Citrus Sinensis ID: 047889

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--
Protein Sequence
AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRSS
Secondary Structure (PSIPRED)
ccccccHHccccEEEEEEcccccHHHHHHHHHHHHHHHcccccEEEEEEEcccccccccccHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
HHHHHHHccccEEEEEEEcccHHHHHcHHHHHHHHHHHcccccEEEEEEEcccccHHccccHHHHHHHHHcc
Coil and Loop (DISEMBL)
AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRSS
Flexible Loop (DISEMBL)
aitsayyrgalgalLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEeyliksrss
Low Complexity Region (SEG)
AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRSS
Disordered region (IsUnstruct)
****AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLI*****
Disordered Region (DISOPRED)
AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS***
Disordered Region (DISEMBL)
AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRSS
Disordered Region (DISPRO)
AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSM*E*********
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRSS
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	72	2.2.26 [Sep-21-2011]
O04486	217	Ras-related protein RABA2	yes	no	0.791	0.262	0.929	3e-25
Q39572	216	Ras-related protein YPTC6	N/A	no	0.875	0.291	0.809	3e-24
P40393	217	Ras-related protein RIC2	no	no	0.888	0.294	0.718	2e-22
Q40195	218	Ras-related protein Rab11	N/A	no	0.888	0.293	0.734	2e-22
Q39434	214	Ras-related protein Rab2B	N/A	no	0.791	0.266	0.807	4e-22
Q9SN35	214	Ras-related protein RABA1	no	no	0.888	0.299	0.703	4e-22
Q40194	218	Ras-related protein Rab11	N/A	no	0.888	0.293	0.718	6e-22
P62494	216	Ras-related protein Rab-1	yes	no	0.791	0.263	0.807	6e-22
P62493	216	Ras-related protein Rab-1	yes	no	0.791	0.263	0.807	6e-22
Q5R9M7	216	Ras-related protein Rab-1	yes	no	0.791	0.263	0.807	6e-22

>sp|O04486|RAA2A_ARATH Ras-related protein RABA2a OS=Arabidopsis thaliana GN=RABA2A PE=2 SV=1

 Score =  114 bits (284), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 53/57 (92%), Positives = 55/57 (96%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGALGALLVYDVTK TTFENVSRWLK+LRDHA SNIVIMLIGNK+DLKHL
Sbjct: 76  AITSAYYRGALGALLVYDVTKPTTFENVSRWLKELRDHADSNIVIMLIGNKTDLKHL 132

Intracellular vesicle trafficking and protein transport.
Arabidopsis thaliana (taxid: 3702)

>sp|Q39572|YPTC6_CHLRE Ras-related protein YPTC6 OS=Chlamydomonas reinhardtii GN=YPTC6 PE=3 SV=1

 Score =  110 bits (274), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 51/63 (80%), Positives = 56/63 (88%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLVYD+TKS TFENV RWLK+LRDHA SNIVIML+GNKSDLKHL + 
Sbjct: 76  AITSAYYRGAVGALLVYDITKSVTFENVERWLKELRDHADSNIVIMLVGNKSDLKHLRDV 135

Query: 61  MCE 63
             E
Sbjct: 136 QTE 138

Chlamydomonas reinhardtii (taxid: 3055)

>sp|P40393|RIC2_ORYSJ Ras-related protein RIC2 OS=Oryza sativa subsp. japonica GN=RIC2 PE=2 SV=2

 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 46/64 (71%), Positives = 55/64 (85%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLVYDVT+ +TFENV RWLK+LRDH   NIV+ML+GNKSDL+HL+  
Sbjct: 78  AITSAYYRGAVGALLVYDVTRHSTFENVERWLKELRDHTDPNIVVMLVGNKSDLRHLVAV 137

Query: 61  MCEE 64
             +E
Sbjct: 138 QTDE 141

Possesses GTPase activity.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q40195|RB11E_LOTJA Ras-related protein Rab11E OS=Lotus japonicus GN=RAB11E PE=2 SV=1

 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 47/64 (73%), Positives = 54/64 (84%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLVYDVT+STTFE   RWLK+LRDH   NIV+MLIGNKSDL+HL+  
Sbjct: 77  AITSAYYRGAVGALLVYDVTRSTTFETAGRWLKELRDHTDPNIVVMLIGNKSDLRHLVTV 136

Query: 61  MCEE 64
             E+
Sbjct: 137 STED 140

Lotus japonicus (taxid: 34305)

>sp|Q39434|RB2BV_BETVU Ras-related protein Rab2BV OS=Beta vulgaris GN=RAB2BV PE=2 SV=1

 Score =  103 bits (256), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGA+GALLVYD+TK  TF+NV RWL++LRDHA SNIVIM+ GNKSDLKHL
Sbjct: 76  AITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIMMAGNKSDLKHL 132

Beta vulgaris (taxid: 161934)

>sp|Q9SN35|RAA1D_ARATH Ras-related protein RABA1d OS=Arabidopsis thaliana GN=RABA1D PE=2 SV=1

 Score =  103 bits (256), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 45/64 (70%), Positives = 55/64 (85%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLVYDVT+ +TFENV RWL++LRDH   NIV+ML+GNKSDL+HL+  
Sbjct: 77  AITSAYYRGAVGALLVYDVTRHSTFENVERWLRELRDHTDPNIVVMLVGNKSDLRHLVAV 136

Query: 61  MCEE 64
             E+
Sbjct: 137 QTED 140

Intracellular vesicle trafficking and protein transport.

Arabidopsis thaliana (taxid: 3702)

>sp|Q40194|RB11D_LOTJA Ras-related protein Rab11D OS=Lotus japonicus GN=RAB11D PE=2 SV=1

 Score =  102 bits (255), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 46/64 (71%), Positives = 54/64 (84%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLVYDVT+  TFEN +RWLK+LRDH   NIV+MLIGNKSDL+HL+  
Sbjct: 77  AITSAYYRGAVGALLVYDVTRRATFENAARWLKELRDHTDPNIVVMLIGNKSDLRHLVAV 136

Query: 61  MCEE 64
             E+
Sbjct: 137 PTED 140

Lotus japonicus (taxid: 34305)

>sp|P62494|RB11A_RAT Ras-related protein Rab-11A OS=Rattus norvegicus GN=Rab11a PE=1 SV=3

 Score =  102 bits (254), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct: 75  AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 131

Regulates endocytic recycling. May exert its functions by interacting with multiple effector proteins in different complexes. Acts as a major regulator of membrane delivery during cytokinesis. Together with MYO5B and RAB8A participates in epithelial cell polarization. Together with RAB3IP, RAB8A, the exocyst complex, PARD3, PRKCI, ANXA2, CDC42 and DNMBP promotes transcytosis of PODXL to the apical membrane initiation sites (AMIS), apical surface formation and lumenogenesis. Together with MYO5B participates in CFTR trafficking to the plasma membrane and TF (Transferrin) recycling in nonpolarized cells. Required in a complex with MYO5B and RAB11FIP2 for the transport of NPC1L1 to the plasma membrane. Participates in the sorting and basolateral transport of CDH1 from the Golgi apparatus to the plasma membrane. Regulates the recycling of FCGRT (receptor of Fc region of monomeric Ig G) to basolateral membranes.

Rattus norvegicus (taxid: 10116)

>sp|P62493|RB11A_RABIT Ras-related protein Rab-11A OS=Oryctolagus cuniculus GN=RAB11A PE=2 SV=3

 Score =  102 bits (254), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct: 75  AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 131

Regulates endocytic recycling. May exert its functions by interacting with multiple effector proteins in different complexes. Acts as a major regulator of membrane delivery during cytokinesis. Together with MYO5B and RAB8A participates in epithelial cell polarization. Together with RAB3IP, RAB8A, the exocyst complex, PARD3, PRKCI, ANXA2, CDC42 and DNMBP promotes transcytosis of PODXL to the apical membrane initiation sites (AMIS), apical surface formation and lumenogenesis. Together with MYO5B participates in CFTR trafficking to the plasma membrane and TF (Transferrin) recycling in nonpolarized cells. Required in a complex with MYO5B and RAB11FIP2 for the transport of NPC1L1 to the plasma membrane. Participates in the sorting and basolateral transport of CDH1 from the Golgi apparatus to the plasma membrane. Regulates the recycling of FCGRT (receptor of Fc region of monomeric Ig G) to basolateral membranes.

Oryctolagus cuniculus (taxid: 9986)

>sp|Q5R9M7|RB11A_PONAB Ras-related protein Rab-11A OS=Pongo abelii GN=RAB11A PE=2 SV=3

 Score =  102 bits (254), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct: 75  AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 131

Regulates endocytic recycling. May exert its functions by interacting with multiple effector proteins in different complexes. Acts as a major regulator of membrane delivery during cytokinesis. Together with MYO5B and RAB8A participates in epithelial cell polarization. Together with RAB3IP, RAB8A, the exocyst complex, PARD3, PRKCI, ANXA2, CDC42 and DNMBP promotes transcytosis of PODXL to the apical membrane initiation sites (AMIS), apical surface formation and lumenogenesis. Together with MYO5B participates in CFTR trafficking to the plasma membrane and TF (Transferrin) recycling in nonpolarized cells. Required in a complex with MYO5B and RAB11FIP2 for the transport of NPC1L1 to the plasma membrane. Participates in the sorting and basolateral transport of CDH1 from the Golgi apparatus to the plasma membrane. Regulates the recycling of FCGRT (receptor of Fc region of monomeric Ig G) to basolateral membranes.

Pongo abelii (taxid: 9601)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	72
297849266	217	hypothetical protein ARALYDRAFT_888208 [	0.791	0.262	0.929	9e-24
15217568	217	Ras-related protein RABA2a [Arabidopsis	0.791	0.262	0.929	1e-23
224120066	218	predicted protein [Populus trichocarpa]	0.791	0.261	0.929	1e-23
224129448	215	predicted protein [Populus trichocarpa]	0.791	0.265	0.929	2e-23
225465200	215	PREDICTED: ras-related protein RABA2a [V	0.791	0.265	0.929	2e-23
351728017	216	uncharacterized protein LOC100499980 [Gl	0.791	0.263	0.912	2e-23
255570960	215	protein with unknown function [Ricinus c	0.791	0.265	0.912	3e-23
358249314	217	uncharacterized protein LOC100797258 [Gl	0.791	0.262	0.912	3e-23
226491888	217	ras-related protein Rab11C [Zea mays] gi	0.791	0.262	0.912	6e-23
148910011	213	unknown [Picea sitchensis]	0.888	0.300	0.796	1e-22

>gi|297849266|ref|XP_002892514.1| hypothetical protein ARALYDRAFT_888208 [Arabidopsis lyrata subsp. lyrata] gi|297338356|gb|EFH68773.1| hypothetical protein ARALYDRAFT_888208 [Arabidopsis lyrata subsp. lyrata]

 Score =  114 bits (284), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 53/57 (92%), Positives = 55/57 (96%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGALGALLVYDVTK TTFENVSRWLK+LRDHA SNIVIMLIGNK+DLKHL
Sbjct: 76  AITSAYYRGALGALLVYDVTKPTTFENVSRWLKELRDHADSNIVIMLIGNKTDLKHL 132

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15217568|ref|NP_172434.1| Ras-related protein RABA2a [Arabidopsis thaliana] gi|3024516|sp|O04486.1|RAA2A_ARATH RecName: Full=Ras-related protein RABA2a; Short=AtRABA2a; AltName: Full=Ras-related protein Rab11C; Short=AtRab11C; Flags: Precursor gi|2160157|gb|AAB60720.1| Strong similarity to A. thaliana ara-2 (gb|ATHARA2). ESTs gb|ATTS2483,gb|ATTS2484,gb|AA042159 come from this gene [Arabidopsis thaliana] gi|2231303|gb|AAB61994.1| ras-related small GTPase [Arabidopsis thaliana] gi|15010638|gb|AAK73978.1| At1g09630/F21M12_2 [Arabidopsis thaliana] gi|21553810|gb|AAM62903.1| putative RAS-related protein RAB11C [Arabidopsis thaliana] gi|22137284|gb|AAM91487.1| At1g09630/F21M12_2 [Arabidopsis thaliana] gi|332190350|gb|AEE28471.1| Ras-related protein RABA2a [Arabidopsis thaliana]

 Score =  114 bits (284), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 53/57 (92%), Positives = 55/57 (96%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGALGALLVYDVTK TTFENVSRWLK+LRDHA SNIVIMLIGNK+DLKHL
Sbjct: 76  AITSAYYRGALGALLVYDVTKPTTFENVSRWLKELRDHADSNIVIMLIGNKTDLKHL 132

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224120066|ref|XP_002331128.1| predicted protein [Populus trichocarpa] gi|222872856|gb|EEF09987.1| predicted protein [Populus trichocarpa]

 Score =  113 bits (283), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 53/57 (92%), Positives = 55/57 (96%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGALGALLVYDVTK TTFENVSRWLK+LRDHA SNIVIMLIGNK+DLKHL
Sbjct: 76  AITSAYYRGALGALLVYDVTKPTTFENVSRWLKELRDHADSNIVIMLIGNKTDLKHL 132

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224129448|ref|XP_002328719.1| predicted protein [Populus trichocarpa] gi|118484335|gb|ABK94045.1| unknown [Populus trichocarpa] gi|222839017|gb|EEE77368.1| predicted protein [Populus trichocarpa]

 Score =  113 bits (282), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 53/57 (92%), Positives = 55/57 (96%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGALGALLVYDVTK TTFENVSRWLK+LRDHA SNIVIMLIGNK+DLKHL
Sbjct: 76  AITSAYYRGALGALLVYDVTKPTTFENVSRWLKELRDHADSNIVIMLIGNKTDLKHL 132

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225465200|ref|XP_002264444.1| PREDICTED: ras-related protein RABA2a [Vitis vinifera] gi|297739506|emb|CBI29688.3| unnamed protein product [Vitis vinifera]

 Score =  112 bits (281), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 53/57 (92%), Positives = 55/57 (96%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGALGALLVYDVTK TTFENVSRWLK+LRDHA SNIVIMLIGNK+DLKHL
Sbjct: 76  AITSAYYRGALGALLVYDVTKPTTFENVSRWLKELRDHADSNIVIMLIGNKTDLKHL 132

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351728017|ref|NP_001235133.1| uncharacterized protein LOC100499980 [Glycine max] gi|255628259|gb|ACU14474.1| unknown [Glycine max]

 Score =  112 bits (281), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 52/57 (91%), Positives = 55/57 (96%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGALGALLVYDVTK TTFENVSRWLK+LRDHA +NIVIMLIGNK+DLKHL
Sbjct: 76  AITSAYYRGALGALLVYDVTKPTTFENVSRWLKELRDHADANIVIMLIGNKTDLKHL 132

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255570960|ref|XP_002526431.1| protein with unknown function [Ricinus communis] gi|223534211|gb|EEF35926.1| protein with unknown function [Ricinus communis]

 Score =  112 bits (280), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 52/57 (91%), Positives = 55/57 (96%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGALGALLVYDVTK TTFENVSRWLK+LRDHA +NIVIMLIGNK+DLKHL
Sbjct: 76  AITSAYYRGALGALLVYDVTKPTTFENVSRWLKELRDHADANIVIMLIGNKTDLKHL 132

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358249314|ref|NP_001240030.1| uncharacterized protein LOC100797258 [Glycine max] gi|255645100|gb|ACU23049.1| unknown [Glycine max]

 Score =  112 bits (280), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 52/57 (91%), Positives = 55/57 (96%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGALGALLVYDVTK TTFENVSRWLK+LRDHA +NIVIMLIGNK+DLKHL
Sbjct: 76  AITSAYYRGALGALLVYDVTKPTTFENVSRWLKELRDHADANIVIMLIGNKTDLKHL 132

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226491888|ref|NP_001147252.1| ras-related protein Rab11C [Zea mays] gi|195609118|gb|ACG26389.1| ras-related protein Rab11C [Zea mays]

 Score =  111 bits (277), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 52/57 (91%), Positives = 54/57 (94%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGALGALLVYDVTK TTFENVSRWLK+LRDHA  NIVIMLIGNK+DLKHL
Sbjct: 76  AITSAYYRGALGALLVYDVTKPTTFENVSRWLKELRDHADYNIVIMLIGNKTDLKHL 132

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|148910011|gb|ABR18090.1| unknown [Picea sitchensis]

 Score =  110 bits (275), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/64 (79%), Positives = 56/64 (87%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLVYD+TK TTFENV RWLK+LRDHA SNIVIML+GNKSDLKHL   
Sbjct: 76  AITSAYYRGAVGALLVYDITKPTTFENVGRWLKELRDHADSNIVIMLVGNKSDLKHLRGV 135

Query: 61  MCEE 64
             E+
Sbjct: 136 STED 139

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	72
TAIR|locus:2024276	217	RAB11c "RAB GTPase 11C" [Arabi	0.791	0.262	0.929	1.8e-23
ASPGD|ASPL0000062894	210	srgE [Emericella nidulans (tax	0.888	0.304	0.734	4.9e-21
UNIPROTKB|Q5ZJN2	216	RAB11A "Ras-related protein Ra	0.791	0.263	0.807	4.9e-21
UNIPROTKB|F2Z4D5	216	RAB11A "Ras-related protein Ra	0.791	0.263	0.807	4.9e-21
UNIPROTKB|Q2TA29	216	RAB11A "Ras-related protein Ra	0.791	0.263	0.807	4.9e-21
UNIPROTKB|Q3MHP2	218	RAB11B "Ras-related protein Ra	0.791	0.261	0.807	4.9e-21
UNIPROTKB|J9JHN1	218	RAB11B "Uncharacterized protei	0.791	0.261	0.807	4.9e-21
UNIPROTKB|P62490	216	RAB11A "Ras-related protein Ra	0.791	0.263	0.807	4.9e-21
UNIPROTKB|B4DMK0	179	RAB11B "cDNA FLJ61134, highly	0.791	0.318	0.807	4.9e-21
UNIPROTKB|B4DT13	155	RAB11A "cDNA FLJ51542, highly	0.791	0.367	0.807	4.9e-21

TAIR|locus:2024276 RAB11c "RAB GTPase 11C" [Arabidopsis thaliana (taxid:3702)]

 Score = 270 (100.1 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 53/57 (92%), Positives = 55/57 (96%)

Query:     1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
             AITSAYYRGALGALLVYDVTK TTFENVSRWLK+LRDHA SNIVIMLIGNK+DLKHL
Sbjct:    76 AITSAYYRGALGALLVYDVTKPTTFENVSRWLKELRDHADSNIVIMLIGNKTDLKHL 132

GO:0005525 "GTP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM;IDA

GO:0007264 "small GTPase mediated signal transduction" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0000910 "cytokinesis" evidence=IMP

GO:0005768 "endosome" evidence=IDA

GO:0009504 "cell plate" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0016192 "vesicle-mediated transport" evidence=RCA

GO:0019932 "second-messenger-mediated signaling" evidence=RCA

ASPGD|ASPL0000062894 srgE [Emericella nidulans (taxid:162425)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 47/64 (73%), Positives = 56/64 (87%)

Query:     1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
             AITSAYYRGA+GALLVYD++K  T++NV+RWLK+LRDHA SNIVIML+GNKSDL+HL   
Sbjct:    73 AITSAYYRGAVGALLVYDISKHQTYDNVNRWLKELRDHADSNIVIMLVGNKSDLRHLRAV 132

Query:    61 MCEE 64
               EE
Sbjct:   133 PTEE 136

GO:0034498 "early endosome to Golgi transport" evidence=IEA

GO:0033205 "cell cycle cytokinesis" evidence=IEA

GO:0042144 "vacuole fusion, non-autophagic" evidence=IEA

GO:0071852 "fungal-type cell wall organization or biogenesis" evidence=IEA

GO:0006887 "exocytosis" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

GO:0007264 "small GTPase mediated signal transduction" evidence=IEA

GO:0005768 "endosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005741 "mitochondrial outer membrane" evidence=IEA

GO:0003924 "GTPase activity" evidence=IEA

UNIPROTKB|Q5ZJN2 RAB11A "Ras-related protein Rab-11A" [Gallus gallus (taxid:9031)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query:     1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
             AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct:    75 AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 131

GO:0007264 "small GTPase mediated signal transduction" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0055038 "recycling endosome membrane" evidence=IEA

GO:0000910 "cytokinesis" evidence=IEA

GO:0003924 "GTPase activity" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005802 "trans-Golgi network" evidence=IEA

GO:0016192 "vesicle-mediated transport" evidence=IEA

GO:0031175 "neuron projection development" evidence=IEA

GO:0043234 "protein complex" evidence=IEA

GO:0072659 "protein localization to plasma membrane" evidence=IEA

GO:0032154 "cleavage furrow" evidence=ISS

UNIPROTKB|F2Z4D5 RAB11A "Ras-related protein Rab-11A" [Bos taurus (taxid:9913)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query:     1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
             AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct:    75 AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 131

GO:0072659 "protein localization to plasma membrane" evidence=IEA

GO:0055037 "recycling endosome" evidence=IEA

GO:0043234 "protein complex" evidence=IEA

GO:0032154 "cleavage furrow" evidence=IEA

GO:0031175 "neuron projection development" evidence=IEA

GO:0016192 "vesicle-mediated transport" evidence=IEA

GO:0005802 "trans-Golgi network" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0003924 "GTPase activity" evidence=IEA

GO:0000910 "cytokinesis" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0007264 "small GTPase mediated signal transduction" evidence=IEA

UNIPROTKB|Q2TA29 RAB11A "Ras-related protein Rab-11A" [Bos taurus (taxid:9913)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query:     1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
             AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct:    75 AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 131

GO:0006184 "GTP catabolic process" evidence=ISS

GO:0045335 "phagocytic vesicle" evidence=ISS

GO:0055037 "recycling endosome" evidence=ISS

GO:0032402 "melanosome transport" evidence=ISS

GO:0072659 "protein localization to plasma membrane" evidence=ISS

GO:0031175 "neuron projection development" evidence=ISS

GO:0032154 "cleavage furrow" evidence=ISS

GO:0003924 "GTPase activity" evidence=ISS

GO:0055038 "recycling endosome membrane" evidence=IEA

GO:0030670 "phagocytic vesicle membrane" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

GO:0007264 "small GTPase mediated signal transduction" evidence=IEA

UNIPROTKB|Q3MHP2 RAB11B "Ras-related protein Rab-11B" [Bos taurus (taxid:9913)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query:     1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
             AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct:    75 AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 131

GO:0045335 "phagocytic vesicle" evidence=ISS

GO:0055037 "recycling endosome" evidence=ISS

GO:0032402 "melanosome transport" evidence=ISS

GO:0005525 "GTP binding" evidence=ISS

GO:0019003 "GDP binding" evidence=ISS

GO:0003924 "GTPase activity" evidence=ISS

GO:0030670 "phagocytic vesicle membrane" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0007264 "small GTPase mediated signal transduction" evidence=IEA

UNIPROTKB|J9JHN1 RAB11B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query:     1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
             AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct:    75 AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 131

GO:0005525 "GTP binding" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0007264 "small GTPase mediated signal transduction" evidence=IEA

UNIPROTKB|P62490 RAB11A "Ras-related protein Rab-11A" [Canis lupus familiaris (taxid:9615)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query:     1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
             AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct:    75 AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 131

GO:0045335 "phagocytic vesicle" evidence=ISS

GO:0055037 "recycling endosome" evidence=ISS

GO:0032402 "melanosome transport" evidence=ISS

GO:0072659 "protein localization to plasma membrane" evidence=ISS

GO:0031175 "neuron projection development" evidence=ISS

GO:0032154 "cleavage furrow" evidence=ISS

GO:0003924 "GTPase activity" evidence=ISS

GO:0055038 "recycling endosome membrane" evidence=IEA

GO:0030670 "phagocytic vesicle membrane" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0043234 "protein complex" evidence=IEA

GO:0016192 "vesicle-mediated transport" evidence=IEA

GO:0005802 "trans-Golgi network" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0000910 "cytokinesis" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

GO:0007264 "small GTPase mediated signal transduction" evidence=IEA

UNIPROTKB|B4DMK0 RAB11B "cDNA FLJ61134, highly similar to Ras-related protein Rab-11B" [Homo sapiens (taxid:9606)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query:     1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
             AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct:    75 AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 131

GO:0007264 "small GTPase mediated signal transduction" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

UNIPROTKB|B4DT13 RAB11A "cDNA FLJ51542, highly similar to Ras-related protein Rab-11B" [Homo sapiens (taxid:9606)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query:     1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
             AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct:    75 AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 131

GO:0007264 "small GTPase mediated signal transduction" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5R9M7	RB11A_PONAB	No assigned EC number	0.8070	0.7916	0.2638	yes	no
P17610	YPT3_SCHPO	No assigned EC number	0.7031	0.8888	0.2990	yes	no
Q2TA29	RB11A_BOVIN	No assigned EC number	0.8070	0.7916	0.2638	yes	no
Q52NJ1	RB11A_PIG	No assigned EC number	0.8070	0.7916	0.2638	yes	no
Q5ZJN2	RB11A_CHICK	No assigned EC number	0.8070	0.7916	0.2638	yes	no
O04486	RAA2A_ARATH	No assigned EC number	0.9298	0.7916	0.2626	yes	no
P62491	RB11A_HUMAN	No assigned EC number	0.8070	0.7916	0.2638	yes	no
P62490	RB11A_CANFA	No assigned EC number	0.8070	0.7916	0.2638	yes	no
P62493	RB11A_RABIT	No assigned EC number	0.8070	0.7916	0.2638	yes	no
P62492	RB11A_MOUSE	No assigned EC number	0.8070	0.7916	0.2638	yes	no
P62494	RB11A_RAT	No assigned EC number	0.8070	0.7916	0.2638	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	72
cd01868	165	cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-	4e-39
smart00175	164	smart00175, RAB, Rab subfamily of small GTPases	2e-32
PLN03110	216	PLN03110, PLN03110, Rab GTPase; Provisional	2e-31
cd00154	159	cd00154, Rab, Ras-related in brain (Rab) family of	5e-27
pfam00071	162	pfam00071, Ras, Ras family	2e-26
cd01866	168	cd01866, Rab2, Rab GTPase family 2 (Rab2)	1e-25
PLN03108	210	PLN03108, PLN03108, Rab family protein; Provisiona	1e-22
cd01864	165	cd01864, Rab19, Rab GTPase family 19 (Rab19)	3e-22
cd01860	163	cd01860, Rab5_related, Rab-related GTPase family i	8e-21
cd01867	167	cd01867, Rab8_Rab10_Rab13_like, Rab GTPase familie	5e-20
cd04113	161	cd04113, Rab4, Rab GTPase family 4 (Rab4)	1e-19
cd04122	166	cd04122, Rab14, Rab GTPase family 14 (Rab14)	1e-19
cd04123	162	cd04123, Rab21, Rab GTPase family 21 (Rab21)	1e-18
cd01869	166	cd01869, Rab1_Ypt1, Rab GTPase family 1 includes t	8e-18
cd01863	161	cd01863, Rab18, Rab GTPase family 18 (Rab18)	3e-16
cd01861	161	cd01861, Rab6, Rab GTPase family 6 (Rab6)	1e-15
cd04120	202	cd04120, Rab12, Rab GTPase family 12 (Rab12)	5e-15
cd04112	191	cd04112, Rab26, Rab GTPase family 26 (Rab26)	1e-14
cd04111	211	cd04111, Rab39, Rab GTPase family 39 (Rab39)	1e-14
cd04107	201	cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab1	4e-14
cd01865	165	cd01865, Rab3, Rab GTPase family 3 contains Rab3A,	3e-13
PTZ00099	176	PTZ00099, PTZ00099, rab6; Provisional	4e-12
cd04127	180	cd04127, Rab27A, Rab GTPase family 27a (Rab27a)	1e-11
COG1100	219	COG1100, COG1100, GTPase SAR1 and related small G	2e-11
cd04110	199	cd04110, Rab35, Rab GTPase family 35 (Rab35)	2e-11
cd04114	169	cd04114, Rab30, Rab GTPase family 30 (Rab30)	4e-11
cd01862	172	cd01862, Rab7, Rab GTPase family 7 (Rab7)	2e-10
cd04109	213	cd04109, Rab28, Rab GTPase family 28 (Rab28)	2e-10
cd04119	168	cd04119, RJL, Rab GTPase family J-like (RabJ-like)	3e-10
TIGR00231	162	TIGR00231, small_GTP, small GTP-binding protein do	4e-10
cd04115	170	cd04115, Rab33B_Rab33A, Rab GTPase family 33 inclu	4e-10
cd04108	170	cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab3	6e-10
cd04117	164	cd04117, Rab15, Rab GTPase family 15 (Rab15)	1e-09
PLN03118	211	PLN03118, PLN03118, Rab family protein; Provisiona	2e-09
cd04101	167	cd04101, RabL4, Rab GTPase-like family 4 (Rab-like	3e-09
cd04121	189	cd04121, Rab40, Rab GTPase family 40 (Rab40) conta	6e-09
cd00877	166	cd00877, Ran, Ras-related nuclear proteins (Ran)/T	9e-09
cd04118	193	cd04118, Rab24, Rab GTPase family 24 (Rab24)	1e-08
PLN03071	219	PLN03071, PLN03071, GTP-binding nuclear protein Ra	1e-08
cd04106	162	cd04106, Rab23_like, Rab GTPase family 23 (Rab23)-	3e-08
PTZ00132	215	PTZ00132, PTZ00132, GTP-binding nuclear protein Ra	4e-08
cd00876	160	cd00876, Ras, Rat sarcoma (Ras) family of small gu	1e-07
cd00157	171	cd00157, Rho, Ras homology family (Rho) of small g	5e-07
smart00176	200	smart00176, RAN, Ran (Ras-related nuclear proteins	7e-07
cd04124	161	cd04124, RabL2, Rab GTPase-like family 2 (Rab-like	8e-07
cd04146	166	cd04146, RERG_RasL11_like, Ras-related and Estroge	1e-06
smart00174	174	smart00174, RHO, Rho (Ras homology) subfamily of R	9e-06
cd04145	164	cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3	2e-05
smart00173	164	smart00173, RAS, Ras subfamily of RAS small GTPase	2e-05
smart00010	166	smart00010, small_GTPase, Small GTPase of the Ras	3e-05
cd00882	161	cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like s	4e-05
pfam08477	116	pfam08477, Miro, Miro-like protein	4e-05
PTZ00369	189	PTZ00369, PTZ00369, Ras-like protein; Provisional	5e-05
cd04144	190	cd04144, Ras2, Rat sarcoma (Ras) family 2 of small	5e-05
cd01893	168	cd01893, Miro1, Mitochondrial Rho family 1 (Miro1)	7e-05
cd04133	173	cd04133, Rop_like, Rho-related protein from plants	8e-05
cd04137	180	cd04137, RheB, Ras Homolog Enriched in Brain (RheB	9e-05
cd04126	220	cd04126, Rab20, Rab GTPase family 20 (Rab20)	1e-04
cd04132	197	cd04132, Rho4_like, Ras homology family 4 (Rho4) o	1e-04
cd04141	172	cd04141, Rit_Rin_Ric, Ras-like protein in all tiss	5e-04
cd04139	163	cd04139, RalA_RalB, Ral (Ras-like) family containi	5e-04
cd04148	219	cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfam	6e-04
cd04136	164	cd04136, Rap_like, Rap-like family consists of Rap	6e-04
cd04138	162	cd04138, H_N_K_Ras_like, Ras GTPase family contain	0.001
cd04176	163	cd04176, Rap2, Rap2 family GTPase consists of Rap2	0.002
cd04175	164	cd04175, Rap1, Rap1 family GTPase consists of Rap1	0.002
cd04130	173	cd04130, Wrch_1, Wnt-1 responsive Cdc42 homolog (W	0.003

>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25

 Score =  126 bits (318), Expect = 4e-39
 Identities = 48/57 (84%), Positives = 54/57 (94%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGA+GALLVYD+TK +TFENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct: 67  AITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHADSNIVIMLVGNKSDLRHL 123

Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. 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. Length = 165

>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases

 Score =  108 bits (273), Expect = 2e-32
 Identities = 36/56 (64%), Positives = 48/56 (85%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           +ITS+YYRGA+GALLVYD+T   +FEN+  WLK+LR++A  N+VIML+GNKSDL+ 
Sbjct: 64  SITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNVVIMLVGNKSDLEE 119

Rab GTPases are implicated in vesicle trafficking. Length = 164

>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional

 Score =  108 bits (270), Expect = 2e-31
 Identities = 45/57 (78%), Positives = 51/57 (89%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGA+GALLVYD+TK  TF+NV RWL++LRDHA SNIVIM+ GNKSDL HL
Sbjct: 76  AITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIMMAGNKSDLNHL 132

Length = 216

>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases)

 Score = 95.2 bits (238), Expect = 5e-27
 Identities = 33/54 (61%), Positives = 45/54 (83%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           +ITS+YYRGA GA+LVYDVT   +FEN+ +WL +L+++A  NI I+L+GNKSDL
Sbjct: 64  SITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIILVGNKSDL 117

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. Length = 159

>gnl|CDD|215692 pfam00071, Ras, Ras family

 Score = 94.1 bits (235), Expect = 2e-26
 Identities = 29/56 (51%), Positives = 40/56 (71%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           A+   YYRGA G LLVYD+T   +FENV +WL+++  HA  N+ I+L+GNK DL+ 
Sbjct: 63  ALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIVLVGNKCDLED 118

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. Length = 162

>gnl|CDD|206658 cd01866, Rab2, Rab GTPase family 2 (Rab2)

 Score = 92.1 bits (229), Expect = 1e-25
 Identities = 33/56 (58%), Positives = 44/56 (78%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           +IT +YYRGA GALLVYD+T+  TF +++ WL+D R H+ SN+ IMLIGNK DL+ 
Sbjct: 68  SITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCDLES 123

Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. 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. Length = 168

>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional

 Score = 85.0 bits (210), Expect = 1e-22
 Identities = 34/56 (60%), Positives = 44/56 (78%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           +IT +YYRGA GALLVYD+T+  TF +++ WL+D R HA +N+ IMLIGNK DL H
Sbjct: 70  SITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCDLAH 125

Length = 210

>gnl|CDD|133267 cd01864, Rab19, Rab GTPase family 19 (Rab19)

 Score = 83.3 bits (206), Expect = 3e-22
 Identities = 25/53 (47%), Positives = 41/53 (77%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           IT +YYR A GA++ YD+T+ ++FE+V  W++++  +  SN+V++LIGNK DL
Sbjct: 68  ITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDL 120

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. Length = 165

>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion

 Score = 79.5 bits (197), Expect = 8e-21
 Identities = 26/49 (53%), Positives = 35/49 (71%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           YYRGA  A++VYD+T   +FE    W+K+L++H   NIVI L GNK+DL
Sbjct: 70  YYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIVIALAGNKADL 118

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. Length = 163

>gnl|CDD|206659 cd01867, Rab8_Rab10_Rab13_like, Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13)

 Score = 77.7 bits (192), Expect = 5e-20
 Identities = 25/55 (45%), Positives = 42/55 (76%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           IT++YYRGA+G +LVYD+T   +FEN+  W++++ +HA  ++  ML+GNK D++ 
Sbjct: 68  ITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVERMLVGNKCDMEE 122

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. Length = 167

>gnl|CDD|206696 cd04113, Rab4, Rab GTPase family 4 (Rab4)

 Score = 76.7 bits (189), Expect = 1e-19
 Identities = 29/54 (53%), Positives = 39/54 (72%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++T +YYRGA GALLVYD+T   +F  ++ WL D R  A  +IVI+L+GNK DL
Sbjct: 64  SVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLASPDIVIILVGNKKDL 117

Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. 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. Length = 161

>gnl|CDD|133322 cd04122, Rab14, Rab GTPase family 14 (Rab14)

 Score = 76.8 bits (189), Expect = 1e-19
 Identities = 30/54 (55%), Positives = 41/54 (75%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           A+T +YYRGA GAL+VYD+T+ +T+ ++S WL D R+    N VI LIGNK+DL
Sbjct: 66  AVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADL 119

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. Length = 166

>gnl|CDD|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21)

 Score = 74.2 bits (183), Expect = 1e-18
 Identities = 25/55 (45%), Positives = 41/55 (74%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           A+   YYR A GA+LVYD+T + +F+ V +W+K+L+   G+NI ++++GNK DL+
Sbjct: 64  ALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLE 118

The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate 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. Length = 162

>gnl|CDD|206661 cd01869, Rab1_Ypt1, Rab GTPase family 1 includes the yeast homolog Ypt1

 Score = 72.0 bits (177), Expect = 8e-18
 Identities = 27/54 (50%), Positives = 39/54 (72%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           ITS+YYRGA G ++VYDVT   +F NV +WL+++  +A  N+  +L+GNK DL 
Sbjct: 67  ITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLT 120

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. Length = 166

>gnl|CDD|206656 cd01863, Rab18, Rab GTPase family 18 (Rab18)

 Score = 67.7 bits (166), Expect = 3e-16
 Identities = 27/55 (49%), Positives = 38/55 (69%), Gaps = 1/55 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDL 54
            +TS+YYRGA G +LVYDVT+  TF+N+  WL +L  ++   + V ML+GNK D 
Sbjct: 64  TLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDK 118

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. Length = 161

>gnl|CDD|206654 cd01861, Rab6, Rab GTPase family 6 (Rab6)

 Score = 66.1 bits (162), Expect = 1e-15
 Identities = 21/51 (41%), Positives = 38/51 (74%)

Query: 4   SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
            +Y R +  A++VYD+T   +F+N  +W+ D+RD  G++++I+L+GNK+DL
Sbjct: 67  PSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDL 117

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. Length = 161

>gnl|CDD|206699 cd04120, Rab12, Rab GTPase family 12 (Rab12)

 Score = 65.4 bits (159), Expect = 5e-15
 Identities = 25/53 (47%), Positives = 39/53 (73%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSD 53
           +ITSAYYR A G +LVYD+TK  TF+++ +W+K +  +A  +  ++L+GNK D
Sbjct: 64  SITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLD 116

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. Length = 202

>gnl|CDD|206695 cd04112, Rab26, Rab GTPase family 26 (Rab26)

 Score = 64.1 bits (156), Expect = 1e-14
 Identities = 26/54 (48%), Positives = 42/54 (77%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++T AYYR A   LL+YDVT  ++F+N+  WL ++ ++A S++VIML+GNK+D+
Sbjct: 65  SVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIMLLGNKADM 118

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. Length = 191

>gnl|CDD|133311 cd04111, Rab39, Rab GTPase family 39 (Rab39)

 Score = 64.4 bits (157), Expect = 1e-14
 Identities = 24/55 (43%), Positives = 37/55 (67%), Gaps = 1/55 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDH-AGSNIVIMLIGNKSDL 54
           +IT +YYR ++G LLV+D+T   +FE+V  WL++ R H      V +L+G+K DL
Sbjct: 67  SITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCDL 121

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. Length = 211

>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32 (Rab32)

 Score = 63.1 bits (154), Expect = 4e-14
 Identities = 26/57 (45%), Positives = 36/57 (63%), Gaps = 4/57 (7%)

Query: 3   TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDH----AGSNIVIMLIGNKSDLK 55
           T  YY+GA+GA++V+DVT+ +TFE V +W  DL        G  I  +L+ NK DLK
Sbjct: 67  TRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLLANKCDLK 123

Rab38/Rab32 subfamily. Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. 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. Length = 201

>gnl|CDD|206657 cd01865, Rab3, Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D

 Score = 60.3 bits (146), Expect = 3e-13
 Identities = 22/54 (40%), Positives = 37/54 (68%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           IT+AYYRGA+G +L+YD+T   +F  V  W   ++ ++  N  ++L+GNK D++
Sbjct: 66  ITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDME 119

The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. 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. Length = 165

>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional

 Score = 57.4 bits (138), Expect = 4e-12
 Identities = 24/70 (34%), Positives = 46/70 (65%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           ++  +Y R +  A++VYD+T   +FEN ++W++D+ +  G +++I L+GNK+DL  L   
Sbjct: 44  SLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKV 103

Query: 61  MCEEYLIKSR 70
             EE + K++
Sbjct: 104 TYEEGMQKAQ 113

Length = 176

>gnl|CDD|206700 cd04127, Rab27A, Rab GTPase family 27a (Rab27a)

 Score = 56.0 bits (135), Expect = 1e-11
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDLKHL-- 57
           ++T+A++R A+G LL++D+T   +F NV  W+  L+ HA   N  I+LIGNK+DL     
Sbjct: 78  SLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVLIGNKADLPDQRE 137

Query: 58  -----LNSMCEEY 65
                   + ++Y
Sbjct: 138 VSERQARELADKY 150

The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated insulin secretion, making it a potential target for diabetes therapy. When bound to JFC1 in prostate cells, Rab27a is believed to regulate the exocytosis of prostate- specific markers. 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. Length = 180

>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General function prediction only]

 Score = 56.1 bits (135), Expect = 2e-11
 Identities = 24/57 (42%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKST-TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           ++   YYRGA G L+VYD T    + E    WL++LR+ A  ++ I+L+GNK DL  
Sbjct: 69  SLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFD 125

Length = 219

>gnl|CDD|133310 cd04110, Rab35, Rab GTPase family 35 (Rab35)

 Score = 55.6 bits (134), Expect = 2e-11
 Identities = 24/52 (46%), Positives = 35/52 (67%), Gaps = 1/52 (1%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSD 53
           ITS YYRG  G ++VYDVT   +F NV RWL+++  +    +  +L+GNK+D
Sbjct: 71  ITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCDD-VCKVLVGNKND 121

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. Length = 199

>gnl|CDD|133314 cd04114, Rab30, Rab GTPase family 30 (Rab30)

 Score = 54.5 bits (131), Expect = 4e-11
 Identities = 20/54 (37%), Positives = 35/54 (64%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           +IT +YYR A   +L YD+T   +F  +  WL+++  +A + ++ +L+GNK DL
Sbjct: 71  SITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNKIDL 124

Rab30 subfamily. Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. 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. Length = 169

>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7)

 Score = 53.1 bits (128), Expect = 2e-10
 Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 4/55 (7%)

Query: 4   SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG----SNIVIMLIGNKSDL 54
            A+YRGA   +LVYDVT   +FE++  W  +    A      N   +++GNK DL
Sbjct: 67  VAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFVVLGNKIDL 121

Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. 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. Length = 172

>gnl|CDD|206694 cd04109, Rab28, Rab GTPase family 28 (Rab28)

 Score = 53.3 bits (128), Expect = 2e-10
 Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 3/54 (5%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRWL---KDLRDHAGSNIVIMLIGNKSDLKH 56
           Y  GA    LVYD+T S +FEN+  WL   K + + + +   ++L+GNK+DL+H
Sbjct: 70  YIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTDLEH 123

Rab28 subfamily. First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumably the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. 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. Length = 213

>gnl|CDD|133319 cd04119, RJL, Rab GTPase family J-like (RabJ-like)

 Score = 52.4 bits (126), Expect = 3e-10
 Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 5/54 (9%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-----NIVIMLIGNKSDL 54
           +Y+   G LLVYDVT   +FE +  WLK+++   G      NIV+++  NK DL
Sbjct: 69  FYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKIDL 122

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. 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. Length = 168

>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain

 Score = 52.0 bits (125), Expect = 4e-10
 Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 1   AITSAYYRGALGALLVYDVTK--STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AI   YYR    +L V+D+        E + +  K++  HA S + I+L+GNK DL+  
Sbjct: 66  AIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKIDLRDA 124

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]. Length = 162

>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and Rab33B

 Score = 52.1 bits (125), Expect = 4e-10
 Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKH 56
           YYR     + VYDVT   +F ++  W+++   H+  + +  +L+GNK DL+ 
Sbjct: 72  YYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLRE 123

Rab33B/Rab33A subfamily. Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. 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. Length = 170

>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36 (Rab36)

 Score = 51.4 bits (123), Expect = 6e-10
 Identities = 21/54 (38%), Positives = 37/54 (68%), Gaps = 1/54 (1%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDL 54
           I S YYRGA   ++V+D+T   + E+  +WL+D L+++  S++++ L+G K DL
Sbjct: 65  IASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDL 118

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. Length = 170

>gnl|CDD|206698 cd04117, Rab15, Rab GTPase family 15 (Rab15)

 Score = 50.4 bits (120), Expect = 1e-09
 Identities = 20/52 (38%), Positives = 35/52 (67%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSD 53
           IT  YYR A G  LVYD++   +++++ +W+ D+ ++A   +  +LIGNK+D
Sbjct: 65  ITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKAD 116

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. Length = 164

>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional

 Score = 50.8 bits (121), Expect = 2e-09
 Identities = 26/54 (48%), Positives = 37/54 (68%), Gaps = 2/54 (3%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSR-WLKDLRDHA-GSNIVIMLIGNKSD 53
           +TS+YYR A G +LVYDVT+  TF N+S  W K++  ++   + V ML+GNK D
Sbjct: 78  LTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVD 131

Length = 211

>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4)

 Score = 49.4 bits (118), Expect = 3e-09
 Identities = 19/41 (46%), Positives = 27/41 (65%), Gaps = 1/41 (2%)

Query: 15  LVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDL 54
           +VYDVT   +F N SRW+  +R H+ G +   +L+GNK DL
Sbjct: 82  VVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCDL 122

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. Length = 167

>gnl|CDD|133321 cd04121, Rab40, Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c

 Score = 49.2 bits (117), Expect = 6e-09
 Identities = 21/53 (39%), Positives = 35/53 (66%), Gaps = 1/53 (1%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           I  +Y RGA G +LVYD+T   +F+ + RW+K++ +HA   +  +L+GN+  L
Sbjct: 71  IFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHA-PGVPKILVGNRLHL 122

The Rab40 subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. 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. Length = 189

>gnl|CDD|206643 cd00877, Ran, Ras-related nuclear proteins (Ran)/TC4 family of small GTPases

 Score = 48.5 bits (116), Expect = 9e-09
 Identities = 21/53 (39%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 4   SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
             YY     A++++DVT   T++NV  W +DL      NI I+L GNK D+K 
Sbjct: 67  DGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCE-NIPIVLCGNKVDIKD 118

Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is bound to chromatin and confined to the nucleus. Ran itself is mobile and is actively imported into the nucleus by a mechanism involving NTF-2. Together with the compartmentalization of its regulators, this is thought to produce a relatively high concentration of RanGTP in the nucleus. Length = 166

>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24)

 Score = 48.7 bits (116), Expect = 1e-08
 Identities = 23/54 (42%), Positives = 35/54 (64%), Gaps = 1/54 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           A++  YYRGA  A++ YD+T S++FE    W+K+L++    +  I L G KSDL
Sbjct: 65  AMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNLE-EHCKIYLCGTKSDL 117

Rab24 is distinct from other Rabs in several ways. It exists primarily in the GTP-bound state, having a low intrinsic GTPase activity; it is not efficiently geranyl-geranylated at the C-terminus; it does not form a detectable complex with Rab GDP-dissociation inhibitors (GDIs); and it has recently been shown to undergo tyrosine phosphorylation when overexpressed in vitro. The specific function of Rab24 still remains unknown. It is found in a transport route between ER-cis-Golgi and late endocytic compartments. It is putatively involved in an autophagic pathway, possibly directing misfolded proteins in the ER to degradative pathways. 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. Length = 193

>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional

 Score = 48.6 bits (116), Expect = 1e-08
 Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 5   AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            YY     A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 81  GYYIHGQCAIIMFDVTARLTYKNVPTWHRDLC-RVCENIPIVLCGNKVDVK 130

Length = 219

>gnl|CDD|133306 cd04106, Rab23_like, Rab GTPase family 23 (Rab23)-like

 Score = 47.1 bits (112), Expect = 3e-08
 Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           AIT AYYRGA   +LV+  T   +FE +  W + +    G +I ++L+  K DL  
Sbjct: 66  AITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAECG-DIPMVLVQTKIDLLD 120

Rab23-like subfamily. Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signaling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. 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. Length = 162

>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional

 Score = 47.0 bits (112), Expect = 4e-08
 Identities = 20/50 (40%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           YY     A++++DVT   T++NV  W +D+      NI I+L+GNK D+K
Sbjct: 78  YYIKGQCAIIMFDVTSRITYKNVPNWHRDIV-RVCENIPIVLVGNKVDVK 126

Length = 215

>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases)

 Score = 45.2 bits (108), Expect = 1e-07
 Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKDLRD-HAGSNIVIMLIGNKSDLKH 56
           Y R   G +LVY +T   +FE +    + +       ++ I+L+GNK DL++
Sbjct: 67  YIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCDLEN 118

The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 160

>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine triphosphatases (GTPases)

 Score = 43.7 bits (104), Expect = 5e-07
 Identities = 15/42 (35%), Positives = 27/42 (64%), Gaps = 2/42 (4%)

Query: 14  LLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
           LL + V   ++FENV ++W  +++ +   N+ I+L+G K DL
Sbjct: 76  LLCFSVDSPSSFENVKTKWYPEIKHYCP-NVPIILVGTKIDL 116

Members of the Rho (Ras homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Since crystal structures often lack C-terminal residues, this feature is not available for annotation in many of the CDs in the hierarchy. Length = 171

>gnl|CDD|128473 smart00176, RAN, Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases

 Score = 43.8 bits (103), Expect = 7e-07
 Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           YY     A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 64  YYIQGQCAIIMFDVTARVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDVK 112

Ran is involved in the active transport of proteins through nuclear pores. Length = 200

>gnl|CDD|133324 cd04124, RabL2, Rab GTPase-like family 2 (Rab-like2)

 Score = 43.3 bits (102), Expect = 8e-07
 Identities = 19/51 (37%), Positives = 35/51 (68%), Gaps = 1/51 (1%)

Query: 4   SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++YY  A   +LV+DVT+  T++N+S+W ++LR++    I  +++ NK DL
Sbjct: 67  ASYYHKAHACILVFDVTRKITYKNLSKWYEELREYR-PEIPCIVVANKIDL 116

RabL2 (Rab-like2) subfamily. RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share > 98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown. 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. Length = 161

>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like families

 Score = 43.0 bits (102), Expect = 1e-06
 Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA--GSNIVIMLIGNKSDLKH 56
                 R A G +LVY +T  ++F+ VS+ L+ +R+       I ++L+GNK+DL H
Sbjct: 65  SLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADLLH 121

RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack estrogen receptor and are correlated with poor clinical prognosis. Elevated RERG expression correlated with favorable patient outcome in a breast tumor subtype that is positive for estrogen receptor expression. In contrast to most Ras proteins, RERG overexpression inhibited the growth of breast tumor cells in vitro and in vivo. RasL11 was found to be ubiquitously expressed in human tissue, but down-regulated in prostate tumors. Both RERG and RasL11 lack the C-terminal CaaX prenylation motif, where a = an aliphatic amino acid and X = any amino acid, and are localized primarily in the cytoplasm. Both are believed to have tumor suppressor activity. Length = 166

>gnl|CDD|197554 smart00174, RHO, Rho (Ras homology) subfamily of Ras-like small GTPases

 Score = 40.3 bits (95), Expect = 9e-06
 Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 5/55 (9%)

Query: 14  LLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDL---KHLLNSMCEE 64
           L+ + V    +FENV  +W  +++     N+ I+L+G K DL   K  L  + ++
Sbjct: 74  LICFSVDSPASFENVKEKWYPEVKHFC-PNVPIILVGTKLDLRNDKSTLEELSKK 127

Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms. Length = 174

>gnl|CDD|133345 cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3

 Score = 39.7 bits (93), Expect = 2e-05
 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKH 56
           A+   Y R   G LLV+ VT   +FE V ++    LR        ++L+GNK+DL+H
Sbjct: 65  AMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEH 121

The M-Ras/R-Ras-like subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 164

>gnl|CDD|214541 smart00173, RAS, Ras subfamily of RAS small GTPases

 Score = 39.1 bits (92), Expect = 2e-05
 Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 5/54 (9%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRW---LKDLRDHAGSNIVIMLIGNKSDLKH 56
           Y R   G LLVY +T   +FE + ++   +  ++D    ++ I+L+GNK DL+ 
Sbjct: 68  YMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDR--DDVPIVLVGNKCDLES 119

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades. Length = 164

>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily; ill-defined subfamily

 Score = 38.7 bits (91), Expect = 3e-05
 Identities = 18/54 (33%), Positives = 33/54 (61%), Gaps = 5/54 (9%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRW---LKDLRDHAGSNIVIMLIGNKSDLKH 56
           Y R   G LLVY +T   +FE ++++   +  ++D    ++ I+L+GNK DL++
Sbjct: 70  YMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRD--DVPIVLVGNKCDLEN 121

SMART predicts Ras-like small GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies. Others that could not be classified in this way are predicted to be members of the small GTPase superfamily without predictions of the subfamily. Length = 166

>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases)

 Score = 38.6 bits (90), Expect = 4e-05
 Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 2/54 (3%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
            +     RGA   LLV D T   + E+    +          I I+L+GNK DL
Sbjct: 67  ELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLR--KEGIPIILVGNKIDL 118

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. Length = 161

>gnl|CDD|219856 pfam08477, Miro, Miro-like protein

 Score = 37.8 bits (88), Expect = 4e-05
 Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 4/47 (8%)

Query: 8   RGALGALLVYDVTKSTTFENVSR---WLKDLRDHAGSNIVIMLIGNK 51
           + A   LLVYD+T   +   VSR   WL +LR   G  I ++L+GNK
Sbjct: 70  KWADAILLVYDLTDRESLNEVSRLIAWLPNLRK-LGGKIPVILVGNK 115

Mitochondrial Rho proteins (Miro-1, and Miro-2), are atypical Rho GTPases. They have a unique domain organisation, 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. Length = 116

>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional

 Score = 38.7 bits (90), Expect = 5e-05
 Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKHL 57
           A+   Y R   G L VY +T  ++FE ++ + +  LR      + ++L+GNK DL   
Sbjct: 68  AMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDSE 125

Length = 189

>gnl|CDD|133344 cd04144, Ras2, Rat sarcoma (Ras) family 2 of small guanosine triphosphatases (GTPases)

 Score = 38.7 bits (90), Expect = 5e-05
 Identities = 19/59 (32%), Positives = 35/59 (59%), Gaps = 3/59 (5%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLR---DHAGSNIVIMLIGNKSDLKH 56
           A+   + R   G +LVY +T  +TFE V R+ + ++   D + +++ IM++GNK D  +
Sbjct: 62  ALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVY 120

The Ras2 subfamily, found exclusively in fungi, was first identified in Ustilago maydis. In U. maydis, Ras2 is regulated by Sql2, a protein that is homologous to GEFs (guanine nucleotide exchange factors) of the CDC25 family. Ras2 has been shown to induce filamentous growth, but the signaling cascade through which Ras2 and Sql2 regulate cell morphology is not known. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Length = 190

>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal

 Score = 38.1 bits (89), Expect = 7e-05
 Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 2/42 (4%)

Query: 14  LLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
            LVY V + +T E + ++WL  +R      + I+L+GNKSDL
Sbjct: 77  CLVYSVDRPSTLERIRTKWLPLIRRLGV-KVPIILVGNKSDL 117

Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature. Length = 168

>gnl|CDD|206705 cd04133, Rop_like, Rho-related protein from plants (Rop)-like

 Score = 37.9 bits (88), Expect = 8e-05
 Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 2/50 (4%)

Query: 7   YRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLK 55
           YRGA   LL + +    ++ENV  +W+ +LR H    + I+L+G K DL+
Sbjct: 70  YRGADVFLLAFSLISKASYENVLKKWIPELR-HYAPGVPIVLVGTKLDLR 118

The Rop (Rho-related protein from plants) subfamily plays a role in diverse cellular processes, including cytoskeletal organization, pollen and vegetative cell growth, hormone responses, stress responses, and pathogen resistance. Rops are able to regulate several downstream pathways to amplify a specific signal by acting as master switches early in the signaling cascade. They transmit a variety of extracellular and intracellular signals. Rops are involved in establishing cell polarity in root-hair development, root-hair elongation, pollen-tube growth, cell-shape formation, responses to hormones such as abscisic acid (ABA) and auxin, responses to abiotic stresses such as oxygen deprivation, and disease resistance and disease susceptibility. An individual Rop can have a unique function or an overlapping function shared with other Rop proteins; in addition, a given Rop-regulated function can be controlled by one or multiple Rop proteins. For example, Rop1, Rop3, and Rop5 are all involved in pollen-tube growth; Rop2 plays a role in response to low-oxygen environments, cell-morphology, and root-hair development; root-hair development is also regulated by Rop4 and Rop6; Rop6 is also responsible for ABA response, and ABA response is also regulated by Rop10. Plants retain some of the regulatory mechanisms that are shared by other members of the Rho family, but have also developed a number of unique modes for regulating Rops. Unique RhoGEFs have been identified that are exclusively active toward Rop proteins, such as those containing the domain PRONE (plant-specific Rop nucleotide exchanger). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 173

>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small GTPase

 Score = 37.6 bits (88), Expect = 9e-05
 Identities = 19/44 (43%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 12  GALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDL 54
           G +LVY VT   +FE V      + D  G  ++ I+L+GNKSDL
Sbjct: 75  GYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDL 118

Rheb (Ras Homolog Enriched in Brain) subfamily. Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that leads to cell growth and cell-cycle progression. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Length = 180

>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20)

 Score = 37.6 bits (87), Expect = 1e-04
 Identities = 21/71 (29%), Positives = 31/71 (43%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSM 61
           + S Y RGA   +L YDV+   + E +      L D A  + +  ++GNK DL       
Sbjct: 60  LGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTEEGALA 119

Query: 62  CEEYLIKSRSS 72
            +E     R S
Sbjct: 120 GQEKDAGDRVS 130

Rab20 is one of several Rab proteins that appear to be restricted in expression to the apical domain of murine polarized epithelial cells. It is expressed on the apical side of polarized kidney tubule and intestinal epithelial cells, and in non-polarized cells. It also localizes to vesico-tubular structures below the apical brush border of renal proximal tubule cells and in the apical region of duodenal epithelial cells. Rab20 has also been shown to colocalize with vacuolar H+-ATPases (V-ATPases) in mouse kidney cells, suggesting a role in the regulation of V-ATPase traffic in specific portions of the nephron. It was also shown to be one of several proteins whose expression is upregulated in human myelodysplastic syndrome (MDS) patients. 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. Length = 220

>gnl|CDD|206704 cd04132, Rho4_like, Ras homology family 4 (Rho4) of small guanosine triphosphatases (GTPases)-like

 Score = 37.3 bits (87), Expect = 1e-04
 Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 2/43 (4%)

Query: 14  LLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLK 55
           L+ Y V   T+ +NV  +W  ++  H      I+L+G K+DL+
Sbjct: 80  LICYSVDNPTSLDNVEDKWYPEVN-HFCPGTPIVLVGLKTDLR 121

Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Length = 197

>gnl|CDD|206712 cd04141, Rit_Rin_Ric, Ras-like protein in all tissues (Rit), Ras-like protein in neurons (Rin) and Ras-related protein which interacts with calmodulin (Ric)

 Score = 35.6 bits (82), Expect = 5e-04
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDL-RDHAGSNIVIMLIGNKSDLKHLLN 59
           A+   Y R   G ++ Y VT   +F+  S + + + R     +I ++L+GNK DL+    
Sbjct: 65  AMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKVDLEQQRQ 124

Query: 60  SMCEEYLIKSRSS 72
              EE    +R  
Sbjct: 125 VTTEEGRNLAREF 137

Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to signal in parallel with the Ras pathway or stimulate the Ras pathway at some upstream point, and binding of calmodulin to Ric may negatively regulate Ric activity. Length = 172

>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly homologous RalA and RalB

 Score = 35.5 bits (82), Expect = 5e-04
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSR-WLKDLRDHAGSNIVIMLIGNKSDLKH 56
           AI   Y+R   G LLV+ +T   +F  ++    + LR     N+ ++L+GNK DL+ 
Sbjct: 63  AIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLED 119

The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (>80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exocyst and for localizing the exocyst to the leading edge of migrating cells. In human cancer cells, RalA is required to support anchorage-independent proliferation and RalB is required to suppress apoptosis. RalA has been shown to localize to the plasma membrane while RalB is localized to the intracellular vesicles. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 163

>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras GTPases

 Score = 35.8 bits (83), Expect = 6e-04
 Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 14  LLVYDVTKSTTFENVSRWLKDLRD-HAGSNIVIMLIGNKSDL 54
           ++VY VT  ++FE  S     LR      +I I+L+GNKSDL
Sbjct: 77  VIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILVGNKSDL 118

RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues. RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function. Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells. RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton. Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ras superfamily members. The N-terminal extension is not conserved among family members; the C-terminal extension is reported to be conserved among the family and lack the CaaX prenylation motif typical of membrane-associated Ras proteins. However, a putative CaaX motif has been identified in the alignment of the C-terminal residues of this CD. Length = 219

>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and RSR1

 Score = 35.2 bits (81), Expect = 6e-04
 Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 9/59 (15%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-----GSNIVIMLIGNKSDL 54
           A+   Y +   G  LVY +T   +F +    L+DLR+         ++ ++L+GNK DL
Sbjct: 64  AMRDLYIKNGQGFALVYSITAQQSFND----LQDLREQILRVKDTEDVPMILVGNKCDL 118

The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. Rap2 is involved in multiple functions, including activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton and activation of the Wnt/beta-catenin signaling pathway in embryonic Xenopus. A number of effector proteins for Rap2 have been identified, including isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK), and the RalGEFs RalGDS, RGL, and Rlf, which also interact with Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and Rap2. In budding yeasts, it is involved in selecting a site for bud growth, which directs the establishment of cell polarization. The Rho family GTPase Cdc42 and its GEF, Cdc24, then establish an axis of polarized growth. It is believed that Cdc42 interacts directly with RSR1 in vivo. In filamentous fungi such as Ashbya gossypii, RSR1 is a key regulator of polar growth in the hypha. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 164

>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras and K-Ras4A/4B

 Score = 34.7 bits (80), Expect = 0.001
 Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDL 54
           A+   Y R   G L V+ +    +FE++  + +   R     ++ ++L+GNK DL
Sbjct: 64  AMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDL 118

H-Ras/N-Ras/K-Ras subfamily. H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1. Others are proposed to play negative regulatory roles in oncogenesis, including RASSF and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 162

>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and Rap2c

 Score = 34.4 bits (79), Expect = 0.002
 Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 3/53 (5%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKD--LRDHAGSNIVIMLIGNKSDLKH 56
           Y +   G ++VY +    TF+++ + ++D  +R      + I+L+GNK DL+ 
Sbjct: 69  YIKNGQGFIVVYSLVNQQTFQDI-KPMRDQIVRVKGYEKVPIILVGNKVDLES 120

The Rap2 subgroup is part of the Rap subfamily of the Ras family. It consists of Rap2a, Rap2b, and Rap2c. Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton. In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments. In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway. The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation. A number of additional effector proteins for Rap2 have been identified, including the RalGEFs RalGDS, RGL, and Rlf, which also interact with Rap1 and Ras. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 163

>gnl|CDD|133375 cd04175, Rap1, Rap1 family GTPase consists of Rap1a and Rap1b isoforms

 Score = 34.0 bits (78), Expect = 0.002
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 9/60 (15%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-----GSNIVIMLIGNKSDLK 55
           A+   Y +   G +LVY +T  +TF +    L+DLR+         ++ ++L+GNK DL+
Sbjct: 64  AMRDLYMKNGQGFVLVYSITAQSTFND----LQDLREQILRVKDTEDVPMILVGNKCDLE 119

The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature. Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. High expression of Rap1 has been observed in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines; interestingly, in the SCCs, the active GTP-bound form localized to the nucleus, while the inactive GDP-bound form localized to the cytoplasm. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. Rap1a, which is stimulated by T-cell receptor (TCR) activation, is a positive regulator of T cells by directing integrin activation and augmenting lymphocyte responses. In murine hippocampal neurons, Rap1b determines which neurite will become the axon and directs the recruitment of Cdc42, which is required for formation of dendrites and axons. In murine platelets, Rap1b is required for normal homeostasis in vivo and is involved in integrin activation. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 164

>gnl|CDD|133330 cd04130, Wrch_1, Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho family GTPase similar to Cdc42

 Score = 33.5 bits (77), Expect = 0.003
 Identities = 14/43 (32%), Positives = 28/43 (65%), Gaps = 2/43 (4%)

Query: 14  LLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLK 55
           LL + V   ++F+N+S +W+ ++R H      I+L+G ++DL+
Sbjct: 76  LLCFSVVNPSSFQNISEKWIPEIRKHN-PKAPIILVGTQADLR 117

Wrch-1 (Wnt-1 responsive Cdc42 homolog) is a Rho family GTPase that shares significant sequence and functional similarity with Cdc42. Wrch-1 was first identified in mouse mammary epithelial cells, where its transcription is upregulated in Wnt-1 transformation. Wrch-1 contains N- and C-terminal extensions relative to cdc42, suggesting potential differences in cellular localization and function. The Wrch-1 N-terminal extension contains putative SH3 domain-binding motifs and has been shown to bind the SH3 domain-containing protein Grb2, which increases the level of active Wrch-1 in cells. Unlike Cdc42, which localizes to the cytosol and perinuclear membranes, Wrch-1 localizes extensively with the plasma membrane and endosomes. The membrane association, localization, and biological activity of Wrch-1 indicate an atypical model of regulation distinct from other Rho family GTPases. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 173

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	72
KOG0084	205	consensus GTPase Rab1/YPT1, small G protein superf	99.93
KOG0078	207	consensus GTP-binding protein SEC4, small G protei	99.91
KOG0098	216	consensus GTPase Rab2, small G protein superfamily	99.91
KOG0092	200	consensus GTPase Rab5/YPT51 and related small G pr	99.91
KOG0087	222	consensus GTPase Rab11/YPT3, small G protein super	99.91
KOG0088	218	consensus GTPase Rab21, small G protein superfamil	99.9
KOG0093	193	consensus GTPase Rab3, small G protein superfamily	99.88
KOG0080	209	consensus GTPase Rab18, small G protein superfamil	99.87
KOG0094	221	consensus GTPase Rab6/YPT6/Ryh1, small G protein s	99.86
KOG0086	214	consensus GTPase Rab4, small G protein superfamily	99.85
cd04120	202	Rab12 Rab12 subfamily. Rab12 was first identified	99.85
KOG0079	198	consensus GTP-binding protein H-ray, small G prote	99.85
cd04121	189	Rab40 Rab40 subfamily. This subfamily contains Rab	99.84
cd04133	176	Rop_like Rop subfamily. The Rop (Rho-related prote	99.83
cd04172	182	Rnd3_RhoE_Rho8 Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE	99.83
KOG0091	213	consensus GTPase Rab39, small G protein superfamil	99.83
cd04131	178	Rnd Rnd subfamily. The Rnd subfamily contains Rnd1	99.82
KOG0083	192	consensus GTPase Rab26/Rab37, small G protein supe	99.82
KOG0395	196	consensus Ras-related GTPase [General function pre	99.81
cd04174	232	Rnd1_Rho6 Rnd1/Rho6 subfamily. Rnd1/Rho6 is a memb	99.8
KOG0081	219	consensus GTPase Rab27, small G protein superfamil	99.8
cd01875	191	RhoG RhoG subfamily. RhoG is a GTPase with high se	99.8
cd01873	195	RhoBTB RhoBTB subfamily. Members of the RhoBTB sub	99.79
PTZ00099	176	rab6; Provisional	99.79
cd04122	166	Rab14 Rab14 subfamily. Rab14 GTPases are localized	99.79
PF00071	162	Ras: Ras family; InterPro: IPR001806 Small GTPases	99.79
cd04117	161	Rab15 Rab15 subfamily. Rab15 colocalizes with the	99.78
cd04141	172	Rit_Rin_Ric Rit/Rin/Ric subfamily. Rit (Ras-like p	99.78
cd04126	220	Rab20 Rab20 subfamily. Rab20 is one of several Rab	99.78
KOG0095	213	consensus GTPase Rab30, small G protein superfamil	99.78
cd04102	202	RabL3 RabL3 (Rab-like3) subfamily. RabL3s are nove	99.77
PLN00023	334	GTP-binding protein; Provisional	99.76
cd01874	175	Cdc42 Cdc42 subfamily. Cdc42 is an essential GTPas	99.76
KOG0394	210	consensus Ras-related GTPase [General function pre	99.76
KOG0097	215	consensus GTPase Rab14, small G protein superfamil	99.75
cd04107	201	Rab32_Rab38 Rab38/Rab32 subfamily. Rab32 and Rab38	99.74
cd04127	180	Rab27A Rab27a subfamily. The Rab27a subfamily cons	99.74
cd04103	158	Centaurin_gamma Centaurin gamma. The centaurins (a	99.74
cd04109	215	Rab28 Rab28 subfamily. First identified in maize,	99.73
cd01865	165	Rab3 Rab3 subfamily. The Rab3 subfamily contains R	99.73
cd01867	167	Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Yp	99.73
cd04144	190	Ras2 Ras2 subfamily. The Ras2 subfamily, found exc	99.72
cd01871	174	Rac1_like Rac1-like subfamily. The Rac1-like subfa	99.72
cd04173	222	Rnd2_Rho7 Rnd2/Rho7 subfamily. Rnd2/Rho7 is a memb	99.72
cd04136	163	Rap_like Rap-like subfamily. The Rap subfamily con	99.71
smart00176	200	RAN Ran (Ras-related nuclear proteins) /TC4 subfam	99.71
cd04134	189	Rho3 Rho3 subfamily. Rho3 is a member of the Rho f	99.71
cd04115	170	Rab33B_Rab33A Rab33B/Rab33A subfamily. Rab33B is u	99.71
cd01869	166	Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in ev	99.71
cd04176	163	Rap2 Rap2 subgroup. The Rap2 subgroup is part of t	99.71
cd04175	164	Rap1 Rap1 subgroup. The Rap1 subgroup is part of t	99.71
cd01868	165	Rab11_like Rab11-like. Rab11a, Rab11b, and Rab25 a	99.71
cd04125	188	RabA_like RabA-like subfamily. RabA was first iden	99.71
cd01864	165	Rab19 Rab19 subfamily. Rab19 proteins are associat	99.71
cd04112	191	Rab26 Rab26 subfamily. First identified in rat pan	99.7
PLN03110	216	Rab GTPase; Provisional	99.7
smart00174	174	RHO Rho (Ras homology) subfamily of Ras-like small	99.7
cd04146	165	RERG_RasL11_like RERG/RasL11-like subfamily. RERG	99.7
KOG4252	246	consensus GTP-binding protein [Signal transduction	99.69
cd04106	162	Rab23_lke Rab23-like subfamily. Rab23 is a member	99.69
PTZ00369	189	Ras-like protein; Provisional	99.69
cd04111	211	Rab39 Rab39 subfamily. Found in eukaryotes, Rab39	99.69
cd01866	168	Rab2 Rab2 subfamily. Rab2 is localized on cis-Golg	99.69
cd04110	199	Rab35 Rab35 subfamily. Rab35 is one of several Rab	99.68
PLN03108	210	Rab family protein; Provisional	99.68
cd04140	165	ARHI_like ARHI subfamily. ARHI (A Ras homolog memb	99.68
cd04128	182	Spg1 Spg1p. Spg1p (septum-promoting GTPase) was fi	99.68
cd04113	161	Rab4 Rab4 subfamily. Rab4 has been implicated in n	99.68
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	99.67
cd04116	170	Rab9 Rab9 subfamily. Rab9 is found in late endosom	99.67
PLN03071	219	GTP-binding nuclear protein Ran; Provisional	99.67
cd04142	198	RRP22 RRP22 subfamily. RRP22 (Ras-related protein	99.67
cd04130	173	Wrch_1 Wrch-1 subfamily. Wrch-1 (Wnt-1 responsive	99.66
cd04143	247	Rhes_like Rhes_like subfamily. This subfamily incl	99.66
cd04145	164	M_R_Ras_like M-Ras/R-Ras-like subfamily. This subf	99.66
KOG0393	198	consensus Ras-related small GTPase, Rho type [Gene	99.65
cd04148	221	RGK RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Ki	99.64
cd04132	187	Rho4_like Rho4-like subfamily. Rho4 is a GTPase th	99.64
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	99.63
cd04108	170	Rab36_Rab34 Rab34/Rab36 subfamily. Rab34, found pr	99.63
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	99.63
cd04123	162	Rab21 Rab21 subfamily. The localization and functi	99.62
cd04101	164	RabL4 RabL4 (Rab-like4) subfamily. RabL4s are nove	99.62
KOG3883	198	consensus Ras family small GTPase [Signal transduc	99.62
cd04177	168	RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the	99.61
cd01892	169	Miro2 Miro2 subfamily. Miro (mitochondrial Rho) pr	99.61
cd01861	161	Rab6 Rab6 subfamily. Rab6 is involved in microtubu	99.61
cd04138	162	H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras,	99.6
cd00877	166	Ran Ran (Ras-related nuclear proteins) /TC4 subfam	99.6
cd04162	164	Arl9_Arfrp2_like Arl9/Arfrp2-like subfamily. Arl9	99.59
cd01860	163	Rab5_related Rab5-related subfamily. This subfamil	99.59
cd04118	193	Rab24 Rab24 subfamily. Rab24 is distinct from othe	99.58
cd04135	174	Tc10 TC10 subfamily. TC10 is a Rho family protein	99.57
cd04129	187	Rho2 Rho2 subfamily. Rho2 is a fungal GTPase that	99.56
cd04114	169	Rab30 Rab30 subfamily. Rab30 appears to be associa	99.56
PLN03118	211	Rab family protein; Provisional	99.55
cd04158	169	ARD1 ARD1 subfamily. ARD1 (ADP-ribosylation factor	99.55
cd04149	168	Arf6 Arf6 subfamily. Arf6 (ADP ribosylation factor	99.55
cd01863	161	Rab18 Rab18 subfamily. Mammalian Rab18 is implicat	99.54
cd04124	161	RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily	99.54
smart00177	175	ARF ARF-like small GTPases; ARF, ADP-ribosylation	99.52
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	99.51
PLN00223	181	ADP-ribosylation factor; Provisional	99.51
cd04161	167	Arl2l1_Arl13_like Arl2l1/Arl13 subfamily. Arl2l1 (	99.49
cd00876	160	Ras Ras family. The Ras family of the Ras superfam	99.49
cd04150	159	Arf1_5_like Arf1-Arf5-like subfamily. This subfami	99.49
cd01870	175	RhoA_like RhoA-like subfamily. The RhoA subfamily	99.49
cd04147	198	Ras_dva Ras-dva subfamily. Ras-dva (Ras - dorsal-v	99.47
cd00154	159	Rab Rab family. Rab GTPases form the largest famil	99.47
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	99.47
TIGR00157	245	ribosome small subunit-dependent GTPase A. The Aqu	99.45
PTZ00133	182	ADP-ribosylation factor; Provisional	99.43
cd04137	180	RheB Rheb (Ras Homolog Enriched in Brain) subfamil	99.43
cd01893	166	Miro1 Miro1 subfamily. Miro (mitochondrial Rho) pr	99.42
cd04154	173	Arl2 Arl2 subfamily. Arl2 (Arf-like 2) GTPases are	99.42
cd00157	171	Rho Rho (Ras homology) family. Members of the Rho	99.42
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	99.38
cd04152	183	Arl4_Arl7 Arl4/Arl7 subfamily. Arl4 (Arf-like 4) i	99.38
cd04157	162	Arl6 Arl6 subfamily. Arl6 (Arf-like 6) forms a sub	99.36
smart00178	184	SAR Sar1p-like members of the Ras-family of small	99.35
cd00879	190	Sar1 Sar1 subfamily. Sar1 is an essential componen	99.34
cd04153	174	Arl5_Arl8 Arl5/Arl8 subfamily. Arl5 (Arf-like 5) a	99.31
PTZ00132	215	GTP-binding nuclear protein Ran; Provisional	99.31
cd04156	160	ARLTS1 ARLTS1 subfamily. ARLTS1 (Arf-like tumor su	99.31
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	99.3
cd00878	158	Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-lik	99.28
COG1100	219	GTPase SAR1 and related small G proteins [General	99.28
smart00010	124	small_GTPase Small GTPase of the Ras superfamily;	99.25
PF00025	175	Arf: ADP-ribosylation factor family The prints ent	99.25
cd04151	158	Arl1 Arl1 subfamily. Arl1 (Arf-like 1) localizes t	99.22
cd01898	170	Obg Obg subfamily. The Obg nucleotide binding prot	99.15
KOG0070	181	consensus GTP-binding ADP-ribosylation factor Arf1	99.12
KOG1673	205	consensus Ras GTPases [General function prediction	99.12
KOG0096	216	consensus GTPase Ran/TC4/GSP1 (nuclear protein tra	99.11
TIGR02528	142	EutP ethanolamine utilization protein, EutP. This	99.11
PRK12299	335	obgE GTPase CgtA; Reviewed	99.11
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	99.09
KOG0073	185	consensus GTP-binding ADP-ribosylation factor-like	99.06
KOG4423	229	consensus GTP-binding protein-like, RAS superfamil	99.06
KOG1707	625	consensus Predicted Ras related/Rac-GTP binding pr	98.98
cd01890	179	LepA LepA subfamily. LepA belongs to the GTPase fa	98.97
KOG0071	180	consensus GTP-binding ADP-ribosylation factor Arf6	98.95
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	98.95
KOG0075	186	consensus GTP-binding ADP-ribosylation factor-like	98.93
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	98.92
cd01881	176	Obg_like The Obg-like subfamily consists of five w	98.88
TIGR03156	351	GTP_HflX GTP-binding protein HflX. This protein fa	98.87
cd04105	203	SR_beta Signal recognition particle receptor, beta	98.83
cd01897	168	NOG NOG1 is a nucleolar GTP-binding protein presen	98.8
TIGR02729	329	Obg_CgtA Obg family GTPase CgtA. This model descri	98.78
PRK11058	426	GTPase HflX; Provisional	98.76
cd00882	157	Ras_like_GTPase Ras-like GTPase superfamily. The R	98.75
KOG0076	197	consensus GTP-binding ADP-ribosylation factor-like	98.74
cd01891	194	TypA_BipA TypA (tyrosine phosphorylated protein A)	98.7
TIGR00450	442	mnmE_trmE_thdF tRNA modification GTPase TrmE. TrmE	98.65
TIGR00231	161	small_GTP small GTP-binding protein domain. This m	98.56
PRK12289	352	GTPase RsgA; Reviewed	98.55
PRK12297	424	obgE GTPase CgtA; Reviewed	98.54
cd01885	222	EF2 EF2 (for archaea and eukarya). Translocation r	98.54
PRK03003	472	GTP-binding protein Der; Reviewed	98.52
PRK05291	449	trmE tRNA modification GTPase TrmE; Reviewed	98.51
cd01879	158	FeoB Ferrous iron transport protein B (FeoB) subfa	98.51
PRK15467	158	ethanolamine utilization protein EutP; Provisional	98.51
KOG0074	185	consensus GTP-binding ADP-ribosylation factor-like	98.51
cd04171	164	SelB SelB subfamily. SelB is an elongation factor	98.5
PRK03003	472	GTP-binding protein Der; Reviewed	98.46
COG2229	187	Predicted GTPase [General function prediction only	98.43
TIGR03597	360	GTPase_YqeH ribosome biogenesis GTPase YqeH. This	98.42
cd01855	190	YqeH YqeH. YqeH is an essential GTP-binding protei	98.42
cd01895	174	EngA2 EngA2 subfamily. This CD represents the seco	98.41
cd01854	287	YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtil	98.41
PRK04213	201	GTP-binding protein; Provisional	98.4
KOG0072	182	consensus GTP-binding ADP-ribosylation factor-like	98.37
KOG0077	193	consensus Vesicle coat complex COPII, GTPase subun	98.35
cd01887	168	IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryo	98.34
cd04164	157	trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein	98.34
TIGR01393	595	lepA GTP-binding protein LepA. LepA (GUF1 in Sacca	98.33
PRK12298	390	obgE GTPase CgtA; Reviewed	98.33
PRK12288	347	GTPase RsgA; Reviewed	98.29
TIGR03594	429	GTPase_EngA ribosome-associated GTPase EngA. EngA	98.26
PRK00098	298	GTPase RsgA; Reviewed	98.24
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	98.23
PRK12296	500	obgE GTPase CgtA; Reviewed	98.2
cd00066	317	G-alpha G protein alpha subunit. The alpha subunit	98.19
TIGR00491	590	aIF-2 translation initiation factor aIF-2/yIF-2. T	98.19
cd00881	189	GTP_translation_factor GTP translation factor fami	98.18
PRK15494	339	era GTPase Era; Provisional	98.17
smart00275	342	G_alpha G protein alpha subunit. Subunit of G prot	98.15
cd04167	213	Snu114p Snu114p subfamily. Snu114p is one of sever	98.08
PRK09518	712	bifunctional cytidylate kinase/GTPase Der; Reviewe	98.06
cd01894	157	EngA1 EngA1 subfamily. This CD represents the firs	98.03
cd04168	237	TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), T	98.03
TIGR00437	591	feoB ferrous iron transporter FeoB. FeoB (773 amin	98.01
TIGR00483	426	EF-1_alpha translation elongation factor EF-1 alph	98.0
cd00880	163	Era_like Era (E. coli Ras-like protein)-like. This	97.99
cd01857	141	HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to t	97.96
PF09439	181	SRPRB: Signal recognition particle receptor beta s	97.95
PRK05433	600	GTP-binding protein LepA; Provisional	97.95
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	97.93
PRK00093	435	GTP-binding protein Der; Reviewed	97.91
PF06858	58	NOG1: Nucleolar GTP-binding protein 1 (NOG1); Inte	97.89
PRK04004	586	translation initiation factor IF-2; Validated	97.86
cd01859	156	MJ1464 MJ1464. This family represents archaeal GTP	97.85
KOG1707	625	consensus Predicted Ras related/Rac-GTP binding pr	97.85
PRK00089	292	era GTPase Era; Reviewed	97.85
CHL00189	742	infB translation initiation factor 2; Provisional	97.84
TIGR00487	587	IF-2 translation initiation factor IF-2. This mode	97.83
cd04169	267	RF3 RF3 subfamily. Peptide chain release factor 3	97.83
TIGR03598	179	GTPase_YsxC ribosome biogenesis GTP-binding protei	97.8
TIGR01394	594	TypA_BipA GTP-binding protein TypA/BipA. This bact	97.77
PRK09518	712	bifunctional cytidylate kinase/GTPase Der; Reviewe	97.76
PRK00093	435	GTP-binding protein Der; Reviewed	97.75
TIGR00475	581	selB selenocysteine-specific elongation factor Sel	97.75
PRK13351	687	elongation factor G; Reviewed	97.73
PRK05306	787	infB translation initiation factor IF-2; Validated	97.72
TIGR03594	429	GTPase_EngA ribosome-associated GTPase EngA. EngA	97.72
KOG1489	366	consensus Predicted GTP-binding protein (ODN super	97.6
cd01888	203	eIF2_gamma eIF2-gamma (gamma subunit of initiation	97.6
cd01889	192	SelB_euk SelB subfamily. SelB is an elongation fac	97.59
PRK14845	1049	translation initiation factor IF-2; Provisional	97.55
PRK09554	772	feoB ferrous iron transport protein B; Reviewed	97.55
cd01896	233	DRG The developmentally regulated GTP-binding prot	97.54
cd01858	157	NGP_1 NGP-1. Autoantigen NGP-1 (Nucleolar G-protei	97.51
COG2262	411	HflX GTPases [General function prediction only]	97.46
PRK12317	425	elongation factor 1-alpha; Reviewed	97.42
PRK00741	526	prfC peptide chain release factor 3; Provisional	97.38
cd01849	155	YlqF_related_GTPase YlqF-related GTPases. These pr	97.35
PRK10218	607	GTP-binding protein; Provisional	97.31
cd04170	268	EF-G_bact Elongation factor G (EF-G) subfamily. Tr	97.3
cd04166	208	CysN_ATPS CysN_ATPS subfamily. CysN, together with	97.29
TIGR00503	527	prfC peptide chain release factor 3. This translat	97.29
PRK13796	365	GTPase YqeH; Provisional	97.26
cd01883	219	EF1_alpha Eukaryotic elongation factor 1 (EF1) alp	97.15
PRK04000	411	translation initiation factor IF-2 subunit gamma;	97.15
TIGR00484	689	EF-G translation elongation factor EF-G. After pep	97.12
PF00009	188	GTP_EFTU: Elongation factor Tu GTP binding domain;	97.1
PRK09866	741	hypothetical protein; Provisional	97.06
cd04104	197	p47_IIGP_like p47 (47-kDa) family. The p47 GTPase	97.04
PRK01889	356	GTPase RsgA; Reviewed	96.97
PRK12740	668	elongation factor G; Reviewed	96.92
TIGR03680	406	eif2g_arch translation initiation factor 2 subunit	96.92
PF04670	232	Gtr1_RagA: Gtr1/RagA G protein conserved region; I	96.91
PRK00454	196	engB GTP-binding protein YsxC; Reviewed	96.9
KOG4273	418	consensus Uncharacterized conserved protein [Funct	96.82
COG0536	369	Obg Predicted GTPase [General function prediction	96.81
cd01886	270	EF-G Elongation factor G (EF-G) subfamily. Translo	96.8
cd01876	170	YihA_EngB The YihA (EngB) subfamily. This subfamil	96.78
COG1084	346	Predicted GTPase [General function prediction only	96.66
cd04178	172	Nucleostemin_like Nucleostemin-like. Nucleostemin	96.65
PLN00043	447	elongation factor 1-alpha; Provisional	96.57
cd01856	171	YlqF YlqF. Proteins of the YlqF family contain all	96.52
PRK10512	614	selenocysteinyl-tRNA-specific translation factor;	96.48
TIGR00485	394	EF-Tu translation elongation factor TU. This align	96.48
KOG0082	354	consensus G-protein alpha subunit (small G protein	96.47
PF00503	389	G-alpha: G-protein alpha subunit; InterPro: IPR001	96.44
PF02421	156	FeoB_N: Ferrous iron transport protein B; InterPro	96.39
cd01850	276	CDC_Septin CDC/Septin. Septins are a conserved fam	96.33
PRK12736	394	elongation factor Tu; Reviewed	96.31
TIGR03596	276	GTPase_YlqF ribosome biogenesis GTP-binding protei	96.2
PRK13768	253	GTPase; Provisional	96.13
cd04165	224	GTPBP1_like GTPBP1-like. Mammalian GTP binding pro	96.13
TIGR00490	720	aEF-2 translation elongation factor aEF-2. This mo	96.05
COG0486	454	ThdF Predicted GTPase [General function prediction	96.03
cd01884	195	EF_Tu EF-Tu subfamily. This subfamily includes ort	96.02
PRK09563	287	rbgA GTPase YlqF; Reviewed	96.0
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	95.9
KOG0090	238	consensus Signal recognition particle receptor, be	95.73
KOG0705	749	consensus GTPase-activating protein Centaurin gamm	95.72
PRK12739	691	elongation factor G; Reviewed	95.65
PRK12735	396	elongation factor Tu; Reviewed	95.48
cd03110	179	Fer4_NifH_child This protein family's function is	95.47
COG1160	444	Predicted GTPases [General function prediction onl	95.43
KOG3886	295	consensus GTP-binding protein [Signal transduction	95.27
COG0532	509	InfB Translation initiation factor 2 (IF-2; GTPase	94.97
TIGR02034	406	CysN sulfate adenylyltransferase, large subunit. H	94.83
CHL00071	409	tufA elongation factor Tu	94.73
PLN03126	478	Elongation factor Tu; Provisional	94.69
PRK05124	474	cysN sulfate adenylyltransferase subunit 1; Provis	94.64
PTZ00416	836	elongation factor 2; Provisional	94.58
PRK00007	693	elongation factor G; Reviewed	94.48
PF14331	266	ImcF-related_N: ImcF-related N-terminal domain	94.44
PF00350	168	Dynamin_N: Dynamin family; InterPro: IPR001401 Mem	94.32
COG1159	298	Era GTPase [General function prediction only]	94.31
PLN00116	843	translation elongation factor EF-2 subunit; Provis	94.07
PLN03127	447	Elongation factor Tu; Provisional	93.91
TIGR03348	1169	VI_IcmF type VI secretion protein IcmF. Members of	93.89
COG1162	301	Predicted GTPases [General function prediction onl	93.79
PRK00049	396	elongation factor Tu; Reviewed	93.75
PRK05506	632	bifunctional sulfate adenylyltransferase subunit 1	93.5
KOG0468	971	consensus U5 snRNP-specific protein [Translation,	93.44
TIGR00101	199	ureG urease accessory protein UreG. This model rep	93.44
KOG1145	683	consensus Mitochondrial translation initiation fac	93.31
KOG1490	620	consensus GTP-binding protein CRFG/NOG1 (ODN super	92.96
PRK07560	731	elongation factor EF-2; Reviewed	92.93
smart00053	240	DYNc Dynamin, GTPase. Large GTPases that mediate v	92.82
KOG1423	379	consensus Ras-like GTPase ERA [Cell cycle control,	92.72
COG1160	444	Predicted GTPases [General function prediction onl	92.5
cd01882	225	BMS1 Bms1. Bms1 is an essential, evolutionarily co	92.5
KOG0462	650	consensus Elongation factor-type GTP-binding prote	92.17
PTZ00327	460	eukaryotic translation initiation factor 2 gamma s	92.15
cd02038	139	FleN-like FleN is a member of the Fer4_NifH superf	91.3
PF03709	115	OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal	90.77
PF11111	176	CENP-M: Centromere protein M (CENP-M); InterPro: I	90.55
COG4963	366	CpaE Flp pilus assembly protein, ATPase CpaE [Intr	90.4
COG1149	284	MinD superfamily P-loop ATPase containing an inser	90.36
COG1161	322	Predicted GTPases [General function prediction onl	90.07
KOG2484	435	consensus GTPase [General function prediction only	89.41
cd02067	119	B12-binding B12 binding domain (B12-BD). This doma	89.28
KOG3929	363	consensus Uncharacterized conserved protein [Funct	89.02
COG0480	697	FusA Translation elongation factors (GTPases) [Tra	88.67
KOG1191	531	consensus Mitochondrial GTPase [Translation, ribos	88.56
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	88.39
KOG1424	562	consensus Predicted GTP-binding protein MMR1 [Gene	88.28
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	87.91
KOG1954	532	consensus Endocytosis/signaling protein EHD1 [Sign	87.27
cd03111	106	CpaE_like This protein family consists of proteins	86.78
COG0218	200	Predicted GTPase [General function prediction only	86.62
KOG0447	980	consensus Dynamin-like GTP binding protein [Genera	86.15
PRK13505	557	formate--tetrahydrofolate ligase; Provisional	85.77
COG1010	249	CobJ Precorrin-3B methylase [Coenzyme metabolism]	85.69
COG0050	394	TufB GTPases - translation elongation factors [Tra	85.37
COG3523	1188	IcmF Type VI protein secretion system component Va	85.19
PTZ00141	446	elongation factor 1- alpha; Provisional	83.4
cd02071	122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	82.63
PF14784	126	ECIST_Cterm: C-terminal domain of the ECSIT protei	82.5
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	82.1
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	81.98
COG0481	603	LepA Membrane GTPase LepA [Cell envelope biogenesi	81.9
PF08468	155	MTS_N: Methyltransferase small domain N-terminal;	81.08

