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Conserved domains on  [gi|1246743216|ref|NP_001342799|]
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GTP-binding protein involved in beta-tubulin folding Alp41 [Schizosaccharomyces pombe]

Protein Classification

ADP-ribosylation factor-like protein 2( domain architecture ID 10134969)

ADP-ribosylation factor-like protein 2 (Arl2) is a small GTP-binding protein which cycles between an inactive GDP-bound and an active GTP-bound form, and the rate of cycling is regulated by guanine nucleotide exchange factors (GEF)and GTPase-activating proteins (GAP)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
 3-175 2.55e-102

Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.


:

Pssm-ID: 206720 [Multi-domain]  Cd Length: 173  Bit Score: 291.92  E-value: 2.55e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   3 LLTILRQQKLKEREVRVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFE 82
Cdd:cd04154     1 LLTILRKTKQKEREMRILMLGLDNAGKTTILKKFNGEDISTISPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  83 STEAIIWVVDSLDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTG 162
Cdd:cd04154    81 STDALIWVVDSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLELDSIKSHHWRIFGCSAVTG 160

                         170
                  ....*....|...
gi 1246743216 163 LNIKDAISWLAND 175
Cdd:cd04154   161 ENLLDGIDWLVDD 173
 
Name Accession Description Interval E-value
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
 3-175 2.55e-102

Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.


Pssm-ID: 206720 [Multi-domain]  Cd Length: 173  Bit Score: 291.92  E-value: 2.55e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   3 LLTILRQQKLKEREVRVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFE 82
Cdd:cd04154     1 LLTILRKTKQKEREMRILMLGLDNAGKTTILKKFNGEDISTISPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  83 STEAIIWVVDSLDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTG 162
Cdd:cd04154    81 STDALIWVVDSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLELDSIKSHHWRIFGCSAVTG 160

                         170
                  ....*....|...
gi 1246743216 163 LNIKDAISWLAND 175
Cdd:cd04154   161 ENLLDGIDWLVDD 173
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 17-176 5.36e-65

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 196.68  E-value: 5.36e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  17 VRVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDD 96
Cdd:pfam00025   1 MRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  97 LRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISWLANDL 176
Cdd:pfam00025  81 DRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHELKDRPWEIQGCSAVTGEGLDEGLDWLSNYI 160
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 1-176 2.56e-44

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 145.11  E-value: 2.56e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   1 MGL-LTILRQQKLKEREVRVLLLGLDNAGKTTIL-KCLLNEDVNEVsPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWK 78
Cdd:PLN00223    1 MGLsFTKLFSRLFAKKEMRILMVGLDAAGKTTILyKLKLGEIVTTI-PTIGFNVETVEYKNISFTVWDVGGQDKIRPLWR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  79 NYFESTEAIIWVVDSLDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVS 158
Cdd:PLN00223   80 HYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRHWYIQSTC 159

                         170
                  ....*....|....*...
gi 1246743216 159 ALTGLNIKDAISWLANDL 176
Cdd:PLN00223  160 ATSGEGLYEGLDWLSNNI 177
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 15-177 4.73e-44

ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).


Pssm-ID: 128474 [Multi-domain]  Cd Length: 175  Bit Score: 144.29  E-value: 4.73e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   15 REVRVLLLGLDNAGKTTIL-KCLLNEDVNEVsPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDS 93
Cdd:smart00177  12 KEMRILMVGLDAAGKTTILyKLKLGESVTTI-PTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDS 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   94 LDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISWLA 173
Cdd:smart00177  91 NDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRNWYIQPTCATSGDGLYEGLTWLS 170


                   ....
gi 1246743216  174 NDLK 177
Cdd:smart00177 171 NNLK 174
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
15-173 1.19e-13

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 65.39  E-value: 1.19e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  15 REVRVLLLGLDNAGKTTILKCLLNEDVN--EVSPTFGFQIRTLEVE----GLRFTIWDIGGQ---KTLRNFWKNYFESTE 85
Cdd:COG1100     2 GEKKIVVVGTGGVGKTSLVNRLVGDIFSleKYLSTNGVTIDKKELKldglDVDLVIWDTPGQdefRETRQFYARQLTGAS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  86 AIIWVVDSlddlRLEECRNTLQELL--VEEKLLFTSILVLANKSDVsgaLSSEEISKILNISKYKSSH--WRIFSVSALT 161
Cdd:COG1100    82 LYLFVVDG----TREETLQSLYELLesLRRLGKKSPIILVLNKIDL---YDEEEIEDEERLKEALSEDniVEVVATSAKT 154

                         170
                  ....*....|..
gi 1246743216 162 GLNIKDAISWLA 173
Cdd:COG1100   155 GEGVEELFAALA 166
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 16-169 6.22e-11

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 58.15  E-value: 6.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  16 EVRVLLLGLDNAGKTTILKCLLNEDVNEVS--PTFGFQIRTLEVE----GLRFTIWDIGGQKTLRNFWKNYFESTEAIIW 89
Cdd:TIGR00231   1 DIKIVIVGHPNVGKSTLLNSLLGNKGSITEyyPGTTRNYVTTVIEedgkTYKFNLLDTAGQEDYDAIRRLYYPQVERSLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  90 VVDSldDLRLEECRNTLQELLVEEKLLFTS---ILVLANKSDVSGALSSEEISKILNISKYKsshwRIFSVSALTGLNIK 166
Cdd:TIGR00231  81 VFDI--VILVLDVEEILEKQTKEIIHHADSgvpIILVGNKIDLKDADLKTHVASEFAKLNGE----PIIPLSAETGKNID 154


                  ...
gi 1246743216 167 DAI 169
Cdd:TIGR00231 155 SAF 157
 
Name Accession Description Interval E-value
Arl2 cd04154
Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind ...
 3-175 2.55e-102

Arf-like 2 (Arl2) GTPase; Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.


Pssm-ID: 206720 [Multi-domain]  Cd Length: 173  Bit Score: 291.92  E-value: 2.55e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   3 LLTILRQQKLKEREVRVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFE 82
Cdd:cd04154     1 LLTILRKTKQKEREMRILMLGLDNAGKTTILKKFNGEDISTISPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  83 STEAIIWVVDSLDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTG 162
Cdd:cd04154    81 STDALIWVVDSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLELDSIKSHHWRIFGCSAVTG 160

                         170
                  ....*....|...
gi 1246743216 163 LNIKDAISWLAND 175
Cdd:cd04154   161 ENLLDGIDWLVDD 173
Arf_Arl cd00878
ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl ...
 18-174 2.48e-68

ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases; Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions.


Pssm-ID: 206644 [Multi-domain]  Cd Length: 158  Bit Score: 205.12  E-value: 2.48e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDDL 97
Cdd:cd00878     1 RILMLGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRE 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1246743216  98 RLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISWLAN 174
Cdd:cd00878    81 RIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGLDWLIE 157
Arf pfam00025
ADP-ribosylation factor family; Pfam combines a number of different Prosite families together
 17-176 5.36e-65

ADP-ribosylation factor family; Pfam combines a number of different Prosite families together


Pssm-ID: 459636 [Multi-domain]  Cd Length: 160  Bit Score: 196.68  E-value: 5.36e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  17 VRVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDD 96
Cdd:pfam00025   1 MRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  97 LRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISWLANDL 176
Cdd:pfam00025  81 DRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHELKDRPWEIQGCSAVTGEGLDEGLDWLSNYI 160
Arl3 cd04155
Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most ...
 3-173 2.69e-64

Arf-like 3 (Arl3) GTPase; Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.


Pssm-ID: 206721 [Multi-domain]  Cd Length: 174  Bit Score: 195.69  E-value: 2.69e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   3 LLTILRQ-QKLKEREVRVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYF 81
Cdd:cd04155     1 LLSILRKlKPSSRQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  82 ESTEAIIWVVDSLDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALT 161
Cdd:cd04155    81 ENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVAEALNLHDIRDRSWHIQACSAKT 160

                         170
                  ....*....|..
gi 1246743216 162 GLNIKDAISWLA 173
Cdd:cd04155   161 GEGLQEGMNWVC 172
Arl1 cd04151
ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi ...
 18-175 9.14e-51

ADP ribosylation factor 1 (Arf1); Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability.


Pssm-ID: 206718 [Multi-domain]  Cd Length: 158  Bit Score: 160.65  E-value: 9.14e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDDL 97
Cdd:cd04151     1 RILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRD 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1246743216  98 RLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISWLAND 175
Cdd:cd04151    81 RLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKLGLSELKDRTWQIFKTSATKGEGLDEGMDWLVNT 158
Arl5_Arl8 cd04153
Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like ...
 14-174 6.44e-50

Arf-like 5 (Arl5) and 8 (Arl8) GTPases; Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.


Pssm-ID: 133353 [Multi-domain]  Cd Length: 174  Bit Score: 159.05  E-value: 6.44e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  14 EREVRVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDS 93
Cdd:cd04153    13 RKEYKVIIVGLDNAGKTTILYQFLLGEVVHTSPTIGSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVIDS 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  94 LDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISWLA 173
Cdd:cd04153    93 TDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISESLGLTSIRDHTWHIQGCCALTGEGLPEGLDWIA 172


                  .
gi 1246743216 174 N 174
Cdd:cd04153   173 S 173
ARLTS1 cd04156
Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), ...
 18-173 4.47e-45

Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11); ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in high-risk familial breast cancer.


Pssm-ID: 133356 [Multi-domain]  Cd Length: 160  Bit Score: 146.41  E-value: 4.47e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEG-LRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDD 96
Cdd:cd04156     1 QVLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLEKhLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDE 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1246743216  97 LRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSH-WRIFSVSALTGLNIKDAISWLA 173
Cdd:cd04156    81 ARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRFKLKKYCSDRdWYVQPCSAVTGEGLAEAFRKLA 158
PLN00223 PLN00223
ADP-ribosylation factor; Provisional
 1-176 2.56e-44

ADP-ribosylation factor; Provisional


Pssm-ID: 165788  Cd Length: 181  Bit Score: 145.11  E-value: 2.56e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   1 MGL-LTILRQQKLKEREVRVLLLGLDNAGKTTIL-KCLLNEDVNEVsPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWK 78
Cdd:PLN00223    1 MGLsFTKLFSRLFAKKEMRILMVGLDAAGKTTILyKLKLGEIVTTI-PTIGFNVETVEYKNISFTVWDVGGQDKIRPLWR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  79 NYFESTEAIIWVVDSLDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVS 158
Cdd:PLN00223   80 HYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRHWYIQSTC 159

                         170
                  ....*....|....*...
gi 1246743216 159 ALTGLNIKDAISWLANDL 176
Cdd:PLN00223  160 ATSGEGLYEGLDWLSNNI 177
ARF smart00177
ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular ...
 15-177 4.73e-44

ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).


Pssm-ID: 128474 [Multi-domain]  Cd Length: 175  Bit Score: 144.29  E-value: 4.73e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   15 REVRVLLLGLDNAGKTTIL-KCLLNEDVNEVsPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDS 93
Cdd:smart00177  12 KEMRILMVGLDAAGKTTILyKLKLGESVTTI-PTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDS 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   94 LDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISWLA 173
Cdd:smart00177  91 NDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRNWYIQPTCATSGDGLYEGLTWLS 170


                   ....
gi 1246743216  174 NDLK 177
Cdd:smart00177 171 NNLK 174
Arf1_5_like cd04150
ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like ...
 17-174 2.39e-43

ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5); The Arf1-Arf5-like subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents and other lower eukaryotes, lack Arf2. Human Arf3 shares 96% sequence identity with Arf1 and is believed to generally function interchangeably with Arf1. Human Arf4 in the activated (GTP-bound) state has been shown to interact with the cytoplasmic domain of epidermal growth factor receptor (EGFR) and mediate the EGF-dependent activation of phospholipase D2 (PLD2), leading to activation of the activator protein 1 (AP-1) transcription factor. Arf4 has also been shown to recognize the C-terminal sorting signal of rhodopsin and regulate its incorporation into specialized post-Golgi rhodopsin transport carriers (RTCs). There is some evidence that Arf5 functions at the early-Golgi and the trans-Golgi to affect Golgi-associated alpha-adaptin homology Arf-binding proteins (GGAs).


Pssm-ID: 206717 [Multi-domain]  Cd Length: 159  Bit Score: 141.78  E-value: 2.39e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  17 VRVLLLGLDNAGKTTIL-KCLLNEDVNEVsPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLD 95
Cdd:cd04150     1 MRILMVGLDAAGKTTILyKLKLGEIVTTI-PTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSND 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1246743216  96 DLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISWLAN 174
Cdd:cd04150    80 RERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKLGLHSLRNRNWYIQATCATSGDGLYEGLDWLSN 158
PTZ00133 PTZ00133
ADP-ribosylation factor; Provisional
 1-180 7.95e-43

ADP-ribosylation factor; Provisional


Pssm-ID: 173423  Cd Length: 182  Bit Score: 141.14  E-value: 7.95e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   1 MGL-LTILRQQKLKEREVRVLLLGLDNAGKTTIL-KCLLNEDVNEVsPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWK 78
Cdd:PTZ00133    1 MGLwLSSAFKSLFGKKEVRILMVGLDAAGKTTILyKLKLGEVVTTI-PTIGFNVETVEYKNLKFTMWDVGGQDKLRPLWR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  79 NYFESTEAIIWVVDSLDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVS 158
Cdd:PTZ00133   80 HYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSVRQRNWYIQGCC 159

                         170       180
                  ....*....|....*....|..
gi 1246743216 159 ALTGLNIKDAISWLANDLKEIK 180
Cdd:PTZ00133  160 ATTAQGLYEGLDWLSANIKKSM 181
Arf6 cd04149
ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins ...
 13-175 2.20e-41

ADP ribosylation factor 6 (Arf6); Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed to function at multiple sites on the plasma membrane through interaction with a specific set of GEFs, GAPs, and effectors. Arf6 has been implicated in breast cancer and melanoma cell invasion, and in actin remodelling at the invasion site of Chlamydia infection.


Pssm-ID: 206716  Cd Length: 168  Bit Score: 137.21  E-value: 2.20e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  13 KEREVRVLLLGLDNAGKTTIL-KCLLNEDVNEVsPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVV 91
Cdd:cd04149     6 GNKEMRILMLGLDAAGKTTILyKLKLGQSVTTI-PTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVV 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  92 DSLDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISW 171
Cdd:cd04149    85 DSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTW 164


                  ....
gi 1246743216 172 LAND 175
Cdd:cd04149   165 LSSN 168
Arfrp1 cd04160
Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a ...
 19-172 4.55e-40

Arf-related protein 1 (Arfrp1); Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.


Pssm-ID: 206725 [Multi-domain]  Cd Length: 168  Bit Score: 133.62  E-value: 4.55e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  19 VLLLGLDNAGKTTIL---KCLLNEDV-----NEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWV 90
Cdd:cd04160     2 VLILGLDNAGKTTFLeqtKTKFSKNYkglnpSKITPTVGLNIGTIEVGKARLMFWDLGGQEELRSLWDKYYAESHGVIYV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  91 VDSLDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILN--ISKYKSSHWRIFSVSALTGLNIKDA 168
Cdd:cd04160    82 IDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLPDALSVAEIKEVFDdcIALIGRRDCLVQPVSALEGEGVEEG 161


                  ....
gi 1246743216 169 ISWL 172
Cdd:cd04160   162 IEWL 165
Sar1 cd00879
Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII ...
 15-173 8.65e-38

Sar1 is an essential component of COPII vesicle coats; Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.