>KOG0084 consensus GTPase Rab1/YPT1, small G protein superfamily, and related GTP-binding proteins [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=99.93  E-value=3.1e-26  Score=130.61  Aligned_cols=71  Identities=41%  Similarity=0.674  Sum_probs=67.7

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.+|||+|||+|+|||+|+++||+++..|+.+++.+...++|++|||||+|+.+.+.|+.++|+.||.+
T Consensus        73 tit~syYR~ahGii~vyDiT~~~SF~~v~~Wi~Ei~~~~~~~v~~lLVGNK~Dl~~~~~v~~~~a~~fa~~  143 (205)
T KOG0084|consen   73 TITSSYYRGAHGIIFVYDITKQESFNNVKRWIQEIDRYASENVPKLLVGNKCDLTEKRVVSTEEAQEFADE  143 (205)
T ss_pred             hhhHhhccCCCeEEEEEEcccHHHhhhHHHHHHHhhhhccCCCCeEEEeeccccHhheecCHHHHHHHHHh
Confidence            47789999999999999999999999999999999999988999999999999999999999999999864

>KOG0078 consensus GTP-binding protein SEC4, small G protein superfamily, and related Ras family GTP-binding proteins [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=99.91  E-value=1e-24  Score=125.37  Aligned_cols=71  Identities=44%  Similarity=0.785  Sum_probs=67.8

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++++.|||+|+|+++|||+++..||+++..|++.+.++.+.++|++|||||+|+.++|+|+.+.++++|++
T Consensus        76 ti~~sYyrgA~gi~LvyDitne~Sfeni~~W~~~I~e~a~~~v~~~LvGNK~D~~~~R~V~~e~ge~lA~e  146 (207)
T KOG0078|consen   76 TITTAYYRGAMGILLVYDITNEKSFENIRNWIKNIDEHASDDVVKILVGNKCDLEEKRQVSKERGEALARE  146 (207)
T ss_pred             HHHHHHHhhcCeeEEEEEccchHHHHHHHHHHHHHHhhCCCCCcEEEeeccccccccccccHHHHHHHHHH
Confidence            36789999999999999999999999999999999999988999999999999999999999999999975

>KOG0098 consensus GTPase Rab2, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.91  E-value=1.1e-24  Score=123.78  Aligned_cols=71  Identities=49%  Similarity=0.803  Sum_probs=68.0

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      |+++.|||+|.|++||||+++++||+++..|+.+++++..+++.++|+|||+||...|.|+.||+++||++
T Consensus        70 sv~~syYr~a~GalLVydit~r~sF~hL~~wL~D~rq~~~~NmvImLiGNKsDL~~rR~Vs~EEGeaFA~e  140 (216)
T KOG0098|consen   70 SVTRSYYRGAAGALLVYDITRRESFNHLTSWLEDARQHSNENMVIMLIGNKSDLEARREVSKEEGEAFARE  140 (216)
T ss_pred             HHHHHHhccCcceEEEEEccchhhHHHHHHHHHHHHHhcCCCcEEEEEcchhhhhccccccHHHHHHHHHH
Confidence            46789999999999999999999999999999999999889999999999999999999999999999986

>KOG0092 consensus GTPase Rab5/YPT51 and related small G protein superfamily GTPases [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.91  E-value=1.9e-24  Score=122.93  Aligned_cols=71  Identities=41%  Similarity=0.682  Sum_probs=68.1

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +|.|+|||+|+++|+|||+++.+||..++.|++++++..++++.+.|||||+||.+.|+|..+|+..+|.+
T Consensus        69 slapMYyRgA~AAivvYDit~~~SF~~aK~WvkeL~~~~~~~~vialvGNK~DL~~~R~V~~~ea~~yAe~  139 (200)
T KOG0092|consen   69 SLAPMYYRGANAAIVVYDITDEESFEKAKNWVKELQRQASPNIVIALVGNKADLLERREVEFEEAQAYAES  139 (200)
T ss_pred             ccccceecCCcEEEEEEecccHHHHHHHHHHHHHHHhhCCCCeEEEEecchhhhhhcccccHHHHHHHHHh
Confidence            57899999999999999999999999999999999999888999999999999999999999999999975

>KOG0087 consensus GTPase Rab11/YPT3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.91  E-value=3.3e-24  Score=123.42  Aligned_cols=71  Identities=68%  Similarity=0.995  Sum_probs=68.1

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++++.|||+|.|+++|||++.+.+|+++.+|+.+++.+.+++++++|||||+||.+.|.|+.+++..+|++
T Consensus        78 AitSaYYrgAvGAllVYDITr~~Tfenv~rWL~ELRdhad~nivimLvGNK~DL~~lraV~te~~k~~Ae~  148 (222)
T KOG0087|consen   78 AITSAYYRGAVGALLVYDITRRQTFENVERWLKELRDHADSNIVIMLVGNKSDLNHLRAVPTEDGKAFAEK  148 (222)
T ss_pred             cccchhhcccceeEEEEechhHHHHHHHHHHHHHHHhcCCCCeEEEEeecchhhhhccccchhhhHhHHHh
Confidence            46789999999999999999999999999999999999999999999999999999999999999999974

>KOG0088 consensus GTPase Rab21, small G protein superfamily [General function prediction only]

Probab=99.90  E-value=9.9e-24  Score=117.90  Aligned_cols=71  Identities=38%  Similarity=0.668  Sum_probs=67.7

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +|.|.|||+++|+++|||++|+.||+.++.|..+++...+..+.+++||||+||.++|.|+.+|++.+|++
T Consensus        77 ALGPIYYRgSnGalLVyDITDrdSFqKVKnWV~Elr~mlGnei~l~IVGNKiDLEeeR~Vt~qeAe~YAes  147 (218)
T KOG0088|consen   77 ALGPIYYRGSNGALLVYDITDRDSFQKVKNWVLELRTMLGNEIELLIVGNKIDLEEERQVTRQEAEAYAES  147 (218)
T ss_pred             ccCceEEeCCCceEEEEeccchHHHHHHHHHHHHHHHHhCCeeEEEEecCcccHHHhhhhhHHHHHHHHHh
Confidence            46799999999999999999999999999999999999888999999999999999999999999999875

>KOG0093 consensus GTPase Rab3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.88  E-value=8.4e-23  Score=112.92  Aligned_cols=70  Identities=33%  Similarity=0.598  Sum_probs=65.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|||+|+|+|+|||++|.+||+.++.|..++..+.-.++|+++|||||||.++|.++.|.++.+++.
T Consensus        86 iTTayyRgamgfiLmyDitNeeSf~svqdw~tqIktysw~naqvilvgnKCDmd~eRvis~e~g~~l~~~  155 (193)
T KOG0093|consen   86 ITTAYYRGAMGFILMYDITNEESFNSVQDWITQIKTYSWDNAQVILVGNKCDMDSERVISHERGRQLADQ  155 (193)
T ss_pred             HHHHHhhccceEEEEEecCCHHHHHHHHHHHHHheeeeccCceEEEEecccCCccceeeeHHHHHHHHHH
Confidence            6788999999999999999999999999999999888768999999999999999999999999998864

>KOG0080 consensus GTPase Rab18, small G protein superfamily [General function prediction only]

Probab=99.87  E-value=1.5e-22  Score=113.31  Aligned_cols=71  Identities=42%  Similarity=0.601  Sum_probs=66.8

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +|+++|||+|.|+|+|||++.+++|..+..|++++..+.. +++..++||||+|-..+|.|+.+|+.+||++
T Consensus        75 tLTpSyyRgaqGiIlVYDVT~Rdtf~kLd~W~~Eld~Ystn~diikmlVgNKiDkes~R~V~reEG~kfAr~  146 (209)
T KOG0080|consen   75 TLTPSYYRGAQGIILVYDVTSRDTFVKLDIWLKELDLYSTNPDIIKMLVGNKIDKESERVVDREEGLKFARK  146 (209)
T ss_pred             ccCHhHhccCceeEEEEEccchhhHHhHHHHHHHHHhhcCCccHhHhhhcccccchhcccccHHHHHHHHHh
Confidence            5889999999999999999999999999999999988875 6788999999999988999999999999986

>KOG0094 consensus GTPase Rab6/YPT6/Ryh1, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.86  E-value=1e-21  Score=112.38  Aligned_cols=71  Identities=37%  Similarity=0.675  Sum_probs=66.0

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCC-CCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~-~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +|.|.|+|++.++|+|||++++.||+++.+|++.++...++ ++.++|||||.||.++|+++.+|+...|++
T Consensus        86 slipsY~Rds~vaviVyDit~~~Sfe~t~kWi~dv~~e~gs~~viI~LVGnKtDL~dkrqvs~eEg~~kAke  157 (221)
T KOG0094|consen   86 SLIPSYIRDSSVAVIVYDITDRNSFENTSKWIEDVRRERGSDDVIIFLVGNKTDLSDKRQVSIEEGERKAKE  157 (221)
T ss_pred             hhhhhhccCCeEEEEEEeccccchHHHHHHHHHHHHhccCCCceEEEEEcccccccchhhhhHHHHHHHHHH
Confidence            57899999999999999999999999999999999887765 588999999999999999999999988874

>KOG0086 consensus GTPase Rab4, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.85  E-value=1.4e-21  Score=108.85  Aligned_cols=70  Identities=43%  Similarity=0.677  Sum_probs=67.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      .++.|||+|.|.++|||+++++||+.+..|+..++...++++.++|+|||.||.++|+|+..|+.+||++
T Consensus        74 VtRsYYRGAAGAlLVYD~TsrdsfnaLtnWL~DaR~lAs~nIvviL~GnKkDL~~~R~VtflEAs~FaqE  143 (214)
T KOG0086|consen   74 VTRSYYRGAAGALLVYDITSRDSFNALTNWLTDARTLASPNIVVILCGNKKDLDPEREVTFLEASRFAQE  143 (214)
T ss_pred             HHHHHhccccceEEEEeccchhhHHHHHHHHHHHHhhCCCcEEEEEeCChhhcChhhhhhHHHHHhhhcc
Confidence            5689999999999999999999999999999999999889999999999999999999999999999975

>cd04120 Rab12 Rab12 subfamily

Probab=99.85  E-value=5.7e-21  Score=110.56  Aligned_cols=70  Identities=36%  Similarity=0.576  Sum_probs=64.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||+++||+++|||+++++||+.+..|++.+++....++|+++||||+||..++.++.+++.++|++
T Consensus        65 l~~~y~~~ad~iIlVfDvtd~~Sf~~l~~w~~~i~~~~~~~~piilVgNK~DL~~~~~v~~~~~~~~a~~  134 (202)
T cd04120          65 ITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETDREISRQQGEKFAQQ  134 (202)
T ss_pred             HHHHHhcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCcEEEEEECcccccccccCHHHHHHHHHh
Confidence            5788999999999999999999999999999988877667899999999999988899999999988853

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

>KOG0079 consensus GTP-binding protein H-ray, small G protein superfamily [General function prediction only]

Probab=99.85  E-value=2.2e-21  Score=107.47  Aligned_cols=69  Identities=38%  Similarity=0.648  Sum_probs=64.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      |+..||++.+++++|||+++.+||.+++.|++++++.. +.+|.+|||||.|+++.|.|..++|++||..
T Consensus        73 itstyyrgthgv~vVYDVTn~ESF~Nv~rWLeei~~nc-dsv~~vLVGNK~d~~~RrvV~t~dAr~~A~~  141 (198)
T KOG0079|consen   73 ITSTYYRGTHGVIVVYDVTNGESFNNVKRWLEEIRNNC-DSVPKVLVGNKNDDPERRVVDTEDARAFALQ  141 (198)
T ss_pred             HHHHHccCCceEEEEEECcchhhhHhHHHHHHHHHhcC-ccccceecccCCCCccceeeehHHHHHHHHh
Confidence            56889999999999999999999999999999999887 6899999999999999999999999999864

>cd04121 Rab40 Rab40 subfamily

Probab=99.84  E-value=1e-20  Score=108.55  Aligned_cols=69  Identities=32%  Similarity=0.614  Sum_probs=63.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||+++|++++|||++++.||+++..|++++.+.. +++|++|||||.||.+.+.++.++++++|++
T Consensus        71 l~~~~~~~ad~illVfD~t~~~Sf~~~~~w~~~i~~~~-~~~piilVGNK~DL~~~~~v~~~~~~~~a~~  139 (189)
T cd04121          71 IFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHA-PGVPKILVGNRLHLAFKRQVATEQAQAYAER  139 (189)
T ss_pred             HHHHHhcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCEEEEEECccchhccCCCHHHHHHHHHH
Confidence            56789999999999999999999999999999997765 6899999999999998899999999999864

This subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. 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 d

>cd04133 Rop_like Rop subfamily

Probab=99.83  E-value=3.6e-20  Score=105.26  Aligned_cols=69  Identities=28%  Similarity=0.454  Sum_probs=61.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCcccc----------cCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKHLL----------NSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~----------~v~~~e~~~~a~   70 (72)
                      +++.||++++++++|||+++++||+++ +.|+.++.+.. +++|++|||||+||.+.+          .++.+++.++|+
T Consensus        65 ~~~~~~~~a~~~ilvyd~~~~~Sf~~~~~~w~~~i~~~~-~~~piilvgnK~Dl~~~~~~~~~~~~~~~v~~~~~~~~a~  143 (176)
T cd04133          65 LRPLSYRGADVFVLAFSLISRASYENVLKKWVPELRHYA-PNVPIVLVGTKLDLRDDKQYLADHPGASPITTAQGEELRK  143 (176)
T ss_pred             cchhhcCCCcEEEEEEEcCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEeChhhccChhhhhhccCCCCCCHHHHHHHHH
Confidence            678899999999999999999999998 78999998765 579999999999997653          589999999987


Q ss_pred             c
Q 047889           71 S   71 (72)
Q Consensus        71 ~   71 (72)
                      +
T Consensus       144 ~  144 (176)
T cd04133         144 Q  144 (176)
T ss_pred             H
Confidence            5

The Rop (Rho-related protein from plants) subfamily plays a role in diverse cellular processes, including cytoskeletal organization, pollen and vegetative cell growth, hormone responses, stress responses, and pathogen resistance. Rops are able to regulate several downstream pathways to amplify a specific signal by acting as master switches early in the signaling cascade. They transmit a variety of extracellular and intracellular signals. Rops are involved in establishing cell polarity in root-hair development, root-hair elongation, pollen-tube growth, cell-shape formation, responses to hormones such as abscisic acid (ABA) and auxin, responses to abiotic stresses such as oxygen deprivation, and disease resistance and disease susceptibility. An individual Rop can have a unique function or an overlapping function shared with other Rop proteins; in addition, a given Rop-regulated function can be controlled by one or multiple Rop proteins. For example,

>cd04172 Rnd3_RhoE_Rho8 Rnd3/RhoE/Rho8 subfamily

Probab=99.83  E-value=4.1e-20  Score=105.42  Aligned_cols=69  Identities=19%  Similarity=0.447  Sum_probs=61.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCcc------------cccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKH------------LLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~------------~~~v~~~e~~~~   68 (72)
                      +++.||+++|++++|||++++.||+++ ..|++.+++.. +++|++|||||+||.+            .+.|+.++|.++
T Consensus        69 ~~~~~~~~ad~~ilvyDit~~~Sf~~~~~~w~~~i~~~~-~~~piilVgNK~DL~~~~~~~~~~~~~~~~~v~~~~~~~~  147 (182)
T cd04172          69 VRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFC-PNTKMLLVGCKSDLRTDLTTLVELSNHRQTPVSYDQGANM  147 (182)
T ss_pred             hhhhhcCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHC-CCCCEEEEeEChhhhcChhhHHHHHhcCCCCCCHHHHHHH
Confidence            568899999999999999999999998 89999998875 6799999999999964            357999999999


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      |++
T Consensus       148 a~~  150 (182)
T cd04172         148 AKQ  150 (182)
T ss_pred             HHH
Confidence            975

Rnd3/RhoE/Rho8 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7. Rnd3/RhoE is known to bind the serine-threonine kinase ROCK I. Unphosphorylated Rnd3/RhoE associates primarily with membranes, but ROCK I-phosphorylated Rnd3/RhoE localizes in the cytosol. Phosphorylation of Rnd3/RhoE correlates with its activity in disrupting RhoA-induced stress fibers and inhibiting Ras-induced fibroblast transformation. In cells that lack stress fibers, such as macrophages and monocytes, Rnd3/RhoE induces a redistribution of actin, causing morphological changes in the cell. In addition, Rnd3/RhoE has been shown to inhibit cell cycle progression in G1 phase at a point upstream of the pRb family pocket protein checkpoint. Rnd3/RhoE has also been shown to inhibit Ras- and Raf-induced fibroblast transformation. In mammary epithelial tumor cells, Rnd3/RhoE regulates the assembly of the apical junction complex and tight

>KOG0091 consensus GTPase Rab39, small G protein superfamily [General function prediction only]

Probab=99.83  E-value=2.2e-20  Score=104.86  Aligned_cols=71  Identities=38%  Similarity=0.660  Sum_probs=64.3

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-C-CCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-S-NIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~-~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      |++.+|||++-|+++|||++|++||++++.|+++...+.+ + .+...|||+|+||...|+|+.|||+++|++
T Consensus        73 sitksyyrnsvgvllvyditnr~sfehv~~w~~ea~m~~q~P~k~VFlLVGhKsDL~SqRqVt~EEaEklAa~  145 (213)
T KOG0091|consen   73 SITKSYYRNSVGVLLVYDITNRESFEHVENWVKEAAMATQGPDKVVFLLVGHKSDLQSQRQVTAEEAEKLAAS  145 (213)
T ss_pred             HHHHHHhhcccceEEEEeccchhhHHHHHHHHHHHHHhcCCCCeeEEEEeccccchhhhccccHHHHHHHHHh
Confidence            5789999999999999999999999999999999877664 4 455789999999999999999999999975

>cd04131 Rnd Rnd subfamily

Probab=99.82  E-value=8.5e-20  Score=103.71  Aligned_cols=69  Identities=19%  Similarity=0.463  Sum_probs=61.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCcc------------cccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKH------------LLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~------------~~~v~~~e~~~~   68 (72)
                      +++.||++++++++|||+++++||+++ ..|++.+++.. +++|++|||||+||.+            .+.++.+++.++
T Consensus        65 ~~~~~~~~a~~~ilvfdit~~~Sf~~~~~~w~~~i~~~~-~~~~iilVgnK~DL~~~~~~~~~~~~~~~~~v~~~e~~~~  143 (178)
T cd04131          65 VRPLCYPDSDAVLICFDISRPETLDSVLKKWRGEIQEFC-PNTKVLLVGCKTDLRTDLSTLMELSHQRQAPVSYEQGCAI  143 (178)
T ss_pred             cchhhcCCCCEEEEEEECCChhhHHHHHHHHHHHHHHHC-CCCCEEEEEEChhhhcChhHHHHHHhcCCCCCCHHHHHHH
Confidence            578899999999999999999999996 89999998875 6799999999999964            356999999999


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      |++
T Consensus       144 a~~  146 (178)
T cd04131         144 AKQ  146 (178)
T ss_pred             HHH
Confidence            975

The Rnd subfamily contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These novel Rho family proteins have substantial structural differences compared to other Rho members, including N- and C-terminal extensions relative to other Rhos. Rnd3/RhoE is farnesylated at the C-terminal prenylation site, unlike most other Rho proteins that are geranylgeranylated. In addition, Rnd members are unable to hydrolyze GTP and are resistant to GAP activity. They are believed to exist only in the GTP-bound conformation, and are antagonists of RhoA activity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.

>KOG0083 consensus GTPase Rab26/Rab37, small G protein superfamily [General function prediction only]

Probab=99.82  E-value=6.2e-21  Score=104.39  Aligned_cols=71  Identities=32%  Similarity=0.599  Sum_probs=66.5

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      |.+..|||+||+.+++||++++.||++++.|+.++.++....+.+.++|||+|+..+|.|..++++++|+.
T Consensus        62 svt~ayyrda~allllydiankasfdn~~~wlsei~ey~k~~v~l~llgnk~d~a~er~v~~ddg~kla~~  132 (192)
T KOG0083|consen   62 SVTHAYYRDADALLLLYDIANKASFDNCQAWLSEIHEYAKEAVALMLLGNKCDLAHERAVKRDDGEKLAEA  132 (192)
T ss_pred             hhhHhhhcccceeeeeeecccchhHHHHHHHHHHHHHHHHhhHhHhhhccccccchhhccccchHHHHHHH
Confidence            45678999999999999999999999999999999999888899999999999999999999999999863

>KOG0395 consensus Ras-related GTPase [General function prediction only]

Probab=99.81  E-value=1.3e-19  Score=104.62  Aligned_cols=70  Identities=31%  Similarity=0.470  Sum_probs=63.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +...|+++++|+++||+++++.||+.+..+++++.+... ..+|+++||||+||...|.|+.+||.++|+.
T Consensus        67 ~~~~~~~~~~gF~lVysitd~~SF~~~~~l~~~I~r~~~~~~~PivlVGNK~Dl~~~R~V~~eeg~~la~~  137 (196)
T KOG0395|consen   67 MRDLYIRNGDGFLLVYSITDRSSFEEAKQLREQILRVKGRDDVPIILVGNKCDLERERQVSEEEGKALARS  137 (196)
T ss_pred             HHHHhhccCcEEEEEEECCCHHHHHHHHHHHHHHHHhhCcCCCCEEEEEEcccchhccccCHHHHHHHHHh
Confidence            567899999999999999999999999999999966554 6789999999999999999999999998764

>cd04174 Rnd1_Rho6 Rnd1/Rho6 subfamily

Probab=99.80  E-value=2.8e-19  Score=105.41  Aligned_cols=69  Identities=22%  Similarity=0.424  Sum_probs=61.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCcc------------cccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKH------------LLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~------------~~~v~~~e~~~~   68 (72)
                      +++.||++|+++++|||+++++||+++ ..|++++.+.. +++|++|||||+||.+            .+.|+.++|.++
T Consensus        77 ~~~~~~~~ad~vIlVyDit~~~Sf~~~~~~w~~~i~~~~-~~~piilVgNK~DL~~~~~~~~~l~~~~~~~Vs~~e~~~~  155 (232)
T cd04174          77 VRPLCYSDSDAVLLCFDISRPETVDSALKKWKAEIMDYC-PSTRILLIGCKTDLRTDLSTLMELSNQKQAPISYEQGCAL  155 (232)
T ss_pred             HHHHHcCCCcEEEEEEECCChHHHHHHHHHHHHHHHHhC-CCCCEEEEEECcccccccchhhhhccccCCcCCHHHHHHH
Confidence            567899999999999999999999985 89999998765 5789999999999965            378999999999


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      |++
T Consensus       156 a~~  158 (232)
T cd04174         156 AKQ  158 (232)
T ss_pred             HHH
Confidence            975

Rnd1/Rho6 is a member of the novel Rho subfamily Rnd, together with Rnd2/Rho7 and Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not hydrolyze it to GDP, indicating that it is constitutively active. In rat, Rnd1/Rho6 is highly expressed in the cerebral cortex and hippocampus during synapse formation, and plays a role in spine formation. Rnd1/Rho6 is also expressed in the liver and in endothelial cells, and is upregulated in uterine myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8, Rnd1/Rho6 is believed to function as an antagonist to RhoA. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.

>KOG0081 consensus GTPase Rab27, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.80  E-value=1.2e-19  Score=101.68  Aligned_cols=71  Identities=35%  Similarity=0.583  Sum_probs=65.0

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ||+..|||+|.|++++||+++..||-+++.|+.+++.+. ..+.-||++|||+||.+.|.|+.+++.++|++
T Consensus        82 SLTTAFfRDAMGFlLiFDlT~eqSFLnvrnWlSQL~~hAYcE~PDivlcGNK~DL~~~R~Vs~~qa~~La~k  153 (219)
T KOG0081|consen   82 SLTTAFFRDAMGFLLIFDLTSEQSFLNVRNWLSQLQTHAYCENPDIVLCGNKADLEDQRVVSEDQAAALADK  153 (219)
T ss_pred             HHHHHHHHhhccceEEEeccchHHHHHHHHHHHHHHHhhccCCCCEEEEcCccchhhhhhhhHHHHHHHHHH
Confidence            467889999999999999999999999999999998875 35677999999999999999999999999875

>cd01875 RhoG RhoG subfamily

Probab=99.80  E-value=5.4e-19  Score=101.12  Aligned_cols=69  Identities=19%  Similarity=0.404  Sum_probs=59.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      +++.||+++|++++|||++++.||+.+. .|.+.+.... +++|++|||||.||.+.            +.++.+++.++
T Consensus        67 l~~~~~~~a~~~ilvydit~~~Sf~~~~~~w~~~i~~~~-~~~piilvgNK~DL~~~~~~~~~~~~~~~~~v~~~~~~~~  145 (191)
T cd01875          67 LRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHHC-PNVPILLVGTKKDLRNDADTLKKLKEQGQAPITPQQGGAL  145 (191)
T ss_pred             hhhhhccCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhC-CCCCEEEEEeChhhhcChhhHHHHhhccCCCCCHHHHHHH
Confidence            6788999999999999999999999996 6988887654 67999999999999754            34788899998


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      |++
T Consensus       146 a~~  148 (191)
T cd01875         146 AKQ  148 (191)
T ss_pred             HHH
Confidence            864

RhoG is a GTPase with high sequence similarity to members of the Rac subfamily, including the regions involved in effector recognition and binding. However, RhoG does not bind to known Rac1 and Cdc42 effectors, including proteins containing a Cdc42/Rac interacting binding (CRIB) motif. Instead, RhoG interacts directly with Elmo, an upstream regulator of Rac1, in a GTP-dependent manner and forms a ternary complex with Dock180 to induce activation of Rac1. The RhoG-Elmo-Dock180 pathway is required for activation of Rac1 and cell spreading mediated by integrin, as well as for neurite outgrowth induced by nerve growth factor. Thus RhoG activates Rac1 through Elmo and Dock180 to control cell morphology. RhoG has also been shown to play a role in caveolar trafficking and has a novel role in signaling the neutrophil respiratory burst stimulated by G protein-coupled receptor (GPCR) agonists. Most Rho proteins contain a lipid modification site at the C-termin

>cd01873 RhoBTB RhoBTB subfamily

Probab=99.79  E-value=6.4e-19  Score=101.47  Aligned_cols=69  Identities=19%  Similarity=0.274  Sum_probs=60.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCcc-------------------cccCC
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKH-------------------LLNSM   61 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~-------------------~~~v~   61 (72)
                      +++.||+++|++++|||++++.||+++. .|++.+.... +++|+++||||+||.+                   .+.|+
T Consensus        80 ~~~~~~~~ad~iilv~d~t~~~Sf~~~~~~w~~~i~~~~-~~~piilvgNK~DL~~~~~~~~~~~~~~~~~~~~~~~~V~  158 (195)
T cd01873          80 DRRFAYGRSDVVLLCFSIASPNSLRNVKTMWYPEIRHFC-PRVPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILP  158 (195)
T ss_pred             hhcccCCCCCEEEEEEECCChhHHHHHHHHHHHHHHHhC-CCCCEEEEEEchhccccccchhhhcccccccccccCCccC
Confidence            4567999999999999999999999996 6999887765 5789999999999964                   47899


Q ss_pred             HHHHHHHHhc
Q 047889           62 CEEYLIKSRS   71 (72)
Q Consensus        62 ~~e~~~~a~~   71 (72)
                      .++|.++|++
T Consensus       159 ~~e~~~~a~~  168 (195)
T cd01873         159 PETGRAVAKE  168 (195)
T ss_pred             HHHHHHHHHH
Confidence            9999999975

Members of the RhoBTB subfamily of Rho GTPases are present in vertebrates, Drosophila, and Dictyostelium. RhoBTB proteins are characterized by a modular organization, consisting of a GTPase domain, a proline rich region, a tandem of two BTB (Broad-Complex, Tramtrack, and Bric a brac) domains, and a C-terminal region of unknown function. RhoBTB proteins may act as docking points for multiple components participating in signal transduction cascades. RhoBTB genes appeared upregulated in some cancer cell lines, suggesting a participation of RhoBTB proteins in the pathogenesis of particular tumors. Note that the Dictyostelium RacA GTPase domain is more closely related to Rac proteins than to RhoBTB proteins, where RacA actually belongs. Thus, the Dictyostelium RacA is not included here. Most Rho proteins contain a lipid modification site at the C-terminus; however, RhoBTB is one of few Rho subfamilies that lack this feature.

>PTZ00099 rab6; Provisional

Probab=99.79  E-value=1.1e-18  Score=99.14  Aligned_cols=69  Identities=35%  Similarity=0.725  Sum_probs=61.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.||++||++++|||++++.||+.+..|+..+......++|++|||||+||...+.+..+++..+++
T Consensus        45 ~~~~~~~~ad~~ilv~D~t~~~sf~~~~~w~~~i~~~~~~~~piilVgNK~DL~~~~~v~~~e~~~~~~  113 (176)
T PTZ00099         45 LIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQ  113 (176)
T ss_pred             ccHHHhCCCcEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCeEEEEEECcccccccCCCHHHHHHHHH
Confidence            567899999999999999999999999999999876655679999999999998778899989888775

>cd04122 Rab14 Rab14 subfamily

Probab=99.79  E-value=9.9e-19  Score=97.59  Aligned_cols=70  Identities=44%  Similarity=0.746  Sum_probs=63.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||++++++++|||+++++||+.+..|++.+.....++.|+++||||+|+...+.++.+++.+++++
T Consensus        67 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~iiiv~nK~Dl~~~~~~~~~~~~~~~~~  136 (166)
T cd04122          67 VTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLEAQRDVTYEEAKQFADE  136 (166)
T ss_pred             HHHHHhcCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccCcCHHHHHHHHHH
Confidence            3567999999999999999999999999999998777667899999999999998889999999988864

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 GT

>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases

Probab=99.79  E-value=8.8e-19  Score=97.12  Aligned_cols=70  Identities=30%  Similarity=0.579  Sum_probs=64.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.+++++|++++|||+++++||+.+..|++.+....+.++|++|+|||.|+.+.+.++.+++.++|++
T Consensus        64 ~~~~~~~~~~~~ii~fd~~~~~S~~~~~~~~~~i~~~~~~~~~iivvg~K~D~~~~~~v~~~~~~~~~~~  133 (162)
T PF00071_consen   64 LRDIFYRNSDAIIIVFDVTDEESFENLKKWLEEIQKYKPEDIPIIVVGNKSDLSDEREVSVEEAQEFAKE  133 (162)
T ss_dssp             HHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGGSSSCHHHHHHHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccceeeeccccccccccchhhHHHHHHHH
Confidence            3467899999999999999999999999999999988766799999999999999999999999999875

This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_A ....

>cd04117 Rab15 Rab15 subfamily

Probab=99.78  E-value=1.9e-18  Score=96.38  Aligned_cols=70  Identities=30%  Similarity=0.538  Sum_probs=63.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|++++|++++|||+++++||+.+..|++.+.+....++|+++||||.|+.+.+.++.+++..+++.
T Consensus        65 ~~~~~~~~~~~~i~v~d~~~~~sf~~~~~~~~~~~~~~~~~~~iilvgnK~Dl~~~~~v~~~~~~~~~~~  134 (161)
T cd04117          65 ITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQKRQVGDEQGNKLAKE  134 (161)
T ss_pred             hHHHHhcCCcEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccCCCHHHHHHHHHH
Confidence            4578999999999999999999999999999999877656799999999999998899999999988864

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

>cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily

Probab=99.78  E-value=1.4e-18  Score=97.99  Aligned_cols=70  Identities=27%  Similarity=0.397  Sum_probs=62.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||++++++++|||++++.||+.+..|...+.+.. ..++|+++||||+|+.+.+.++.+++.+++++
T Consensus        66 l~~~~~~~~d~~ilv~d~~~~~Sf~~~~~~~~~i~~~~~~~~~piilvgNK~Dl~~~~~v~~~~~~~~a~~  136 (172)
T cd04141          66 MRDQYMRCGEGFIICYSVTDRHSFQEASEFKKLITRVRLTEDIPLVLVGNKVDLESQRQVTTEEGRNLARE  136 (172)
T ss_pred             HhHHHhhcCCEEEEEEECCchhHHHHHHHHHHHHHHhcCCCCCCEEEEEEChhhhhcCccCHHHHHHHHHH
Confidence            56889999999999999999999999999988887654 36799999999999988889999999998864

Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to sign

>cd04126 Rab20 Rab20 subfamily

Probab=99.78  E-value=1.8e-18  Score=101.29  Aligned_cols=70  Identities=27%  Similarity=0.420  Sum_probs=62.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc-------------------cccCCH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH-------------------LLNSMC   62 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~-------------------~~~v~~   62 (72)
                      +++.||++++++|+|||+++++||+.+..|+..+.+....++|++|||||+||.+                   .|.|+.
T Consensus        60 l~~~~~~~ad~~IlV~Dvt~~~Sf~~l~~~~~~l~~~~~~~~piIlVgNK~DL~~~~~~~~~~~~~~~~~~~~~~r~v~~  139 (220)
T cd04126          60 LGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTEEGALAGQEKDAGDRVSPEDQRQVTL  139 (220)
T ss_pred             hHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECcccccccccccccccccccccccccccCCH
Confidence            4678999999999999999999999999888887766556799999999999976                   689999


Q ss_pred             HHHHHHHhc
Q 047889           63 EEYLIKSRS   71 (72)
Q Consensus        63 ~e~~~~a~~   71 (72)
                      +++.++|++
T Consensus       140 ~e~~~~a~~  148 (220)
T cd04126         140 EDAKAFYKR  148 (220)
T ss_pred             HHHHHHHHH
Confidence            999999875

Rab20 is one of several Rab proteins that appear to be restricted in expression to the apical domain of murine polarized epithelial cells. It is expressed on the apical side of polarized kidney tubule and intestinal epithelial cells, and in non-polarized cells. It also localizes to vesico-tubular structures below the apical brush border of renal proximal tubule cells and in the apical region of duodenal epithelial cells. Rab20 has also been shown to colocalize with vacuolar H+-ATPases (V-ATPases) in mouse kidney cells, suggesting a role in the regulation of V-ATPase traffic in specific portions of the nephron. It was also shown to be one of several proteins whose expression is upregulated in human myelodysplastic syndrome (MDS) patients. 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-bo

>KOG0095 consensus GTPase Rab30, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.78  E-value=4.3e-19  Score=98.69  Aligned_cols=70  Identities=30%  Similarity=0.518  Sum_probs=65.8

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      |++.+|||.|+++|++||++-..||+-++.|+.++.++....+..++||||.|+.+.|+|+.+-+++|++
T Consensus        71 sitqsyyrsahalilvydiscqpsfdclpewlreie~yan~kvlkilvgnk~d~~drrevp~qigeefs~  140 (213)
T KOG0095|consen   71 SITQSYYRSAHALILVYDISCQPSFDCLPEWLREIEQYANNKVLKILVGNKIDLADRREVPQQIGEEFSE  140 (213)
T ss_pred             HHHHHHhhhcceEEEEEecccCcchhhhHHHHHHHHHHhhcceEEEeeccccchhhhhhhhHHHHHHHHH
Confidence            4678999999999999999999999999999999999988889999999999999999999999998875

>cd04102 RabL3 RabL3 (Rab-like3) subfamily

Probab=99.77  E-value=1.5e-18  Score=100.49  Aligned_cols=63  Identities=25%  Similarity=0.418  Sum_probs=55.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-------------------CCCCeEEEEeeCCCCcccccCCH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-------------------GSNIVIMLIGNKSDLKHLLNSMC   62 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-------------------~~~~~~vlvgnK~Dl~~~~~v~~   62 (72)
                      +++.||++++++|+|||+++++||+++..|++++.+..                   +.++|++|||||+|+.++|.+..
T Consensus        70 l~~~~yr~ad~iIlVyDvtn~~Sf~~l~~W~~ei~~~~~~~~~~~~~~~~~~~~~~~~~~~PiilVGnK~Dl~~~r~~~~  149 (202)
T cd04102          70 TRAVFYNQVNGIILVHDLTNRKSSQNLQRWSLEALNKDTFPTGLLVTNGDYDSEQFGGNQIPLLVIGTKLDQIPEKESSG  149 (202)
T ss_pred             HHHHHhCcCCEEEEEEECcChHHHHHHHHHHHHHHHhhccccccccccccccccccCCCCceEEEEEECccchhhcccch
Confidence            56789999999999999999999999999999987631                   24699999999999988887776


Q ss_pred             HH
Q 047889           63 EE   64 (72)
Q Consensus        63 ~e   64 (72)
                      ++
T Consensus       150 ~~  151 (202)
T cd04102         150 NL  151 (202)
T ss_pred             HH
Confidence            64

RabL3s 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, RabL3 lacks a prenylation site at the C-terminus. The specific function of RabL3 remains unknown.

>PLN00023 GTP-binding protein; Provisional

Probab=99.76  E-value=4.9e-18  Score=103.98  Aligned_cols=70  Identities=17%  Similarity=0.326  Sum_probs=60.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC------------CCCeEEEEeeCCCCcccc---c---CCHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG------------SNIVIMLIGNKSDLKHLL---N---SMCE   63 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~------------~~~~~vlvgnK~Dl~~~~---~---v~~~   63 (72)
                      +++.||++++++|+|||+++++||+++..|++.+.....            .++|++|||||+||..++   .   +..+
T Consensus        99 L~~~yyr~AdgiILVyDITdr~SFenL~kWl~eI~~~~~~s~p~~s~~~~~~~ipIILVGNK~DL~~~~~~r~~s~~~~e  178 (334)
T PLN00023         99 CRSLFYSQINGVIFVHDLSQRRTKTSLQKWASEVAATGTFSAPLGSGGPGGLPVPYIVIGNKADIAPKEGTRGSSGNLVD  178 (334)
T ss_pred             hhHHhccCCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcccccccccccccCCCCcEEEEEECccccccccccccccccHH
Confidence            678899999999999999999999999999999987631            258999999999997643   3   4688


Q ss_pred             HHHHHHhc
Q 047889           64 EYLIKSRS   71 (72)
Q Consensus        64 e~~~~a~~   71 (72)
                      +++++|++
T Consensus       179 ~a~~~A~~  186 (334)
T PLN00023        179 AARQWVEK  186 (334)
T ss_pred             HHHHHHHH
Confidence            99999875

>cd01874 Cdc42 Cdc42 subfamily

Probab=99.76  E-value=5.2e-18  Score=95.97  Aligned_cols=69  Identities=22%  Similarity=0.378  Sum_probs=59.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      +++.||+++|++++|||+++++||+.+. .|...+.... +++|+++||||+|+...            +.++.+++.++
T Consensus        65 ~~~~~~~~a~~~ilv~d~~~~~s~~~~~~~w~~~i~~~~-~~~piilvgnK~Dl~~~~~~~~~l~~~~~~~v~~~~~~~~  143 (175)
T cd01874          65 LRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHC-PKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETGEKL  143 (175)
T ss_pred             hhhhhcccCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEECHhhhhChhhHHHhhhccCCCcCHHHHHHH
Confidence            5678999999999999999999999996 6998887654 57999999999998653            67889999988


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       144 a~~  146 (175)
T cd01874         144 ARD  146 (175)
T ss_pred             HHH
Confidence            764

Cdc42 is an essential GTPase that belongs to the Rho family of Ras-like GTPases. These proteins act as molecular switches by responding to exogenous and/or endogenous signals and relaying those signals to activate downstream components of a biological pathway. Cdc42 transduces signals to the actin cytoskeleton to initiate and maintain polarized growth and to mitogen-activated protein morphogenesis. In the budding yeast Saccharomyces cerevisiae, Cdc42 plays an important role in multiple actin-dependent morphogenetic events such as bud emergence, mating-projection formation, and pseudohyphal growth. In mammalian cells, Cdc42 regulates a variety of actin-dependent events and induces the JNK/SAPK protein kinase cascade, which leads to the activation of transcription factors within the nucleus. Cdc42 mediates these processes through interactions with a myriad of downstream effectors, whose number and regulation we are just starting to understand. In addi

>KOG0394 consensus Ras-related GTPase [General function prediction only]

Probab=99.76  E-value=3.2e-18  Score=97.41  Aligned_cols=71  Identities=30%  Similarity=0.491  Sum_probs=62.6

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC----CCCeEEEEeeCCCCcc--cccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG----SNIVIMLIGNKSDLKH--LLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~----~~~~~vlvgnK~Dl~~--~~~v~~~e~~~~a~~   71 (72)
                      ||.-.|||+||+++++||++++.||+++..|.+++....+    ...|.||+|||+|+.+  .|+|+.+.|.+||++
T Consensus        73 sLg~aFYRgaDcCvlvydv~~~~Sfe~L~~Wr~EFl~qa~~~~Pe~FPFVilGNKiD~~~~~~r~VS~~~Aq~WC~s  149 (210)
T KOG0394|consen   73 SLGVAFYRGADCCVLVYDVNNPKSFENLENWRKEFLIQASPQDPETFPFVILGNKIDVDGGKSRQVSEKKAQTWCKS  149 (210)
T ss_pred             hcccceecCCceEEEEeecCChhhhccHHHHHHHHHHhcCCCCCCcccEEEEcccccCCCCccceeeHHHHHHHHHh
Confidence            4667899999999999999999999999999999765543    4589999999999976  399999999999975

>KOG0097 consensus GTPase Rab14, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.75  E-value=2e-18  Score=95.51  Aligned_cols=70  Identities=44%  Similarity=0.748  Sum_probs=66.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      .+++|||++.|.++|||++.+++++++..|+...+....++..++++|||.||...|.|+.+|+++||.+
T Consensus        76 vtrsyyrgaagalmvyditrrstynhlsswl~dar~ltnpnt~i~lignkadle~qrdv~yeeak~faee  145 (215)
T KOG0097|consen   76 VTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLESQRDVTYEEAKEFAEE  145 (215)
T ss_pred             HHHHHhccccceeEEEEehhhhhhhhHHHHHhhhhccCCCceEEEEecchhhhhhcccCcHHHHHHHHhh
Confidence            4689999999999999999999999999999999988888999999999999999999999999999875

>cd04107 Rab32_Rab38 Rab38/Rab32 subfamily

Probab=99.74  E-value=1.6e-17  Score=95.52  Aligned_cols=70  Identities=41%  Similarity=0.689  Sum_probs=61.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc----CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA----GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~----~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||++++++++|||+++++||+.+..|+..+....    ..++|++|||||+|+...+.+..+++.+++++
T Consensus        66 ~~~~~~~~a~~~ilv~D~t~~~s~~~~~~~~~~i~~~~~~~~~~~~piilv~NK~Dl~~~~~~~~~~~~~~~~~  139 (201)
T cd04107          66 MTRVYYRGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPCLLLANKCDLKKRLAKDGEQMDQFCKE  139 (201)
T ss_pred             hHHHHhCCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhcccCCCCCcEEEEEECCCcccccccCHHHHHHHHHH
Confidence            56789999999999999999999999999999886542    25789999999999987788999999988764

Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. 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.

>cd04127 Rab27A Rab27a subfamily

Probab=99.74  E-value=1.6e-17  Score=93.51  Aligned_cols=70  Identities=36%  Similarity=0.588  Sum_probs=61.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||+++++||..+..|+..+..... ++.|+++||||+|+.+.+.++.+++.+++++
T Consensus        79 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piiiv~nK~Dl~~~~~v~~~~~~~~~~~  149 (180)
T cd04127          79 LTTAFFRDAMGFLLIFDLTNEQSFLNVRNWMSQLQTHAYCENPDIVLCGNKADLEDQRQVSEEQAKALADK  149 (180)
T ss_pred             HHHHHhCCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEeCccchhcCccCHHHHHHHHHH
Confidence            457789999999999999999999999999999877643 5789999999999988888999999888764

The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated

>cd04103 Centaurin_gamma Centaurin gamma

Probab=99.74  E-value=1.2e-17  Score=93.25  Aligned_cols=68  Identities=12%  Similarity=0.181  Sum_probs=59.6

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCc--ccccCCHHHHHHHHhc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLK--HLLNSMCEEYLIKSRS   71 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~--~~~~v~~~e~~~~a~~   71 (72)
                      ..|++++|++++|||+++++||+.+..|++++..... +++|+++||||.|+.  ..+.++.+++.+++++
T Consensus        60 ~~~~~~~~~~ilv~d~~~~~sf~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~~~~~v~~~~~~~~~~~  130 (158)
T cd04103          60 AQFASWVDAVIFVFSLENEASFQTVYNLYHQLSSYRNISEIPLILVGTQDAISESNPRVIDDARARQLCAD  130 (158)
T ss_pred             hhHHhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEeeHHHhhhcCCcccCHHHHHHHHHH
Confidence            4688999999999999999999999999999987653 679999999999995  3578999999888853

The centaurins (alpha, beta, gamma, and delta) are large, multi-domain proteins that all contain an ArfGAP domain and ankyrin repeats, and in some cases, numerous additional domains. Centaurin gamma contains an additional GTPase domain near its N-terminus. The specific function of this GTPase domain has not been well characterized, but centaurin gamma 2 (CENTG2) may play a role in the development of autism. Centaurin gamma 1 is also called PIKE (phosphatidyl inositol (PI) 3-kinase enhancer) and centaurin gamma 2 is also known as AGAP (ArfGAP protein with a GTPase-like domain, ankyrin repeats and a Pleckstrin homology domain) or GGAP. Three isoforms of PIKE have been identified. PIKE-S (short) and PIKE-L (long) are brain-specific isoforms, with PIKE-S restricted to the nucleus and PIKE-L found in multiple cellular compartments. A third isoform, PIKE-A was identified in human glioblastoma brain cancers and has been found in various tissues.

>cd04109 Rab28 Rab28 subfamily

Probab=99.73  E-value=2.5e-17  Score=95.72  Aligned_cols=70  Identities=31%  Similarity=0.520  Sum_probs=61.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC---CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG---SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||+++|++++|||+++++||+.+..|+..+.+...   .++|+++||||+|+.+.+.++.+++.++++.
T Consensus        66 l~~~~~~~ad~iilV~D~t~~~s~~~~~~w~~~l~~~~~~~~~~~piilVgNK~DL~~~~~v~~~~~~~~~~~  138 (215)
T cd04109          66 MLDKYIYGAHAVFLVYDVTNSQSFENLEDWYSMVRKVLKSSETQPLVVLVGNKTDLEHNRTVKDDKHARFAQA  138 (215)
T ss_pred             HHHHHhhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhccccCCCceEEEEEECcccccccccCHHHHHHHHHH
Confidence            456899999999999999999999999999999987642   4578999999999988889999998888764

First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumbly the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. 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

>cd01865 Rab3 Rab3 subfamily

Probab=99.73  E-value=3e-17  Score=91.59  Aligned_cols=70  Identities=33%  Similarity=0.586  Sum_probs=61.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..++++++++++|||++++++|+.+..|++.+.+.....+|+++||||+|+.+.+.+..+++.++++.
T Consensus        66 ~~~~~~~~~~~~l~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piivv~nK~Dl~~~~~~~~~~~~~~~~~  135 (165)
T cd01865          66 ITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDMEDERVVSSERGRQLADQ  135 (165)
T ss_pred             HHHHHccCCcEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCCEEEEEECcccCcccccCHHHHHHHHHH
Confidence            4577899999999999999999999999999999876656899999999999988888888888877653

The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. 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 promot

>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2

Probab=99.73  E-value=4.4e-17  Score=91.06  Aligned_cols=70  Identities=40%  Similarity=0.740  Sum_probs=62.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..+++++|++++|||+++++||+.+..|+..+.+....++|+++||||+|+.+.+.+..+++.++++.
T Consensus        68 ~~~~~~~~ad~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~p~iiv~nK~Dl~~~~~~~~~~~~~~~~~  137 (167)
T cd01867          68 ITTAYYRGAMGIILVYDITDEKSFENIRNWMRNIEEHASEDVERMLVGNKCDMEEKRVVSKEEGEALADE  137 (167)
T ss_pred             HHHHHhCCCCEEEEEEECcCHHHHHhHHHHHHHHHHhCCCCCcEEEEEECcccccccCCCHHHHHHHHHH
Confidence            3567899999999999999999999999999999877657899999999999998888888888887753

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 inhi

>cd04144 Ras2 Ras2 subfamily

Probab=99.72  E-value=3.3e-17  Score=93.52  Aligned_cols=69  Identities=29%  Similarity=0.454  Sum_probs=60.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC---CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG---SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.||+++|++++|||+++++||+.+..|+..+.....   .+.|+++||||+|+.+++.++.+++.++++
T Consensus        63 ~~~~~~~~ad~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilvgNK~Dl~~~~~v~~~~~~~~~~  134 (190)
T cd04144          63 LRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVYEREVSTEEGAALAR  134 (190)
T ss_pred             HHHHHHHhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcccCCCCCEEEEEEChhccccCccCHHHHHHHHH
Confidence            467899999999999999999999999999998876542   578999999999998888898888887765

The Ras2 subfamily, found exclusively in fungi, was first identified in Ustilago maydis. In U. maydis, Ras2 is regulated by Sql2, a protein that is homologous to GEFs (guanine nucleotide exchange factors) of the CDC25 family. Ras2 has been shown to induce filamentous growth, but the signaling cascade through which Ras2 and Sql2 regulate cell morphology is not known. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.

>cd01871 Rac1_like Rac1-like subfamily

Probab=99.72  E-value=4e-17  Score=92.27  Aligned_cols=69  Identities=25%  Similarity=0.450  Sum_probs=59.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      +++.||+++|++|+|||+++++||+.+. .|+..+.... +++|+++||||+||.+.            +.++.+++.++
T Consensus        65 ~~~~~~~~~d~~ilv~d~~~~~sf~~~~~~~~~~~~~~~-~~~piilvgnK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  143 (174)
T cd01871          65 LRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHC-PNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAM  143 (174)
T ss_pred             hhhhhcCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEeeChhhccChhhHHHHhhccCCCCCHHHHHHH
Confidence            5678999999999999999999999995 6988887654 67999999999999643            35889999988


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       144 ~~~  146 (174)
T cd01871         144 AKE  146 (174)
T ss_pred             HHH
Confidence            864

The Rac1-like subfamily consists of Rac1, Rac2, and Rac3 proteins, plus the splice variant Rac1b that contains a 19-residue insertion near switch II relative to Rac1. While Rac1 is ubiquitously expressed, Rac2 and Rac3 are largely restricted to hematopoietic and neural tissues respectively. Rac1 stimulates the formation of actin lamellipodia and membrane ruffles. It also plays a role in cell-matrix adhesion and cell anoikis. In intestinal epithelial cells, Rac1 is an important regulator of migration and mediates apoptosis. Rac1 is also essential for RhoA-regulated actin stress fiber and focal adhesion complex formation. In leukocytes, Rac1 and Rac2 have distinct roles in regulating cell morphology, migration, and invasion, but are not essential for macrophage migration or chemotaxis. Rac3 has biochemical properties that are closely related to Rac1, such as effector interaction, nucleotide binding, and hydrolysis; Rac2 has a slower nucleoti

>cd04173 Rnd2_Rho7 Rnd2/Rho7 subfamily

Probab=99.72  E-value=5.6e-17  Score=95.13  Aligned_cols=69  Identities=17%  Similarity=0.435  Sum_probs=58.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      +++.||+++|++++|||+++++||+++ ..|...+.... +++|++|||||+||...            ..++.+++..+
T Consensus        65 l~~~~~~~~d~illvfdis~~~Sf~~i~~~w~~~~~~~~-~~~piiLVgnK~DL~~~~~~~~~~~~~~~~pIs~e~g~~~  143 (222)
T cd04173          65 VRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEFC-PNAKVVLVGCKLDMRTDLATLRELSKQRLIPVTHEQGTVL  143 (222)
T ss_pred             HhHHhccCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhC-CCCCEEEEEECcccccchhhhhhhhhccCCccCHHHHHHH
Confidence            568899999999999999999999999 56887776554 67999999999999652            24888899998


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      |++
T Consensus       144 ak~  146 (222)
T cd04173         144 AKQ  146 (222)
T ss_pred             HHH
Confidence            875

Rnd2/Rho7 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in radially migrating cells in the brain while they are within the subventricular zone of the hippocampus and cerebral cortex. These migrating cells typically develop into pyramidal neurons. Cells that exogenously expressed Rnd2/Rho7 failed to migrate to upper layers of the brain, suggesting that Rnd2/Rho7 plays a role in the radial migration and morphological changes of developing pyramidal neurons, and that Rnd2/Rho7 degradation is necessary for proper cellular migration. The Rnd2/Rho7 GEF Rapostlin is found primarily in the brain and together with Rnd2/Rho7 induces dendrite branching. Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA antagonists, Rnd2/Rho7 binds the GEF Pragmin and significantly stimulates RhoA activity and Rho-A mediated cell contraction. Rnd2/Rho7 is also found to be expressed in sperma

>cd04136 Rap_like Rap-like subfamily

Probab=99.71  E-value=6.8e-17  Score=89.43  Aligned_cols=69  Identities=25%  Similarity=0.405  Sum_probs=60.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.|+++++++++|||++++++|+.+..|...+.+... .+.|+++||||+|+.+.+.+..+++.++++
T Consensus        65 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~  134 (163)
T cd04136          65 MRDLYIKNGQGFVLVYSITSQSSFNDLQDLREQILRVKDTENVPMVLVGNKCDLEDERVVSREEGQALAR  134 (163)
T ss_pred             HHHHHhhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccceecHHHHHHHHH
Confidence            467899999999999999999999999999999877543 579999999999998777888888777765

The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres.

>smart00176 RAN Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases

Probab=99.71  E-value=6.4e-17  Score=93.57  Aligned_cols=66  Identities=33%  Similarity=0.553  Sum_probs=55.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.||++++++++|||++++.||+.+..|++++.+.. +++|++|||||+|+.. +.+..++. .+++
T Consensus        60 l~~~~~~~ad~~ilV~D~t~~~S~~~i~~w~~~i~~~~-~~~piilvgNK~Dl~~-~~v~~~~~-~~~~  125 (200)
T smart00176       60 LRDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRVC-ENIPIVLCGNKVDVKD-RKVKAKSI-TFHR  125 (200)
T ss_pred             hhHHHhcCCCEEEEEEECCChHHHHHHHHHHHHHHHhC-CCCCEEEEEECccccc-ccCCHHHH-HHHH
Confidence            56789999999999999999999999999999998765 6899999999999964 55665443 4543

Ran is involved in the active transport of proteins through nuclear pores.

>cd04134 Rho3 Rho3 subfamily

Probab=99.71  E-value=7.3e-17  Score=92.10  Aligned_cols=69  Identities=26%  Similarity=0.482  Sum_probs=58.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCcccc------------cCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHLL------------NSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~------------~v~~~e~~~~   68 (72)
                      +++.||++++++++|||+++++||+.+. .|+..+.... +++|+++||||+||.+.+            .++.+++.++
T Consensus        64 l~~~~~~~a~~~ilv~dv~~~~sf~~~~~~~~~~i~~~~-~~~piilvgNK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  142 (189)
T cd04134          64 LRSLSYADTDVIMLCFSVDSPDSLENVESKWLGEIREHC-PGVKLVLVALKCDLREARNERDDLQRYGKHTISYEEGLAV  142 (189)
T ss_pred             cccccccCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEEChhhccChhhHHHHhhccCCCCCHHHHHHH
Confidence            5678999999999999999999999995 6999988654 579999999999997654            3667778777


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       143 ~~~  145 (189)
T cd04134         143 AKR  145 (189)
T ss_pred             HHH
Confidence            653

Rho3 is a member of the Rho family found only in fungi. Rho3 is believed to regulate cell polarity by interacting with the diaphanous/formin family protein For3 to control both the actin cytoskeleton and microtubules. Rho3 is also believed to have a direct role in exocytosis that is independent of its role in regulating actin polarity. The function in exocytosis may be two-pronged: first, in the transport of post-Golgi vesicles from the mother cell to the bud, mediated by myosin (Myo2); second, in the docking and fusion of vesicles to the plasma membrane, mediated by an exocyst (Exo70) protein. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.

>cd04115 Rab33B_Rab33A Rab33B/Rab33A subfamily

Probab=99.71  E-value=8.4e-17  Score=90.24  Aligned_cols=70  Identities=24%  Similarity=0.516  Sum_probs=62.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|++++|++++|||+++++||..+..|++.+..... .++|+++||||+|+...+.++.+++.++++.
T Consensus        68 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~~~~~~~~~~~~~~~  138 (170)
T cd04115          68 MVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQIQVPTDLAQRFADA  138 (170)
T ss_pred             hHHHhhcCCCEEEEEEECCCHHHHHhHHHHHHHHHHhcCCCCCCEEEEEECccchhhcCCCHHHHHHHHHH
Confidence            456789999999999999999999999999999877643 6799999999999998889998888888753

Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. 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

>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily

Probab=99.71  E-value=8.3e-17  Score=89.64  Aligned_cols=69  Identities=41%  Similarity=0.647  Sum_probs=61.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|+++++++++|||+++++||..+..|+..+.....++.|++++|||+|+...+.+..+++..+++
T Consensus        67 ~~~~~~~~~~~ii~v~d~~~~~s~~~l~~~~~~~~~~~~~~~~~iiv~nK~Dl~~~~~~~~~~~~~~~~  135 (166)
T cd01869          67 ITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTDKRVVDYSEAQEFAD  135 (166)
T ss_pred             HHHHHhCcCCEEEEEEECcCHHHHHhHHHHHHHHHHhCCCCCcEEEEEEChhcccccCCCHHHHHHHHH
Confidence            456789999999999999999999999999999987665679999999999998888888888888875

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 t

>cd04176 Rap2 Rap2 subgroup

Probab=99.71  E-value=9.6e-17  Score=89.09  Aligned_cols=69  Identities=22%  Similarity=0.390  Sum_probs=60.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.|++++|++++|||+++++||+++..|+..+.+... .+.|+++||||+|+..++.+..+++..+++
T Consensus        65 ~~~~~~~~ad~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piviv~nK~Dl~~~~~~~~~~~~~~~~  134 (163)
T cd04176          65 MRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESEREVSSAEGRALAE  134 (163)
T ss_pred             hHHHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccchhcCccCHHHHHHHHH
Confidence            567899999999999999999999999999998877543 679999999999998777888777777764

The Rap2 subgroup is part of the Rap subfamily of the Ras family. It consists of Rap2a, Rap2b, and Rap2c. Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton. In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments. In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway. The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation. A number of additional effector proteins for Rap2 have been identified, incl

>cd04175 Rap1 Rap1 subgroup

Probab=99.71  E-value=7.8e-17  Score=89.62  Aligned_cols=69  Identities=23%  Similarity=0.369  Sum_probs=60.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.|++++|++++|||+++++||+.+..|...+.+.. ..+.|++++|||+|+.+.+.++.+++.++++
T Consensus        65 ~~~~~~~~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~  134 (164)
T cd04175          65 MRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLAR  134 (164)
T ss_pred             HHHHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCcchhccEEcHHHHHHHHH
Confidence            56789999999999999999999999999999987654 3679999999999998877888888777765

The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature. Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. High expression of Rap1 has been observed in the n

>cd01868 Rab11_like Rab11-like

Probab=99.71  E-value=1.1e-16  Score=89.00  Aligned_cols=69  Identities=71%  Similarity=1.038  Sum_probs=62.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.|+++++++++|||++++.+|..+..|+..+.+....++|+++||||+|+...+.+..+++..+++
T Consensus        68 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~pi~vv~nK~Dl~~~~~~~~~~~~~~~~  136 (165)
T cd01868          68 ITSAYYRGAVGALLVYDITKKQTFENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTEEAKAFAE  136 (165)
T ss_pred             HHHHHHCCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECccccccccCCHHHHHHHHH
Confidence            457789999999999999999999999999999988765679999999999998888888888888775

Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP

>cd04125 RabA_like RabA-like subfamily

Probab=99.71  E-value=1.2e-16  Score=90.92  Aligned_cols=69  Identities=35%  Similarity=0.559  Sum_probs=61.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.+++++|++++|||+++++||+.+..|+..+........|++++|||+|+.+.+.+..+++..+++
T Consensus        65 ~~~~~~~~~d~iilv~d~~~~~s~~~i~~~~~~i~~~~~~~~~~ivv~nK~Dl~~~~~v~~~~~~~~~~  133 (188)
T cd04125          65 LNNSYYRGAHGYLLVYDVTDQESFENLKFWINEINRYARENVIKVIVANKSDLVNNKVVDSNIAKSFCD  133 (188)
T ss_pred             hHHHHccCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECCCCcccccCCHHHHHHHHH
Confidence            456789999999999999999999999999999987765679999999999998888888888888775

RabA was first identified in D. discoideum, where its expression levels were compared to other Rabs in growing and developing cells. The RabA mRNA levels were below the level of detection by Northern blot analysis, suggesting a very low level of expression. The function of RabA remains unknown. 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.

>cd01864 Rab19 Rab19 subfamily

Probab=99.71  E-value=1.2e-16  Score=88.98  Aligned_cols=70  Identities=39%  Similarity=0.739  Sum_probs=62.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..+++++|++++|||++++.||+.++.|+..+.......+|+++||||+|+.+.+.+..+++.++++.
T Consensus        68 ~~~~~~~~~d~~llv~d~~~~~s~~~~~~~~~~i~~~~~~~~p~ivv~nK~Dl~~~~~~~~~~~~~~~~~  137 (165)
T cd01864          68 ITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDLEEQREVLFEEACTLAEK  137 (165)
T ss_pred             HHHHHhccCCEEEEEEECcCHHHHHhHHHHHHHHHHhCCCCCcEEEEEECcccccccccCHHHHHHHHHH
Confidence            3567899999999999999999999999999999876657899999999999988888888888888764

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 chracterized. 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.

>cd04112 Rab26 Rab26 subfamily

Probab=99.70  E-value=1.2e-16  Score=91.24  Aligned_cols=69  Identities=36%  Similarity=0.652  Sum_probs=61.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||+++++||+++..|+..+.+.....+|+++||||+|+..++.+..+++..+++
T Consensus        66 ~~~~~~~~ad~~i~v~D~~~~~s~~~~~~~~~~i~~~~~~~~piiiv~NK~Dl~~~~~~~~~~~~~l~~  134 (191)
T cd04112          66 VTHAYYRDAHALLLLYDITNKASFDNIRAWLTEIKEYAQEDVVIMLLGNKADMSGERVVKREDGERLAK  134 (191)
T ss_pred             hhHHHccCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEEcccchhccccCHHHHHHHHH
Confidence            356789999999999999999999999999999988766689999999999998778888888888765

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.

>PLN03110 Rab GTPase; Provisional

Probab=99.70  E-value=1.1e-16  Score=93.15  Aligned_cols=69  Identities=65%  Similarity=0.993  Sum_probs=62.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.|+++++++++|||++++.+|+.+..|+..+.+..+.++|+++||||+|+...+.+..+++..+++
T Consensus        77 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~piiiv~nK~Dl~~~~~~~~~~~~~l~~  145 (216)
T PLN03110         77 ITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIMMAGNKSDLNHLRSVAEEDGQALAE  145 (216)
T ss_pred             HHHHHhCCCCEEEEEEECCChHHHHHHHHHHHHHHHhCCCCCeEEEEEEChhcccccCCCHHHHHHHHH
Confidence            457799999999999999999999999999999988766789999999999998888898888888765

>smart00174 RHO Rho (Ras homology) subfamily of Ras-like small GTPases

Probab=99.70  E-value=1.4e-16  Score=89.22  Aligned_cols=69  Identities=23%  Similarity=0.404  Sum_probs=58.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      +++.+++++|++++|||+++++||+.+. .|+..+.... ++.|+++||||+|+..+            +.++.+++.++
T Consensus        62 ~~~~~~~~~d~~ilv~d~~~~~s~~~~~~~~~~~i~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  140 (174)
T smart00174       62 LRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFC-PNTPIILVGTKLDLREDKSTLRELSKQKQEPVTYEQGEAL  140 (174)
T ss_pred             hchhhcCCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhC-CCCCEEEEecChhhhhChhhhhhhhcccCCCccHHHHHHH
Confidence            4677899999999999999999999995 6999887764 68999999999999653            34888888888


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       141 ~~~  143 (174)
T smart00174      141 AKR  143 (174)
T ss_pred             HHH
Confidence            764

Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.

>cd04146 RERG_RasL11_like RERG/RasL11-like subfamily

Probab=99.70  E-value=1.5e-16  Score=88.61  Aligned_cols=69  Identities=29%  Similarity=0.393  Sum_probs=60.6

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc--CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA--GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ...+++++|++++|||+++++||+.+..|+..+....  ..++|+++||||+|+...+.++.+++.+++++
T Consensus        65 ~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~v~~~~~~~~~~~  135 (165)
T cd04146          65 LERSIRWADGFVLVYSITDRSSFDEISQLKQLIREIKKRDREIPVILVGNKADLLHYRQVSTEEGEKLASE  135 (165)
T ss_pred             HHHHHHhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCchHHhCccCHHHHHHHHHH
Confidence            4568899999999999999999999999999887754  35799999999999988888999998888764

RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack estrogen receptor and are correlated with poor clinical prognosis. Elevated RERG expression correlated with favorable patient outcome in a breast tumor subtype that is positive for estrogen receptor expression. In contrast to most Ras proteins, RERG overexpression inhibited the growth of breast tumor cells in vitro and in vivo. RasL11 was found to be ubiquitously expressed in human tissue, but down-regulated in prostate tumors. Both RERG and RasL11 lack the C-terminal CaaX prenylation motif, where a = an aliphatic amino acid and X = any amino acid, and are localized primarily in the cytoplasm. Both are believed to have tu

>KOG4252 consensus GTP-binding protein [Signal transduction mechanisms]

Probab=99.69  E-value=5.1e-17  Score=92.66  Aligned_cols=69  Identities=29%  Similarity=0.428  Sum_probs=64.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|||+|.+.++||+.+|+.||+.+..|+++++... .++|.++|-||+||.++.+++.++++.++++
T Consensus        85 ItkAyyrgaqa~vLVFSTTDr~SFea~~~w~~kv~~e~-~~IPtV~vqNKIDlveds~~~~~evE~lak~  153 (246)
T KOG4252|consen   85 ITKAYYRGAQASVLVFSTTDRYSFEATLEWYNKVQKET-ERIPTVFVQNKIDLVEDSQMDKGEVEGLAKK  153 (246)
T ss_pred             HHHHHhccccceEEEEecccHHHHHHHHHHHHHHHHHh-ccCCeEEeeccchhhHhhhcchHHHHHHHHH
Confidence            56789999999999999999999999999999998766 7899999999999999999999999888864

>cd04106 Rab23_lke Rab23-like subfamily

Probab=99.69  E-value=1.7e-16  Score=87.86  Aligned_cols=69  Identities=30%  Similarity=0.510  Sum_probs=61.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|+++++++++|||+++++||+.+..|+..+.... .++|+++||||+|+..++.++.+++.++++.
T Consensus        67 ~~~~~~~~~~~~v~v~d~~~~~s~~~l~~~~~~~~~~~-~~~p~iiv~nK~Dl~~~~~v~~~~~~~~~~~  135 (162)
T cd04106          67 ITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAEC-GDIPMVLVQTKIDLLDQAVITNEEAEALAKR  135 (162)
T ss_pred             hHHHHhcCCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCEEEEEEChhcccccCCCHHHHHHHHHH
Confidence            45779999999999999999999999999999987654 6799999999999988888888888887753

Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signalling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with G

>PTZ00369 Ras-like protein; Provisional

Probab=99.69  E-value=2e-16  Score=90.19  Aligned_cols=69  Identities=23%  Similarity=0.400  Sum_probs=60.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.|+++++++++|||+++++||+.+..|...+.+... .++|++++|||+|+.+.+.++.+++.++++
T Consensus        69 l~~~~~~~~d~iilv~D~s~~~s~~~~~~~~~~i~~~~~~~~~piiiv~nK~Dl~~~~~i~~~~~~~~~~  138 (189)
T PTZ00369         69 MRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDSERQVSTGEGQELAK  138 (189)
T ss_pred             hHHHHhhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccCHHHHHHHHH
Confidence            467899999999999999999999999999998876543 589999999999998878888888877765

>cd04111 Rab39 Rab39 subfamily

Probab=99.69  E-value=2.1e-16  Score=91.81  Aligned_cols=70  Identities=37%  Similarity=0.663  Sum_probs=61.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||+++|++++|||+++++||+.+..|+..+.+... ..+|+++||||+|+...+.++.+++.++++.
T Consensus        68 ~~~~~~~~~d~iilv~D~~~~~Sf~~l~~~~~~i~~~~~~~~~~iilvgNK~Dl~~~~~v~~~~~~~~~~~  138 (211)
T cd04111          68 ITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCDLESQRQVTREEAEKLAKD  138 (211)
T ss_pred             HHHHHhcCCcEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEccccccccccCHHHHHHHHHH
Confidence            456899999999999999999999999999999877653 4688999999999988888999999888764

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.

>cd01866 Rab2 Rab2 subfamily

Probab=99.69  E-value=2.5e-16  Score=88.15  Aligned_cols=70  Identities=50%  Similarity=0.806  Sum_probs=62.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||+++++||+.+..|+..+++...+.+|+++||||.|+...+.++.+++..++++
T Consensus        69 ~~~~~~~~~d~il~v~d~~~~~s~~~~~~~~~~~~~~~~~~~pvivv~nK~Dl~~~~~~~~~~~~~~~~~  138 (168)
T cd01866          69 ITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCDLESRREVSYEEGEAFAKE  138 (168)
T ss_pred             HHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEECcccccccCCCHHHHHHHHHH
Confidence            4567899999999999999999999999999999876557899999999999987788888888887653

Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. 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 featur

>cd04110 Rab35 Rab35 subfamily

Probab=99.68  E-value=2.8e-16  Score=90.34  Aligned_cols=68  Identities=37%  Similarity=0.648  Sum_probs=60.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|+++++++++|||+++++||+.+..|++.+.... +.+|+++||||+|+.+.+.+..+++..+++
T Consensus        71 ~~~~~~~~a~~iilv~D~~~~~s~~~~~~~~~~i~~~~-~~~piivVgNK~Dl~~~~~~~~~~~~~~~~  138 (199)
T cd04110          71 ITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNC-DDVCKVLVGNKNDDPERKVVETEDAYKFAG  138 (199)
T ss_pred             HHHHHhCCCcEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCEEEEEECcccccccccCHHHHHHHHH
Confidence            46789999999999999999999999999999987654 679999999999998877888888887765

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

>PLN03108 Rab family protein; Provisional

Probab=99.68  E-value=3.5e-16  Score=90.74  Aligned_cols=70  Identities=51%  Similarity=0.815  Sum_probs=62.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|++++|++++|||+++++||+.+..|+..+........|++++|||+|+.+.+.++.+++.+++++
T Consensus        71 ~~~~~~~~ad~~vlv~D~~~~~s~~~l~~~~~~~~~~~~~~~piiiv~nK~Dl~~~~~~~~~~~~~~~~~  140 (210)
T PLN03108         71 ITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCDLAHRRAVSTEEGEQFAKE  140 (210)
T ss_pred             HHHHHhccCCEEEEEEECCcHHHHHHHHHHHHHHHHhcCCCCcEEEEEECccCccccCCCHHHHHHHHHH
Confidence            4567899999999999999999999999999988776657899999999999998888999999988864

>cd04140 ARHI_like ARHI subfamily

Probab=99.68  E-value=3.2e-16  Score=87.44  Aligned_cols=69  Identities=25%  Similarity=0.299  Sum_probs=59.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC---CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG---SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..++++++++++|||+++++||+.+..|++.+.+...   +++|+++||||+|+...+.+..+++..+++
T Consensus        65 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~v~~~~~~~~~~  136 (165)
T cd04140          65 MQRLSISKGHAFILVYSVTSKQSLEELKPIYELICEIKGNNIEKIPIMLVGNKCDESHKREVSSNEGAACAT  136 (165)
T ss_pred             HHHHHhhcCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCCEEEEEECccccccCeecHHHHHHHHH
Confidence            356789999999999999999999999999988876542   579999999999998778888888877764

ARHI (A Ras homolog member I) is a member of the Ras family with several unique structural and functional properties. ARHI is expressed in normal human ovarian and breast tissue, but its expression is decreased or eliminated in breast and ovarian cancer. ARHI contains an N-terminal extension of 34 residues (human) that is required to retain its tumor suppressive activity. Unlike most other Ras family members, ARHI is maintained in the constitutively active (GTP-bound) state in resting cells and has modest GTPase activity. ARHI inhibits STAT3 (signal transducers and activators of transcription 3), a latent transcription factor whose abnormal activation plays a critical role in oncogenesis. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to

>cd04128 Spg1 Spg1p

Probab=99.68  E-value=2.5e-16  Score=89.72  Aligned_cols=69  Identities=19%  Similarity=0.401  Sum_probs=54.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc-----cccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH-----LLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~-----~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||+++++||+++..|+.++.+..+..+| ++||||+|+..     ++....+++.++|++
T Consensus        65 ~~~~~~~~a~~iilv~D~t~~~s~~~i~~~~~~~~~~~~~~~p-ilVgnK~Dl~~~~~~~~~~~~~~~~~~~a~~  138 (182)
T cd04128          65 MLPLVCNDAVAILFMFDLTRKSTLNSIKEWYRQARGFNKTAIP-ILVGTKYDLFADLPPEEQEEITKQARKYAKA  138 (182)
T ss_pred             hhHHHCcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCE-EEEEEchhccccccchhhhhhHHHHHHHHHH
Confidence            5678999999999999999999999999999999876555677 68899999942     222234667777653

Spg1p (septum-promoting GTPase) was first identified in the fission yeast S. pombe, where it regulates septum formation in the septation initiation network (SIN) through the cdc7 protein kinase. Spg1p is an essential gene that localizes to the spindle pole bodies. When GTP-bound, it binds cdc7 and causes it to translocate to spindle poles. Sid4p (septation initiation defective) is required for localization of Spg1p to the spindle pole body, and the ability of Spg1p to promote septum formation from any point in the cell cycle depends on Sid4p. Spg1p is negatively regulated by Byr4 and cdc16, which form a two-component GTPase activating protein (GAP) for Spg1p. The existence of a SIN-related pathway in plants has been proposed. 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

>cd04113 Rab4 Rab4 subfamily

Probab=99.68  E-value=4.7e-16  Score=86.15  Aligned_cols=70  Identities=47%  Similarity=0.734  Sum_probs=62.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.++++++++++|||++++++|..+..|+..++....+++|++++|||.|+...+.+..+++..+++.
T Consensus        65 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iivv~nK~D~~~~~~~~~~~~~~~~~~  134 (161)
T cd04113          65 VTRSYYRGAAGALLVYDITNRTSFEALPTWLSDARALASPNIVVILVGNKSDLADQREVTFLEASRFAQE  134 (161)
T ss_pred             hHHHHhcCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEEchhcchhccCCHHHHHHHHHH
Confidence            3567899999999999999999999999999998877667899999999999988888888898887764

Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. 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 p

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=99.67  E-value=5.4e-16  Score=85.87  Aligned_cols=70  Identities=34%  Similarity=0.631  Sum_probs=60.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-----CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-----SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-----~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||++++++|+.+..|+..+.....     ...|+++||||+|+.+++.+..+++..++++
T Consensus        65 ~~~~~~~~~d~~ilv~D~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  139 (168)
T cd04119          65 VRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLTKHRAVSEDEGRLWAES  139 (168)
T ss_pred             HHHHHhccCCEEEEEEECCCHHHHHhHHHHHHHHHHhccccccCCCceEEEEEEchhcccccccCHHHHHHHHHH
Confidence            457889999999999999999999999999999877653     4699999999999987778888888877653

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. 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.