Pssm-ID: 206645 [Multi-domain]  Cd Length: 191  Bit Score: 128.55  E-value: 8.65e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  15 REVRVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSL 94
Cdd:cd00879    18 KEAKIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  95 DDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKY---------KSSHWR---IFSVSALTG 162
Cdd:cd00879    98 DPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEEELREALGLYGTttgkggvslKVSNIRpveVFMCSVVKR 177

                         170
                  ....*....|.
gi 1246743216 163 LNIKDAISWLA 173
Cdd:cd00879   178 QGYGEGFRWLS 188
Arl6 cd04157
Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small ...
 19-174 1.17e-37

Arf-like 6 (Arl6) GTPase; Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


Pssm-ID: 206722 [Multi-domain]  Cd Length: 162  Bit Score: 127.55  E-value: 1.17e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  19 VLLLGLDNAGKTTILKCLLNEDVN--EVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDD 96
Cdd:cd04157     2 ILVLGLDNSGKTTIINQLKPSNAQsqNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  97 LRLEECRNTLqELLVEEKLLFTS---ILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISWLA 173
Cdd:cd04157    82 LRMVVAKDEL-ELLLNHPDIKHRripILFYANKMDLPDALTAVKITQLLCLENIKDKPWHIFASSALTGEGLDEGVDWLQ 160


                  .
gi 1246743216 174 N 174
Cdd:cd04157   161 A 161
ARD1 cd04158
(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein ...
 18-176 5.49e-36

(ADP-ribosylation factor domain protein 1 (ARD1); ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membrane. Two Tyr-based motifs in the Arf domain are responsible for Golgi localization, while the GAP domain controls lysosomal localization.


Pssm-ID: 206723 [Multi-domain]  Cd Length: 169  Bit Score: 123.60  E-value: 5.49e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDDL 97
Cdd:cd04158     1 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  98 RLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSH-WRIFSVSALTGLNIKDAISWLANDL 176
Cdd:cd04158    81 RVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTELLSLHKLCCGRsWYIQGCDARSGMGLYEGLDWLSRQL 160
Arl10_like cd04159
Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from ...
 21-172 3.96e-32

Arf-like 9 (Arl9) and 10 (Arl10) GTPases; Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.


Pssm-ID: 206724 [Multi-domain]  Cd Length: 159  Bit Score: 113.18  E-value: 3.96e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  21 LLGLDNAGKTTILKCLLNED-VNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDDLRL 99
Cdd:cd04159     4 LVGLQNSGKTTLVNVIASGQfSEDTIPTVGFNMRKVTKGNVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREKL 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1246743216 100 EECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISWL 172
Cdd:cd04159    84 EVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIEQMNLKSITDREVSCYSISAKEKTNIDIVLDWL 156
Arl4_Arl7 cd04152
Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular ...
 19-172 5.78e-30

Arf-like 4 (Arl4) and 7 (Arl7) GTPases; Arl4 (Arf-like 4) is highly expressed in testicular germ cells, and is found in the nucleus and nucleolus. In mice, Arl4 is developmentally expressed during embryogenesis, and a role in somite formation and central nervous system differentiation has been proposed. Arl7 has been identified as the only Arf/Arl protein to be induced by agonists of liver X-receptor and retinoid X-receptor and by cholesterol loading in human macrophages. Arl7 is proposed to play a role in transport between a perinuclear compartment and the plasma membrane, apparently linked to the ABCA1-mediated cholesterol secretion pathway. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.


Pssm-ID: 206719 [Multi-domain]  Cd Length: 183  Bit Score: 108.35  E-value: 5.78e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  19 VLLLGLDNAGKTTILKCL-LNEDVNEVsPTFGFQIRTLEV-----EGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVD 92
Cdd:cd04152     6 IVMLGLDSAGKTTVLYRLkFNEFVNTV-PTKGFNTEKIKVslgnaKGVTFHFWDVGGQEKLRPLWKSYTRCTDGIVFVVD 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  93 SLDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISK-YKSSHWRIFSVSALTGLNIKDAISW 171
Cdd:cd04152    85 SVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPNALPVSEVEKLLALHElSSSTPWHVQPACAIIGEGLQEGLEK 164


                  .
gi 1246743216 172 L 172
Cdd:cd04152   165 L 165
Arl2l1_Arl13_like cd04161
Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a ...
 19-172 5.85e-30

Arl2-like protein 1 (Arl2l1) and Arl13; Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.


Pssm-ID: 133361 [Multi-domain]  Cd Length: 167  Bit Score: 107.86  E-value: 5.85e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  19 VLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDDLR 98
Cdd:cd04161     2 LLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDDR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  99 LEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKY---KSSHWRIFSVSALTGLN------IKDAI 169
Cdd:cd04161    82 VQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYLSLEKLvneNKSLCHIEPCSAIEGLGkkidpsIVEGL 161


                  ...
gi 1246743216 170 SWL 172
Cdd:cd04161   162 RWL 164
Arl9_Arfrp2_like cd04162
Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first ...
 19-145 8.38e-29

Arf-like 9 (Arl9)/Arfrp2-like GTPase; Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project. It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2). This is a novel subfamily identified in human cancers that is uncharacterized to date.


Pssm-ID: 133362 [Multi-domain]  Cd Length: 164  Bit Score: 104.84  E-value: 8.38e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  19 VLLLGLDNAGKTTILKCLLNEDVNE-VSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDDL 97
Cdd:cd04162     2 ILVLGLDGAGKTSLLHSLSSERSLEsVVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYWKRYLSGSQGLIFVVDSADSE 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1246743216  98 RLEECRNTLQELLVEEKLLftSILVLANKSDVSGALSSEEISKILNIS 145
Cdd:cd04162    82 RLPLARQELHQLLQHPPDL--PLVVLANKQDLPAARSVQEIHKELELE 127
SAR smart00178
Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene ...
 6-173 4.59e-28

Sar1p-like members of the Ras-family of small GTPases; Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 197556 [Multi-domain]  Cd Length: 184  Bit Score: 103.48  E-value: 4.59e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216    6 ILRQQKLKEREVRVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTE 85
Cdd:smart00178   7 ILASLGLWNKHAKILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAIGNIKFTTFDLGGHQQARRLWKDYFPEVN 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   86 AIIWVVDSLDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNISKYKSSHWR-------IFSVS 158
Cdd:smart00178  87 GIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDELRYALGLTNTTTGKGKvgvrpveVFMCS 166

                          170
                   ....*....|....*
gi 1246743216  159 ALTGLNIKDAISWLA 173
Cdd:smart00178 167 VVRRMGYGEGFKWLS 181
Ras_like_GTPase cd00882
Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like ...
 20-174 5.78e-18

Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.


Pssm-ID: 206648 [Multi-domain]  Cd Length: 161  Bit Score: 76.73  E-value: 5.78e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  20 LLLGLDNAGKTTILKCLLNEDVNEVS----PTFGFQIRTLEVE--GLRFTIWDIGGQKTLRNFW-----KNYFESTEAII 88
Cdd:cd00882     1 VVVGRGGVGKSSLLNALLGGEVGEVSdvpgTTRDPDVYVKELDkgKVKLVLVDTPGLDEFGGLGreelaRLLLRGADLIL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  89 WVVDSLDDLRLEECRNTLQELLVEEKLLftsILVLANKSDVSGAlsSEEISKILNISKYKSSHWRIFSVSALTGLNIKDA 168
Cdd:cd00882    81 LVVDSTDRESEEDAKLLILRRLRKEGIP---IILVGNKIDLLEE--REVEELLRLEELAKILGVPVFEVSAKTGEGVDEL 155


                  ....*.
gi 1246743216 169 ISWLAN 174
Cdd:cd00882   156 FEKLIE 161
Gem1 COG1100
GTPase SAR1 family domain [General function prediction only];
15-173 1.19e-13

GTPase SAR1 family domain [General function prediction only];


Pssm-ID: 440717 [Multi-domain]  Cd Length: 177  Bit Score: 65.39  E-value: 1.19e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  15 REVRVLLLGLDNAGKTTILKCLLNEDVN--EVSPTFGFQIRTLEVE----GLRFTIWDIGGQ---KTLRNFWKNYFESTE 85
Cdd:COG1100     2 GEKKIVVVGTGGVGKTSLVNRLVGDIFSleKYLSTNGVTIDKKELKldglDVDLVIWDTPGQdefRETRQFYARQLTGAS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  86 AIIWVVDSlddlRLEECRNTLQELL--VEEKLLFTSILVLANKSDVsgaLSSEEISKILNISKYKSSH--WRIFSVSALT 161
Cdd:COG1100    82 LYLFVVDG----TREETLQSLYELLesLRRLGKKSPIILVLNKIDL---YDEEEIEDEERLKEALSEDniVEVVATSAKT 154

                         170
                  ....*....|..
gi 1246743216 162 GLNIKDAISWLA 173
Cdd:COG1100   155 GEGVEELFAALA 166
Rab cd00154
Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases ...
 17-173 5.64e-13

Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases); Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible.


Pssm-ID: 206640 [Multi-domain]  Cd Length: 159  Bit Score: 63.24  E-value: 5.64e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  17 VRVLLLGLDNAGKTTILKCLLNEDVNE-VSPTFG--FQIRTLEVEGLRFT--IWDIGGQKTLRNFWKNYFESTEAIIWVV 91
Cdd:cd00154     1 FKIVLIGDSGVGKTSLLLRFVDNKFSEnYKSTIGvdFKSKTIEVDGKKVKlqIWDTAGQERFRSITSSYYRGAHGAILVY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  92 D-----SLDDLR--LEECRNTLQELLVeekllftsILVLANKSDVSG--ALSSEEISKIlniskYKSSHWRIFSVSALTG 162
Cdd:cd00154    81 DvtnreSFENLDkwLNELKEYAPPNIP--------IILVGNKSDLEDerQVSTEEAQQF-----AKENGLLFFETSAKTG 147

                         170
                  ....*....|.
gi 1246743216 163 LNIKDAISWLA 173
Cdd:cd00154   148 ENVDEAFESLA 158
PLN03118 PLN03118
Rab family protein; Provisional
 18-179 6.05e-13

Rab family protein; Provisional


Pssm-ID: 215587 [Multi-domain]  Cd Length: 211  Bit Score: 64.31  E-value: 6.05e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLNEDVNEVSPTFG--FQIRTLEVEG--LRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVds 93
Cdd:PLN03118   16 KILLIGDSGVGKSSLLVSFISSSVEDLAPTIGvdFKIKQLTVGGkrLKLTIWDTAGQERFRTLTSSYYRNAQGIILVY-- 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  94 ldDLRLEECRNTLQELLVEEKLLFTS-----ILVLANKSDVSgalSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDA 168
Cdd:PLN03118   94 --DVTRRETFTNLSDVWGKEVELYSTnqdcvKMLVGNKVDRE---SERDVSREEGMALAKEHGCLFLECSAKTRENVEQC 168

                         170
                  ....*....|.
gi 1246743216 169 ISWLANDLKEI 179
Cdd:PLN03118  169 FEELALKIMEV 179
Era_like cd00880
E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family ...
 21-165 5.11e-11

E. coli Ras-like protein (Era)-like GTPase; The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family.


Pssm-ID: 206646 [Multi-domain]  Cd Length: 161  Bit Score: 58.03  E-value: 5.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  21 LLGLDNAGKTTILKCLLNEDVNEVSPTFGF----QIRTLEVEGLR-FTIWD------IGGQKTLRNF-WKNYFESTEAII 88
Cdd:cd00880     2 IFGRPNVGKSSLLNALLGQNVGIVSPIPGTtrdpVRKEWELLPLGpVVLIDtpgldeEGGLGRERVEeARQVADRADLVL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1246743216  89 WVVDSldDLRLEECRNTLQELLVEEKllftSILVLANKSDVSGAlsSEEISKILNISKYKSSHWRIFSVSALTGLNI 165
Cdd:cd00880    82 LVVDS--DLTPVEEEAKLGLLRERGK----PVLLVLNKIDLVPE--SEEEELLRERKLELLPDLPVIAVSALPGEGI 150
small_GTP TIGR00231
small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this ...
 16-169 6.22e-11

small GTP-binding protein domain; Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General]


Pssm-ID: 272973 [Multi-domain]  Cd Length: 162  Bit Score: 58.15  E-value: 6.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  16 EVRVLLLGLDNAGKTTILKCLLNEDVNEVS--PTFGFQIRTLEVE----GLRFTIWDIGGQKTLRNFWKNYFESTEAIIW 89
Cdd:TIGR00231   1 DIKIVIVGHPNVGKSTLLNSLLGNKGSITEyyPGTTRNYVTTVIEedgkTYKFNLLDTAGQEDYDAIRRLYYPQVERSLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  90 VVDSldDLRLEECRNTLQELLVEEKLLFTS---ILVLANKSDVSGALSSEEISKILNISKYKsshwRIFSVSALTGLNIK 166
Cdd:TIGR00231  81 VFDI--VILVLDVEEILEKQTKEIIHHADSgvpIILVGNKIDLKDADLKTHVASEFAKLNGE----PIIPLSAETGKNID 154


                  ...
gi 1246743216 167 DAI 169
Cdd:TIGR00231 155 SAF 157
Ras pfam00071
Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop ...
 18-178 1.95e-10

Ras family; Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.


Pssm-ID: 425451 [Multi-domain]  Cd Length: 162  Bit Score: 56.75  E-value: 1.95e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLNEDVNEVS-PTFG--FQIRTLEVEG--LRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVD 92
Cdd:pfam00071   1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYiPTIGvdFYTKTIEVDGktVKLQIWDTAGQERFRALRPLYYRGADGFLLVYD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  93 SLDDLRLEECRNTLQELLvEEKLLFTSILVLANKSDVSG--ALSSEEISKIlniskYKSSHWRIFSVSALTGLNIKDAIS 170
Cdd:pfam00071  81 ITSRDSFENVKKWVEEIL-RHADENVPIVLVGNKCDLEDqrVVSTEEGEAL-----AKELGLPFMETSAKTNENVEEAFE 154


                  ....*...
gi 1246743216 171 WLANDLKE 178
Cdd:pfam00071 155 ELAREILK 162
SR_beta cd04105
Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms ...
 19-142 1.17e-09

Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms the heterodimeric signal recognition particle (SRP); Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer.