>cd04116 Rab9 Rab9 subfamily

Probab=99.67  E-value=5.6e-16  Score=86.57  Aligned_cols=69  Identities=29%  Similarity=0.487  Sum_probs=59.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc----CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA----GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~----~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|++++|++++|||+++++||+.+..|...+....    ..++|+++||||+|+. ++.++.+++.+++++
T Consensus        70 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~-~~~~~~~~~~~~~~~  142 (170)
T cd04116          70 LRTPFYRGSDCCLLTFAVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVVLGNKNDIP-ERQVSTEEAQAWCRE  142 (170)
T ss_pred             hHHHHhcCCCEEEEEEECCCHHHHHhHHHHHHHHHHhcccccCCCCcEEEEEECcccc-ccccCHHHHHHHHHH
Confidence            46789999999999999999999999999998876643    2468999999999997 578888899888764

Rab9 is found in late endosomes, together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kD (TIP47). Rab9 is a key mediator of vesicular transport from late endosomes to the trans-Golgi network (TGN) by redirecting the MPRs. Rab9 has been identified as a key component for the replication of several viruses, including HIV1, Ebola, Marburg, and measles, making it a potential target for inhibiting a variety of viruses. 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, CX

>PLN03071 GTP-binding nuclear protein Ran; Provisional

Probab=99.67  E-value=4.4e-16  Score=90.94  Aligned_cols=66  Identities=33%  Similarity=0.550  Sum_probs=55.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.||++++++|+|||+++++||+.+..|++.+.+.. +++|++|||||+|+.. +.+..+++ ++++
T Consensus        78 ~~~~~~~~~~~~ilvfD~~~~~s~~~i~~w~~~i~~~~-~~~piilvgNK~Dl~~-~~v~~~~~-~~~~  143 (219)
T PLN03071         78 LRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRVC-ENIPIVLCGNKVDVKN-RQVKAKQV-TFHR  143 (219)
T ss_pred             hhHHHcccccEEEEEEeCCCHHHHHHHHHHHHHHHHhC-CCCcEEEEEEchhhhh-ccCCHHHH-HHHH
Confidence            56789999999999999999999999999999998764 6799999999999964 45555554 4443

>cd04142 RRP22 RRP22 subfamily

Probab=99.67  E-value=6e-16  Score=89.25  Aligned_cols=66  Identities=20%  Similarity=0.257  Sum_probs=57.3

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc---CCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA---GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~---~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      .+++++|++++|||+++++||+.+..|++.+.+..   ...+|+++||||+|+...+.+..+++.++++
T Consensus        76 ~~~~~ad~iilv~D~~~~~S~~~~~~~~~~i~~~~~~~~~~~piiivgNK~Dl~~~~~~~~~~~~~~~~  144 (198)
T cd04142          76 RGLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQRHRFAPRHVLSVLVR  144 (198)
T ss_pred             hhhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcccCCCCCCEEEEEECccccccccccHHHHHHHHH
Confidence            45789999999999999999999999999887764   3679999999999998878888888777654

RRP22 (Ras-related protein on chromosome 22) subfamily consists of proteins that inhibit cell growth and promote caspase-independent cell death. Unlike most Ras proteins, RRP22 is down-regulated in many human tumor cells due to promoter methylation. RRP22 localizes to the nucleolus in a GTP-dependent manner, suggesting a novel function in modulating transport of nucleolar components. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Like most Ras family proteins, RRP22 is farnesylated.

>cd04130 Wrch_1 Wrch-1 subfamily

Probab=99.66  E-value=7.5e-16  Score=86.57  Aligned_cols=69  Identities=20%  Similarity=0.432  Sum_probs=59.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCcc------------cccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKH------------LLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~------------~~~v~~~e~~~~   68 (72)
                      +++.|++++|++++|||+++++||+.+ ..|+..+.... ++.|++++|||.|+..            ++.+..+++.++
T Consensus        64 ~~~~~~~~a~~~i~v~d~~~~~sf~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  142 (173)
T cd04130          64 LRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHN-PKAPIILVGTQADLRTDVNVLIQLARYGEKPVSQSRAKAL  142 (173)
T ss_pred             ccccccCCCcEEEEEEECCCHHHHHHHHHHHHHHHHhhC-CCCCEEEEeeChhhccChhHHHHHhhcCCCCcCHHHHHHH
Confidence            567899999999999999999999998 47998887643 5799999999999963            467888899988


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       143 a~~  145 (173)
T cd04130         143 AEK  145 (173)
T ss_pred             HHH
Confidence            864

Wrch-1 (Wnt-1 responsive Cdc42 homolog) is a Rho family GTPase that shares significant sequence and functional similarity with Cdc42. Wrch-1 was first identified in mouse mammary epithelial cells, where its transcription is upregulated in Wnt-1 transformation. Wrch-1 contains N- and C-terminal extensions relative to cdc42, suggesting potential differences in cellular localization and function. The Wrch-1 N-terminal extension contains putative SH3 domain-binding motifs and has been shown to bind the SH3 domain-containing protein Grb2, which increases the level of active Wrch-1 in cells. Unlike Cdc42, which localizes to the cytosol and perinuclear membranes, Wrch-1 localizes extensively with the plasma membrane and endosomes. The membrane association, localization, and biological activity of Wrch-1 indicate an atypical model of regulation distinct from other Rho family GTPases. Most Rho proteins contain a lipid modification site at the C-terminus,

>cd04143 Rhes_like Rhes_like subfamily

Probab=99.66  E-value=7.9e-16  Score=91.42  Aligned_cols=69  Identities=17%  Similarity=0.202  Sum_probs=59.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc---------CCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA---------GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~---------~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.|++++|++|+|||+++++||+.+..|++++.+..         ..+.|+++||||+|+..++.+..+++.+++.
T Consensus        64 ~~~~~~~~ad~iIlVfdv~~~~Sf~~i~~~~~~I~~~k~~~~~~~~~~~~~piIivgNK~Dl~~~~~v~~~ei~~~~~  141 (247)
T cd04143          64 MRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKADRDFPREVQRDEVEQLVG  141 (247)
T ss_pred             HHHHHhccCCEEEEEEeCCCHHHHHHHHHHHHHHHHhhcccccccccCCCCcEEEEEECccchhccccCHHHHHHHHH
Confidence            45678999999999999999999999999999986541         2579999999999998778889888887754

This subfamily includes Rhes (Ras homolog enriched in striatum) and Dexras1/AGS1 (activator of G-protein signaling 1). These proteins are homologous, but exhibit significant differences in tissue distribution and subcellular localization. Rhes is found primarily in the striatum of the brain, but is also expressed in other areas of the brain, such as the cerebral cortex, hippocampus, inferior colliculus, and cerebellum. Rhes expression is controlled by thyroid hormones. In rat PC12 cells, Rhes is farnesylated and localizes to the plasma membrane. Rhes binds and activates PI3K, and plays a role in coupling serpentine membrane receptors with heterotrimeric G-protein signaling. Rhes has recently been shown to be reduced under conditions of dopamine supersensitivity and may play a role in determining dopamine receptor sensitivity. Dexras1/AGS1 is a dexamethasone-induced Ras protein that is expressed primarily in the brain, with low expression l

>cd04145 M_R_Ras_like M-Ras/R-Ras-like subfamily

Probab=99.66  E-value=7.9e-16  Score=85.21  Aligned_cols=70  Identities=30%  Similarity=0.454  Sum_probs=60.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||++++++|+.+..|+..+.+.. ..++|++++|||+|+...+.+..+++.+++++
T Consensus        66 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~piiiv~NK~Dl~~~~~~~~~~~~~~~~~  136 (164)
T cd04145          66 MREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEHQRKVSREEGQELARK  136 (164)
T ss_pred             HHHHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCCEEEEeeCccccccceecHHHHHHHHHH
Confidence            45689999999999999999999999999999887653 35799999999999988778888888877653

This subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an ali

>KOG0393 consensus Ras-related small GTPase, Rho type [General function prediction only]

Probab=99.65  E-value=5.6e-16  Score=89.33  Aligned_cols=69  Identities=29%  Similarity=0.517  Sum_probs=61.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      +++..|.++|.+++||++.+++||+++ ..|+.+++.+. +++|++|||+|.||+.+            ..|+.+++.++
T Consensus        69 lRplsY~~tdvfl~cfsv~~p~S~~nv~~kW~pEi~~~c-p~vpiiLVGtk~DLr~d~~~~~~l~~~~~~~Vt~~~g~~l  147 (198)
T KOG0393|consen   69 LRPLSYPQTDVFLLCFSVVSPESFENVKSKWIPEIKHHC-PNVPIILVGTKADLRDDPSTLEKLQRQGLEPVTYEQGLEL  147 (198)
T ss_pred             ccccCCCCCCEEEEEEEcCChhhHHHHHhhhhHHHHhhC-CCCCEEEEeehHHhhhCHHHHHHHHhccCCcccHHHHHHH
Confidence            567889999999999999999999998 78999999887 89999999999999853            26888999988


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      |++
T Consensus       148 A~~  150 (198)
T KOG0393|consen  148 AKE  150 (198)
T ss_pred             HHH
Confidence            875

>cd04148 RGK RGK subfamily

Probab=99.64  E-value=1.7e-15  Score=88.55  Aligned_cols=68  Identities=26%  Similarity=0.312  Sum_probs=59.0

Q ss_pred             ccchhh-CCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            3 TSAYYR-GALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         3 ~~~y~~-~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ...+++ ++|++++|||++++.||+.+..|+..+.+... .++|+++||||+|+...+.++.+++.+++.
T Consensus        65 ~~~~~~~~ad~iilV~d~td~~S~~~~~~~~~~l~~~~~~~~~piilV~NK~Dl~~~~~v~~~~~~~~a~  134 (221)
T cd04148          65 EDSCMQYQGDAFVVVYSVTDRSSFERASELRIQLRRNRQLEDRPIILVGNKSDLARSREVSVQEGRACAV  134 (221)
T ss_pred             HhHHhhcCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEChhccccceecHHHHHHHHH
Confidence            345677 99999999999999999999999998877643 579999999999998888899888887765

The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues. RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function. Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells. RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton. Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ra

>cd04132 Rho4_like Rho4-like subfamily

Probab=99.64  E-value=1.7e-15  Score=85.82  Aligned_cols=69  Identities=22%  Similarity=0.380  Sum_probs=57.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccc----ccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHL----LNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~----~~v~~~e~~~~a~~   71 (72)
                      +++.|++++|++++|||+++++||+.+. .|+..+.... +++|+++||||.|+...    +.+..+++.++++.
T Consensus        65 ~~~~~~~~ad~ii~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~v~~~~~~~~~~~  138 (187)
T cd04132          65 LRPLSYPDVDVLLICYAVDNPTSLDNVEDKWFPEVNHFC-PGTPIMLVGLKTDLRKDKNLDRKVTPAQAESVAKK  138 (187)
T ss_pred             HHHHhCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEeChhhhhCccccCCcCHHHHHHHHHH
Confidence            4567899999999999999999999995 6988876553 67999999999999653    35778888887753

Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=99.63  E-value=2e-15  Score=83.75  Aligned_cols=70  Identities=29%  Similarity=0.449  Sum_probs=59.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||++++++|+.+..|...+.+... .+.|+++||||+|+...+.+..+++..+++.
T Consensus        64 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~pii~v~nK~Dl~~~~~~~~~~~~~~~~~  134 (164)
T smart00173       64 MRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLESERVVSTEEGKELARQ  134 (164)
T ss_pred             HHHHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccceEcHHHHHHHHHH
Confidence            456789999999999999999999999999988866543 5789999999999988778888888777653

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>cd04108 Rab36_Rab34 Rab34/Rab36 subfamily

Probab=99.63  E-value=2.9e-15  Score=84.36  Aligned_cols=69  Identities=30%  Similarity=0.597  Sum_probs=56.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCccccc--CCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLN--SMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~--v~~~e~~~~a~   70 (72)
                      +++.||+++|++++|||+++++||+.+..|++.+.+.. +..+|+++||||.|+...+.  +..+++.++++
T Consensus        65 ~~~~~~~~ad~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~iilVgnK~Dl~~~~~~~~~~~~~~~~~~  136 (170)
T cd04108          65 IASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDLSSPAQYALMEQDAIKLAA  136 (170)
T ss_pred             hHHHHhcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEChhcCccccccccHHHHHHHHH
Confidence            56789999999999999999999999999999986553 34688999999999965443  34566666654

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 re

>smart00175 RAB Rab subfamily of small GTPases

Probab=99.63  E-value=3.7e-15  Score=82.45  Aligned_cols=70  Identities=54%  Similarity=0.848  Sum_probs=61.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..+++++|++++|||++++.+|+.+..|+..+.....+++|+++++||+|+...+.+..+++.++++.
T Consensus        65 ~~~~~~~~~d~~ilv~d~~~~~s~~~~~~~l~~~~~~~~~~~pivvv~nK~D~~~~~~~~~~~~~~~~~~  134 (164)
T smart00175       65 ITSSYYRGAVGALLVYDITNRESFENLKNWLKELREYADPNVVIMLVGNKSDLEDQRQVSREEAEAFAEE  134 (164)
T ss_pred             HHHHHhCCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEEchhcccccCCCHHHHHHHHHH
Confidence            3567899999999999999999999999999998877657899999999999987778888888877653

Rab GTPases are implicated in vesicle trafficking.

>cd04123 Rab21 Rab21 subfamily

Probab=99.62  E-value=5.8e-15  Score=81.31  Aligned_cols=69  Identities=36%  Similarity=0.668  Sum_probs=60.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.+++++|++++|||++++++|+.+..|++.+......++|++++|||+|+...+.+..++..++++
T Consensus        65 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piiiv~nK~D~~~~~~~~~~~~~~~~~  133 (162)
T cd04123          65 LGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLERQRVVSKSEAEEYAK  133 (162)
T ss_pred             hhHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccCCCHHHHHHHHH
Confidence            467789999999999999999999999999999887765689999999999998777887777776654

The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate 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

>cd04101 RabL4 RabL4 (Rab-like4) subfamily

Probab=99.62  E-value=5.4e-15  Score=82.04  Aligned_cols=68  Identities=29%  Similarity=0.501  Sum_probs=58.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +.+.+++++|++++|||++++++|+.+..|++.+.... ..+|+++||||+|+.+.+.+..+++..+++
T Consensus        68 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~-~~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~  135 (164)
T cd04101          68 MVSNYWESPSVFILVYDVSNKASFENCSRWVNKVRTAS-KHMPGVLVGNKMDLADKAEVTDAQAQAFAQ  135 (164)
T ss_pred             HHHHHhCCCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCEEEEEECcccccccCCCHHHHHHHHH
Confidence            45678999999999999999999999999999988764 679999999999998777788777666553

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.

>KOG3883 consensus Ras family small GTPase [Signal transduction mechanisms]

Probab=99.62  E-value=3.2e-15  Score=83.45  Aligned_cols=70  Identities=20%  Similarity=0.298  Sum_probs=62.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      |.++||.-+||+++||+..|++||+.+.-..+.|....+ ..+||+++|||+|+.+.+.+..+-|..||++
T Consensus        77 Lprhy~q~aDafVLVYs~~d~eSf~rv~llKk~Idk~KdKKEvpiVVLaN~rdr~~p~~vd~d~A~~Wa~r  147 (198)
T KOG3883|consen   77 LPRHYFQFADAFVLVYSPMDPESFQRVELLKKEIDKHKDKKEVPIVVLANKRDRAEPREVDMDVAQIWAKR  147 (198)
T ss_pred             hhHhHhccCceEEEEecCCCHHHHHHHHHHHHHHhhccccccccEEEEechhhcccchhcCHHHHHHHHhh
Confidence            457899999999999999999999998777777766665 6799999999999999999999999999875

>cd04177 RSR1 RSR1 subgroup

Probab=99.61  E-value=6.8e-15  Score=82.27  Aligned_cols=70  Identities=24%  Similarity=0.388  Sum_probs=60.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.++++++++++|||++++++|+.+..|.+.+.+.. ..+.|++++|||.|+...+.++.+++.+++++
T Consensus        65 ~~~~~~~~~~~~vlv~~~~~~~s~~~~~~~~~~i~~~~~~~~~piiiv~nK~D~~~~~~~~~~~~~~~~~~  135 (168)
T cd04177          65 MRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLEDDRQVSREDGVSLSQQ  135 (168)
T ss_pred             hhHHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCCEEEEEEChhccccCccCHHHHHHHHHH
Confidence            56789999999999999999999999999999887644 36799999999999988888888888777653

RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key featu

>cd01892 Miro2 Miro2 subfamily

Probab=99.61  E-value=2.5e-15  Score=84.50  Aligned_cols=67  Identities=19%  Similarity=0.155  Sum_probs=53.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.||+++|++++|||.+++.+|+.+..|+..+...  .++|+++||||+|+.+.+.+..+++.++++
T Consensus        70 ~~~~~~~~~d~~llv~d~~~~~s~~~~~~~~~~~~~~--~~~p~iiv~NK~Dl~~~~~~~~~~~~~~~~  136 (169)
T cd01892          70 LNDAELAACDVACLVYDSSDPKSFSYCAEVYKKYFML--GEIPCLFVAAKADLDEQQQRYEVQPDEFCR  136 (169)
T ss_pred             cchhhhhcCCEEEEEEeCCCHHHHHHHHHHHHHhccC--CCCeEEEEEEcccccccccccccCHHHHHH
Confidence            4677899999999999999999999999998876432  479999999999997666554444555543

Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.

>cd01861 Rab6 Rab6 subfamily

Probab=99.61  E-value=9e-15  Score=80.84  Aligned_cols=69  Identities=35%  Similarity=0.689  Sum_probs=59.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +...++++++++++|||+++++||+.+..|+..+......+.|++++|||+|+.+.+.+..++...+++
T Consensus        65 ~~~~~~~~~~~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilv~nK~D~~~~~~~~~~~~~~~~~  133 (161)
T cd01861          65 LIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDKRQVSTEEGEKKAK  133 (161)
T ss_pred             HHHHHhccCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCEEEEEEEChhccccCccCHHHHHHHHH
Confidence            356789999999999999999999999999999876654579999999999997777788888777664

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

>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily

Probab=99.60  E-value=6.9e-15  Score=81.03  Aligned_cols=68  Identities=19%  Similarity=0.397  Sum_probs=57.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.|+++++++++|||++++.+|+.+..|+..+.+... .+.|+++||||+|+.. +.+..+++.++++
T Consensus        65 l~~~~~~~~~~~i~v~~~~~~~s~~~~~~~~~~i~~~~~~~~~piivv~nK~Dl~~-~~~~~~~~~~~~~  133 (162)
T cd04138          65 MRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAA-RTVSSRQGQDLAK  133 (162)
T ss_pred             HHHHHHhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccc-ceecHHHHHHHHH
Confidence            467899999999999999999999999999998877643 5799999999999976 5667777777654

H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.

>cd00877 Ran Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases

Probab=99.60  E-value=9e-15  Score=81.98  Aligned_cols=65  Identities=34%  Similarity=0.593  Sum_probs=53.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      +++.+|+++|++++|||+++++||..++.|+..+.... .++|+++||||+|+.. +.+.. ++.+++
T Consensus        65 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~piiiv~nK~Dl~~-~~~~~-~~~~~~  129 (166)
T cd00877          65 LRDGYYIGGQCAIIMFDVTSRVTYKNVPNWHRDLVRVC-GNIPIVLCGNKVDIKD-RKVKA-KQITFH  129 (166)
T ss_pred             ccHHHhcCCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCcEEEEEEchhccc-ccCCH-HHHHHH
Confidence            46789999999999999999999999999999998876 4899999999999973 44443 334444

Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is

>cd04162 Arl9_Arfrp2_like Arl9/Arfrp2-like subfamily

Probab=99.59  E-value=2.6e-15  Score=84.06  Aligned_cols=59  Identities=22%  Similarity=0.348  Sum_probs=50.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCC
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSM   61 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~   61 (72)
                      +++.||+++|++++|||.+++.+|..++.|+..+.... +++|+++||||+|+...+.+.
T Consensus        60 ~~~~~~~~ad~ii~V~D~t~~~s~~~~~~~l~~~~~~~-~~~piilv~NK~Dl~~~~~~~  118 (164)
T cd04162          60 YWKRYLSGSQGLIFVVDSADSERLPLARQELHQLLQHP-PDLPLVVLANKQDLPAARSVQ  118 (164)
T ss_pred             HHHHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHhCC-CCCcEEEEEeCcCCcCCCCHH
Confidence            46789999999999999999999999999988886543 689999999999998765443

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.

>cd01860 Rab5_related Rab5-related subfamily

Probab=99.59  E-value=1.9e-14  Score=79.70  Aligned_cols=69  Identities=39%  Similarity=0.693  Sum_probs=60.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.+++++|++++|||.+++++|.....|+..+.....+.+|+++++||+|+...+.+..+++..+++
T Consensus        66 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iivv~nK~D~~~~~~~~~~~~~~~~~  134 (163)
T cd01860          66 LAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQRNASPNIIIALVGNKADLESKRQVSTEEAQEYAD  134 (163)
T ss_pred             HHHHHhccCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECccccccCcCCHHHHHHHHH
Confidence            346789999999999999999999999999999987765789999999999998777888888777765

This 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 mo

>cd04118 Rab24 Rab24 subfamily

Probab=99.58  E-value=2e-14  Score=81.92  Aligned_cols=68  Identities=34%  Similarity=0.552  Sum_probs=56.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc----cccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH----LLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~----~~~v~~~e~~~~a~   70 (72)
                      ++..||+++|++++|||++++.||+.+..|++.++... ++.|+++||||.|+..    .+.+..+++.++++
T Consensus        66 ~~~~~~~~~d~iilv~d~~~~~s~~~~~~~~~~i~~~~-~~~piilv~nK~Dl~~~~~~~~~v~~~~~~~~~~  137 (193)
T cd04118          66 MSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNLE-EHCKIYLCGTKSDLIEQDRSLRQVDFHDVQDFAD  137 (193)
T ss_pred             hhHhhcCCCCEEEEEEECCCHHHHHHHHHHHHHHHhcC-CCCCEEEEEEcccccccccccCccCHHHHHHHHH
Confidence            45678999999999999999999999999999987754 5799999999999853    24566677777654

Rab24 is distinct from other Rabs in several ways. It exists primarily in the GTP-bound state, having a low intrinsic GTPase activity; it is not efficiently geranyl-geranylated at the C-terminus; it does not form a detectable complex with Rab GDP-dissociation inhibitors (GDIs); and it has recently been shown to undergo tyrosine phosphorylation when overexpressed in vitro. The specific function of Rab24 still remains unknown. It is found in a transport route between ER-cis-Golgi and late endocytic compartments. It is putatively involved in an autophagic pathway, possibly directing misfolded proteins in the ER to degradative pathways. 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 facilita

>cd04135 Tc10 TC10 subfamily

Probab=99.57  E-value=2.8e-14  Score=79.87  Aligned_cols=69  Identities=20%  Similarity=0.387  Sum_probs=57.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      +++.++++++++++|||++++++|+.+. .|...+... .++.|++++|||+|+.+.            +.++.+++..+
T Consensus        64 ~~~~~~~~~~~~ilv~~~~~~~s~~~~~~~~~~~l~~~-~~~~piivv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  142 (174)
T cd04135          64 LRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEY-APNVPYLLVGTQIDLRDDPKTLARLNDMKEKPVTVEQGQKL  142 (174)
T ss_pred             cccccCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHhh-CCCCCEEEEeEchhhhcChhhHHHHhhccCCCCCHHHHHHH
Confidence            4677899999999999999999999995 788888765 478999999999998543            36778888887


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      ++.
T Consensus       143 ~~~  145 (174)
T cd04135         143 AKE  145 (174)
T ss_pred             HHH
Confidence            753

TC10 is a Rho family protein that has been shown to induce microspike formation and neurite outgrowth in vitro. Its expression changes dramatically after peripheral nerve injury, suggesting an important role in promoting axonal outgrowth and regeneration. TC10 regulates translocation of insulin-stimulated GLUT4 in adipocytes and has also been shown to bind directly to Golgi COPI coat proteins. GTP-bound TC10 in vitro can bind numerous potential effectors. Depending on its subcellular localization and distinct functional domains, TC10 can differentially regulate two types of filamentous actin in adipocytes. TC10 mRNAs are highly expressed in three types of mouse muscle tissues: leg skeletal muscle, cardiac muscle, and uterus; they were also present in brain, with higher levels in adults than in newborns. TC10 has also been shown to play a role in regulating the expression of cystic fibrosis transmembrane conductance regulator (CFTR) through interacti

>cd04129 Rho2 Rho2 subfamily

Probab=99.56  E-value=3.5e-14  Score=80.87  Aligned_cols=68  Identities=22%  Similarity=0.383  Sum_probs=56.4

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCcc----------cccCCHHHHHHHHhc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKH----------LLNSMCEEYLIKSRS   71 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~----------~~~v~~~e~~~~a~~   71 (72)
                      .+.+++++++++++||++++++|+.+. .|+..++... +++|+++||||+|+.+          .+.++.+++.+++++
T Consensus        66 ~~~~~~~a~~~llv~~i~~~~s~~~~~~~~~~~i~~~~-~~~piilvgnK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (187)
T cd04129          66 RPLSYSKAHVILIGFAVDTPDSLENVRTKWIEEVRRYC-PNVPVILVGLKKDLRQDAVAKEEYRTQRFVPIQQGKRVAKE  144 (187)
T ss_pred             chhhcCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEeeChhhhhCcccccccccCCcCCHHHHHHHHHH
Confidence            346788999999999999999999996 6999987765 5699999999999954          356777788877753

Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors).

>cd04114 Rab30 Rab30 subfamily

Probab=99.56  E-value=4.7e-14  Score=78.58  Aligned_cols=68  Identities=29%  Similarity=0.518  Sum_probs=58.5

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +..|++++|++++|||++++.+|+.+..|+..+.......+|++++|||+|+.+.+.+..+.+..+.+
T Consensus        73 ~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~l~~~~~~~~~~i~v~NK~D~~~~~~i~~~~~~~~~~  140 (169)
T cd04114          73 TQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNKIDLAERREVSQQRAEEFSD  140 (169)
T ss_pred             HHHHhcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccccCHHHHHHHHH
Confidence            46789999999999999999999999999998877665679999999999998777877766666554

Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. 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.

>PLN03118 Rab family protein; Provisional

Probab=99.55  E-value=4.6e-14  Score=81.71  Aligned_cols=69  Identities=41%  Similarity=0.605  Sum_probs=57.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHH-HHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSR-WLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~-~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++++|..+.. |...+..... .+.|+++||||+|+...+.++.+++..+++
T Consensus        78 ~~~~~~~~~d~~vlv~D~~~~~sf~~~~~~~~~~~~~~~~~~~~~~ilv~NK~Dl~~~~~i~~~~~~~~~~  148 (211)
T PLN03118         78 LTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVDRESERDVSREEGMALAK  148 (211)
T ss_pred             HHHHHHhcCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccCccCHHHHHHHHH
Confidence            45789999999999999999999999965 7666654432 568999999999998878888888877765

>cd04158 ARD1 ARD1 subfamily

Probab=99.55  E-value=3.8e-14  Score=79.50  Aligned_cols=66  Identities=17%  Similarity=0.211  Sum_probs=54.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      +++.|++++|++++|||.+++++|..+..|+..+.+.. ..+.|++++|||+|+..  .++.+++.+++
T Consensus        59 ~~~~~~~~ad~ii~V~D~s~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~--~~~~~~~~~~~  125 (169)
T cd04158          59 LWKHYYLNTQAVVFVVDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAG--ALSVEEMTELL  125 (169)
T ss_pred             HHHHHhccCCEEEEEEeCCcHHHHHHHHHHHHHHhcChhhCCCCEEEEEeCcCccc--CCCHHHHHHHh
Confidence            35678999999999999999999999999988886543 25689999999999964  46777776654

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 membra

>cd04149 Arf6 Arf6 subfamily

Probab=99.55  E-value=3.3e-14  Score=79.90  Aligned_cols=66  Identities=20%  Similarity=0.318  Sum_probs=52.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      +++.||+++|++++|||.+++.+|+.+..|+.++.... ..++|++|||||+|+.+  .++.+++.++.
T Consensus        69 ~~~~~~~~a~~ii~v~D~t~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~--~~~~~~i~~~~  135 (168)
T cd04149          69 LWRHYYTGTQGLIFVVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPD--AMKPHEIQEKL  135 (168)
T ss_pred             HHHHHhccCCEEEEEEeCCchhhHHHHHHHHHHHhcCHhhcCCcEEEEEECcCCcc--CCCHHHHHHHc
Confidence            35679999999999999999999999988776664322 25689999999999975  35666666543

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 t

>cd01863 Rab18 Rab18 subfamily

Probab=99.54  E-value=8.3e-14  Score=77.05  Aligned_cols=68  Identities=47%  Similarity=0.725  Sum_probs=57.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +...+++++|++++|||++++.+|+.+..|+..+.+... .+.|++++|||+|+. .+.+..+++.++++
T Consensus        65 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~iv~nK~D~~-~~~~~~~~~~~~~~  133 (161)
T cd01863          65 LTSSYYRGAQGVILVYDVTRRDTFTNLETWLNELETYSTNNDIVKMLVGNKIDKE-NREVTREEGLKFAR  133 (161)
T ss_pred             hhHHHhCCCCEEEEEEECCCHHHHHhHHHHHHHHHHhCCCCCCcEEEEEECCccc-ccccCHHHHHHHHH
Confidence            356788999999999999999999999999999887753 679999999999997 35667777777765

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 mos

>cd04124 RabL2 RabL2 subfamily

Probab=99.54  E-value=6.7e-14  Score=77.92  Aligned_cols=54  Identities=35%  Similarity=0.733  Sum_probs=48.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +++.|++++|++++|||++++.+|+.+..|+..+.+.. ++.|++++|||+|+..
T Consensus        65 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~p~ivv~nK~Dl~~  118 (161)
T cd04124          65 MHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYR-PEIPCIVVANKIDLDP  118 (161)
T ss_pred             hhHHHhCCCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCcEEEEEECccCch
Confidence            56789999999999999999999999999999997654 5799999999999853

RabL2 (Rab-like2) subfamily. RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share 98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown. 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-b

>smart00177 ARF ARF-like small GTPases; ARF, ADP-ribosylation factor

Probab=99.52  E-value=1e-13  Score=78.30  Aligned_cols=55  Identities=22%  Similarity=0.387  Sum_probs=46.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~   56 (72)
                      +++.||++++++++|||++++++|+.+..|+..+.+.. ..++|++|||||+|+.+
T Consensus        73 ~~~~~~~~ad~ii~v~D~t~~~s~~~~~~~l~~~~~~~~~~~~piilv~NK~Dl~~  128 (175)
T smart00177       73 LWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPD  128 (175)
T ss_pred             HHHHHhCCCCEEEEEEECCCHHHHHHHHHHHHHHhhCHhhcCCcEEEEEeCcCccc
Confidence            45779999999999999999999999988887775432 25789999999999975

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).

>cd01862 Rab7 Rab7 subfamily

Probab=99.51  E-value=2e-13  Score=76.02  Aligned_cols=69  Identities=30%  Similarity=0.504  Sum_probs=57.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC----CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG----SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~----~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++++++++||++++.+|+.+..|.+.+.....    .++|+++||||+|+..++.++.++...+++
T Consensus        65 ~~~~~~~~~d~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~  137 (172)
T cd01862          65 LGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPSDPENFPFVVLGNKIDLEEKRQVSTKKAQQWCQ  137 (172)
T ss_pred             HHHHHhcCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCccCCCCceEEEEEECcccccccccCHHHHHHHHH
Confidence            456789999999999999999999999999887655432    379999999999998667777777776654

Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. 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-

>PLN00223 ADP-ribosylation factor; Provisional

Probab=99.51  E-value=1.1e-13  Score=78.70  Aligned_cols=55  Identities=18%  Similarity=0.343  Sum_probs=46.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHh-cCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDH-AGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~-~~~~~~~vlvgnK~Dl~~   56 (72)
                      +++.||+++|++|+|||.+++++|..+..|+..+... ..+++|++|+|||+|++.
T Consensus        77 ~~~~~~~~a~~iI~V~D~s~~~s~~~~~~~l~~~l~~~~~~~~piilv~NK~Dl~~  132 (181)
T PLN00223         77 LWRHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPN  132 (181)
T ss_pred             HHHHHhccCCEEEEEEeCCcHHHHHHHHHHHHHHhcCHhhCCCCEEEEEECCCCCC
Confidence            4678999999999999999999999998877766432 225799999999999975

>cd04161 Arl2l1_Arl13_like Arl2l1/Arl13 subfamily

Probab=99.49  E-value=1.1e-13  Score=77.62  Aligned_cols=57  Identities=32%  Similarity=0.476  Sum_probs=49.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~   58 (72)
                      +++.||++++++++|||.+++.+|+.+..|+..+.+... .+.|+++||||+|+...+
T Consensus        59 ~~~~~~~~a~~ii~V~D~s~~~s~~~~~~~l~~l~~~~~~~~~piliv~NK~Dl~~~~  116 (167)
T cd04161          59 IWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNAL  116 (167)
T ss_pred             HHHHHHcCCCEEEEEEECCchhHHHHHHHHHHHHHcCccccCCcEEEEEeCCCCcCCC
Confidence            457899999999999999999999999999988865532 579999999999997644

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.

>cd00876 Ras Ras family

Probab=99.49  E-value=2.5e-13  Score=74.65  Aligned_cols=69  Identities=28%  Similarity=0.421  Sum_probs=59.8

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ...++++++++++|||+++++++..+..|...+.+... ...|++++|||+|+...+.++.+++.+++++
T Consensus        64 ~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~~~~~~~~~~~~~~~~  133 (160)
T cd00876          64 RDLYIRQGDGFILVYSITDRESFEEIKGYREQILRVKDDEDIPIVLVGNKCDLENERQVSKEEGKALAKE  133 (160)
T ss_pred             HHHHHhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECCcccccceecHHHHHHHHHH
Confidence            45788999999999999999999999999888877654 5899999999999988778888888877653

The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of m

>cd04150 Arf1_5_like Arf1-Arf5-like subfamily

Probab=99.49  E-value=1.8e-13  Score=76.25  Aligned_cols=55  Identities=18%  Similarity=0.364  Sum_probs=45.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHh-cCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDH-AGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~-~~~~~~~vlvgnK~Dl~~   56 (72)
                      +++.||+++|++++|||.+++.+|+.+..|+..+... .....|++|+|||+|+.+
T Consensus        60 ~~~~~~~~ad~~i~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~  115 (159)
T cd04150          60 LWRHYFQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPN  115 (159)
T ss_pred             HHHHHhcCCCEEEEEEeCCCHHHHHHHHHHHHHHHhcHHhcCCCEEEEEECCCCCC
Confidence            4578899999999999999999999998877666432 224689999999999965

This 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

>cd01870 RhoA_like RhoA-like subfamily

Probab=99.49  E-value=3.8e-13  Score=75.33  Aligned_cols=68  Identities=22%  Similarity=0.404  Sum_probs=54.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      +++.+++++|++++|||+++++||+.+. .|...+.... .+.|+++||||+|+...            +.+..+++.++
T Consensus        65 ~~~~~~~~~d~~i~v~~~~~~~s~~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~i~~~~~~~v~~~~~~~~  143 (175)
T cd01870          65 LRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFC-PNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDM  143 (175)
T ss_pred             ccccccCCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhC-CCCCEEEEeeChhcccChhhhhhhhhccCCCccHHHHHHH
Confidence            3457889999999999999999999994 6888887653 57999999999998542            34566777777


Q ss_pred             Hh
Q 047889           69 SR   70 (72)
Q Consensus        69 a~   70 (72)
                      ++
T Consensus       144 ~~  145 (175)
T cd01870         144 AN  145 (175)
T ss_pred             HH
Confidence            65

The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. RhoA and RhoC are observed only in geranyl

>cd04147 Ras_dva Ras-dva subfamily

Probab=99.47  E-value=5.4e-13  Score=76.63  Aligned_cols=67  Identities=21%  Similarity=0.287  Sum_probs=55.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcc-cccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKH-LLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~-~~~v~~~e~~~~   68 (72)
                      +++.|++++|++++|||++++.+|+.+..|+..+.+... .++|+++|+||.|+.. ++.+..+++.+.
T Consensus        63 ~~~~~~~~ad~vilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~NK~Dl~~~~~~v~~~~~~~~  131 (198)
T cd04147          63 MRKLSIQNSDAFALVYAVDDPESFEEVERLREEILEVKEDKFVPIVVVGNKADSLEEERQVPAKDALST  131 (198)
T ss_pred             HHHHHhhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEEccccccccccccHHHHHHH
Confidence            456789999999999999999999999999988877654 5799999999999965 466666555443

Ras-dva (Ras - dorsal-ventral anterior localization) subfamily consists of a set of proteins characterized only in Xenopus leavis, to date. In Xenopus Ras-dva expression is activated by the transcription factor Otx2 and begins during gastrulation throughout the anterior ectoderm. Ras-dva expression is inhibited in the anterior neural plate by factor Xanf1. Downregulation of Ras-dva results in head development abnormalities through the inhibition of several regulators of the anterior neural plate and folds patterning, including Otx2, BF-1, Xag2, Pax6, Slug, and Sox9. Downregulation of Ras-dva also interferes with the FGF-8a signaling within the anterior ectoderm. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.

>cd00154 Rab Rab family

Probab=99.47  E-value=5.7e-13  Score=72.67  Aligned_cols=68  Identities=47%  Similarity=0.785  Sum_probs=59.5

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ...+++++|++++|||.+++++++.+..|+..+........|+++++||+|+..+..+..++..++++
T Consensus        66 ~~~~~~~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~~~~~~~~~~~~~~~  133 (159)
T cd00154          66 TPSYYRGAHGAILVYDITNRESFENLDKWLKELKEYAPENIPIILVGNKIDLEDQRQVSTEEAQQFAK  133 (159)
T ss_pred             HHHHhcCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEEcccccccccccHHHHHHHHH
Confidence            46788999999999999999999999999999887765679999999999997566778888887765

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 di

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=99.47  E-value=6.1e-13  Score=73.43  Aligned_cols=69  Identities=28%  Similarity=0.438  Sum_probs=57.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.+++++++++++||++++.+|..+..|+..+..... .+.|+++|+||+|+...+.+..++...+++
T Consensus        64 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piiiv~NK~D~~~~~~~~~~~~~~~~~  133 (164)
T cd04139          64 IRDNYHRSGEGFLLVFSITDMESFTATAEFREQILRVKDDDNVPLLLVGNKCDLEDKRQVSSEEAANLAR  133 (164)
T ss_pred             HHHHHhhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEccccccccccCHHHHHHHHH
Confidence            356789999999999999999999999999988877643 579999999999997756666666665554

The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo

>TIGR00157 ribosome small subunit-dependent GTPase A

Probab=99.45  E-value=4e-13  Score=79.82  Aligned_cols=65  Identities=18%  Similarity=0.145  Sum_probs=52.9

Q ss_pred             CcccchhhCCCEEEEEEECCChh-hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHH
Q 047889            1 AITSAYYRGALGALLVYDVTKST-TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIK   68 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~   68 (72)
                      +|.+.|++++|++++|||++++. ||+.+..|+..+..   .++|+++|+||+||.+++.+..+++..+
T Consensus        28 ~L~r~~~~n~D~viiV~d~~~p~~s~~~l~r~l~~~~~---~~i~~vIV~NK~DL~~~~~~~~~~~~~~   93 (245)
T TIGR00157        28 ELTRPIVANIDQIVIVSSAVLPELSLNQLDRFLVVAEA---QNIEPIIVLNKIDLLDDEDMEKEQLDIY   93 (245)
T ss_pred             eEECcccccCCEEEEEEECCCCCCCHHHHHHHHHHHHH---CCCCEEEEEECcccCCCHHHHHHHHHHH
Confidence            36788999999999999999988 89999999876653   5699999999999976555554555444

The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option).

>PTZ00133 ADP-ribosylation factor; Provisional

Probab=99.43  E-value=1e-12  Score=74.78  Aligned_cols=55  Identities=20%  Similarity=0.368  Sum_probs=45.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHh-cCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDH-AGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~-~~~~~~~vlvgnK~Dl~~   56 (72)
                      +++.||+++|++|+|||.+++++|+....++..+... ...++|++|||||.|+.+
T Consensus        77 ~~~~~~~~ad~iI~v~D~t~~~s~~~~~~~l~~~~~~~~~~~~piilv~NK~Dl~~  132 (182)
T PTZ00133         77 LWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPN  132 (182)
T ss_pred             HHHHHhcCCCEEEEEEeCCCHHHHHHHHHHHHHHHhCHhhcCCCEEEEEeCCCCCC
Confidence            4577999999999999999999999998777666332 225689999999999965

>cd04137 RheB Rheb (Ras Homolog Enriched in Brain) subfamily

Probab=99.43  E-value=1.5e-12  Score=73.37  Aligned_cols=68  Identities=32%  Similarity=0.394  Sum_probs=56.9

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +..++.++++++++||+++..+|+.+..|+..+.+.. ..+.|+++++||+|+...+.+..+++..+++
T Consensus        66 ~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~NK~Dl~~~~~~~~~~~~~~~~  134 (180)
T cd04137          66 PQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHTQRQVSTEEGKELAE  134 (180)
T ss_pred             HHHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEchhhhhcCccCHHHHHHHHH
Confidence            4578899999999999999999999999888876643 3578999999999998777777777666654

Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that le

>cd01893 Miro1 Miro1 subfamily

Probab=99.42  E-value=1.3e-12  Score=73.00  Aligned_cols=55  Identities=36%  Similarity=0.554  Sum_probs=47.1

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHLLN   59 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~   59 (72)
                      ..+++++|++++|||++++.||+.+. .|.+.++... .+.|+++||||+|+.+.+.
T Consensus        65 ~~~~~~ad~~ilv~d~~~~~s~~~~~~~~~~~i~~~~-~~~pviiv~nK~Dl~~~~~  120 (166)
T cd01893          65 AAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRLG-VKVPIILVGNKSDLRDGSS  120 (166)
T ss_pred             hhhcccCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEEchhcccccc
Confidence            45678999999999999999999984 6888887765 5799999999999976554

Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.

>cd04154 Arl2 Arl2 subfamily

Probab=99.42  E-value=1.2e-12  Score=73.58  Aligned_cols=66  Identities=20%  Similarity=0.236  Sum_probs=51.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHh-cCCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDH-AGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~-~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      ++..||+++|++++|||.+++.+|..+..|+..+... ...++|+++||||+|+.+.  ...++..++.
T Consensus        74 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~--~~~~~~~~~~  140 (173)
T cd04154          74 YWRNYFESTDALIWVVDSSDRLRLDDCKRELKELLQEERLAGATLLILANKQDLPGA--LSEEEIREAL  140 (173)
T ss_pred             HHHHHhCCCCEEEEEEECCCHHHHHHHHHHHHHHHhChhhcCCCEEEEEECcccccC--CCHHHHHHHh
Confidence            3567899999999999999999999998888776543 2367999999999999753  2445554443

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.

>cd00157 Rho Rho (Ras homology) family

Probab=99.42  E-value=1.6e-12  Score=72.29  Aligned_cols=68  Identities=26%  Similarity=0.447  Sum_probs=54.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCcccc-----------cCCHHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKHLL-----------NSMCEEYLIKS   69 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~-----------~v~~~e~~~~a   69 (72)
                      +.+.+++.+|++++|||++++.+|... ..|+..+.... .+.|+++||||+|+...+           .+..+++.+++
T Consensus        64 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~p~ivv~nK~Dl~~~~~~~~~~~~~~~~v~~~~~~~~~  142 (171)
T cd00157          64 LRPLSYPNTDVFLICFSVDSPSSFENVKTKWIPEIRHYC-PNVPIILVGTKIDLRDDENTLKKLEKGKEPITPEEGEKLA  142 (171)
T ss_pred             cchhhcCCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhC-CCCCEEEEEccHHhhhchhhhhhcccCCCccCHHHHHHHH
Confidence            356778899999999999999999987 56888877655 589999999999996644           34566666665


Q ss_pred             h
Q 047889           70 R   70 (72)
Q Consensus        70 ~   70 (72)
                      .
T Consensus       143 ~  143 (171)
T cd00157         143 K  143 (171)
T ss_pred             H
Confidence            4

Members of the Rho family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho protein

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=99.38  E-value=1.8e-12  Score=68.77  Aligned_cols=48  Identities=40%  Similarity=0.685  Sum_probs=38.2

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHH---HHHHHHhcCCCCeEEEEeeCCC
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRW---LKDLRDHAGSNIVIMLIGNKSD   53 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~---~~~~~~~~~~~~~~vlvgnK~D   53 (72)
                      .++.++|++++|||+++++||+.+..+   +..+.... .++|+++||||.|
T Consensus        69 ~~~~~~d~~ilv~D~s~~~s~~~~~~~~~~l~~~~~~~-~~~piilv~nK~D  119 (119)
T PF08477_consen   69 FFLKKADAVILVYDLSDPESLEYLSQLLKWLKNIRKRD-KNIPIILVGNKSD  119 (119)
T ss_dssp             HHHHHSCEEEEEEECCGHHHHHHHHHHHHHHHHHHHHS-SCSEEEEEEE-TC
T ss_pred             chhhcCcEEEEEEcCCChHHHHHHHHHHHHHHHHHccC-CCCCEEEEEeccC
Confidence            357889999999999999999998555   55554433 5699999999998

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), 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 []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>cd04152 Arl4_Arl7 Arl4/Arl7 subfamily

Probab=99.38  E-value=4.6e-12  Score=72.00  Aligned_cols=64  Identities=19%  Similarity=0.279  Sum_probs=51.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLI   67 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~   67 (72)
                      +++.|+++++++++|||.+++.+++.+..|+..+..... .+.|+++++||+|+..  .+..++...
T Consensus        68 ~~~~~~~~~d~ii~v~D~~~~~~~~~~~~~~~~i~~~~~~~~~p~iiv~NK~D~~~--~~~~~~~~~  132 (183)
T cd04152          68 LWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITRFSENQGVPVLVLANKQDLPN--ALSVSEVEK  132 (183)
T ss_pred             HHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHhhhhcCCCcEEEEEECcCccc--cCCHHHHHH
Confidence            457789999999999999999999999999888765432 5799999999999864  344444443

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.

>cd04157 Arl6 Arl6 subfamily

Probab=99.36  E-value=5e-12  Score=69.79  Aligned_cols=55  Identities=25%  Similarity=0.395  Sum_probs=47.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc---CCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA---GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~---~~~~~~vlvgnK~Dl~~   56 (72)
                      ++..||++++++++|+|.+++.+|..+..|+..+.+..   ..++|+++||||+|+..
T Consensus        61 ~~~~~~~~~d~ii~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~iiv~NK~Dl~~  118 (162)
T cd04157          61 LWEHYYKNIQGIIFVIDSSDRLRLVVVKDELELLLNHPDIKHRRVPILFFANKMDLPD  118 (162)
T ss_pred             HHHHHHccCCEEEEEEeCCcHHHHHHHHHHHHHHHcCcccccCCCCEEEEEeCccccC
Confidence            45788999999999999999999999998888875532   25799999999999965

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 A

>smart00178 SAR Sar1p-like members of the Ras-family of small GTPases

Probab=99.35  E-value=6.3e-12  Score=71.54  Aligned_cols=64  Identities=19%  Similarity=0.280  Sum_probs=51.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLI   67 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~   67 (72)
                      ++..||++++++++|+|.+++.+|.....|+..+.+.. ..+.|+++++||+|+..  .++.++..+
T Consensus        77 ~~~~~~~~ad~ii~vvD~~~~~~~~~~~~~l~~l~~~~~~~~~piliv~NK~Dl~~--~~~~~~i~~  141 (184)
T smart00178       77 LWKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPY--AASEDELRY  141 (184)
T ss_pred             HHHHHhCCCCEEEEEEECCcHHHHHHHHHHHHHHHcChhhcCCCEEEEEeCccccC--CCCHHHHHH
Confidence            45789999999999999999999999988877765432 25789999999999864  566666543

Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus.

>cd00879 Sar1 Sar1 subfamily

Probab=99.34  E-value=1.1e-11  Score=70.37  Aligned_cols=65  Identities=22%  Similarity=0.312  Sum_probs=53.1

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      +..|+++++++++|+|.+++.+|.....|+..+.+... .+.|++++|||+|+..  .+..++..+..
T Consensus        80 ~~~~~~~ad~iilV~D~~~~~s~~~~~~~~~~i~~~~~~~~~pvivv~NK~Dl~~--~~~~~~~~~~~  145 (190)
T cd00879          80 WKDYFPEVDGIVFLVDAADPERFQESKEELDSLLSDEELANVPFLILGNKIDLPG--AVSEEELRQAL  145 (190)
T ss_pred             HHHHhccCCEEEEEEECCcHHHHHHHHHHHHHHHcCccccCCCEEEEEeCCCCCC--CcCHHHHHHHh
Confidence            46789999999999999999999998888887765432 5699999999999964  56677766654

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.

>cd04153 Arl5_Arl8 Arl5/Arl8 subfamily

Probab=99.31  E-value=1.7e-11  Score=69.07  Aligned_cols=55  Identities=25%  Similarity=0.338  Sum_probs=45.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~   56 (72)
                      +++.||+++|++++|+|.+++++|..+..|+..+.+.. ..++|+++++||+|+.+
T Consensus        75 ~~~~~~~~~d~vi~V~D~s~~~~~~~~~~~l~~~~~~~~~~~~p~viv~NK~Dl~~  130 (174)
T cd04153          75 SWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKG  130 (174)
T ss_pred             HHHHHhhcCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhcCCCEEEEEECCCCCC
Confidence            35678999999999999999999999888777765433 25699999999999965

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.

>PTZ00132 GTP-binding nuclear protein Ran; Provisional

Probab=99.31  E-value=1.6e-11  Score=71.19  Aligned_cols=59  Identities=34%  Similarity=0.626  Sum_probs=50.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMC   62 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~   62 (72)
                      ++..|+++++++++|||++++.||..+..|+..+.... .++|++++|||+|+.+ +.+..
T Consensus        74 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~i~lv~nK~Dl~~-~~~~~  132 (215)
T PTZ00132         74 LRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRVC-ENIPIVLVGNKVDVKD-RQVKA  132 (215)
T ss_pred             hhHHHhccCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCEEEEEECccCcc-ccCCH
Confidence            45678999999999999999999999999999987664 6799999999999864 34443

>cd04156 ARLTS1 ARLTS1 subfamily

Probab=99.31  E-value=1.7e-11  Score=67.69  Aligned_cols=54  Identities=20%  Similarity=0.337  Sum_probs=45.9

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~   56 (72)
                      +..|+++++++++|+|.+++.+|..+..|+..+.+.. ..+.|+++|+||+|+..
T Consensus        61 ~~~~~~~~~~iv~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~  115 (160)
T cd04156          61 WKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPG  115 (160)
T ss_pred             HHHHhccCCEEEEEEECCcHHHHHHHHHHHHHHHhchhhcCCCEEEEEECccccc
Confidence            4568999999999999999999999988888775432 25799999999999964

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 h

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=99.30  E-value=1.9e-11  Score=67.90  Aligned_cols=65  Identities=22%  Similarity=0.297  Sum_probs=51.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~   68 (72)
                      ++..++++++++++|+|.++++++.....|+..+.+.. ..++|+++++||+|+..  .+..++..++
T Consensus        66 ~~~~~~~~~~~~v~vvd~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~NK~D~~~--~~~~~~~~~~  131 (167)
T cd04160          66 LWDKYYAECHAIIYVIDSTDRERFEESKSALEKVLRNEALEGVPLLILANKQDLPD--ALSVEEIKEV  131 (167)
T ss_pred             HHHHHhCCCCEEEEEEECchHHHHHHHHHHHHHHHhChhhcCCCEEEEEEcccccc--CCCHHHHHHH
Confidence            34678999999999999999999999988888875543 25799999999999865  3444554443

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.

>cd00878 Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases

Probab=99.28  E-value=3.3e-11  Score=66.51  Aligned_cols=56  Identities=21%  Similarity=0.370  Sum_probs=47.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCccc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~   57 (72)
                      +++.++++++++++|||.+++.+|..+..|+..+.... ....|+++++||+|+...
T Consensus        59 ~~~~~~~~~~~~i~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~piiiv~nK~D~~~~  115 (158)
T cd00878          59 LWKHYYENTNGIIFVVDSSDRERIEEAKEELHKLLNEEELKGVPLLIFANKQDLPGA  115 (158)
T ss_pred             HHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHhCcccCCCcEEEEeeccCCccc
Confidence            35678899999999999999999999988888775543 367999999999999763

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. Thu

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=99.28  E-value=1.7e-11  Score=70.86  Aligned_cols=57  Identities=42%  Similarity=0.705  Sum_probs=49.2

Q ss_pred             cccchhhCCCEEEEEEECCC-hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccc
Q 047889            2 ITSAYYRGALGALLVYDVTK-STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~-~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      +++.||+++++++++||.++ ..+++....|...+....+...|++++|||+|+...+
T Consensus        70 ~~~~y~~~~~~~l~~~d~~~~~~~~~~~~~~~~~l~~~~~~~~~iilv~nK~Dl~~~~  127 (219)
T COG1100          70 LRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFDEQ  127 (219)
T ss_pred             HHHHHhcCCCEEEEEEecccchhhhHHHHHHHHHHHHhCCCCceEEEEecccccccch
Confidence            57899999999999999999 4556666999999988765679999999999998764

>smart00010 small_GTPase Small GTPase of the Ras superfamily; ill-defined subfamily

Probab=99.25  E-value=5.2e-11  Score=63.19  Aligned_cols=68  Identities=18%  Similarity=0.145  Sum_probs=56.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +...++++++++++||+.+++.+++.+  |...+......++|.+++|||.|+.+++.+..+++..+++.
T Consensus        39 ~~~~~~~s~~~~~~v~~~~~~~s~~~~--~~~~i~~~~k~dl~~~~~~nk~dl~~~~~~~~~~~~~~~~~  106 (124)
T smart00010       39 YDPTSYESFDVVLQCWRVDDRDSADNK--NVPEVLVGNKSDLPILVGGNRDVLEEERQVATEEGLEFAET  106 (124)
T ss_pred             ccccccCCCCEEEEEEEccCHHHHHHH--hHHHHHhcCCCCCcEEEEeechhhHhhCcCCHHHHHHHHHH
Confidence            356789999999999999999999877  88777655556789999999999976667888888777764

SMART predicts Ras-like small GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies. Others that could not be classified in this way are predicted to be members of the small GTPase superfamily without predictions of the subfamily.

>PF00025 Arf: ADP-ribosylation factor family The prints entry specific to Sar1 proteins The Prosite entry specific to Sar1 proteins; InterPro: IPR006689 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases

Probab=99.25  E-value=1e-10  Score=66.27  Aligned_cols=64  Identities=25%  Similarity=0.377  Sum_probs=52.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLI   67 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~   67 (72)
                      +|+.||.+++|+|+|.|.++++.+......+..+.... ..++|+++++||+|+++  .++.++...
T Consensus        74 ~w~~y~~~~~~iIfVvDssd~~~l~e~~~~L~~ll~~~~~~~~piLIl~NK~D~~~--~~~~~~i~~  138 (175)
T PF00025_consen   74 LWKSYFQNADGIIFVVDSSDPERLQEAKEELKELLNDPELKDIPILILANKQDLPD--AMSEEEIKE  138 (175)
T ss_dssp             GGGGGHTTESEEEEEEETTGGGGHHHHHHHHHHHHTSGGGTTSEEEEEEESTTSTT--SSTHHHHHH
T ss_pred             cceeeccccceeEEEEecccceeecccccchhhhcchhhcccceEEEEeccccccC--cchhhHHHh
Confidence            68899999999999999999999999987777765533 26799999999999875  455565543

This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other. The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.; GO: 0005525 GTP binding; PDB: 2H57_B 2W83_B 3N5C_B 2J5X_A 3LVR_E 2BAO_A 3LVQ_E 2A5F_A 3PCR_B 1E0S_A ....

>cd04151 Arl1 Arl1 subfamily

Probab=99.22  E-value=6.4e-11  Score=65.55  Aligned_cols=55  Identities=18%  Similarity=0.296  Sum_probs=43.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHH-HHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDL-RDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~-~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +++.|+++++++++|+|.+++.++.....|+..+ +.....+.|+++++||+|+.+
T Consensus        59 ~~~~~~~~~~~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~piiiv~nK~Dl~~  114 (158)
T cd04151          59 YWRCYYSNTDAIIYVVDSTDRDRLGTAKEELHAMLEEEELKGAVLLVFANKQDMPG  114 (158)
T ss_pred             HHHHHhcCCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhcCCcEEEEEeCCCCCC
Confidence            3567899999999999999999998876665544 322235799999999999964

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.

>cd01898 Obg Obg subfamily

Probab=99.15  E-value=2.2e-10  Score=63.74  Aligned_cols=51  Identities=18%  Similarity=0.052  Sum_probs=43.2

Q ss_pred             CCCEEEEEEECCCh-hhHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCccccc
Q 047889            9 GALGALLVYDVTKS-TTFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLKHLLN   59 (72)
Q Consensus         9 ~a~~~i~v~d~~~~-~s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~~~~   59 (72)
                      .+|++++|+|.+++ .+++.+..|.+.+.+...  ...|+++|+||+|+.....
T Consensus        78 ~~d~vi~v~D~~~~~~~~~~~~~~~~~l~~~~~~~~~~p~ivv~NK~Dl~~~~~  131 (170)
T cd01898          78 RTRLLLHVIDLSGDDDPVEDYKTIRNELELYNPELLEKPRIVVLNKIDLLDEEE  131 (170)
T ss_pred             hCCEEEEEEecCCCCCHHHHHHHHHHHHHHhCccccccccEEEEEchhcCCchh
Confidence            59999999999999 899999999998877642  3689999999999965443

The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain.

>KOG0070 consensus GTP-binding ADP-ribosylation factor Arf1 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.12  E-value=5.1e-10  Score=63.84  Aligned_cols=63  Identities=19%  Similarity=0.320  Sum_probs=51.6

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHH
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEY   65 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~   65 (72)
                      .+|++||++++++|+|.|.+|++.+...+.-+..+..+.. ..+|+++.+||.|++.  ..+..|.
T Consensus        76 ~lW~~Y~~~t~~lIfVvDS~Dr~Ri~eak~eL~~~l~~~~l~~~~llv~aNKqD~~~--als~~ei  139 (181)
T KOG0070|consen   76 PLWKHYFQNTQGLIFVVDSSDRERIEEAKEELHRMLAEPELRNAPLLVFANKQDLPG--ALSAAEI  139 (181)
T ss_pred             cchhhhccCCcEEEEEEeCCcHHHHHHHHHHHHHHHcCcccCCceEEEEechhhccc--cCCHHHH
Confidence            3689999999999999999999999998776666655544 6899999999999986  4444443

>KOG1673 consensus Ras GTPases [General function prediction only]

Probab=99.12  E-value=1.1e-10  Score=65.63  Aligned_cols=52  Identities=23%  Similarity=0.523  Sum_probs=45.6

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      .|.-..++-+++++||++.+++++++..|+.+.+...+..+| ++||+|.|+-
T Consensus        86 lPiac~dsvaIlFmFDLt~r~TLnSi~~WY~QAr~~NktAiP-ilvGTKyD~f  137 (205)
T KOG1673|consen   86 LPIACKDSVAILFMFDLTRRSTLNSIKEWYRQARGLNKTAIP-ILVGTKYDLF  137 (205)
T ss_pred             CceeecCcEEEEEEEecCchHHHHHHHHHHHHHhccCCccce-EEeccchHhh
Confidence            456678899999999999999999999999999887767788 7899999973

>KOG0096 consensus GTPase Ran/TC4/GSP1 (nuclear protein transport pathway), small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.11  E-value=8.2e-11  Score=67.67  Aligned_cols=54  Identities=41%  Similarity=0.696  Sum_probs=49.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++.-||-++.|.|++||++.+-++.++..|..++.... .++|||++|||.|..+
T Consensus        75 lrdgyyI~~qcAiimFdVtsr~t~~n~~rwhrd~~rv~-~NiPiv~cGNKvDi~~  128 (216)
T KOG0096|consen   75 LRDGYYIQGQCAIIMFDVTSRFTYKNVPRWHRDLVRVR-ENIPIVLCGNKVDIKA  128 (216)
T ss_pred             cccccEEecceeEEEeeeeehhhhhcchHHHHHHHHHh-cCCCeeeeccceeccc
Confidence            45779999999999999999999999999999998877 6699999999999865

>TIGR02528 EutP ethanolamine utilization protein, EutP

Probab=99.11  E-value=1.1e-10  Score=63.57  Aligned_cols=57  Identities=14%  Similarity=-0.079  Sum_probs=42.2

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +|+++|++++|||++++.++.. ..|.+..      ..|+++|+||+|+.+ +.+..+++.++++
T Consensus        59 ~~~~ad~vilv~d~~~~~s~~~-~~~~~~~------~~p~ilv~NK~Dl~~-~~~~~~~~~~~~~  115 (142)
T TIGR02528        59 TAADADVIALVQSATDPESRFP-PGFASIF------VKPVIGLVTKIDLAE-ADVDIERAKELLE  115 (142)
T ss_pred             HhhcCCEEEEEecCCCCCcCCC-hhHHHhc------cCCeEEEEEeeccCC-cccCHHHHHHHHH
Confidence            4789999999999999999865 3453321      139999999999965 4556666666654

This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site.

>PRK12299 obgE GTPase CgtA; Reviewed

Probab=99.11  E-value=3.4e-10  Score=70.02  Aligned_cols=63  Identities=14%  Similarity=0.067  Sum_probs=49.3

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCcccccCCHHHHHHH
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLKHLLNSMCEEYLIK   68 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~~~~v~~~e~~~~   68 (72)
                      ++..++++++|+|++++++++.+..|.+++..+.+  .+.|+++|+||+|+.+...+..++...+
T Consensus       233 hie~a~vlI~ViD~s~~~s~e~~~~~~~EL~~~~~~L~~kp~IIV~NKiDL~~~~~~~~~~~~~~  297 (335)
T PRK12299        233 HIERTRLLLHLVDIEAVDPVEDYKTIRNELEKYSPELADKPRILVLNKIDLLDEEEEREKRAALE  297 (335)
T ss_pred             HhhhcCEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhcccCCeEEEEECcccCCchhHHHHHHHHH
Confidence            34568999999999998899999999999987653  4689999999999976544444444433

>cd04159 Arl10_like Arl10-like subfamily

Probab=99.09  E-value=6.1e-10  Score=60.71  Aligned_cols=55  Identities=29%  Similarity=0.421  Sum_probs=45.5

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCccc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~   57 (72)
                      +..|++++|++++|+|.+++.++.....|+..+.... ..+.|+++|+||+|+...
T Consensus        61 ~~~~~~~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~p~iiv~nK~D~~~~  116 (159)
T cd04159          61 WERYCRGVNAIVYVVDAADRTALEAAKNELHDLLEKPSLEGIPLLVLGNKNDLPGA  116 (159)
T ss_pred             HHHHHhcCCEEEEEEECCCHHHHHHHHHHHHHHHcChhhcCCCEEEEEeCccccCC
Confidence            4678999999999999999999999887777764432 257899999999998654

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.

>KOG0073 consensus GTP-binding ADP-ribosylation factor-like protein ARL2 [Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]

Probab=99.06  E-value=1.3e-09  Score=61.55  Aligned_cols=55  Identities=18%  Similarity=0.319  Sum_probs=45.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHH-HHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDL-RDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~-~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .|+.||..+||+|+|+|..|+..|+.....+..+ .+..-...|+++++||.|++.
T Consensus        76 ~W~nYfestdglIwvvDssD~~r~~e~~~~L~~lL~eerlaG~~~Lvlank~dl~~  131 (185)
T KOG0073|consen   76 YWKNYFESTDGLIWVVDSSDRMRMQECKQELTELLVEERLAGAPLLVLANKQDLPG  131 (185)
T ss_pred             HHHHhhhccCeEEEEEECchHHHHHHHHHHHHHHHhhhhhcCCceEEEEecCcCcc
Confidence            5789999999999999999999999986665554 333335689999999999984

>KOG4423 consensus GTP-binding protein-like, RAS superfamily [Signal transduction mechanisms]

Probab=99.06  E-value=1.7e-10  Score=66.42  Aligned_cols=56  Identities=43%  Similarity=0.773  Sum_probs=49.2

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc----CCCCeEEEEeeCCCCcc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA----GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~----~~~~~~vlvgnK~Dl~~   56 (72)
                      .|+..||+.+++.++|||+++.-+|+.+..|.+++....    +..+|+++.+||||+..
T Consensus        90 ~mtrVyykea~~~~iVfdvt~s~tfe~~skwkqdldsk~qLpng~Pv~~vllankCd~e~  149 (229)
T KOG4423|consen   90 NMTRVYYKEAHGAFIVFDVTRSLTFEPVSKWKQDLDSKLQLPNGTPVPCVLLANKCDQEK  149 (229)
T ss_pred             ceEEEEecCCcceEEEEEccccccccHHHHHHHhccCcccCCCCCcchheeccchhccCh
Confidence            378899999999999999999999999999999986543    25688999999999865

>KOG1707 consensus Predicted Ras related/Rac-GTP binding protein [Defense mechanisms]

Probab=98.98  E-value=1.6e-09  Score=70.50  Aligned_cols=55  Identities=33%  Similarity=0.471  Sum_probs=47.7

Q ss_pred             hhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcC--CCCeEEEEeeCCCCcccccC
Q 047889            6 YYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAG--SNIVIMLIGNKSDLKHLLNS   60 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~~~~v   60 (72)
                      =.+.||.+.++|+++++++++.+ ..|++.+++..+  .++|+||||||+|+......
T Consensus        76 EirkA~vi~lvyavd~~~T~D~ist~WLPlir~~~~~~~~~PVILvGNK~d~~~~~~~  133 (625)
T KOG1707|consen   76 EIRKADVICLVYAVDDESTVDRISTKWLPLIRQLFGDYHETPVILVGNKSDNGDNENN  133 (625)
T ss_pred             HHhhcCEEEEEEecCChHHhhhhhhhhhhhhhcccCCCccCCEEEEeeccCCcccccc
Confidence            36789999999999999999999 679999988763  57999999999999765444

>cd01890 LepA LepA subfamily

Probab=98.97  E-value=3.2e-09  Score=59.59  Aligned_cols=50  Identities=28%  Similarity=0.355  Sum_probs=40.0

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +..+++++|++++|||.++..++.....|....    ..++|+++|+||+|+.+
T Consensus        84 ~~~~~~~ad~~i~v~D~~~~~~~~~~~~~~~~~----~~~~~iiiv~NK~Dl~~  133 (179)
T cd01890          84 VSRSLAACEGALLLVDATQGVEAQTLANFYLAL----ENNLEIIPVINKIDLPS  133 (179)
T ss_pred             HHHHHHhcCeEEEEEECCCCccHhhHHHHHHHH----HcCCCEEEEEECCCCCc
Confidence            456899999999999999987777777664332    24689999999999864

LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and eukaryota (e.g. yeast GUF1p), but is missing from archaea. This pattern of phyletic distribution suggests that LepA evolved through a duplication of the EF-G gene in bacteria, followed by early transfer into the eukaryotic lineage, most likely from the promitochondrial endosymbiont. Yeast GUF1p is not essential and mutant cells did not reveal any marked phenotype.

>KOG0071 consensus GTP-binding ADP-ribosylation factor Arf6 (dArf3) [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.95  E-value=5.1e-09  Score=58.15  Aligned_cols=65  Identities=23%  Similarity=0.374  Sum_probs=51.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~   68 (72)
                      +|++||.+..|+|+|.|..++..++..+.-+..+.+... .+.|+++.+||.|++.  ..+++|...+
T Consensus        77 lWrhYy~gtqglIFV~Dsa~~dr~eeAr~ELh~ii~~~em~~~~~LvlANkQDlp~--A~~pqei~d~  142 (180)
T KOG0071|consen   77 LWRHYYTGTQGLIFVVDSADRDRIEEARNELHRIINDREMRDAIILILANKQDLPD--AMKPQEIQDK  142 (180)
T ss_pred             HHHhhccCCceEEEEEeccchhhHHHHHHHHHHHhCCHhhhcceEEEEecCccccc--ccCHHHHHHH
Confidence            688999999999999999999888887665555444332 6799999999999987  5556665544

>cd01878 HflX HflX subfamily

Probab=98.95  E-value=4e-09  Score=60.60  Aligned_cols=51  Identities=25%  Similarity=0.181  Sum_probs=43.9

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ++++|++++|+|.+++.++..+..|.+.+......+.|+++|+||+|+...
T Consensus       118 ~~~~d~ii~v~D~~~~~~~~~~~~~~~~l~~~~~~~~~viiV~NK~Dl~~~  168 (204)
T cd01878         118 VAEADLLLHVVDASDPDYEEQIETVEKVLKELGAEDIPMILVLNKIDLLDD  168 (204)
T ss_pred             HhcCCeEEEEEECCCCChhhHHHHHHHHHHHcCcCCCCEEEEEEccccCCh
Confidence            678999999999999999998888888777655467899999999998653

A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.

>KOG0075 consensus GTP-binding ADP-ribosylation factor-like protein [General function prediction only]

Probab=98.93  E-value=3e-09  Score=59.40  Aligned_cols=56  Identities=29%  Similarity=0.453  Sum_probs=47.2

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKH   56 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~   56 (72)
                      ++|..|||+++++++|.|..+++.+...+.-+..+....+ ..+|+++.|||.|+++
T Consensus        80 smWerycR~v~aivY~VDaad~~k~~~sr~EL~~LL~k~~l~gip~LVLGnK~d~~~  136 (186)
T KOG0075|consen   80 SMWERYCRGVSAIVYVVDAADPDKLEASRSELHDLLDKPSLTGIPLLVLGNKIDLPG  136 (186)
T ss_pred             HHHHHHhhcCcEEEEEeecCCcccchhhHHHHHHHhcchhhcCCcEEEecccccCcc
Confidence            4688999999999999999999999888766666544333 7899999999999976

>cd04155 Arl3 Arl3 subfamily

Probab=98.92  E-value=1.2e-08  Score=57.00  Aligned_cols=54  Identities=19%  Similarity=0.297  Sum_probs=43.9

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHh-cCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDH-AGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~-~~~~~~~vlvgnK~Dl~~   56 (72)
                      +..++++++++++|+|.++..+|.....|+..+... ....+|+++++||+|+..
T Consensus        75 ~~~~~~~~~~ii~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~  129 (173)
T cd04155          75 WRNYFENTDCLIYVIDSADKKRLEEAGAELVELLEEEKLAGVPVLVFANKQDLAT  129 (173)
T ss_pred             HHHHhcCCCEEEEEEeCCCHHHHHHHHHHHHHHHhChhhcCCCEEEEEECCCCcc
Confidence            356789999999999999999999887776665433 235799999999999864

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.

>cd01881 Obg_like The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1

Probab=98.88  E-value=1.1e-08  Score=56.92  Aligned_cols=55  Identities=20%  Similarity=0.132  Sum_probs=44.2

Q ss_pred             hhhCCCEEEEEEECCCh------hhHHHHHHHHHHHHHhcC-------CCCeEEEEeeCCCCcccccC
Q 047889            6 YYRGALGALLVYDVTKS------TTFENVSRWLKDLRDHAG-------SNIVIMLIGNKSDLKHLLNS   60 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~------~s~~~~~~~~~~~~~~~~-------~~~~~vlvgnK~Dl~~~~~v   60 (72)
                      ++++++++++|+|.+++      .++.....|...+.....       ...|+++|+||+|+......
T Consensus        71 ~~~~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ivv~NK~Dl~~~~~~  138 (176)
T cd01881          71 HIRRADAILHVVDASEDDDIGGVDPLEDYEILNAELKLYDLETILGLLTAKPVIYVLNKIDLDDAEEL  138 (176)
T ss_pred             HHhccCEEEEEEeccCCccccccCHHHHHHHHHHHHHHhhhhhHHHHHhhCCeEEEEEchhcCchhHH
Confidence            56789999999999998      588888888888765432       36899999999999764443

Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the initiation of sporulation and DNA replication in the bacteria Caulobacter and Bacillus, but its exact molecular role is unknown. Furthermore, several OBG family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. Nog1 is a nucleolar protein that might function in ribosome assembly. The DRG and Nog1 subfamilies are ubiquitous in archaea and eukaryotes, the Ygr210 subfamily is present in archaea and fungi, and the Obg and YyaF/YchF subfamilies are ubiquitous in bacteria and eukaryotes. The Obg/Nog1 and DRG subfamilies appear to

>TIGR03156 GTP_HflX GTP-binding protein HflX

Probab=98.87  E-value=7.2e-09  Score=64.52  Aligned_cols=51  Identities=27%  Similarity=0.193  Sum_probs=43.6

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++++||++++|+|.+++.+++.+..|.+.+......+.|+++|+||+|+..
T Consensus       265 ~~~~ADlil~VvD~s~~~~~~~~~~~~~~L~~l~~~~~piIlV~NK~Dl~~  315 (351)
T TIGR03156       265 EVREADLLLHVVDASDPDREEQIEAVEKVLEELGAEDIPQLLVYNKIDLLD  315 (351)
T ss_pred             HHHhCCEEEEEEECCCCchHHHHHHHHHHHHHhccCCCCEEEEEEeecCCC
Confidence            478999999999999999998888887777665545789999999999965

This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial members are designated HflX, following the naming convention in Escherichia coli where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function. Over large numbers of other bacterial genomes, the pairing with hfq is more significant than with hflK and hlfC. The gene from Homo sapiens in this family has been named PGPL (pseudoautosomal GTP-binding protein-like).

>cd04105 SR_beta Signal recognition particle receptor, beta subunit (SR-beta)

Probab=98.83  E-value=2.3e-08  Score=57.99  Aligned_cols=54  Identities=20%  Similarity=0.324  Sum_probs=42.8

Q ss_pred             cchhhCC-CEEEEEEECCCh-hhHHHHHHHHHHHHHhc---CCCCeEEEEeeCCCCccc
Q 047889            4 SAYYRGA-LGALLVYDVTKS-TTFENVSRWLKDLRDHA---GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         4 ~~y~~~a-~~~i~v~d~~~~-~s~~~~~~~~~~~~~~~---~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..||+++ +++|+|+|.++. +++..+..|+..+....   .+.+|+++++||+|+...
T Consensus        66 ~~~~~~~~~~vV~VvD~~~~~~~~~~~~~~l~~il~~~~~~~~~~pvliv~NK~Dl~~a  124 (203)
T cd04105          66 LETLKNSAKGIVFVVDSATFQKNLKDVAEFLYDILTDLEKVKNKIPVLIACNKQDLFTA  124 (203)
T ss_pred             HHHHhccCCEEEEEEECccchhHHHHHHHHHHHHHHHHhhccCCCCEEEEecchhhccc
Confidence            4678898 999999999998 78888877765553321   257999999999998653

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 typ

>cd01897 NOG NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans

Probab=98.80  E-value=2e-08  Score=55.74  Aligned_cols=51  Identities=16%  Similarity=0.272  Sum_probs=39.5

Q ss_pred             CCCEEEEEEECCChhhH--HHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccC
Q 047889            9 GALGALLVYDVTKSTTF--ENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS   60 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~--~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v   60 (72)
                      .+|++++|+|.+++.++  +....|++.+.... .+.|+++|+||+|+...+.+
T Consensus        79 ~~d~~l~v~d~~~~~~~~~~~~~~~~~~l~~~~-~~~pvilv~NK~Dl~~~~~~  131 (168)
T cd01897          79 LRAAVLFLFDPSETCGYSLEEQLSLFEEIKPLF-KNKPVIVVLNKIDLLTFEDL  131 (168)
T ss_pred             ccCcEEEEEeCCcccccchHHHHHHHHHHHhhc-CcCCeEEEEEccccCchhhH
Confidence            36899999999988754  66677888876543 47999999999999764443

NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes. Thus, defects in NOG1 can lead to defects in 60S biogenesis. The S. cerevisiae NOG1 gene is essential for cell viability, and mutations in the predicted G motifs abrogate function. It is a member of the ODN family of GTP-binding proteins that also includes the bacterial Obg and DRG proteins.

>TIGR02729 Obg_CgtA Obg family GTPase CgtA

Probab=98.78  E-value=3.2e-08  Score=61.20  Aligned_cols=50  Identities=16%  Similarity=0.127  Sum_probs=41.8

Q ss_pred             hCCCEEEEEEECCCh---hhHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCccc
Q 047889            8 RGALGALLVYDVTKS---TTFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~---~s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~~   57 (72)
                      ..++++++|+|+++.   ++++.+..|.+++.....  ...|+++|+||+|+.+.
T Consensus       234 erad~ll~VvD~s~~~~~~~~e~l~~l~~EL~~~~~~l~~kp~IIV~NK~DL~~~  288 (329)
T TIGR02729       234 ERTRVLLHLIDISPLDGRDPIEDYEIIRNELKKYSPELAEKPRIVVLNKIDLLDE  288 (329)
T ss_pred             HhhCEEEEEEcCccccccCHHHHHHHHHHHHHHhhhhhccCCEEEEEeCccCCCh
Confidence            369999999999987   788888889888876643  46899999999999654

This model describes a univeral, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. This GTPase, related to the nucleolar protein Obg, is designated CgtA in bacteria. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure. Recent work done in Vibrio cholerae shows an essential role in the stringent response, in which RelA-dependent ability to synthesize the alarmone ppGpp is required for deletion of this GTPase to be lethal.

>PRK11058 GTPase HflX; Provisional

Probab=98.76  E-value=3.7e-08  Score=62.76  Aligned_cols=51  Identities=25%  Similarity=0.182  Sum_probs=42.3

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++++||++++|+|.+++.+++.+..|...+......+.|+++|+||+|+..
T Consensus       273 ~~~~ADlIL~VvDaS~~~~~e~l~~v~~iL~el~~~~~pvIiV~NKiDL~~  323 (426)
T PRK11058        273 ETRQATLLLHVVDAADVRVQENIEAVNTVLEEIDAHEIPTLLVMNKIDMLD  323 (426)
T ss_pred             HhhcCCEEEEEEeCCCccHHHHHHHHHHHHHHhccCCCCEEEEEEcccCCC
Confidence            468899999999999999998887666666655445799999999999864

>cd00882 Ras_like_GTPase Ras-like GTPase superfamily

Probab=98.75  E-value=9.9e-08  Score=50.86  Aligned_cols=55  Identities=53%  Similarity=0.827  Sum_probs=43.4

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHH-HHHhcCCCCeEEEEeeCCCCcccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~-~~~~~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      ..+++.++++++|+|.+++.++.....|... .........|+++++||+|+....
T Consensus        63 ~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivv~nk~D~~~~~  118 (157)
T cd00882          63 RLYYRGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGNKIDLPEER  118 (157)
T ss_pred             HHHhcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhhccCCCcEEEEEecccccccc
Confidence            3477899999999999999999999887322 333334789999999999987543

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 regulate initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Memb

>KOG0076 consensus GTP-binding ADP-ribosylation factor-like protein yARL3 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.74  E-value=9.6e-09  Score=58.58  Aligned_cols=56  Identities=23%  Similarity=0.388  Sum_probs=48.1

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHH-hcCCCCeEEEEeeCCCCcc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRD-HAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~-~~~~~~~~vlvgnK~Dl~~   56 (72)
                      |||..||-.+||+|+++|.++++.|+....-++.+.. ....++|+++.+||.|+.+
T Consensus        84 Slw~~yY~~~H~ii~viDa~~~eR~~~~~t~~~~v~~~E~leg~p~L~lankqd~q~  140 (197)
T KOG0076|consen   84 SLWKKYYWLAHGIIYVIDATDRERFEESKTAFEKVVENEKLEGAPVLVLANKQDLQN  140 (197)
T ss_pred             HHHHHHHHHhceeEEeecCCCHHHHHHHHHHHHHHHHHHHhcCCchhhhcchhhhhh
Confidence            5788999999999999999999999999776666543 3347899999999999976

>cd01891 TypA_BipA TypA (tyrosine phosphorylated protein A)/BipA subfamily

Probab=98.70  E-value=6.5e-08  Score=55.35  Aligned_cols=51  Identities=18%  Similarity=0.153  Sum_probs=37.0

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ...|++++|++++|||.++. .+.....|+..+..   .++|+++|+||+|+...
T Consensus        82 ~~~~~~~~d~~ilV~d~~~~-~~~~~~~~~~~~~~---~~~p~iiv~NK~Dl~~~  132 (194)
T cd01891          82 VERVLSMVDGVLLLVDASEG-PMPQTRFVLKKALE---LGLKPIVVINKIDRPDA  132 (194)
T ss_pred             HHHHHHhcCEEEEEEECCCC-ccHHHHHHHHHHHH---cCCCEEEEEECCCCCCC
Confidence            46789999999999999874 23333444444432   46899999999999653

BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella typhimurium after exposure to bactericidal/permeability-inducing protein (a cationic antimicrobial protein produced by neutrophils), and has since been identified in E. coli as well. The properties thus far described for BipA are related to its role in the process of pathogenesis by enteropathogenic E. coli. It appears to be involved in the regulation of several processes important for infection, including rearrangements of the cytoskeleton of the host, bacterial resistance to host defense peptides, flagellum-mediated cell motility, and expression of K5 capsular genes. It has been proposed that BipA may utilize a novel mechanism to regulate the expression of target genes. In addition, BipA from enteropathogenic E. co

>TIGR00450 mnmE_trmE_thdF tRNA modification GTPase TrmE

Probab=98.65  E-value=6.3e-08  Score=61.93  Aligned_cols=48  Identities=27%  Similarity=0.257  Sum_probs=39.7

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..|++++|++++|||.+++.+++..  |+..+..   .+.|+++|+||+|+..
T Consensus       277 ~~~~~~aD~il~V~D~s~~~s~~~~--~l~~~~~---~~~piIlV~NK~Dl~~  324 (442)
T TIGR00450       277 FKAIKQADLVIYVLDASQPLTKDDF--LIIDLNK---SKKPFILVLNKIDLKI  324 (442)
T ss_pred             HHHHhhCCEEEEEEECCCCCChhHH--HHHHHhh---CCCCEEEEEECccCCC
Confidence            4688999999999999999888775  7665542   4689999999999964

TrmE, also called MnmE and previously designated ThdF (thiophene and furan oxidation protein), is a GTPase involved in tRNA modification to create 5-methylaminomethyl-2-thiouridine in the wobble position of some tRNAs. This protein and GidA form an alpha2/beta2 heterotetramer.