Pssm-ID: 206691 [Multi-domain]  Cd Length: 202  Bit Score: 55.02  E-value: 1.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  19 VLLLGLDNAGKTTILKCLLNEdvnEVSPTFGFQ------IRTLEVEGLRFTIWDIGGQKTLRN-FWKNYFESTEAIIWVV 91
Cdd:cd04105     3 VLLLGPSDSGKTALFTKLTTG---KVRSTVTSIepnvasFYSNSSKGKKLTLVDVPGHEKLRDkLLEYLKASLKAIVFVV 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1246743216  92 DSLDDLRleECRNT---LQELLVEEKLLFTS--ILVLANKSDVSGALSSEEISKIL 142
Cdd:cd04105    80 DSATFQK--NIRDVaefLYDILTDLEKIKNKipILIACNKQDLFTAKPAKKIKELL 133
G-alpha pfam00503
G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular ...
 46-129 3.18e-09

G-protein alpha subunit; G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring of residues centered on the nucleotide binding site. A Ggamma is found fused to an inactive Galpha in the Dictyostelium protein gbqA.


Pssm-ID: 459835 [Multi-domain]  Cd Length: 316  Bit Score: 54.90  E-value: 3.18e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  46 PTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVdSLD--DLRLEECRNTLQelLVEEKLLF------ 117
Cdd:pfam00503 153 KTTGIIETKFEFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVV-SLSeyDQVLYEDDSTNR--MEESLKLFeeicns 229

                          90
                  ....*....|....*..
gi 1246743216 118 -----TSILVLANKSDV 129
Cdd:pfam00503 230 pwfknTPIILFLNKKDL 246
RAB smart00175
Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.
 17-179 1.15e-08

Rab subfamily of small GTPases; Rab GTPases are implicated in vesicle trafficking.


Pssm-ID: 197555 [Multi-domain]  Cd Length: 164  Bit Score: 51.74  E-value: 1.15e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   17 VRVLLLGLDNAGKTtilkCLL-----NEDVNEVSPTFG--FQIRTLEVEG--LRFTIWDIGGQKTLRNFWKNYFESTEAI 87
Cdd:smart00175   1 FKIILIGDSGVGKS----SLLsrftdGKFSEQYKSTIGvdFKTKTIEVDGkrVKLQIWDTAGQERFRSITSSYYRGAVGA 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   88 IWVVD-----SLDDLR--LEECRNTLQELLVeekllftsILVLANKSDVSG--ALSSEE---ISKILNISkyksshwrIF 155
Cdd:smart00175  77 LLVYDitnreSFENLEnwLKELREYASPNVV--------IMLVGNKSDLEEqrQVSREEaeaFAEEHGLP--------FF 140

                          170       180
                   ....*....|....*....|....
gi 1246743216  156 SVSALTGLNIKDAISWLANDLKEI 179
Cdd:smart00175 141 ETSAKTNTNVEEAFEELAREILKR 164
Rab36_Rab34 cd04108
Rab GTPase families 34 (Rab34) and 36 (Rab36); Rab34/Rab36 subfamily. Rab34, found primarily ...
 50-173 3.32e-08

Rab GTPase families 34 (Rab34) and 36 (Rab36); Rab34/Rab36 subfamily. Rab34, found primarily in the Golgi, interacts with its effector, Rab-interacting lysosomal protein (RILP). This enables its participation in microtubular dynenin-dynactin-mediated repositioning of lysosomes from the cell periphery to the Golgi. A Rab34 (Rah) isoform that lacks the consensus GTP-binding region has been identified in mice. This isoform is associated with membrane ruffles and promotes macropinosome formation. Rab36 has been mapped to human chromosome 22q11.2, a region that is homozygously deleted in malignant rhabdoid tumors (MRTs). However, experimental assessments do not implicate Rab36 as a tumor suppressor that would enable tumor formation through a loss-of-function mechanism. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206693 [Multi-domain]  Cd Length: 170  Bit Score: 50.65  E-value: 3.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  50 FQIRTLEVEGLRFT--IWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDDLRLEECRNTLQELLVEEKLLFTSILVLANKS 127
Cdd:cd04108    37 FEMERFEVLGVPFSlqLWDTAGQERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKK 116

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1246743216 128 DVS--GALSSEEISKILNISKYKSSHWrifSVSALTGLNIKDAISWLA 173
Cdd:cd04108   117 DLSspAQYALMEQDAIKLAREMKAEYW---AVSALTGENVRDFFFRVA 161
MMR_HSR1 pfam01926
50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete ...
 18-126 6.27e-08

50S ribosome-binding GTPase; The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide.


Pssm-ID: 460387 [Multi-domain]  Cd Length: 113  Bit Score: 48.77  E-value: 6.27e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLNEDVnEVSPTFG----FQIRTLEVEGLRFTIWDIGG-------QKTLRNFWKNYFEStEA 86
Cdd:pfam01926   1 RVALVGRPNVGKSTLINALTGAKA-IVSDYPGttrdPNEGRLELKGKQIILVDTPGliegaseGEGLGRAFLAIIEA-DL 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1246743216  87 IIWVVDSLDDLRLEEcrNTLQELLVEEKllfTSILVLANK 126
Cdd:pfam01926  79 ILFVVDSEEGITPLD--EELLELLRENK---KPIILVLNK 113
Rab15 cd04117
Rab GTPase family 15 (Rab15); Rab15 colocalizes with the transferrin receptor in early ...
 18-92 8.78e-08

Rab GTPase family 15 (Rab15); Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206698 [Multi-domain]  Cd Length: 164  Bit Score: 49.59  E-value: 8.78e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILkCLLNEdvNEVSP----TFG--FQIRTLEVEGL--RFTIWDIGGQKTLRNFWKNYFESTEAIIW 89
Cdd:cd04117     2 RLLLIGDSGVGKTCLL-CRFTD--NEFHSshisTIGvdFKMKTIEVDGIkvRIQIWDTAGQERYQTITKQYYRRAQGIFL 78


                  ...
gi 1246743216  90 VVD 92
Cdd:cd04117    79 VYD 81
Rab8_Rab10_Rab13_like cd01867
Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to ...
 18-178 1.21e-07

Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13); Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206659 [Multi-domain]  Cd Length: 167  Bit Score: 49.19  E-value: 1.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTtilkCLLNEDVNEV-SPTF------GFQIRTLEVEG--LRFTIWDIGGQKTLRNFWKNYFESTEAII 88
Cdd:cd01867     5 KLLLIGDSGVGKS----CLLLRFSEDSfNPSFistigiDFKIRTIELDGkkIKLQIWDTAGQERFRTITTSYYRGAMGII 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  89 WVVDSLDDLRLEECRNTLQELlveEKLLFTSI--LVLANKSDVSgalSSEEISKILNISKYKSSHWRIFSVSALTGLNIK 166
Cdd:cd01867    81 LVYDITDEKSFENIKNWMRNI---DEHASEDVerMLVGNKCDME---EKRVVSKEEGEALAREYGIKFLETSAKANINVE 154

                         170
                  ....*....|..
gi 1246743216 167 DAISWLANDLKE 178
Cdd:cd01867   155 EAFLTLAKDILK 166
RocCOR cd09914
Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family; RocCOR (or Roco) protein ...
 16-166 1.96e-07

Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family; RocCOR (or Roco) protein family is characterized by a superdomain containing a Ras-like GTPase domain, called Roc (Ras of complex proteins), and a characteristic second domain called COR (C-terminal of Roc). A kinase domain and diverse regulatory domains are also often found in Roco proteins. Their functions are diverse; in Dictyostelium discoideum, which encodes 11 Roco proteins, they are involved in cell division, chemotaxis and development, while in human, where 4 Roco proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded, these proteins are involved in epilepsy and cancer. Mutations in LRRK2 (leucine-rich repeat kinase 2) are known to cause familial Parkinson's disease.


Pssm-ID: 206741 [Multi-domain]  Cd Length: 161  Bit Score: 48.49  E-value: 1.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  16 EVRVLLLGLDNAGKTTILKCLLNEDVNE-VSPTFGFQIRTLEVEG-----LRFTIWDIGGQKTLRNFwKNYFESTEAIIW 89
Cdd:cd09914     1 EAKLMLVGQGGVGKTSLCKQLIGEKFDGdESSTHGINVQDWKIPAperkkIRLNVWDFGGQEIYHAT-HQFFLTSRSLYL 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1246743216  90 VVdslDDLRLEECRNTLQELL--VEEKLLFTSILVLANKSDVSgalSSEEISKILNISKYKSSHWRIFSVSALTGLNIK 166
Cdd:cd09914    80 LV---FDLRTGDEVSRVPYWLrqIKAFGGVSPVILVGTHIDES---CDEDILKKALNKKFPAIINDIHFVSCKNGKGIA 152
Rab1_Ypt1 cd01869
Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in ...
 50-178 1.03e-06

Rab GTPase family 1 includes the yeast homolog Ypt1; Rab1/Ypt1 subfamily. Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206661 [Multi-domain]  Cd Length: 166  Bit Score: 46.55  E-value: 1.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  50 FQIRTLEVEG--LRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDDLRLEECRNTLQELlveEKLLFTSI--LVLAN 125
Cdd:cd01869    39 FKIRTIELDGktVKLQIWDTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEI---DRYASENVnkLLVGN 115

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1246743216 126 KSD-----VSGALSSEEISKILNISkyksshwrIFSVSALTGLNIKDAISWLANDLKE 178
Cdd:cd01869   116 KCDltdkkVVDYTEAKEFADELGIP--------FLETSAKNATNVEEAFMTMAREIKK 165
Rab18 cd01863
Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic ...
 17-92 2.26e-06

Rab GTPase family 18 (Rab18); Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206656 [Multi-domain]  Cd Length: 161  Bit Score: 45.38  E-value: 2.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  17 VRVLLLGLDNAGKTTILKCLLNEDVNE-VSPTFG--FQIRTLEVEGLRF--TIWDIGGQKTLRNFWKNYFESTEAIIWVV 91
Cdd:cd01863     1 LKILLIGDSGVGKSSLLLRFTDDTFDEdLSSTIGvdFKVKTVTVDGKKVklAIWDTAGQERFRTLTSSYYRGAQGVILVY 80


                  .
gi 1246743216  92 D 92
Cdd:cd01863    81 D 81
Roc pfam08477
Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial ...
 18-128 3.10e-06

Ras of Complex, Roc, domain of DAPkinase; Roc, or Ras of Complex, proteins are mitochondrial Rho proteins (Miro-1, and Miro-2) and atypical Rho GTPases. Full-length proteins have a unique domain organization, with tandem GTP-binding domains and two EF hand domains (pfam00036) that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.


Pssm-ID: 462490 [Multi-domain]  Cd Length: 114  Bit Score: 44.04  E-value: 3.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLNEDVNE-VSPTFGFQIRTLEVEG-------LRFTIWDIGGQKTLRNFWKNYFESTEAIIW 89
Cdd:pfam08477   1 KVVLLGDSGVGKTSLLKRFVDDTFDPkYKSTIGVDFKTKTVLEnddngkkIKLNIWDTAGQERFRSLHPFYYRGAAAALL 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1246743216  90 VVDSLDDLRLEECRNTLQELLVEEKllftsILVLANKSD 128
Cdd:pfam08477  81 VYDSRTFSNLKYWLRELKKYAGNSP-----VILVGNKID 114
PLN03110 PLN03110
Rab GTPase; Provisional
 18-179 5.06e-06

Rab GTPase; Provisional


Pssm-ID: 178657 [Multi-domain]  Cd Length: 216  Bit Score: 45.30  E-value: 5.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTIL-KCLLNEDVNEVSPTFG--FQIRTLEVEG--LRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVD 92
Cdd:PLN03110   14 KIVLIGDSGVGKSNILsRFTRNEFCLESKSTIGveFATRTLQVEGktVKAQIWDTAGQERYRAITSAYYRGAVGALLVYD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  93 -----SLDDLR--LEECRNTLQELLVeekllftsILVLANKSDVSGALS-SEEISKILNISKYKSshwrIFSVSALTGLN 164
Cdd:PLN03110   94 itkrqTFDNVQrwLRELRDHADSNIV--------IMMAGNKSDLNHLRSvAEEDGQALAEKEGLS----FLETSALEATN 161

                         170
                  ....*....|....*
gi 1246743216 165 IKDAISWLANDLKEI 179
Cdd:PLN03110  162 VEKAFQTILLEIYHI 176
G_alpha smart00275
G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding ...
 46-147 8.33e-06

G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding site


Pssm-ID: 214595 [Multi-domain]  Cd Length: 342  Bit Score: 44.88  E-value: 8.33e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   46 PTFGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLD-DLRLEE--CRNTLQELLveekLLF----- 117
Cdd:smart00275 170 PTTGIQETAFIVKKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVALSEyDQVLEEdeSTNRMQESL----NLFesicn 245

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1246743216  118 ------TSILVLANKSDVsgalsSEEISKILNISKY 147
Cdd:smart00275 246 srwfanTSIILFLNKIDL-----FEEKIKKVPLVDY 276
Rab12 cd04120
Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was ...
 18-97 1.20e-05

Rab GTPase family 12 (Rab12); Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206699 [Multi-domain]  Cd Length: 202  Bit Score: 43.85  E-value: 1.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLNEDVNEVSPT---FGFQIRTLEVEG--LRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVD 92
Cdd:cd04120     2 QVIIIGSRGVGKTSLMERFTDDTFCEACKStvgVDFKIKTVELRGkkIRLQIWDTAGQERFNSITSAYYRSAKGIILVYD 81

                          90
                  ....*....|
gi 1246743216  93 -----SLDDL 97
Cdd:cd04120    82 itkkeTFDDL 91
trmE cd04164
trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in ...
 17-174 1.49e-05

trmE is a tRNA modification GTPase; TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.


Pssm-ID: 206727 [Multi-domain]  Cd Length: 159  Bit Score: 43.25  E-value: 1.49e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  17 VRVLLLGLDNAGKTTILKCLLNEDVNEVSPTFGfqirT--------LEVEGLRFTIWD-------------IGGQKTlrn 75
Cdd:cd04164     4 IKVVIAGKPNVGKSSLLNALAGRDRAIVSDIAG----TtrdvieeeIDLGGIPVRLIDtaglretedeiekIGIERA--- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  76 fwKNYFESTEAIIWVVDSLDDLrleecrnTLQELLVEEKLLFTSILVLANKSDVSGALSSEEISKILNiskyksshwrIF 155
Cdd:cd04164    77 --REAIEEADLVLLVVDASEGL-------DEEDLEILELPAKKPVIVVLNKSDLLSDAEGISELNGKP----------II 137

                         170
                  ....*....|....*....
gi 1246743216 156 SVSALTGLNIKDAISWLAN 174
Cdd:cd04164   138 AISAKTGEGIDELKEALLE 156
Rab39 cd04111
Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell ...
 18-184 1.50e-05

Rab GTPase family 39 (Rab39); Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines. It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133311 [Multi-domain]  Cd Length: 211  Bit Score: 43.59  E-value: 1.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLNEDVNEVS-PTFG--FQIRTLEVE-GLR--FTIWDIGGQKTLRNFWKNYFESTEAIIWVV 91
Cdd:cd04111     4 RLIVIGDSTVGKSSLLKRFTEGRFAEVSdPTVGvdFFSRLIEIEpGVRikLQLWDTAGQERFRSITRSYYRNSVGVLLVF 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  92 DSLDDLRLEECRNTLQEllVEEKLLFTSI--LVLANKSDVSgalSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAI 169
Cdd:cd04111    84 DITNRESFEHVHDWLEE--ARSHIQPHRPvfILVGHKCDLE---SQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAF 158

                         170
                  ....*....|....*.
gi 1246743216 170 SWLANDLKE-IKLGTI 184
Cdd:cd04111   159 ELLTQEIYErIKRGEL 174
G-alpha cd00066
Alpha subunit of G proteins (guanine nucleotide binding); The alpha subunit of G proteins ...
 56-120 3.27e-05

Alpha subunit of G proteins (guanine nucleotide binding); The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G proteins, which in turn route the signals to several distinct intracellular signaling pathways. The alpha subunit of G proteins is a weak GTPase. In the resting state, heterotrimeric G proteins are associated at the cytosolic face of the plasma membrane and the alpha subunit binds to GDP. Upon activation by a receptor GDP is replaced with GTP, and the G-alpha/GTP complex dissociates from the beta and gamma subunits. This results in activation of downstream signaling pathways, such as cAMP synthesis by adenylyl cyclase, which is terminated when GTP is hydrolized and the heterotrimers reconstitute.