>TIGR00231 small_GTP small GTP-binding protein domain

Probab=98.56  E-value=3.4e-07  Score=49.40  Aligned_cols=56  Identities=34%  Similarity=0.539  Sum_probs=44.9

Q ss_pred             ccchhhCCCEEEEEEECCCh-hhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCcccc
Q 047889            3 TSAYYRGALGALLVYDVTKS-TTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~-~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      +..+++++++++.++|+... .++.... .|...+......+.|+++++||.|+....
T Consensus        67 ~~~~~~~~~~~i~~~d~~~~v~~~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~~~  124 (161)
T TIGR00231        67 RRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESNVPIILVGNKIDLRDAK  124 (161)
T ss_pred             HHHHHhhhhEEEEEEEEeeeehhhhhHhHHHHHHHHHhcccCCcEEEEEEcccCCcch
Confidence            45668899999999999988 7888775 77777766553488999999999997643

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.

>PRK12289 GTPase RsgA; Reviewed

Probab=98.55  E-value=5.6e-07  Score=56.26  Aligned_cols=52  Identities=25%  Similarity=0.287  Sum_probs=40.9

Q ss_pred             cccchhhCCCEEEEEEECCChh-hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKST-TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      |.+..+.++|.+++|+|+.++. +...+..|+..+..   .++|+++|+||+||..
T Consensus        82 L~R~~~aNvD~vLlV~d~~~p~~~~~~LdR~L~~a~~---~~ip~ILVlNK~DLv~  134 (352)
T PRK12289         82 LDRPPVANADQILLVFALAEPPLDPWQLSRFLVKAES---TGLEIVLCLNKADLVS  134 (352)
T ss_pred             eechhhhcCCEEEEEEECCCCCCCHHHHHHHHHHHHH---CCCCEEEEEEchhcCC
Confidence            3455789999999999999876 56667778765532   5689999999999953

>PRK12297 obgE GTPase CgtA; Reviewed

Probab=98.54  E-value=5.3e-07  Score=57.56  Aligned_cols=49  Identities=20%  Similarity=0.194  Sum_probs=40.2

Q ss_pred             hCCCEEEEEEECCCh---hhHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKS---TTFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~---~s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~   56 (72)
                      ..++++++|+|+++.   +++++...|.+++..+..  ...|+++|+||+|+..
T Consensus       235 er~~llI~VID~s~~~~~dp~e~~~~i~~EL~~y~~~L~~kP~IVV~NK~DL~~  288 (424)
T PRK12297        235 ERTRVIVHVIDMSGSEGRDPIEDYEKINKELKLYNPRLLERPQIVVANKMDLPE  288 (424)
T ss_pred             hhCCEEEEEEeCCccccCChHHHHHHHHHHHhhhchhccCCcEEEEEeCCCCcC
Confidence            348999999999865   678888888888877643  4689999999999853

>cd01885 EF2 EF2 (for archaea and eukarya)

Probab=98.54  E-value=5.3e-07  Score=53.18  Aligned_cols=60  Identities=23%  Similarity=0.117  Sum_probs=42.5

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc-ccccCCHHHHHH
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK-HLLNSMCEEYLI   67 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~-~~~~v~~~e~~~   67 (72)
                      ..+++.+|++++|+|.++..+......|. .+.   ...+|+++++||+|+. .++.++++++..
T Consensus        91 ~~~l~~aD~~ilVvD~~~g~~~~t~~~l~-~~~---~~~~p~ilviNKiD~~~~e~~~~~~~~~~  151 (222)
T cd01885          91 TAALRLCDGALVVVDAVEGVCVQTETVLR-QAL---KERVKPVLVINKIDRLILELKLSPEEAYQ  151 (222)
T ss_pred             HHHHHhcCeeEEEEECCCCCCHHHHHHHH-HHH---HcCCCEEEEEECCCcchhhhcCCHHHHHH
Confidence            46789999999999999876555433322 222   2357999999999975 556777776644

Translocation requires hydrolysis of a molecule of GTP and is mediated by EF-G in bacteria and by eEF2 in eukaryotes. The eukaryotic elongation factor eEF2 is a GTPase involved in the translocation of the peptidyl-tRNA from the A site to the P site on the ribosome. The 95-kDa protein is highly conserved, with 60% amino acid sequence identity between the human and yeast proteins. Two major mechanisms are known to regulate protein elongation and both involve eEF2. First, eEF2 can be modulated by reversible phosphorylation. Increased levels of phosphorylated eEF2 reduce elongation rates presumably because phosphorylated eEF2 fails to bind the ribosomes. Treatment of mammalian cells with agents that raise the cytoplasmic Ca2+ and cAMP levels reduce elongation rates by activating the kinase responsible for phosphorylating eEF2. In contrast, treatment of cells with insulin increases elongation rates by promoting eEF2 dephosphorylation. Seco

>PRK03003 GTP-binding protein Der; Reviewed

Probab=98.52  E-value=2.5e-07  Score=59.49  Aligned_cols=49  Identities=29%  Similarity=0.262  Sum_probs=37.4

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++++|++++|+|.++..++.. ..|...++.   .+.|+++|+||+|+..
T Consensus       112 ~~~~~~aD~il~VvD~~~~~s~~~-~~i~~~l~~---~~~piilV~NK~Dl~~  160 (472)
T PRK03003        112 EVAMRTADAVLFVVDATVGATATD-EAVARVLRR---SGKPVILAANKVDDER  160 (472)
T ss_pred             HHHHHhCCEEEEEEECCCCCCHHH-HHHHHHHHH---cCCCEEEEEECccCCc
Confidence            457899999999999999866543 344444443   4689999999999864

>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed

Probab=98.51  E-value=1.8e-07  Score=59.92  Aligned_cols=47  Identities=23%  Similarity=0.134  Sum_probs=38.5

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      .+++++|++++|||.+++.+++....|..      ..+.|+++|+||+|+...
T Consensus       290 ~~~~~aD~il~VvD~s~~~s~~~~~~l~~------~~~~piiiV~NK~DL~~~  336 (449)
T PRK05291        290 EAIEEADLVLLVLDASEPLTEEDDEILEE------LKDKPVIVVLNKADLTGE  336 (449)
T ss_pred             HHHHhCCEEEEEecCCCCCChhHHHHHHh------cCCCCcEEEEEhhhcccc
Confidence            47889999999999999988887655543      356899999999999653

>cd01879 FeoB Ferrous iron transport protein B (FeoB) subfamily

Probab=98.51  E-value=4.6e-07  Score=49.61  Aligned_cols=53  Identities=11%  Similarity=-0.064  Sum_probs=37.4

Q ss_pred             ccchhh--CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCC
Q 047889            3 TSAYYR--GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSM   61 (72)
Q Consensus         3 ~~~y~~--~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~   61 (72)
                      +..|+.  ++|++++|+|.+++++..   .|..++..   .+.|+++++||+|+.....+.
T Consensus        66 ~~~~~~~~~~d~vi~v~d~~~~~~~~---~~~~~~~~---~~~~~iiv~NK~Dl~~~~~~~  120 (158)
T cd01879          66 ARDFLLGEKPDLIVNVVDATNLERNL---YLTLQLLE---LGLPVVVALNMIDEAEKRGIK  120 (158)
T ss_pred             HHHHhcCCCCcEEEEEeeCCcchhHH---HHHHHHHH---cCCCEEEEEehhhhcccccch
Confidence            345664  999999999998865532   34444433   358999999999997654443

E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.

>PRK15467 ethanolamine utilization protein EutP; Provisional

Probab=98.51  E-value=4.1e-07  Score=50.85  Aligned_cols=54  Identities=11%  Similarity=0.032  Sum_probs=38.4

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      ++++|++++|+|.++..++  +..|+..+    ....|+++++||+|+.+   ...++..+++
T Consensus        62 ~~~ad~il~v~d~~~~~s~--~~~~~~~~----~~~~~ii~v~nK~Dl~~---~~~~~~~~~~  115 (158)
T PRK15467         62 LQDVDMLIYVHGANDPESR--LPAGLLDI----GVSKRQIAVISKTDMPD---ADVAATRKLL  115 (158)
T ss_pred             HhcCCEEEEEEeCCCcccc--cCHHHHhc----cCCCCeEEEEEccccCc---ccHHHHHHHH
Confidence            6799999999999998876  33454333    13578999999999964   2344555544

>KOG0074 consensus GTP-binding ADP-ribosylation factor-like protein ARL3 [General function prediction only]

Probab=98.51  E-value=2.3e-07  Score=51.77  Aligned_cols=55  Identities=27%  Similarity=0.444  Sum_probs=46.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .|..||.+.|++|+|.|.+|+..|+.+. ++.+.+.+..-..+|+.+.+||.|+-.
T Consensus        78 yWsNYyenvd~lIyVIDS~D~krfeE~~~el~ELleeeKl~~vpvlIfankQdllt  133 (185)
T KOG0074|consen   78 YWSNYYENVDGLIYVIDSTDEKRFEEISEELVELLEEEKLAEVPVLIFANKQDLLT  133 (185)
T ss_pred             hhhhhhhccceEEEEEeCCchHhHHHHHHHHHHHhhhhhhhccceeehhhhhHHHh
Confidence            4788999999999999999999999994 555555555557899999999999854

>cd04171 SelB SelB subfamily

Probab=98.50  E-value=7e-07  Score=49.08  Aligned_cols=47  Identities=23%  Similarity=0.051  Sum_probs=32.8

Q ss_pred             chhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            5 AYYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      .+++++|++++|+|.++   +.+++.+.    .+...  ...|+++++||+|+...
T Consensus        70 ~~~~~ad~ii~V~d~~~~~~~~~~~~~~----~~~~~--~~~~~ilv~NK~Dl~~~  119 (164)
T cd04171          70 AGAGGIDLVLLVVAADEGIMPQTREHLE----ILELL--GIKRGLVVLTKADLVDE  119 (164)
T ss_pred             hhhhcCCEEEEEEECCCCccHhHHHHHH----HHHHh--CCCcEEEEEECccccCH
Confidence            46789999999999987   44544332    22222  22489999999999653

SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryo

>PRK03003 GTP-binding protein Der; Reviewed

Probab=98.46  E-value=5.7e-07  Score=57.86  Aligned_cols=48  Identities=21%  Similarity=0.170  Sum_probs=38.3

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+++++|++++|+|.++..++..+. ++..+..   .+.|+++|+||+|+.+
T Consensus       289 ~~i~~ad~vilV~Da~~~~s~~~~~-~~~~~~~---~~~piIiV~NK~Dl~~  336 (472)
T PRK03003        289 AAIEAAEVAVVLIDASEPISEQDQR-VLSMVIE---AGRALVLAFNKWDLVD  336 (472)
T ss_pred             HHHhcCCEEEEEEeCCCCCCHHHHH-HHHHHHH---cCCCEEEEEECcccCC
Confidence            3578999999999999998888764 3444433   4689999999999964

>COG2229 Predicted GTPase [General function prediction only]

Probab=98.43  E-value=2e-06  Score=49.45  Aligned_cols=61  Identities=25%  Similarity=0.295  Sum_probs=45.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLI   67 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~   67 (72)
                      ++..+.+++.|.|++.|-+.+..| .....++.+....  .+|+++..||.||.+  ..++++..+
T Consensus        84 m~~~l~~ga~gaivlVDss~~~~~-~a~~ii~f~~~~~--~ip~vVa~NK~DL~~--a~ppe~i~e  144 (187)
T COG2229          84 MWEILSRGAVGAIVLVDSSRPITF-HAEEIIDFLTSRN--PIPVVVAINKQDLFD--ALPPEKIRE  144 (187)
T ss_pred             HHHHHhCCcceEEEEEecCCCcch-HHHHHHHHHhhcc--CCCEEEEeeccccCC--CCCHHHHHH
Confidence            467789999999999999999998 4445555554432  399999999999987  444444433

>TIGR03597 GTPase_YqeH ribosome biogenesis GTPase YqeH

Probab=98.42  E-value=4.6e-07  Score=56.68  Aligned_cols=60  Identities=15%  Similarity=0.135  Sum_probs=42.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~   68 (72)
                      +.+.|+++++++++|+|+.+..     ..|.+.+.+.. .+.|+++|+||+||.. +.+..++..++
T Consensus        56 ~l~~~~~~~~~Il~VvD~~d~~-----~s~~~~l~~~~-~~~piilV~NK~DLl~-k~~~~~~~~~~  115 (360)
T TIGR03597        56 LLNSLGDSNALIVYVVDIFDFE-----GSLIPELKRFV-GGNPVLLVGNKIDLLP-KSVNLSKIKEW  115 (360)
T ss_pred             HHhhcccCCcEEEEEEECcCCC-----CCccHHHHHHh-CCCCEEEEEEchhhCC-CCCCHHHHHHH
Confidence            3467888999999999997654     33666666554 3678999999999964 34445555443

This family describes YqeH, a member of a larger family of GTPases involved in ribosome biogenesis. Like YqlF, it shows a cyclical permutation relative to GTPases EngA (in which the GTPase domain is duplicated), Era, and others. Members of this protein family are found in a relatively small number of bacterial species, including Bacillus subtilis but not Escherichia coli.

>cd01855 YqeH YqeH

Probab=98.42  E-value=4.5e-07  Score=51.80  Aligned_cols=49  Identities=24%  Similarity=0.236  Sum_probs=35.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +...|++++|++++|+|.+++..     .|...+.... .+.|+++|+||+|+..
T Consensus        27 ~l~~~~~~ad~il~VvD~~~~~~-----~~~~~l~~~~-~~~~~ilV~NK~Dl~~   75 (190)
T cd01855          27 LLSSISPKKALVVHVVDIFDFPG-----SLIPRLRLFG-GNNPVILVGNKIDLLP   75 (190)
T ss_pred             HHHhcccCCcEEEEEEECccCCC-----ccchhHHHhc-CCCcEEEEEEchhcCC
Confidence            34678999999999999988642     1333332222 4689999999999864

YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases.

>cd01895 EngA2 EngA2 subfamily

Probab=98.41  E-value=1.5e-06  Score=47.86  Aligned_cols=49  Identities=22%  Similarity=0.142  Sum_probs=36.3

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      +++++|++++|+|.+++.+..... +...+..   .+.|+++++||+|+...+
T Consensus        81 ~~~~~d~vi~v~d~~~~~~~~~~~-~~~~~~~---~~~~~iiv~nK~Dl~~~~  129 (174)
T cd01895          81 AIERADVVLLVIDATEGITEQDLR-IAGLILE---EGKALVIVVNKWDLVEKD  129 (174)
T ss_pred             HHhhcCeEEEEEeCCCCcchhHHH-HHHHHHh---cCCCEEEEEeccccCCcc
Confidence            567899999999999987765542 3333322   358999999999997643

This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. 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. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.

>cd01854 YjeQ_engC YjeQ/EngC

Probab=98.41  E-value=5.7e-07  Score=54.70  Aligned_cols=49  Identities=14%  Similarity=0.124  Sum_probs=41.4

Q ss_pred             hhhCCCEEEEEEECCChh-hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            6 YYRGALGALLVYDVTKST-TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      .+.++|.+++|+|.+++. ++..+..|+..+..   .++|+++|.||+||.++
T Consensus        75 i~anvD~vllV~d~~~p~~s~~~ldr~L~~~~~---~~ip~iIVlNK~DL~~~  124 (287)
T cd01854          75 IAANVDQLVIVVSLNEPFFNPRLLDRYLVAAEA---AGIEPVIVLTKADLLDD  124 (287)
T ss_pred             EEEeCCEEEEEEEcCCCCCCHHHHHHHHHHHHH---cCCCEEEEEEHHHCCCh
Confidence            377899999999999998 88888889877654   35899999999999653

YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.

>PRK04213 GTP-binding protein; Provisional

Probab=98.40  E-value=9.3e-08  Score=54.78  Aligned_cols=17  Identities=24%  Similarity=0.038  Sum_probs=14.4

Q ss_pred             CCCeEEEEeeCCCCccc
Q 047889           41 SNIVIMLIGNKSDLKHL   57 (72)
Q Consensus        41 ~~~~~vlvgnK~Dl~~~   57 (72)
                      .++|+++|+||+|+...
T Consensus       129 ~~~p~iiv~NK~Dl~~~  145 (201)
T PRK04213        129 LGIPPIVAVNKMDKIKN  145 (201)
T ss_pred             cCCCeEEEEECccccCc
Confidence            46999999999999653

>KOG0072 consensus GTP-binding ADP-ribosylation factor-like protein ARL1 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.37  E-value=1.7e-06  Score=48.42  Aligned_cols=55  Identities=15%  Similarity=0.212  Sum_probs=43.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHH-HHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSR-WLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~-~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +|+.||.+.+++|+|.|.+|+........ ++..+++..-....+++++||.|...
T Consensus        78 yWRcYy~dt~avIyVVDssd~dris~a~~el~~mL~E~eLq~a~llv~anKqD~~~  133 (182)
T KOG0072|consen   78 YWRCYYADTDAVIYVVDSSDRDRISIAGVELYSMLQEEELQHAKLLVFANKQDYSG  133 (182)
T ss_pred             HHHHHhcccceEEEEEeccchhhhhhhHHHHHHHhccHhhcCceEEEEeccccchh
Confidence            57899999999999999999987766643 44444444445688999999999865

>KOG0077 consensus Vesicle coat complex COPII, GTPase subunit SAR1 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.35  E-value=1.6e-06  Score=49.44  Aligned_cols=54  Identities=17%  Similarity=0.283  Sum_probs=45.5

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~   56 (72)
                      +..||-.+|++++.+|.-+++.|...+.-++.+.... -.++|+++.|||+|.+.
T Consensus        81 wkdyf~~v~~iv~lvda~d~er~~es~~eld~ll~~e~la~vp~lilgnKId~p~  135 (193)
T KOG0077|consen   81 WKDYFPQVDAIVYLVDAYDQERFAESKKELDALLSDESLATVPFLILGNKIDIPY  135 (193)
T ss_pred             HHHHHhhhceeEeeeehhhHHHhHHHHHHHHHHHhHHHHhcCcceeecccccCCC
Confidence            5679999999999999999999999877666654433 26899999999999876

>cd01887 IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily

Probab=98.34  E-value=2.1e-06  Score=47.47  Aligned_cols=47  Identities=19%  Similarity=0.114  Sum_probs=34.0

Q ss_pred             ccchhhCCCEEEEEEECCCh---hhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKS---TTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~---~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +..+++.+|++++|+|.++.   .++..+.    .+..   .+.|+++|+||+|+..
T Consensus        67 ~~~~~~~~d~il~v~d~~~~~~~~~~~~~~----~~~~---~~~p~ivv~NK~Dl~~  116 (168)
T cd01887          67 RARGASLTDIAILVVAADDGVMPQTIEAIK----LAKA---ANVPFIVALNKIDKPN  116 (168)
T ss_pred             HHHHHhhcCEEEEEEECCCCccHHHHHHHH----HHHH---cCCCEEEEEEceeccc
Confidence            45678899999999999884   3343322    2222   4589999999999864

IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess three characteristic segments, including a divergent N-terminal region followed by conserved central and C-terminal segments. This core region is conserved among all known eukaryotic and archaeal IF2/eIF5Bs and eubacterial IF2s.

>cd04164 trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes

Probab=98.34  E-value=1.7e-06  Score=47.14  Aligned_cols=47  Identities=23%  Similarity=0.137  Sum_probs=37.6

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      .+++.+|++++|+|.+++.+......|..      ....|+++|+||+|+.+.
T Consensus        76 ~~~~~~~~~v~v~d~~~~~~~~~~~~~~~------~~~~~vi~v~nK~D~~~~  122 (157)
T cd04164          76 EAIEEADLVLFVIDASRGLDEEDLEILEL------PADKPIIVVLNKSDLLPD  122 (157)
T ss_pred             HHHhhCCEEEEEEECCCCCCHHHHHHHHh------hcCCCEEEEEEchhcCCc
Confidence            46778999999999999888777655432      356899999999998653

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.

>TIGR01393 lepA GTP-binding protein LepA

Probab=98.33  E-value=2.3e-06  Score=56.66  Aligned_cols=50  Identities=24%  Similarity=0.295  Sum_probs=39.9

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ...+++.+|++++|+|.++..++.....|...+.    .++|+++|+||+|+..
T Consensus        87 v~~~l~~aD~aILVvDat~g~~~qt~~~~~~~~~----~~ipiIiViNKiDl~~  136 (595)
T TIGR01393        87 VSRSLAACEGALLLVDAAQGIEAQTLANVYLALE----NDLEIIPVINKIDLPS  136 (595)
T ss_pred             HHHHHHhCCEEEEEecCCCCCCHhHHHHHHHHHH----cCCCEEEEEECcCCCc
Confidence            3568899999999999999877777777654332    3579999999999964

LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function is unknown.

>PRK12298 obgE GTPase CgtA; Reviewed

Probab=98.33  E-value=2.8e-06  Score=53.80  Aligned_cols=52  Identities=21%  Similarity=0.140  Sum_probs=41.9

Q ss_pred             hhhCCCEEEEEEECC---ChhhHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCccc
Q 047889            6 YYRGALGALLVYDVT---KSTTFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         6 y~~~a~~~i~v~d~~---~~~s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~~   57 (72)
                      ++..++++++|+|++   +.+.++....|.+++.....  ...|+++|.||+|+...
T Consensus       234 ~i~radvlL~VVD~s~~~~~d~~e~~~~l~~eL~~~~~~L~~kP~IlVlNKiDl~~~  290 (390)
T PRK12298        234 HLERCRVLLHLIDIAPIDGSDPVENARIIINELEKYSPKLAEKPRWLVFNKIDLLDE  290 (390)
T ss_pred             HHHhCCEEEEEeccCcccccChHHHHHHHHHHHHhhhhhhcCCCEEEEEeCCccCCh
Confidence            467899999999998   56778888888888876542  46899999999999653

>PRK12288 GTPase RsgA; Reviewed

Probab=98.29  E-value=2.8e-06  Score=53.07  Aligned_cols=45  Identities=20%  Similarity=0.218  Sum_probs=38.2

Q ss_pred             CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            9 GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++|.+++|++++...++..+..|+..+..   .++|.++|+||+||..
T Consensus       120 NvD~vlIV~s~~p~~s~~~Ldr~L~~a~~---~~i~~VIVlNK~DL~~  164 (347)
T PRK12288        120 NIDQIVIVSAVLPELSLNIIDRYLVACET---LGIEPLIVLNKIDLLD  164 (347)
T ss_pred             EccEEEEEEeCCCCCCHHHHHHHHHHHHh---cCCCEEEEEECccCCC
Confidence            48999999999988899999999775542   4589999999999964

>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA

Probab=98.26  E-value=4.5e-06  Score=52.85  Aligned_cols=47  Identities=23%  Similarity=0.197  Sum_probs=36.2

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      .+++.+|++++|+|.++..+..... +...+.+   .+.|+++|+||+|+.
T Consensus       250 ~~~~~ad~~ilV~D~~~~~~~~~~~-~~~~~~~---~~~~iiiv~NK~Dl~  296 (429)
T TIGR03594       250 KAIERADVVLLVLDATEGITEQDLR-IAGLILE---AGKALVIVVNKWDLV  296 (429)
T ss_pred             HHHHhCCEEEEEEECCCCccHHHHH-HHHHHHH---cCCcEEEEEECcccC
Confidence            3688999999999999887766653 3333332   458999999999996

EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability.

>PRK00098 GTPase RsgA; Reviewed

Probab=98.24  E-value=2.6e-06  Score=52.09  Aligned_cols=47  Identities=21%  Similarity=0.236  Sum_probs=37.6

Q ss_pred             hhCCCEEEEEEECCChhhHHH-HHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFEN-VSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~-~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..++|.+++|+|++++.++.. +..|+..+..   .++|+++|+||+||.+
T Consensus        78 aaniD~vllV~d~~~p~~~~~~idr~L~~~~~---~~ip~iIVlNK~DL~~  125 (298)
T PRK00098         78 AANVDQAVLVFAAKEPDFSTDLLDRFLVLAEA---NGIKPIIVLNKIDLLD  125 (298)
T ss_pred             eecCCEEEEEEECCCCCCCHHHHHHHHHHHHH---CCCCEEEEEEhHHcCC
Confidence            378999999999998876555 4778766643   4689999999999963

>TIGR00436 era GTP-binding protein Era

Probab=98.23  E-value=4.7e-06  Score=50.14  Aligned_cols=47  Identities=23%  Similarity=0.123  Sum_probs=36.3

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+++++|++++|+|.++..+..  ..+...+..   .+.|+++|+||+|+..
T Consensus        75 ~~l~~aDvvl~VvD~~~~~~~~--~~i~~~l~~---~~~p~ilV~NK~Dl~~  121 (270)
T TIGR00436        75 SAIGGVDLILFVVDSDQWNGDG--EFVLTKLQN---LKRPVVLTRNKLDNKF  121 (270)
T ss_pred             HHHhhCCEEEEEEECCCCCchH--HHHHHHHHh---cCCCEEEEEECeeCCC
Confidence            4678999999999999887765  344444443   4589999999999864

Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.

>PRK12296 obgE GTPase CgtA; Reviewed

Probab=98.20  E-value=5.2e-06  Score=54.06  Aligned_cols=53  Identities=13%  Similarity=0.087  Sum_probs=38.5

Q ss_pred             hhhCCCEEEEEEECCC----hhhHHHHHHHHHHHHHhcC-----------CCCeEEEEeeCCCCcccc
Q 047889            6 YYRGALGALLVYDVTK----STTFENVSRWLKDLRDHAG-----------SNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~----~~s~~~~~~~~~~~~~~~~-----------~~~~~vlvgnK~Dl~~~~   58 (72)
                      ++..++++++|+|.++    ++.+..+..|..++..+..           ...|+++|+||+|+.+.+
T Consensus       233 hieradvLv~VVD~s~~e~~rdp~~d~~~i~~EL~~y~~~l~~~~~~~~l~~kP~IVVlNKiDL~da~  300 (500)
T PRK12296        233 HIERCAVLVHVVDCATLEPGRDPLSDIDALEAELAAYAPALDGDLGLGDLAERPRLVVLNKIDVPDAR  300 (500)
T ss_pred             HHHhcCEEEEEECCcccccccCchhhHHHHHHHHHHhhhcccccchhhhhcCCCEEEEEECccchhhH
Confidence            4567899999999986    3456666666666654431           368999999999997543

>cd00066 G-alpha G protein alpha subunit

Probab=98.19  E-value=3.1e-06  Score=52.22  Aligned_cols=55  Identities=15%  Similarity=0.184  Sum_probs=41.3

Q ss_pred             cccchhhCCCEEEEEEECCCh----------hhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKS----------TTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~----------~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~   56 (72)
                      .|.+||.+++++++|.|+++.          ..+......++.+-+... .+.|++|++||.|+-.
T Consensus       177 kW~~~f~~v~~iifvv~lsd~d~~~~e~~~~nrl~esl~~f~~i~~~~~~~~~pill~~NK~D~f~  242 (317)
T cd00066         177 KWIHCFEDVTAIIFVVALSEYDQVLFEDESTNRMQESLNLFDSICNSRWFANTSIILFLNKKDLFE  242 (317)
T ss_pred             hHHHHhCCCCEEEEEEEchhcccccccCCcchHHHHHHHHHHHHHhCccccCCCEEEEccChHHHH
Confidence            467899999999999999974          456555555555544332 5799999999999744

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.

>TIGR00491 aIF-2 translation initiation factor aIF-2/yIF-2

Probab=98.19  E-value=3.8e-06  Score=55.58  Aligned_cols=48  Identities=21%  Similarity=0.098  Sum_probs=36.9

Q ss_pred             cccchhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++..+++.+|++++|+|.++   +.+++.+..+    +.   .++|+++++||+|+..
T Consensus        85 l~~~~~~~aD~~IlVvD~~~g~~~qt~e~i~~l----~~---~~vpiIVv~NK~Dl~~  135 (590)
T TIGR00491        85 LRKRGGALADLAILIVDINEGFKPQTQEALNIL----RM---YKTPFVVAANKIDRIP  135 (590)
T ss_pred             HHHHHHhhCCEEEEEEECCcCCCHhHHHHHHHH----HH---cCCCEEEEEECCCccc
Confidence            34568899999999999997   6677665432    22   3589999999999963

This model describes archaeal and eukaryotic orthologs of bacterial IF-2. Like IF-2, it helps convey the initiator tRNA to the ribosome, although the initiator is N-formyl-Met in bacteria and Met here. This protein is not closely related to the subunits of eIF-2 of eukaryotes, which is also involved in the initiation of translation. The aIF-2 of Methanococcus jannaschii contains a large intein interrupting a region of very strongly conserved sequence very near the amino end; this model does not correctly align the sequences from Methanococcus jannaschii and Pyrococcus horikoshii in this region.

>cd00881 GTP_translation_factor GTP translation factor family

Probab=98.18  E-value=8.5e-06  Score=45.68  Aligned_cols=50  Identities=22%  Similarity=0.192  Sum_probs=36.8

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +..+++.+|++++|+|.++..+... ..++..+..   ...|+++++||+|+..
T Consensus        79 ~~~~~~~~d~~i~v~d~~~~~~~~~-~~~~~~~~~---~~~~i~iv~nK~D~~~  128 (189)
T cd00881          79 VIRGLSVSDGAILVVDANEGVQPQT-REHLRIARE---GGLPIIVAINKIDRVG  128 (189)
T ss_pred             HHHHHHhcCEEEEEEECCCCCcHHH-HHHHHHHHH---CCCCeEEEEECCCCcc
Confidence            3567889999999999987665443 233333333   5689999999999965

This family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation. In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function.

>PRK15494 era GTPase Era; Provisional

Probab=98.17  E-value=8.5e-06  Score=50.69  Aligned_cols=46  Identities=33%  Similarity=0.459  Sum_probs=32.9

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +++++|++++|+|..+  +|.... .|++.+...   +.|.++|+||+|+..
T Consensus       128 ~l~~aDvil~VvD~~~--s~~~~~~~il~~l~~~---~~p~IlViNKiDl~~  174 (339)
T PRK15494        128 SLHSADLVLLIIDSLK--SFDDITHNILDKLRSL---NIVPIFLLNKIDIES  174 (339)
T ss_pred             HhhhCCEEEEEEECCC--CCCHHHHHHHHHHHhc---CCCEEEEEEhhcCcc
Confidence            4679999999998544  566663 455555433   356678999999964

>smart00275 G_alpha G protein alpha subunit

Probab=98.15  E-value=6.1e-06  Score=51.46  Aligned_cols=55  Identities=13%  Similarity=0.147  Sum_probs=41.7

Q ss_pred             cccchhhCCCEEEEEEECCCh----------hhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKS----------TTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~----------~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~   56 (72)
                      .|..||.+++++++|.|+++-          ..+......++.+-+.. -.++|++|++||.|+-.
T Consensus       200 kW~~~f~~v~~IiFvvdlSd~d~~~~Ed~~~nrl~esl~~f~~l~~~~~~~~~piil~~NK~D~~~  265 (342)
T smart00275      200 KWIHCFDNVTAIIFCVALSEYDQVLEEDESTNRMQESLNLFESICNSRWFANTSIILFLNKIDLFE  265 (342)
T ss_pred             hHHHHhCCCCEEEEEEECcccccchhccCcchHHHHHHHHHHHHHcCccccCCcEEEEEecHHhHH
Confidence            467899999999999999973          45666655555554432 26799999999999854

Subunit of G proteins that contains the guanine nucleotide binding site

>cd04167 Snu114p Snu114p subfamily

Probab=98.08  E-value=1.5e-05  Score=46.42  Aligned_cols=48  Identities=29%  Similarity=0.295  Sum_probs=35.4

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      ..+++.+|++++|+|.++..++.. ..|+..+..   ...|+++++||+|+.
T Consensus        89 ~~~~~~aD~~llVvD~~~~~~~~~-~~~~~~~~~---~~~p~iiviNK~D~~  136 (213)
T cd04167          89 AAALRLSDGVVLVVDVVEGVTSNT-ERLIRHAIL---EGLPIVLVINKIDRL  136 (213)
T ss_pred             HHHHHhCCEEEEEEECCCCCCHHH-HHHHHHHHH---cCCCEEEEEECcccC
Confidence            456889999999999988766543 334444332   348999999999974

Snu114p is one of several proteins that make up the U5 small nuclear ribonucleoprotein (snRNP) particle. U5 is a component of the spliceosome, which catalyzes the splicing of pre-mRNA to remove introns. Snu114p is homologous to EF-2, but typically contains an additional N-terminal domain not found in Ef-2. This protein is part of the GTP translation factor family and the Ras superfamily, characterized by five G-box motifs.

>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed

Probab=98.06  E-value=1.3e-05  Score=53.99  Aligned_cols=47  Identities=19%  Similarity=0.209  Sum_probs=37.3

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +++.+|++++|+|.++..++..+.-| ..+..   .+.|+++|+||+|+.+
T Consensus       529 ~i~~advvilViDat~~~s~~~~~i~-~~~~~---~~~piIiV~NK~DL~~  575 (712)
T PRK09518        529 AIERSELALFLFDASQPISEQDLKVM-SMAVD---AGRALVLVFNKWDLMD  575 (712)
T ss_pred             HhhcCCEEEEEEECCCCCCHHHHHHH-HHHHH---cCCCEEEEEEchhcCC
Confidence            46889999999999999888876543 33432   4589999999999964

>cd01894 EngA1 EngA1 subfamily

Probab=98.03  E-value=1.8e-05  Score=43.08  Aligned_cols=49  Identities=27%  Similarity=0.121  Sum_probs=34.4

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      .+++++|++++|+|..+..+.... .....++.   ...|+++|+||+|+.+.
T Consensus        72 ~~~~~~d~ii~v~d~~~~~~~~~~-~~~~~~~~---~~~piiiv~nK~D~~~~  120 (157)
T cd01894          72 LAIEEADVILFVVDGREGLTPADE-EIAKYLRK---SKKPVILVVNKVDNIKE  120 (157)
T ss_pred             HHHHhCCEEEEEEeccccCCccHH-HHHHHHHh---cCCCEEEEEECcccCCh
Confidence            467889999999999876554432 12222332   35899999999999763

This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. 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. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.

>cd04168 TetM_like Tet(M)-like subfamily

Probab=98.03  E-value=1.8e-05  Score=47.09  Aligned_cols=49  Identities=22%  Similarity=0.167  Sum_probs=36.8

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++.... ....++..+..   .++|+++++||+|+..
T Consensus        82 ~~~l~~aD~~IlVvd~~~g~~~-~~~~~~~~~~~---~~~P~iivvNK~D~~~  130 (237)
T cd04168          82 ERSLSVLDGAILVISAVEGVQA-QTRILWRLLRK---LNIPTIIFVNKIDRAG  130 (237)
T ss_pred             HHHHHHhCeEEEEEeCCCCCCH-HHHHHHHHHHH---cCCCEEEEEECccccC
Confidence            4578999999999999886543 33445555544   3589999999999874

Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.

>TIGR00437 feoB ferrous iron transporter FeoB

Probab=98.01  E-value=1e-05  Score=53.58  Aligned_cols=55  Identities=13%  Similarity=-0.115  Sum_probs=36.2

Q ss_pred             CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            9 GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++|+++.|+|.++.+.   ...+..++.   ..+.|+++++||+|+.+++.+.. +..++++
T Consensus        72 ~aDvvI~VvDat~ler---~l~l~~ql~---~~~~PiIIVlNK~Dl~~~~~i~~-d~~~L~~  126 (591)
T TIGR00437        72 KPDLVVNVVDASNLER---NLYLTLQLL---ELGIPMILALNLVDEAEKKGIRI-DEEKLEE  126 (591)
T ss_pred             CCCEEEEEecCCcchh---hHHHHHHHH---hcCCCEEEEEehhHHHHhCCChh-hHHHHHH
Confidence            7899999999887432   223333333   24689999999999976555542 3444443

FeoB (773 amino acids in E. coli), a cytoplasmic membrane protein required for iron(II) update, is encoded in an operon with FeoA (75 amino acids), which is also required, and is regulated by Fur. There appear to be two copies in Archaeoglobus fulgidus and Clostridium acetobutylicum.

>TIGR00483 EF-1_alpha translation elongation factor EF-1 alpha

Probab=98.00  E-value=1.5e-05  Score=50.80  Aligned_cols=49  Identities=18%  Similarity=0.001  Sum_probs=32.3

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHH--HHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKD--LRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~--~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +++++|++++|+|.++.+++.. ..+...  +.... ...|+++++||+|+..
T Consensus       105 ~~~~aD~~ilVvDa~~~~~~~~-~~t~~~~~~~~~~-~~~~iIVviNK~Dl~~  155 (426)
T TIGR00483       105 GASQADAAVLVVAVGDGEFEVQ-PQTREHAFLARTL-GINQLIVAINKMDSVN  155 (426)
T ss_pred             hhhhCCEEEEEEECCCCCcccC-CchHHHHHHHHHc-CCCeEEEEEEChhccC
Confidence            4578999999999999865422 222111  22222 3357999999999963

This model represents the counterpart of bacterial EF-Tu for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1 alpha). The trusted cutoff is set fairly high so that incomplete sequences will score between suggested and trusted cutoff levels.

>cd00880 Era_like Era (E

Probab=97.99  E-value=1.8e-05  Score=42.53  Aligned_cols=49  Identities=27%  Similarity=0.154  Sum_probs=37.9

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      .+++.+|++++++|..+..+..... |.....   ....|+++|+||+|+..+
T Consensus        71 ~~~~~~d~il~v~~~~~~~~~~~~~-~~~~~~---~~~~~~ivv~nK~D~~~~  119 (163)
T cd00880          71 RVLERADLILFVVDADLRADEEEEK-LLELLR---ERGKPVLLVLNKIDLLPE  119 (163)
T ss_pred             HHHHhCCEEEEEEeCCCCCCHHHHH-HHHHHH---hcCCeEEEEEEccccCCh
Confidence            4788999999999999988776655 333332   357899999999998653

coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), 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 se

>cd01857 HSR1_MMR1 HSR1/MMR1

Probab=97.96  E-value=1.8e-05  Score=43.36  Aligned_cols=47  Identities=19%  Similarity=0.273  Sum_probs=34.3

Q ss_pred             hhhCCCEEEEEEECCChhhHH--HHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFE--NVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~--~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ....+|++++|+|..++.+..  .+..|+...   . .+.|+++|.||+|+..
T Consensus         8 ~i~~aD~vl~ViD~~~p~~~~~~~l~~~l~~~---~-~~k~~iivlNK~DL~~   56 (141)
T cd01857           8 VVERSDIVVQIVDARNPLLFRPPDLERYVKEV---D-PRKKNILLLNKADLLT   56 (141)
T ss_pred             HHhhCCEEEEEEEccCCcccCCHHHHHHHHhc---c-CCCcEEEEEechhcCC
Confidence            456899999999999876544  344444322   2 4689999999999854

Human HSR1, is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N terminus.

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=97.95  E-value=6.2e-05  Score=43.37  Aligned_cols=52  Identities=25%  Similarity=0.406  Sum_probs=35.2

Q ss_pred             hhhCCCEEEEEEECCC-hhhHHHHHHHHHHHHHhc---CCCCeEEEEeeCCCCccc
Q 047889            6 YYRGALGALLVYDVTK-STTFENVSRWLKDLRDHA---GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~-~~s~~~~~~~~~~~~~~~---~~~~~~vlvgnK~Dl~~~   57 (72)
                      |..++.|+|+|.|.+. +..+..+..++-.+....   ...+|+++++||.|+...
T Consensus        72 ~~~~~k~IIfvvDSs~~~~~~~~~Ae~Ly~iL~~~~~~~~~~piLIacNK~Dl~~A  127 (181)
T PF09439_consen   72 YLSNAKGIIFVVDSSTDQKELRDVAEYLYDILSDTEVQKNKPPILIACNKQDLFTA  127 (181)
T ss_dssp             HHGGEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHCCTT--EEEEEEE-TTSTT-
T ss_pred             chhhCCEEEEEEeCccchhhHHHHHHHHHHHHHhhhhccCCCCEEEEEeCcccccc
Confidence            5678999999999874 566777755544443222   367999999999999763

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.

>PRK05433 GTP-binding protein LepA; Provisional

Probab=97.95  E-value=3.3e-05  Score=51.35  Aligned_cols=50  Identities=26%  Similarity=0.304  Sum_probs=38.0

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +..+++.+|++++|+|.++.........|....    ..++|+++|+||+|+..
T Consensus        91 v~~sl~~aD~aILVVDas~gv~~qt~~~~~~~~----~~~lpiIvViNKiDl~~  140 (600)
T PRK05433         91 VSRSLAACEGALLVVDASQGVEAQTLANVYLAL----ENDLEIIPVLNKIDLPA  140 (600)
T ss_pred             HHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHH----HCCCCEEEEEECCCCCc
Confidence            356789999999999999876665555554322    14689999999999864

>cd04163 Era Era subfamily

Probab=97.93  E-value=4.6e-05  Score=41.49  Aligned_cols=47  Identities=23%  Similarity=0.223  Sum_probs=33.1

Q ss_pred             chhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .++.++|++++|+|.+++.  ... ..+...+..   ...|+++++||+|+..
T Consensus        78 ~~~~~~d~i~~v~d~~~~~--~~~~~~~~~~~~~---~~~~~iiv~nK~Dl~~  125 (168)
T cd04163          78 SALKDVDLVLFVVDASEPI--GEGDEFILELLKK---SKTPVILVLNKIDLVK  125 (168)
T ss_pred             HHHHhCCEEEEEEECCCcc--CchHHHHHHHHHH---hCCCEEEEEEchhccc
Confidence            4578899999999999872  222 223333333   2589999999999974

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.

>PRK00093 GTP-binding protein Der; Reviewed

Probab=97.91  E-value=4.4e-05  Score=48.54  Aligned_cols=47  Identities=26%  Similarity=0.198  Sum_probs=33.8

Q ss_pred             cchhhCCCEEEEEEECCChhhHH--HHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFE--NVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~--~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++++|++++|+|.++..+..  .+..|+.   .   .+.|+++|+||+|+..
T Consensus        75 ~~~~~~ad~il~vvd~~~~~~~~~~~~~~~l~---~---~~~piilv~NK~D~~~  123 (435)
T PRK00093         75 ELAIEEADVILFVVDGRAGLTPADEEIAKILR---K---SNKPVILVVNKVDGPD  123 (435)
T ss_pred             HHHHHhCCEEEEEEECCCCCCHHHHHHHHHHH---H---cCCcEEEEEECccCcc
Confidence            35678999999999998754432  2334432   2   2689999999999754

>PF06858 NOG1: Nucleolar GTP-binding protein 1 (NOG1); InterPro: IPR010674 This domain represents a conserved region of approximately 60 residues in length within nucleolar GTP-binding protein 1 (NOG1)

Probab=97.89  E-value=0.00015  Score=34.53  Aligned_cols=43  Identities=21%  Similarity=0.316  Sum_probs=27.3

Q ss_pred             CCEEEEEEECCChhhH--HHHHHHHHHHHHhcCCCCeEEEEeeCCC
Q 047889           10 ALGALLVYDVTKSTTF--ENVSRWLKDLRDHAGSNIVIMLIGNKSD   53 (72)
Q Consensus        10 a~~~i~v~d~~~~~s~--~~~~~~~~~~~~~~~~~~~~vlvgnK~D   53 (72)
                      .+++++++|++....+  +.=...+++++..- ++.|+++|.||+|
T Consensus        14 ~~~ilfi~D~Se~CGysie~Q~~L~~~ik~~F-~~~P~i~V~nK~D   58 (58)
T PF06858_consen   14 ADAILFIIDPSEQCGYSIEEQLSLFKEIKPLF-PNKPVIVVLNKID   58 (58)
T ss_dssp             -SEEEEEE-TT-TTSS-HHHHHHHHHHHHHHT-TTS-EEEEE--TT
T ss_pred             cceEEEEEcCCCCCCCCHHHHHHHHHHHHHHc-CCCCEEEEEeccC
Confidence            4679999999987644  44345566666655 5899999999998

The NOG1 family includes eukaryotic, bacterial and archaeal proteins. In Saccharomyces cerevisiae, the NOG1 gene has been shown to be essential for cell viability, suggesting that NOG1 may play an important role in nucleolar functions. In particular, NOG1 is believed to be functionally linked to ribosome biogenesis, which occurs in the nucleolus. In eukaryotes, NOG1 mutants were found to disrupt the biogenesis of the 60S ribosomal subunit []. The DRG and OBG proteins as well as the prokaryotic NOG-like proteins are homologous throughout their length to the amino half of eukaryotic NOG1, which contains the GTP binding motifs (IPR006073 from INTERPRO); the N-terminal GTP-binding motif is required for function.; GO: 0005525 GTP binding; PDB: 2E87_A.

>PRK04004 translation initiation factor IF-2; Validated

Probab=97.86  E-value=4.5e-05  Score=50.61  Aligned_cols=46  Identities=22%  Similarity=0.144  Sum_probs=35.5

Q ss_pred             ccchhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            3 TSAYYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      +..+++.+|++++|+|.++   +.+++.+..+    ..   .++|+++++||+|+.
T Consensus        88 ~~~~~~~aD~~IlVvDa~~g~~~qt~e~i~~~----~~---~~vpiIvviNK~D~~  136 (586)
T PRK04004         88 RKRGGALADIAILVVDINEGFQPQTIEAINIL----KR---RKTPFVVAANKIDRI  136 (586)
T ss_pred             HHHhHhhCCEEEEEEECCCCCCHhHHHHHHHH----HH---cCCCEEEEEECcCCc
Confidence            3456778999999999997   7777766432    22   468999999999985

>cd01859 MJ1464 MJ1464

Probab=97.85  E-value=1.7e-05  Score=43.92  Aligned_cols=50  Identities=14%  Similarity=0.100  Sum_probs=33.9

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .++..+++|.+++|+|.+++..... ..+...+.   ..+.|+++|.||+|+..
T Consensus         6 ~~~i~~~aD~vl~V~D~~~~~~~~~-~~l~~~~~---~~~~p~iiv~NK~Dl~~   55 (156)
T cd01859           6 VRRIIKESDVVLEVLDARDPELTRS-RKLERYVL---ELGKKLLIVLNKADLVP   55 (156)
T ss_pred             HHHHHhhCCEEEEEeeCCCCcccCC-HHHHHHHH---hCCCcEEEEEEhHHhCC
Confidence            4567788999999999987653222 11222221   23579999999999853

This family represents archaeal GTPase typified by the protein MJ1464 from Methanococcus jannaschii. The members of this family show a circular permutation of the GTPase signature motifs so that C-terminal strands 5, 6, and 7 (strands 6 contain the NKxD motif) are relocated to the N terminus.

>KOG1707 consensus Predicted Ras related/Rac-GTP binding protein [Defense mechanisms]

Probab=97.85  E-value=3.6e-05  Score=50.86  Aligned_cols=61  Identities=21%  Similarity=0.231  Sum_probs=44.3

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ..+|.+.++||.+++.||..+....+.....  ..+|+++|+.|.|+.+..+...-+-.++++
T Consensus       494 ~~cDv~~~~YDsS~p~sf~~~a~v~~~~~~~--~~~Pc~~va~K~dlDe~~Q~~~iqpde~~~  554 (625)
T KOG1707|consen  494 AACDVACLVYDSSNPRSFEYLAEVYNKYFDL--YKIPCLMVATKADLDEVPQRYSIQPDEFCR  554 (625)
T ss_pred             ceeeeEEEecccCCchHHHHHHHHHHHhhhc--cCCceEEEeeccccchhhhccCCChHHHHH
Confidence            4579999999999999999987765554322  679999999999997754322222244444

>PRK00089 era GTPase Era; Reviewed

Probab=97.85  E-value=6.4e-05  Score=45.55  Aligned_cols=46  Identities=22%  Similarity=0.194  Sum_probs=31.7

Q ss_pred             hhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+.++|++++|+|.++..  ... ....+.+.   ..+.|+++|+||+|+..
T Consensus        81 ~~~~~D~il~vvd~~~~~--~~~~~~i~~~l~---~~~~pvilVlNKiDl~~  127 (292)
T PRK00089         81 SLKDVDLVLFVVDADEKI--GPGDEFILEKLK---KVKTPVILVLNKIDLVK  127 (292)
T ss_pred             HHhcCCEEEEEEeCCCCC--ChhHHHHHHHHh---hcCCCEEEEEECCcCCC
Confidence            567899999999998832  222 22222232   24689999999999963

>CHL00189 infB translation initiation factor 2; Provisional

Probab=97.84  E-value=3.3e-05  Score=52.41  Aligned_cols=48  Identities=21%  Similarity=0.215  Sum_probs=35.4

Q ss_pred             cccchhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++..+++.+|++++|+|.++   +.+++.+..    +.   ..++|+++++||+|+..
T Consensus       311 mr~rg~~~aDiaILVVDA~dGv~~QT~E~I~~----~k---~~~iPiIVViNKiDl~~  361 (742)
T CHL00189        311 MRSRGANVTDIAILIIAADDGVKPQTIEAINY----IQ---AANVPIIVAINKIDKAN  361 (742)
T ss_pred             HHHHHHHHCCEEEEEEECcCCCChhhHHHHHH----HH---hcCceEEEEEECCCccc
Confidence            34568899999999999887   445544332    22   24689999999999965

>TIGR00487 IF-2 translation initiation factor IF-2

Probab=97.83  E-value=8e-05  Score=49.47  Aligned_cols=48  Identities=21%  Similarity=0.177  Sum_probs=34.0

Q ss_pred             cccchhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++..+++.+|++++|+|.++   +.+++.+.    .+   ...++|+++++||+|+.+
T Consensus       151 ~r~rga~~aDiaILVVda~dgv~~qT~e~i~----~~---~~~~vPiIVviNKiDl~~  201 (587)
T TIGR00487       151 MRARGAKVTDIVVLVVAADDGVMPQTIEAIS----HA---KAANVPIIVAINKIDKPE  201 (587)
T ss_pred             HHHhhhccCCEEEEEEECCCCCCHhHHHHHH----HH---HHcCCCEEEEEECccccc
Confidence            34557788999999999886   34444321    12   224689999999999864

This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognized by the pfam model GTP_EFTU.

>cd04169 RF3 RF3 subfamily

Probab=97.83  E-value=8.1e-05  Score=45.03  Aligned_cols=49  Identities=20%  Similarity=0.142  Sum_probs=33.9

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++...- ....++.....   .++|+++++||+|+..
T Consensus        89 ~~~l~~aD~~IlVvda~~g~~~-~~~~i~~~~~~---~~~P~iivvNK~D~~~  137 (267)
T cd04169          89 YRTLTAVDSAVMVIDAAKGVEP-QTRKLFEVCRL---RGIPIITFINKLDREG  137 (267)
T ss_pred             HHHHHHCCEEEEEEECCCCccH-HHHHHHHHHHh---cCCCEEEEEECCccCC
Confidence            3467889999999999875321 22333333332   4689999999999864

Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide. The class II release factor RF3 then initiates the release of the class I RF from the ribosome. RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state. GDP/GTP exchange occurs, followed by the release of the class I RF. Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome. RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts.

>TIGR03598 GTPase_YsxC ribosome biogenesis GTP-binding protein YsxC/EngB

Probab=97.80  E-value=7.3e-05  Score=42.25  Aligned_cols=48  Identities=21%  Similarity=0.336  Sum_probs=33.2

Q ss_pred             chhhC---CCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRG---ALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~---a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .|++.   ++++++|+|.+++-+...... +..+..   ...|+++++||+|+..
T Consensus        93 ~~l~~~~~~~~ii~vvd~~~~~~~~~~~~-~~~~~~---~~~pviiv~nK~D~~~  143 (179)
T TIGR03598        93 EYLEKRENLKGVVLLMDIRHPLKELDLEM-LEWLRE---RGIPVLIVLTKADKLK  143 (179)
T ss_pred             HHHHhChhhcEEEEEecCCCCCCHHHHHH-HHHHHH---cCCCEEEEEECcccCC
Confidence            45654   579999999988655555422 233332   3689999999999864

Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes.

>TIGR01394 TypA_BipA GTP-binding protein TypA/BipA

Probab=97.77  E-value=9.8e-05  Score=49.12  Aligned_cols=51  Identities=18%  Similarity=0.130  Sum_probs=38.1

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      ..+++.+|++++|+|.++- .....+.|+..+..   .++|.+++.||+|+...+
T Consensus        82 ~~~l~~aD~alLVVDa~~G-~~~qT~~~l~~a~~---~~ip~IVviNKiD~~~a~  132 (594)
T TIGR01394        82 ERVLGMVDGVLLLVDASEG-PMPQTRFVLKKALE---LGLKPIVVINKIDRPSAR  132 (594)
T ss_pred             HHHHHhCCEEEEEEeCCCC-CcHHHHHHHHHHHH---CCCCEEEEEECCCCCCcC
Confidence            4578899999999998763 34455666666654   358899999999996543

This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP-binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.

>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed

Probab=97.76  E-value=7.9e-05  Score=50.33  Aligned_cols=48  Identities=21%  Similarity=0.150  Sum_probs=34.8

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++.  +... ..|.+.++.   .+.|+++|+||+|+..
T Consensus       349 ~~~~~~aD~iL~VvDa~~~--~~~~d~~i~~~Lr~---~~~pvIlV~NK~D~~~  397 (712)
T PRK09518        349 QIAVSLADAVVFVVDGQVG--LTSTDERIVRMLRR---AGKPVVLAVNKIDDQA  397 (712)
T ss_pred             HHHHHhCCEEEEEEECCCC--CCHHHHHHHHHHHh---cCCCEEEEEECccccc
Confidence            3468899999999999763  2222 245555543   5689999999999854

>PRK00093 GTP-binding protein Der; Reviewed

Probab=97.75  E-value=0.0001  Score=46.92  Aligned_cols=47  Identities=23%  Similarity=0.167  Sum_probs=35.7

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +++.+|++++|+|.++..+..... +...+.+   ...|+++++||+|+..
T Consensus       252 ~~~~ad~~ilViD~~~~~~~~~~~-i~~~~~~---~~~~~ivv~NK~Dl~~  298 (435)
T PRK00093        252 AIERADVVLLVIDATEGITEQDLR-IAGLALE---AGRALVIVVNKWDLVD  298 (435)
T ss_pred             HHHHCCEEEEEEeCCCCCCHHHHH-HHHHHHH---cCCcEEEEEECccCCC
Confidence            678899999999999887766543 3333333   3589999999999863

>TIGR00475 selB selenocysteine-specific elongation factor SelB

Probab=97.75  E-value=0.00012  Score=48.58  Aligned_cols=46  Identities=28%  Similarity=0.179  Sum_probs=33.6

Q ss_pred             chhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCccc
Q 047889            5 AYYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKHL   57 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~~   57 (72)
                      .++.++|++++|+|.++   +.+++.+.    .+..   .++| +++|+||+|+.++
T Consensus        69 ~g~~~aD~aILVVDa~~G~~~qT~ehl~----il~~---lgi~~iIVVlNK~Dlv~~  118 (581)
T TIGR00475        69 AGGGGIDAALLVVDADEGVMTQTGEHLA----VLDL---LGIPHTIVVITKADRVNE  118 (581)
T ss_pred             hhhccCCEEEEEEECCCCCcHHHHHHHH----HHHH---cCCCeEEEEEECCCCCCH
Confidence            45678999999999998   56665543    2222   2466 9999999999653

In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.

>PRK13351 elongation factor G; Reviewed

Probab=97.73  E-value=9.9e-05  Score=49.60  Aligned_cols=49  Identities=20%  Similarity=0.225  Sum_probs=38.2

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++..+......|. .+..   .++|+++++||+|+..
T Consensus        91 ~~~l~~aD~~ilVvd~~~~~~~~~~~~~~-~~~~---~~~p~iiviNK~D~~~  139 (687)
T PRK13351         91 ERSLRVLDGAVVVFDAVTGVQPQTETVWR-QADR---YGIPRLIFINKMDRVG  139 (687)
T ss_pred             HHHHHhCCEEEEEEeCCCCCCHHHHHHHH-HHHh---cCCCEEEEEECCCCCC
Confidence            46789999999999999887776655552 3332   3589999999999875

>PRK05306 infB translation initiation factor IF-2; Validated

Probab=97.72  E-value=5.8e-05  Score=51.58  Aligned_cols=47  Identities=17%  Similarity=0.111  Sum_probs=34.1

Q ss_pred             ccchhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +..+++.+|++++|+|.++   +.+++.+.       .....++|+++++||+|+..
T Consensus       354 ~~rga~~aDiaILVVdAddGv~~qT~e~i~-------~a~~~~vPiIVviNKiDl~~  403 (787)
T PRK05306        354 RARGAQVTDIVVLVVAADDGVMPQTIEAIN-------HAKAAGVPIIVAINKIDKPG  403 (787)
T ss_pred             HHhhhhhCCEEEEEEECCCCCCHhHHHHHH-------HHHhcCCcEEEEEECccccc
Confidence            4456788999999999987   44544432       12224689999999999964

>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA

Probab=97.72  E-value=0.00014  Score=46.13  Aligned_cols=50  Identities=30%  Similarity=0.174  Sum_probs=34.4

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..+++.+|++++|+|..+..+.... .+...+++   .+.|+++|+||+|+...
T Consensus        73 ~~~~~~ad~vl~vvD~~~~~~~~d~-~i~~~l~~---~~~piilVvNK~D~~~~  122 (429)
T TIGR03594        73 EIAIEEADVILFVVDGREGLTPEDE-EIAKWLRK---SGKPVILVANKIDGKKE  122 (429)
T ss_pred             HHHHhhCCEEEEEEeCCCCCCHHHH-HHHHHHHH---hCCCEEEEEECccCCcc
Confidence            3567899999999999875443321 12222333   35899999999998653

EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability.

>KOG1489 consensus Predicted GTP-binding protein (ODN superfamily) [General function prediction only]

Probab=97.60  E-value=0.00027  Score=44.13  Aligned_cols=48  Identities=19%  Similarity=0.340  Sum_probs=39.7

Q ss_pred             hCCCEEEEEEECCCh---hhHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCc
Q 047889            8 RGALGALLVYDVTKS---TTFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLK   55 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~---~s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~   55 (72)
                      ..++.+++|.|++.+   +.+++++....++..+..  .+-|.++|+||+|++
T Consensus       273 ER~~~l~fVvD~s~~~~~~p~~~~~lL~~ELe~yek~L~~rp~liVaNKiD~~  325 (366)
T KOG1489|consen  273 ERCKGLLFVVDLSGKQLRNPWQQLQLLIEELELYEKGLADRPALIVANKIDLP  325 (366)
T ss_pred             HhhceEEEEEECCCcccCCHHHHHHHHHHHHHHHhhhhccCceEEEEeccCch
Confidence            468899999999999   888888877777765543  678999999999995

>cd01888 eIF2_gamma eIF2-gamma (gamma subunit of initiation factor 2)

Probab=97.60  E-value=0.00018  Score=41.62  Aligned_cols=44  Identities=25%  Similarity=0.215  Sum_probs=29.5

Q ss_pred             hhCCCEEEEEEECCCh----hhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKS----TTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~----~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..++|++++|+|.+++    .+++.+..|    ...  ...|++++.||+|+..
T Consensus       104 ~~~~D~~llVvd~~~~~~~~~t~~~l~~~----~~~--~~~~iiivvNK~Dl~~  151 (203)
T cd01888         104 AAVMDGALLLIAANEPCPQPQTSEHLAAL----EIM--GLKHIIIVQNKIDLVK  151 (203)
T ss_pred             hhcCCEEEEEEECCCCCCCcchHHHHHHH----HHc--CCCcEEEEEEchhccC
Confidence            4466999999999873    344443333    221  2247899999999964

eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B. eIF2B is a heteropentamer, and the epsilon chain binds eIF2. Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma. It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role. eIF2-gamma is found only in eukaryotes and archaea. It is closely related to SelB, the sel

>cd01889 SelB_euk SelB subfamily

Probab=97.59  E-value=0.00028  Score=40.25  Aligned_cols=45  Identities=22%  Similarity=0.135  Sum_probs=30.0

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +.+|++++|+|.++.........+.  +...  ...|+++++||+|+..
T Consensus        90 ~~~d~vi~VvD~~~~~~~~~~~~~~--~~~~--~~~~~iiv~NK~Dl~~  134 (192)
T cd01889          90 QIIDLMLLVVDATKGIQTQTAECLV--IGEI--LCKKLIVVLNKIDLIP  134 (192)
T ss_pred             hhCCEEEEEEECCCCccHHHHHHHH--HHHH--cCCCEEEEEECcccCC
Confidence            3568999999998754444333332  1122  2469999999999863

SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and euk

>PRK14845 translation initiation factor IF-2; Provisional

Probab=97.55  E-value=0.00021  Score=50.22  Aligned_cols=46  Identities=28%  Similarity=0.223  Sum_probs=34.6

Q ss_pred             cchhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++   +.+++.+..    +..   .++|+++++||+|+..
T Consensus       544 ~~g~~~aDivlLVVDa~~Gi~~qT~e~I~~----lk~---~~iPiIVViNKiDL~~  592 (1049)
T PRK14845        544 KRGGSLADLAVLVVDINEGFKPQTIEAINI----LRQ---YKTPFVVAANKIDLIP  592 (1049)
T ss_pred             HhhcccCCEEEEEEECcccCCHhHHHHHHH----HHH---cCCCEEEEEECCCCcc
Confidence            445678999999999986   666666543    222   3579999999999953

>PRK09554 feoB ferrous iron transport protein B; Reviewed

Probab=97.55  E-value=0.00033  Score=47.91  Aligned_cols=54  Identities=17%  Similarity=-0.043  Sum_probs=37.7

Q ss_pred             CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            9 GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      .+|++++|+|.++.+.   ...|..++.+.   +.|++++.||+|+.+++.+. .+..+++
T Consensus        85 ~aD~vI~VvDat~ler---~l~l~~ql~e~---giPvIvVlNK~Dl~~~~~i~-id~~~L~  138 (772)
T PRK09554         85 DADLLINVVDASNLER---NLYLTLQLLEL---GIPCIVALNMLDIAEKQNIR-IDIDALS  138 (772)
T ss_pred             CCCEEEEEecCCcchh---hHHHHHHHHHc---CCCEEEEEEchhhhhccCcH-HHHHHHH
Confidence            7899999999887543   33455555543   58999999999987655553 3344443

>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins

Probab=97.54  E-value=0.00086  Score=39.78  Aligned_cols=24  Identities=38%  Similarity=0.224  Sum_probs=18.5

Q ss_pred             chhhCCCEEEEEEECCChh-hHHHH
Q 047889            5 AYYRGALGALLVYDVTKST-TFENV   28 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~-s~~~~   28 (72)
                      .+++++|++++|+|.+++. ....+
T Consensus        73 ~~~~~ad~il~V~D~t~~~~~~~~~   97 (233)
T cd01896          73 AVARTADLILMVLDATKPEGHREIL   97 (233)
T ss_pred             HhhccCCEEEEEecCCcchhHHHHH
Confidence            4688999999999998866 34333

GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.

>cd01858 NGP_1 NGP-1

Probab=97.51  E-value=0.00023  Score=39.55  Aligned_cols=46  Identities=17%  Similarity=0.251  Sum_probs=31.9

Q ss_pred             hhCCCEEEEEEECCChhh--HHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTT--FENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s--~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +.++|.+++|.|..++..  -..+..+   +... ..+.|+++|.||+|+..
T Consensus         6 l~~aD~il~VvD~~~p~~~~~~~i~~~---l~~~-~~~~p~ilVlNKiDl~~   53 (157)
T cd01858           6 IDSSDVVIQVLDARDPMGTRCKHVEEY---LKKE-KPHKHLIFVLNKCDLVP   53 (157)
T ss_pred             hhhCCEEEEEEECCCCccccCHHHHHH---HHhc-cCCCCEEEEEEchhcCC
Confidence            568999999999988742  2222332   3322 24589999999999954

Autoantigen NGP-1 (Nucleolar G-protein gene 1) has been shown to localize in the nucleolus and nucleolar organizers in all cell types analyzed, which is indicative of a function in ribosomal assembly. NGP-1 and its homologs show a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with NKXD motif) are relocated to the N terminus.

>COG2262 HflX GTPases [General function prediction only]

Probab=97.46  E-value=0.00076  Score=43.14  Aligned_cols=49  Identities=27%  Similarity=0.243  Sum_probs=40.3

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..||.++.|.|.++|...+.+..-.+-+.+..-.++|+++|-||+|+-.
T Consensus       270 ~~aDlllhVVDaSdp~~~~~~~~v~~vL~el~~~~~p~i~v~NKiD~~~  318 (411)
T COG2262         270 KEADLLLHVVDASDPEILEKLEAVEDVLAEIGADEIPIILVLNKIDLLE  318 (411)
T ss_pred             hcCCEEEEEeecCChhHHHHHHHHHHHHHHcCCCCCCEEEEEecccccC
Confidence            4689999999999998877777766667666556799999999999643

>PRK12317 elongation factor 1-alpha; Reviewed

Probab=97.42  E-value=0.00039  Score=44.39  Aligned_cols=48  Identities=17%  Similarity=0.014  Sum_probs=30.1

Q ss_pred             hhCCCEEEEEEECCChhhHHH-HHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFEN-VSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~-~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+++|++++|+|.+++.++.. ...+...+...  ...|+++++||+|+..
T Consensus       105 ~~~aD~~ilVvDa~~~~~~~~~~~~~~~~~~~~--~~~~iivviNK~Dl~~  153 (425)
T PRK12317        105 ASQADAAVLVVAADDAGGVMPQTREHVFLARTL--GINQLIVAINKMDAVN  153 (425)
T ss_pred             hhcCCEEEEEEEcccCCCCCcchHHHHHHHHHc--CCCeEEEEEEcccccc
Confidence            457999999999987422212 12222223222  2246899999999964

>PRK00741 prfC peptide chain release factor 3; Provisional

Probab=97.38  E-value=0.00057  Score=45.00  Aligned_cols=49  Identities=20%  Similarity=0.154  Sum_probs=34.4

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++.-. .....++.....   .++|+++++||+|+..
T Consensus        97 ~~~l~~aD~aIlVvDa~~gv~-~~t~~l~~~~~~---~~iPiiv~iNK~D~~~  145 (526)
T PRK00741         97 YRTLTAVDSALMVIDAAKGVE-PQTRKLMEVCRL---RDTPIFTFINKLDRDG  145 (526)
T ss_pred             HHHHHHCCEEEEEEecCCCCC-HHHHHHHHHHHh---cCCCEEEEEECCcccc
Confidence            356889999999999987432 123334333332   4689999999999865

>cd01849 YlqF_related_GTPase YlqF-related GTPases

Probab=97.35  E-value=0.00042  Score=38.47  Aligned_cols=43  Identities=19%  Similarity=0.046  Sum_probs=29.0

Q ss_pred             CEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889           11 LGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus        11 ~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      |.+++|.|..++.+...  .++.. ......+.|+++|.||+|+..
T Consensus         1 Dvvl~VvD~~~p~~~~~--~~i~~-~~~~~~~~p~IiVlNK~Dl~~   43 (155)
T cd01849           1 DVILEVLDARDPLGTRS--PDIER-VLIKEKGKKLILVLNKADLVP   43 (155)
T ss_pred             CEEEEEEeccCCccccC--HHHHH-HHHhcCCCCEEEEEechhcCC
Confidence            67899999988765442  23331 111225689999999999954

These proteins are found in bacteria, eukaryotes, and archaea. They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases.

>PRK10218 GTP-binding protein; Provisional

Probab=97.31  E-value=0.00097  Score=44.65  Aligned_cols=51  Identities=16%  Similarity=-0.009  Sum_probs=35.4

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      +..+++.+|++++|+|.++.... ..+.++..+..   .++|.+++.||+|+...
T Consensus        85 v~~~l~~aDg~ILVVDa~~G~~~-qt~~~l~~a~~---~gip~IVviNKiD~~~a  135 (607)
T PRK10218         85 VERVMSMVDSVLLVVDAFDGPMP-QTRFVTKKAFA---YGLKPIVVINKVDRPGA  135 (607)
T ss_pred             HHHHHHhCCEEEEEEecccCccH-HHHHHHHHHHH---cCCCEEEEEECcCCCCC
Confidence            35688999999999999874322 22333334433   35788999999998753

>cd04170 EF-G_bact Elongation factor G (EF-G) subfamily

Probab=97.30  E-value=0.0016  Score=39.12  Aligned_cols=49  Identities=22%  Similarity=0.223  Sum_probs=35.6

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++.........|. .+..   .++|.+++.||+|+..
T Consensus        82 ~~~l~~aD~~i~Vvd~~~g~~~~~~~~~~-~~~~---~~~p~iivvNK~D~~~  130 (268)
T cd04170          82 RAALRAADAALVVVSAQSGVEVGTEKLWE-FADE---AGIPRIIFINKMDRER  130 (268)
T ss_pred             HHHHHHCCEEEEEEeCCCCCCHHHHHHHH-HHHH---cCCCEEEEEECCccCC
Confidence            45678899999999998866554434442 3332   4589999999999875

Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group

>cd04166 CysN_ATPS CysN_ATPS subfamily

Probab=97.29  E-value=0.0017  Score=37.76  Aligned_cols=48  Identities=25%  Similarity=0.070  Sum_probs=29.6

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .++.+|++++|+|.++... .........+...  ...++++|.||+|+..
T Consensus        97 ~~~~ad~~llVvD~~~~~~-~~~~~~~~~~~~~--~~~~iIvviNK~D~~~  144 (208)
T cd04166          97 GASTADLAILLVDARKGVL-EQTRRHSYILSLL--GIRHVVVAVNKMDLVD  144 (208)
T ss_pred             hhhhCCEEEEEEECCCCcc-HhHHHHHHHHHHc--CCCcEEEEEEchhccc
Confidence            4678999999999987532 1111222222222  2245788999999864

CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which catalyzes ATP hydrolysis, is a member of the ATP pyrophosphatase (ATP PPase) family. CysN hydrolysis of GTP is required for CysD hydrolysis of ATP; however, CysN hydrolysis of GTP is not dependent on CysD hydrolysis of ATP. CysN is an example of lateral gene transfer followed by acquisition of new function. In many organisms, an ATPS exists which is not GTP-dependent and shares no sequence or structural similarity to CysN.

>TIGR00503 prfC peptide chain release factor 3

Probab=97.29  E-value=0.00083  Score=44.26  Aligned_cols=48  Identities=19%  Similarity=0.134  Sum_probs=33.3

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+++.+|++++|+|.++.- ......+++..+.   .++|+++++||+|+..
T Consensus        99 ~~l~~aD~aIlVvDa~~gv-~~~t~~l~~~~~~---~~~PiivviNKiD~~~  146 (527)
T TIGR00503        99 RTLTAVDNCLMVIDAAKGV-ETRTRKLMEVTRL---RDTPIFTFMNKLDRDI  146 (527)
T ss_pred             HHHHhCCEEEEEEECCCCC-CHHHHHHHHHHHh---cCCCEEEEEECccccC
Confidence            4678899999999988631 1223344443332   4689999999999864

This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus.

>PRK13796 GTPase YqeH; Provisional

Probab=97.26  E-value=0.0011  Score=41.77  Aligned_cols=53  Identities=21%  Similarity=0.240  Sum_probs=34.2

Q ss_pred             CCC-EEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHH
Q 047889            9 GAL-GALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIK   68 (72)
Q Consensus         9 ~a~-~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~   68 (72)
                      .++ .+++|.|+.+..     ..|.+.+.+.. .+.|+++|+||+||.. +.+..++..++
T Consensus        68 ~~~~lIv~VVD~~D~~-----~s~~~~L~~~~-~~kpviLViNK~DLl~-~~~~~~~i~~~  121 (365)
T PRK13796         68 DSDALVVNVVDIFDFN-----GSWIPGLHRFV-GNNPVLLVGNKADLLP-KSVKKNKVKNW  121 (365)
T ss_pred             ccCcEEEEEEECccCC-----CchhHHHHHHh-CCCCEEEEEEchhhCC-CccCHHHHHHH
Confidence            345 778889987743     33555665544 3678999999999954 34444444433

>cd01883 EF1_alpha Eukaryotic elongation factor 1 (EF1) alpha subfamily

Probab=97.15  E-value=0.0014  Score=38.36  Aligned_cols=46  Identities=24%  Similarity=0.076  Sum_probs=29.2

Q ss_pred             hhCCCEEEEEEECCChhh---H----HHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKSTT---F----ENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s---~----~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      .+.+|++++|.|.++...   |    .....| ......  ...|++++.||+|+.
T Consensus        98 ~~~~d~~i~VvDa~~~~~~~~~~~~~~~~~~~-~~~~~~--~~~~iiivvNK~Dl~  150 (219)
T cd01883          98 ASQADVAVLVVDARKGEFEAGFEKGGQTREHA-LLARTL--GVKQLIVAVNKMDDV  150 (219)
T ss_pred             hhhCCEEEEEEECCCCccccccccccchHHHH-HHHHHc--CCCeEEEEEEccccc
Confidence            456999999999988421   1    112222 222221  236899999999997

EF1 is responsible for the GTP-dependent binding of aminoacyl-tRNAs to the ribosomes. EF1 is composed of four subunits: the alpha chain which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This subfamily is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha interacts with the actin of the eukaryotic cytoskeleton and may thereby play a role in cellular transformation and apoptosis. EF-Tu can have no such role in bacteria. In humans, the isoform eEF1A2 is overexpressed in 2/3 of breast cancers and has been identified as a putative oncogene. This subfamily also includes Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation in

>PRK04000 translation initiation factor IF-2 subunit gamma; Validated

Probab=97.15  E-value=0.0013  Score=42.06  Aligned_cols=46  Identities=28%  Similarity=0.290  Sum_probs=29.7

Q ss_pred             chhhC---CCEEEEEEECCCh----hhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRG---ALGALLVYDVTKS----TTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~---a~~~i~v~d~~~~----~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .|+++   +|++++|+|.++.    .+.+.+..    +...  ...|+++|+||+|+.+
T Consensus       101 ~~~~~~~~~D~~llVVDa~~~~~~~~t~~~l~~----l~~~--~i~~iiVVlNK~Dl~~  153 (411)
T PRK04000        101 TMLSGAALMDGAILVIAANEPCPQPQTKEHLMA----LDII--GIKNIVIVQNKIDLVS  153 (411)
T ss_pred             HHHHHHhhCCEEEEEEECCCCCCChhHHHHHHH----HHHc--CCCcEEEEEEeecccc
Confidence            34454   5999999999953    34443332    2221  2246899999999965

>TIGR00484 EF-G translation elongation factor EF-G

Probab=97.12  E-value=0.0012  Score=44.65  Aligned_cols=49  Identities=18%  Similarity=0.191  Sum_probs=35.3

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++.........| ..+..   .++|+++++||+|+..
T Consensus        93 ~~~l~~~D~~ilVvda~~g~~~~~~~~~-~~~~~---~~~p~ivviNK~D~~~  141 (689)
T TIGR00484        93 ERSLRVLDGAVAVLDAVGGVQPQSETVW-RQANR---YEVPRIAFVNKMDKTG  141 (689)
T ss_pred             HHHHHHhCEEEEEEeCCCCCChhHHHHH-HHHHH---cCCCEEEEEECCCCCC
Confidence            3568899999999999876554433333 23332   3589999999999875

After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.

>PF00009 GTP_EFTU: Elongation factor Tu GTP binding domain; InterPro: IPR000795 Elongation factors belong to a family of proteins that promote the GTP-dependent binding of aminoacyl tRNA to the A site of ribosomes during protein biosynthesis, and catalyse the translocation of the synthesised protein chain from the A to the P site

Probab=97.10  E-value=0.0038  Score=35.59  Aligned_cols=45  Identities=36%  Similarity=0.352  Sum_probs=30.6

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      .+.+|++++|.|..+.-.-.. ...+..+..   .++|++++.||+|+.
T Consensus        91 ~~~~D~ailvVda~~g~~~~~-~~~l~~~~~---~~~p~ivvlNK~D~~  135 (188)
T PF00009_consen   91 LRQADIAILVVDANDGIQPQT-EEHLKILRE---LGIPIIVVLNKMDLI  135 (188)
T ss_dssp             HTTSSEEEEEEETTTBSTHHH-HHHHHHHHH---TT-SEEEEEETCTSS
T ss_pred             ecccccceeeeeccccccccc-ccccccccc---cccceEEeeeeccch
Confidence            567999999999986533322 222333333   458899999999987

The proteins are all relatively similar in the vicinity of their C-termini, and are also highly similar to a range of proteins that includes the nodulation Q protein from Rhizobium meliloti (Sinorhizobium meliloti), bacterial tetracycline resistance proteins [] and the omnipotent suppressor protein 2 from yeast. In both prokaryotes and eukaryotes, there are three distinct types of elongation factors, EF-1alpha (EF-Tu), which binds GTP and an aminoacyl-tRNAand delivers the latter to the A site of ribosomes; EF-1beta (EF-Ts), which interacts with EF-1a/EF-Tu to displace GDP and thus allows the regeneration of GTP-EF-1a; and EF-2 (EF-G), which binds GTP and peptidyl-tRNA and translocates the latter from the A site to the P site. In EF-1-alpha, a specific region has been shown [] to be involved in a conformational change mediated by the hydrolysis of GTP to GDP. This region is conserved in both EF-1alpha/EF-Tu as well as EF-2/EF-G and thus seems typical for GTP-dependent proteins which bind non-initiator tRNAs to the ribosome. The GTP-binding protein synthesis factor family also includes the eukaryotic peptide chain release factor GTP-binding subunits [] and prokaryotic peptide chain release factor 3 (RF-3) []; the prokaryotic GTP-binding protein lepA and its homologue in yeast (GUF1) and Caenorhabditis elegans (ZK1236.1); yeast HBS1 []; rat statin S1 []; and the prokaryotic selenocysteine-specific elongation factor selB [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 3IZW_C 1DG1_G 2BVN_B 3IZV_C 3MMP_C 1OB2_A 1EFU_A 3FIH_Z 3TR5_A 1TUI_C ....

>PRK09866 hypothetical protein; Provisional

Probab=97.06  E-value=0.0051  Score=41.91  Aligned_cols=49  Identities=16%  Similarity=0.174  Sum_probs=33.3

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+..+|.+++|.|.+...+... ....+.++... ...|+++|.||+|+..
T Consensus       255 qL~eADvVLFVVDat~~~s~~D-eeIlk~Lkk~~-K~~PVILVVNKIDl~d  303 (741)
T PRK09866        255 QLARASAVLAVLDYTQLKSISD-EEVREAILAVG-QSVPLYVLVNKFDQQD  303 (741)
T ss_pred             HHhhCCEEEEEEeCCCCCChhH-HHHHHHHHhcC-CCCCEEEEEEcccCCC
Confidence            4778999999999987544333 12233343322 3369999999999854

>cd04104 p47_IIGP_like p47 (47-kDa) family

Probab=97.04  E-value=0.0011  Score=38.26  Aligned_cols=42  Identities=12%  Similarity=0.126  Sum_probs=29.2

Q ss_pred             hhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      +.++|.++++-+    .+|... ..|++.+...   ..|+++|+||+|+.
T Consensus        78 ~~~~d~~l~v~~----~~~~~~d~~~~~~l~~~---~~~~ilV~nK~D~~  120 (197)
T cd04104          78 FSEYDFFIIISS----TRFSSNDVKLAKAIQCM---GKKFYFVRTKVDRD  120 (197)
T ss_pred             ccCcCEEEEEeC----CCCCHHHHHHHHHHHHh---CCCEEEEEecccch
Confidence            567888888732    335555 4566666554   47899999999983

The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma). ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis. TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro. IRG-47 is involved in resistance to T. gondii infection. LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections. IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues. In macrophages, IIGP1 interacts with hook3, a microtubule binding protei

>PRK01889 GTPase RsgA; Reviewed

Probab=96.97  E-value=0.0033  Score=39.61  Aligned_cols=47  Identities=15%  Similarity=0.203  Sum_probs=34.9

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      -.++|.+++|.+....-+...+..++..+..   .+++.++|.||+||.+
T Consensus       110 aANvD~vliV~s~~p~~~~~~ldr~L~~a~~---~~i~piIVLNK~DL~~  156 (356)
T PRK01889        110 AANVDTVFIVCSLNHDFNLRRIERYLALAWE---SGAEPVIVLTKADLCE  156 (356)
T ss_pred             EEeCCEEEEEEecCCCCChhHHHHHHHHHHH---cCCCEEEEEEChhcCC
Confidence            3678999999999755566666666655544   3467788999999965

>PRK12740 elongation factor G; Reviewed

Probab=96.92  E-value=0.0026  Score=42.79  Aligned_cols=49  Identities=16%  Similarity=0.137  Sum_probs=36.3

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++.........|. .+..   .++|++++.||+|+..
T Consensus        78 ~~~l~~aD~vllvvd~~~~~~~~~~~~~~-~~~~---~~~p~iiv~NK~D~~~  126 (668)
T PRK12740         78 ERALRVLDGAVVVVCAVGGVEPQTETVWR-QAEK---YGVPRIIFVNKMDRAG  126 (668)
T ss_pred             HHHHHHhCeEEEEEeCCCCcCHHHHHHHH-HHHH---cCCCEEEEEECCCCCC
Confidence            35678899999999998876665544442 3332   4589999999999865

>TIGR03680 eif2g_arch translation initiation factor 2 subunit gamma

Probab=96.92  E-value=0.0029  Score=40.38  Aligned_cols=44  Identities=30%  Similarity=0.214  Sum_probs=28.7

Q ss_pred             hhCCCEEEEEEECCCh----hhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKS----TTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~----~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ...+|++++|+|.++.    .+.+.+.    .+...  ...|++++.||+|+.+
T Consensus       101 ~~~aD~aIlVVDa~~g~~~~qt~e~l~----~l~~~--gi~~iIVvvNK~Dl~~  148 (406)
T TIGR03680       101 AALMDGALLVIAANEPCPQPQTKEHLM----ALEII--GIKNIVIVQNKIDLVS  148 (406)
T ss_pred             HHHCCEEEEEEECCCCccccchHHHHH----HHHHc--CCCeEEEEEEccccCC
Confidence            3457999999999863    2333332    22222  2246899999999964

eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA.