Pssm-ID: 206639 [Multi-domain]  Cd Length: 315  Bit Score: 43.28  E-value: 3.27e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1246743216  56 EVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVdSLD--DLRLEECRNT--LQELLVeeklLFTSI 120
Cdd:cd00066   157 SIKNLKFRMFDVGGQRSERKKWIHCFEDVTAIIFVV-ALSeyDQVLVEDESVnrMQESLK----LFDSI 220
PLN03108 PLN03108
Rab family protein; Provisional
 48-185 4.37e-05

Rab family protein; Provisional


Pssm-ID: 178655 [Multi-domain]  Cd Length: 210  Bit Score: 42.24  E-value: 4.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  48 FGFQIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVdsldDLRLEECRNTLQELLVEEKLLFTS---ILVLA 124
Cdd:PLN03108   43 FGARMITIDNKPIKLQIWDTAGQESFRSITRSYYRGAAGALLVY----DITRRETFNHLASWLEDARQHANAnmtIMLIG 118

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1246743216 125 NKSDVSG--ALSSEEiskilnISKYKSSHWRIF-SVSALTGLNIKDA-ISWLANDLKEIKLGTID 185
Cdd:PLN03108  119 NKCDLAHrrAVSTEE------GEQFAKEHGLIFmEASAKTAQNVEEAfIKTAAKIYKKIQDGVFD 177
Rab26 cd04112
Rab GTPase family 26 (Rab26); Rab26 subfamily. First identified in rat pancreatic acinar cells, ...
 18-177 6.07e-05

Rab GTPase family 26 (Rab26); Rab26 subfamily. First identified in rat pancreatic acinar cells, Rab26 is believed to play a role in recruiting mature granules to the plasma membrane upon beta-adrenergic stimulation. Rab26 belongs to the Rab functional group III, which are considered key regulators of intracellular vesicle transport during exocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 206695 [Multi-domain]  Cd Length: 191  Bit Score: 41.77  E-value: 6.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTIL------KCLLNEDVNEVSptFGFQIRTLEVEGLR--FTIWDIGGQKTLRNFWKNYFESTEAIIW 89
Cdd:cd04112     2 KVMLVGDSGVGKTCLLvrfkdgAFLAGSFIATVG--IQFTNKVVTVDGVKvkLQIWDTAGQERFRSVTHAYYRDAHALLL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  90 VVD-----SLDDLR--LEECRNTLQELLVeekllftsILVLANKSDVSG--ALSSEEISKILniskyKSSHWRIFSVSAL 160
Cdd:cd04112    80 LYDvtnksSFDNIRawLTEILEYAQSDVV--------IMLLGNKADMSGerVVKREDGERLA-----KEYGVPFMETSAK 146

                         170
                  ....*....|....*..
gi 1246743216 161 TGLNIKDAISWLANDLK 177
Cdd:cd04112   147 TGLNVELAFTAVAKELK 163
Rab35 cd04110
Rab GTPase family 35 (Rab35); Rab35 is one of several Rab proteins to be found to participate ...
 50-109 8.72e-05

Rab GTPase family 35 (Rab35); Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.


Pssm-ID: 133310 [Multi-domain]  Cd Length: 199  Bit Score: 41.38  E-value: 8.72e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1246743216  50 FQIRTLEVEGLR--FTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDDLRLEECRNTLQEL 109
Cdd:cd04110    43 FKIRTVEINGERvkLQIWDTAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEI 104
Rab6 cd01861
Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways ...
 18-176 4.60e-04

Rab GTPase family 6 (Rab6); Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206654 [Multi-domain]  Cd Length: 161  Bit Score: 38.76  E-value: 4.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLNEDV-NEVSPTFG--FQIRTLEVEG--LRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVD 92
Cdd:cd01861     2 KLVFLGDQSVGKTSIITRFMYDTFdNQYQATIGidFLSKTMYVDDktVRLQLWDTAGQERFRSLIPSYIRDSSVAVVVYD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  93 -----SLDDLR--LEECRNtlqellveEKLLFTSILVLANKSDVSgalSSEEISKILNISKYKSSHWRIFSVSALTGLNI 165
Cdd:cd01861    82 itnrqSFDNTDkwIDDVRD--------ERGNDVIIVLVGNKTDLS---DKRQVSTEEGEKKAKENNAMFIETSAKAGHNV 150

                         170
                  ....*....|.
gi 1246743216 166 KDAISWLANDL 176
Cdd:cd01861   151 KQLFKKIAQAL 161
Rab5_related cd01860
Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The ...
 16-167 4.74e-04

Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion; The Rab5-related subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 206653 [Multi-domain]  Cd Length: 163  Bit Score: 39.07  E-value: 4.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  16 EVRVLLLGLDNAGKTTI-LKCLLNEDVNEVSPTFG--F--QIRTLEVEGLRFTIWDIGGQKTLRNFWKNYFESTEAIIWV 90
Cdd:cd01860     1 QFKLVLLGDSSVGKSSIvLRFVKNEFSENQESTIGaaFltQTVNLDDTTVKFEIWDTAGQERYRSLAPMYYRGAAAAIVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  91 VDSLDDLRLEECRNTLQELlvEEKLLFTSILVLA-NKSDVSG--ALSSEEiskilnISKYKSSHWRIFS-VSALTGLNIK 166
Cdd:cd01860    81 YDITSEESFEKAKSWVKEL--QEHGPPNIVIALAgNKADLESkrQVSTEE------AQEYADENGLLFMeTSAKTGENVN 152


                  .
gi 1246743216 167 D 167
Cdd:cd01860   153 E 153
Rab19 cd01864
Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. ...
 18-130 4.82e-04

Rab GTPase family 19 (Rab19); Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet characterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133267 [Multi-domain]  Cd Length: 165  Bit Score: 38.95  E-value: 4.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLNEDVNEVS-PTFG--FQIRTLEVEG--LRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVD 92
Cdd:cd01864     5 KIILIGDSNVGKTCVVQRFKSGTFSERQgNTIGvdFTMKTLEIQGkrVKLQIWDTAGQERFRTITQSYYRSANGAIIAYD 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1246743216  93 SlddlrleECRNTLQEL--LVEEKLLFTS----ILVLANKSDVS 130
Cdd:cd01864    85 I-------TRRSSFESVphWIEEVEKYGAsnvvLLLIGNKCDLE 121
G_alpha smart00275
G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding ...
 6-95 1.41e-03

G protein alpha subunit; Subunit of G proteins that contains the guanine nucleotide binding site


Pssm-ID: 214595 [Multi-domain]  Cd Length: 342  Bit Score: 38.33  E-value: 1.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216    6 ILRQQKLKEREVRVLLLGLDNAGKTTILKcllnedvnevsptfgfQIRTLEVEGlrFTiwdiggQKTLRNF----WKNYF 81
Cdd:smart00275  11 LEEERKKKKREVKLLLLGAGESGKSTILK----------------QMRILHGDG--FS------QEERREYrpliYSNIL 66

                           90
                   ....*....|....
gi 1246743216   82 ESTEAIIWVVDSLD 95
Cdd:smart00275  67 ESMKALVDAMEELN 80
RAN smart00176
Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the ...
 22-176 1.71e-03

Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases; Ran is involved in the active transport of proteins through nuclear pores.