>PF04670 Gtr1_RagA: Gtr1/RagA G protein conserved region; InterPro: IPR006762 GTR1 was first identified in Saccharomyces cerevisiae (Baker's yeast) as a suppressor of a mutation in RCC1

Probab=96.91  E-value=0.0043  Score=37.10  Aligned_cols=51  Identities=22%  Similarity=0.303  Sum_probs=35.7

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHH---HHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENV---SRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~---~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      ...|+++.++|+|+|..+.+-.+.+   ...+..+.+.+ +++.+.+.-+|+|+.
T Consensus        71 ~~if~~v~~LIyV~D~qs~~~~~~l~~~~~~i~~l~~~s-p~~~v~vfiHK~D~l  124 (232)
T PF04670_consen   71 EEIFSNVGVLIYVFDAQSDDYDEDLAYLSDCIEALRQYS-PNIKVFVFIHKMDLL  124 (232)
T ss_dssp             HHHHCTESEEEEEEETT-STCHHHHHHHHHHHHHHHHHS-TT-EEEEEEE-CCCS
T ss_pred             HHHHhccCEEEEEEEcccccHHHHHHHHHHHHHHHHHhC-CCCeEEEEEeecccC
Confidence            4578999999999999955544444   44445555554 789999999999984

RCC1 catalyzes guanine nucleotide exchange on Ran, a well characterised nuclear Ras-like small G protein that plays an essential role in the import and export of proteins and RNAs across the nuclear membrane through the nuclear pore complex. RCC1 is located inside the nucleus, bound to chromatin. The concentration of GTP within the cell is ~30 times higher than the concentration of GDP, thus resulting in the preferential production of the GTP form of Ran by RCC1 within the nucleus. Gtr1p is located within both the cytoplasm and the nucleus and has been reported to play a role in cell growth. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1 and Rag A and Gtr1p belong to the sixth subfamily of the Ras-like small GTPase superfamily []. ; GO: 0005525 GTP binding, 0005634 nucleus, 0005737 cytoplasm; PDB: 3R7W_B 2Q3F_B 3LLU_A.

>PRK00454 engB GTP-binding protein YsxC; Reviewed

Probab=96.90  E-value=0.0038  Score=35.37  Aligned_cols=48  Identities=19%  Similarity=0.318  Sum_probs=29.7

Q ss_pred             chhhCC---CEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGA---LGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a---~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .|++.+   +++++++|.+++.+.... .+...+..   ...|+++++||+|+..
T Consensus        99 ~~~~~~~~~~~~~~v~d~~~~~~~~~~-~i~~~l~~---~~~~~iiv~nK~Dl~~  149 (196)
T PRK00454         99 EYLRTRENLKGVVLLIDSRHPLKELDL-QMIEWLKE---YGIPVLIVLTKADKLK  149 (196)
T ss_pred             HHHHhCccceEEEEEEecCCCCCHHHH-HHHHHHHH---cCCcEEEEEECcccCC
Confidence            455654   577888888776543321 11122222   3588999999999854

>KOG4273 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.82  E-value=0.0017  Score=39.88  Aligned_cols=46  Identities=22%  Similarity=0.400  Sum_probs=33.8

Q ss_pred             CCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889           10 ALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus        10 a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..+++++||++..+.+..++.|+..-.-.  .--..+.+|||.|....
T Consensus        79 l~a~vmvfdlse~s~l~alqdwl~htdin--sfdillcignkvdrvph  124 (418)
T KOG4273|consen   79 LQAFVMVFDLSEKSGLDALQDWLPHTDIN--SFDILLCIGNKVDRVPH  124 (418)
T ss_pred             eeeEEEEEeccchhhhHHHHhhccccccc--cchhheecccccccccc
Confidence            36899999999999999999997643222  11234668999997543

>COG0536 Obg Predicted GTPase [General function prediction only]

Probab=96.81  E-value=0.0063  Score=38.45  Aligned_cols=49  Identities=18%  Similarity=0.147  Sum_probs=36.4

Q ss_pred             hCCCEEEEEEECCChh---hHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKST---TFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~---s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~   56 (72)
                      ..+..++.|.|++..+   -.++......++..+..  .+.|.++|.||+|+..
T Consensus       236 ERt~vL~hviD~s~~~~~dp~~~~~~i~~EL~~Y~~~L~~K~~ivv~NKiD~~~  289 (369)
T COG0536         236 ERTRVLLHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKPRIVVLNKIDLPL  289 (369)
T ss_pred             HhhheeEEEEecCcccCCCHHHHHHHHHHHHHHhhHHhccCceEEEEeccCCCc
Confidence            3567888899998665   36666666667766653  5789999999999643

>cd01886 EF-G Elongation factor G (EF-G) subfamily

Probab=96.80  E-value=0.005  Score=37.40  Aligned_cols=49  Identities=18%  Similarity=0.136  Sum_probs=32.9

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|.|..+...-. ....+..+..   .+.|++++.||+|+..
T Consensus        82 ~~~l~~aD~ailVVDa~~g~~~~-t~~~~~~~~~---~~~p~ivviNK~D~~~  130 (270)
T cd01886          82 ERSLRVLDGAVAVFDAVAGVEPQ-TETVWRQADR---YNVPRIAFVNKMDRTG  130 (270)
T ss_pred             HHHHHHcCEEEEEEECCCCCCHH-HHHHHHHHHH---cCCCEEEEEECCCCCC
Confidence            35788999999999987642211 1223333332   4589999999999864

Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group conta

>cd01876 YihA_EngB The YihA (EngB) subfamily

Probab=96.78  E-value=0.0047  Score=33.59  Aligned_cols=40  Identities=23%  Similarity=0.355  Sum_probs=26.6

Q ss_pred             CCEEEEEEECCChhh--HHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889           10 ALGALLVYDVTKSTT--FENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus        10 a~~~i~v~d~~~~~s--~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      .+++++++|.++..+  ...+..|+..      ...|+++++||+|+.
T Consensus        82 ~~~~~~v~d~~~~~~~~~~~~~~~l~~------~~~~vi~v~nK~D~~  123 (170)
T cd01876          82 LKGVVLLIDSRHGPTEIDLEMLDWLEE------LGIPFLVVLTKADKL  123 (170)
T ss_pred             hhEEEEEEEcCcCCCHhHHHHHHHHHH------cCCCEEEEEEchhcC
Confidence            467888998876632  2223344322      247899999999984

This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target.

>COG1084 Predicted GTPase [General function prediction only]

Probab=96.66  E-value=0.008  Score=37.78  Aligned_cols=46  Identities=20%  Similarity=0.301  Sum_probs=34.5

Q ss_pred             CCEEEEEEECCChh--hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889           10 ALGALLVYDVTKST--TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus        10 a~~~i~v~d~~~~~--s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      +++++++||.+...  +++.=.+.+.+++....  .|+++|.||.|+.+.
T Consensus       248 ~~~IlF~~D~Se~cgy~lE~Q~~L~~eIk~~f~--~p~v~V~nK~D~~~~  295 (346)
T COG1084         248 AGVILFLFDPSETCGYSLEEQISLLEEIKELFK--APIVVVINKIDIADE  295 (346)
T ss_pred             cCeEEEEEcCccccCCCHHHHHHHHHHHHHhcC--CCeEEEEecccccch
Confidence            46788999998765  44554566777776653  899999999998753

>cd04178 Nucleostemin_like Nucleostemin-like

Probab=96.65  E-value=0.0082  Score=34.22  Aligned_cols=44  Identities=25%  Similarity=0.178  Sum_probs=27.6

Q ss_pred             CEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889           11 LGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus        11 ~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      |.++++.|..++.+-.. ..+.+.+. ....+.|+++|.||+|+..
T Consensus         1 DvVl~VvDar~p~~~~~-~~i~~~~~-l~~~~kp~IlVlNK~DL~~   44 (172)
T cd04178           1 DVILEVLDARDPLGCRC-PQVEEAVL-QAGGNKKLVLVLNKIDLVP   44 (172)
T ss_pred             CEEEEEEECCCCCCCCC-HHHHHHHH-hccCCCCEEEEEehhhcCC
Confidence            67899999887643211 22222221 1224589999999999954

Nucleostemin (NS) is a nucleolar protein that functions as a regulator of cell growth and proliferation in stem cells and in several types of cancer cells, but is not expressed in the differentiated cells of most mammalian adult tissues. NS shuttles between the nucleolus and nucleoplasm bidirectionally at a rate that is fast and independent of cell type. Lowering GTP levels decreases the nucleolar retention of NS, and expression of NS is abruptly down-regulated during differentiation prior to terminal cell division. Found only in eukaryotes, NS consists of an N-terminal basic domain, a coiled-coil domain, a GTP-binding domain, an intermediate domain, and a C-terminal acidic domain. Experimental evidence indicates that NS uses its GTP-binding property as a molecular switch to control the transition between the nucleolus and nucleoplasm, and this process involves interaction between the basic, GTP-binding, and intermediate domains of the

>PLN00043 elongation factor 1-alpha; Provisional

Probab=96.57  E-value=0.008  Score=39.00  Aligned_cols=47  Identities=21%  Similarity=0.095  Sum_probs=30.6

Q ss_pred             chhhCCCEEEEEEECCChhhHH-------HHHHHHHHHHHhcCCCC-eEEEEeeCCCCc
Q 047889            5 AYYRGALGALLVYDVTKSTTFE-------NVSRWLKDLRDHAGSNI-VIMLIGNKSDLK   55 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~-------~~~~~~~~~~~~~~~~~-~~vlvgnK~Dl~   55 (72)
                      ..++.+|++++|+|.++ .+|+       ..+..+..+..   ..+ +++++.||+|+.
T Consensus       104 ~g~~~aD~aIlVVda~~-G~~e~g~~~~~qT~eh~~~~~~---~gi~~iIV~vNKmD~~  158 (447)
T PLN00043        104 TGTSQADCAVLIIDSTT-GGFEAGISKDGQTREHALLAFT---LGVKQMICCCNKMDAT  158 (447)
T ss_pred             hhhhhccEEEEEEEccc-CceecccCCCchHHHHHHHHHH---cCCCcEEEEEEcccCC
Confidence            35678999999999986 3343       23222222222   346 478899999986

>cd01856 YlqF YlqF

Probab=96.52  E-value=0.0031  Score=35.50  Aligned_cols=46  Identities=22%  Similarity=0.081  Sum_probs=30.6

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ....+||.+++|+|..++..-.. ..+.+.+     .+.|.++|.||+|+.+
T Consensus        15 ~~i~~aD~il~v~D~~~~~~~~~-~~i~~~~-----~~k~~ilVlNK~Dl~~   60 (171)
T cd01856          15 EKLKLVDLVIEVRDARIPLSSRN-PLLEKIL-----GNKPRIIVLNKADLAD   60 (171)
T ss_pred             HHHhhCCEEEEEeeccCccCcCC-hhhHhHh-----cCCCEEEEEehhhcCC
Confidence            34678999999999987653221 1111111     2468899999999954

Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga) and in all eukaryotes.

>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional

Probab=96.48  E-value=0.018  Score=38.85  Aligned_cols=44  Identities=23%  Similarity=0.117  Sum_probs=30.0

Q ss_pred             hhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      .+.++|++++|+|.++   +.+.+.+.    .+..   .++| +++|.||+|+.+
T Consensus        71 g~~~~D~~lLVVda~eg~~~qT~ehl~----il~~---lgi~~iIVVlNKiDlv~  118 (614)
T PRK10512         71 GVGGIDHALLVVACDDGVMAQTREHLA----ILQL---TGNPMLTVALTKADRVD  118 (614)
T ss_pred             HhhcCCEEEEEEECCCCCcHHHHHHHH----HHHH---cCCCeEEEEEECCccCC
Confidence            4668999999999887   44544432    2222   2244 679999999964

>TIGR00485 EF-Tu translation elongation factor TU

Probab=96.48  E-value=0.013  Score=37.23  Aligned_cols=44  Identities=23%  Similarity=0.246  Sum_probs=26.3

Q ss_pred             CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            9 GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      ++|++++|+|.++...-. ....+..+..   ..+| ++++.||+|+.+
T Consensus        98 ~~D~~ilVvda~~g~~~q-t~e~l~~~~~---~gi~~iIvvvNK~Dl~~  142 (394)
T TIGR00485        98 QMDGAILVVSATDGPMPQ-TREHILLARQ---VGVPYIVVFLNKCDMVD  142 (394)
T ss_pred             hCCEEEEEEECCCCCcHH-HHHHHHHHHH---cCCCEEEEEEEecccCC
Confidence            469999999998732111 1122222332   2456 457899999864

This alignment models orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts, one of several GTP-binding translation factors found by the more general pfam model GTP_EFTU. The eukaryotic conterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this model. EF-Tu is one of the most abundant proteins in bacteria, as well as one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation.

>KOG0082 consensus G-protein alpha subunit (small G protein superfamily) [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]

Probab=96.47  E-value=0.006  Score=38.58  Aligned_cols=55  Identities=13%  Similarity=0.189  Sum_probs=38.6

Q ss_pred             ccchhhCCCEEEEEEECCChhh----------HHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCccc
Q 047889            3 TSAYYRGALGALLVYDVTKSTT----------FENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s----------~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~   57 (72)
                      |-++|.+++++|+|.++++-.-          +......++.+-++.- .+.+++|.-||.||-++
T Consensus       212 WihcFe~v~aviF~vslSeYdq~l~ED~~~NRM~eS~~LF~sI~n~~~F~~tsiiLFLNK~DLFeE  277 (354)
T KOG0082|consen  212 WIHCFEDVTAVIFCVSLSEYDQVLEEDETTNRMHESLKLFESICNNKWFANTSIILFLNKKDLFEE  277 (354)
T ss_pred             HHHhhcCCCEEEEEEehhhhhhhcccccchhHHHHHHHHHHHHhcCcccccCcEEEEeecHHHHHH
Confidence            4678999999999999986432          2223344555544332 57899999999999654

>PF00503 G-alpha: G-protein alpha subunit; InterPro: IPR001019 Guanine nucleotide binding proteins (G proteins) are membrane-associated, heterotrimeric proteins composed of three subunits: alpha (IPR001019 from INTERPRO), beta (IPR001632 from INTERPRO) and gamma (IPR001770 from INTERPRO) []

Probab=96.44  E-value=0.0061  Score=38.61  Aligned_cols=53  Identities=15%  Similarity=0.195  Sum_probs=36.5

Q ss_pred             ccchhhCCCEEEEEEECCCh----------hhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCc
Q 047889            3 TSAYYRGALGALLVYDVTKS----------TTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLK   55 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~----------~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~   55 (72)
                      |-+||.+++++|+|.++++-          ..+......++.+-+.. -.+.|++|+.||.|+-
T Consensus       253 W~~~F~~v~~vif~vsls~ydq~~~ed~~~nrl~esl~lF~~i~~~~~~~~~~iil~lnK~D~f  316 (389)
T PF00503_consen  253 WIHCFEDVTAVIFVVSLSEYDQTLYEDPNTNRLHESLNLFESICNNPWFKNTPIILFLNKIDLF  316 (389)
T ss_dssp             GGGGGTTESEEEEEEEGGGGGSBESSSTTSBHHHHHHHHHHHHHTSGGGTTSEEEEEEE-HHHH
T ss_pred             HHHHhccccEEEEeecccchhhhhcccchHHHHHHHHHHHHHHHhCcccccCceEEeeecHHHH
Confidence            56899999999999998642          23444444455554332 2579999999999973

G proteins and their receptors (GPCRs) form one of the most prevalent signalling systems in mammalian cells, regulating systems as diverse as sensory perception, cell growth and hormonal regulation []. At the cell surface, the binding of ligands such as hormones and neurotransmitters to a GPCR activates the receptor by causing a conformational change, which in turn activates the bound G protein on the intracellular-side of the membrane. The activated receptor promotes the exchange of bound GDP for GTP on the G protein alpha subunit. GTP binding changes the conformation of switch regions within the alpha subunit, which allows the bound trimeric G protein (inactive) to be released from the receptor, and to dissociate into active alpha subunit (GTP-bound) and beta/gamma dimer. The alpha subunit and the beta/gamma dimer go on to activate distinct downstream effectors, such as adenylyl cyclase, phosphodiesterases, phospholipase C, and ion channels. These effectors in turn regulate the intracellular concentrations of secondary messengers, such as cAMP, diacylglycerol, sodium or calcium cations, which ultimately lead to a physiological response, usually via the downstream regulation of gene transcription. The cycle is completed by the hydrolysis of alpha subunit-bound GTP to GDP, resulting in the re-association of the alpha and beta/gamma subunits and their binding to the receptor, which terminates the signal []. The length of the G protein signal is controlled by the duration of the GTP-bound alpha subunit, which can be regulated by RGS (regulator of G protein signalling) proteins (IPR000342 from INTERPRO) or by covalent modifications []. There are several isoforms of each subunit, many of which have splice variants, which together can make up hundreds of combinations of G proteins. The specific combination of subunits in heterotrimeric G proteins affects not only which receptor it can bind to, but also which downstream target is affected, providing the means to target specific physiological processes in response to specific external stimuli [, ]. G proteins carry lipid modifications on one or more of their subunits to target them to the plasma membrane and to contribute to protein interactions. This family consists of the G protein alpha subunit, which acts as a weak GTPase. G protein classes are defined based on the sequence and function of their alpha subunits, which in mammals fall into four main categories: G(S)alpha, G(Q)alpha, G(I)alpha and G(12)alpha; there are also fungal and plant classes of alpha subunits. The alpha subunit consists of two domains: a GTP-binding domain and a helical insertion domain (IPR011025 from INTERPRO). The GTP-binding domain is homologous to Ras-like small GTPases, and includes switch regions I and II, which change conformation during activation. The switch regions are loops of alpha-helices with conformations sensitive to guanine nucleotides. The helical insertion domain is inserted into the GTP-binding domain before switch region I and is unique to heterotrimeric G proteins. This helical insertion domain functions to sequester the guanine nucleotide at the interface with the GTP-binding domain and must be displaced to enable nucleotide dissociation.; GO: 0004871 signal transducer activity, 0019001 guanyl nucleotide binding, 0007186 G-protein coupled receptor protein signaling pathway; PDB: 3QI2_B 3QE0_A 2IK8_A 2OM2_A 2GTP_B 2XNS_B 3ONW_B 1KJY_A 2EBC_A 1Y3A_B ....

>PF02421 FeoB_N: Ferrous iron transport protein B; InterPro: IPR011619 Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions

Probab=96.39  E-value=0.0049  Score=34.80  Aligned_cols=46  Identities=17%  Similarity=0.062  Sum_probs=33.0

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccccc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLN   59 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~   59 (72)
                      ...|+++.|.|.++.+   .-.....++.+.   ..|++++.||+|....+.
T Consensus        77 ~~~D~ii~VvDa~~l~---r~l~l~~ql~e~---g~P~vvvlN~~D~a~~~g  122 (156)
T PF02421_consen   77 EKPDLIIVVVDATNLE---RNLYLTLQLLEL---GIPVVVVLNKMDEAERKG  122 (156)
T ss_dssp             TSSSEEEEEEEGGGHH---HHHHHHHHHHHT---TSSEEEEEETHHHHHHTT
T ss_pred             cCCCEEEEECCCCCHH---HHHHHHHHHHHc---CCCEEEEEeCHHHHHHcC
Confidence            5789999999988744   323344455543   599999999999865443

FeoB has been identified as part of this transport system and may play a role in the transport of ferrous iron. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent [].; GO: 0005525 GTP binding, 0015093 ferrous iron transmembrane transporter activity, 0015684 ferrous iron transport, 0016021 integral to membrane; PDB: 3TAH_B 3B1X_A 3SS8_A 3B1W_C 3B1V_A 3LX5_A 3B1Y_A 3LX8_A 3B1Z_A 3K53_B ....

>cd01850 CDC_Septin CDC/Septin

Probab=96.33  E-value=0.0056  Score=37.31  Aligned_cols=15  Identities=20%  Similarity=0.202  Sum_probs=13.0

Q ss_pred             CCeEEEEeeCCCCcc
Q 047889           42 NIVIMLIGNKSDLKH   56 (72)
Q Consensus        42 ~~~~vlvgnK~Dl~~   56 (72)
                      .+|+++|+||+|+..
T Consensus       143 ~v~vi~VinK~D~l~  157 (276)
T cd01850         143 RVNIIPVIAKADTLT  157 (276)
T ss_pred             cCCEEEEEECCCcCC
Confidence            689999999999843

Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities.

>PRK12736 elongation factor Tu; Reviewed

Probab=96.31  E-value=0.021  Score=36.38  Aligned_cols=45  Identities=22%  Similarity=0.232  Sum_probs=27.9

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      ..+|++++|+|.++... ......+..+...   .+| ++++.||+|+.+
T Consensus        97 ~~~d~~llVvd~~~g~~-~~t~~~~~~~~~~---g~~~~IvviNK~D~~~  142 (394)
T PRK12736         97 AQMDGAILVVAATDGPM-PQTREHILLARQV---GVPYLVVFLNKVDLVD  142 (394)
T ss_pred             hhCCEEEEEEECCCCCc-hhHHHHHHHHHHc---CCCEEEEEEEecCCcc
Confidence            45799999999876321 1112222233332   467 678999999863

>TIGR03596 GTPase_YlqF ribosome biogenesis GTP-binding protein YlqF

Probab=96.20  E-value=0.0076  Score=36.59  Aligned_cols=46  Identities=20%  Similarity=0.202  Sum_probs=30.8

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .....+|.+++|.|...+.+...  .++....    .+.|+++|.||+|+.+
T Consensus        17 ~~l~~aDvVl~V~Dar~p~~~~~--~~i~~~l----~~kp~IiVlNK~DL~~   62 (276)
T TIGR03596        17 EKLKLVDVVIEVLDARIPLSSRN--PMIDEIR----GNKPRLIVLNKADLAD   62 (276)
T ss_pred             HHHhhCCEEEEEEeCCCCCCCCC--hhHHHHH----CCCCEEEEEEccccCC
Confidence            34568999999999977654322  1111111    2478999999999953

Members of this protein family are GTP-binding proteins involved in ribosome biogenesis, including the essential YlqF protein of Bacillus subtilis, which is an essential protein. They are related to Era, EngA, and other GTPases of ribosome biogenesis, but are circularly permuted. This family is not universal, and is not present in Escherichia coli, and so is not as well studied as some other GTPases. This model is built for bacterial members.

>PRK13768 GTPase; Provisional

Probab=96.13  E-value=0.0071  Score=36.36  Aligned_cols=47  Identities=15%  Similarity=0.008  Sum_probs=30.0

Q ss_pred             CCEEEEEEECCChhhHHHH--HHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889           10 ALGALLVYDVTKSTTFENV--SRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus        10 a~~~i~v~d~~~~~s~~~~--~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ++++++++|.....+....  ..|+...... ..+.|+++|.||+|+...
T Consensus       129 ~~~ii~liD~~~~~~~~d~~~~~~l~~~~~~-~~~~~~i~v~nK~D~~~~  177 (253)
T PRK13768        129 KSVVVFLIDAVLAKTPSDFVSLLLLALSVQL-RLGLPQIPVLNKADLLSE  177 (253)
T ss_pred             CeEEEEEechHHhCCHHHHHHHHHHHHHHHH-HcCCCEEEEEEhHhhcCc
Confidence            7899999999654433332  2232222222 246899999999998653

>cd04165 GTPBP1_like GTPBP1-like

Probab=96.13  E-value=0.032  Score=33.04  Aligned_cols=44  Identities=20%  Similarity=0.113  Sum_probs=29.5

Q ss_pred             CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            9 GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+|++++|.|...... .....++..+..   .++|++++.||+|+..
T Consensus       109 ~~D~~llVvda~~g~~-~~d~~~l~~l~~---~~ip~ivvvNK~D~~~  152 (224)
T cd04165         109 APDYAMLVVAANAGII-GMTKEHLGLALA---LNIPVFVVVTKIDLAP  152 (224)
T ss_pred             CCCEEEEEEECCCCCc-HHHHHHHHHHHH---cCCCEEEEEECccccC
Confidence            5799999999865432 222334444443   3478999999999854

Mammalian GTP binding protein 1 (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1 are GTPases whose specific functions remain unknown. In mouse, GTPBP1 is expressed in macrophages, in smooth muscle cells of various tissues and in some neurons of the cerebral cortex; GTPBP2 tissue distribution appears to overlap that of GTPBP1. In human leukemia and macrophage cell lines, expression of both GTPBP1 and GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The chromosomal location of both genes has been identified in humans, with GTPBP1 located in chromosome 22q12-13.1 and GTPBP2 located in chromosome 6p21-12. Human glioblastoma multiforme (GBM), a highly-malignant astrocytic glioma and the most common cancer in the central nervous system, has been linked to chromosomal deletions and a translocation on chromosome 6. The GBM translocation results in a fusion of GTPBP2 and PTPRZ1, a protein involved in oligodendrocyte differentiation, recovery, and

>TIGR00490 aEF-2 translation elongation factor aEF-2

Probab=96.05  E-value=0.013  Score=40.04  Aligned_cols=48  Identities=19%  Similarity=0.102  Sum_probs=31.3

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      ...++.+|++++|+|..+--.-.....|. .+.   ..+.|++++.||+|..
T Consensus       104 ~~al~~aD~~llVvda~~g~~~~t~~~~~-~~~---~~~~p~ivviNKiD~~  151 (720)
T TIGR00490       104 TRAMRAVDGAIVVVCAVEGVMPQTETVLR-QAL---KENVKPVLFINKVDRL  151 (720)
T ss_pred             HHHHHhcCEEEEEEecCCCCCccHHHHHH-HHH---HcCCCEEEEEEChhcc
Confidence            34678999999999987632222222222 222   2356788999999985

This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD.

>COG0486 ThdF Predicted GTPase [General function prediction only]

Probab=96.03  E-value=0.018  Score=37.58  Aligned_cols=47  Identities=23%  Similarity=0.207  Sum_probs=32.4

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      -..+||.+++|+|.+.+.+=....     +.+....+.|+++|.||.||..+
T Consensus       293 ~i~~ADlvL~v~D~~~~~~~~d~~-----~~~~~~~~~~~i~v~NK~DL~~~  339 (454)
T COG0486         293 AIEEADLVLFVLDASQPLDKEDLA-----LIELLPKKKPIIVVLNKADLVSK  339 (454)
T ss_pred             HHHhCCEEEEEEeCCCCCchhhHH-----HHHhcccCCCEEEEEechhcccc
Confidence            356899999999999862211111     11123467899999999999764

>cd01884 EF_Tu EF-Tu subfamily

Probab=96.02  E-value=0.051  Score=31.51  Aligned_cols=45  Identities=24%  Similarity=0.251  Sum_probs=28.3

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~   55 (72)
                      ...+|++++|.|....-. ......+..+..   .++| ++++-||+|+.
T Consensus        86 ~~~~D~~ilVvda~~g~~-~~~~~~~~~~~~---~~~~~iIvviNK~D~~  131 (195)
T cd01884          86 AAQMDGAILVVSATDGPM-PQTREHLLLARQ---VGVPYIVVFLNKADMV  131 (195)
T ss_pred             hhhCCEEEEEEECCCCCc-HHHHHHHHHHHH---cCCCcEEEEEeCCCCC
Confidence            457899999999876322 112223333333   2355 77889999985

This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors. The eukaryotic counterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this family. EF-Tu is one of the most abundant proteins in bacteria, as well as, one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation.

>PRK09563 rbgA GTPase YlqF; Reviewed

Probab=96.00  E-value=0.0092  Score=36.45  Aligned_cols=45  Identities=27%  Similarity=0.190  Sum_probs=30.6

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      -...+|.+++|.|...+.+.+.  .++.+..    .+.|+++|.||+|+.+
T Consensus        21 ~l~~aDvIL~VvDar~p~~~~~--~~l~~~~----~~kp~iiVlNK~DL~~   65 (287)
T PRK09563         21 NLKLVDVVIEVLDARIPLSSEN--PMIDKII----GNKPRLLILNKSDLAD   65 (287)
T ss_pred             HhhhCCEEEEEEECCCCCCCCC--hhHHHHh----CCCCEEEEEEchhcCC
Confidence            4567999999999877654322  1222221    2578999999999953

>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse

Probab=95.90  E-value=0.079  Score=27.68  Aligned_cols=40  Identities=25%  Similarity=0.301  Sum_probs=26.6

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeC
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNK   51 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK   51 (72)
                      +..+|++++|+|..++.. +.....++.++    ...|+++|.||
T Consensus        77 ~~~~d~ii~vv~~~~~~~-~~~~~~~~~l~----~~~~~i~v~NK  116 (116)
T PF01926_consen   77 ISKSDLIIYVVDASNPIT-EDDKNILRELK----NKKPIILVLNK  116 (116)
T ss_dssp             HCTESEEEEEEETTSHSH-HHHHHHHHHHH----TTSEEEEEEES
T ss_pred             HHHCCEEEEEEECCCCCC-HHHHHHHHHHh----cCCCEEEEEcC
Confidence            368899999999777422 12223333332    56899999998

These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....

>KOG0090 consensus Signal recognition particle receptor, beta subunit (small G protein superfamily) [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.73  E-value=0.11  Score=31.18  Aligned_cols=48  Identities=21%  Similarity=0.254  Sum_probs=32.4

Q ss_pred             CCCEEEEEEECC-ChhhHHHHHHHHHHHHHhc---CCCCeEEEEeeCCCCcc
Q 047889            9 GALGALLVYDVT-KSTTFENVSRWLKDLRDHA---GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         9 ~a~~~i~v~d~~-~~~s~~~~~~~~~~~~~~~---~~~~~~vlvgnK~Dl~~   56 (72)
                      .+-|+++|.|.. ...-...+..++-++....   ...+|++++.||.|+..
T Consensus       108 ~akaiVFVVDSa~f~k~vrdvaefLydil~~~~~~~~~~~vLIaCNKqDl~t  159 (238)
T KOG0090|consen  108 SAKAIVFVVDSATFLKNVRDVAEFLYDILLDSRVKKNKPPVLIACNKQDLFT  159 (238)
T ss_pred             cceeEEEEEeccccchhhHHHHHHHHHHHHhhccccCCCCEEEEecchhhhh
Confidence            688888888754 3445566655544443222   36789999999999965

>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]

Probab=95.72  E-value=0.014  Score=39.22  Aligned_cols=66  Identities=12%  Similarity=0.207  Sum_probs=48.8

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcc--cccCCHHHHHHHH
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKH--LLNSMCEEYLIKS   69 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~--~~~v~~~e~~~~a   69 (72)
                      .+|-..+|++|+||.+.+..+|+.+..+.-.+.... -..+|++++|++--...  .+.+...++.+++
T Consensus        90 aQft~wvdavIfvf~~~d~~s~q~v~~l~~~l~~~r~r~~i~l~lvgtqd~iS~~~~rv~~da~~r~l~  158 (749)
T KOG0705|consen   90 AQFCQWVDAVVFVFSVEDEQSFQAVQALAHEMSSYRNISDLPLILVGTQDHISAKRPRVITDDRARQLS  158 (749)
T ss_pred             hhhhhhccceEEEEEeccccCHHHHHHHHhhcccccccccchHHhhcCcchhhcccccccchHHHHHHH
Confidence            467788999999999999999999988766664333 26789999998865433  3455556665554

>PRK12739 elongation factor G; Reviewed

Probab=95.65  E-value=0.04  Score=37.58  Aligned_cols=48  Identities=17%  Similarity=0.120  Sum_probs=32.5

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..++.+|++++|.|..+...-... ..+..+..   .+.|++++.||+|+..
T Consensus        92 ~al~~~D~~ilVvDa~~g~~~qt~-~i~~~~~~---~~~p~iv~iNK~D~~~  139 (691)
T PRK12739         92 RSLRVLDGAVAVFDAVSGVEPQSE-TVWRQADK---YGVPRIVFVNKMDRIG  139 (691)
T ss_pred             HHHHHhCeEEEEEeCCCCCCHHHH-HHHHHHHH---cCCCEEEEEECCCCCC
Confidence            457789999999998765332222 22223332   3578899999999875

>PRK12735 elongation factor Tu; Reviewed

Probab=95.48  E-value=0.079  Score=33.85  Aligned_cols=45  Identities=18%  Similarity=0.211  Sum_probs=27.6

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEE-EEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIM-LIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~v-lvgnK~Dl~~   56 (72)
                      ..+|++++|+|..+... ......+..+..   ..+|.+ ++.||+|+.+
T Consensus        97 ~~aD~~llVvda~~g~~-~qt~e~l~~~~~---~gi~~iivvvNK~Dl~~  142 (396)
T PRK12735         97 AQMDGAILVVSAADGPM-PQTREHILLARQ---VGVPYIVVFLNKCDMVD  142 (396)
T ss_pred             ccCCEEEEEEECCCCCc-hhHHHHHHHHHH---cCCCeEEEEEEecCCcc
Confidence            46799999999876322 122222333332   346744 6799999964

>cd03110 Fer4_NifH_child This protein family's function is unkown

Probab=95.47  E-value=0.18  Score=28.36  Aligned_cols=47  Identities=30%  Similarity=0.360  Sum_probs=34.9

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+..+|.++++...+ ..++..+..+.+.+++.   +.|+.+|.||.|...
T Consensus       111 ~l~~aD~vliv~~~~-~~~~~~~~~~~~~l~~~---~~~~~vV~N~~~~~~  157 (179)
T cd03110         111 SLTGADAALLVTEPT-PSGLHDLERAVELVRHF---GIPVGVVINKYDLND  157 (179)
T ss_pred             HHHcCCEEEEEecCC-cccHHHHHHHHHHHHHc---CCCEEEEEeCCCCCc
Confidence            457799999998876 55777777777766653   356789999999753

It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.

>COG1160 Predicted GTPases [General function prediction only]

Probab=95.43  E-value=0.036  Score=36.12  Aligned_cols=43  Identities=26%  Similarity=0.244  Sum_probs=28.6

Q ss_pred             hhCCCEEEEEEECCChh-hHH-HHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKST-TFE-NVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~-s~~-~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      +..||++++|.|...-- .-+ .+..|   ++   ..+.|++||.||+|-.
T Consensus        81 i~eADvilfvVD~~~Git~~D~~ia~~---Lr---~~~kpviLvvNK~D~~  125 (444)
T COG1160          81 IEEADVILFVVDGREGITPADEEIAKI---LR---RSKKPVILVVNKIDNL  125 (444)
T ss_pred             HHhCCEEEEEEeCCCCCCHHHHHHHHH---HH---hcCCCEEEEEEcccCc
Confidence            46799999999976521 111 12222   23   2568999999999975

>KOG3886 consensus GTP-binding protein [Signal transduction mechanisms]

Probab=95.27  E-value=0.096  Score=31.97  Aligned_cols=52  Identities=19%  Similarity=0.271  Sum_probs=39.5

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHH---HHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLK---DLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~---~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..-|++.++++.|||+...+--.++.++.+   .+.++ ++...++..-.|.||..
T Consensus        76 d~iF~nV~vli~vFDves~e~~~D~~~yqk~Le~ll~~-SP~AkiF~l~hKmDLv~  130 (295)
T KOG3886|consen   76 DNIFRNVQVLIYVFDVESREMEKDFHYYQKCLEALLQN-SPEAKIFCLLHKMDLVQ  130 (295)
T ss_pred             hhhheeheeeeeeeeccchhhhhhHHHHHHHHHHHHhc-CCcceEEEEEeechhcc
Confidence            456789999999999999876666665554   33444 37788899999999964

>COG0532 InfB Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]

Probab=94.97  E-value=0.11  Score=34.59  Aligned_cols=41  Identities=22%  Similarity=0.201  Sum_probs=30.9

Q ss_pred             CCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            9 GALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         9 ~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      =+|.+++|.+.++   |++.+.+.+.    +   ..++|+++..||+|..+
T Consensus        78 vtDIaILVVa~dDGv~pQTiEAI~ha----k---~a~vP~iVAiNKiDk~~  121 (509)
T COG0532          78 VTDIAILVVAADDGVMPQTIEAINHA----K---AAGVPIVVAINKIDKPE  121 (509)
T ss_pred             cccEEEEEEEccCCcchhHHHHHHHH----H---HCCCCEEEEEecccCCC
Confidence            3688999999887   5666654442    2   35799999999999874

>TIGR02034 CysN sulfate adenylyltransferase, large subunit

Probab=94.83  E-value=0.1  Score=33.45  Aligned_cols=47  Identities=21%  Similarity=-0.002  Sum_probs=28.0

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ...+|++++|+|......-....+|. .+...  ...+++++.||+|+..
T Consensus       101 ~~~aD~allVVda~~G~~~qt~~~~~-~~~~~--~~~~iivviNK~D~~~  147 (406)
T TIGR02034       101 ASTADLAVLLVDARKGVLEQTRRHSY-IASLL--GIRHVVLAVNKMDLVD  147 (406)
T ss_pred             HhhCCEEEEEEECCCCCccccHHHHH-HHHHc--CCCcEEEEEEeccccc
Confidence            45789999999986532111112221 22222  2235889999999864

Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules. With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulfurase) and cysC (APS kinase).

>CHL00071 tufA elongation factor Tu

Probab=94.73  E-value=0.17  Score=32.51  Aligned_cols=46  Identities=17%  Similarity=0.175  Sum_probs=29.3

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      ...+|++++|.|...... ......+..+..   ..+| ++++.||+|+.+
T Consensus        96 ~~~~D~~ilVvda~~g~~-~qt~~~~~~~~~---~g~~~iIvvvNK~D~~~  142 (409)
T CHL00071         96 AAQMDGAILVVSAADGPM-PQTKEHILLAKQ---VGVPNIVVFLNKEDQVD  142 (409)
T ss_pred             HHhCCEEEEEEECCCCCc-HHHHHHHHHHHH---cCCCEEEEEEEccCCCC
Confidence            356899999999875321 222223333333   3467 778999999864

>PLN03126 Elongation factor Tu; Provisional

Probab=94.69  E-value=0.15  Score=33.56  Aligned_cols=45  Identities=16%  Similarity=0.152  Sum_probs=29.1

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      ..+|++++|.|..+-.. .....++..+...   .+| ++++.||+|+.+
T Consensus       166 ~~aD~ailVVda~~G~~-~qt~e~~~~~~~~---gi~~iIvvvNK~Dl~~  211 (478)
T PLN03126        166 AQMDGAILVVSGADGPM-PQTKEHILLAKQV---GVPNMVVFLNKQDQVD  211 (478)
T ss_pred             hhCCEEEEEEECCCCCc-HHHHHHHHHHHHc---CCCeEEEEEecccccC
Confidence            46799999999875422 2223333334333   467 788999999854

>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional

Probab=94.64  E-value=0.12  Score=33.97  Aligned_cols=47  Identities=17%  Similarity=-0.048  Sum_probs=27.7

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+.+|++++|.|.+....=....+| ..+...  ...|++++.||+|+..
T Consensus       128 l~~aD~allVVDa~~G~~~qt~~~~-~l~~~l--g~~~iIvvvNKiD~~~  174 (474)
T PRK05124        128 ASTCDLAILLIDARKGVLDQTRRHS-FIATLL--GIKHLVVAVNKMDLVD  174 (474)
T ss_pred             HhhCCEEEEEEECCCCccccchHHH-HHHHHh--CCCceEEEEEeecccc
Confidence            3678999999998653211111122 112222  1246889999999864

>PTZ00416 elongation factor 2; Provisional

Probab=94.58  E-value=0.075  Score=37.11  Aligned_cols=45  Identities=24%  Similarity=0.234  Sum_probs=30.6

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      .+.+|++++|.|..+--.-..-..| ..+..   .+.|++++.||+|+.
T Consensus       113 l~~~D~ailVvda~~g~~~~t~~~~-~~~~~---~~~p~iv~iNK~D~~  157 (836)
T PTZ00416        113 LRVTDGALVVVDCVEGVCVQTETVL-RQALQ---ERIRPVLFINKVDRA  157 (836)
T ss_pred             HhcCCeEEEEEECCCCcCccHHHHH-HHHHH---cCCCEEEEEEChhhh
Confidence            4679999999998774322222223 33333   358999999999985

>PRK00007 elongation factor G; Reviewed

Probab=94.48  E-value=0.14  Score=35.04  Aligned_cols=46  Identities=20%  Similarity=0.256  Sum_probs=30.7

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+.+|++++|.|...--.-.....| ..+..   ...|++++.||+|+..
T Consensus        96 l~~~D~~vlVvda~~g~~~qt~~~~-~~~~~---~~~p~iv~vNK~D~~~  141 (693)
T PRK00007         96 LRVLDGAVAVFDAVGGVEPQSETVW-RQADK---YKVPRIAFVNKMDRTG  141 (693)
T ss_pred             HHHcCEEEEEEECCCCcchhhHHHH-HHHHH---cCCCEEEEEECCCCCC
Confidence            4678999999997654333332323 23333   3478899999999875

>PF14331 ImcF-related_N: ImcF-related N-terminal domain

Probab=94.44  E-value=0.18  Score=30.70  Aligned_cols=48  Identities=21%  Similarity=0.312  Sum_probs=31.9

Q ss_pred             CCCEEEEEEECCChh-------hHHH----HHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            9 GALGALLVYDVTKST-------TFEN----VSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~-------s~~~----~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      -.+|+|++.|+.+.-       .+..    ++.-+.++.+..+..+|+.++-+|+|+-.
T Consensus        25 PlnGvil~vs~~~Ll~~~~~~r~l~~~a~~lR~rL~el~~~lg~~~PVYvv~Tk~D~l~   83 (266)
T PF14331_consen   25 PLNGVILTVSVDDLLNADEAERELEALARALRQRLEELQRTLGVRLPVYVVFTKCDLLP   83 (266)
T ss_pred             CCCEEEEEEEHHHHhcCChhhhHHHHHHHHHHHHHHHHHHHhCCCCCeEeeeECCCccc
Confidence            359999999987421       2222    23334444444457899999999999843

>PF00350 Dynamin_N: Dynamin family; InterPro: IPR001401 Membrane transport between compartments in eukaryotic cells requires proteins that allow the budding and scission of nascent cargo vesicles from one compartment and their targeting and fusion with another

Probab=94.32  E-value=0.15  Score=28.12  Aligned_cols=47  Identities=19%  Similarity=0.167  Sum_probs=30.5

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCC
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKS   52 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~   52 (72)
                      +..|+..+|++++|.+.+..-+-.....+.+.....   ...+++|-||.
T Consensus       122 ~~~~~~~~d~vi~V~~~~~~~~~~~~~~l~~~~~~~---~~~~i~V~nk~  168 (168)
T PF00350_consen  122 TEEYLPKADVVIFVVDANQDLTESDMEFLKQMLDPD---KSRTIFVLNKA  168 (168)
T ss_dssp             HHHHHSTTEEEEEEEETTSTGGGHHHHHHHHHHTTT---CSSEEEEEE-G
T ss_pred             HHHhhccCCEEEEEeccCcccchHHHHHHHHHhcCC---CCeEEEEEcCC
Confidence            457889999999999998865544444444444332   23378888874

Dynamins are large GTPases that belong to a protein superfamily [] that, in eukaryotic cells, includes classical dynamins, dynamin-like proteins, OPA1, Mx proteins, mitofusins and guanylate-binding proteins/atlastins [, , , ], and are involved in the scission of a wide range of vesicles and organelles. They play a role in many processes including budding of transport vesicles, division of organelles, cytokinesis and pathogen resistance. The minimal distinguishing architectural features that are common to all dynamins and are distinct from other GTPases are the structure of the large GTPase domain (300 amino acids) and the presence of two additional domains; the middle domain and the GTPase effector domain (GED), which are involved in oligomerization and regulation of the GTPase activity. This entry represents the GTPase domain, containing the GTP-binding motifs that are needed for guanine-nucleotide binding and hydrolysis. The conservation of these motifs is absolute except for the the final motif in guanylate-binding proteins. The GTPase catalytic activity can be stimulated by oligomerisation of the protein, which is mediated by interactions between the GTPase domain, the middle domain and the GED.; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1JWY_B 1JX2_B 3ZVR_A 2AKA_B 3L43_B 2X2F_D 2X2E_D 3SNH_A 3ZYS_D 3ZYC_D ....

>COG1159 Era GTPase [General function prediction only]

Probab=94.31  E-value=0.19  Score=31.28  Aligned_cols=49  Identities=18%  Similarity=0.121  Sum_probs=32.3

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      .-+.++|.+++|.|.+..-.-. -...++.++.   .+.|++++.||+|....
T Consensus        81 ~sl~dvDlilfvvd~~~~~~~~-d~~il~~lk~---~~~pvil~iNKID~~~~  129 (298)
T COG1159          81 SALKDVDLILFVVDADEGWGPG-DEFILEQLKK---TKTPVILVVNKIDKVKP  129 (298)
T ss_pred             HHhccCcEEEEEEeccccCCcc-HHHHHHHHhh---cCCCeEEEEEccccCCc
Confidence            3467899999999988743211 1122333333   46899999999997553

>PLN00116 translation elongation factor EF-2 subunit; Provisional

Probab=94.07  E-value=0.14  Score=35.90  Aligned_cols=45  Identities=27%  Similarity=0.203  Sum_probs=30.7

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      .+.+|++++|.|...--.-.....|. .+.   ..++|++++.||+|+.
T Consensus       119 l~~~D~ailVvda~~Gv~~~t~~~~~-~~~---~~~~p~i~~iNK~D~~  163 (843)
T PLN00116        119 LRITDGALVVVDCIEGVCVQTETVLR-QAL---GERIRPVLTVNKMDRC  163 (843)
T ss_pred             HhhcCEEEEEEECCCCCcccHHHHHH-HHH---HCCCCEEEEEECCccc
Confidence            46789999999987643333223332 232   2468999999999986

>PLN03127 Elongation factor Tu; Provisional

Probab=93.91  E-value=0.25  Score=32.25  Aligned_cols=45  Identities=16%  Similarity=0.200  Sum_probs=28.0

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      ..+|++++|.|.++... ......+..+..   ..+| ++++-||+|+.+
T Consensus       146 ~~aD~allVVda~~g~~-~qt~e~l~~~~~---~gip~iIvviNKiDlv~  191 (447)
T PLN03127        146 AQMDGGILVVSAPDGPM-PQTKEHILLARQ---VGVPSLVVFLNKVDVVD  191 (447)
T ss_pred             hhCCEEEEEEECCCCCc-hhHHHHHHHHHH---cCCCeEEEEEEeeccCC
Confidence            35899999999875321 112222223332   3477 578899999864

>TIGR03348 VI_IcmF type VI secretion protein IcmF

Probab=93.89  E-value=0.11  Score=37.61  Aligned_cols=47  Identities=21%  Similarity=0.352  Sum_probs=35.2

Q ss_pred             CCCEEEEEEECCChhh-----H----HHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            9 GALGALLVYDVTKSTT-----F----ENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s-----~----~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      -.||+|++.|+.+.-.     .    ..++..+.++.+..+-.+|+.++.+|+|+-
T Consensus       201 plnGvil~vs~~~Ll~~~~~~~~~~a~~lR~rl~el~~~lg~~~PVYvv~Tk~Dll  256 (1169)
T TIGR03348       201 PLNGVVVTVSLADLLTADPAERKAHARAIRQRLQELREQLGARFPVYLVLTKADLL  256 (1169)
T ss_pred             CCCeEEEEEEHHHHhCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCEEEEEecchhh
Confidence            4799999999876421     1    345666677766666789999999999974

Members of this protein family are IcmF homologs and tend to be associated with type VI secretion systems.

>COG1162 Predicted GTPases [General function prediction only]

Probab=93.79  E-value=0.54  Score=29.42  Aligned_cols=47  Identities=19%  Similarity=0.173  Sum_probs=31.5

Q ss_pred             hCCCEEEEEEECCChh-hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            8 RGALGALLVYDVTKST-TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      .+.|-.+++++..+|+ +...+..++-.+..   .++.-+++-||+||.++
T Consensus        78 ~n~d~~iiIvs~~~P~~~~~~ldR~Lv~ae~---~gi~pvIvlnK~DL~~~  125 (301)
T COG1162          78 ANNDQAIIVVSLVDPDFNTNLLDRYLVLAEA---GGIEPVIVLNKIDLLDD  125 (301)
T ss_pred             cccceEEEEEeccCCCCCHHHHHHHHHHHHH---cCCcEEEEEEccccCcc
Confidence            3466667777777776 67777666544433   34555777999999763

>PRK00049 elongation factor Tu; Reviewed

Probab=93.75  E-value=0.29  Score=31.34  Aligned_cols=46  Identities=17%  Similarity=0.191  Sum_probs=29.2

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEE-EEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIM-LIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~v-lvgnK~Dl~~   56 (72)
                      ...+|++++|.|...... ......+..+..   ..+|.+ ++.||+|+..
T Consensus        96 ~~~aD~~llVVDa~~g~~-~qt~~~~~~~~~---~g~p~iiVvvNK~D~~~  142 (396)
T PRK00049         96 AAQMDGAILVVSAADGPM-PQTREHILLARQ---VGVPYIVVFLNKCDMVD  142 (396)
T ss_pred             hccCCEEEEEEECCCCCc-hHHHHHHHHHHH---cCCCEEEEEEeecCCcc
Confidence            357899999999876422 222233333433   247765 5899999863

>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional

Probab=93.50  E-value=0.27  Score=33.34  Aligned_cols=47  Identities=21%  Similarity=0.036  Sum_probs=28.2

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ...+|++++|.|.+.... .........+...  ...+++++.||+|+.+
T Consensus       125 ~~~aD~~llVvda~~g~~-~~t~e~~~~~~~~--~~~~iivvvNK~D~~~  171 (632)
T PRK05506        125 ASTADLAIILVDARKGVL-TQTRRHSFIASLL--GIRHVVLAVNKMDLVD  171 (632)
T ss_pred             HHhCCEEEEEEECCCCcc-ccCHHHHHHHHHh--CCCeEEEEEEeccccc
Confidence            457899999999865321 1111111122222  2357889999999864

>KOG0468 consensus U5 snRNP-specific protein [Translation, ribosomal structure and biogenesis]

Probab=93.44  E-value=0.12  Score=35.82  Aligned_cols=45  Identities=27%  Similarity=0.349  Sum_probs=31.7

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCC
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL   54 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl   54 (72)
                      -++-+|++++++|+.+--.++. ...++.   ....+.|+++|.||.|.
T Consensus       217 ~l~~sDgvVlvvDv~EGVmlnt-Er~ikh---aiq~~~~i~vviNKiDR  261 (971)
T KOG0468|consen  217 SLRLSDGVVLVVDVAEGVMLNT-ERIIKH---AIQNRLPIVVVINKVDR  261 (971)
T ss_pred             HhhhcceEEEEEEcccCceeeH-HHHHHH---HHhccCcEEEEEehhHH
Confidence            4677999999999876555543 222222   22367999999999996

>TIGR00101 ureG urease accessory protein UreG

Probab=93.44  E-value=0.18  Score=29.30  Aligned_cols=39  Identities=23%  Similarity=0.168  Sum_probs=24.5

Q ss_pred             CCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889           10 ALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus        10 a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +++++.|+|.++-.+...  .+..++      ...-+++.||+|+..
T Consensus       113 ~~~~i~vvD~~~~~~~~~--~~~~qi------~~ad~~~~~k~d~~~  151 (199)
T TIGR00101       113 ADLTIFVIDVAAGDKIPR--KGGPGI------TRSDLLVINKIDLAP  151 (199)
T ss_pred             hCcEEEEEEcchhhhhhh--hhHhHh------hhccEEEEEhhhccc
Confidence            678999999987665321  111111      122388999999974

This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel.

>KOG1145 consensus Mitochondrial translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]

Probab=93.31  E-value=0.34  Score=32.91  Aligned_cols=41  Identities=22%  Similarity=0.186  Sum_probs=30.9

Q ss_pred             CCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            9 GALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         9 ~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      -+|.+++|...+|   +.+.+.+++       ..+.++|+++.-||+|-++
T Consensus       224 vtDIvVLVVAadDGVmpQT~EaIkh-------Ak~A~VpiVvAinKiDkp~  267 (683)
T KOG1145|consen  224 VTDIVVLVVAADDGVMPQTLEAIKH-------AKSANVPIVVAINKIDKPG  267 (683)
T ss_pred             cccEEEEEEEccCCccHhHHHHHHH-------HHhcCCCEEEEEeccCCCC
Confidence            4688999998876   566665544       2346799999999999764

>KOG1490 consensus GTP-binding protein CRFG/NOG1 (ODN superfamily) [General function prediction only]

Probab=92.96  E-value=0.59  Score=31.52  Aligned_cols=52  Identities=15%  Similarity=0.144  Sum_probs=33.9

Q ss_pred             EEEEEEECCChhh--HHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHH
Q 047889           12 GALLVYDVTKSTT--FENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEE   64 (72)
Q Consensus        12 ~~i~v~d~~~~~s--~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e   64 (72)
                      +|+++-|++..-.  ...=-..+..++... .+-|.++|.||+|+-....++.+.
T Consensus       250 aVLYfmDLSe~CGySva~QvkLfhsIKpLF-aNK~~IlvlNK~D~m~~edL~~~~  303 (620)
T KOG1490|consen  250 AVLYFMDLSEMCGYSVAAQVKLYHSIKPLF-ANKVTILVLNKIDAMRPEDLDQKN  303 (620)
T ss_pred             hheeeeechhhhCCCHHHHHHHHHHhHHHh-cCCceEEEeecccccCccccCHHH
Confidence            4777888887653  333233444554443 678999999999986655555443

>PRK07560 elongation factor EF-2; Reviewed

Probab=92.93  E-value=0.27  Score=33.88  Aligned_cols=46  Identities=20%  Similarity=0.139  Sum_probs=29.6

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      ..+.+|++++|.|...--.-..-..|. .+...   ..|.+++.||+|+.
T Consensus       107 ~l~~~D~avlVvda~~g~~~~t~~~~~-~~~~~---~~~~iv~iNK~D~~  152 (731)
T PRK07560        107 AMRAVDGAIVVVDAVEGVMPQTETVLR-QALRE---RVKPVLFINKVDRL  152 (731)
T ss_pred             HHHhcCEEEEEEECCCCCCccHHHHHH-HHHHc---CCCeEEEEECchhh
Confidence            467899999999977643322223332 22222   35778999999975

>smart00053 DYNc Dynamin, GTPase

Probab=92.82  E-value=0.52  Score=28.45  Aligned_cols=50  Identities=10%  Similarity=-0.009  Sum_probs=28.9

Q ss_pred             ccchhhCC-CEEEEEEECCC-hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGA-LGALLVYDVTK-STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a-~~~i~v~d~~~-~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ...|+++. +.+++|.|.+. .... .....   ++...+...|+++|.||.|..+
T Consensus       155 v~~yi~~~~~IIL~Vvda~~d~~~~-d~l~i---a~~ld~~~~rti~ViTK~D~~~  206 (240)
T smart00053      155 IKQFISKEECLILAVTPANVDLANS-DALKL---AKEVDPQGERTIGVITKLDLMD  206 (240)
T ss_pred             HHHHHhCccCeEEEEEECCCCCCch-hHHHH---HHHHHHcCCcEEEEEECCCCCC
Confidence            45677755 46777776543 2211 11122   2222235689999999999864

Large GTPases that mediate vesicle trafficking. Dynamin participates in the endocytic uptake of receptors, associated ligands, and plasma membrane following an exocytic event.

>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]

Probab=92.72  E-value=0.12  Score=32.76  Aligned_cols=46  Identities=28%  Similarity=0.244  Sum_probs=31.9

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..||++++++|.++....-+ ++.+..+..+  ..+|-+||.||.|...
T Consensus       154 q~AD~vvVv~Das~tr~~l~-p~vl~~l~~y--s~ips~lvmnkid~~k  199 (379)
T KOG1423|consen  154 QNADCVVVVVDASATRTPLH-PRVLHMLEEY--SKIPSILVMNKIDKLK  199 (379)
T ss_pred             hhCCEEEEEEeccCCcCccC-hHHHHHHHHH--hcCCceeeccchhcch
Confidence            46899999999997443222 2333445544  4688999999999754

>COG1160 Predicted GTPases [General function prediction only]

Probab=92.50  E-value=1.1  Score=29.47  Aligned_cols=57  Identities=23%  Similarity=0.181  Sum_probs=37.2

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHH
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLI   67 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~   67 (72)
                      ...++.+++|.|.+.+-+-...+ ....+.+   ...++++|-||-|+-++...+.++.++
T Consensus       258 I~~a~vvllviDa~~~~~~qD~~-ia~~i~~---~g~~~vIvvNKWDl~~~~~~~~~~~k~  314 (444)
T COG1160         258 IERADVVLLVIDATEGISEQDLR-IAGLIEE---AGRGIVIVVNKWDLVEEDEATMEEFKK  314 (444)
T ss_pred             HhhcCEEEEEEECCCCchHHHHH-HHHHHHH---cCCCeEEEEEccccCCchhhHHHHHHH
Confidence            34689999999998875533321 2222332   457889999999987655455555443

>cd01882 BMS1 Bms1

Probab=92.50  E-value=0.57  Score=27.68  Aligned_cols=46  Identities=22%  Similarity=0.133  Sum_probs=28.0

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      .+.+|.++++.|.+....... ...+..+..   ...| +++|.||.|+..
T Consensus       101 ak~aDvVllviDa~~~~~~~~-~~i~~~l~~---~g~p~vi~VvnK~D~~~  147 (225)
T cd01882         101 AKVADLVLLLIDASFGFEMET-FEFLNILQV---HGFPRVMGVLTHLDLFK  147 (225)
T ss_pred             HHhcCEEEEEEecCcCCCHHH-HHHHHHHHH---cCCCeEEEEEeccccCC
Confidence            457899999999875433222 222333332   2356 455999999853

Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes.

>KOG0462 consensus Elongation factor-type GTP-binding protein [Translation, ribosomal structure and biogenesis]

Probab=92.17  E-value=0.87  Score=31.02  Aligned_cols=48  Identities=25%  Similarity=0.322  Sum_probs=30.2

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      +.-++|++++.|-..--.-+.+..++.-+    ..+..+|.|-||+|++..+
T Consensus       146 laac~G~lLvVDA~qGvqAQT~anf~lAf----e~~L~iIpVlNKIDlp~ad  193 (650)
T KOG0462|consen  146 LAACDGALLVVDASQGVQAQTVANFYLAF----EAGLAIIPVLNKIDLPSAD  193 (650)
T ss_pred             hhhcCceEEEEEcCcCchHHHHHHHHHHH----HcCCeEEEeeeccCCCCCC
Confidence            34589999999977532222222222222    1457788999999998754

>PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional

Probab=92.15  E-value=0.65  Score=30.58  Aligned_cols=46  Identities=20%  Similarity=0.128  Sum_probs=27.6

Q ss_pred             hCCCEEEEEEECCChh-hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKST-TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+|++++|.|.++.. .-....++ ..+...  .-.+++++-||+|+.+
T Consensus       139 ~~~D~alLVVda~~g~~~~qT~ehl-~i~~~l--gi~~iIVvlNKiDlv~  185 (460)
T PTZ00327        139 AVMDAALLLIAANESCPQPQTSEHL-AAVEIM--KLKHIIILQNKIDLVK  185 (460)
T ss_pred             hhCCEEEEEEECCCCccchhhHHHH-HHHHHc--CCCcEEEEEecccccC
Confidence            3579999999998631 11111222 222222  2246889999999864

>cd02038 FleN-like FleN is a member of the Fer4_NifH superfamily

Probab=91.30  E-value=1.4  Score=24.00  Aligned_cols=49  Identities=12%  Similarity=0.217  Sum_probs=32.9

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      ..+..+|.++++.+.+ ..++......++.+.+.. ...++.++.|+.+-.
T Consensus        62 ~~l~~aD~vviv~~~~-~~s~~~~~~~l~~l~~~~-~~~~~~lVvN~~~~~  110 (139)
T cd02038          62 DFFLAADEVIVVTTPE-PTSITDAYALIKKLAKQL-RVLNFRVVVNRAESP  110 (139)
T ss_pred             HHHHhCCeEEEEcCCC-hhHHHHHHHHHHHHHHhc-CCCCEEEEEeCCCCH
Confidence            3466789988887764 566666655555665433 445677899999743

It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by influencing FleQ activity.

>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure

Probab=90.77  E-value=1.1  Score=23.83  Aligned_cols=40  Identities=13%  Similarity=0.355  Sum_probs=27.2

Q ss_pred             CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCC
Q 047889            9 GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKS   52 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~   52 (72)
                      +..|+++-||   .+..+.....++.++... .++|+++++++-
T Consensus        38 ~i~avvi~~d---~~~~~~~~~ll~~i~~~~-~~iPVFl~~~~~   77 (115)
T PF03709_consen   38 DIAAVVISWD---GEEEDEAQELLDKIRERN-FGIPVFLLAERD   77 (115)
T ss_dssp             TEEEEEEECH---HHHHHHHHHHHHHHHHHS-TT-EEEEEESCC
T ss_pred             CeeEEEEEcc---cccchhHHHHHHHHHHhC-CCCCEEEEecCC
Confidence            3445555555   555666677888887765 889999999855

Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.

>PF11111 CENP-M: Centromere protein M (CENP-M); InterPro: IPR020987 The prime candidate for specifying centromere identity is the array of nucleosomes assembles associated with CENP-A []

Probab=90.55  E-value=2.2  Score=24.79  Aligned_cols=62  Identities=6%  Similarity=-0.014  Sum_probs=40.9

Q ss_pred             CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            9 GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ..|-++++.|+++..||..++.=+..+....--.. ++++++-....+...+...+..++|.+
T Consensus        64 rIDlIVFvinl~sk~SL~~ve~SL~~vd~~fflGK-VCfl~t~a~~~~~~sv~~~~V~kla~~  125 (176)
T PF11111_consen   64 RIDLIVFVINLHSKYSLQSVEASLSHVDPSFFLGK-VCFLATNAGRESHCSVHPNEVRKLAAT  125 (176)
T ss_pred             eeEEEEEEEecCCcccHHHHHHHHhhCChhhhccc-eEEEEcCCCcccccccCHHHHHHHHHH
Confidence            35889999999999999988665444432211112 344445555455568888888888764

CENP-A recruits a nucleosome associated complex (CENP-A-NAC complex) comprised of CENP-M which this entry represents, along with two other proteins []. Assembly of the CENP-A NAC at centromeres is partly dependent on CENP-M. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival [].

>COG4963 CpaE Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]

Probab=90.40  E-value=1.5  Score=28.28  Aligned_cols=52  Identities=15%  Similarity=0.217  Sum_probs=43.4

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      +..+..++|.+++|.+. +-.++.+.++.++.+++...++.+..++.||.+-+
T Consensus       233 t~~vL~~Sd~iviv~e~-sl~slR~ak~lld~l~~~r~~~~~p~lv~n~~~~~  284 (366)
T COG4963         233 TRQVLSGSDEIVIVAEP-SLASLRNAKELLDELKRLRPNDPKPILVLNRVGVP  284 (366)
T ss_pred             HHHHHhcCCeEEEEecc-cHHHHHHHHHHHHHHHHhCCCCCCceEEeeecCCC
Confidence            35677899999999986 46788888899999998887888889999999864

>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]

Probab=90.36  E-value=2.8  Score=26.14  Aligned_cols=45  Identities=24%  Similarity=0.264  Sum_probs=34.2

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      ..++|.+++|--.| +..+.+++..++.....   ++|..+|-||.++.
T Consensus       183 l~~aD~ai~VTEPT-p~glhD~kr~~el~~~f---~ip~~iViNr~~~g  227 (284)
T COG1149         183 LKGADLAILVTEPT-PFGLHDLKRALELVEHF---GIPTGIVINRYNLG  227 (284)
T ss_pred             hccCCEEEEEecCC-ccchhHHHHHHHHHHHh---CCceEEEEecCCCC
Confidence            56889999886554 66778887777666654   49999999999654

>COG1161 Predicted GTPases [General function prediction only]

Probab=90.07  E-value=0.4  Score=30.02  Aligned_cols=45  Identities=20%  Similarity=0.159  Sum_probs=30.9

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ....+|.++-|.|.-++.+...     ..+.+.. ...|.++|.||+||..
T Consensus        31 ~~~~~d~vvevvDar~P~~s~~-----~~l~~~v-~~k~~i~vlNK~DL~~   75 (322)
T COG1161          31 VLKSVDVVVEVVDARDPLGTRN-----PELERIV-KEKPKLLVLNKADLAP   75 (322)
T ss_pred             hcccCCEEEEEEeccccccccC-----ccHHHHH-ccCCcEEEEehhhcCC
Confidence            4456899999999999876443     2233333 2344499999999965

>KOG2484 consensus GTPase [General function prediction only]

Probab=89.41  E-value=1.3  Score=28.95  Aligned_cols=44  Identities=25%  Similarity=0.153  Sum_probs=30.7

Q ss_pred             CCCEEEEEEECCChhhHHH--HHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            9 GALGALLVYDVTKSTTFEN--VSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+|.+|-|.|--||.+-..  +..|.   .+ .+++-..|+|-||.||..
T Consensus       146 ~sDVVleVlDARDPlgtR~~~vE~~V---~~-~~gnKkLILVLNK~DLVP  191 (435)
T KOG2484|consen  146 ASDVVLEVLDARDPLGTRCPEVEEAV---LQ-AHGNKKLILVLNKIDLVP  191 (435)
T ss_pred             hhheEEEeeeccCCCCCCChhHHHHH---Hh-ccCCceEEEEeehhccCC
Confidence            5799999999999976443  23332   11 224577899999999843

>cd02067 B12-binding B12 binding domain (B12-BD)

Probab=89.28  E-value=1.6  Score=22.96  Aligned_cols=40  Identities=10%  Similarity=0.137  Sum_probs=27.9

Q ss_pred             EEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCC
Q 047889           13 ALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKS   52 (72)
Q Consensus        13 ~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~   52 (72)
                      -+++++.++...+..+..+.+.+++....++++++-|+-.
T Consensus        52 dvV~iS~~~~~~~~~~~~~i~~l~~~~~~~~~i~vGG~~~   91 (119)
T cd02067          52 DAIGLSGLLTTHMTLMKEVIEELKEAGLDDIPVLVGGAIV   91 (119)
T ss_pred             CEEEEeccccccHHHHHHHHHHHHHcCCCCCeEEEECCCC
Confidence            3555566677788899999999988743267766666543

This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.

>KOG3929 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.02  E-value=2.9  Score=26.26  Aligned_cols=14  Identities=21%  Similarity=0.548  Sum_probs=12.1

Q ss_pred             CCeEEEEeeCCCCc
Q 047889           42 NIVIMLIGNKSDLK   55 (72)
Q Consensus        42 ~~~~vlvgnK~Dl~   55 (72)
                      .+|+++||.|.|--
T Consensus       190 P~PV~IVgsKYDvF  203 (363)
T KOG3929|consen  190 PVPVVIVGSKYDVF  203 (363)
T ss_pred             CCceEEeccchhhh
Confidence            48899999999964

>COG0480 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]

Probab=88.67  E-value=0.84  Score=31.65  Aligned_cols=46  Identities=22%  Similarity=0.219  Sum_probs=30.5

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .|-.||+++|+|...--....-.-|. ++.   ..++|.+++-||+|...
T Consensus        97 lrvlDgavvVvdaveGV~~QTEtv~r-qa~---~~~vp~i~fiNKmDR~~  142 (697)
T COG0480          97 LRVLDGAVVVVDAVEGVEPQTETVWR-QAD---KYGVPRILFVNKMDRLG  142 (697)
T ss_pred             HHhhcceEEEEECCCCeeecHHHHHH-HHh---hcCCCeEEEEECccccc
Confidence            45679999999987643333223332 232   35699999999999743

>KOG1191 consensus Mitochondrial GTPase [Translation, ribosomal structure and biogenesis]

Probab=88.56  E-value=0.7  Score=30.90  Aligned_cols=51  Identities=27%  Similarity=0.205  Sum_probs=31.4

Q ss_pred             hhCCCEEEEEEEC--CChhhHHHHHHHHHHHHHhc------CCCCeEEEEeeCCCCccc
Q 047889            7 YRGALGALLVYDV--TKSTTFENVSRWLKDLRDHA------GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         7 ~~~a~~~i~v~d~--~~~~s~~~~~~~~~~~~~~~------~~~~~~vlvgnK~Dl~~~   57 (72)
                      .+.||.+++|+|.  ++-++-..+...++......      ...-|++++.||.|+..+
T Consensus       346 ~~~advi~~vvda~~~~t~sd~~i~~~l~~~~~g~~~~~~~~~~~~~i~~~nk~D~~s~  404 (531)
T KOG1191|consen  346 IERADVILLVVDAEESDTESDLKIARILETEGVGLVVIVNKMEKQRIILVANKSDLVSK  404 (531)
T ss_pred             HhhcCEEEEEecccccccccchHHHHHHHHhccceEEEeccccccceEEEechhhccCc
Confidence            4578999999998  44444333333333322111      134789999999999664

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=88.39  E-value=0.35  Score=28.04  Aligned_cols=15  Identities=27%  Similarity=0.299  Sum_probs=12.4

Q ss_pred             CeEEEEeeCCCCccc
Q 047889           43 IVIMLIGNKSDLKHL   57 (72)
Q Consensus        43 ~~~vlvgnK~Dl~~~   57 (72)
                      .|.+++.||.|+.+.
T Consensus       149 ~a~iiv~NK~Dl~~~  163 (207)
T TIGR00073       149 EADLIVINKADLAEA  163 (207)
T ss_pred             hCCEEEEEHHHcccc
Confidence            567999999999653

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>KOG1424 consensus Predicted GTP-binding protein MMR1 [General function prediction only]

Probab=88.28  E-value=1.6  Score=29.45  Aligned_cols=46  Identities=15%  Similarity=0.148  Sum_probs=30.9

Q ss_pred             CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            9 GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+|.++.+.|.-+|--|.. ......+.+. ++....+|+-||.||-.
T Consensus       174 rSDivvqIVDARnPllfr~-~dLe~Yvke~-d~~K~~~LLvNKaDLl~  219 (562)
T KOG1424|consen  174 RSDIVVQIVDARNPLLFRS-PDLEDYVKEV-DPSKANVLLVNKADLLP  219 (562)
T ss_pred             hcceEEEEeecCCccccCC-hhHHHHHhcc-ccccceEEEEehhhcCC
Confidence            5799999999998866543 2222223322 24466789999999854

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=87.91  E-value=3.9  Score=25.07  Aligned_cols=46  Identities=17%  Similarity=0.140  Sum_probs=29.6

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      -+++|.++.|.|.+ .+|+....+..+...+.  .--++.+|.||.|-.
T Consensus       153 ~~~vD~vivVvDpS-~~sl~taeri~~L~~el--g~k~i~~V~NKv~e~  198 (255)
T COG3640         153 IEGVDLVIVVVDPS-YKSLRTAERIKELAEEL--GIKRIFVVLNKVDEE  198 (255)
T ss_pred             ccCCCEEEEEeCCc-HHHHHHHHHHHHHHHHh--CCceEEEEEeeccch
Confidence            45789999999865 44555444433333322  236799999999854

>KOG1954 consensus Endocytosis/signaling protein EHD1 [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=87.27  E-value=2.7  Score=27.71  Aligned_cols=48  Identities=21%  Similarity=0.297  Sum_probs=29.6

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      |-..+|.++++||....+--......++.++   +..-.+-+|-||.|..+
T Consensus       178 FaeR~D~IiLlfD~hKLDIsdEf~~vi~aLk---G~EdkiRVVLNKADqVd  225 (532)
T KOG1954|consen  178 FAERVDRIILLFDAHKLDISDEFKRVIDALK---GHEDKIRVVLNKADQVD  225 (532)
T ss_pred             HHHhccEEEEEechhhccccHHHHHHHHHhh---CCcceeEEEeccccccC
Confidence            3456899999999765543333333333443   34455667779999643

>cd03111 CpaE_like This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster

Probab=86.78  E-value=3  Score=21.62  Aligned_cols=45  Identities=27%  Similarity=0.169  Sum_probs=31.4

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCC-CCeEEEEeeC
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNK   51 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~-~~~~vlvgnK   51 (72)
                      .+..+|.++++.+ .+..++..+..+.+.+++...+ ...+.+|.|+
T Consensus        61 ~l~~aD~vlvvv~-~~~~s~~~~~~~~~~l~~~~~~~~~~~~lVvNr  106 (106)
T cd03111          61 ALDQADRVFLVTQ-QDLPSIRNAKRLLELLRVLDYSLPAKIELVLNR  106 (106)
T ss_pred             HHHHcCeEEEEec-CChHHHHHHHHHHHHHHHcCCCCcCceEEEecC
Confidence            4567888888775 4577888888888877765433 4556677775

The function of these proteins are unkown. The Caulobacter pilus assembly contains 7 genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF. These genes are clustered together on chromosome.

>COG0218 Predicted GTPase [General function prediction only]

Probab=86.62  E-value=3.5  Score=24.44  Aligned_cols=43  Identities=16%  Similarity=0.195  Sum_probs=25.5

Q ss_pred             CCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889           10 ALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus        10 a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      -.+++++.|.-.+..-.+. ..++.+..   .++|++++.||+|--.
T Consensus       107 L~~vvlliD~r~~~~~~D~-em~~~l~~---~~i~~~vv~tK~DKi~  149 (200)
T COG0218         107 LKGVVLLIDARHPPKDLDR-EMIEFLLE---LGIPVIVVLTKADKLK  149 (200)
T ss_pred             heEEEEEEECCCCCcHHHH-HHHHHHHH---cCCCeEEEEEccccCC
Confidence            3566777776544332221 22233333   5699999999999643

>KOG0447 consensus Dynamin-like GTP binding protein [General function prediction only]

Probab=86.15  E-value=2.9  Score=28.97  Aligned_cols=64  Identities=14%  Similarity=0.093  Sum_probs=40.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~   68 (72)
                      |...|+.+.+++|+|..=.+   .+.-+.-...+-... +.....++|.+|.||.++...++...+++
T Consensus       441 msKayM~NPNAIILCIQDGS---VDAERSnVTDLVsq~DP~GrRTIfVLTKVDlAEknlA~PdRI~kI  505 (980)
T KOG0447|consen  441 ISKAYMQNPNAIILCIQDGS---VDAERSIVTDLVSQMDPHGRRTIFVLTKVDLAEKNVASPSRIQQI  505 (980)
T ss_pred             HHHHHhcCCCeEEEEeccCC---cchhhhhHHHHHHhcCCCCCeeEEEEeecchhhhccCCHHHHHHH
Confidence            56789999999999974322   222222223332222 34566789999999988766666655543

>PRK13505 formate--tetrahydrofolate ligase; Provisional

Probab=85.77  E-value=2.7  Score=28.56  Aligned_cols=41  Identities=15%  Similarity=0.160  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889           25 FENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      |.++.+-++.++.   -.+|++++-||.|...+.+  .+..+++|+
T Consensus       358 l~NL~RHIenvr~---FGvPvVVAINKFd~DTe~E--i~~I~~~c~  398 (557)
T PRK13505        358 FANLERHIENIRK---FGVPVVVAINKFVTDTDAE--IAALKELCE  398 (557)
T ss_pred             HHHHHHHHHHHHH---cCCCEEEEEeCCCCCCHHH--HHHHHHHHH
Confidence            3444444444443   3699999999999875322  233444544

>COG1010 CobJ Precorrin-3B methylase [Coenzyme metabolism]

Probab=85.69  E-value=4.1  Score=24.88  Aligned_cols=45  Identities=18%  Similarity=0.236  Sum_probs=35.7

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCC
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKS   52 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~   52 (72)
                      ..+|-++..|+.-++..=+++..-++-+.++.+++.|+.++-|--
T Consensus       153 A~adfVi~~YNP~s~~R~~~~~~a~eil~~~r~~~tpVgivrnag  197 (249)
T COG1010         153 AEADFVIALYNPISKRRPEQLGRAFEILREHRSPDTPVGIVRNAG  197 (249)
T ss_pred             hhCCEEEEEECCccccchHHHHHHHHHHHHhcCCCCcEEEEecCC
Confidence            357889999998887766677777778888888899998886644

>COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]

Probab=85.37  E-value=0.85  Score=29.00  Aligned_cols=42  Identities=29%  Similarity=0.271  Sum_probs=26.4

Q ss_pred             CCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCccc
Q 047889            9 GALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKHL   57 (72)
Q Consensus         9 ~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~~   57 (72)
                      +.|+.|+|.+-++   |.+-+++.    ..++   -.+| ++++-||+|+.++
T Consensus        98 qmDgAILVVsA~dGpmPqTrEHiL----larq---vGvp~ivvflnK~Dmvdd  143 (394)
T COG0050          98 QMDGAILVVAATDGPMPQTREHIL----LARQ---VGVPYIVVFLNKVDMVDD  143 (394)
T ss_pred             hcCccEEEEEcCCCCCCcchhhhh----hhhh---cCCcEEEEEEecccccCc
Confidence            3589999998887   33333321    1122   3465 6777899999764

>COG3523 IcmF Type VI protein secretion system component VasK [Intracellular trafficking, secretion, and vesicular transport]

Probab=85.19  E-value=2.4  Score=31.32  Aligned_cols=48  Identities=23%  Similarity=0.313  Sum_probs=33.5

Q ss_pred             CCCEEEEEEECCChhh---------HHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            9 GALGALLVYDVTKSTT---------FENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s---------~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      --||+|+..|+.+.-+         ...++.-+.++.+.-.-..|+.|+.||.|+-.
T Consensus       214 piNGiiltlsv~~L~~~~~~~~~~~~~~LR~RL~El~~tL~~~~PVYl~lTk~Dll~  270 (1188)
T COG3523         214 PLNGIILTLSVSDLLTADPAEREALARTLRARLQELRETLHARLPVYLVLTKADLLP  270 (1188)
T ss_pred             CCceEEEEEEHHHHcCCCHHHHHHHHHHHHHHHHHHHHhhccCCceEEEEecccccc
Confidence            4589999998875311         22244445666665567899999999999843

>PTZ00141 elongation factor 1- alpha; Provisional

Probab=83.40  E-value=2.3  Score=27.87  Aligned_cols=46  Identities=20%  Similarity=0.021  Sum_probs=27.1

Q ss_pred             hhCCCEEEEEEECCChh---hH---HHHHHHHHHHHHhcCCCCe-EEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKST---TF---ENVSRWLKDLRDHAGSNIV-IMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~---s~---~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~   55 (72)
                      ...+|++++|.|.+.-.   .|   ...+..+..+..   -.+| ++++-||+|+.
T Consensus       106 ~~~aD~ailVVda~~G~~e~~~~~~~qT~eh~~~~~~---~gi~~iiv~vNKmD~~  158 (446)
T PTZ00141        106 TSQADVAILVVASTAGEFEAGISKDGQTREHALLAFT---LGVKQMIVCINKMDDK  158 (446)
T ss_pred             hhhcCEEEEEEEcCCCceecccCCCccHHHHHHHHHH---cCCCeEEEEEEccccc
Confidence            35789999999987531   11   122222222332   2455 67899999953

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain

Probab=82.63  E-value=5.6  Score=21.22  Aligned_cols=42  Identities=12%  Similarity=0.011  Sum_probs=27.8

Q ss_pred             CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCC
Q 047889            9 GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKS   52 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~   52 (72)
                      +++.+.+.  ..+..+...++.+.+.+++...+.+++++-|+..
T Consensus        50 ~~d~V~iS--~~~~~~~~~~~~~~~~L~~~~~~~i~i~~GG~~~   91 (122)
T cd02071          50 DVDVIGLS--SLSGGHMTLFPEVIELLRELGAGDILVVGGGIIP   91 (122)
T ss_pred             CCCEEEEc--ccchhhHHHHHHHHHHHHhcCCCCCEEEEECCCC
Confidence            45555554  4467778888999999888754566666665543

This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.

>PF14784 ECIST_Cterm: C-terminal domain of the ECSIT protein

Probab=82.50  E-value=4.8  Score=22.14  Aligned_cols=37  Identities=14%  Similarity=0.435  Sum_probs=25.4

Q ss_pred             CEEEEEEECCChhhHHHHHHHHHHHHHhcC--CCCeEEE
Q 047889           11 LGALLVYDVTKSTTFENVSRWLKDLRDHAG--SNIVIML   47 (72)
Q Consensus        11 ~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~vl   47 (72)
                      ||.|+..-++...+=..+..|+..+++.++  ..+|+++
T Consensus        85 dGti~Amc~tg~~~~~sL~~WI~~Lq~~NP~L~~ipV~F  123 (126)
T PF14784_consen   85 DGTIFAMCMTGTSDKDSLLSWIRGLQETNPNLAQIPVLF  123 (126)
T ss_pred             cceEEEEEeccCCCHHHHHHHHHHHHhhCCchhcceEEE
Confidence            566666656666666667779999988654  4677664

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=82.10  E-value=3.6  Score=24.73  Aligned_cols=45  Identities=18%  Similarity=0.116  Sum_probs=21.3

Q ss_pred             CCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889           10 ALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus        10 a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .-+++++.|...   +..|-..  ++-.+.....-+.|.+.|-||+|+..
T Consensus       123 ~~~~v~LvD~~~~~~~~~f~s~--~L~s~s~~~~~~lP~vnvlsK~Dl~~  170 (238)
T PF03029_consen  123 RLVVVFLVDSSFCSDPSKFVSS--LLLSLSIMLRLELPHVNVLSKIDLLS  170 (238)
T ss_dssp             --EEEEEE-GGG-SSHHHHHHH--HHHHHHHHHHHTSEEEEEE--GGGS-
T ss_pred             ceEEEEEEecccccChhhHHHH--HHHHHHHHhhCCCCEEEeeeccCccc
Confidence            345666766553   3333322  22122111124699999999999976

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=81.98  E-value=4.3  Score=22.73  Aligned_cols=53  Identities=19%  Similarity=0.026  Sum_probs=32.4

Q ss_pred             CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            9 GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      +||.++++.|.+++.+.-.     +.+...  -+.|++=|-+|+|+.. .....+.++++.
T Consensus        63 dad~V~ll~dat~~~~~~p-----P~fa~~--f~~pvIGVITK~Dl~~-~~~~i~~a~~~L  115 (143)
T PF10662_consen   63 DADVVLLLQDATEPRSVFP-----PGFASM--FNKPVIGVITKIDLPS-DDANIERAKKWL  115 (143)
T ss_pred             hCCEEEEEecCCCCCccCC-----chhhcc--cCCCEEEEEECccCcc-chhhHHHHHHHH
Confidence            6899999999988754210     111111  2478899999999983 123344444443

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>COG0481 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]

Probab=81.90  E-value=7.7  Score=26.41  Aligned_cols=46  Identities=28%  Similarity=0.344  Sum_probs=29.2

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +..|.|.+++.|-+.----+.+...+--+    ..+..++-|-||+||+.
T Consensus        97 LAACEGalLvVDAsQGveAQTlAN~YlAl----e~~LeIiPViNKIDLP~  142 (603)
T COG0481          97 LAACEGALLVVDASQGVEAQTLANVYLAL----ENNLEIIPVLNKIDLPA  142 (603)
T ss_pred             HhhCCCcEEEEECccchHHHHHHHHHHHH----HcCcEEEEeeecccCCC
Confidence            44578899999987532222222222222    25678888999999986

>PF08468 MTS_N: Methyltransferase small domain N-terminal; InterPro: IPR013675 This domain is found to the N terminus of the methyltransferase small domain (IPR007848 from INTERPRO) in bacterial proteins []

Probab=81.08  E-value=7.8  Score=21.88  Aligned_cols=41  Identities=17%  Similarity=0.248  Sum_probs=24.9

Q ss_pred             CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCC
Q 047889            9 GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSD   53 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~D   53 (72)
                      ++|.+|+.|--..    .....++..+....+.+.+++|||-|..
T Consensus        69 ~~D~vvly~PKaK----~e~~~lL~~l~~~L~~g~~i~vVGEnk~  109 (155)
T PF08468_consen   69 DFDTVVLYWPKAK----AEAQYLLANLLSHLPPGTEIFVVGENKG  109 (155)
T ss_dssp             T-SEEEEE--SSH----HHHHHHHHHHHTTS-TT-EEEEEEEGGG
T ss_pred             CCCEEEEEccCcH----HHHHHHHHHHHHhCCCCCEEEEEecCcc
Confidence            5788888875433    3455566677766667899999997653

; GO: 0008990 rRNA (guanine-N2-)-methyltransferase activity, 0006364 rRNA processing; PDB: 2PJD_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	72
1oiv_A	191	X-Ray Structure Of The Small G Protein Rab11a In Co		8e-23
1yzk_A	184	Gppnhp Bound Rab11 Gtpase Length = 184		8e-23
2hv8_A	172	Crystal Structure Of Gtp-Bound Rab11 In Complex Wit		8e-23
1oiw_A	191	X-ray Structure Of The Small G Protein Rab11a In Co		9e-23
2f9l_A	199	3d Structure Of Inactive Human Rab11b Gtpase Length		2e-22
3bfk_A	181	Crystal Structure Of Plasmodium Falciparum Rab11a I		2e-22
2d7c_A	167	Crystal Structure Of Human Rab11 In Complex With Fi		5e-22
2gzd_A	173	Crystal Structure Of Rab11 In Complex With Rab11-Fi		5e-22
3cpj_B	223	Crystal Structure Of Ypt31 In Complex With Yeast Ra		7e-18
2oil_A	193	Crystal Structure Of Human Rab25 In Complex With Gd		7e-18
3tso_A	178	Structure Of The Cancer Associated Rab25 Protein In		7e-18
3rwm_B	185	Crystal Structure Of Ypt32 In Complex With Gppnhp L		2e-17
2a5j_A	191	Crystal Structure Of Human Rab2b Length = 191		3e-16
1z0a_A	174	Gdp-Bound Rab2a Gtpase Length = 174		4e-16
2hup_A	201	Crystal Structure Of Human Rab43 In Complex With Gd		2e-14
1z0f_A	179	Gdp-Bound Rab14 Gtpase Length = 179		2e-13
4drz_A	196	Crystal Structure Of Human Rab14 Length = 196		2e-13
2eqb_A	174	Crystal Structure Of The Rab Gtpase Sec4p, The Sec2		5e-13
3cph_A	213	Crystal Structure Of Sec4 In Complex With Rab-Gdi L		6e-13
1g17_A	170	Crystal Structure Of Sec4-Guanosine-5'-(Beta,Gamma)		7e-13
2ocy_C	170	Complex Of The Guanine Exchange Factor Sec2p And Th		3e-12
3qbt_A	174	Crystal Structure Of Ocrl1 540-678 In Complex With		3e-12
2fu5_C	183	Structure Of Rab8 In Complex With Mss4 Length = 183		3e-12
1g16_A	170	Crystal Structure Of Sec4-Gdp Length = 170		4e-12
2o52_A	200	Crystal Structure Of Human Rab4b In Complex With Gd		8e-12
2bmd_A	186	High Resolution Structure Of Gdp-Bound Human Rab4a		1e-11
1yu9_A	175	Gppnhp-Bound Rab4a Length = 175		1e-11
1z0k_A	172	Structure Of Gtp-Bound Rab4q67l Gtpase In Complex W		2e-11
4i1o_A	181	Crystal Structure Of The Legionella Pneumophila Gap		3e-11
3jza_A	175	Crystal Structure Of Human Rab1b In Complex With Th		3e-11
4fmc_B	171	Espg-Rab1 Complex Length = 171		4e-11
3l0i_B	199	Complex Structure Of Sidm/drra With The Wild Type R		4e-11
4fmd_F	164	Espg-Rab1 Complex Structure At 3.05 A Length = 164		4e-11
4fmb_B	171	Vira-Rab1 Complex Structure Length = 171		4e-11
3sfv_A	181	Crystal Structure Of The Gdp-Bound Rab1a S25n Mutan		4e-11
3tkl_A	196	Crystal Structure Of The Gtp-Bound Rab1a In Complex		5e-11
2fol_A	191	Crystal Structure Of Human Rab1a In Complex With Gd		5e-11
1yvd_A	169	Gppnhp-Bound Rab22 Gtpase Length = 169		6e-11
1z0j_A	170	Structure Of Gtp-Bound Rab22q64l Gtpase In Complex		6e-11
4fmc_F	117	Espg-Rab1 Complex Length = 117		7e-11
1z07_A	166	Gppnhp-Bound Rab5c G55q Mutant Gtpase Length = 166		8e-11
1huq_A	164	1.8a Crystal Structure Of The Monomeric Gtpase Rab5		8e-11
1z0d_A	167	Gdp-bound Rab5c Gtpase Length = 167		9e-11
2rhd_A	175	Crystal Structure Of Cryptosporidium Parvum Small G		1e-10
2fg5_A	192	Crystal Structure Of Human Rab31 In Complex With A		1e-10
2bcg_Y	206	Structure Of Doubly Prenylated Ypt1:gdi Complex Len		3e-10
1ukv_Y	206	Structure Of Rabgdp-Dissociation Inhibitor In Compl		3e-10
2efc_B	181	Ara7-GdpATVPS9A Length = 181		3e-10
1tu4_A	171	Crystal Structure Of Rab5-Gdp Complex Length = 171		3e-10
2il1_A	192	Crystal Structure Of A Predicted Human Gtpase In Co		3e-10
1n6i_A	170	Crystal Structure Of Human Rab5a A30p Mutant Comple		4e-10
1n6p_A	170	Crystal Structure Of Human Rab5a A30e Mutant Comple		4e-10
1yzn_A	185	Gppnhp-Bound Ypt1p Gtpase Length = 185		4e-10
1n6h_A	170	Crystal Structure Of Human Rab5a Length = 170		4e-10
1tu3_A	171	Crystal Structure Of Rab5 Complex With Rabaptin5 C-		4e-10
1n6n_A	170	Crystal Structure Of Human Rab5a A30r Mutant Comple		4e-10
3mjh_A	168	Crystal Structure Of Human Rab5a In Complex With Th		4e-10
1n6o_A	170	Crystal Structure Of Human Rab5a A30k Mutant Comple		4e-10
1n6r_A	170	Crystal Structure Of Human Rab5a A30l Mutant Comple		4e-10
2hei_A	179	Crystal Structure Of Human Rab5b In Complex With Gd		5e-10
1d5c_A	162	Crystal Structure Of Plasmodium Falciparum Rab6 Com		5e-10
1yzq_A	170	Gppnhp-Bound Rab6 Gtpase Length = 170		5e-10
4dkx_A	216	Crystal Structure Of The Rab 6a'(Q72l) Length = 216		6e-10
2y8e_A	179	Crystal Structure Of D. Melanogaster Rab6 Gtpase Bo		6e-10
2wwx_A	175	Crystal Structure Of The SidmDRRA(GEFGDF DOMAIN)-Ra		6e-10
2fe4_A	171	The Crystal Structure Of Human Neuronal Rab6b In It		8e-10
3cwz_A	188	Strucure Of Rab6(Gtp)-R6ip1 Complex Length = 188		1e-09
2g6b_A	180	Crystal Structure Of Human Rab26 In Complex With A		1e-09
2gil_A	162	Structure Of The Extremely Slow Gtpase Rab6a In The		1e-09
3bbp_A	211	Rab6-Gtp:gcc185 Rab Binding Domain Complex Length =		1e-09
3dz8_A	191	Crystal Structure Of Human Rab3b Gtpase Bound With		2e-09
1yzu_A	170	Gppnhp-Bound Rab21 Gtpase At 2.50 A Resolution Leng		2e-09
1yzt_A	184	Gppnhp-Bound Rab21 Gtpase At 2.05 A Resolution Leng		3e-09
1z08_A	170	Gppnhp-Bound Rab21 Q53g Mutant Gtpase Length = 170		3e-09
1ek0_A	170	Gppnhp-Bound Ypt51 At 1.48 A Resolution Length = 17		3e-09
3rab_A	169	Gppnhp-bound Rab3a At 2.0 A Resolution Length = 169		4e-09
2gf9_A	189	Crystal Structure Of Human Rab3d In Complex With Gd		5e-09
2p5s_A	199	Rab Domain Of Human Rasef In Complex With Gdp Lengt		2e-08
3tw8_B	181	Gef Domain Of Dennd 1b In Complex With Rab Gtpase R		2e-08
1zbd_A	203	Structural Basis Of Rab Effector Specificity: Cryst		4e-08
3bc1_A	195	Crystal Structure Of The Complex Rab27a-slp2a Lengt		4e-08
1x3s_A	195	Crystal Structure Of Human Rab18 In Complex With Gp		6e-08
2ew1_A	201	Crystal Structure Of Rab30 In Complex With A Gtp An		1e-07
2f7s_A	217	The Crystal Structure Of Human Rab27b Bound To Gdp		1e-07
2if0_A	200	Crystal Structure Of Mouse Rab27b Bound To Gdp In M		2e-07
2iez_A	220	Crystal Structure Of Mouse Rab27b Bound To Gdp In M		2e-07
2hxs_A	178	Crystal Structure Of Rab28a Gtpase In The Inactive		4e-07
4djt_A	218	Crystal Structure Of A Nuclear Gtp-Binding Protein		9e-07
2iey_A	195	Crystal Structure Of Mouse Rab27b Bound To Gdp In H		2e-06
2zet_A	203	Crystal Structure Of The Small Gtpase Rab27b Comple		2e-06
1ky2_A	182	Gppnhp-Bound Ypt7p At 1.6 A Resolution Length = 182		3e-06
1z22_A	168	Gdp-Bound Rab23 Gtpase Crystallized In C222(1) Spac		1e-05
3clv_A	208	Crystal Structure Of Rab5a From Plasmodium Falcipar		2e-05
3ea5_A	216	Kap95p Binding Induces The Switch Loops Of Rangdp T		2e-05
1qg2_A	216	Canine Gdp-Ran R76e Mutant Length = 216		2e-05
1byu_A	216	Canine Gdp-Ran Length = 216		2e-05
1a2k_C	216	Gdpran-Ntf2 Complex Length = 216		2e-05
1qg4_A	216	Canine Gdp-Ran F72y Mutant Length = 216		2e-05
1rrp_A	204	Structure Of The Ran-Gppnhp-Ranbd1 Complex Length =		2e-05
3ran_A	216	Canine Gdp-Ran Q69l Mutant Length = 216		2e-05
2bku_A	177	Kap95p:rangtp Complex Length = 177		3e-05
1wa5_A	176	Crystal Structure Of The Exportin Cse1p Complexed W		3e-05
3nby_C	176	Crystal Structure Of The Pki Nes-Crm1-Rangtp Nuclea		3e-05
3nc1_C	182	Crystal Structure Of The Crm1-Rangtp Complex Length		3e-05
3gj4_A	221	Crystal Structure Of Human Rangdp-Nup153znf3 Comple		4e-05
3gj0_A	221	Crystal Structure Of Human Rangdp Length = 221		4e-05
1qbk_C	216	Structure Of The Karyopherin Beta2-ran Gppnhp Nucle		4e-05
3m1i_A	219	Crystal Structure Of Yeast Crm1 (Xpo1p) In Complex		4e-05
3icq_B	171	Karyopherin Nuclear State Length = 171		4e-05
2x19_A	172	Crystal Structure Of Importin13 - Rangtp Complex Le		4e-05
2g77_B	198	Crystal Structure Of Gyp1 Tbc Domain In Complex Wit		6e-05
1z06_A	189	Gppnhp-Bound Rab33 Gtpase Length = 189		7e-05
1vg0_B	207	The Crystal Structures Of The Rep-1 Protein In Comp		1e-04
1t91_A	207	Crystal Structure Of Human Small Gtpase Rab7(Gtp) L		1e-04
2ery_A	172	The Crystal Structure Of The Ras Related Protein Rr		1e-04
1vg1_A	185	Gdp-bound Rab7 Length = 185		1e-04
3law_A	207	Structure Of Gtp-Bound L129f Mutant Rab7 Length = 2		2e-04
1yzl_A	179	Gppnhp-Bound Rab9 Gtpase Length = 179		4e-04
2atv_A	196	The Crystal Structure Of Human Rerg In The Gdp Boun		7e-04

>pdb|1OIV|A Chain A, X-Ray Structure Of The Small G Protein Rab11a In Complex With Gdp Length = 191

Iteration: 1
 Score =  102 bits (253), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 47/64 (73%), Positives = 54/64 (84%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL   
Sbjct: 93  AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAV 152
Query: 61  MCEE 64
             +E
Sbjct: 153 PTDE 156

>pdb|1YZK|A Chain A, Gppnhp Bound Rab11 Gtpase Length = 184

Iteration: 1
 Score =  101 bits (252), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 47/64 (73%), Positives = 54/64 (84%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL   
Sbjct: 84  AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAV 143
Query: 61  MCEE 64
             +E
Sbjct: 144 PTDE 147

>pdb|2HV8|A Chain A, Crystal Structure Of Gtp-Bound Rab11 In Complex With Fip3 Length = 172

Iteration: 1
 Score =  101 bits (252), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 47/64 (73%), Positives = 54/64 (84%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL   
Sbjct: 72  AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAV 131
Query: 61  MCEE 64
             +E
Sbjct: 132 PTDE 135

>pdb|1OIW|A Chain A, X-ray Structure Of The Small G Protein Rab11a In Complex With Gtpgammas Length = 191

Iteration: 1
 Score =  101 bits (252), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 47/64 (73%), Positives = 54/64 (84%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL   
Sbjct: 93  AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAV 152
Query: 61  MCEE 64
             +E
Sbjct: 153 PTDE 156

>pdb|2F9L|A Chain A, 3d Structure Of Inactive Human Rab11b Gtpase Length = 199

Iteration: 1
 Score =  100 bits (250), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 53/63 (84%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSM 61
           ITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL    
Sbjct: 70  ITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVP 129
Query: 62  CEE 64
            +E
Sbjct: 130 TDE 132

>pdb|3BFK|A Chain A, Crystal Structure Of Plasmodium Falciparum Rab11a In Complex With Gdp Length = 181

Iteration: 1
 Score =  100 bits (248), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 44/57 (77%), Positives = 53/57 (92%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGA+GALLVYD+TK  +FEN+ +WLK+LRD+A SNIVI+L+GNKSDLKHL
Sbjct: 72  AITSAYYRGAVGALLVYDITKKNSFENIEKWLKELRDNADSNIVILLVGNKSDLKHL 128

>pdb|2D7C|A Chain A, Crystal Structure Of Human Rab11 In Complex With Fip3 Rab- Binding Domain Length = 167

Iteration: 1
 Score = 99.4 bits (246), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 46/64 (71%), Positives = 53/64 (82%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVI L+GNKSDL+HL   
Sbjct: 69  AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIXLVGNKSDLRHLRAV 128
Query: 61  MCEE 64
             +E
Sbjct: 129 PTDE 132

>pdb|2GZD|A Chain A, Crystal Structure Of Rab11 In Complex With Rab11-Fip2 Length = 173

Iteration: 1
 Score = 99.4 bits (246), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 46/64 (71%), Positives = 53/64 (82%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVI L+GNKSDL+HL   
Sbjct: 75  AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIXLVGNKSDLRHLRAV 134
Query: 61  MCEE 64
             +E
Sbjct: 135 PTDE 138

>pdb|3CPJ|B Chain B, Crystal Structure Of Ypt31 In Complex With Yeast Rab-Gdi Length = 223

Iteration: 1
 Score = 85.5 bits (210), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 51/64 (79%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GAL+VYD++KS+++EN + WL +LR++A  N+ + LIGNKSDL HL   
Sbjct: 77  AITSAYYRGAVGALIVYDISKSSSYENCNHWLSELRENADDNVAVGLIGNKSDLAHLRAV 136
Query: 61  MCEE 64
             EE
Sbjct: 137 PTEE 140

>pdb|2OIL|A Chain A, Crystal Structure Of Human Rab25 In Complex With Gdp Length = 193

Iteration: 1
 Score = 85.5 bits (210), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 40/64 (62%), Positives = 48/64 (75%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLV+D+TK  T+  V RWLK+L DHA + IV+ML+GNKSDL      
Sbjct: 89  AITSAYYRGAVGALLVFDLTKHQTYAVVERWLKELYDHAEATIVVMLVGNKSDLSQAREV 148
Query: 61  MCEE 64
             EE
Sbjct: 149 PTEE 152

>pdb|3TSO|A Chain A, Structure Of The Cancer Associated Rab25 Protein In Complex With Fip2 Length = 178

Iteration: 1
 Score = 85.5 bits (210), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 40/64 (62%), Positives = 48/64 (75%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AITSAYYRGA+GALLV+D+TK  T+  V RWLK+L DHA + IV+ML+GNKSDL      
Sbjct: 74  AITSAYYRGAVGALLVFDLTKHQTYAVVERWLKELYDHAEATIVVMLVGNKSDLSQAREV 133
Query: 61  MCEE 64
             EE
Sbjct: 134 PTEE 137

>pdb|3RWM|B Chain B, Crystal Structure Of Ypt32 In Complex With Gppnhp Length = 185

Iteration: 1
 Score = 83.6 bits (205), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 36/57 (63%), Positives = 49/57 (85%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGA+GAL+VYD++KS+++EN + WL +LR++A  N+ + LIGNKSDL HL
Sbjct: 74  AITSAYYRGAVGALIVYDISKSSSYENCNHWLTELRENADDNVAVGLIGNKSDLAHL 130

>pdb|2A5J|A Chain A, Crystal Structure Of Human Rab2b Length = 191

Iteration: 1
 Score = 80.1 bits (196), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 37/64 (57%), Positives = 49/64 (76%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           +IT +YYRGA GALLVYD+T+  TF +++ WL+D R H+ SN+VIMLIGNKSDL+   + 
Sbjct: 85  SITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESRRDV 144
Query: 61  MCEE 64
             EE
Sbjct: 145 KREE 148

>pdb|1Z0A|A Chain A, Gdp-Bound Rab2a Gtpase Length = 174

Iteration: 1
 Score = 79.7 bits (195), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 35/55 (63%), Positives = 46/55 (83%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           +IT +YYRGA GALLVYD+T+  TF +++ WL+D R H+ SN+VIMLIGNKSDL+
Sbjct: 74  SITRSYYRGAAGALLVYDITRRDTFNHLTTWLEDARQHSNSNMVIMLIGNKSDLE 128

>pdb|2HUP|A Chain A, Crystal Structure Of Human Rab43 In Complex With Gdp Length = 201

Iteration: 1
 Score = 73.9 bits (180), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 44/56 (78%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           IT +YYR A GA+L YD+TK ++F +V  W++D+R +AGSNIV +LIGNKSDL  L
Sbjct: 94  ITQSYYRSANGAILAYDITKRSSFLSVPHWIEDVRKYAGSNIVQLLIGNKSDLSEL 149

>pdb|1Z0F|A Chain A, Gdp-Bound Rab14 Gtpase Length = 179

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 32/64 (50%), Positives = 46/64 (71%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           A+T +YYRGA GAL+VYD+T+ +T+ ++S WL D R+    N VI+LIGNK+DL+   + 
Sbjct: 79  AVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIILIGNKADLEAQRDV 138
Query: 61  MCEE 64
             EE
Sbjct: 139 TYEE 142

>pdb|4DRZ|A Chain A, Crystal Structure Of Human Rab14 Length = 196

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 32/64 (50%), Positives = 46/64 (71%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           A+T +YYRGA GAL+VYD+T+ +T+ ++S WL D R+    N VI+LIGNK+DL+   + 
Sbjct: 94  AVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIILIGNKADLEAQRDV 153
Query: 61  MCEE 64
             EE
Sbjct: 154 TYEE 157

>pdb|2EQB|A Chain A, Crystal Structure Of The Rab Gtpase Sec4p, The Sec2p Gef Domain, And Phosphate Complex Length = 174

Iteration: 1
 Score = 69.3 bits (168), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 40/54 (74%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           IT+AYYRGA+G +LVYDVT   TF N+ +W K + +HA     ++L+GNKSD++
Sbjct: 72  ITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDME 125

>pdb|3CPH|A Chain A, Crystal Structure Of Sec4 In Complex With Rab-Gdi Length = 213

Iteration: 1
 Score = 68.9 bits (167), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 40/54 (74%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           IT+AYYRGA+G +LVYDVT   TF N+ +W K + +HA     ++L+GNKSD++
Sbjct: 85  ITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDME 138

>pdb|1G17|A Chain A, Crystal Structure Of Sec4-Guanosine-5'-(Beta,Gamma)- Imidotriphosphate Length = 170

Iteration: 1
 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 40/54 (74%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           IT+AYYRGA+G +LVYD+T   TF N+ +W K + +HA     ++L+GNKSD++
Sbjct: 68  ITTAYYRGAMGIILVYDITDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDME 121

>pdb|2OCY|C Chain C, Complex Of The Guanine Exchange Factor Sec2p And The Rab Gtpase Sec4p Length = 170

Iteration: 1
 Score = 67.0 bits (162), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 28/52 (53%), Positives = 37/52 (71%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSD 53
           IT+AYYRGA G +LVYDVT   TF N+ +W K + +HA     ++L+GNKSD
Sbjct: 68  ITTAYYRGAXGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSD 119

>pdb|3QBT|A Chain A, Crystal Structure Of Ocrl1 540-678 In Complex With Rab8a:gppnhp Length = 174

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 42/53 (79%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           IT+AYYRGA+G +LVYD+T   +F+N+  W++++ +HA +++  M++GNK D+
Sbjct: 71  ITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDV 123

>pdb|2FU5|C Chain C, Structure Of Rab8 In Complex With Mss4 Length = 183

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 42/53 (79%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           IT+AYYRGA+G +LVYD+T   +F+N+  W++++ +HA +++  M++GNK D+
Sbjct: 73  ITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDV 125

>pdb|1G16|A Chain A, Crystal Structure Of Sec4-Gdp Length = 170

Iteration: 1
 Score = 66.2 bits (160), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 27/52 (51%), Positives = 37/52 (71%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSD 53
           IT+AYYRGA G +LVYD+T   TF N+ +W K + +HA     ++L+GNKSD
Sbjct: 68  ITTAYYRGAXGIILVYDITDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSD 119

>pdb|2O52|A Chain A, Crystal Structure Of Human Rab4b In Complex With Gdp Length = 200

Iteration: 1
 Score = 65.5 bits (158), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 29/54 (53%), Positives = 39/54 (72%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++T +YYRGA GALLVYD+T   T+ +++ WL D R  A  NIV++L GNK DL
Sbjct: 89  SVTRSYYRGAAGALLVYDITSRETYNSLAAWLTDARTLASPNIVVILCGNKKDL 142

>pdb|2BMD|A Chain A, High Resolution Structure Of Gdp-Bound Human Rab4a Length = 186

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 38/54 (70%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++T +YYRGA GALLVYD+T   T+  ++ WL D R  A  NIVI+L GNK DL
Sbjct: 74  SVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGNKKDL 127

>pdb|1YU9|A Chain A, Gppnhp-Bound Rab4a Length = 175

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 38/54 (70%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++T +YYRGA GALLVYD+T   T+  ++ WL D R  A  NIVI+L GNK DL
Sbjct: 75  SVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGNKKDL 128

>pdb|1Z0K|A Chain A, Structure Of Gtp-Bound Rab4q67l Gtpase In Complex With The Central Rab Binding Domain Of Rabenosyn-5 Length = 172

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 38/54 (70%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++T +YYRGA GALLVYD+T   T+  ++ WL D R  A  NIVI+L GNK DL
Sbjct: 72  SVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGNKKDL 125

>pdb|4I1O|A Chain A, Crystal Structure Of The Legionella Pneumophila Gap Domain Of Lepb In Complex With Rab1b Bound To Gdp And Bef3 Length = 181

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 47/67 (70%), Gaps = 3/67 (4%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL---KHLL 58
           ITS+YYRGA G ++VYDVT   ++ NV +WL+++  +A  N+  +L+GNKSDL   K + 
Sbjct: 74  ITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVD 133
Query: 59  NSMCEEY 65
           N+  +E+
Sbjct: 134 NTTAKEF 140

>pdb|3JZA|A Chain A, Crystal Structure Of Human Rab1b In Complex With The Gef Domain Of DrraSIDM FROM LEGIONELLA PNEUMOPHILA Length = 175

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 47/67 (70%), Gaps = 3/67 (4%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL---KHLL 58
           ITS+YYRGA G ++VYDVT   ++ NV +WL+++  +A  N+  +L+GNKSDL   K + 
Sbjct: 74  ITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVD 133
Query: 59  NSMCEEY 65
           N+  +E+
Sbjct: 134 NTTAKEF 140

>pdb|4FMC|B Chain B, Espg-Rab1 Complex Length = 171

Iteration: 1
 Score = 62.8 bits (151), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 39/53 (73%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ITS+YYRGA G ++VYDVT   +F NV +WL+++  +A  N+  +L+GNK DL
Sbjct: 71  ITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDL 123

>pdb|3L0I|B Chain B, Complex Structure Of Sidm/drra With The Wild Type Rab1 Length = 199

Iteration: 1
 Score = 62.8 bits (151), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 39/53 (73%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ITS+YYRGA G ++VYDVT   +F NV +WL+++  +A  N+  +L+GNK DL
Sbjct: 98  ITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDL 150

>pdb|4FMD|F Chain F, Espg-Rab1 Complex Structure At 3.05 A Length = 164

Iteration: 1
 Score = 62.8 bits (151), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 39/53 (73%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ITS+YYRGA G ++VYDVT   +F NV +WL+++  +A  N+  +L+GNK DL
Sbjct: 64  ITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDL 116

>pdb|4FMB|B Chain B, Vira-Rab1 Complex Structure Length = 171

Iteration: 1
 Score = 62.8 bits (151), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 39/53 (73%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ITS+YYRGA G ++VYDVT   +F NV +WL+++  +A  N+  +L+GNK DL
Sbjct: 71  ITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDL 123

>pdb|3SFV|A Chain A, Crystal Structure Of The Gdp-Bound Rab1a S25n Mutant In Complex With The Coiled-Coil Domain Of Lida From Legionella Pneumophila Length = 181

Iteration: 1
 Score = 62.8 bits (151), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 39/53 (73%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ITS+YYRGA G ++VYDVT   +F NV +WL+++  +A  N+  +L+GNK DL
Sbjct: 81  ITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDL 133

>pdb|3TKL|A Chain A, Crystal Structure Of The Gtp-Bound Rab1a In Complex With The Coiled- Coil Domain Of Lida From Legionella Pneumophila Length = 196

Iteration: 1
 Score = 62.8 bits (151), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 39/53 (73%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ITS+YYRGA G ++VYDVT   +F NV +WL+++  +A  N+  +L+GNK DL
Sbjct: 81  ITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDL 133

>pdb|2FOL|A Chain A, Crystal Structure Of Human Rab1a In Complex With Gdp Length = 191

Iteration: 1
 Score = 62.8 bits (151), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 39/53 (73%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ITS+YYRGA G ++VYDVT   +F NV +WL+++  +A  N+  +L+GNK DL
Sbjct: 90  ITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDL 142

>pdb|1YVD|A Chain A, Gppnhp-Bound Rab22 Gtpase Length = 169

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 38/61 (62%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           A+   YYRG+  A++VYD+TK  TF  +  W+++LR H   +IV+ + GNK DL  +   
Sbjct: 69  ALAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQHGPPSIVVAIAGNKCDLTDVREV 128
Query: 61  M 61
           M
Sbjct: 129 M 129

>pdb|1Z0J|A Chain A, Structure Of Gtp-Bound Rab22q64l Gtpase In Complex With The Minimal Rab Binding Domain Of Rabenosyn-5 Length = 170

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 38/61 (62%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           A+   YYRG+  A++VYD+TK  TF  +  W+++LR H   +IV+ + GNK DL  +   
Sbjct: 70  ALAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQHGPPSIVVAIAGNKCDLTDVREV 129
Query: 61  M 61
           M
Sbjct: 130 M 130

>pdb|4FMC|F Chain F, Espg-Rab1 Complex Length = 117

Iteration: 1
 Score = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 39/54 (72%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
            ITS+YYRGA G ++VYDVT   +F NV +WL+++  +A  N+  +L+GNK DL
Sbjct: 62  TITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDL 115

>pdb|1Z07|A Chain A, Gppnhp-Bound Rab5c G55q Mutant Gtpase Length = 166

Iteration: 1
 Score = 62.0 bits (149), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 26/49 (53%), Positives = 34/49 (69%)
Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           YYRGA  A++VYD+T + TF     W+K+L+  A  NIVI L GNK+DL
Sbjct: 74  YYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADL 122

>pdb|1HUQ|A Chain A, 1.8a Crystal Structure Of The Monomeric Gtpase Rab5c (Mouse) Length = 164

Iteration: 1
 Score = 62.0 bits (149), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 26/49 (53%), Positives = 34/49 (69%)
Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           YYRGA  A++VYD+T + TF     W+K+L+  A  NIVI L GNK+DL
Sbjct: 72  YYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADL 120

>pdb|1Z0D|A Chain A, Gdp-bound Rab5c Gtpase Length = 167

Iteration: 1
 Score = 62.0 bits (149), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 36/54 (66%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++   YYRGA  A++VYD+T + TF     W+K+L+  A  NIVI L GNK+DL
Sbjct: 69  SLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADL 122

>pdb|2RHD|A Chain A, Crystal Structure Of Cryptosporidium Parvum Small Gtpase Rab1a Length = 175

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 40/54 (74%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
            ITS+YYRGA G ++VYDVT   +F+NV +W++++  +A  N+  +L+GNK DL
Sbjct: 73  TITSSYYRGAHGIIIVYDVTDRDSFDNVKQWIQEIDRYAMENVNKLLVGNKCDL 126

>pdb|2FG5|A Chain A, Crystal Structure Of Human Rab31 In Complex With A Gtp Analogue Length = 192

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 38/54 (70%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++   YYRG+  A++VYD+TK  +F  + +W+K+L++H   NIV+ + GNK DL
Sbjct: 87  SLAPMYYRGSAAAVIVYDITKQDSFYTLKKWVKELKEHGPENIVMAIAGNKCDL 140

>pdb|2BCG|Y Chain Y, Structure Of Doubly Prenylated Ypt1:gdi Complex Length = 206

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 39/55 (70%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            ITS+YYRG+ G ++VYDVT   +F  V  WL+++  +A S ++ +L+GNK DLK
Sbjct: 72  TITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYATSTVLKLLVGNKCDLK 126

>pdb|1UKV|Y Chain Y, Structure Of Rabgdp-Dissociation Inhibitor In Complex With Prenylated Ypt1 Gtpase Length = 206

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 39/55 (70%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            ITS+YYRG+ G ++VYDVT   +F  V  WL+++  +A S ++ +L+GNK DLK
Sbjct: 72  TITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYATSTVLKLLVGNKCDLK 126

>pdb|2EFC|B Chain B, Ara7-GdpATVPS9A Length = 181

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 23/49 (46%), Positives = 34/49 (69%)
Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           YYRGA  A++V+DVT   +FE   +W+++L+     N+V+ L GNKSDL
Sbjct: 81  YYRGAAAAIIVFDVTNQASFERAKKWVQELQAQGNPNMVMALAGNKSDL 129

>pdb|1TU4|A Chain A, Crystal Structure Of Rab5-Gdp Complex Length = 171

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++   YYRGA  A++VYD+T   +F     W+K+L+  A  NIVI L GNK+DL
Sbjct: 71  SLAPXYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADL 124

>pdb|2IL1|A Chain A, Crystal Structure Of A Predicted Human Gtpase In Complex With Gdp Length = 192

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 39/53 (73%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSD 53
           +ITSAYYR A G +LVYD+TK  TF+++ +W+K +  +A  +  ++L+GNK D
Sbjct: 90  SITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLD 142

>pdb|1N6I|A Chain A, Crystal Structure Of Human Rab5a A30p Mutant Complex With Gdp Length = 170

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++   YYRGA  A++VYD+T   +F     W+K+L+  A  NIVI L GNK+DL
Sbjct: 70  SLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADL 123

>pdb|1N6P|A Chain A, Crystal Structure Of Human Rab5a A30e Mutant Complex With Gppnhp Length = 170

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++   YYRGA  A++VYD+T   +F     W+K+L+  A  NIVI L GNK+DL
Sbjct: 70  SLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADL 123

>pdb|1YZN|A Chain A, Gppnhp-Bound Ypt1p Gtpase Length = 185

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 39/55 (70%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            ITS+YYRG+ G ++VYDVT   +F  V  WL+++  +A S ++ +L+GNK DLK
Sbjct: 85  TITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYATSTVLKLLVGNKCDLK 139

>pdb|1N6H|A Chain A, Crystal Structure Of Human Rab5a Length = 170

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++   YYRGA  A++VYD+T   +F     W+K+L+  A  NIVI L GNK+DL
Sbjct: 70  SLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADL 123

>pdb|1TU3|A Chain A, Crystal Structure Of Rab5 Complex With Rabaptin5 C-Terminal Domain Length = 171

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++   YYRGA  A++VYD+T   +F     W+K+L+  A  NIVI L GNK+DL
Sbjct: 71  SLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADL 124

>pdb|1N6N|A Chain A, Crystal Structure Of Human Rab5a A30r Mutant Complex With Gppnhp Length = 170

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++   YYRGA  A++VYD+T   +F     W+K+L+  A  NIVI L GNK+DL
Sbjct: 70  SLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADL 123

>pdb|3MJH|A Chain A, Crystal Structure Of Human Rab5a In Complex With The C2h2 Zinc Finger Of Eea1 Length = 168

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++   YYRGA  A++VYD+T   +F     W+K+L+  A  NIVI L GNK+DL
Sbjct: 69  SLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADL 122

>pdb|1N6O|A Chain A, Crystal Structure Of Human Rab5a A30k Mutant Complex With Gppnhp Length = 170

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++   YYRGA  A++VYD+T   +F     W+K+L+  A  NIVI L GNK+DL
Sbjct: 70  SLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADL 123

>pdb|1N6R|A Chain A, Crystal Structure Of Human Rab5a A30l Mutant Complex With Gppnhp Length = 170

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++   YYRGA  A++VYD+T   +F     W+K+L+  A  NIVI L GNK+DL
Sbjct: 70  SLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADL 123

>pdb|2HEI|A Chain A, Crystal Structure Of Human Rab5b In Complex With Gdp Length = 179

Iteration: 1
 Score = 59.3 bits (142), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ++   YYRGA  A++VYD+T   TF     W+K+L+  A  +IVI L GNK+DL
Sbjct: 72  SLAPMYYRGAQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADL 125

>pdb|1D5C|A Chain A, Crystal Structure Of Plasmodium Falciparum Rab6 Complexed With Gdp Length = 162

Iteration: 1
 Score = 59.3 bits (142), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 45/71 (63%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           ++  +Y R +  A++VYD+T   +FEN ++W++D+ +  G +++I L+GNK+DL  L   
Sbjct: 65  SLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKV 124
Query: 61  MCEEYLIKSRS 71
             EE   K++ 
Sbjct: 125 TYEEGXQKAQE 135

>pdb|1YZQ|A Chain A, Gppnhp-Bound Rab6 Gtpase Length = 170

Iteration: 1
 Score = 59.3 bits (142), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 41/64 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           ++  +Y R +  A++VYD+T   +F+  ++W+ D+R   GS+++IML+GNK+DL      
Sbjct: 70  SLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQV 129
Query: 61  MCEE 64
             EE
Sbjct: 130 SIEE 133

>pdb|4DKX|A Chain A, Crystal Structure Of The Rab 6a'(Q72l) Length = 216

Iteration: 1
 Score = 59.3 bits (142), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 41/64 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           ++  +Y R +  A++VYD+T   +F+  ++W+ D+R   GS+++IML+GNK+DL      
Sbjct: 77  SLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQV 136
Query: 61  MCEE 64
             EE
Sbjct: 137 SIEE 140

>pdb|2Y8E|A Chain A, Crystal Structure Of D. Melanogaster Rab6 Gtpase Bound To Gmppnp Length = 179

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 41/64 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           ++  +Y R +  A++VYD+T + +F   S+W+ D+R   GS+++IML+GNK+DL      
Sbjct: 78  SLIPSYIRDSTVAVVVYDITNTNSFHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQV 137
Query: 61  MCEE 64
             EE
Sbjct: 138 STEE 141

>pdb|2WWX|A Chain A, Crystal Structure Of The SidmDRRA(GEFGDF DOMAIN)-Rab1 (Gtpase Domain) Complex Length = 175

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 38/53 (71%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
           ITS+YYRGA G ++VYDVT   +F NV +WL+++  +A  N+  +L+G K DL
Sbjct: 73  ITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGIKCDL 125

>pdb|2FE4|A Chain A, The Crystal Structure Of Human Neuronal Rab6b In Its Inactive Gdp-Bound Form Length = 171

Iteration: 1
 Score = 58.5 bits (140), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 41/64 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           ++  +Y R +  A++VYD+T   +F+  S+W+ D+R   GS+++IML+GNK+DL      
Sbjct: 66  SLIPSYIRDSTVAVVVYDITNLNSFQQTSKWIDDVRTERGSDVIIMLVGNKTDLADKRQI 125
Query: 61  MCEE 64
             EE
Sbjct: 126 TIEE 129

>pdb|3CWZ|A Chain A, Strucure Of Rab6(Gtp)-R6ip1 Complex Length = 188

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 41/64 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           ++  +Y R +  A++VYD+T   +F+  ++W+ D+R   GS+++IML+GNK+DL      
Sbjct: 70  SLIPSYIRDSTVAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQV 129
Query: 61  MCEE 64
             EE
Sbjct: 130 SIEE 133

>pdb|2G6B|A Chain A, Crystal Structure Of Human Rab26 In Complex With A Gtp Analogue Length = 180

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 38/56 (67%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           ++T AYYR A   LL+YDVT   +F+N+  WL ++ ++A  ++ +ML+GNK D  H
Sbjct: 75  SVTHAYYRDAHALLLLYDVTNKASFDNIQAWLTEIHEYAQHDVALMLLGNKVDSAH 130

>pdb|2GIL|A Chain A, Structure Of The Extremely Slow Gtpase Rab6a In The Gtp Bound Form At 1.8 Resolution Length = 162

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 41/64 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           ++  +Y R +  A++VYD+T   +F+  ++W+ D+R   GS+++IML+GNK+DL      
Sbjct: 65  SLIPSYIRDSTVAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQV 124
Query: 61  MCEE 64
             EE
Sbjct: 125 SIEE 128

>pdb|3BBP|A Chain A, Rab6-Gtp:gcc185 Rab Binding Domain Complex Length = 211

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 41/64 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           ++  +Y R +  A++VYD+T   +F+  ++W+ D+R   GS+++IML+GNK+DL      
Sbjct: 80  SLIPSYIRDSTVAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQV 139
Query: 61  MCEE 64
             EE
Sbjct: 140 SIEE 143

>pdb|3DZ8|A Chain A, Crystal Structure Of Human Rab3b Gtpase Bound With Gdp Length = 191

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 37/55 (67%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           IT+AYYRGA+G +L+YD+T   +F  V  W   ++ ++  N  ++L+GNK D++ 
Sbjct: 88  ITTAYYRGAMGFILMYDITNEESFNAVQDWATQIKTYSWDNAQVILVGNKCDMEE 142

>pdb|1YZU|A Chain A, Gppnhp-Bound Rab21 Gtpase At 2.50 A Resolution Length = 170

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 37/55 (67%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           A+   YYR + GA+LVYD+T   +F+ V  W+K+LR   G+ I + ++GNK DL+
Sbjct: 70  ALGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLE 124

>pdb|1YZT|A Chain A, Gppnhp-Bound Rab21 Gtpase At 2.05 A Resolution Length = 184

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 37/55 (67%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           A+   YYR + GA+LVYD+T   +F+ V  W+K+LR   G+ I + ++GNK DL+
Sbjct: 84  ALGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLE 138

>pdb|1Z08|A Chain A, Gppnhp-Bound Rab21 Q53g Mutant Gtpase Length = 170

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 37/55 (67%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           A+   YYR + GA+LVYD+T   +F+ V  W+K+LR   G+ I + ++GNK DL+
Sbjct: 70  ALGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLE 124

>pdb|1EK0|A Chain A, Gppnhp-Bound Ypt51 At 1.48 A Resolution Length = 170

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 34/53 (64%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSD 53
           ++   YYR A  AL+VYDVTK  +F     W+K+L + A  +I+I L+GNK D
Sbjct: 67  SLAPXYYRNAQAALVVYDVTKPQSFIKARHWVKELHEQASKDIIIALVGNKID 119

>pdb|3RAB|A Chain A, Gppnhp-bound Rab3a At 2.0 A Resolution Length = 169

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 37/54 (68%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           IT+AYYRGA+G +L+YD+T   +F  V  W   ++ ++  N  ++L+GNK D++
Sbjct: 70  ITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDME 123

>pdb|2GF9|A Chain A, Crystal Structure Of Human Rab3d In Complex With Gdp Length = 189

Iteration: 1
 Score = 56.2 bits (134), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 36/54 (66%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           IT+AYYRGA+G LL+YD+    +F  V  W   ++ ++  N  ++L+GNK DL+
Sbjct: 87  ITTAYYRGAMGFLLMYDIANQESFAAVQDWATQIKTYSWDNAQVILVGNKCDLE 140

>pdb|2P5S|A Chain A, Rab Domain Of Human Rasef In Complex With Gdp Length = 199

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 36/55 (65%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           +I  +Y+R A G LL+YDVT   +F N+  W+  + D A   + IML+GNK+D++
Sbjct: 92  SIAKSYFRKADGVLLLYDVTCEKSFLNIREWVDMIEDAAHETVPIMLVGNKADIR 146

>pdb|3TW8|B Chain B, Gef Domain Of Dennd 1b In Complex With Rab Gtpase Rab35 Length = 181

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 24/53 (45%), Positives = 36/53 (67%), Gaps = 1/53 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSD 53
            ITS YYRG  G ++VYDVT + +F NV RWL ++  +   ++  +L+GNK+D
Sbjct: 73  TITSTYYRGTHGVIVVYDVTSAESFVNVKRWLHEINQNC-DDVCRILVGNKND 124

>pdb|1ZBD|A Chain A, Structural Basis Of Rab Effector Specificity: Crystal Structure Of The Small G Protein Rab3a Complexed With The Effector Domain Of Rabphilin-3a Length = 203

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 34/54 (62%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
           IT+AYYRGA G +L YD+T   +F  V  W   ++ ++  N  ++L+GNK D +
Sbjct: 73  ITTAYYRGAXGFILXYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDXE 126

>pdb|3BC1|A Chain A, Crystal Structure Of The Complex Rab27a-slp2a Length = 195

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 40/56 (71%), Gaps = 1/56 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDLK 55
           ++T+A++R A+G LL++D+T   +F NV  W+  L+ HA S N  I+L GNKSDL+
Sbjct: 85  SLTTAFFRDAMGFLLLFDLTNEQSFLNVRNWISQLQMHAYSENPDIVLCGNKSDLE 140

>pdb|1X3S|A Chain A, Crystal Structure Of Human Rab18 In Complex With Gppnhp Length = 195

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSN-IVIMLIGNKSD 53
           +T +YYRGA G +LVYDVT+  TF  +  WL +L  +   N IV  L+GNK D
Sbjct: 80  LTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNXLVGNKID 132

>pdb|2EW1|A Chain A, Crystal Structure Of Rab30 In Complex With A Gtp Analogue Length = 201

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 35/56 (62%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           +IT +YYR A   +L YD+T   +F  +  WL+++  +A + ++ +L+GNK DL  
Sbjct: 90  SITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYASNKVITVLVGNKIDLAE 145

>pdb|2F7S|A Chain A, The Crystal Structure Of Human Rab27b Bound To Gdp Length = 217

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 24/55 (43%), Positives = 39/55 (70%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDL 54
           ++T+A++R A+G LL++D+T   +F NV  W+  L+ +A   N  I+LIGNK+DL
Sbjct: 99  SLTTAFFRDAMGFLLMFDLTSQQSFLNVRNWMSQLQANAYCENPDIVLIGNKADL 153

>pdb|2IF0|A Chain A, Crystal Structure Of Mouse Rab27b Bound To Gdp In Monoclinic Space Group Length = 200

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 39/56 (69%), Gaps = 1/56 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLK 55
           ++T+A++R A+G LL++D+T   +F NV  W+  L+ +A   N  I+LIGNK+DL 
Sbjct: 85  SLTTAFFRDAMGFLLMFDLTSQQSFLNVRNWMSQLQANAYCENPDIVLIGNKADLP 140

>pdb|2IEZ|A Chain A, Crystal Structure Of Mouse Rab27b Bound To Gdp In Monoclinic Space Group Length = 220

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/55 (43%), Positives = 39/55 (70%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDL 54
           ++T+A++R A+G LL++D+T   +F NV  W+  L+ +A   N  I+LIGNK+DL
Sbjct: 85  SLTTAFFRDAMGFLLMFDLTSQQSFLNVRNWMSQLQANAYCENPDIVLIGNKADL 139

>pdb|2HXS|A Chain A, Crystal Structure Of Rab28a Gtpase In The Inactive (Gdp-3'p- Bound) Form Length = 178

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 3/64 (4%)
Query: 6   YYRGALGALLVYDVTKSTTFENVSRW---LKDLRDHAGSNIVIMLIGNKSDLKHLLNSMC 62
           Y  GA G LLVYD+T   +FEN+  W   +K + + + +  ++ L+GNK DL+H+     
Sbjct: 76  YIYGAQGVLLVYDITNYQSFENLEDWYTVVKKVSEESETQPLVALVGNKIDLEHMRTIKP 135
Query: 63  EEYL 66
           E++L
Sbjct: 136 EKHL 139

>pdb|4DJT|A Chain A, Crystal Structure Of A Nuclear Gtp-Binding Protein From Encephalitozoon Cuniculi Bound To Gdp-Mg2+ Length = 218

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 21/55 (38%), Positives = 35/55 (63%)
Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           +   YY GA GA+L +DVT   T +N++RW+K+ +   G+   I++  NK D+K+
Sbjct: 77  LKDVYYIGASGAILFFDVTSRITCQNLARWVKEFQAVVGNEAPIVVCANKIDIKN 131

>pdb|2IEY|A Chain A, Crystal Structure Of Mouse Rab27b Bound To Gdp In Hexagonal Space Group Length = 195

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 36/55 (65%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDL 54
           ++T+A++R A G LL +D+T   +F NV  W   L+ +A   N  I+LIGNK+DL
Sbjct: 85  SLTTAFFRDAXGFLLXFDLTSQQSFLNVRNWXSQLQANAYCENPDIVLIGNKADL 139

>pdb|2ZET|A Chain A, Crystal Structure Of The Small Gtpase Rab27b Complexed With The Slp Homology Domain Of Slac2-AMELANOPHILIN Length = 203

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLK 55
           ++T+A++R A G LL +D+T   +F NV  W   L+ +A   N  I+LIGNK+DL 
Sbjct: 85  SLTTAFFRDAXGFLLXFDLTSQQSFLNVRNWXSQLQANAYCENPDIVLIGNKADLP 140

>pdb|1KY2|A Chain A, Gppnhp-Bound Ypt7p At 1.6 A Resolution Length = 182

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 40/72 (55%), Gaps = 7/72 (9%)
Query: 5   AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSN----IVIMLIGNKSDL---KHL 57
           A+YRGA   +LVYDVT +++FEN+  W  +   HA  N       +++GNK D    K +
Sbjct: 77  AFYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEESKKI 136
Query: 58  LNSMCEEYLIKS 69
           ++    + L KS
Sbjct: 137 VSEKSAQELAKS 148

>pdb|1Z22|A Chain A, Gdp-Bound Rab23 Gtpase Crystallized In C222(1) Space Group Length = 168

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           AIT AYYRGA   +LV+  T   +FE +S W + +    G +I   L+ NK D   LL+ 
Sbjct: 69  AITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAEVG-DIPTALVQNKID---LLDD 124
Query: 61  MC 62
            C
Sbjct: 125 SC 126

>pdb|3CLV|A Chain A, Crystal Structure Of Rab5a From Plasmodium Falciparum, Pfb0500c Length = 208

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/53 (37%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSD 53
           +I   YYRGA  A++V+D++ S T +    W+  L+    SN +I+L+ NK D
Sbjct: 108 SIVPLYYRGATCAIVVFDISNSNTLDRAKTWVNQLK--ISSNYIIILVANKID 158

>pdb|3EA5|A Chain A, Kap95p Binding Induces The Switch Loops Of Rangdp To Adopt The Gtp- Bound Conformation: Implications For Nuclear Import Complex Assembly Dynamics Length = 216

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 74  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 127

>pdb|1QG2|A Chain A, Canine Gdp-Ran R76e Mutant Length = 216

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 74  GLEDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 127

>pdb|1BYU|A Chain A, Canine Gdp-Ran Length = 216

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 74  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 127

>pdb|1A2K|C Chain C, Gdpran-Ntf2 Complex Length = 216

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 74  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 127

>pdb|1QG4|A Chain A, Canine Gdp-Ran F72y Mutant Length = 216

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 74  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 127

>pdb|1RRP|A Chain A, Structure Of The Ran-Gppnhp-Ranbd1 Complex Length = 204

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 67  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 120

>pdb|3RAN|A Chain A, Canine Gdp-Ran Q69l Mutant Length = 216

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 74  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 127

>pdb|2BKU|A Chain A, Kap95p:rangtp Complex Length = 177

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 74  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 127

>pdb|1WA5|A Chain A, Crystal Structure Of The Exportin Cse1p Complexed With Its Cargo (Kap60p) And Rangtp Length = 176

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 74  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 127

>pdb|3NBY|C Chain C, Crystal Structure Of The Pki Nes-Crm1-Rangtp Nuclear Export Complex Length = 176

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 70  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 123

>pdb|3NC1|C Chain C, Crystal Structure Of The Crm1-Rangtp Complex Length = 182

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 76  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 129

>pdb|3GJ4|A Chain A, Crystal Structure Of Human Rangdp-Nup153znf3 Complex Length = 221

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 79  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 132

>pdb|3GJ0|A Chain A, Crystal Structure Of Human Rangdp Length = 221

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 79  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 132

>pdb|1QBK|C Chain C, Structure Of The Karyopherin Beta2-ran Gppnhp Nuclear Transport Complex Length = 216

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++ +DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 74  GLRDGYYIQAQCAIIXFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIK 127

>pdb|3M1I|A Chain A, Crystal Structure Of Yeast Crm1 (Xpo1p) In Complex With Yeas (Yrb1p) And Yeast Rangtp (Gsp1pgtp) Length = 219

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK 55
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K
Sbjct: 76  GLRDGYYINAQCAIIMFDVTSRITYKNVPNWHRDLV-RVCENIPIVLCGNKVDVK 129

>pdb|3ICQ|B Chain B, Karyopherin Nuclear State Length = 171

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K 
Sbjct: 68  GLRDGYYINAQCAIIMFDVTSRITYKNVPNWHRDLV-RVCENIPIVLCGNKVDVKE 122

>pdb|2X19|A Chain A, Crystal Structure Of Importin13 - Rangtp Complex Length = 172

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K 
Sbjct: 69  GLRDGYYINAQCAIIMFDVTSRITYKNVPNWHRDLV-RVCENIPIVLCGNKVDVKE 123

>pdb|2G77|B Chain B, Crystal Structure Of Gyp1 Tbc Domain In Complex With Rab33 Gtpase Bound To Gdp And Alf3 Length = 198

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSN-IVIMLIGNKSDLK 55
           YYR     + VYD T   +F ++  W+++ + H  +N I  +L+GNK DL+
Sbjct: 99  YYRNVHAVVFVYDXTNXASFHSLPAWIEECKQHLLANDIPRILVGNKCDLR 149

>pdb|1Z06|A Chain A, Gppnhp-Bound Rab33 Gtpase Length = 189

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSN-IVIMLIGNKSDLK 55
           ++   YYR     + VYD+T   +F ++  W+++ + H  +N I  +L+GNK DL+
Sbjct: 85  SMVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRILVGNKCDLR 140

>pdb|1VG0|B Chain B, The Crystal Structures Of The Rep-1 Protein In Complex With Monoprenylated Rab7 Protein Length = 207

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 5   AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS----NIVIMLIGNKSDLKH 56
           A+YRGA   +LV+DVT   TF+ +  W  +    A      N   +++GNK DL++
Sbjct: 76  AFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLEN 131

>pdb|1T91|A Chain A, Crystal Structure Of Human Small Gtpase Rab7(Gtp) Length = 207

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 5   AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS----NIVIMLIGNKSDLKH 56
           A+YRGA   +LV+DVT   TF+ +  W  +    A      N   +++GNK DL++
Sbjct: 76  AFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLEN 131

>pdb|2ERY|A Chain A, The Crystal Structure Of The Ras Related Protein Rras2 (Rras2) In The Gdp Bound State Length = 172

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKHLLN 59
           A+   Y R   G LLV+ VT   +FE + ++ +  LR        ++LIGNK+DL H   
Sbjct: 68  AMREQYMRTGEGFLLVFSVTDRGSFEEIYKFQRQILRVKDRDEFPMILIGNKADLDHQRQ 127
Query: 60  SMCEE 64
              EE
Sbjct: 128 VTQEE 132

>pdb|1VG1|A Chain A, Gdp-bound Rab7 Length = 185

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 5   AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS----NIVIMLIGNKSDLKH 56
           A+YRGA   +LV+DVT   TF+ +  W  +    A      N   +++GNK DL++
Sbjct: 76  AFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLEN 131

>pdb|3LAW|A Chain A, Structure Of Gtp-Bound L129f Mutant Rab7 Length = 207

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 5   AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS----NIVIMLIGNKSDLKH 56
           A+YRGA   +LV+DVT   TF+ +  W  +    A      N   +++GNK D ++
Sbjct: 76  AFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDFEN 131

>pdb|1YZL|A Chain A, Gppnhp-Bound Rab9 Gtpase Length = 179

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 4/60 (6%)
Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA----GSNIVIMLIGNKSDLKH 56
           ++ + +YRG+   LL + V  S +F+N+S W K+   +A      +   +++GNK+D+K 
Sbjct: 75  SLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKTDIKE 134

>pdb|2ATV|A Chain A, The Crystal Structure Of Human Rerg In The Gdp Bound State Length = 196

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 4   SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDH--AGSNIVIMLIGNKSDLKHLLNSM 61
             + R   G +LVYD+T   +FE V   LK++ D      N+ ++L+GNK+DL H     
Sbjct: 93  EGHMRWGEGFVLVYDITDRGSFEEVLP-LKNILDEIKKPKNVTLILVGNKADLDHSRQVS 151
Query: 62  CEE 64
            EE
Sbjct: 152 TEE 154

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	72
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	1e-33
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	1e-33
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	1e-33
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	2e-33
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	2e-33
4djt_A	218	GTP-binding nuclear protein GSP1; structural genom	2e-33
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	2e-33
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	2e-33
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	3e-33
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	4e-33
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	6e-33
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	7e-33
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	8e-33
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	9e-33
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	1e-32
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	2e-32
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	2e-32
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	2e-32
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	3e-32
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	3e-32
3bbp_A	211	RAB-6, RAS-related protein RAB-6A; golgi complex,	3e-32
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	3e-32
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	4e-32
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	4e-32
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	5e-32
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	5e-32
3l0i_B	199	RAS-related protein RAB-1A; GEF-GDF-RAB complex, G	7e-32
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	2e-31
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	3e-31
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	3e-31
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	7e-31
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	7e-31
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	7e-31
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	9e-31
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	2e-30
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	2e-30
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	3e-30
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	5e-30
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	1e-29
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	2e-29
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	2e-29
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	1e-28
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	2e-28
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	8e-23
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	1e-22
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	1e-22
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	3e-22
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	9e-22
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	1e-21
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	2e-21
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	2e-21
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	6e-21
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	1e-20
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	2e-20
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	2e-20
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	5e-20
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	1e-19
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	2e-19
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	3e-19
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	4e-19
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	9e-19
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	2e-18
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	3e-18
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	4e-18
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	4e-18
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	1e-17
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	1e-16
3dpu_A	535	RAB family protein; roccor, G-domain, COR, GTP-bin	2e-16
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	9e-16
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	5e-14
3c5h_A	255	Glucocorticoid receptor DNA-binding factor 1; RAS,	1e-10
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	9e-10
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	3e-09
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	6e-09
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	7e-09
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	1e-08
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	2e-08
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	3e-08
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	6e-08
3th5_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	8e-08
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	1e-07
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	2e-07
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	3e-07
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	3e-07
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	4e-06

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A* Length = 170

 Score =  111 bits (281), Expect = 1e-33
 Identities = 24/57 (42%), Positives = 37/57 (64%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           A+   YYRG+  A++VYD+TK  TF  +  W+++LR H   +IV+ + GNK DL  +
Sbjct: 70  ALAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQHGPPSIVVAIAGNKCDLTDV 126

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B* Length = 191

 Score =  112 bits (282), Expect = 1e-33
 Identities = 46/57 (80%), Positives = 52/57 (91%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct: 93  AITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 149

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae} Length = 223

 Score =  113 bits (284), Expect = 1e-33
 Identities = 36/57 (63%), Positives = 49/57 (85%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGA+GAL+VYD++KS+++EN + WL +LR++A  N+ + LIGNKSDL HL
Sbjct: 77  AITSAYYRGAVGALIVYDISKSSSYENCNHWLSELRENADDNVAVGLIGNKSDLAHL 133

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A* Length = 186

 Score =  111 bits (281), Expect = 2e-33
 Identities = 30/57 (52%), Positives = 38/57 (66%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           ++T +YYRGA GALLVYD+T   T+  ++ WL D R  A  NIVI+L GNK DL   
Sbjct: 74  SVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGNKKDLDAD 130

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A* Length = 199

 Score =  112 bits (282), Expect = 2e-33
 Identities = 45/57 (78%), Positives = 51/57 (89%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
            ITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL
Sbjct: 69  RITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHL 125

>4djt_A GTP-binding nuclear protein GSP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid, RAN family; HET: GDP; 1.80A {Encephalitozoon cuniculi} Length = 218

 Score =  112 bits (283), Expect = 2e-33
 Identities = 21/57 (36%), Positives = 35/57 (61%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
            +   YY GA GA+L +DVT   T +N++RW+K+ +   G+   I++  NK D+K+ 
Sbjct: 76  VLKDVYYIGASGAILFFDVTSRITCQNLARWVKEFQAVVGNEAPIVVCANKIDIKNR 132

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B* Length = 181

 Score =  111 bits (280), Expect = 2e-33
 Identities = 23/57 (40%), Positives = 36/57 (63%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           ++   YYRGA  A++V+DVT   +FE   +W+++L+     N+V+ L GNKSDL   
Sbjct: 76  SLAPMYYRGAAAAIIVFDVTNQASFERAKKWVQELQAQGNPNMVMALAGNKSDLLDA 132

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A* Length = 179

 Score =  111 bits (280), Expect = 2e-33
 Identities = 30/57 (52%), Positives = 43/57 (75%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           A+T +YYRGA GAL+VYD+T+ +T+ ++S WL D R+    N VI+LIGNK+DL+  
Sbjct: 79  AVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIILIGNKADLEAQ 135

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A* Length = 170

 Score =  110 bits (278), Expect = 3e-33
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           ++   YYRGA  A++VYD+T   +F     W+K+L+  A  NIVI L GNK+DL + 
Sbjct: 70  SLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANK 126

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A* Length = 170

 Score =  110 bits (277), Expect = 4e-33
 Identities = 24/57 (42%), Positives = 37/57 (64%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           A+   YYR + GA+LVYD+T   +F+ V  W+K+LR   G+ I + ++GNK DL+  
Sbjct: 70  ALGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEKE 126

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens} Length = 193

 Score =  110 bits (278), Expect = 6e-33
 Identities = 38/57 (66%), Positives = 46/57 (80%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AITSAYYRGA+GALLV+D+TK  T+  V RWLK+L DHA + IV+ML+GNKSDL   
Sbjct: 89  AITSAYYRGAVGALLVFDLTKHQTYAVVERWLKELYDHAEATIVVMLVGNKSDLSQA 145

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A* Length = 191

 Score =  110 bits (277), Expect = 7e-33
 Identities = 35/57 (61%), Positives = 46/57 (80%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           +IT +YYRGA GALLVYD+T+  TF +++ WL+D R H+ SN+VIMLIGNKSDL+  
Sbjct: 85  SITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESR 141

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens} Length = 200

 Score =  110 bits (278), Expect = 8e-33
 Identities = 29/57 (50%), Positives = 39/57 (68%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           ++T +YYRGA GALLVYD+T   T+ +++ WL D R  A  NIV++L GNK DL   
Sbjct: 89  SVTRSYYRGAAGALLVYDITSRETYNSLAAWLTDARTLASPNIVVILCGNKKDLDPE 145

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8 Length = 192

 Score =  110 bits (277), Expect = 9e-33
 Identities = 23/57 (40%), Positives = 39/57 (68%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           ++   YYRG+  A++VYD+TK  +F  + +W+K+L++H   NIV+ + GNK DL  +
Sbjct: 87  SLAPMYYRGSAAAVIVYDITKQDSFYTLKKWVKELKEHGPENIVMAIAGNKCDLSDI 143

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A* Length = 206

 Score =  110 bits (277), Expect = 1e-32
 Identities = 26/57 (45%), Positives = 39/57 (68%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
            ITS+YYRG+ G ++VYDVT   +F  V  WL+++  +A S ++ +L+GNK DLK  
Sbjct: 72  TITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYATSTVLKLLVGNKCDLKDK 128

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A* Length = 179

 Score =  109 bits (274), Expect = 2e-32
 Identities = 22/57 (38%), Positives = 39/57 (68%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           ++  +Y R +  A++VYD+T + +F   S+W+ D+R   GS+++IML+GNK+DL   
Sbjct: 78  SLIPSYIRDSTVAVVVYDITNTNSFHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDK 134

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens} Length = 201

 Score =  109 bits (275), Expect = 2e-32
 Identities = 33/57 (57%), Positives = 44/57 (77%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
            IT +YYR A GA+L YD+TK ++F +V  W++D+R +AGSNIV +LIGNKSDL  L
Sbjct: 93  TITQSYYRSANGAILAYDITKRSSFLSVPHWIEDVRKYAGSNIVQLLIGNKSDLSEL 149

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8 Length = 180

 Score =  108 bits (273), Expect = 2e-32
 Identities = 24/57 (42%), Positives = 38/57 (66%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           ++T AYYR A   LL+YDVT   +F+N+  WL ++ ++A  ++ +ML+GNK D  H 
Sbjct: 75  SVTHAYYRDAHALLLLYDVTNKASFDNIQAWLTEIHEYAQHDVALMLLGNKVDSAHE 131

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8 Length = 203

 Score =  109 bits (274), Expect = 3e-32
 Identities = 22/57 (38%), Positives = 37/57 (64%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
            IT+AYYRGA+G +L+YD+T   +F  V  W   ++ ++  N  ++L+GNK D++  
Sbjct: 72  TITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDMEDE 128

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A* Length = 183

 Score =  108 bits (273), Expect = 3e-32
 Identities = 24/57 (42%), Positives = 42/57 (73%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
            IT+AYYRGA+G +LVYD+T   +F+N+  W++++ +HA +++  M++GNK D+   
Sbjct: 72  TITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDK 128

>3bbp_A RAB-6, RAS-related protein RAB-6A; golgi complex, GRIP domain, RAB GTPase, ARL GTPase, golgin, RAB effector, clAsp protein; HET: GTP; 3.00A {Homo sapiens} Length = 211

 Score =  109 bits (274), Expect = 3e-32
 Identities = 21/57 (36%), Positives = 39/57 (68%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           ++  +Y R +  A++VYD+T   +F+  ++W+ D+R   GS+++IML+GNK+DL   
Sbjct: 80  SLIPSYIRDSTVAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADK 136

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens} Length = 192

 Score =  108 bits (273), Expect = 3e-32
 Identities = 25/57 (43%), Positives = 40/57 (70%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           +ITSAYYR A G +LVYD+TK  TF+++ +W+K +  +A  +  ++L+GNK D +  
Sbjct: 90  SITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETD 146

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens} Length = 199

 Score =  108 bits (273), Expect = 4e-32
 Identities = 23/60 (38%), Positives = 37/60 (61%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           +I  +Y+R A G LL+YDVT   +F N+  W+  + D A   + IML+GNK+D++    +
Sbjct: 92  SIAKSYFRKADGVLLLYDVTCEKSFLNIREWVDMIEDAAHETVPIMLVGNKADIRDTAAT 151

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens} Length = 196

 Score =  108 bits (273), Expect = 4e-32
 Identities = 27/57 (47%), Positives = 39/57 (68%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
            ITS+YYRGA G ++VYDVT   +F NV +WL+++  +A  N+  +L+GNK DL   
Sbjct: 80  TITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTK 136

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A* Length = 189

 Score =  108 bits (272), Expect = 5e-32
 Identities = 23/57 (40%), Positives = 36/57 (63%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
            IT+AYYRGA+G LL+YD+    +F  V  W   ++ ++  N  ++L+GNK DL+  
Sbjct: 86  TITTAYYRGAMGFLLMYDIANQESFAAVQDWATQIKTYSWDNAQVILVGNKCDLEDE 142

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8 Length = 201

 Score =  108 bits (272), Expect = 5e-32
 Identities = 20/57 (35%), Positives = 35/57 (61%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           +IT +YYR A   +L YD+T   +F  +  WL+++  +A + ++ +L+GNK DL   
Sbjct: 90  SITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYASNKVITVLVGNKIDLAER 146

>3l0i_B RAS-related protein RAB-1A; GEF-GDF-RAB complex, GTP-binding, guanine-nucleotide exchang GDI-displacement factor; 2.85A {Homo sapiens} Length = 199

 Score =  108 bits (271), Expect = 7e-32
 Identities = 27/57 (47%), Positives = 39/57 (68%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
            ITS+YYRGA G ++VYDVT   +F NV +WL+++  +A  N+  +L+GNK DL   
Sbjct: 97  TITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTK 153

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} Length = 191

 Score =  106 bits (267), Expect = 2e-31
 Identities = 22/57 (38%), Positives = 37/57 (64%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
            IT+AYYRGA+G +L+YD+T   +F  V  W   ++ ++  N  ++L+GNK D++  
Sbjct: 87  TITTAYYRGAMGFILMYDITNEESFNAVQDWATQIKTYSWDNAQVILVGNKCDMEEE 143

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A Length = 170

 Score =  105 bits (265), Expect = 3e-31
 Identities = 27/54 (50%), Positives = 39/54 (72%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
            IT+AYYRGA+G +LVYD+T   TF N+ +W K + +HA     ++L+GNKSD+
Sbjct: 67  TITTAYYRGAMGIILVYDITDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDM 120

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A* Length = 195

 Score =  106 bits (267), Expect = 3e-31
 Identities = 26/58 (44%), Positives = 40/58 (68%), Gaps = 1/58 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDLKHL 57
           ++T+A++R A+G LL++D+T   +F NV  W+  L+ HA S N  I+L GNKSDL+  
Sbjct: 85  SLTTAFFRDAMGFLLLFDLTNEQSFLNVRNWISQLQMHAYSENPDIVLCGNKSDLEDQ 142

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A* Length = 168

 Score =  104 bits (263), Expect = 7e-31
 Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
           AIT AYYRGA   +LV+  T   +FE +S W + +      +I   L+ NK DL   
Sbjct: 69  AITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAEV-GDIPTALVQNKIDLLDD 124

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8 Length = 213

 Score =  105 bits (265), Expect = 7e-31
 Identities = 28/54 (51%), Positives = 39/54 (72%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL 54
            IT+AYYRGA+G +LVYDVT   TF N+ +W K + +HA     ++L+GNKSD+
Sbjct: 84  TITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDM 137

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A* Length = 217

 Score =  106 bits (266), Expect = 7e-31
 Identities = 24/58 (41%), Positives = 39/58 (67%), Gaps = 1/58 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDLKHL 57
           ++T+A++R A+G LL++D+T   +F NV  W+  L+ +A   N  I+LIGNK+DL   
Sbjct: 99  SLTTAFFRDAMGFLLMFDLTSQQSFLNVRNWMSQLQANAYCENPDIVLIGNKADLPDQ 156

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B* Length = 189

 Score =  104 bits (263), Expect = 9e-31
 Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSN-IVIMLIGNKSDLKHL 57
           ++   YYR     + VYD+T   +F ++  W+++ + H  +N I  +L+GNK DL+  
Sbjct: 85  SMVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRILVGNKCDLRSA 142

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A* Length = 178

 Score =  104 bits (261), Expect = 2e-30
 Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 3/60 (5%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWL---KDLRDHAGSNIVIMLIGNKSDLKHL 57
            +   Y  GA G LLVYD+T   +FEN+  W    K + + + +  ++ L+GNK DL+H+
Sbjct: 71  KMLDKYIYGAQGVLLVYDITNYQSFENLEDWYTVVKKVSEESETQPLVALVGNKIDLEHM 130

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens} Length = 181

 Score =  104 bits (261), Expect = 2e-30
 Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL 57
            ITS YYRG  G ++VYDVT + +F NV RWL ++  +   ++  +L+GNK+D    
Sbjct: 73  TITSTYYRGTHGVIVVYDVTSAESFVNVKRWLHEINQNC-DDVCRILVGNKNDDPER 128

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C Length = 208

 Score =  104 bits (261), Expect = 3e-30
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRD---HAGSNIVIMLIGNKSDLKHL 57
              S Y+ G   A+LV+DV+   +FE+   W + L+         +  +L+ NK+DL   
Sbjct: 88  EQISQYWNGVYYAILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANKTDLPPQ 147

>3gj0_A GTP-binding nuclear protein RAN; G protein, GDP, acetylation, cytoplasm, HOST- virus interaction, nucleotide-binding, nucleus, phosphoprotein; HET: GDP; 1.48A {Homo sapiens} PDB: 3gj3_A* 3gj5_A* 3gj4_A* 3gj6_A* 3gj7_A* 3gj8_A* 1i2m_A 1a2k_C 1ibr_A* 1k5d_A* 1k5g_A* 1qbk_C* 3a6p_C* 3ch5_A* 1qg4_A* 3ea5_A* 1qg2_A* 1byu_A* 3ran_A* 3gjx_C* ... Length = 221

 Score =  104 bits (261), Expect = 5e-30
 Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
            +   YY  A  A++++DVT   T++NV  W +DL      NI I+L GNK D+K 
Sbjct: 79  GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKD 133

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A* Length = 177

 Score =  101 bits (255), Expect = 1e-29
 Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 4/60 (6%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA----GSNIVIMLIGNKSDLKH 56
           ++ + +YRG+   LL + V  S +F+N+S W K+   +A      +   +++GNK D+  
Sbjct: 71  SLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDISE 130

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8 Length = 195

 Score =  101 bits (255), Expect = 2e-29
 Identities = 27/55 (49%), Positives = 35/55 (63%), Gaps = 1/55 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSN-IVIMLIGNKSDL 54
            +T +YYRGA G +LVYDVT+  TF  +  WL +L  +   N IV ML+GNK D 
Sbjct: 79  TLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDK 133

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B* Length = 207

 Score =  101 bits (255), Expect = 2e-29
 Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 4/60 (6%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA----GSNIVIMLIGNKSDLKH 56
           ++  A+YRGA   +LV+DVT   TF+ +  W  +    A      N   +++GNK DL++
Sbjct: 72  SLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLEN 131

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum} Length = 208

 Score =  100 bits (250), Expect = 1e-28
 Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 2/56 (3%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           +I   YYRGA  A++V+D++ S T +    W+  L+    SN +I+L+ NK D   
Sbjct: 108 SIVPLYYRGATCAIVVFDISNSNTLDRAKTWVNQLKIS--SNYIIILVANKIDKNK 161

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A* Length = 182

 Score = 98.8 bits (247), Expect = 2e-28
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 4/61 (6%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA----GSNIVIMLIGNKSDLKH 56
           ++  A+YRGA   +LVYDVT +++FEN+  W  +   HA          +++GNK D + 
Sbjct: 73  SLGVAFYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEE 132

Query: 57  L 57
            
Sbjct: 133 S 133

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} Length = 169

 Score = 84.1 bits (209), Expect = 8e-23
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDL-RDHAGSNIVIMLIGNKSDLKH 56
           +     +     L+V+ VT   +F  V   L  L       ++ ++L+GNKSDL  
Sbjct: 68  LQDHCLQTGDAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLAR 123

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A* Length = 192

 Score = 84.3 bits (209), Expect = 1e-22
 Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDLKHLLNS 60
           +     +     L+VY +T   +FE  S     LR    + +I I+L+GNKSDL      
Sbjct: 73  LHDHCMQVGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRXREV 132

Query: 61  MCEE 64
              E
Sbjct: 133 SVSE 136

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B* Length = 184

 Score = 83.9 bits (208), Expect = 1e-22
 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 1   AITSAYYRGALGALLVYDVTK-STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           +    +       L VYD++K     + +  WL +++  A S+  ++L+G   D+  
Sbjct: 71  STHPHFMTQRALYLAVYDLSKGQAEVDAMKPWLFNIKARA-SSSPVILVGTHLDVSD 126

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens} Length = 195

 Score = 83.4 bits (207), Expect = 3e-22
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDL-RDHAGSNIVIMLIGNKSDLKH 56
           +     +     L+V+ VT   +F  V   L  L       ++ ++L+GNKSDL  
Sbjct: 89  LRDHCLQTGDAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLAR 144

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8 Length = 211

 Score = 82.8 bits (205), Expect = 9e-22
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDLKH 56
           +     +     L+VY +T   +FE  S     LR    + +I I+L+GNKSDL  
Sbjct: 104 LHDHCMQVGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVR 159

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A* Length = 166

 Score = 81.4 bits (202), Expect = 1e-21
 Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDLKH 56
            +           ++VY VT   +FE  S     LR    + ++ I+L+GNKSDL  
Sbjct: 64  WLPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVR 120

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A* Length = 168

 Score = 80.6 bits (200), Expect = 2e-21
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKH 56
           AI   Y+R   G L V+ +T+  +F   + + +  LR     N+  +L+GNKSDL+ 
Sbjct: 67  AIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLED 123

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A* Length = 187

 Score = 81.1 bits (201), Expect = 2e-21
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKH 56
           AI   Y+R   G L V+ +T+  +F   + + +  LR     N+  +L+GNKSDL+ 
Sbjct: 81  AIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLED 137

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens} Length = 175

 Score = 79.5 bits (197), Expect = 6e-21
 Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDL-RDHAGSNIVIMLIGNKSDLKH 56
               +  +G    ++VY +    +FE+ S     L R H   ++ I+L+GNK+DL  
Sbjct: 69  WSQESCLQGGSAYVIVYSIADRGSFESASELRIQLRRTHQADHVPIILVGNKADLAR 125

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A* Length = 181

 Score = 78.7 bits (195), Expect = 1e-20
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKH 56
           A+   Y R   G LLV+ +    +F  V +     LR     +  ++L+GNK+DL+ 
Sbjct: 72  AMREQYMRAGHGFLLVFAINDRQSFNEVGKLFTQILRVKDRDDFPVVLVGNKADLES 128

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens} Length = 206

 Score = 79.2 bits (196), Expect = 2e-20
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKH 56
           AI   Y+R   G L V+ +T+  +F   + + +  LR     N+  +L+GNKSDL+ 
Sbjct: 77  AIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLED 133

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens} Length = 201

 Score = 78.8 bits (195), Expect = 2e-20
 Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKH 56
            +  ++  G  G +LVY VT   +F+ +    +     H  + + ++L+GNK+DL  
Sbjct: 87  ILPYSFIIGVHGYVLVYSVTSLHSFQVIESLYQKLHEGHGKTRVPVVLVGNKADLSP 143

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 Length = 170

 Score = 77.1 bits (190), Expect = 5e-20
 Identities = 24/56 (42%), Positives = 34/56 (60%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           ++   YYR A  AL+VYDVTK  +F     W+K+L + A  +I+I L+GNK D   
Sbjct: 67  SLAPXYYRNAQAALVVYDVTKPQSFIKARHWVKELHEQASKDIIIALVGNKIDXLQ 122

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A* Length = 183

 Score = 76.4 bits (189), Expect = 1e-19
 Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDLKH 56
           A+   Y R   G L+VY VT   +FE+V R+ + +       +  ++L+ NK DL H
Sbjct: 81  AMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMH 137

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ... Length = 166

 Score = 75.2 bits (186), Expect = 2e-19
 Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDLKH 56
           A+   Y R   G L V+ +  + +FE++ ++ + ++    S ++ ++L+GNKSDL  
Sbjct: 66  AMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKSDLAA 122

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* Length = 181

 Score = 75.3 bits (186), Expect = 3e-19
 Identities = 19/57 (33%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKH 56
                Y     G +LVY VT   +FE +       L       I IML+GNK DL  
Sbjct: 69  IFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHM 125

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 Length = 172

 Score = 74.9 bits (185), Expect = 4e-19
 Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 2/58 (3%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS--NIVIMLIGNKSDLKH 56
           A+           +LVY +T   + E +    + + +  G   +I IML+GNK D   
Sbjct: 66  AMQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIKGDVESIPIMLVGNKCDESP 123

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R* Length = 167

 Score = 73.7 bits (182), Expect = 9e-19
 Identities = 13/57 (22%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKH 56
           ++   Y +   G +LVY +    +F+++       +R      + ++L+GNK DL+ 
Sbjct: 66  SMRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRYEKVPVILVGNKVDLES 122

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8 Length = 196

 Score = 73.4 bits (181), Expect = 2e-18
 Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDLKH 56
                + R   G +LVYD+T   +FE V      L +     N+ ++L+GNK+DL H
Sbjct: 90  IQREGHMRWGEGFVLVYDITDRGSFEEVLPLKNILDEIKKPKNVTLILVGNKADLDH 146

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A* Length = 190

 Score = 73.0 bits (180), Expect = 3e-18
 Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDL 54
           A+   Y R   G L V+ +  S +F +++ + + ++    S ++ ++L+GNK DL
Sbjct: 84  AMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDL 138

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8 Length = 199

 Score = 73.0 bits (180), Expect = 4e-18
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 2/58 (3%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRD--HAGSNIVIMLIGNKSDLKH 56
           A+           +LV+ VT   + E +    K +     +  +I +ML+GNK D   
Sbjct: 71  AMQRLSISKGHAFILVFSVTSKQSLEELGPIYKLIVQIKGSVEDIPVMLVGNKCDETQ 128

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D* Length = 167

 Score = 72.1 bits (178), Expect = 4e-18
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKH 56
           A+   Y +   G  LVY +T  +TF ++    +  LR     ++ ++L+GNK DL+ 
Sbjct: 66  AMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 122

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A* Length = 189

 Score = 71.5 bits (176), Expect = 1e-17
 Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDL 54
           A+   Y R   G L V+ +  + +FE++  + + ++    S ++ ++L+GNK DL
Sbjct: 67  AMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDL 121

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens} Length = 187

 Score = 68.8 bits (169), Expect = 1e-16
 Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 3/56 (5%)

Query: 4   SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG---SNIVIMLIGNKSDLKH 56
             Y   A   L+VY V    +F++ S +L+ L  HA     +I  +L+GNK D+  
Sbjct: 86  ERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQ 141

>3dpu_A RAB family protein; roccor, G-domain, COR, GTP-binding, nucleotide-binding, SIGN protein; 2.90A {Chlorobaculum tepidum} Length = 535

 Score = 70.8 bits (173), Expect = 2e-16
 Identities = 11/56 (19%), Positives = 22/56 (39%), Gaps = 4/56 (7%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           A    +   +   +L+ D     T  N   WL+ +  + G    ++++ NK D   
Sbjct: 113 ASHQFFMTRSSVYMLLLDS---RTDSNKHYWLRHIEKYGG-KSPVIVVMNKIDENP 164

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} Length = 184

 Score = 66.4 bits (163), Expect = 9e-16
 Identities = 6/50 (12%), Positives = 20/50 (40%), Gaps = 1/50 (2%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDL 54
           +       + V+ +    +F+ V  +   L     +  + ++L+G +  +
Sbjct: 82  FAAWVDAVVFVFSLEDEISFQTVYNYFLRLCSFRNASEVPMVLVGTQDAI 131

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A Length = 178

 Score = 61.9 bits (151), Expect = 5e-14
 Identities = 11/56 (19%), Positives = 22/56 (39%), Gaps = 5/56 (8%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRW---LKDLRDHAGSNIVIMLIG--NKSDLKH 56
           +   A   + V+ +    +F+ VSR    L  LR      + + L+G  ++     
Sbjct: 69  FSGWADAVIFVFSLEDENSFQAVSRLHGQLSSLRGEGRGGLALALVGTQDRISASS 124

>3c5h_A Glucocorticoid receptor DNA-binding factor 1; RAS, GTPase, glucorticoid receptor, structural genomics consortium, SGC, alternative splicing; HET: GNP; 1.80A {Homo sapiens} Length = 255

 Score = 53.5 bits (128), Expect = 1e-10
 Identities = 10/48 (20%), Positives = 23/48 (47%), Gaps = 3/48 (6%)

Query: 12  GALLVYDVTK--STTFENVSRWLKDLRDHAGS-NIVIMLIGNKSDLKH 56
           G LL  DV++  +  F++  +++ +L +        I+++  K D   
Sbjct: 165 GFLLGIDVSRGMNRNFDDQLKFVSNLYNQLAKTKKPIVVVLTKCDEGV 212

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C Length = 182

 Score = 50.8 bits (122), Expect = 9e-10
 Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
           +    YRGA   +L + +    ++ENV  +W+ +L+ +A   + I+L+G K DL
Sbjct: 72  LRPLSYRGADVFILAFSLISKASYENVSKKWIPELKHYA-PGVPIVLVGTKLDL 124

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* Length = 194

 Score = 49.3 bits (118), Expect = 3e-09
 Identities = 13/54 (24%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
           +    Y  +   LL + V   T+F+N+ ++W  +++ +       +L+G K DL
Sbjct: 87  LRPLSYADSDVVLLCFAVNNRTSFDNISTKWEPEIKHYI-DTAKTVLVGLKVDL 139