Pssm-ID: 128473 [Multi-domain]  Cd Length: 200  Bit Score: 37.68  E-value: 1.71e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   22 LGLDNAGKTTILK-CLLNEDVNEVSPTFGFQIRTLEVEG----LRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDD 96
Cdd:smart00176   1 VGDGGTGKTTFVKrHLTGEFEKKYVATLGVEVHPLVFHTnrgpIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTAR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216   97 LRLEECRNTLQELL-VEEKLlftSILVLANKSDVsgalsSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISWLAND 175
Cdd:smart00176  81 VTYKNVPNWHRDLVrVCENI---PIVLCGNKVDV-----KDRKVKAKSITFHRKKNLQYYDISAKSNYNFEKPFLWLARK 152


                   .
gi 1246743216  176 L 176
Cdd:smart00176 153 L 153
Rab14 cd04122
Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, ...
 50-168 1.88e-03

Rab GTPase family 14 (Rab14); Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.


Pssm-ID: 133322 [Multi-domain]  Cd Length: 166  Bit Score: 37.12  E-value: 1.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  50 FQIRTLEVEG--LRFTIWDIGGQKTLRNFWKNYFESTEAIIWVVdsldDLRLEECRNTLQELLVEEKLLF---TSILVLA 124
Cdd:cd04122    39 FGTRIIEVNGqkIKLQIWDTAGQERFRAVTRSYYRGAAGALMVY----DITRRSTYNHLSSWLTDARNLTnpnTVIFLIG 114

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1246743216 125 NKSDVSGA--LSSEEISKILniskyKSSHWRIFSVSALTGLNIKDA 168
Cdd:cd04122   115 NKADLEAQrdVTYEEAKQFA-----DENGLLFLECSAKTGENVEDA 155
Era cd04163
E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is ...
 69-174 2.06e-03

E. coli Ras-like protein (Era) is a multifunctional GTPase; Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.


Pssm-ID: 206726 [Multi-domain]  Cd Length: 168  Bit Score: 37.06  E-value: 2.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  69 GQKTLRNFWKNYfESTEAIIWVVDSLDDLRLEEcRNTLQELlveEKLLFTSILVLaNKSDVsgALSSEEISKILNISKYK 148
Cdd:cd04163    69 GERMVKAAWSAL-KDVDLVLFVVDASEWIGEGD-EFILELL---KKSKTPVILVL-NKIDL--VKDKEDLLPLLEKLKEL 140

                          90       100
                  ....*....|....*....|....*.
gi 1246743216 149 SSHWRIFSVSALTGLNIKDAISWLAN 174
Cdd:cd04163   141 HPFAEIFPISALKGENVDELLEYIVE 166
Gtr1_RagA pfam04670
Gtr1/RagA G protein conserved region; GTR1 was first identified in S. cerevisiae as a ...
 18-110 3.09e-03

Gtr1/RagA G protein conserved region; GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologs of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B.


Pssm-ID: 398377 [Multi-domain]  Cd Length: 231  Bit Score: 37.18  E-value: 3.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILK----CLLNEDVNEVSPTFGFQIRTLEVEG-LRFTIWDIGGQKtlrNFWKNY--------FEST 84
Cdd:pfam04670   1 KVLLMGLSGSGKSSMRSvifsNYSPRDTLRLGATIDVEHSHVRFLGnLVLNLWDCGGQD---DFFDNYltfqkehiFSNV 77

                          90       100
                  ....*....|....*....|....*.
gi 1246743216  85 EAIIWVVDSlDDLRLEECRNTLQELL 110
Cdd:pfam04670  78 GVLIYVFDV-QSREYEEDLARLKETI 102
RabL4 cd04101
Rab GTPase-like family 4 (Rab-like4); RabL4 (Rab-like4) subfamily. RabL4s are novel proteins ...
 64-173 5.19e-03

Rab GTPase-like family 4 (Rab-like4); RabL4 (Rab-like4) subfamily. RabL4s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL4 lacks a prenylation site at the C-terminus. The specific function of RabL4 remains unknown.


Pssm-ID: 206688 [Multi-domain]  Cd Length: 167  Bit Score: 35.97  E-value: 5.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  64 IWDIGGQKTLRNFWKNYFESTEAIIWVVDSLDDLRLEECRNTLQELLVEEKLLFTSILVLANKSDVSG--ALSSEEISKI 141
Cdd:cd04101    57 IFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCDLTDrrEVDAAQAQAL 136

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1246743216 142 LNISKYKsshwrIFSVSALTGLNIKDAISWLA 173
Cdd:cd04101   137 AQANTLK-----FYETSAKEGVGYEAPFLSLA 163
RagC_like cd11385
Rag GTPase, subfamily of Ras-related GTPases, includes Ras-related GTP-binding proteins C and ...
 18-97 6.42e-03

Rag GTPase, subfamily of Ras-related GTPases, includes Ras-related GTP-binding proteins C and D; RagC and RagD are closely related Rag GTPases (ras-related GTP-binding protein C and D) that constitute a unique subgroup of the Ras superfamily, and are functional homologs of Saccharomyces cerevisiae Gtr2. These domains form heterodimers with RagA or RagB, and similarly, Gtr2 dimerizes with Gtr1 in order to function. They play an essential role in regulating amino acid-induced target of rapamycin complex 1 (TORC1) kinase signaling, exocytic cargo sorting at endosomes, and epigenetic control of gene expression. In response to amino acids, the Rag GTPases guide the TORC1 complex to activate the platform containing Rheb proto-oncogene by driving the relocalization of mTORC1 from discrete locations in the cytoplasm to a late endosomal and/or lysosomal compartment that is Rheb-enriched and contains Rab-7.


Pssm-ID: 206745 [Multi-domain]  Cd Length: 175  Bit Score: 35.66  E-value: 6.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246743216  18 RVLLLGLDNAGKTTILKCLLnedvNEVSPTfgfqiRTLEVEG--------------LRFTIWDIGGQktLRNFWKNY--- 80
Cdd:cd11385     1 RILLMGLRRSGKSSIQKVVF----HKMSPN-----ETLFLEStnkitkddisnssfVNFQIWDFPGQ--LDPFDPTLdpe 69

                          90
                  ....*....|....*....
gi 1246743216  81 --FESTEAIIWVVDSLDDL 97
Cdd:cd11385    70 miFSGCGALVFVIDAQDDY 88
obgE PRK12299
GTPase CgtA; Reviewed
 120-180 8.23e-03

GTPase CgtA; Reviewed


Pssm-ID: 237048 [Multi-domain]  Cd Length: 335  Bit Score: 36.20  E-value: 8.23e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1246743216 120 ILVLaNKSDvsgALSSEEISKILNISKYKSSHWRIFSVSALTGLNIKDAISWLANDLKEIK 180
Cdd:PRK12299  275 ILVL-NKID---LLDEEEEREKRAALELAALGGPVFLISAVTGEGLDELLRALWELLEEAR 331
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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