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ... Length = 201

 Score = 48.6 bits (116), Expect = 6e-09
 Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
           +    Y      L+ + +    + EN+  +W  +++     N+ I+L+GNK DL
Sbjct: 89  LRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFC-PNVPIILVGNKKDL 141

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens} Length = 214

 Score = 48.6 bits (116), Expect = 7e-09
 Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 2/54 (3%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
           +   +Y  A   LL +DVT   +F+N+ +RW  ++       + I+++G K+DL
Sbjct: 98  LRPLFYPDASVLLLCFDVTSPNSFDNIFNRWYPEVNHFC-KKVPIIVVGCKTDL 150

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana} Length = 212

 Score = 48.1 bits (115), Expect = 1e-08
 Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 2/50 (4%)

Query: 6   YYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
            YRGA   +L + +    ++ENV  +W+ +LR  A  N+ I+L+G K DL
Sbjct: 77  SYRGADIFVLAFSLISKASYENVLKKWMPELRRFA-PNVPIVLVGTKLDL 125

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B* Length = 184

 Score = 47.4 bits (113), Expect = 2e-08
 Identities = 13/54 (24%), Positives = 30/54 (55%), Gaps = 2/54 (3%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
           +    Y  +   L+ +D+++  T ++V  +W  ++++    N  ++L+G KSDL
Sbjct: 71  VRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFC-PNTKMLLVGCKSDL 123

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8 Length = 207

 Score = 46.7 bits (111), Expect = 3e-08
 Identities = 13/56 (23%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           +    Y      L+ + V    + EN+  +W+ +++     N+ I+L+ NK DL+ 
Sbjct: 89  LRPLSYPDTDVILMCFSVDSPDSLENIPEKWVPEVKHFC-PNVPIILVANKKDLRS 143

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8 Length = 205

 Score = 45.9 bits (109), Expect = 6e-08
 Identities = 13/54 (24%), Positives = 30/54 (55%), Gaps = 2/54 (3%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
           +    Y  +   L+ +D+++  T ++V  +W  ++++    N  ++L+G KSDL
Sbjct: 92  VRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFC-PNTKMLLVGCKSDL 144

>3th5_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTPase, GTP binding, protein binding, signali protein; HET: GNP; 2.30A {Homo sapiens} Length = 204

 Score = 45.5 bits (108), Expect = 8e-08
 Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 6   YYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
            Y      L+ + +    +FENV ++W  ++R H   N  I+L+G K DL
Sbjct: 98  SYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHC-PNTPIILVGTKLDL 146

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens} Length = 201

 Score = 45.1 bits (107), Expect = 1e-07
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 6   YYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
            Y      LL + V   ++F+NV  +W+ ++R H      I+L+G +SDL
Sbjct: 88  CYTNTDIFLLCFSVVSPSSFQNVSEKWVPEIRCHC-PKAPIILVGTQSDL 136

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8 Length = 194

 Score = 44.4 bits (105), Expect = 2e-07
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 6   YYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
            Y      L+ + V    +F+NV   W+ +L+++A  N+  +LIG + DL
Sbjct: 86  SYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAP-NVPFLLIGTQIDL 134

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ... Length = 186

 Score = 44.0 bits (104), Expect = 3e-07
 Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
           +    Y     +L+ + +    +FENV ++W  ++R H   N  I+L+G K DL
Sbjct: 69  LRPLSYPQTDVSLICFSLVSPASFENVRAKWYPEVRHHC-PNTPIILVGTKLDL 121

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A* Length = 214

 Score = 44.1 bits (104), Expect = 3e-07
 Identities = 13/54 (24%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
           +    Y  +   LL +D+++  T ++   +W  ++ D+   +  ++LIG K+DL
Sbjct: 91  VRPLCYSDSDAVLLCFDISRPETVDSALKKWRTEILDYCP-STRVLLIGCKTDL 143

>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A* Length = 332

 Score = 41.1 bits (96), Expect = 4e-06
 Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 2/42 (4%)

Query: 14  LLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDL 54
           L+ + +    +F +V ++W  ++R H   N  I+L+G K DL
Sbjct: 231 LICFSLVSPASFHHVRAKWYPEVRHHC-PNTPIILVGTKLDL 271

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	72
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	99.88
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	99.74
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	99.74
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	99.74
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	99.73
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	99.71
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	99.71
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	99.71
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	99.71
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	99.7
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	99.7
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	99.7
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	99.7
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	99.7
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	99.69
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	99.69
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	99.69
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	99.69
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	99.69
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	99.69
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	99.69
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	99.69
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	99.69
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	99.69
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	99.69
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	99.69
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	99.68
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	99.68
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	99.68
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	99.68
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	99.68
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	99.68
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	99.68
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	99.68
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	99.67
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	99.67
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	99.67
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	99.67
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	99.66
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	99.66
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	99.66
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	99.66
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	99.66
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	99.66
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	99.65
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	99.65
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	99.65
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	99.65
4djt_A	218	GTP-binding nuclear protein GSP1; structural genom	99.64
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	99.64
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	99.64
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	99.64
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	99.64
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	99.63
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	99.63
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	99.63
3l0i_B	199	RAS-related protein RAB-1A; GEF-GDF-RAB complex, G	99.63
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	99.62
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	99.62
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	99.62
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	99.61
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	99.61
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	99.61
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	99.61
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	99.61
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	99.6
3c5h_A	255	Glucocorticoid receptor DNA-binding factor 1; RAS,	99.6
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	99.6
3r7w_B	331	Gtpase2, GTP-binding protein GTR2; RAG gtpases, GT	99.6
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	99.59
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	99.59
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	99.59
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	99.58
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	99.58
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	99.58
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	99.57
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	99.57
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	99.57
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	99.57
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	99.56
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	99.56
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	99.56
3llu_A	196	RAS-related GTP-binding protein C; structural geno	99.55
3r7w_A	307	Gtpase1, GTP-binding protein GTR1; RAG gtpases, GT	99.54
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	99.54
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	99.54
1azs_C	402	GS-alpha; complex (lyase/hydrolase), hydrolase, si	99.53
1cip_A	353	Protein (guanine nucleotide-binding protein alpha-	99.52
2xtz_A	354	Guanine nucleotide-binding protein alpha-1 subuni;	99.52
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	99.51
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	99.51
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	99.5
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	99.5
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	99.49
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	99.48
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	99.47
3ohm_A	327	Guanine nucleotide-binding protein G(Q) subunit A;	99.47
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	99.47
1zcb_A	362	G alpha I/13; GTP-binding, lipoprotein, membrane,	99.46
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	99.46
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	99.46
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	99.45
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	99.45
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	99.45
3th5_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	99.16
4fid_A	340	G protein alpha subunit; RAS-like domain, all-heli	99.44
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	99.44
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	99.43
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	99.43
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	99.42
1nrj_B	218	SR-beta, signal recognition particle receptor beta	99.35
3lvq_E	497	ARF-GAP with SH3 domain, ANK repeat and PH domain	99.33
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	99.31
3o47_A	329	ADP-ribosylation factor GTPase-activating protein	99.31
2ged_A	193	SR-beta, signal recognition particle receptor beta	99.25
2fh5_B	214	SR-beta, signal recognition particle receptor beta	99.19
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	99.18
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	99.14
3dpu_A	535	RAB family protein; roccor, G-domain, COR, GTP-bin	99.13
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	99.11
2wji_A	165	Ferrous iron transport protein B homolog; membrane	99.06
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	98.96
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	98.91
1lnz_A	342	SPO0B-associated GTP-binding protein; GTPase, OBG,	98.91
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	98.86
3l82_B	227	F-box only protein 4; TRFH domain, helix, GTPase d	98.83
2hjg_A	436	GTP-binding protein ENGA; GTPase ENGA KH-domain, h	98.83
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	98.82
4dcu_A	456	GTP-binding protein ENGA; GTPase, GDP, protein bin	98.79
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	98.78
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	98.78
3gee_A	476	MNME, tRNA modification GTPase MNME; G protein, cy	98.77
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	98.77
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	98.66
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	98.65
3a1s_A	258	Iron(II) transport protein B; FEOB, iron transport	98.62
3h2y_A	368	GTPase family protein; GTP-binding protein YQEH, p	98.62
3qq5_A	423	Small GTP-binding protein; hydrogenase, H-cluster,	98.6
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	98.56
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	98.55
1xzp_A	482	Probable tRNA modification GTPase TRME; GTP-bindin	98.55
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	98.53
3l2o_B	312	F-box only protein 4; small G protein fold, UBL co	98.52
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	98.44
3i8s_A	274	Ferrous iron transport protein B; GTPase, GPCR, ir	98.44
1jny_A	435	EF-1-alpha, elongation factor 1-alpha, EF-TU, TUF-	98.42
3geh_A	462	MNME, tRNA modification GTPase MNME; G protein, U3	98.41
1g7s_A	594	Translation initiation factor IF2/EIF5B; translati	98.36
1r5b_A	467	Eukaryotic peptide chain release factor GTP-bindi	98.35
3p26_A	483	Elongation factor 1 alpha-like protein; GTP/GDP bi	98.35
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	98.34
2qag_A	361	Septin-2, protein NEDD5; cell cycle, cell division	98.33
3ec1_A	369	YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase	98.32
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	98.32
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	98.32
2ywe_A	600	GTP-binding protein LEPA; G domain, beta-barrel, f	98.28
2hjg_A	436	GTP-binding protein ENGA; GTPase ENGA KH-domain, h	98.28
3cb4_D	599	GTP-binding protein LEPA; GTPase, OB-fold, membran	98.28
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	98.27
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	98.25
3sjy_A	403	Translation initiation factor 2 subunit gamma; zin	98.24
2j69_A	695	Bacterial dynamin-like protein; FZO, FZL, GTPase,	98.23
3t34_A	360	Dynamin-related protein 1A, linker, dynamin-relat	98.21
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	98.2
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	98.17
1n0u_A	842	EF-2, elongation factor 2; G-protein, CIS-proline,	98.16
3tr5_A	528	RF-3, peptide chain release factor 3; protein synt	98.15
3izq_1	611	HBS1P, elongation factor 1 alpha-like protein; NO-	98.14
1s0u_A	408	EIF-2-gamma, translation initiation factor 2 gamma	98.11
2c78_A	405	Elongation factor TU-A; hydrolase, GTPase, transla	98.1
3izy_P	537	Translation initiation factor IF-2, mitochondrial;	98.09
1d2e_A	397	Elongation factor TU (EF-TU); G-protein, beta-barr	98.08
2qpt_A	550	EH domain-containing protein-2; protein-nucleotide	98.07
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	98.05
3j2k_7	439	ERF3, eukaryotic polypeptide chain release factor	98.01
2elf_A	370	Protein translation elongation factor 1A; tRNA, py	98.01
1zo1_I	501	IF2, translation initiation factor 2; E. coli, rib	98.0
1zun_B	434	Sulfate adenylate transferase, subunit 1/adenylyls	97.99
1f60_A	458	Elongation factor EEF1A; protein-protein complex,	97.97
4dcu_A	456	GTP-binding protein ENGA; GTPase, GDP, protein bin	97.93
1dar_A	691	EF-G, elongation factor G; ribosomal translocase,	97.93
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	97.92
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	97.91
1wb1_A	482	Translation elongation factor SELB; selenocysteine	97.9
1kk1_A	410	EIF2gamma; initiation of translation; HET: GNP; 1.	97.85
2xex_A	693	Elongation factor G; GTPase, translation, biosynth	97.84
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	97.84
3avx_A	1289	Elongation factor TS, elongation factor TU, linke	97.78
2rdo_7	704	EF-G, elongation factor G; elongation factor G, EF	97.76
2h5e_A	529	Peptide chain release factor RF-3; beta barrel, tr	97.75
1puj_A	282	YLQF, conserved hypothetical protein YLQF; structu	97.57
1udx_A	416	The GTP-binding protein OBG; TGS domain, riken str	97.5
2dy1_A	665	Elongation factor G; translocation, GTP complex, s	97.47
1wxq_A	397	GTP-binding protein; structural genomics, riken st	97.37
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	97.26
3mca_A	592	HBS1, elongation factor 1 alpha-like protein; prot	97.24
2x2e_A	353	Dynamin-1; nitration, hydrolase, membrane fission,	97.16
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	97.08
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	97.05
3t5d_A	274	Septin-7; GTP-binding protein, cytoskeleton, signa	96.97
3cnl_A	262	YLQF, putative uncharacterized protein; circular p	96.69
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	96.35
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	96.21
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	96.02
2hf9_A	226	Probable hydrogenase nickel incorporation protein	95.92
1jal_A	363	YCHF protein; nucleotide-binding fold, structural	95.69
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	95.18
3vqt_A	548	RF-3, peptide chain release factor 3; translation,	95.16
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	94.73
3zvr_A	772	Dynamin-1; hydrolase, DRP1, DRP, endocytosis, mito	94.52
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	94.31
4fn5_A	709	EF-G 1, elongation factor G 1; translation, transl	93.51
3j25_A	638	Tetracycline resistance protein TETM; antibiotic r	90.53
4a9a_A	376	Ribosome-interacting GTPase 1; DRG-DFRP complex, r	90.34
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	87.86
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	86.26
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	83.72
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	80.59

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=99.88  E-value=2.5e-22  Score=116.13  Aligned_cols=71  Identities=34%  Similarity=0.672  Sum_probs=66.6

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++++.||++++++++|||+++++||+++..|+..+.....+++|++|||||+||.++|.|+.+++.++|++
T Consensus        77 ~l~~~~~~~a~~~ilv~di~~~~Sf~~i~~~~~~i~~~~~~~~piilVgNK~Dl~~~r~V~~~e~~~~a~~  147 (216)
T 4dkx_A           77 SLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQVSIEEGERKAKE  147 (216)
T ss_dssp             GGHHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTTSSEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             hHHHHHhccccEEEEEeecchhHHHHHHHHHHHHHHHhcCCCCeEEEEeeccchHhcCcccHHHHhhHHHH
Confidence            36789999999999999999999999999999999888778899999999999999999999999999874

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=99.74  E-value=7.6e-18  Score=96.95  Aligned_cols=69  Identities=28%  Similarity=0.322  Sum_probs=60.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +.+.||++++++++|||++++.||+.+..|...+.+.. ..++|++|||||+||.+.+.+..+++..+++
T Consensus       104 l~~~~~~~a~~~ilVydvt~~~sf~~~~~~~~~l~~~~~~~~~piilVgNK~DL~~~r~v~~~e~~~~a~  173 (211)
T 2g3y_A          104 LHDHCMQVGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVSVSEGRACAV  173 (211)
T ss_dssp             HHHCCCCCCSEEEEEEETTCHHHHHHHHHHHHHHHTSGGGTTSCEEEEEECTTCGGGCCSCHHHHHHHHH
T ss_pred             HHHHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCcEEEEEEChHHhcCceEeHHHHHHHHH
Confidence            35678999999999999999999999999998887643 3579999999999998888999988887764

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=99.74  E-value=2.4e-17  Score=91.59  Aligned_cols=69  Identities=36%  Similarity=0.721  Sum_probs=60.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......++|+++||||+|+.+.+.++.+++.++++
T Consensus        73 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~v~~~~~~~~~~  141 (183)
T 2fu5_C           73 ITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLAL  141 (183)
T ss_dssp             -CCTTTTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEEC--CCSCCCSCHHHHHHHHH
T ss_pred             hHHHHHhcCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECccCCccCcCCHHHHHHHHH
Confidence            467899999999999999999999999999999988766789999999999999888899999988875

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=99.74  E-value=1.2e-17  Score=94.43  Aligned_cols=70  Identities=26%  Similarity=0.319  Sum_probs=62.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||++++++++|||++++.||+.+..|+..+..... .++|+++||||+|+.+.+.++.+++.++++.
T Consensus        89 ~~~~~~~~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~v~~~~~~~~a~~  159 (195)
T 3cbq_A           89 LRDHCLQTGDAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVSLEEGRHLAGT  159 (195)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHSTTSCCCEEEEEECTTCTTTCCSCHHHHHHHHHH
T ss_pred             hHHHhhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEeechhccccCCcCHHHHHHHHHH
Confidence            456789999999999999999999999999999877653 5799999999999998889999999988863

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens}

Probab=99.73  E-value=2.6e-17  Score=93.32  Aligned_cols=70  Identities=49%  Similarity=0.750  Sum_probs=63.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......++|+++||||+|+.+++.++.+++.++++.
T Consensus        94 ~~~~~~~~~d~iilv~D~~~~~s~~~~~~~~~~i~~~~~~~~piilv~NK~Dl~~~~~v~~~~~~~~~~~  163 (201)
T 2hup_A           94 ITQSYYRSANGAILAYDITKRSSFLSVPHWIEDVRKYAGSNIVQLLIGNKSDLSELREVSLAEAQSLAEH  163 (201)
T ss_dssp             HHHHHHTTCSEEEEEEETTBHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECCccccccccCHHHHHHHHHH
Confidence            3567899999999999999999999999999999887667899999999999998889999999888763

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=99.71  E-value=9.2e-17  Score=90.64  Aligned_cols=69  Identities=28%  Similarity=0.338  Sum_probs=60.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.||++++++++|||++++.||+.+..|...+.+.. ..++|+++||||+|+...+.+..+++..++.
T Consensus        73 ~~~~~~~~~~~~i~v~dv~~~~s~~~~~~~~~~l~~~~~~~~~piilV~NK~Dl~~~r~v~~~~~~~~a~  142 (192)
T 2cjw_A           73 LHDHCMQVGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRXREVSVSEGRAXAV  142 (192)
T ss_dssp             TGGGHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTTSCCCEEEEEECTTCGGGCCSCHHHHHHHHH
T ss_pred             HHHhhcccCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCeEEEEEechhhhccccccHHHHHHHHH
Confidence            56789999999999999999999999999998887653 3579999999999998888899888887764

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=99.71  E-value=1.5e-16  Score=88.23  Aligned_cols=70  Identities=34%  Similarity=0.371  Sum_probs=61.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++++|+.+..|+..+.+... .++|+++||||+|+.+++.+..+++.+++++
T Consensus        70 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~  140 (181)
T 3t5g_A           70 FPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES  140 (181)
T ss_dssp             CCGGGTTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHC----CCEEEEEECTTCTTTCCSCHHHHHHHHHH
T ss_pred             HHHHHHhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccchhcceecHHHHHHHHHH
Confidence            567899999999999999999999999999999876643 5799999999999998899999999988864

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=99.71  E-value=8.3e-17  Score=88.23  Aligned_cols=70  Identities=26%  Similarity=0.320  Sum_probs=61.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|++++|++++|||++++++|+.+..|+..+..... .++|+++||||+|+.+.+.++.+++.+++++
T Consensus        68 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~  138 (169)
T 3q85_A           68 LQDHCLQTGDAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVSLEEGRHLAGT  138 (169)
T ss_dssp             --CHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHSTTSCCCEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             hhhhhhccCCEEEEEEECCChHHHHHHHHHHHHHHhcccCCCCCEEEEeeCcchhhcccCCHHHHHHHHHH
Confidence            466789999999999999999999999999999877654 4899999999999998899999999988764

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=99.71  E-value=8.5e-17  Score=92.06  Aligned_cols=69  Identities=20%  Similarity=0.416  Sum_probs=61.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHH-HHHHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFEN-VSRWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~-~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      +++.|++++|++++|||+++++||+. +..|+..+.... +++|+++||||+|+.++            +.++.+++.++
T Consensus        91 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~i~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  169 (214)
T 3q3j_B           91 VRPLCYSDSDAVLLCFDISRPETVDSALKKWRTEILDYC-PSTRVLLIGCKTDLRTDLSTLMELSHQKQAPISYEQGCAI  169 (214)
T ss_dssp             TGGGGCTTCSEEEEEEETTCTHHHHHHHTHHHHHHHHHC-TTSEEEEEEECGGGGGCHHHHHHHHHTTCCCCCHHHHHHH
T ss_pred             HHHHHcCCCeEEEEEEECcCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEEChhhccchhhhhhhcccccCccCHHHHHHH
Confidence            57889999999999999999999999 699999998875 68999999999999763            78999999988


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       170 ~~~  172 (214)
T 3q3j_B          170 AKQ  172 (214)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            864

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=99.70  E-value=9.2e-17  Score=90.08  Aligned_cols=70  Identities=33%  Similarity=0.615  Sum_probs=63.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......++|+++||||+|+.+++.+..+++..+++.
T Consensus        88 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  157 (191)
T 3dz8_A           88 ITTAYYRGAMGFILMYDITNEESFNAVQDWATQIKTYSWDNAQVILVGNKCDMEEERVVPTEKGQLLAEQ  157 (191)
T ss_dssp             HHHHHHTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHHccCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCccccccCHHHHHHHHHH
Confidence            3567899999999999999999999999999999887667899999999999998889999998888763

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=99.70  E-value=1.1e-16  Score=88.55  Aligned_cols=67  Identities=13%  Similarity=0.181  Sum_probs=57.5

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc---CCCCeEEEEeeCCCC--cccccCCHHHHHHHHh
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA---GSNIVIMLIGNKSDL--KHLLNSMCEEYLIKSR   70 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~---~~~~~~vlvgnK~Dl--~~~~~v~~~e~~~~a~   70 (72)
                      ..||+++|++++|||+++++||+.+..|++.+....   .+++|+++||||+|+  ...+.++.+++.++++
T Consensus        67 ~~~~~~~d~~ilv~D~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~~~v~~~~~~~~~~  138 (178)
T 2iwr_A           67 AKFSGWADAVIFVFSLEDENSFQAVSRLHGQLSSLRGEGRGGLALALVGTQDRISASSPRVVGDARARALXA  138 (178)
T ss_dssp             HHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHCSSSCCCEEEEEEECTTCBTTBCCCSCHHHHHHHHH
T ss_pred             hHHHHhCCEEEEEEECcCHHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccccCcCCHHHHHHHHH
Confidence            468999999999999999999999999877766543   257999999999999  4567899999988875

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=99.70  E-value=1.2e-16  Score=87.36  Aligned_cols=70  Identities=26%  Similarity=0.296  Sum_probs=54.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||++++++|+.+..|+..+.... ..++|+++||||+|+.+.+.+..+++.++++.
T Consensus        65 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~  135 (166)
T 3q72_A           65 LPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVSVDEGRACAVV  135 (166)
T ss_dssp             --------CCEEEEEEETTCHHHHHHHHHHHHHHHHCC---CCCEEEEEECTTCCSSCCSCHHHHHHHHHH
T ss_pred             hhhhhhhhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeccccccccccCHHHHHHHHHH
Confidence            56789999999999999999999999999999887654 36799999999999998899999998888753

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=99.70  E-value=1.4e-16  Score=89.32  Aligned_cols=69  Identities=55%  Similarity=0.850  Sum_probs=62.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......+.|+++||||+|+.+.+.+..+++.++++
T Consensus        86 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~l~~i~~~~~~~~piilv~nK~Dl~~~~~v~~~~~~~~~~  154 (191)
T 2a5j_A           86 ITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESRRDVKREEGEAFAR  154 (191)
T ss_dssp             CCHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHHHHHHHHH
T ss_pred             hHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECcccCCccccCHHHHHHHHH
Confidence            467899999999999999999999999999999988766789999999999998888899999988875

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=99.70  E-value=9.1e-17  Score=91.41  Aligned_cols=69  Identities=30%  Similarity=0.529  Sum_probs=62.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.......+|+++||||+|+.+.+.+..+++.++++
T Consensus        91 ~~~~~~~~~d~~i~v~D~~~~~s~~~~~~~~~~i~~~~~~~~piilv~NK~Dl~~~~~v~~~~~~~~~~  159 (201)
T 2ew1_A           91 ITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYASNKVITVLVGNKIDLAERREVSQQRAEEFSE  159 (201)
T ss_dssp             HHGGGSTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCSSCHHHHHHHHH
T ss_pred             HHHHHHhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCccccccCHHHHHHHHH
Confidence            356789999999999999999999999999999988766789999999999998888999999888875

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=99.69  E-value=4e-16  Score=88.21  Aligned_cols=70  Identities=37%  Similarity=0.614  Sum_probs=63.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.......+|+++||||+|+.+.+.+..+++.++++.
T Consensus        73 ~~~~~~~~~d~vilv~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  142 (206)
T 2bcg_Y           73 ITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYATSTVLKLLVGNKCDLKDKRVVEYDVAKEFADA  142 (206)
T ss_dssp             CCGGGGTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECTTCTTTCCSCHHHHHHHHHH
T ss_pred             HHHHhccCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCccccccCHHHHHHHHHH
Confidence            5678999999999999999999999999999999887667899999999999998888999998888753

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=99.69  E-value=1.7e-16  Score=86.72  Aligned_cols=70  Identities=37%  Similarity=0.629  Sum_probs=62.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.....+.+|+++||||+|+.+++.+..+++.+++++
T Consensus        71 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilv~nK~Dl~~~~~~~~~~~~~~~~~  140 (170)
T 1r2q_A           71 LAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADD  140 (170)
T ss_dssp             GHHHHHTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             hhHHhccCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECccCccccccCHHHHHHHHHH
Confidence            3567899999999999999999999999999999887667899999999999988888998998888753

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=99.69  E-value=3.3e-16  Score=87.58  Aligned_cols=70  Identities=34%  Similarity=0.595  Sum_probs=62.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......+.|+++||||+|+.+.+.+..+++.+++++
T Consensus        87 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  156 (189)
T 2gf9_A           87 ITTAYYRGAMGFLLMYDIANQESFAAVQDWATQIKTYSWDNAQVILVGNKCDLEDERVVPAEDGRRLADD  156 (189)
T ss_dssp             SGGGGGTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             hHHHhccCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECcccccccCCCHHHHHHHHHH
Confidence            4678999999999999999999999999999999887667899999999999988888988888888753

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=99.69  E-value=1.3e-16  Score=88.53  Aligned_cols=70  Identities=27%  Similarity=0.402  Sum_probs=62.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++++|+.+..|+..+.... ..++|+++||||+|+.+.+.+..+++.+++++
T Consensus        82 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~v~~~~~~~~~~~  152 (183)
T 3kkq_A           82 MREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTRDQGKEMATK  152 (183)
T ss_dssp             SHHHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTSSCCCEEEEEECTTCSTTCCSCHHHHHHHHHH
T ss_pred             HHHHHHhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECCCchhccCcCHHHHHHHHHH
Confidence            45778999999999999999999999999999986644 36799999999999998899999999988763

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=99.69  E-value=1.2e-16  Score=89.66  Aligned_cols=68  Identities=28%  Similarity=0.356  Sum_probs=60.7

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc---CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA---GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~---~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ..|+++++++++|||++++++|+.+..|+..+....   ..++|+++||||+|+.+.+.++.+++.+++++
T Consensus        86 ~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~v~~~~~~~~~~~  156 (187)
T 3c5c_A           86 ERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQYRQVTKAEGVALAGR  156 (187)
T ss_dssp             HHHHTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECGGGGGGCSSCHHHHHHHHHH
T ss_pred             HHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhhccCCCCCEEEEEECcchhhcCccCHHHHHHHHHH
Confidence            468999999999999999999999999999987763   25799999999999998889999999988763

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=99.69  E-value=2.4e-16  Score=88.21  Aligned_cols=70  Identities=40%  Similarity=0.619  Sum_probs=63.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......+.|+++||||+|+...+.+..+++.++++.
T Consensus        81 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~  150 (196)
T 3tkl_A           81 ITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADS  150 (196)
T ss_dssp             THHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCTTTCCSCHHHHHHHHHH
T ss_pred             hHHHHHhhCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECcccccccccCHHHHHHHHHH
Confidence            4567899999999999999999999999999999888767899999999999998889999988888763

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=99.69  E-value=1.2e-16  Score=87.59  Aligned_cols=70  Identities=36%  Similarity=0.650  Sum_probs=61.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......++|+++|+||+|+.+++.++.+++.+++++
T Consensus        71 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  140 (170)
T 1z08_A           71 LGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEKERHVSIQEAESYAES  140 (170)
T ss_dssp             --CCSSTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHHGGGSEEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             hHHHHhccCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCeEEEEEECcccccccccCHHHHHHHHHH
Confidence            4577899999999999999999999999999998776656799999999999998889999999888764

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=99.69  E-value=3.2e-16  Score=86.67  Aligned_cols=70  Identities=34%  Similarity=0.667  Sum_probs=62.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.....+++|+++|+||+|+.+.+.+..+++.+++++
T Consensus        77 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~p~i~v~nK~Dl~~~~~~~~~~~~~~~~~  146 (181)
T 2efe_B           77 LAPMYYRGAAAAIIVFDVTNQASFERAKKWVQELQAQGNPNMVMALAGNKSDLLDARKVTAEDAQTYAQE  146 (181)
T ss_dssp             GTHHHHTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECTTCTTTCCSCHHHHHHHHHH
T ss_pred             hhHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECCcccccccCCHHHHHHHHHH
Confidence            4567899999999999999999999999999999887667899999999999988888999999888753

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=99.69  E-value=2.2e-16  Score=88.67  Aligned_cols=70  Identities=34%  Similarity=0.679  Sum_probs=63.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......++|+++||||+|+.+++.+..+++.+++++
T Consensus        88 ~~~~~~~~~d~iilV~d~~~~~s~~~~~~~~~~i~~~~~~~~piiiv~NK~Dl~~~~~v~~~~~~~~~~~  157 (192)
T 2fg5_A           88 LAPMYYRGSAAAVIVYDITKQDSFYTLKKWVKELKEHGPENIVMAIAGNKCDLSDIREVPLKDAKEYAES  157 (192)
T ss_dssp             GTHHHHTTCSEEEEEEETTCTHHHHHHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHHHHHHHHHT
T ss_pred             hhHHhhccCCEEEEEEeCCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEECcccccccccCHHHHHHHHHH
Confidence            4567899999999999999999999999999999887667899999999999988888999999988764

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=99.69  E-value=3.7e-16  Score=85.48  Aligned_cols=70  Identities=36%  Similarity=0.687  Sum_probs=62.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.....+.+|+++||||+|+.+.+.+..+++..++++
T Consensus        71 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~l~~~~~~~~~iilv~nK~Dl~~~~~v~~~~~~~~~~~  140 (170)
T 1z0j_A           71 LAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQHGPPSIVVAIAGNKCDLTDVREVMERDAKDYADS  140 (170)
T ss_dssp             GTHHHHTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTSEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             ccHhhCcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCcEEEEEECCccccccccCHHHHHHHHHH
Confidence            4567899999999999999999999999999999887667899999999999998888988888888753

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=99.69  E-value=2.1e-16  Score=86.89  Aligned_cols=68  Identities=25%  Similarity=0.372  Sum_probs=58.2

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      .+.|+++++++++|||++++.+|+.+..|+..+.... ..+.|+++||||+|+.+.+.++.+++..+++
T Consensus        71 ~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~l~~~~~~~~~piilv~NK~Dl~~~~~v~~~~~~~~~~  139 (175)
T 2nzj_A           71 QESCLQGGSAYVIVYSIADRGSFESASELRIQLRRTHQADHVPIILVGNKADLARCREVSVEEGRACAV  139 (175)
T ss_dssp             HHHTTTSCSEEEEEEETTCHHHHHHHHHHHHHHHHCC----CCEEEEEECTTCTTTCCSCHHHHHHHHH
T ss_pred             HHhhcccCCEEEEEEECCCHHHHHHHHHHHHHHHHhhccCCCCEEEEEEChhhccccccCHHHHHHHHH
Confidence            4678899999999999999999999999999887653 3579999999999999888899888887765

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=99.69  E-value=2e-16  Score=90.77  Aligned_cols=70  Identities=53%  Similarity=0.866  Sum_probs=60.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......++|+++||||+|+.+.+.++.+++.+++++
T Consensus        78 ~~~~~~~~~d~vilV~D~~~~~s~~~~~~~l~~i~~~~~~~~piilv~nK~Dl~~~~~v~~~~~~~~~~~  147 (223)
T 3cpj_B           78 ITSAYYRGAVGALIVYDISKSSSYENCNHWLSELRENADDNVAVGLIGNKSDLAHLRAVPTEESKTFAQE  147 (223)
T ss_dssp             CCGGGTTTCCEEEEEEC-CCHHHHHHHHHHHHHHHHHCC--CEEEEEECCGGGGGGCCSCHHHHHHHHHH
T ss_pred             hHHHHhccCCEEEEEEeCCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccccCHHHHHHHHHH
Confidence            5678999999999999999999999999999999887667899999999999988888999999888753

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=99.68  E-value=3.3e-16  Score=86.52  Aligned_cols=69  Identities=36%  Similarity=0.623  Sum_probs=60.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......+.|+++|+||+|+.+++.+..+++.++++
T Consensus        76 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~  144 (180)
T 2g6b_A           76 VTHAYYRDAHALLLLYDVTNKASFDNIQAWLTEIHEYAQHDVALMLLGNKVDSAHERVVKREDGEKLAK  144 (180)
T ss_dssp             ---CCGGGCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECCSTTSCCCSCHHHHHHHHH
T ss_pred             HHHHHccCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEECcccCcccccCHHHHHHHHH
Confidence            456789999999999999999999999999999988766789999999999999888899888888875

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C

Probab=99.68  E-value=2.4e-16  Score=88.74  Aligned_cols=70  Identities=24%  Similarity=0.375  Sum_probs=57.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC---CCCeEEEEeeCCCCcc-cccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG---SNIVIMLIGNKSDLKH-LLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~vlvgnK~Dl~~-~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.....   ..+|+++||||+|+.+ .+.++.+++.+++++
T Consensus        89 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~~v~~~~~~~~~~~  162 (208)
T 2yc2_C           89 QISQYWNGVYYAILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANKTDLPPQRHQVRLDMAQDWATT  162 (208)
T ss_dssp             HHSTTCCCCCEEEEEEETTCHHHHHHHHHHHHHHHHHCSCTTSCCEEEEEEECC-------CCCHHHHHHHHHH
T ss_pred             HHHHHHhhCcEEEEEEECCCHHHHHHHHHHHHHHHHhhcccccCCcEEEEEECcccchhhccCCHHHHHHHHHH
Confidence            356789999999999999999999999999999988765   5899999999999988 788999999988764

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=99.68  E-value=2.3e-16  Score=89.23  Aligned_cols=70  Identities=43%  Similarity=0.672  Sum_probs=63.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......++|+++||||+|+..++.++.+++.+++++
T Consensus        90 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~v~~~~~~~~~~~  159 (200)
T 2o52_A           90 VTRSYYRGAAGALLVYDITSRETYNSLAAWLTDARTLASPNIVVILCGNKKDLDPEREVTFLEASRFAQE  159 (200)
T ss_dssp             CCHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHTCTTCEEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHhccCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECCCcccccccCHHHHHHHHHH
Confidence            4677999999999999999999999999999999877667899999999999988888999998888753

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=99.68  E-value=3e-16  Score=87.54  Aligned_cols=69  Identities=19%  Similarity=0.436  Sum_probs=60.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      +++.|++++|++++|||++++.+|+.+ ..|+..+.... ++.|+++||||+|+.++            +.++.+++.++
T Consensus        71 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~i~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  149 (184)
T 1m7b_A           71 VRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFC-PNTKMLLVGCKSDLRTDVSTLVELSNHRQTPVSYDQGANM  149 (184)
T ss_dssp             TGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHC-TTCEEEEEEECGGGGGCHHHHHHHHTTTCCCCCHHHHHHH
T ss_pred             hHHhhcCCCcEEEEEEECCCHHHHHHHHHHHHHHHHHHC-CCCCEEEEEEcchhhcchhhHhhhhhcccCCCCHHHHHHH
Confidence            567899999999999999999999999 78999887765 67999999999999753            67899999888


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       150 ~~~  152 (184)
T 1m7b_A          150 AKQ  152 (184)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            863

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=99.68  E-value=3.4e-16  Score=86.19  Aligned_cols=69  Identities=45%  Similarity=0.749  Sum_probs=62.4

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +..|++++|++++|||++++.+|+.+..|+..+......+.|+++||||+|+.+++.+..+++.+++++
T Consensus        81 ~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  149 (179)
T 1z0f_A           81 TRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIILIGNKADLEAQRDVTYEEAKQFAEE  149 (179)
T ss_dssp             HHHHHHTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             HHHHhccCCEEEEEEeCcCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECcccccccccCHHHHHHHHHH
Confidence            467899999999999999999999999999999887767899999999999988888999999888753

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=99.68  E-value=3.8e-16  Score=87.33  Aligned_cols=70  Identities=24%  Similarity=0.542  Sum_probs=62.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.||+.+..|+..+.... ..+.|+++||||+|+.+.+.+..+++.+++++
T Consensus        86 ~~~~~~~~~d~iilv~D~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~v~~~~~~~~~~~  156 (189)
T 1z06_A           86 MVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRILVGNKCDLRSAIQVPTDLAQKFADT  156 (189)
T ss_dssp             THHHHHTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHCCCSCCCEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             hhHHHhcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccceeCHHHHHHHHHH
Confidence            45778999999999999999999999999999988765 46799999999999988888999999888763

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=99.68  E-value=1.7e-16  Score=89.18  Aligned_cols=69  Identities=35%  Similarity=0.569  Sum_probs=62.5

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +..|++++|++++|||++++.+|+.+..|+..+......+.|+++||||+|+.+.+.+..+++.+++++
T Consensus        92 ~~~~~~~~d~iilV~D~~~~~s~~~~~~~~~~i~~~~~~~~piilV~NK~Dl~~~~~v~~~~~~~~~~~  160 (192)
T 2il1_A           92 TSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETDREITRQQGEKFAQQ  160 (192)
T ss_dssp             HHHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHHHHHHHHHT
T ss_pred             HHHHhcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECcccccccccCHHHHHHHHHh
Confidence            467899999999999999999999999999999887667899999999999988889999999888764

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=99.68  E-value=4.8e-16  Score=87.65  Aligned_cols=70  Identities=33%  Similarity=0.585  Sum_probs=62.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......+.|+++||||+|+.+.+.+..+++.+++++
T Consensus        73 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  142 (203)
T 1zbd_A           73 ITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDMEDERVVSSERGRQLADH  142 (203)
T ss_dssp             HHHTTGGGCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCSSCEEEEEEECTTCTTSCCSCHHHHHHHHHH
T ss_pred             hHHHhhcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECcccCcccccCHHHHHHHHHH
Confidence            3567899999999999999999999999999999877667899999999999988888998888888753

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=99.67  E-value=2.6e-16  Score=87.43  Aligned_cols=69  Identities=45%  Similarity=0.652  Sum_probs=62.1

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +..|++++|++++|||++++.+|+.+..|+..+......++|+++||||+|+...+.++.+++.+++++
T Consensus        76 ~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  144 (186)
T 2bme_A           76 TRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGNKKDLDADREVTFLEASRFAQE  144 (186)
T ss_dssp             HHTTSTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHhcCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECcccccccccCHHHHHHHHHH
Confidence            467899999999999999999999999999998877667899999999999988888998998888753

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=99.67  E-value=5.8e-16  Score=87.47  Aligned_cols=70  Identities=26%  Similarity=0.407  Sum_probs=60.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++++|+.+..|+..+..... .++|+++||||+|+..++.+..+++.+++++
T Consensus        88 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~v~~~~~~~~~~~  158 (201)
T 3oes_A           88 LPYSFIIGVHGYVLVYSVTSLHSFQVIESLYQKLHEGHGKTRVPVVLVGNKADLSPEREVQAVEGKKLAES  158 (201)
T ss_dssp             CCGGGTTTCCEEEEEEETTCHHHHHHHHHHHHHHHC-----CCCEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHHhcCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccCccccccCHHHHHHHHHH
Confidence            567899999999999999999999999999999876543 5799999999999998899999999888763

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=99.67  E-value=1.1e-15  Score=84.34  Aligned_cols=68  Identities=37%  Similarity=0.646  Sum_probs=61.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|..+..|+..+.... ++.|+++||||+|+.+.+.+..+++..+++
T Consensus        74 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~  141 (181)
T 3tw8_B           74 ITSTYYRGTHGVIVVYDVTSAESFVNVKRWLHEINQNC-DDVCRILVGNKNDDPERKVVETEDAYKFAG  141 (181)
T ss_dssp             CCGGGGTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHC-TTSEEEEEEECTTCGGGCCSCHHHHHHHHH
T ss_pred             hHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCEEEEEECCCCchhcccCHHHHHHHHH
Confidence            46789999999999999999999999999999997765 689999999999999888899888888775

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=99.67  E-value=3.8e-16  Score=87.54  Aligned_cols=66  Identities=12%  Similarity=0.182  Sum_probs=58.8

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCC--cccccCCHHHHHHHHhc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDL--KHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl--~~~~~v~~~e~~~~a~~   71 (72)
                      |++++|++++|||++++.||+.+..|+..+..... .++|+++||||+|+  ...+.++.+++.+++++
T Consensus        82 ~~~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~v~~~~~~~~~~~  150 (184)
T 3ihw_A           82 FAAWVDAVVFVFSLEDEISFQTVYNYFLRLCSFRNASEVPMVLVGTQDAISAANPRVIDDSRARKLSTD  150 (184)
T ss_dssp             HHHHCSEEEEEEETTCHHHHHHHHHHHHHHHTTSCGGGSCEEEEEECTTCBTTBCCCSCHHHHHHHHHH
T ss_pred             eecCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccccCHHHHHHHHHH
Confidence            78999999999999999999999999999987653 57999999999999  45688999999988864

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=99.66  E-value=7.2e-16  Score=84.19  Aligned_cols=69  Identities=38%  Similarity=0.598  Sum_probs=61.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc---ccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL---LNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~---~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......++|+++||||+|+...   +.+..+++.++++
T Consensus        68 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~v~~~~~~~~~~  139 (170)
T 1ek0_A           68 LAPXYYRNAQAALVVYDVTKPQSFIKARHWVKELHEQASKDIIIALVGNKIDXLQEGGERKVAREEGEKLAE  139 (170)
T ss_dssp             GHHHHHTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECGGGGGSSCCCCSCHHHHHHHHH
T ss_pred             hhhhhhccCcEEEEEEecCChHHHHHHHHHHHHHHHhcCCCCcEEEEEECCCccccccccCCCHHHHHHHHH
Confidence            45678999999999999999999999999999998876678999999999999765   7788888888775

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=99.66  E-value=7.5e-16  Score=87.77  Aligned_cols=69  Identities=19%  Similarity=0.447  Sum_probs=60.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCcc------------cccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKH------------LLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~------------~~~v~~~e~~~~   68 (72)
                      +++.|+++++++++|||++++.+|+.+ ..|+..+.... ++.|+++||||+|+.+            .+.++.+++.++
T Consensus        92 ~~~~~~~~~d~~ilv~D~~~~~s~~~~~~~~~~~i~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  170 (205)
T 1gwn_A           92 VRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFC-PNTKMLLVGCKSDLRTDVSTLVELSNHRQTPVSYDQGANM  170 (205)
T ss_dssp             TGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHC-TTCEEEEEEECGGGGGCHHHHHHHHTTTCCCCCHHHHHHH
T ss_pred             HHHhhccCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHC-CCCCEEEEEechhhccchhhhhhhcccccCCCCHHHHHHH
Confidence            567899999999999999999999999 78999988765 6799999999999975            367888999888


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       171 ~~~  173 (205)
T 1gwn_A          171 AKQ  173 (205)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            763

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=99.66  E-value=5.3e-16  Score=84.64  Aligned_cols=70  Identities=23%  Similarity=0.350  Sum_probs=61.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|++++|++++|||++++.+|+.+..|+..+.... ..+.|+++||||+|+.+++.++.+++.+++++
T Consensus        67 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  137 (167)
T 1c1y_A           67 MRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQ  137 (167)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSCCCEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCcCCCcEEEEEECccccccccCCHHHHHHHHHH
Confidence            45678999999999999999999999999999887754 36899999999999998888999998888763

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=99.66  E-value=4.3e-16  Score=85.94  Aligned_cols=69  Identities=33%  Similarity=0.567  Sum_probs=59.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC---CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG---SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.....   ...|+++||||+|+.+.+.++.+++.++++
T Consensus        72 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~iilv~nK~Dl~~~~~~~~~~~~~~~~  143 (178)
T 2hxs_A           72 MLDKYIYGAQGVLLVYDITNYQSFENLEDWYTVVKKVSEESETQPLVALVGNKIDLEHMRTIKPEKHLRFCQ  143 (178)
T ss_dssp             THHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHHHHTCCCEEEEEEECGGGGGGCSSCHHHHHHHHH
T ss_pred             hhhHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcccCCCCeEEEEEEccccccccccCHHHHHHHHH
Confidence            457899999999999999999999999999998876532   334489999999998888899999888875

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=99.66  E-value=1.3e-15  Score=85.35  Aligned_cols=69  Identities=23%  Similarity=0.403  Sum_probs=60.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      ++..|++++|++++|||++++.+|..+. .|+..+.... +++|+++||||+|+.+.            +.++.+++.++
T Consensus        82 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  160 (194)
T 2atx_A           82 LRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYA-PNVPFLLIGTQIDLRDDPKTLARLNDMKEKPICVEQGQKL  160 (194)
T ss_dssp             TGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHS-TTCCEEEEEECTTSTTCHHHHHHHTTTTCCCCCHHHHHHH
T ss_pred             HHHHhcCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEEChhhcccccchhhcccccCcccCHHHHHHH
Confidence            5678999999999999999999999997 8999988765 57999999999999763            57888888888


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       161 ~~~  163 (194)
T 2atx_A          161 AKE  163 (194)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            753

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=99.66  E-value=6.1e-16  Score=85.19  Aligned_cols=69  Identities=36%  Similarity=0.680  Sum_probs=61.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......++|+++|+||+|+.+++.+..+++..+++
T Consensus        79 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~  147 (179)
T 2y8e_A           79 LIPSYIRDSTVAVVVYDITNTNSFHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAK  147 (179)
T ss_dssp             GSHHHHHTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTTSSEEEEEEECGGGGGGCCSCHHHHHHHHH
T ss_pred             HHHHHhcCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECCcccccCcCCHHHHHHHHH
Confidence            456789999999999999999999999999999887766789999999999998888899888888765

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=99.65  E-value=1e-15  Score=83.68  Aligned_cols=69  Identities=39%  Similarity=0.751  Sum_probs=60.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......+.|+++||||+|+ ..+.+..+++.+++++
T Consensus        68 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl-~~~~~~~~~~~~~~~~  136 (170)
T 1g16_A           68 ITTAYYRGAMGIILVYDITDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDM-ETRVVTADQGEALAKE  136 (170)
T ss_dssp             CCHHHHTTEEEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTC-TTCCSCHHHHHHHHHH
T ss_pred             hHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECccC-CcCccCHHHHHHHHHH
Confidence            45778999999999999999999999999999998876678999999999999 4577888888887753

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=99.65  E-value=1e-15  Score=85.84  Aligned_cols=69  Identities=20%  Similarity=0.325  Sum_probs=60.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCccc--ccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKHL--LNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~--~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+ ..|+..+.... +++|+++||||+|+.++  +.+..+++.+++++
T Consensus        87 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~~~  158 (194)
T 3reg_A           87 LRPLSYADSDVVLLCFAVNNRTSFDNISTKWEPEIKHYI-DTAKTVLVGLKVDLRKDGSDDVTKQEGDDLCQK  158 (194)
T ss_dssp             TGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHC-TTSEEEEEEECGGGCCTTTTCCCHHHHHHHHHH
T ss_pred             HhHhhccCCcEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEEChhhccCCCCcccHHHHHHHHHh
Confidence            567899999999999999999999998 78988887664 67999999999999753  78899999888763

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=99.65  E-value=4e-16  Score=87.77  Aligned_cols=70  Identities=30%  Similarity=0.362  Sum_probs=62.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++++|+.+..|+..+..... .++|+++||||+|+.+.+.++.+++.+++++
T Consensus        91 ~~~~~~~~~d~iilv~D~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~NK~Dl~~~~~v~~~~~~~~~~~  161 (196)
T 2atv_A           91 QREGHMRWGEGFVLVYDITDRGSFEEVLPLKNILDEIKKPKNVTLILVGNKADLDHSRQVSTEEGEKLATE  161 (196)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTTSCCCEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             chhhhhccCCEEEEEEECcCHHHHHHHHHHHHHHHHhhCCCCCcEEEEEECcccccccccCHHHHHHHHHH
Confidence            356789999999999999999999999999999877643 6899999999999998889999999888753

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=99.65  E-value=7.4e-16  Score=86.29  Aligned_cols=70  Identities=56%  Similarity=0.853  Sum_probs=62.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|..+..|+..+........|+++||||+|+...+.+..+++.++++.
T Consensus        90 ~~~~~~~~~d~vi~v~D~~~~~s~~~~~~~l~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  159 (193)
T 2oil_A           90 ITSAYYRGAVGALLVFDLTKHQTYAVVERWLKELYDHAEATIVVMLVGNKSDLSQAREVPTEEARMFAEN  159 (193)
T ss_dssp             THHHHHTTCCEEEEEEETTCHHHHHTHHHHHHHHHTTSCTTCEEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             hhHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCeEEEEEECCCcccccccCHHHHHHHHHH
Confidence            4567899999999999999999999999999999876667899999999999988888898998888753

>4djt_A GTP-binding nuclear protein GSP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid, RAN family; HET: GDP; 1.80A {Encephalitozoon cuniculi}

Probab=99.64  E-value=1.4e-15  Score=86.65  Aligned_cols=70  Identities=30%  Similarity=0.524  Sum_probs=59.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......+.|+++||||+|+.+.+.+..+++..+++.
T Consensus        77 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  146 (218)
T 4djt_A           77 LKDVYYIGASGAILFFDVTSRITCQNLARWVKEFQAVVGNEAPIVVCANKIDIKNRQKISKKLVMEVLKG  146 (218)
T ss_dssp             CCHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCSSSCEEEEEECTTCC----CCHHHHHHHTTT
T ss_pred             HHHHHhhcCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCccccccCHHHHHHHHHH
Confidence            4678899999999999999999999999999999887767799999999999988888998888887753

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=99.64  E-value=1.2e-15  Score=84.08  Aligned_cols=70  Identities=23%  Similarity=0.387  Sum_probs=60.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHh-cCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDH-AGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~-~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|..+..|+..+... ...++|+++||||+|+.+.+.+..+++.+++++
T Consensus        73 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~v~~~~~~~~~~~  143 (181)
T 2fn4_A           73 MREQYMRAGHGFLLVFAINDRQSFNEVGKLFTQILRVKDRDDFPVVLVGNKADLESQRQVPRSEASAFGAS  143 (181)
T ss_dssp             CHHHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHTSSCCCEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHHhhCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccCHHHHHHHHHH
Confidence            4567899999999999999999999999999888444 346899999999999998888999998888753

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=99.64  E-value=9.4e-16  Score=83.48  Aligned_cols=69  Identities=26%  Similarity=0.437  Sum_probs=61.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++++|+.+..|+..+..... .+.|+++||||+|+.+.+.+..+++.++++
T Consensus        68 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~  137 (168)
T 1u8z_A           68 IRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAD  137 (168)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHCCTTSCEEEEEECGGGGGGCCSCHHHHHHHHH
T ss_pred             HHHHHhhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECccccccCccCHHHHHHHHH
Confidence            356789999999999999999999999999999887664 579999999999998888899999888875

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=99.64  E-value=1.4e-15  Score=82.95  Aligned_cols=68  Identities=34%  Similarity=0.462  Sum_probs=61.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.... .+.|+++|+||+|+.+.+.+..+++.++++
T Consensus        70 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~  137 (168)
T 1z2a_A           70 ITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAEV-GDIPTALVQNKIDLLDDSCIKNEEAEGLAK  137 (168)
T ss_dssp             CCHHHHTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHH-CSCCEEEEEECGGGGGGCSSCHHHHHHHHH
T ss_pred             HHHHHhcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCEEEEEECcccCcccccCHHHHHHHHH
Confidence            45788999999999999999999999999999987766 679999999999998888888888888775

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=99.64  E-value=1.7e-15  Score=84.23  Aligned_cols=68  Identities=40%  Similarity=0.573  Sum_probs=61.0

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +..|++++|++++|||++++.++..+..|+..+..... ..+|+++|+||+|+.+.+.+..+++.++++
T Consensus        87 ~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~  155 (195)
T 3bc1_A           87 TTAFFRDAMGFLLLFDLTNEQSFLNVRNWISQLQMHAYSENPDIVLCGNKSDLEDQRAVKEEEARELAE  155 (195)
T ss_dssp             HHHTTTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSSSSSCCEEEEEECTTCGGGCCSCHHHHHHHHH
T ss_pred             HHHHHcCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccCHHHHHHHHH
Confidence            45789999999999999999999999999999887764 679999999999998888899888888875

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=99.63  E-value=2.5e-15  Score=82.88  Aligned_cols=69  Identities=30%  Similarity=0.501  Sum_probs=58.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC----CCCeEEEEeeCCCCc-ccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG----SNIVIMLIGNKSDLK-HLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~----~~~~~vlvgnK~Dl~-~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.....    ..+|+++||||+|+. ..+.+..+++.++++
T Consensus        74 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~v~~~~~~~~~~  147 (182)
T 1ky3_A           74 LGVAFYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEESKKIVSEKSAQELAK  147 (182)
T ss_dssp             ---CCSTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSCTTTCCEEEEEECTTSCGGGCCSCHHHHHHHHH
T ss_pred             hhHHHhhcCCEEEEEEECCChHHHHHHHHHHHHHHHHhcccCcCCCcEEEEEECCccccccccCCHHHHHHHHH
Confidence            456789999999999999999999999999999877653    678999999999994 456788888888876

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=99.63  E-value=2e-15  Score=84.93  Aligned_cols=69  Identities=26%  Similarity=0.441  Sum_probs=61.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|..+..|+..+..... .++|+++||||+|+.+.+.+..+++.++++
T Consensus        78 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~  147 (206)
T 2bov_A           78 IRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAE  147 (206)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTCSCCCEEEEEECTTCGGGCCSCHHHHHHHHH
T ss_pred             HHHHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeccCccccccccHHHHHHHHH
Confidence            346789999999999999999999999999999887653 579999999999999888899999888875

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=99.63  E-value=2.6e-15  Score=84.50  Aligned_cols=68  Identities=26%  Similarity=0.459  Sum_probs=59.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCcc------------cccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKH------------LLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~------------~~~v~~~e~~~~   68 (72)
                      +++.|++++|++++|||++++.+|..+. .|+..+.... +++|+++||||+|+..            .+.+..+++..+
T Consensus        84 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  162 (201)
T 2q3h_A           84 LRPLCYTNTDIFLLCFSVVSPSSFQNVSEKWVPEIRCHC-PKAPIILVGTQSDLREDVKVLIELDKCKEKPVPEEAAKLL  162 (201)
T ss_dssp             SGGGGGTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHC-SSSCEEEEEECGGGGGCHHHHHHHHTTTCCCCCHHHHHHH
T ss_pred             HhHhhcCCCcEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEECHhhhhchhhhhhhcccccccCCHHHHHHH
Confidence            5678999999999999999999999996 7999988765 5899999999999975            367888888888


Q ss_pred             Hh
Q 047889           69 SR   70 (72)
Q Consensus        69 a~   70 (72)
                      ++
T Consensus       163 ~~  164 (201)
T 2q3h_A          163 AE  164 (201)
T ss_dssp             HH
T ss_pred             HH
Confidence            75

>3l0i_B RAS-related protein RAB-1A; GEF-GDF-RAB complex, GTP-binding, guanine-nucleotide exchang GDI-displacement factor; 2.85A {Homo sapiens}

Probab=99.63  E-value=1.5e-16  Score=89.81  Aligned_cols=69  Identities=39%  Similarity=0.617  Sum_probs=53.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+......++|+++||||+|+...+.+..+++.++++
T Consensus        98 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~p~ilv~nK~Dl~~~~~v~~~~~~~~~~  166 (199)
T 3l0i_B           98 ITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFAD  166 (199)
T ss_dssp             CSCC--CCCSEEEECC-CCCSHHHHHHHHHHHHHHSCC-CCSEEEEC-CCSSCC--CCCCSCC-CHHHH
T ss_pred             HHHHHhhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhccCCCCEEEEEECccCCccccCCHHHHHHHHH
Confidence            467899999999999999999999999999999987766789999999999998877777666666654

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=99.62  E-value=1.9e-15  Score=83.71  Aligned_cols=70  Identities=26%  Similarity=0.435  Sum_probs=61.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|..+..|+..+..... .++|+++|+||+|+.+.+.+..+++.+++++
T Consensus        82 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  152 (187)
T 2a9k_A           82 IRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAEQ  152 (187)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHCCTTCCEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHhccCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccCccCHHHHHHHHHH
Confidence            356789999999999999999999999999999877664 5799999999999988888999998888753

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=99.62  E-value=1.2e-15  Score=86.13  Aligned_cols=68  Identities=32%  Similarity=0.483  Sum_probs=57.8

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc------ccccCCHHHHHHHHh
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK------HLLNSMCEEYLIKSR   70 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~------~~~~v~~~e~~~~a~   70 (72)
                      +..|++++|++++|||++++.+|+.+..|+..+......++|+++||||+|+.      ..+.+..+++.++++
T Consensus        94 ~~~~~~~~d~iilv~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~NK~Dl~~~~~~~~~~~v~~~~~~~~~~  167 (199)
T 2p5s_A           94 AKSYFRKADGVLLLYDVTCEKSFLNIREWVDMIEDAAHETVPIMLVGNKADIRDTAATEGQKCVPGHFGEKLAM  167 (199)
T ss_dssp             HHHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHC---CCEEEEEECGGGHHHHHHTTCCCCCHHHHHHHHH
T ss_pred             HHHHHhhCCEEEEEEECCChHHHHHHHHHHHHHHHhcCCCCCEEEEEECcccccccccccccccCHHHHHHHHH
Confidence            46789999999999999999999999999999987766789999999999996      457788888888775

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=99.62  E-value=5.4e-15  Score=83.65  Aligned_cols=68  Identities=41%  Similarity=0.762  Sum_probs=59.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+........|+++|+||+|+ ..+.+..+++.++++
T Consensus        85 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl-~~~~~~~~~~~~~~~  152 (213)
T 3cph_A           85 ITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDM-ETRVVTADQGEALAK  152 (213)
T ss_dssp             CCHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHTTTCSEEEEEEECTTC-SSCCSCHHHHHHHHH
T ss_pred             HHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCC-cccccCHHHHHHHHH
Confidence            45778999999999999999999999999999998876668999999999999 557788888887765

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=99.61  E-value=6.6e-15  Score=83.26  Aligned_cols=67  Identities=18%  Similarity=0.187  Sum_probs=57.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.||+++|++++|||++++++|..+..|+..+.+.. ..++|+++||||+|+..  .++.+++.++++
T Consensus        85 ~~~~~~~~~d~~i~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~--~~~~~~~~~~~~  152 (198)
T 1f6b_A           85 VWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPE--AISEERLREMFG  152 (198)
T ss_dssp             GGGGGGGGCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTSCEEEEEECTTSTT--CCCHHHHHHHHT
T ss_pred             HHHHHHhcCCEEEEEEECCCHHHHHHHHHHHHHHHhCcccCCCcEEEEEECCCccc--cCCHHHHHHHhC
Confidence            56789999999999999999999999999998886543 36799999999999975  677888777654

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=99.61  E-value=2.8e-15  Score=81.52  Aligned_cols=70  Identities=19%  Similarity=0.350  Sum_probs=61.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|+++++++++|||++++.+|+.+..|...+..... .+.|+++|+||+|+...+.+..+++.+++++
T Consensus        67 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~  137 (167)
T 1kao_A           67 MRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRYEKVPVILVGNKVDLESEREVSSSEGRALAEE  137 (167)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTTSCCCEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHhccCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCcccccccCCHHHHHHHHHH
Confidence            346789999999999999999999999999988876543 6799999999999988888998888888753

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=99.61  E-value=1.1e-15  Score=86.79  Aligned_cols=68  Identities=28%  Similarity=0.465  Sum_probs=57.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccccc--------CCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHLLN--------SMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~--------v~~~e~~~~a~   70 (72)
                      +++.|++++|++++|||++++.+|+.+. .|+..+.... +++|+++||||+|+.+.+.        ++.+++.++++
T Consensus        73 ~~~~~~~~~d~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~v~~~~~~~~~~  149 (212)
T 2j0v_A           73 LRPLSYRGADIFVLAFSLISKASYENVLKKWMPELRRFA-PNVPIVLVGTKLDLRDDKGYLADHTNVITSTQGEELRK  149 (212)
T ss_dssp             --CGGGTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHC-TTCCEEEEEECHHHHTCHHHHHTCSSCCCHHHHHHHHH
T ss_pred             HHHhhccCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEeCHHhhhCccccccccCCCCHHHHHHHHH
Confidence            5678999999999999999999999996 8999998765 5899999999999976654        47888888775

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A*

Probab=99.61  E-value=1.5e-15  Score=86.46  Aligned_cols=69  Identities=35%  Similarity=0.536  Sum_probs=60.6

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +..|++++|++++|||++++.+|+.+..|+..+..... ..+|+++|+||+|+.+.+.+..+++.++++.
T Consensus       101 ~~~~~~~~d~iilV~D~~~~~s~~~~~~~l~~i~~~~~~~~~piilV~NK~Dl~~~~~v~~~~~~~~~~~  170 (217)
T 2f7s_A          101 TTAFFRDAMGFLLMFDLTSQQSFLNVRNWMSQLQANAYCENPDIVLIGNKADLPDQREVNERQARELADK  170 (217)
T ss_dssp             HHHHHTTCCEEEEEEETTCHHHHHHHHHHHHTCCCCCTTTCCEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             HHHHhcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCcCCCCEEEEEECCccccccccCHHHHHHHHHH
Confidence            46789999999999999999999999999888765543 6799999999999988888999998888753

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=99.61  E-value=7.6e-15  Score=80.84  Aligned_cols=68  Identities=29%  Similarity=0.500  Sum_probs=59.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC----CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG----SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~----~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.....    .++|+++||||+|+. .+.+..+++.++++
T Consensus        72 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~p~i~v~nK~Dl~-~~~~~~~~~~~~~~  143 (177)
T 1wms_A           72 LRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDIS-ERQVSTEEAQAWCR  143 (177)
T ss_dssp             HHGGGGTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTCSCTTTSCEEEEEECTTCS-SCSSCHHHHHHHHH
T ss_pred             hHHHHHhcCCEEEEEEECcCHHHHHHHHHHHHHHHHHccccccCCCcEEEEEECCccc-ccccCHHHHHHHHH
Confidence            356889999999999999999999999999999877653    678999999999997 57888899988876

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=99.60  E-value=1.9e-15  Score=83.63  Aligned_cols=68  Identities=26%  Similarity=0.454  Sum_probs=58.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccccc----------CCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHLLN----------SMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~----------v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+. .|+..+.... ++.|+++||||+|+.+.+.          ++.+++.++++
T Consensus        72 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~v~~~~~~~~~~  150 (182)
T 3bwd_D           72 LRPLSYRGADVFILAFSLISKASYENVSKKWIPELKHYA-PGVPIVLVGTKLDLRDDKQFFIDHPGAVPITTVQGEELKK  150 (182)
T ss_dssp             TGGGGGTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHC-TTCCEEEEEECHHHHTCHHHHHHC--CCCCCHHHHHHHHH
T ss_pred             hHHhhccCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEechhhhcCcccccccccCCCCCHHHHHHHHH
Confidence            5678999999999999999999999997 7999888765 5799999999999976554          47888888775

>3c5h_A Glucocorticoid receptor DNA-binding factor 1; RAS, GTPase, glucorticoid receptor, structural genomics consortium, SGC, alternative splicing; HET: GNP; 1.80A {Homo sapiens}

Probab=99.60  E-value=1.1e-15  Score=89.70  Aligned_cols=60  Identities=18%  Similarity=0.177  Sum_probs=49.3

Q ss_pred             CCCEEEEEEECCCh--hhHHHHHHHHHHHHHh-cCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            9 GALGALLVYDVTKS--TTFENVSRWLKDLRDH-AGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         9 ~a~~~i~v~d~~~~--~s~~~~~~~~~~~~~~-~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++|++++|||++++  .||+.+..|+..+... ...++|+++||||+|+.+++.+  +++.++++
T Consensus       162 ~ad~vilV~D~t~~~~~s~~~~~~~l~~i~~~~~~~~~piilV~NK~Dl~~~~~v--~~~~~~~~  224 (255)
T 3c5h_A          162 LVDGFLLGIDVSRGMNRNFDDQLKFVSNLYNQLAKTKKPIVVVLTKCDEGVERYI--RDAHTFAL  224 (255)
T ss_dssp             ECCEEEEEEECBC----CHHHHHHHHHHHHHHHHHTTCCEEEEEECGGGBCHHHH--HHHHHHHH
T ss_pred             cCCEEEEEEECCCCchhhHHHHHHHHHHHHHHhccCCCCEEEEEEcccccccHHH--HHHHHHHH
Confidence            89999999999999  9999999999998765 3367999999999999876665  56777764

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=99.60  E-value=7.9e-15  Score=82.86  Aligned_cols=69  Identities=22%  Similarity=0.410  Sum_probs=59.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      ++..|++++|++++|||++++++|+.+ ..|...+.... ++.|+++||||+|+.+.            +.+..+++.++
T Consensus        89 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  167 (201)
T 2gco_A           89 LRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFC-PNVPIILVGNKKDLRQDEHTRRELAKMKQEPVRSEEGRDM  167 (201)
T ss_dssp             TGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHS-TTCCEEEEEECGGGTTCHHHHHHHHTTTCCCCCHHHHHHH
T ss_pred             HHHHhcCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEecHHhhcCccchhhhcccccCcCCHHHHHHH
Confidence            567899999999999999999999999 78988887764 57999999999999765            56888888887


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       168 ~~~  170 (201)
T 2gco_A          168 ANR  170 (201)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            753

>3r7w_B Gtpase2, GTP-binding protein GTR2; RAG gtpases, GTR1P, GTR2P, MTOR, protein transport; HET: GNP; 2.77A {Saccharomyces cerevisiae} PDB: 4arz_B*

Probab=99.60  E-value=9.4e-16  Score=93.41  Aligned_cols=68  Identities=12%  Similarity=0.024  Sum_probs=52.5

Q ss_pred             ccchhhCCCEEEEEEECCCh--hhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc-------ccCCHHHHHHHHhc
Q 047889            3 TSAYYRGALGALLVYDVTKS--TTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL-------LNSMCEEYLIKSRS   71 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~--~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~-------~~v~~~e~~~~a~~   71 (72)
                      ++.||++++|+|+|||++++  +++..+..|+..+... .+++|++++|||+||..+       |.|..++++++|++
T Consensus        66 ~~~yyr~a~~~IlV~Ditd~~~~~~~~l~~~l~~~~~~-~~~ipillvgNK~DL~~~~~R~~~~R~V~~~~~~~la~~  142 (331)
T 3r7w_B           66 SERLFKSVGALVYVIDSQDEYINAITNLAMIIEYAYKV-NPSINIEVLIHKVDGLSEDFKVDAQRDIMQRTGEELLEL  142 (331)
T ss_dssp             HHHHHTTCSEEEEECCCSSCTTHHHHHHHHHHHHHHHH-CTTCEEEEECCCCCSSCSHHHHHHHHHHHHHHHHTTSSS
T ss_pred             hhhhccCCCEEEEEEECCchHHHHHHHHHHHHHHHhhc-CCCCcEEEEEECcccCchhhhhhHHHHhhHHHHHHHHhh
Confidence            57899999999999999998  3333333445555444 368999999999999764       67888899998874

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=99.59  E-value=3.9e-15  Score=84.99  Aligned_cols=69  Identities=26%  Similarity=0.474  Sum_probs=53.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      +++.|++++|++++|||++++.+|+.+. .|+..+.... +++|+++||||+|+...            +.++.+++.++
T Consensus        98 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  176 (214)
T 2j1l_A           98 LRPLFYPDASVLLLCFDVTSPNSFDNIFNRWYPEVNHFC-KKVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEM  176 (214)
T ss_dssp             -------CEEEEEEEEETTCHHHHHHHHHTHHHHHHHHC-SSCCEEEEEECGGGGSCHHHHHHHHHTTCCCCCHHHHHHH
T ss_pred             HHHHHhccCCEEEEEEECcCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEEChhhhccchhhhhhcccccCcccHHHHHHH
Confidence            4577899999999999999999999996 7999887765 67999999999999765            36888888888


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       177 ~~~  179 (214)
T 2j1l_A          177 ARS  179 (214)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            753

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=99.59  E-value=8.8e-15  Score=81.63  Aligned_cols=69  Identities=42%  Similarity=0.656  Sum_probs=59.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|..+..|+..+..... ..+|+++|+||+|+. .+.+..+++.+++++
T Consensus        80 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~p~ilv~nK~Dl~-~~~~~~~~~~~~~~~  149 (195)
T 1x3s_A           80 LTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKE-NREVDRNEGLKFARK  149 (195)
T ss_dssp             SHHHHHTTCCEEEEEEETTCHHHHHTHHHHHHHHTTCCSCSCCEEEEEEECTTSS-SCCSCHHHHHHHHHH
T ss_pred             hhHHHhccCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCcCCCcEEEEEECCcCc-ccccCHHHHHHHHHH
Confidence            457789999999999999999999999999999876543 579999999999994 467888888888753

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=99.59  E-value=1.5e-14  Score=81.27  Aligned_cols=67  Identities=18%  Similarity=0.246  Sum_probs=56.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.|++++|++++|||+++++||+.+..|+..+.+.. ..+.|+++||||+|+.+  .++.+++.+..+
T Consensus        83 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~--~~~~~~~~~~~~  150 (190)
T 1m2o_B           83 LWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIAELKDVPFVILGNKIDAPN--AVSEAELRSALG  150 (190)
T ss_dssp             SGGGGCTTCCEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCCEEEEEECTTSTT--CCCHHHHHHHTT
T ss_pred             HHHHHHhcCCEEEEEEECCChHHHHHHHHHHHHHHcchhhcCCCEEEEEECCCCcC--CCCHHHHHHHhC
Confidence            46789999999999999999999999999998886543 26799999999999976  677777776543

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=99.58  E-value=6.1e-15  Score=81.67  Aligned_cols=69  Identities=25%  Similarity=0.466  Sum_probs=59.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      ++..|++++|++++|||++++.+|..+. .|+..+.... ++.|+++||||+|+.+.            +.++.+++.++
T Consensus        69 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  147 (186)
T 1mh1_A           69 LRPLSYPQTDVSLICFSLVSPASFENVRAKWYPEVRHHC-PNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAM  147 (186)
T ss_dssp             TGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHS-TTSCEEEEEECHHHHTCHHHHHHHHHTTCCCCCHHHHHHH
T ss_pred             HHHHhccCCcEEEEEEECCChhhHHHHHHHHHHHHHHhC-CCCCEEEEeEcccccccchhhhhhcccccccCCHHHHHHH
Confidence            4678999999999999999999999997 7998888765 48999999999999653            57888888888


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       148 ~~~  150 (186)
T 1mh1_A          148 AKE  150 (186)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            753

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=99.58  E-value=4.3e-15  Score=82.85  Aligned_cols=67  Identities=19%  Similarity=0.182  Sum_probs=56.0

Q ss_pred             cccchhhCCCEEEEEEECC------ChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVT------KSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~------~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|++++|++++|||++      ++++|+.+..|+..++. ...++|+++||||+|+.+  .++.+++.+++++
T Consensus        90 ~~~~~~~~~d~~i~v~D~~~~~~~~~~~s~~~l~~~l~~~~~-~~~~~piilv~NK~Dl~~--~~~~~~~~~~~~~  162 (198)
T 3t1o_A           90 SRKLILRGVDGIVFVADSAPNRLRANAESMRNMRENLAEYGL-TLDDVPIVIQVNKRDLPD--ALPVEMVRAVVDP  162 (198)
T ss_dssp             HHHHHTTTCCEEEEEEECCGGGHHHHHHHHHHHHHHHHHTTC-CTTSSCEEEEEECTTSTT--CCCHHHHHHHHCT
T ss_pred             HHHHHHhcCCEEEEEEECCcchhhHhHHHHHHHHHHHHhhcc-ccCCCCEEEEEEchhccc--ccCHHHHHHHHHh
Confidence            4567999999999999999      67888888889888743 237899999999999976  4888898888764

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=99.58  E-value=1.8e-14  Score=81.13  Aligned_cols=68  Identities=29%  Similarity=0.468  Sum_probs=58.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC----CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG----SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~----~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|..+..|+..+.....    .+.|+++||||+|+. .+.+..+++.++++
T Consensus        73 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~-~~~~~~~~~~~~~~  144 (207)
T 1vg8_A           73 LGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLE-NRQVATKRAQAWCY  144 (207)
T ss_dssp             SCCGGGTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSSGGGSCEEEEEECTTSS-CCCSCHHHHHHHHH
T ss_pred             hHHHHHhCCcEEEEEEECCCHHHHHHHHHHHHHHHHhcccccCCCCcEEEEEECCCCc-ccccCHHHHHHHHH
Confidence            467899999999999999999999999999998876543    478999999999998 56788888888775

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=99.57  E-value=5.5e-15  Score=83.85  Aligned_cols=69  Identities=25%  Similarity=0.446  Sum_probs=59.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCcccc------------cCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHLL------------NSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~------------~v~~~e~~~~   68 (72)
                      ++..|++++|++++|||++++.+|+.+. .|+..+.... ++.|+++||||+|+...+            .++.+++..+
T Consensus        94 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  172 (204)
T 4gzl_A           94 LRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHC-PNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAM  172 (204)
T ss_dssp             TGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHC-SSCCEEEEEECHHHHTCHHHHHHHHHTTCCCCCHHHHHHH
T ss_pred             HHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEechhhccchhhhhhhhccccccccHHHHHHH
Confidence            5678999999999999999999999996 8998888775 789999999999997654            3778888877


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       173 ~~~  175 (204)
T 4gzl_A          173 AKE  175 (204)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            753

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=99.57  E-value=1.8e-14  Score=81.72  Aligned_cols=69  Identities=19%  Similarity=0.382  Sum_probs=59.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      ++..|++++|++++|||++++.+|..+ ..|+..+.... ++.|+++||||+|+...            +.+..+++.++
T Consensus        89 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  167 (207)
T 2fv8_A           89 LRPLSYPDTDVILMCFSVDSPDSLENIPEKWVPEVKHFC-PNVPIILVANKKDLRSDEHVRTELARMKQEPVRTDDGRAM  167 (207)
T ss_dssp             TGGGGCTTCCEEEEEEETTCHHHHHHHHHTHHHHHHHHS-TTCCEEEEEECGGGGGCHHHHHHHHHTTCCCCCHHHHHHH
T ss_pred             HHHhhcCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEEchhhhccccchhhhhhcccCCCCHHHHHHH
Confidence            467899999999999999999999999 78988887754 67999999999999765            56788888887


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       168 ~~~  170 (207)
T 2fv8_A          168 AVR  170 (207)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            753

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=99.57  E-value=2.3e-14  Score=79.52  Aligned_cols=68  Identities=21%  Similarity=0.425  Sum_probs=59.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.|++++|++++|||++++.+|+.+..|+..+..... .+.|+++||||+|+.+ +.+..+++.++++
T Consensus        68 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~i~v~nK~Dl~~-~~~~~~~~~~~~~  136 (189)
T 4dsu_A           68 MRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPS-RTVDTKQAQDLAR  136 (189)
T ss_dssp             THHHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTCSCCCEEEEEECTTSSS-CSSCHHHHHHHHH
T ss_pred             HHHHHHhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECccCcc-cccCHHHHHHHHH
Confidence            467889999999999999999999999999999877543 6799999999999974 6778888887765

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=99.57  E-value=5.8e-15  Score=80.68  Aligned_cols=68  Identities=24%  Similarity=0.304  Sum_probs=58.7

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +..|++++|++++|||++++.+|+.+..|+..+.+...  ++.|+++||||+|+...+.+..+++..+++
T Consensus        68 ~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~i~~~~~~~~~~pii~v~nK~Dl~~~~~v~~~~~~~~~~  137 (172)
T 2erx_A           68 QRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIKGDVESIPIMLVGNKCDESPSREVQSSEAEALAR  137 (172)
T ss_dssp             HHHHHHHCSEEEEEEETTCHHHHHTTHHHHHHHHHHHC---CCCEEEEEECGGGGGGCCSCHHHHHHHHH
T ss_pred             HHHhcccCCEEEEEEECcCHHHHHHHHHHHHHHHHHhCCCCCCCEEEEEEccccccccccCHHHHHHHHH
Confidence            46788999999999999999999999999888877543  579999999999998888888888887765

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=99.56  E-value=3.6e-14  Score=79.17  Aligned_cols=67  Identities=31%  Similarity=0.566  Sum_probs=58.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|++++|++++|||++++.+|..+..|+..+....  ..|+++|+||+| ..++.+..+++.+++++
T Consensus       109 ~~~~~~~~~d~~i~v~D~~~~~s~~~~~~~~~~i~~~~--~~piilv~NK~D-~~~~~~~~~~~~~~~~~  175 (208)
T 3clv_A          109 IVPLYYRGATCAIVVFDISNSNTLDRAKTWVNQLKISS--NYIIILVANKID-KNKFQVDILEVQKYAQD  175 (208)
T ss_dssp             THHHHHTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHS--CCEEEEEEECTT-CC-CCSCHHHHHHHHHH
T ss_pred             HHHHHhcCCCEEEEEEECCCHHHHHHHHHHHHHHHhhC--CCcEEEEEECCC-cccccCCHHHHHHHHHH
Confidence            45678999999999999999999999999999988765  399999999999 55678899999888764

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=99.56  E-value=3.9e-14  Score=78.99  Aligned_cols=69  Identities=20%  Similarity=0.403  Sum_probs=56.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|+++++++++|||++++.+|+.+..|+..+..... .++|+++||||+|+.. +.+..+++.+++++
T Consensus        85 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~p~ilv~nK~Dl~~-~~~~~~~~~~~~~~  154 (190)
T 3con_A           85 MRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPT-RTVDTKQAHELAKS  154 (190)
T ss_dssp             -----CTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHHTCSCCCEEEEEECTTCSC-CCSCHHHHHHHHHH
T ss_pred             HHHHhhCcCCEEEEEEECcCHHHHHHHHHHHHHHHHHhCCCCCeEEEEEECCcCCc-ccCCHHHHHHHHHH
Confidence            457889999999999999999999999999999877653 5799999999999976 67888888888753

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=99.56  E-value=3.7e-15  Score=89.45  Aligned_cols=64  Identities=14%  Similarity=0.076  Sum_probs=52.6

Q ss_pred             CcccchhhCCCEEEEEEECCChh-hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            1 AITSAYYRGALGALLVYDVTKST-TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      ++++.||+++|++++|||++++. +|+.+..|+..+..   .++|++|||||+||.+++.+  +++.+++
T Consensus        76 ~l~~~~~~~ad~vilV~D~~~~~~s~~~l~~~l~~~~~---~~~piilv~NK~DL~~~~~v--~~~~~~~  140 (301)
T 1u0l_A           76 LLTKPHVANVDQVILVVTVKMPETSTYIIDKFLVLAEK---NELETVMVINKMDLYDEDDL--RKVRELE  140 (301)
T ss_dssp             EETTTTEESCCEEEEEECSSTTCCCHHHHHHHHHHHHH---TTCEEEEEECCGGGCCHHHH--HHHHHHH
T ss_pred             eeeccccccCCEEEEEEeCCCCCCCHHHHHHHHHHHHH---CCCCEEEEEeHHHcCCchhH--HHHHHHH
Confidence            36789999999999999999997 79999999987765   46999999999999765544  4455544

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=99.55  E-value=1.4e-14  Score=81.54  Aligned_cols=66  Identities=9%  Similarity=0.015  Sum_probs=54.3

Q ss_pred             cchhhCCCEEEEEEECCCh--hhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc-------cccCCHHHHHHHHh
Q 047889            4 SAYYRGALGALLVYDVTKS--TTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH-------LLNSMCEEYLIKSR   70 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~--~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~-------~~~v~~~e~~~~a~   70 (72)
                      +.||+++|++++|||++++  +++..+..|+..+.... +++|+++||||+|+..       .+.+..+++.++++
T Consensus        90 ~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~l~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~v~~~~~~~~~~  164 (196)
T 3llu_A           90 EMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVN-PDMNFEVFIHKVDGLSDDHKIETQRDIHQRANDDLAD  164 (196)
T ss_dssp             HHHHHTCSEEEEEEETTSCCHHHHHHHHHHHHHHHHHC-TTCEEEEEEECGGGSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccCCEEEEEEECCCchHHHHHHHHHHHHHHHhcC-CCCcEEEEEeccccCchhhhhHHHhHHHHHHHHHHHH
Confidence            6899999999999999998  77777778877775443 6899999999999754       46677777777776

>3r7w_A Gtpase1, GTP-binding protein GTR1; RAG gtpases, GTR1P, GTR2P, MTOR, protein transport; HET: GNP; 2.77A {Saccharomyces cerevisiae} PDB: 4arz_A*

Probab=99.54  E-value=1.3e-14  Score=87.17  Aligned_cols=70  Identities=16%  Similarity=0.217  Sum_probs=57.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc--CCCCeEEEEeeCCCCcc--ccc----CCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA--GSNIVIMLIGNKSDLKH--LLN----SMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~~~vlvgnK~Dl~~--~~~----v~~~e~~~~a~~   71 (72)
                      +++.||+++|++++|||++++++|+.+..|...+....  .+++|+++||||+|+.+  .+.    +..+++.+++++
T Consensus        73 ~~~~~~~~ad~vi~V~D~t~~~s~~~l~~~~~~l~~l~~~~~~~piilv~NK~Dl~~~~~r~~~~~v~~~~~~~~~~~  150 (307)
T 3r7w_A           73 QKDHIFQMVQVLIHVFDVESTEVLKDIEIFAKALKQLRKYSPDAKIFVLLHKMDLVQLDKREELFQIMMKNLSETSSE  150 (307)
T ss_dssp             THHHHHTTCSEEEEEEETTCSCHHHHHHHHHHHHHHHHHHCTTCEEEEEEECGGGSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhccCCEEEEEEECCChhhHHHHHHHHHHHHHHHHhCCCCeEEEEEecccccchhhhhHHHHHHHHHHHHHHHH
Confidence            45778899999999999999999999988766554432  36799999999999977  565    777888888764

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=99.54  E-value=5.2e-14  Score=76.26  Aligned_cols=67  Identities=22%  Similarity=0.437  Sum_probs=58.2

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +..|++++|++++|||++++.+|+.+..|+..+..... .+.|+++|+||+|+.. +.+..+++.++++
T Consensus        68 ~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~i~~~~~~~~~p~iiv~nK~Dl~~-~~~~~~~~~~~~~  135 (166)
T 2ce2_X           68 RDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKSDLAA-RTVESRQAQDLAR  135 (166)
T ss_dssp             HHHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHTCSCCCEEEEEECTTCSC-CCSCHHHHHHHHH
T ss_pred             HHHhhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEEchhhhh-cccCHHHHHHHHH
Confidence            45689999999999999999999999999999877653 4799999999999976 6777888888765

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=99.54  E-value=4.3e-15  Score=83.00  Aligned_cols=68  Identities=18%  Similarity=0.275  Sum_probs=54.8

Q ss_pred             cccchhhCCCEEEEEEECCCh-hhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCC---HHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKS-TTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSM---CEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~-~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~---~~e~~~~a~   70 (72)
                      +++.|+++++++++|||++++ .+|+.+..|+..+.... +++|+++||||+|+.+.+.+.   .+++.++++
T Consensus        72 ~~~~~~~~~~~~i~v~d~~~~~~s~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~~~  143 (184)
T 2zej_A           72 THPHFMTQRALYLAVYDLSKGQAEVDAMKPWLFNIKARA-SSSPVILVGTHLDVSDEKQRKACMSKITKELLN  143 (184)
T ss_dssp             TSHHHHHHSEEEEEEEEGGGCHHHHHTHHHHHHHHHHHC-TTCEEEEEEECGGGCCHHHHHHHHHHHHHHTTT
T ss_pred             hhHHHccCCcEEEEEEeCCcchhHHHHHHHHHHHHHhhC-CCCcEEEEEECCCcccchhhHHHHHHHHHHHHH
Confidence            567899999999999999997 58999999999987654 579999999999998765543   344555553

>1azs_C GS-alpha; complex (lyase/hydrolase), hydrolase, signal transducing protein, cyclase, effector enzyme; HET: GSP FKP; 2.30A {Bos taurus} SCOP: a.66.1.1 c.37.1.8 PDB: 1azt_A* 3c14_C* 3c15_C* 3c16_C* 1cjt_C* 1cjk_C* 1cju_C* 1cjv_C* 1tl7_C* 1cs4_C* 1u0h_C* 2gvd_C* 2gvz_C* 3e8a_C* 3g82_C* 3maa_C* 1cul_C* 3sn6_A*

Probab=99.53  E-value=6.9e-15  Score=91.53  Aligned_cols=59  Identities=14%  Similarity=0.157  Sum_probs=51.6

Q ss_pred             CcccchhhCCCEEEEEEECCC----------hhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCccccc
Q 047889            1 AITSAYYRGALGALLVYDVTK----------STTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLN   59 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~----------~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~   59 (72)
                      ++++.||++++++|+|||+++          ..+|+.+..|++.+.+.. ..++|++|+|||+||.+++.
T Consensus       232 ~~w~~yf~~a~~iIfV~dis~ydq~l~ed~~~ns~~e~~~~~~~i~~~~~~~~~piiLvgNK~DL~~~ki  301 (402)
T 1azs_C          232 RKWIQCFNDVTAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKV  301 (402)
T ss_dssp             GGGGGGTTTCCEEEEEEETTGGGCBCTTTSCSBHHHHHHHHHHHHHTCTTCSSCCEEEEEECHHHHHHHH
T ss_pred             hhhHhhccCCCEEEEEEECcccccccccccccchHHHHHHHHHHHHhcccCCCCeEEEEEEChhhhhhhh
Confidence            368999999999999999999          899999999999987653 36799999999999966543

>1cip_A Protein (guanine nucleotide-binding protein alpha-1 subunit); GTPase, hydrolase; HET: GNP; 1.50A {Rattus norvegicus} SCOP: a.66.1.1 c.37.1.8 PDB: 1agr_A* 1bof_A* 1gdd_A* 1gfi_A* 1gia_A* 1gp2_A* 3ffa_A* 3ffb_A* 1gg2_A* 1git_A* 1svs_A* 1svk_A* 2zjz_A* 2zjy_A* 3ums_A* 2pz2_A* 2pz3_A* 1as0_A* 1as2_A* 1as3_A* ...

Probab=99.52  E-value=8.1e-15  Score=89.89  Aligned_cols=70  Identities=13%  Similarity=0.145  Sum_probs=58.8

Q ss_pred             CcccchhhCCCEEEEEEECCC----------hhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccc-----------
Q 047889            1 AITSAYYRGALGALLVYDVTK----------STTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLL-----------   58 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~----------~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~-----------   58 (72)
                      ++|..||++++++|+|||+++          ..+|.....|++.+.+.. ..++|++|+|||+||.+++           
T Consensus       208 ~~w~~yf~~a~~iIfV~dls~~d~~l~ed~~~nr~~e~~~~~~~i~~~~~~~~~piiLv~NK~DL~~~ki~~~~l~~~fp  287 (353)
T 1cip_A          208 KKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYP  287 (353)
T ss_dssp             GGGGGGCTTCSEEEEEEEGGGGGCEETTEEEEEHHHHHHHHHHHHHTCGGGTTSEEEEEEECHHHHHHHHTTSCGGGTCT
T ss_pred             HHHHHHHhcCCEEEEEEECccccccccccchhhhHHHHHHHHHHHHcCccccCCcEEEEEECcCchhhhccccchhhccc
Confidence            368899999999999999999          578999999998887643 2679999999999996544           


Q ss_pred             ----cCCHHHHHHHHh
Q 047889           59 ----NSMCEEYLIKSR   70 (72)
Q Consensus        59 ----~v~~~e~~~~a~   70 (72)
                          .++.+++.++++
T Consensus       288 ~~~g~~~~~e~~~~~~  303 (353)
T 1cip_A          288 EYAGSNTYEEAAAYIQ  303 (353)
T ss_dssp             TCCSCSCHHHHHHHHH
T ss_pred             ccCCCCCHHHHHHHHH
Confidence                478889988875

>2xtz_A Guanine nucleotide-binding protein alpha-1 subuni; hydrolase, G-protein signaling, SELF-activation, RAS-like DO; HET: GSP; 2.34A {Arabidopsis thaliana}

Probab=99.52  E-value=6.6e-15  Score=90.32  Aligned_cols=58  Identities=10%  Similarity=0.091  Sum_probs=50.3

Q ss_pred             CcccchhhCCCEEEEEEECC----------ChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccc
Q 047889            1 AITSAYYRGALGALLVYDVT----------KSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~----------~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~   58 (72)
                      ++++.||++++++|+|||++          +..+|+.+..|++.+.+.. ..++|++|+|||+||.+++
T Consensus       198 ~~~~~y~~~~~~iI~v~dis~ydq~l~e~~~~~s~~~~~~~~~~i~~~~~~~~~piiLvgNK~DL~~~k  266 (354)
T 2xtz_A          198 RKWIHLFEGVTAVIFCAAISEYDQTLFEDEQKNRMMETKELFDWVLKQPCFEKTSFMLFLNKFDIFEKK  266 (354)
T ss_dssp             GGTGGGCTTEEEEEEEEEGGGTTCBCSSCTTSBHHHHHHHHHHHHHTCGGGSSCEEEEEEECHHHHHHH
T ss_pred             HHHHHHhCCCCEEEEEEECcccccccccccchhHHHHHHHHHHHHHhccccCCCeEEEEEECcchhhhh
Confidence            36899999999999999998          8899999999998887653 2679999999999996544

>3gj0_A GTP-binding nuclear protein RAN; G protein, GDP, acetylation, cytoplasm, HOST- virus interaction, nucleotide-binding, nucleus, phosphoprotein; HET: GDP; 1.48A {Homo sapiens} SCOP: c.37.1.8 PDB: 3gj3_A* 3gj5_A* 3gj4_A* 3gj6_A* 3gj7_A* 3gj8_A* 1i2m_A 1a2k_C 1ibr_A* 1k5d_A* 1k5g_A* 1qbk_C* 3a6p_C* 3ch5_A* 4gmx_A* 4gpt_A* 4hat_A* 4hau_A* 4hav_A* 4haw_A* ...

Probab=99.51  E-value=3.8e-14  Score=80.94  Aligned_cols=56  Identities=39%  Similarity=0.658  Sum_probs=50.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      ++..|++++|++++|||++++.+|..+..|+..+.... .++|+++||||+|+.+.+
T Consensus        80 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~p~ilv~nK~Dl~~~~  135 (221)
T 3gj0_A           80 LRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKDRK  135 (221)
T ss_dssp             CCHHHHTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHS-TTCCEEEEEECTTSSSCS
T ss_pred             HHHHHHhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCEEEEEECCcccccc
Confidence            56789999999999999999999999999999998775 689999999999997643

>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A*

Probab=99.51  E-value=5.7e-14  Score=83.87  Aligned_cols=69  Identities=22%  Similarity=0.422  Sum_probs=59.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      ++..|++++|++++|||++++.+|..+. .|+..+.... +++|+++||||+|+...            +.++.+++.++
T Consensus       219 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  297 (332)
T 2wkq_A          219 LRPLSYPQTDVFLICFSLVSPASFHHVRAKWYPEVRHHC-PNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAM  297 (332)
T ss_dssp             TGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHC-TTSCEEEEEECHHHHTCHHHHHHHHHTTCCCCCHHHHHHH
T ss_pred             HHHHhccCCCEEEEEEeCCCHHHHHHHHHHHHHHHHhhC-CCCcEEEEEEchhcccccchhhhccccccccccHHHHHHH
Confidence            5678999999999999999999999996 7988887765 48999999999999653            67888888888


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      +++
T Consensus       298 ~~~  300 (332)
T 2wkq_A          298 AKE  300 (332)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            764

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=99.50  E-value=6.1e-14  Score=78.50  Aligned_cols=68  Identities=22%  Similarity=0.290  Sum_probs=57.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.....  .++|+++||||+|+.. +.+..+++..+++
T Consensus        72 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~piilv~nK~Dl~~-~~~~~~~~~~~~~  141 (199)
T 2gf0_A           72 MQRLSISKGHAFILVFSVTSKQSLEELGPIYKLIVQIKGSVEDIPVMLVGNKCDETQ-REVDTREAQAVAQ  141 (199)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHTTHHHHHHHHHHHSCGGGSCEEEEEECTTCSS-CSSCHHHHHHHHH
T ss_pred             HHHHhhccCCEEEEEEECcCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccCCc-cccCHHHHHHHHH
Confidence            356789999999999999999999999999888876543  4789999999999975 6778888877765

>2h57_A ADP-ribosylation factor-like protein 6; GTP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GTP; 2.00A {Homo sapiens}

Probab=99.50  E-value=3.1e-13  Score=75.50  Aligned_cols=66  Identities=20%  Similarity=0.270  Sum_probs=54.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC---CCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG---SNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.....   .+.|+++||||+|+..  .+..++..++.
T Consensus        83 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~--~~~~~~~~~~~  151 (190)
T 2h57_A           83 LWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKHRRIPILFFANKMDLRD--AVTSVKVSQLL  151 (190)
T ss_dssp             GGGGGGGGCSEEEEEEETTCHHHHHHHHHHHHHHHHSTTTTTSCCCEEEEEECTTSTT--CCCHHHHHHHH
T ss_pred             HHHHHHhcCCEEEEEEECCCHHHHHHHHHHHHHHHhChhhccCCCeEEEEEeCcCccc--CCCHHHHHHHh
Confidence            457899999999999999999999999999888876533   5799999999999975  44556655544

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=99.49  E-value=3.5e-13  Score=75.96  Aligned_cols=70  Identities=66%  Similarity=0.993  Sum_probs=61.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|+++++++++|||++++.+|+.+..|+..+........|++++|||+|+.+.+.+..+++.+++++
T Consensus        70 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~i~~v~nK~Dl~~~~~~~~~~a~~l~~~  139 (199)
T 2f9l_A           70 ITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEK  139 (199)
T ss_dssp             CCHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             hhHHHHhcCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCeEEEEEECcccccccCcCHHHHHHHHHH
Confidence            4567889999999999999999999999999888766556789999999999998888998999888763

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=99.48  E-value=3.1e-13  Score=75.34  Aligned_cols=64  Identities=19%  Similarity=0.188  Sum_probs=52.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLI   67 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~   67 (72)
                      ++..|++++|++++|||+++++||+.+..|+..+.... ..+.|+++||||+|+.+  ....++..+
T Consensus        76 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~--~~~~~~i~~  140 (187)
T 1zj6_A           76 SWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKE--CMTVAEISQ  140 (187)
T ss_dssp             GGHHHHTTCCEEEEEEETTCTTTHHHHHHHHHHHHTSGGGTTCEEEEEEECTTSTT--CCCHHHHHH
T ss_pred             HHHHHhcCCCEEEEEEeCCCHHHHHHHHHHHHHHHhchhhCCCeEEEEEECCCCcC--CCCHHHHHH
Confidence            45678999999999999999999999999998887653 26799999999999975  344444443

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=99.47  E-value=5.5e-13  Score=74.07  Aligned_cols=63  Identities=19%  Similarity=0.201  Sum_probs=51.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYL   66 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~   66 (72)
                      ++..|++++|++++|||++++++|+.+..|+..+.... ..+.|+++||||+|+..  ....++..
T Consensus        81 ~~~~~~~~~d~ii~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~--~~~~~~i~  144 (181)
T 2h17_A           81 SWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKE--CMTVAEIS  144 (181)
T ss_dssp             GGGGGGTTCCEEEEEEETTCTTTHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTT--CCCHHHHH
T ss_pred             HHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHhChhhCCCeEEEEEECCCccc--CCCHHHHH
Confidence            46789999999999999999999999999988876542 36799999999999975  33344443

>3ohm_A Guanine nucleotide-binding protein G(Q) subunit A; PH domain, EF hand, TIM barrel, C2 domain, GTPase, lipase, C binding, GTP binding; HET: GDP; 2.70A {Mus musculus} PDB: 2bcj_Q* 2rgn_A* 3ah8_A*

Probab=99.47  E-value=5.6e-14  Score=85.54  Aligned_cols=69  Identities=10%  Similarity=0.060  Sum_probs=57.4

Q ss_pred             CcccchhhCCCEEEEEEECC----------ChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccc-----------
Q 047889            1 AITSAYYRGALGALLVYDVT----------KSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLL-----------   58 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~----------~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~-----------   58 (72)
                      ++|.+||++++|+|+|||++          +.++|.....|++.+.+... .++|++|+|||+||.+++           
T Consensus       182 ~~w~~yf~~~~~iIfV~dls~ydq~l~d~~~~nr~~es~~~~~~i~~~~~~~~~~iiL~~NK~DL~~~ki~~~~l~~~fp  261 (327)
T 3ohm_A          182 RKWIHCFENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNSSVILFLNKKDLLEEKIMYSHLVDYFP  261 (327)
T ss_dssp             TTGGGGCSSCSEEEEEEEGGGGGCBCSSCTTSBHHHHHHHHHHHHHTSGGGTTCEEEEEEECHHHHHHHTTTSCGGGTCT
T ss_pred             HHHHHHhCCCCEEEEEEECccccccccccccHhHHHHHHHHHHHHhhhhccCCceEEEEEECchhhhhhhccchHhhhch
Confidence            47899999999999999665          77888888888888765432 679999999999997766           


Q ss_pred             -----cCCHHHHHHHH
Q 047889           59 -----NSMCEEYLIKS   69 (72)
Q Consensus        59 -----~v~~~e~~~~a   69 (72)
                           .++.++|.++.
T Consensus       262 ~y~g~~~~~e~a~~fi  277 (327)
T 3ohm_A          262 EYDGPQRDAQAAREFI  277 (327)
T ss_dssp             TCCSCSSCHHHHHHHH
T ss_pred             hccCCCCCHHHHHHHH
Confidence                 57888998874

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=99.47  E-value=3.6e-13  Score=73.30  Aligned_cols=55  Identities=18%  Similarity=0.311  Sum_probs=47.4

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCccc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~   57 (72)
                      ++.|++++|++++|||++++++|..+..|+..+.... ..+.|+++||||+|+.+.
T Consensus        61 ~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~  116 (164)
T 1r8s_A           61 WRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNA  116 (164)
T ss_dssp             HHHHTTTCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC
T ss_pred             HHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhcCCeEEEEEECcCCcCC
Confidence            4678999999999999999999999999988876532 367999999999999763

>1zcb_A G alpha I/13; GTP-binding, lipoprotein, membrane, transducer, signaling PR; HET: GDP; 2.00A {Mus musculus} SCOP: a.66.1.1 c.37.1.8 PDB: 3ab3_A* 3cx8_A* 3cx7_A* 3cx6_A* 1zca_A*

Probab=99.46  E-value=5.6e-14  Score=86.42  Aligned_cols=68  Identities=13%  Similarity=0.101  Sum_probs=57.4

Q ss_pred             cccchhhCCCEEEEEEECCC----------hhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccc------------
Q 047889            2 ITSAYYRGALGALLVYDVTK----------STTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLL------------   58 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~----------~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~------------   58 (72)
                      ++..||++++++|+|||+++          +.+|..+..|+..+.+.. ..++|++|+|||+||.+++            
T Consensus       217 ~w~~~f~~~~~iIfv~dls~~dq~l~ed~~~n~~~es~~~~~~i~~~~~~~~~piILv~NK~DL~~~ki~~~~l~~~fp~  296 (362)
T 1zcb_A          217 RWFECFDSVTSILFLVSSSEFDQVLMEDRQTNRLTESLNIFETIVNNRVFSNVSIILFLNKTDLLEEKVQVVSIKDYFLE  296 (362)
T ss_dssp             -CTTSCTTCCEEEEEEETTCTTCEETTEEEEEHHHHHHHHHHHHHTCGGGTTSEEEEEEECHHHHHHHTTTCCGGGTCTT
T ss_pred             hHHHHhCCCCEEEEEEECccccccccccccccHHHHHHHHHHHHhcchhhCCCCEEEEEEChhhhhhhccccchhhcCcc
Confidence            67899999999999999999          789999999998887643 3679999999999997544            


Q ss_pred             ----cCCHHHHHHHH
Q 047889           59 ----NSMCEEYLIKS   69 (72)
Q Consensus        59 ----~v~~~e~~~~a   69 (72)
                          .++.+++.+++
T Consensus       297 y~g~~~~~~e~~~~~  311 (362)
T 1zcb_A          297 FEGDPHCLRDVQKFL  311 (362)
T ss_dssp             CCSCTTCHHHHHHHH
T ss_pred             ccCCCCCHHHHHHHH
Confidence                37788888876

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=99.46  E-value=4.6e-13  Score=75.27  Aligned_cols=70  Identities=66%  Similarity=0.993  Sum_probs=61.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +.+.|+++++++++|||+++..+|+.+..|+..+........|+++++||+|+.+.+.+..+++.+++++
T Consensus        94 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~i~~v~nK~Dl~~~~~~~~~~a~~l~~~  163 (191)
T 1oix_A           94 ITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEK  163 (191)
T ss_dssp             CCHHHHTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             hhHHHhhcCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECcccccccccCHHHHHHHHHH
Confidence            4577889999999999999999999999999888765556789999999999998888888999888764

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=99.46  E-value=7.8e-13  Score=73.46  Aligned_cols=56  Identities=20%  Similarity=0.300  Sum_probs=48.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCccc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~   57 (72)
                      ++..|++++|++++|||++++.+|+.+..|+..+.... ..+.|+++||||+|+.+.
T Consensus        78 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~  134 (186)
T 1ksh_A           78 YWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGA  134 (186)
T ss_dssp             TGGGGCTTCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC
T ss_pred             HHHHHhcCCCEEEEEEECcCHHHHHHHHHHHHHHHhChhcCCCcEEEEEeCccCCCC
Confidence            46789999999999999999999999999988876542 267999999999999764

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=99.45  E-value=4.4e-13  Score=74.69  Aligned_cols=56  Identities=21%  Similarity=0.308  Sum_probs=47.7

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~   58 (72)
                      +..|++++|++++|||++++++|+.+..|+..+.... ..+.|+++||||+|+.+.+
T Consensus        77 ~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~~  133 (181)
T 1fzq_A           77 WRSYFENTDILIYVIDSADRKRFEETGQELTELLEEEKLSCVPVLIFANKQDLLTAA  133 (181)
T ss_dssp             HHHHHTTCSEEEEEEETTCGGGHHHHHHHHHHHTTCGGGTTCCEEEEEECTTSTTCC
T ss_pred             HHHHhCCCCEEEEEEECcCHHHHHHHHHHHHHHHhChhhcCCCEEEEEECcCcccCC
Confidence            4678999999999999999999999999988775432 3679999999999997643

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=99.45  E-value=5.4e-13  Score=74.62  Aligned_cols=56  Identities=16%  Similarity=0.270  Sum_probs=48.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC--------CCCeEEEEeeCCCCccc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG--------SNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~--------~~~~~vlvgnK~Dl~~~   57 (72)
                      ++..|++++|++++|||++++++|..+..|+..+.....        .++|+++||||+|+...
T Consensus        79 ~~~~~~~~~d~ii~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~  142 (199)
T 4bas_A           79 LWETYYDNIDAVIFVVDSSDHLRLCVVKSEIQAMLKHEDIRRELPGGGRVPFLFFANKMDAAGA  142 (199)
T ss_dssp             GGGGGCTTCSEEEEEEETTCGGGHHHHHHHHHHHHTSHHHHSBCTTSCBCCEEEEEECTTSTTC
T ss_pred             HHHHHHhcCCEEEEEEECCcHHHHHHHHHHHHHHHhChhhhhcccccCCCCEEEEEECcCCCCC
Confidence            567899999999999999999999999999888765421        37999999999999764

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=99.45  E-value=6.9e-13  Score=74.54  Aligned_cols=56  Identities=16%  Similarity=0.345  Sum_probs=48.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCccc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~   57 (72)
                      +++.|++++|++++|||++++++|+.+..|+..+.... ..+.|+++||||+|+.+.
T Consensus        89 ~~~~~~~~~d~iilv~D~~~~~s~~~~~~~l~~~~~~~~~~~~piilv~NK~Dl~~~  145 (192)
T 2b6h_A           89 LWRHYFQNTQGLIFVVDSNDRERVQESADELQKMLQEDELRDAVLLVFANKQDMPNA  145 (192)
T ss_dssp             THHHHHHTCCEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC
T ss_pred             HHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHhcccccCCCeEEEEEECCCCCCC
Confidence            45678999999999999999999999999988876532 257999999999999763

>3th5_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTPase, GTP binding, protein binding, signali protein; HET: GNP; 2.30A {Homo sapiens}

Probab=99.16  E-value=8.4e-15  Score=82.75  Aligned_cols=68  Identities=25%  Similarity=0.451  Sum_probs=55.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCcccc------------cCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHLL------------NSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~------------~v~~~e~~~~   68 (72)
                      ++..|++++|++++|||++++.+|+.+. .|+..+.... +++|+++||||+|+.+.+            .+..+++.++
T Consensus        94 ~~~~~~~~~d~iilv~D~~~~~s~~~~~~~~~~~l~~~~-~~~piilv~NK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  172 (204)
T 3th5_A           94 LRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHC-PNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAM  172 (204)
Confidence            4567899999999999999999999996 8988887654 479999999999997643            5566666666


Q ss_pred             Hh
Q 047889           69 SR   70 (72)
Q Consensus        69 a~   70 (72)
                      ++
T Consensus       173 ~~  174 (204)
T 3th5_A          173 AK  174 (204)
Confidence            54

>4fid_A G protein alpha subunit; RAS-like domain, all-helical domain, GTP binding, nucleotide signaling protein, transducer, lipoprotein; HET: MLY MSE GDP; 2.62A {Entamoeba histolytica}

Probab=99.44  E-value=5.1e-14  Score=86.08  Aligned_cols=56  Identities=16%  Similarity=0.183  Sum_probs=48.8

Q ss_pred             cccchhhCCCEEEEEEECC----------ChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCccc
Q 047889            2 ITSAYYRGALGALLVYDVT----------KSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~----------~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~   57 (72)
                      +|..||++++|+|+|||++          +..+|.....|+..+.+... .++|++|+|||+||.++
T Consensus       177 ~w~~yy~~a~~iIfV~diS~ydq~l~e~~~~nr~~es~~~~~~i~~~~~~~~~piiLv~NK~DL~~e  243 (340)
T 4fid_A          177 XWVSFFSDVDCAIFVTSLAEYDMKLYEDGNTSRLTESIAVFKDIMTNEFLKGAVKLIFLNKMDLFEE  243 (340)
T ss_dssp             HHHTTSCSCSEEEEEEEGGGTTCBCC--CCSBHHHHHHHHHHHHHHCGGGTTSEEEEEEECHHHHHH
T ss_pred             cHHHHhccCCEEEEEEECCccccccccccccchHHHHHHHHHHHhhhhccCCCeEEEEEECchhhhh
Confidence            5789999999999999999          78999999999888866543 68999999999999654

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=99.44  E-value=2e-13  Score=74.63  Aligned_cols=56  Identities=14%  Similarity=0.224  Sum_probs=48.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCccc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~   57 (72)
                      ++..|++++|++++|||++++.+|..+..|+..+.... ..+.|+++||||+|+.+.
T Consensus        67 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~  123 (171)
T 1upt_A           67 YWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQA  123 (171)
T ss_dssp             GGGGGCTTCSEEEEEEETTCCTTHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC
T ss_pred             HHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhCCCEEEEEEECCCCcCC
Confidence            46789999999999999999999999998888775543 267999999999999764

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=99.43  E-value=1.7e-13  Score=76.42  Aligned_cols=56  Identities=20%  Similarity=0.248  Sum_probs=48.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCccc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~   57 (72)
                      +++.|++++|++++|||++++++|..+..|+..+.... ..+.|+++||||+|+.+.
T Consensus        82 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~  138 (189)
T 2x77_A           82 YWRCYFSDTDAVIYVVDSTDRDRMGVAKHELYALLDEDELRKSLLLIFANKQDLPDA  138 (189)
T ss_dssp             CCSSSSTTCCEEEEEEETTCCTTHHHHHHHHHHHHTCSTTTTCEEEEEEECTTSTTC
T ss_pred             HHHHHhhcCCEEEEEEeCCCHHHHHHHHHHHHHHHhhhhcCCCeEEEEEECCCCcCC
Confidence            45779999999999999999999999998888776543 257999999999999764

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=99.43  E-value=1.1e-12  Score=72.50  Aligned_cols=63  Identities=17%  Similarity=0.220  Sum_probs=51.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYL   66 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~   66 (72)
                      ++..|++++|++++|||.+++.+|+.+..|+..+.... ..+.|+++|+||+|+.+.  ...++..
T Consensus        78 ~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~~~i~  141 (183)
T 1moz_A           78 YWRCYYADTAAVIFVVDSTDKDRMSTASKELHLMLQEEELQDAALLVFANKQDQPGA--LSASEVS  141 (183)
T ss_dssp             TGGGTTTTEEEEEEEEETTCTTTHHHHHHHHHHHTTSSTTSSCEEEEEEECTTSTTC--CCHHHHH
T ss_pred             HHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHcChhhCCCeEEEEEECCCCCCC--CCHHHHH
Confidence            46789999999999999999999999999988886653 367999999999999753  3444443

>1zd9_A ADP-ribosylation factor-like 10B; transport protein, GDP-binding, membrane trafficking, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2al7_A* 2h18_A*

Probab=99.42  E-value=1.3e-12  Score=72.98  Aligned_cols=55  Identities=25%  Similarity=0.401  Sum_probs=47.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~   56 (72)
                      ++..|++++|++++|||++++++|..+..|+..+.... ..++|+++||||+|+..
T Consensus        83 ~~~~~~~~~d~ii~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~  138 (188)
T 1zd9_A           83 MWERYCRGVSAIVYMVDAADQEKIEASKNELHNLLDKPQLQGIPVLVLGNKRDLPG  138 (188)
T ss_dssp             THHHHHTTCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCCEEEEEECTTSTT
T ss_pred             HHHHHHccCCEEEEEEECCCHHHHHHHHHHHHHHHhCcccCCCCEEEEEECCCCcc
Confidence            45678999999999999999999999999988876542 26799999999999975

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=99.35  E-value=1.5e-12  Score=74.01  Aligned_cols=59  Identities=22%  Similarity=0.314  Sum_probs=48.6

Q ss_pred             ccchhhC----CCEEEEEEECC-ChhhHHHHHHHHHHHHHh----cCCCCeEEEEeeCCCCcccccCC
Q 047889            3 TSAYYRG----ALGALLVYDVT-KSTTFENVSRWLKDLRDH----AGSNIVIMLIGNKSDLKHLLNSM   61 (72)
Q Consensus         3 ~~~y~~~----a~~~i~v~d~~-~~~s~~~~~~~~~~~~~~----~~~~~~~vlvgnK~Dl~~~~~v~   61 (72)
                      +..|+++    ++++++|||.+ ++.+|..+..|+..+...    ...++|+++|+||+|+...+.+.
T Consensus        72 ~~~~~~~~~~~~~~~i~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~  139 (218)
T 1nrj_B           72 LSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTARPPS  139 (218)
T ss_dssp             HHHHHHHHGGGEEEEEEEEETTSCTTCCHHHHHHHHHHHHHHHHHSTTCCCEEEEEECTTSTTCCCHH
T ss_pred             HHHHHHhccccCCEEEEEEECCCChHHHHHHHHHHHHHHhcccccccCCCCEEEEEEchHhcccCCHH
Confidence            3467776    89999999999 899999999998887654    33689999999999998766544

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=99.31  E-value=2e-12  Score=77.71  Aligned_cols=65  Identities=11%  Similarity=0.008  Sum_probs=51.2

Q ss_pred             cccchhhCCCEEEEEEECCChh-hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCC-HHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKST-TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSM-CEEYLIKS   69 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~-~~e~~~~a   69 (72)
                      +.+.|++++|++++|||++++. +++.+..|+..+..   .++|+++|+||+||.+++.+. .++..+++
T Consensus        72 l~r~~~~naD~vliV~d~~~p~~s~~~l~~~l~~~~~---~~~~~ilV~NK~DL~~~~~v~~~~~~~~~~  138 (302)
T 2yv5_A           72 LIRPKVANVDRVIIVETLKMPEFNNYLLDNMLVVYEY---FKVEPVIVFNKIDLLNEEEKKELERWISIY  138 (302)
T ss_dssp             EETTEEESCCEEEEEECSTTTTCCHHHHHHHHHHHHH---TTCEEEEEECCGGGCCHHHHHHHHHHHHHH
T ss_pred             HhHHHHHhcCEEEEEEECCCCCCCHHHHHHHHHHHHh---CCCCEEEEEEcccCCCccccHHHHHHHHHH
Confidence            5678999999999999999996 99999999887754   569999999999997644333 34444443

>3o47_A ADP-ribosylation factor GTPase-activating protein ribosylation factor 1; structural genomics consortium, GTPase activation; HET: GDP; 2.80A {Homo sapiens}

Probab=99.31  E-value=7.7e-12  Score=75.81  Aligned_cols=56  Identities=18%  Similarity=0.322  Sum_probs=47.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCccc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~   57 (72)
                      ++..|++++|++|+|||++++.+|..+..|+..+.... ..++|+++||||+|+.+.
T Consensus       225 ~~~~~~~~ad~vilV~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilV~NK~Dl~~~  281 (329)
T 3o47_A          225 LWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNA  281 (329)
T ss_dssp             SHHHHHTTEEEEEEEEETTCSSSHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC
T ss_pred             HHHHHhccCCEEEEEEECCchHHHHHHHHHHHHHHhhhccCCCeEEEEEECccCCcc
Confidence            46779999999999999999999999988777764433 368999999999999764

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=99.25  E-value=2.6e-11  Score=67.60  Aligned_cols=58  Identities=22%  Similarity=0.327  Sum_probs=46.7

Q ss_pred             ccchhhC----CCEEEEEEECC-ChhhHHHHHHHHHHHHHh----cCCCCeEEEEeeCCCCcccccC
Q 047889            3 TSAYYRG----ALGALLVYDVT-KSTTFENVSRWLKDLRDH----AGSNIVIMLIGNKSDLKHLLNS   60 (72)
Q Consensus         3 ~~~y~~~----a~~~i~v~d~~-~~~s~~~~~~~~~~~~~~----~~~~~~~vlvgnK~Dl~~~~~v   60 (72)
                      +..|+++    +|++++|||.+ ++.+|..+..|+..+...    ...++|+++||||+|+...+.+
T Consensus       108 ~~~~~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~  174 (193)
T 2ged_A          108 LSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTARPP  174 (193)
T ss_dssp             HHHHHHHHGGGEEEEEEEEETTCCHHHHHHHHHHHHHHHHHHHHHSTTCCCEEEEEECTTSTTCCCH
T ss_pred             HHHHHHhhcccCCEEEEEEECCCCchhHHHHHHHHHHHHhhhhhccccCCCEEEEEEchHhcCCCCH
Confidence            3456665    89999999999 999999998888777554    2357999999999999875543

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=99.19  E-value=8.1e-11  Score=66.63  Aligned_cols=57  Identities=16%  Similarity=0.213  Sum_probs=42.7

Q ss_pred             cccchhhCCCEEEEEEECCChh-hHHHHHH-HHHHHHHh--cCCCCeEEEEeeCCCCcccc
Q 047889            2 ITSAYYRGALGALLVYDVTKST-TFENVSR-WLKDLRDH--AGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~-s~~~~~~-~~~~~~~~--~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      +++.|+++++++++|||+++.. ++..+.. |...+...  ...++|+++||||+|+...+
T Consensus        71 ~~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~  131 (214)
T 2fh5_B           71 LLDRFKSSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAK  131 (214)
T ss_dssp             HHHHHGGGEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHTSTTCCEEEEEEECTTSTTCC
T ss_pred             HHHHHHhhCCEEEEEEECCCcCHHHHHHHHHHHHHHhhhhhcccCCCEEEEEECCCCCCcc
Confidence            4567899999999999999964 5766655 44444432  23579999999999997654

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=99.18  E-value=6.9e-11  Score=67.84  Aligned_cols=58  Identities=16%  Similarity=0.049  Sum_probs=42.9

Q ss_pred             chhhCCCEEEEEEECCChhhHHH--HHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHH
Q 047889            5 AYYRGALGALLVYDVTKSTTFEN--VSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCE   63 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~   63 (72)
                      .+++.+|++++|||++++.+|..  ...|+..+.... ++.|+++||||+|+.+.+.+..+
T Consensus       104 ~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~l~~~~-~~~piilv~nK~Dl~~~~~~~~~  163 (228)
T 2qu8_A          104 ALAHINGVILFIIDISEQCGLTIKEQINLFYSIKSVF-SNKSIVIGFNKIDKCNMDSLSID  163 (228)
T ss_dssp             HHHTSSEEEEEEEETTCTTSSCHHHHHHHHHHHHTCC--CCCEEEEEECGGGCC--CCCHH
T ss_pred             HhhccccEEEEEEecccccCcchHHHHHHHHHHHHhh-cCCcEEEEEeCcccCCchhhHHH
Confidence            35788999999999999988752  245665555432 47999999999999887777765

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=99.14  E-value=1.6e-11  Score=67.95  Aligned_cols=51  Identities=16%  Similarity=0.195  Sum_probs=43.1

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+++++|++++|||.+++.+++ ...|++.+.+....++|+++||||+|+.+
T Consensus        79 ~~~~~ad~~i~v~D~~~~~s~~-~~~~~~~~~~~~~~~~p~ilv~NK~Dl~~  129 (172)
T 2gj8_A           79 QEIEQADRVLFMVDGTTTDAVD-PAEIWPEFIARLPAKLPITVVRNKADITG  129 (172)
T ss_dssp             HHHHTCSEEEEEEETTTCCCCS-HHHHCHHHHHHSCTTCCEEEEEECHHHHC
T ss_pred             HHHHhCCEEEEEEECCCCCCHH-HHHHHHHHHHhcccCCCEEEEEECccCCc
Confidence            4789999999999999999887 45788877766556799999999999854

>3dpu_A RAB family protein; roccor, G-domain, COR, GTP-binding, nucleotide-binding, SIGN protein; 2.90A {Chlorobaculum tepidum}

Probab=99.13  E-value=1.1e-10  Score=74.47  Aligned_cols=65  Identities=14%  Similarity=0.162  Sum_probs=54.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +...|+++++++++|||.++.   +.+..|...+.... ++.|+++||||+|+...+.+..+++.+++.
T Consensus       114 ~~~~~l~~~d~ii~V~D~s~~---~~~~~~~~~l~~~~-~~~pvilV~NK~Dl~~~~~v~~~~~~~~~~  178 (535)
T 3dpu_A          114 SHQFFMTRSSVYMLLLDSRTD---SNKHYWLRHIEKYG-GKSPVIVVMNKIDENPSYNIEQKKINERFP  178 (535)
T ss_dssp             TCHHHHHSSEEEEEEECGGGG---GGHHHHHHHHHHHS-SSCCEEEEECCTTTCTTCCCCHHHHHHHCG
T ss_pred             HHHHHccCCcEEEEEEeCCCc---hhHHHHHHHHHHhC-CCCCEEEEEECCCcccccccCHHHHHHHHH
Confidence            456789999999999998765   55677999988775 579999999999998888888888877654

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=99.11  E-value=2.9e-11  Score=67.02  Aligned_cols=65  Identities=15%  Similarity=0.099  Sum_probs=48.2

Q ss_pred             ccchhhC-CCEEEEEEECCChhhHHHH-HHHHHH--------H-HHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            3 TSAYYRG-ALGALLVYDVTKSTTFENV-SRWLKD--------L-RDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         3 ~~~y~~~-a~~~i~v~d~~~~~s~~~~-~~~~~~--------~-~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ...|+++ +++++++|++.+..+|..+ ..|...        + ......++|+++||||+|+...+   .+++.++++
T Consensus        72 ~~~~~~~~~~~~~~v~~v~d~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~---~~~~~~~~~  147 (190)
T 2cxx_A           72 IVHFIEDNAKNIDVAVLVVDGKAAPEIIKRWEKRGEIPIDVEFYQFLRELDIPTIVAVNKLDKIKNV---QEVINFLAE  147 (190)
T ss_dssp             HHHHHHHHGGGCCEEEEEEETTHHHHHHHHHHHTTCCCHHHHHHHHHHHTTCCEEEEEECGGGCSCH---HHHHHHHHH
T ss_pred             HHHHHHhhhccCCEEEEEEcchhhhhHHHhhhccCccHHHHHHHHHHHhcCCceEEEeehHhccCcH---HHHHHHHHH
Confidence            3567887 9999999999999999988 677653        2 22223579999999999997654   445555554

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=99.06  E-value=1.3e-10  Score=63.76  Aligned_cols=61  Identities=16%  Similarity=0.031  Sum_probs=44.3

Q ss_pred             ccchhh--CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            3 TSAYYR--GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         3 ~~~y~~--~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      .+.|++  +++++++|+|.++.++   ...|+.++.+   .+.|+++||||+|+...+.+.. ++.++++
T Consensus        73 ~~~~~~~~~~~~~i~v~D~~~~~~---~~~~~~~~~~---~~~p~ilv~nK~Dl~~~~~~~~-~~~~~~~  135 (165)
T 2wji_A           73 ARDYIINEKPDLVVNIVDATALER---NLYLTLQLME---MGANLLLALNKMDLAKSLGIEI-DVDKLEK  135 (165)
T ss_dssp             HHHHHHHHCCSEEEEEEETTCHHH---HHHHHHHHHH---TTCCEEEEEECHHHHHHTTCCC-CHHHHHH
T ss_pred             HHHHHhcCCCCEEEEEecCCchhH---hHHHHHHHHh---cCCCEEEEEEchHhccccChhh-HHHHHHH
Confidence            356776  8999999999998654   4457777654   3689999999999976655543 3444443

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=98.96  E-value=1e-09  Score=65.94  Aligned_cols=63  Identities=13%  Similarity=-0.020  Sum_probs=50.3

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      ..+++++|++++|+|.++..++.....|++.+..   .+.|+++|+||+|+...+....+....++
T Consensus        87 ~~~l~~aD~il~VvD~~~~~~~~~~~~~~~~l~~---~~~pvilV~NK~Dl~~~~~~~~~~~~~l~  149 (308)
T 3iev_A           87 KQSLEEADVILFMIDATEGWRPRDEEIYQNFIKP---LNKPVIVVINKIDKIGPAKNVLPLIDEIH  149 (308)
T ss_dssp             HHHHHHCSEEEEEEETTTBSCHHHHHHHHHHTGG---GCCCEEEEEECGGGSSSGGGGHHHHHHHH
T ss_pred             HHHhhcCCEEEEEEeCCCCCCchhHHHHHHHHHh---cCCCEEEEEECccCCCCHHHHHHHHHHHH
Confidence            4688999999999999999999998888887765   35899999999999744455555555544

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=98.91  E-value=4.6e-09  Score=57.50  Aligned_cols=48  Identities=19%  Similarity=0.162  Sum_probs=36.0

Q ss_pred             cccchhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++..+++++|++++|||.++   +.+++.+       ......++|+++||||+|+..
T Consensus        71 ~~~~~~~~~d~~i~v~d~~~~~~~~~~~~l-------~~~~~~~~p~ilv~nK~Dl~~  121 (178)
T 2lkc_A           71 MRARGAQVTDIVILVVAADDGVMPQTVEAI-------NHAKAANVPIIVAINKMDKPE  121 (178)
T ss_dssp             SCCSSCCCCCEEEEEEETTCCCCHHHHHHH-------HHHGGGSCCEEEEEETTTSSC
T ss_pred             HHHHHHhhCCEEEEEEECCCCCcHHHHHHH-------HHHHhCCCCEEEEEECccCCc
Confidence            45678899999999999998   4444433       222235689999999999975

>1lnz_A SPO0B-associated GTP-binding protein; GTPase, OBG, stringent factor, stress response, sporulation, large G-protein, structural genomics, PSI; HET: G4P; 2.60A {Bacillus subtilis} SCOP: b.117.1.1 c.37.1.8

Probab=98.91  E-value=2.1e-09  Score=65.72  Aligned_cols=55  Identities=13%  Similarity=0.201  Sum_probs=46.0

Q ss_pred             ccchhhC---CCEEEEEEECCC---hhhHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCccc
Q 047889            3 TSAYYRG---ALGALLVYDVTK---STTFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         3 ~~~y~~~---a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~~   57 (72)
                      ...|++.   ++++++|+|+++   +.+++.+..|..++.....  ...|+++|+||+|+...
T Consensus       227 ~~~fl~~i~~~d~ll~VvD~s~~~~~~~~~~~~~~~~eL~~~~~~l~~~p~ilV~NK~Dl~~~  289 (342)
T 1lnz_A          227 GHQFLRHIERTRVIVHVIDMSGLEGRDPYDDYLTINQELSEYNLRLTERPQIIVANKMDMPEA  289 (342)
T ss_dssp             HHHHHHHHHHCCEEEEEEESSCSSCCCHHHHHHHHHHHHHHSCSSTTTSCBCBEEECTTSTTH
T ss_pred             HHHHHHHHHhccEEEEEEECCcccccChHHHHHHHHHHHHHhhhhhcCCCEEEEEECccCCCC
Confidence            3456554   999999999999   8899999999999987653  47999999999999753

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=98.86  E-value=7.5e-10  Score=61.32  Aligned_cols=60  Identities=18%  Similarity=0.054  Sum_probs=43.4

Q ss_pred             ccchhh--CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            3 TSAYYR--GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         3 ~~~y~~--~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      +..|++  .++++++|+|.++   ++....|+..+..   .+.|+++||||+|+...+.+. +++.+++
T Consensus        77 ~~~~~~~~~~~~~i~v~d~~~---~~~~~~~~~~~~~---~~~piilv~nK~Dl~~~~~~~-~~~~~~~  138 (188)
T 2wjg_A           77 ARDYIINEKPDLVVNIVDATA---LERNLYLTLQLME---MGANLLLALNKMDLAKSLGIE-IDVDKLE  138 (188)
T ss_dssp             HHHHHHHHCCSEEEEEEEGGG---HHHHHHHHHHHHT---TTCCEEEEEECHHHHHHTTCC-CCHHHHH
T ss_pred             HHHHHhccCCCEEEEEecchh---HHHHHHHHHHHHh---cCCCEEEEEEhhhccccccch-HHHHHHH
Confidence            455665  4999999999765   5666778777754   468999999999997665554 3444444

>3l82_B F-box only protein 4; TRFH domain, helix, GTPase domain, acetylation, ADP- ribosylation, alternative splicing, cell cycle, cell division; 2.40A {Homo sapiens}

Probab=98.83  E-value=4.2e-09  Score=61.21  Aligned_cols=63  Identities=10%  Similarity=-0.005  Sum_probs=44.3

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHH----hc-CCCCeEEEEeeCC-CCcccccCCHHHHH
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRD----HA-GSNIVIMLIGNKS-DLKHLLNSMCEEYL   66 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~----~~-~~~~~~vlvgnK~-Dl~~~~~v~~~e~~   66 (72)
                      ++|+.||.++||+|+|.|.+|++.++ .+.-+.++..    .. ..++|++|.+||. |++.  .++..|..
T Consensus       117 plWr~Yy~~TdglIfVVDSsD~~R~e-ak~EL~eL~~mL~ee~~L~gapLLVlANKqqDlp~--Ams~~EI~  185 (227)
T 3l82_B          117 PQIQKVCEVVDGFIYVANAEAHKRHE-WQDEFSHIMAMTDPAFGSSGRPLLVLSCISQGDVK--RMPCFYLA  185 (227)
T ss_dssp             CCHHHHHHHCSEEEEEEECBTTCCCC-HHHHHHHHHHHSCTTSSCSCSCEEEEEEESSTTSC--BCCHHHHH
T ss_pred             HHHHHHhcCCCEEEEEeccccHhHHH-HHHHHHHHHHHhcchhhhCCCeEEEEeCCCcCccC--CCCHHHHH
Confidence            47899999999999999999987655 3333322222    11 1578999999995 7754  56666544

>2hjg_A GTP-binding protein ENGA; GTPase ENGA KH-domain, hydrolase; HET: GDP; 2.50A {Bacillus subtilis}

Probab=98.83  E-value=8.1e-09  Score=64.51  Aligned_cols=57  Identities=14%  Similarity=0.075  Sum_probs=46.0

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHH
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEY   65 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~   65 (72)
                      .+++++|++++|+|.++..+++.. .|...+..   .+.|+++|+||+|+.+++.++.++.
T Consensus       253 ~~~~~ad~~llv~D~~~~~s~~~~-~~~~~~~~---~~~~iiiv~NK~Dl~~~~~~~~~~~  309 (436)
T 2hjg_A          253 KAIDRSEVVAVVLDGEEGIIEQDK-RIAGYAHE---AGKAVVIVVNKWDAVDKDESTMKEF  309 (436)
T ss_dssp             HHHHHCSEEEEEEETTTCCCHHHH-HHHHHHHH---TTCEEEEEEECGGGSCCCTTHHHHH
T ss_pred             HHHHhCCEEEEEEcCCcCCcHHHH-HHHHHHHH---cCCcEEEEEECccCCCcchHHHHHH
Confidence            478899999999999999888875 47666654   4689999999999987666655544

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=98.82  E-value=4.9e-09  Score=58.27  Aligned_cols=55  Identities=15%  Similarity=0.156  Sum_probs=40.3

Q ss_pred             ccchhhCC---CEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCC
Q 047889            3 TSAYYRGA---LGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSM   61 (72)
Q Consensus         3 ~~~y~~~a---~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~   61 (72)
                      ...|++++   +++++|+|.+++.++.... +...+..   .+.|+++|+||+|+...+.+.
T Consensus        96 ~~~~~~~~~~~~~~i~v~d~~~~~~~~~~~-~~~~~~~---~~~p~i~v~nK~Dl~~~~~~~  153 (195)
T 1svi_A           96 IETYITTREELKAVVQIVDLRHAPSNDDVQ-MYEFLKY---YGIPVIVIATKADKIPKGKWD  153 (195)
T ss_dssp             HHHHHHHCTTEEEEEEEEETTSCCCHHHHH-HHHHHHH---TTCCEEEEEECGGGSCGGGHH
T ss_pred             HHHHHhhhhcCCEEEEEEECCCCCCHHHHH-HHHHHHH---cCCCEEEEEECcccCChHHHH
Confidence            45677777   9999999999988877643 1222222   568999999999997765543

>4dcu_A GTP-binding protein ENGA; GTPase, GDP, protein binding, hydrolase; HET: GDP; 2.00A {Bacillus subtilis} PDB: 4dct_A* 4dcs_A* 4dcv_A* 2hjg_A*

Probab=98.79  E-value=1.6e-08  Score=63.50  Aligned_cols=62  Identities=16%  Similarity=0.077  Sum_probs=47.3

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      .|++.+|++++|+|.++..+ +....|...+.+   .+.|+++|+||+|+.+++.+..+++.+.++
T Consensus       273 ~~~~~ad~~llviD~~~~~~-~~~~~~~~~~~~---~~~~~ilv~NK~Dl~~~~~~~~~~~~~~~~  334 (456)
T 4dcu_A          273 KAIDRSEVVAVVLDGEEGII-EQDKRIAGYAHE---AGKAVVIVVNKWDAVDKDESTMKEFEENIR  334 (456)
T ss_dssp             HHHHHCSEEEEEEETTTCCC-HHHHHHHHHHHH---TTCEEEEEEECGGGSCCCSSHHHHHHHHHH
T ss_pred             HHHhhCCEEEEEEeCCCCcC-HHHHHHHHHHHH---cCCCEEEEEEChhcCCCchHHHHHHHHHHH
Confidence            37889999999999987543 233456555554   458999999999998878888787776654

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=98.78  E-value=2.7e-08  Score=60.74  Aligned_cols=53  Identities=11%  Similarity=0.166  Sum_probs=44.1

Q ss_pred             hhhCCCEEEEEEECCChh--hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccccc
Q 047889            6 YYRGALGALLVYDVTKST--TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLN   59 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~--s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~   59 (72)
                      +...+|++++|+|.+++.  +++....|+..+..... +.|+++|+||+|+.....
T Consensus       243 ~~~~ad~illV~D~s~~~~~~~~~~~~~~~~i~~~~~-~~piilV~NK~Dl~~~~~  297 (357)
T 2e87_A          243 LRYLGNLIIYIFDPSEHCGFPLEEQIHLFEEVHGEFK-DLPFLVVINKIDVADEEN  297 (357)
T ss_dssp             GGGTCSEEEEEECTTCTTSSCHHHHHHHHHHHHHHTT-TSCEEEEECCTTTCCHHH
T ss_pred             HHhcCCEEEEEEeCCccccCCHHHHHHHHHHHHHhcC-CCCEEEEEECcccCChHH
Confidence            455799999999999987  78888899988877653 799999999999976443

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=98.78  E-value=1.4e-08  Score=54.62  Aligned_cols=50  Identities=14%  Similarity=0.061  Sum_probs=35.5

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..+++++|++++|||.+++.+...  .|+..+...  .+.|+++||||+|+.+.
T Consensus        74 ~~~~~~~~~~i~v~d~~~~~~~~~--~~~~~~~~~--~~~p~ilv~nK~Dl~~~  123 (161)
T 2dyk_A           74 DRALEDAEVVLFAVDGRAELTQAD--YEVAEYLRR--KGKPVILVATKVDDPKH  123 (161)
T ss_dssp             HHHTTTCSEEEEEEESSSCCCHHH--HHHHHHHHH--HTCCEEEEEECCCSGGG
T ss_pred             HHHHHhCCEEEEEEECCCcccHhH--HHHHHHHHh--cCCCEEEEEECcccccc
Confidence            457899999999999998644332  222222222  46899999999999764

>3gee_A MNME, tRNA modification GTPase MNME; G protein, cytoplasm, GTP- binding, hydrolase, magnesium, metal-binding, nucleotide- binding, potassium; HET: GDP FON; 2.95A {Chlorobium tepidum} PDB: 3gei_A*

Probab=98.77  E-value=1.1e-08  Score=64.91  Aligned_cols=55  Identities=13%  Similarity=0.042  Sum_probs=41.4

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccC
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS   60 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v   60 (72)
                      ..|++++|++++|+|.+++.++..+..+...+...  .+.|+++|+||+|+...+.+
T Consensus       307 ~~~~~~aD~vl~VvD~s~~~s~~~~~~~~~~l~~l--~~~piIvV~NK~Dl~~~~~~  361 (476)
T 3gee_A          307 RMKMAEADLILYLLDLGTERLDDELTEIRELKAAH--PAAKFLTVANKLDRAANADA  361 (476)
T ss_dssp             -CCCSSCSEEEEEEETTTCSSGGGHHHHHHHHHHC--TTSEEEEEEECTTSCTTTHH
T ss_pred             HhhcccCCEEEEEEECCCCcchhhhHHHHHHHHhc--CCCCEEEEEECcCCCCccch
Confidence            45889999999999999998886544444333333  26999999999999765544

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=98.77  E-value=7.9e-09  Score=57.20  Aligned_cols=62  Identities=18%  Similarity=0.173  Sum_probs=41.2

Q ss_pred             ccchhhCC---CEEEEEEECCChhhH--HHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc--ccCCHHHHHHHHh
Q 047889            3 TSAYYRGA---LGALLVYDVTKSTTF--ENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL--LNSMCEEYLIKSR   70 (72)
Q Consensus         3 ~~~y~~~a---~~~i~v~d~~~~~s~--~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~--~~v~~~e~~~~a~   70 (72)
                      .+.|++++   +++++|+|.++..+.  ..+..|+..      .+.|+++||||+|+.+.  +.+..+++.++++
T Consensus        95 ~~~~~~~~~~~~~vi~v~d~~~~~~~~~~~~~~~~~~------~~~p~i~v~nK~Dl~~~~~~~~~~~~~~~~~~  163 (195)
T 3pqc_A           95 VEDYFKNRWSLQMVFLLVDGRIPPQDSDLMMVEWMKS------LNIPFTIVLTKMDKVKMSERAKKLEEHRKVFS  163 (195)
T ss_dssp             HHHHHHHCTTEEEEEEEEETTSCCCHHHHHHHHHHHH------TTCCEEEEEECGGGSCGGGHHHHHHHHHHHHH
T ss_pred             HHHHHhcCcCceEEEEEecCCCCCCHHHHHHHHHHHH------cCCCEEEEEEChhcCChHHHHHHHHHHHHHHh
Confidence            34677776   999999998876443  333444332      25899999999999643  3444556665554

>3b1v_A Ferrous iron uptake transporter protein B; G protein, iron transport, GTPase, transmembrane, potassium; HET: GGM; 1.85A {Streptococcus thermophilus} PDB: 3b1w_A* 3lx5_A* 3lx8_A* 3ss8_A* 3b1z_A 3b1y_A* 3b1x_A* 3tah_A*

Probab=98.66  E-value=1.1e-08  Score=60.77  Aligned_cols=60  Identities=18%  Similarity=0.013  Sum_probs=43.0

Q ss_pred             ccchhh--CCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            3 TSAYYR--GALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         3 ~~~y~~--~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      .+.|++  ++|++++|+|.++.+++   ..|..++.+   .++|+++++||+|+...+.+. .++.+++
T Consensus        72 ~~~~~~~~~~d~vi~V~D~t~~e~~---~~~~~~l~~---~~~p~ilv~NK~Dl~~~~~~~-~~~~~l~  133 (272)
T 3b1v_A           72 ARDYLLSQRADSILNVVDATNLERN---LYLTTQLIE---TGIPVTIALNMIDVLDGQGKK-INVDKLS  133 (272)
T ss_dssp             HHHHHHTTCCSEEEEEEEGGGHHHH---HHHHHHHHH---TCSCEEEEEECHHHHHHTTCC-CCHHHHH
T ss_pred             HHHHHhcCCCCEEEEEecCCchHhH---HHHHHHHHh---cCCCEEEEEEChhhCCcCCcH-HHHHHHH
Confidence            456776  59999999999887654   456666654   468999999999997655554 2344443

>1wf3_A GTP-binding protein; GTPase, riken structural genomics/prote initiative, RSGI, structural genomics, hydrolase; HET: GNP; 1.88A {Thermus thermophilus} SCOP: c.37.1.8 d.52.3.1

Probab=98.65  E-value=4.6e-08  Score=58.76  Aligned_cols=51  Identities=22%  Similarity=0.305  Sum_probs=38.4

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHH-HHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWL-KDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~-~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..|++++|++++|+|.+++.+..  ..|+ +.+.... ++.|+++|+||+|+...
T Consensus        81 ~~~l~~ad~il~VvD~~~~~~~~--~~~i~~~l~~~~-~~~p~ilV~NK~Dl~~~  132 (301)
T 1wf3_A           81 YEALADVNAVVWVVDLRHPPTPE--DELVARALKPLV-GKVPILLVGNKLDAAKY  132 (301)
T ss_dssp             HHHTSSCSEEEEEEETTSCCCHH--HHHHHHHHGGGT-TTSCEEEEEECGGGCSS
T ss_pred             HHHHhcCCEEEEEEECCCCCChH--HHHHHHHHHhhc-CCCCEEEEEECcccCCc
Confidence            46889999999999999875544  3443 4555442 47999999999999753

>3a1s_A Iron(II) transport protein B; FEOB, iron transporter, small GTPase, G protein, GDI; HET: GDP; 1.50A {Thermotoga maritima} PDB: 3a1t_A* 3a1u_A* 3a1v_A* 3a1w_A

Probab=98.62  E-value=1.7e-08  Score=59.40  Aligned_cols=52  Identities=15%  Similarity=0.058  Sum_probs=39.5

Q ss_pred             cchh--hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCC
Q 047889            4 SAYY--RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSM   61 (72)
Q Consensus         4 ~~y~--~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~   61 (72)
                      +.|+  .++|++++|+|.++.++..   .|..++.+   .++|+++|+||+|+...+.+.
T Consensus        76 ~~~~~~~~~d~ii~V~D~t~~~~~~---~~~~~l~~---~~~pvilv~NK~Dl~~~~~i~  129 (258)
T 3a1s_A           76 RDYLLKGDADLVILVADSVNPEQSL---YLLLEILE---MEKKVILAMTAIDEAKKTGMK  129 (258)
T ss_dssp             HHHHHHSCCSEEEEEEETTSCHHHH---HHHHHHHT---TTCCEEEEEECHHHHHHTTCC
T ss_pred             HHHHhhcCCCEEEEEeCCCchhhHH---HHHHHHHh---cCCCEEEEEECcCCCCccchH
Confidence            4566  4899999999999876543   46666654   368999999999997665554

>3h2y_A GTPase family protein; GTP-binding protein YQEH, possibly involved in replication initiation, csgid, IDP90222; HET: DGI; 1.80A {Bacillus anthracis str}

Probab=98.62  E-value=3.2e-08  Score=60.94  Aligned_cols=60  Identities=20%  Similarity=0.265  Sum_probs=43.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~   68 (72)
                      +.+.++++++++++|+|++++.     ..|.+.+.+.. .+.|+++|+||+||... .+..++..++
T Consensus        62 ~l~~i~~~~~~il~VvD~~d~~-----~~~~~~l~~~~-~~~p~ilV~NK~DL~~~-~~~~~~~~~~  121 (368)
T 3h2y_A           62 ILNGIGKSDALVVKIVDIFDFN-----GSWLPGLHRFV-GNNKVLLVGNKADLIPK-SVKHDKVKHW  121 (368)
T ss_dssp             HHHHHHHSCCEEEEEEETTSHH-----HHCCTTHHHHS-SSSCEEEEEECGGGSCT-TSCHHHHHHH
T ss_pred             HHHHHhccCcEEEEEEECCCCc-----ccHHHHHHHHh-CCCcEEEEEEChhcCCc-ccCHHHHHHH
Confidence            3467889999999999999864     45766676654 47899999999999653 3344444333

>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation, GTP-binding domain, maturation enzyme, oxidoreductase; 2.99A {Thermotoga neapolitana}

Probab=98.60  E-value=5.2e-08  Score=61.08  Aligned_cols=58  Identities=16%  Similarity=0.092  Sum_probs=41.9

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      ..+++++|++++|+|.+..+   ....|+..+.+.   +.|+++|+||+|+...+..  +.+.+++
T Consensus       108 ~~~l~~aD~vllVvD~~~~~---~~~~~l~~l~~~---~~piIvV~NK~Dl~~~~~~--~~~~~l~  165 (423)
T 3qq5_A          108 RRVFYRADCGILVTDSAPTP---YEDDVVNLFKEM---EIPFVVVVNKIDVLGEKAE--ELKGLYE  165 (423)
T ss_dssp             HHHHTSCSEEEEECSSSCCH---HHHHHHHHHHHT---TCCEEEECCCCTTTTCCCT--HHHHHSS
T ss_pred             HHHHhcCCEEEEEEeCCChH---HHHHHHHHHHhc---CCCEEEEEeCcCCCCccHH--HHHHHHH
Confidence            34889999999999984333   335677666654   6899999999999876554  4444443

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=98.56  E-value=1.7e-07  Score=54.98  Aligned_cols=55  Identities=9%  Similarity=0.035  Sum_probs=41.1

Q ss_pred             CCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCC--CeEEEEeeCCCCcccccCCHHH
Q 047889            9 GALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSN--IVIMLIGNKSDLKHLLNSMCEE   64 (72)
Q Consensus         9 ~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~--~~~vlvgnK~Dl~~~~~v~~~e   64 (72)
                      ++|++++|++++... +... ..|++.+.+..+.+  .|+++|+||+|+...+....++
T Consensus       116 ~~~~il~V~~~d~~~-~~~~~~~~~~~l~~~~~~~~~~~~ivv~nK~Dl~~~~~~~~e~  173 (262)
T 3def_A          116 TIDVLLYVDRLDVYA-VDELDKQVVIAITQTFGKEIWCKTLLVLTHAQFSPPDELSYET  173 (262)
T ss_dssp             EECEEEEEEESSCSC-CCHHHHHHHHHHHHHHCGGGGGGEEEEEECTTCCCSTTCCHHH
T ss_pred             CCCEEEEEEcCCCCC-CCHHHHHHHHHHHHHhchhhhcCEEEEEeCcccCCCCCccHHH
Confidence            789999999998765 5444 57888887765433  4899999999997655555554

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=98.55  E-value=1.7e-07  Score=55.09  Aligned_cols=57  Identities=12%  Similarity=0.024  Sum_probs=41.3

Q ss_pred             hhCCCEEEEEEECCChhhHHHH-HHHHHHHHHhcCCC--CeEEEEeeCCCCcccccCCHHH
Q 047889            7 YRGALGALLVYDVTKSTTFENV-SRWLKDLRDHAGSN--IVIMLIGNKSDLKHLLNSMCEE   64 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~-~~~~~~~~~~~~~~--~~~vlvgnK~Dl~~~~~v~~~e   64 (72)
                      ++++|++++|+|++.. ++... ..|+..+....+.+  .|+++|+||+|+...+.++.++
T Consensus       117 ~~~~d~il~v~~~d~~-~~~~~~~~~~~~l~~~~~~~~~~~iivV~nK~Dl~~~~~~~~~~  176 (270)
T 1h65_A          117 DKTIDVLLYVDRLDAY-RVDNLDKLVAKAITDSFGKGIWNKAIVALTHAQFSPPDGLPYDE  176 (270)
T ss_dssp             TCEECEEEEEEESSCC-CCCHHHHHHHHHHHHHHCGGGGGGEEEEEECCSCCCGGGCCHHH
T ss_pred             cCCCCEEEEEEeCCCC-cCCHHHHHHHHHHHHHhCcccccCEEEEEECcccCCcCCCCHHH
Confidence            3579999999999764 45444 57887776654333  6999999999997665555544

>1xzp_A Probable tRNA modification GTPase TRME; GTP-binding, THF-binding, hydrolase; 2.30A {Thermotoga maritima} SCOP: a.24.25.1 c.37.1.8 d.250.1.2 PDB: 1xzq_A* 1xzp_B 1xzq_B*

Probab=98.55  E-value=2.8e-07  Score=58.59  Aligned_cols=57  Identities=21%  Similarity=0.074  Sum_probs=42.2

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHH
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIK   68 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~   68 (72)
                      ..|++.+|++++|+|.+++.+++...-| +.+     .+.|+++|+||+|+...  +..++..++
T Consensus       318 ~~~~~~aD~vl~VvD~s~~~s~~~~~il-~~l-----~~~piivV~NK~DL~~~--~~~~~~~~~  374 (482)
T 1xzp_A          318 LQEIEKADIVLFVLDASSPLDEEDRKIL-ERI-----KNKRYLVVINKVDVVEK--INEEEIKNK  374 (482)
T ss_dssp             HHHHHHCSEEEEEEETTSCCCHHHHHHH-HHH-----TTSSEEEEEEECSSCCC--CCHHHHHHH
T ss_pred             HHHhhcccEEEEEecCCCCCCHHHHHHH-HHh-----cCCCEEEEEECcccccc--cCHHHHHHH
Confidence            4688999999999999999888764322 222     36899999999999753  455555443

>3iby_A Ferrous iron transport protein B; G protein, G domain, iron uptake, cell inner membrane, cell GTP-binding, ION transport, membrane; 2.50A {Legionella pneumophila}

Probab=98.53  E-value=2e-08  Score=59.04  Aligned_cols=51  Identities=10%  Similarity=-0.052  Sum_probs=38.3

Q ss_pred             ccchh--hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccccc
Q 047889            3 TSAYY--RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLN   59 (72)
Q Consensus         3 ~~~y~--~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~   59 (72)
                      .+.|+  +++|++++|+|.++.+++..+..|   +.+   .+.|+++|+||+|+...+.
T Consensus        75 ~~~~~~~~~~d~vi~VvDas~~~~~~~l~~~---l~~---~~~pvilv~NK~Dl~~~~~  127 (256)
T 3iby_A           75 AAQSVIDLEYDCIINVIDACHLERHLYLTSQ---LFE---LGKPVVVALNMMDIAEHRG  127 (256)
T ss_dssp             HHHHHHHSCCSEEEEEEEGGGHHHHHHHHHH---HTT---SCSCEEEEEECHHHHHHTT
T ss_pred             HHHHHhhCCCCEEEEEeeCCCchhHHHHHHH---HHH---cCCCEEEEEEChhcCCcCC
Confidence            45677  899999999999997766554333   332   3689999999999866543

>3l2o_B F-box only protein 4; small G protein fold, UBL conjugation pathway, ubiquitin Pro ligase, protein binding-cell cycle complex; 2.80A {Homo sapiens}

Probab=98.52  E-value=1.2e-07  Score=57.36  Aligned_cols=62  Identities=8%  Similarity=-0.052  Sum_probs=43.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHH----HHHHhc-CCCCeEEEEeeC-CCCcccccCCHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLK----DLRDHA-GSNIVIMLIGNK-SDLKHLLNSMCEEYL   66 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~----~~~~~~-~~~~~~vlvgnK-~Dl~~~~~v~~~e~~   66 (72)
                      +|+.||.++||+|+|.|.+|++.++ .+.-+.    .+.+.. ..++|++|.+|| .|++.  .++.+|..
T Consensus       203 lWr~Yy~~tdglIfVVDSsDreRle-ak~EL~eL~~mL~e~~~l~~apLLVfANKkQDlp~--Ams~~EI~  270 (312)
T 3l2o_B          203 QIQKVCEVVDGFIYVANAEAHKRHE-WQDEFSHIMAMTDPAFGSSGRPLLVLSCISQGDVK--RMPCFYLA  270 (312)
T ss_dssp             HHHHHHHHCSEEEECCBCBTTCCCC-HHHHHHHHHHHHCHHHHCTTCCEEEEEEESSTTSC--BCCHHHHH
T ss_pred             HHHHHhcCCCEEEEEecCCcHhHHH-HHHHHHHHHHHhcchhhcCCCeEEEEeCCcccccC--CCCHHHHH
Confidence            6789999999999999999998665 322222    222221 257999999997 58864  56666543

>2qtf_A Protein HFLX, GTP-binding protein; beta-alpha-barrels, nucleotide-binding, nucleotide binding protein; 2.00A {Sulfolobus solfataricus P2} PDB: 2qth_A* 3kxi_A* 3kxl_A 3kxk_A

Probab=98.44  E-value=7.5e-07  Score=54.82  Aligned_cols=51  Identities=25%  Similarity=0.146  Sum_probs=42.2

Q ss_pred             hhhCCCEEEEEEECCChh--hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKST--TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~--s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +++.+|++++|+|.+++.  ++..+..|.+.+......+.|+++|+||+|+..
T Consensus       254 ~~~~aD~il~VvD~s~~~~~~~~~~~~~~~~L~~l~~~~~p~ilV~NK~Dl~~  306 (364)
T 2qtf_A          254 EAKYSDALILVIDSTFSENLLIETLQSSFEILREIGVSGKPILVTLNKIDKIN  306 (364)
T ss_dssp             GGGGSSEEEEEEETTSCHHHHHHHHHHHHHHHHHHTCCSCCEEEEEECGGGCC
T ss_pred             HHHhCCEEEEEEECCCCcchHHHHHHHHHHHHHHhCcCCCCEEEEEECCCCCC
Confidence            468899999999999987  677777777777665546789999999999865

>3i8s_A Ferrous iron transport protein B; GTPase, GPCR, iron uptake, FEO, cell inner membrane, cell ME GTP-binding, ION transport, membrane; 1.80A {Escherichia coli} PDB: 3i8x_A* 3i92_A* 3hyr_A 3hyt_A* 2wic_A* 2wib_A* 2wia_A*

Probab=98.44  E-value=1e-07  Score=56.40  Aligned_cols=46  Identities=17%  Similarity=-0.002  Sum_probs=34.8

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccccc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLN   59 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~   59 (72)
                      +++|++++|+|.++.++...   |..++.+.   ++|+++|+||+|+.+.+.
T Consensus        84 ~~~d~ii~VvD~~~~~~~~~---~~~~l~~~---~~p~ivv~NK~Dl~~~~~  129 (274)
T 3i8s_A           84 GDADLLINVVDASNLERNLY---LTLQLLEL---GIPCIVALNMLDIAEKQN  129 (274)
T ss_dssp             TCCSEEEEEEEGGGHHHHHH---HHHHHHHH---TCCEEEEEECHHHHHHTT
T ss_pred             cCCCEEEEEecCCChHHHHH---HHHHHHhc---CCCEEEEEECccchhhhh
Confidence            69999999999998765544   44444443   589999999999865443

>1jny_A EF-1-alpha, elongation factor 1-alpha, EF-TU, TUF-1; GTPase, alpha/beta structure, protein biosynthesis, translation; HET: GDP; 1.80A {Sulfolobus solfataricus} SCOP: b.43.3.1 b.44.1.1 c.37.1.8 PDB: 1skq_A* 3agj_A*

Probab=98.42  E-value=9.2e-08  Score=59.83  Aligned_cols=52  Identities=23%  Similarity=0.199  Sum_probs=38.8

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc----CCCC-eEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA----GSNI-VIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~----~~~~-~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++ .+|+.+..|..+..++.    ...+ |+++++||+|+.+
T Consensus       102 ~~~~~~aD~~ilVvDa~~-gsfe~~~~~~~qt~~~~~~~~~~~~~~iivviNK~Dl~~  158 (435)
T 1jny_A          102 ITGASQADAAILVVSAKK-GEYEAGMSVEGQTREHIILAKTMGLDQLIVAVNKMDLTE  158 (435)
T ss_dssp             HHTSSCCSEEEEEEECST-THHHHHHSTTCHHHHHHHHHHHTTCTTCEEEEECGGGSS
T ss_pred             HhhhhhcCEEEEEEECCC-CccccccccchHHHHHHHHHHHcCCCeEEEEEEcccCCC
Confidence            457889999999999998 88887665554444332    1233 6899999999975

>3geh_A MNME, tRNA modification GTPase MNME; G protein, U34, GTP-binding, HYDR magnesium, metal-binding, nucleotide-binding, potassium, TR processing; HET: GDP FON; 3.20A {Nostoc SP}

Probab=98.41  E-value=5.9e-07  Score=56.83  Aligned_cols=50  Identities=20%  Similarity=0.116  Sum_probs=37.7

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLN   59 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~   59 (72)
                      ..+++++|++++|+|.+++.+... ..|++.+.     ..|+++|+||+|+...+.
T Consensus       298 ~~~~~~aD~vl~VvD~s~~~~~~~-~~i~~~l~-----~~piivV~NK~Dl~~~~~  347 (462)
T 3geh_A          298 RQAANTADLVLLTIDAATGWTTGD-QEIYEQVK-----HRPLILVMNKIDLVEKQL  347 (462)
T ss_dssp             -CCCCSCSEEEEEEETTTCSCHHH-HHHHHHHT-----TSCEEEEEECTTSSCGGG
T ss_pred             hhhhhcCCEEEEEeccCCCCCHHH-HHHHHhcc-----CCcEEEEEECCCCCcchh
Confidence            347889999999999999877655 44544442     369999999999976543

>1g7s_A Translation initiation factor IF2/EIF5B; translational GTPase; HET: GDP; 2.00A {Methanothermobacterthermautotrophicus} SCOP: b.43.3.1 b.43.3.1 c.20.1.1 c.37.1.8 PDB: 1g7r_A* 1g7t_A*

Probab=98.36  E-value=1.1e-06  Score=57.17  Aligned_cols=48  Identities=23%  Similarity=0.144  Sum_probs=38.2

Q ss_pred             cccchhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++..+++.+|++++|+|.++   +.+++.+..+    ..   .++|+++++||+|+..
T Consensus        86 ~~~r~~~~aD~aILVvDa~~Gv~~qT~e~l~~l----~~---~~vPiIVViNKiDl~~  136 (594)
T 1g7s_A           86 LRKRGGALADLAILIVDINEGFKPQTQEALNIL----RM---YRTPFVVAANKIDRIH  136 (594)
T ss_dssp             SBCSSSBSCSEEEEEEETTTCCCHHHHHHHHHH----HH---TTCCEEEEEECGGGST
T ss_pred             HHHHHHhhCCEEEEEEECCCCccHhHHHHHHHH----HH---cCCeEEEEeccccccc
Confidence            45667888999999999999   7888765532    22   4689999999999964

>1r5b_A Eukaryotic peptide chain release factor GTP-bindi subunit; translation termination, peptide release, GTPase, translatio; 2.35A {Schizosaccharomyces pombe} SCOP: b.43.3.1 b.44.1.1 c.37.1.8 PDB: 1r5n_A* 1r5o_A* 3e20_A

Probab=98.35  E-value=1.2e-07  Score=59.80  Aligned_cols=53  Identities=17%  Similarity=0.040  Sum_probs=35.5

Q ss_pred             cchhhCCCEEEEEEECCCh---hhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKS---TTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~---~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++|+|+|.++.   .+|+...+|.+.+......++| +++++||+|+..
T Consensus       139 ~~~~~~aD~~ilVvDa~~g~~e~sf~~~~qt~e~l~~~~~~~vp~iivviNK~Dl~~  195 (467)
T 1r5b_A          139 INGASQADIGVLVISARRGEFEAGFERGGQTREHAVLARTQGINHLVVVINKMDEPS  195 (467)
T ss_dssp             ---TTSCSEEEEEEECSTTHHHHTTSTTCCHHHHHHHHHHTTCSSEEEEEECTTSTT
T ss_pred             HhhcccCCEEEEEEeCCcCccccccCCCCcHHHHHHHHHHcCCCEEEEEEECccCCC
Confidence            4567889999999999985   4555444444444332224577 999999999953

>3p26_A Elongation factor 1 alpha-like protein; GTP/GDP binding domain, beta-barrel, translational GTPase, D structural genomics; 2.50A {Saccharomyces cerevisiae} PDB: 3p27_A*

Probab=98.35  E-value=5.7e-07  Score=56.91  Aligned_cols=60  Identities=15%  Similarity=-0.021  Sum_probs=35.4

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHH------HHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHH
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENV------SRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEY   65 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~------~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~   65 (72)
                      ..+++++|++++|+|.++..++..+      ......+...  ...|+++|+||+|+.+.+....++.
T Consensus       129 ~~~~~~aD~~llVvDa~~g~~~~~~~~~~qt~e~~~~~~~~--~~~~iIvviNK~Dl~~~~~~~~~~i  194 (483)
T 3p26_A          129 IMGISQADMAILCVDCSTNAFESGFDLDGQTKEHMLLASSL--GIHNLIIAMNKMDNVDWSQQRFEEI  194 (483)
T ss_dssp             HHHHTTCSEEEEEEECCC------CCCCHHHHHHHHHHHHT--TCCCEEEEEECGGGGTTCHHHHHHH
T ss_pred             HHhhhhCCEEEEEEECCCCccccccchhhhHHHHHHHHHHc--CCCcEEEEEECcCcccchHHHHHHH
Confidence            4678999999999999997654332      1122222221  2356999999999976444443433

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=98.34  E-value=2.6e-07  Score=52.32  Aligned_cols=51  Identities=20%  Similarity=0.148  Sum_probs=35.6

Q ss_pred             cchhhC---CCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccc
Q 047889            4 SAYYRG---ALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         4 ~~y~~~---a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      ..|++.   +|++++|+|.++..+.. -..|+..+..   ...|+++|+||+|+...+
T Consensus       107 ~~~~~~~~~~d~vi~v~d~~~~~~~~-~~~~~~~l~~---~~~p~i~v~nK~Dl~~~~  160 (223)
T 4dhe_A          107 SSYLQTRPQLCGMILMMDARRPLTEL-DRRMIEWFAP---TGKPIHSLLTKCDKLTRQ  160 (223)
T ss_dssp             HHHHHHCTTEEEEEEEEETTSCCCHH-HHHHHHHHGG---GCCCEEEEEECGGGSCHH
T ss_pred             HHHHhcCcCcCEEEEEEeCCCCCCHH-HHHHHHHHHh---cCCCEEEEEeccccCChh
Confidence            356666   77799999998754422 2345555544   468999999999997543

>2qag_A Septin-2, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=98.33  E-value=1e-07  Score=58.51  Aligned_cols=62  Identities=15%  Similarity=0.207  Sum_probs=41.3

Q ss_pred             chhhCCCEE-----------EEEEECCC-hhhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCcccccCCH--HHHHHHH
Q 047889            5 AYYRGALGA-----------LLVYDVTK-STTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMC--EEYLIKS   69 (72)
Q Consensus         5 ~y~~~a~~~-----------i~v~d~~~-~~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~--~e~~~~a   69 (72)
                      .|+++++++           +++|++++ ..+|..+. .|+..+    ...+|+++|+||+|+...+.+..  +++.+++
T Consensus       128 ~yl~~~~~~~r~~~~d~rv~~~vy~I~~~~~~l~~~d~~~~~~l----~~~~piIlV~NK~Dl~~~~ev~~~k~~i~~~~  203 (361)
T 2qag_A          128 RYLHDESGLNRRHIIDNRVHCCFYFISPFGHGLKPLDVAFMKAI----HNKVNIVPVIAKADTLTLKERERLKKRILDEI  203 (361)
T ss_dssp             HHHHHHTCSCCC-CCCCCCCEEEEEECSSSSSCCHHHHHHHHHT----CS-SCEEEEEECCSSSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHhhhhccccccCCceEEEEEEEecCCCCcchhHHHHHHHh----ccCCCEEEEEECCCCCCHHHHHHHHHHHHHHH
Confidence            566666655           48888887 66777664 454443    36789999999999987665544  4555554


Q ss_pred             h
Q 047889           70 R   70 (72)
Q Consensus        70 ~   70 (72)
                      +
T Consensus       204 ~  204 (361)
T 2qag_A          204 E  204 (361)
T ss_dssp             T
T ss_pred             H
Confidence            3

>3ec1_A YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase, signaling protein; HET: GDP; 2.36A {Geobacillus stearothermophilus}

Probab=98.32  E-value=2.2e-07  Score=57.15  Aligned_cols=48  Identities=21%  Similarity=0.246  Sum_probs=38.0

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+.++++++++++|+|++++.+     .|.+.+.+.. .+.|+++|+||+||..
T Consensus        65 L~~~~~~~~lil~VvD~~d~~~-----s~~~~l~~~l-~~~piilV~NK~DLl~  112 (369)
T 3ec1_A           65 LHRIGESKALVVNIVDIFDFNG-----SFIPGLPRFA-ADNPILLVGNKADLLP  112 (369)
T ss_dssp             HHHHHHHCCEEEEEEETTCSGG-----GCCSSHHHHC-TTSCEEEEEECGGGSC
T ss_pred             HHHhhccCcEEEEEEECCCCCC-----chhhHHHHHh-CCCCEEEEEEChhcCC
Confidence            4567889999999999999874     4555555554 4789999999999965

>1mky_A Probable GTP-binding protein ENGA; GTPase, DER, KH-domain, tandem G-domains, ligand binding protein; HET: GDP; 1.90A {Thermotoga maritima} SCOP: c.37.1.8 c.37.1.8 d.52.5.1

Probab=98.32  E-value=1.3e-06  Score=54.65  Aligned_cols=48  Identities=29%  Similarity=0.339  Sum_probs=35.2

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHH--HHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFEN--VSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +..|+++||++++|+|.++..+...  +..|+   +.   .+.|+++|+||+|+..
T Consensus        75 ~~~~~~~ad~il~V~D~~~~~~~~d~~i~~~l---~~---~~~p~ilv~NK~D~~~  124 (439)
T 1mky_A           75 TLNMIREADLVLFVVDGKRGITKEDESLADFL---RK---STVDTILVANKAENLR  124 (439)
T ss_dssp             HHHHHTTCSEEEEEEETTTCCCHHHHHHHHHH---HH---HTCCEEEEEESCCSHH
T ss_pred             HHHHHHhCCEEEEEEECCCCCCHHHHHHHHHH---HH---cCCCEEEEEeCCCCcc
Confidence            3568999999999999987655433  23332   22   2589999999999864

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=98.32  E-value=4.4e-07  Score=52.31  Aligned_cols=54  Identities=19%  Similarity=0.088  Sum_probs=32.0

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCcccccC
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLKHLLNS   60 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~~~~v   60 (72)
                      .+++++|++++|+|+++...-  ...|+..+.....  ...|+++|+||+|+...+.+
T Consensus       108 ~~~~~~~~~l~v~d~~~~~~~--~~~~l~~~~~~~~~~~~~~~iiv~nK~D~~~~~~~  163 (239)
T 3lxx_A          108 LTSPGPHALLLVVPLGRYTEE--EHKATEKILKMFGERARSFMILIFTRKDDLGDTNL  163 (239)
T ss_dssp             HTTTCCSEEEEEEETTCCSSH--HHHHHHHHHHHHHHHHGGGEEEEEECGGGC-----
T ss_pred             hcCCCCcEEEEEeeCCCCCHH--HHHHHHHHHHHhhhhccceEEEEEeCCccCCcccH
Confidence            456788999999998764431  1233333322111  23689999999998654443

>2ywe_A GTP-binding protein LEPA; G domain, beta-barrel, ferredoxin-like domain, structural GE NPPSFA; 2.05A {Aquifex aeolicus} PDB: 2ywf_A* 2ywg_A* 2ywh_A*

Probab=98.28  E-value=3.8e-06  Score=54.72  Aligned_cols=50  Identities=28%  Similarity=0.392  Sum_probs=41.0

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..+++.+|++++|+|.++..++.....|.....    .++|+++++||+|+...
T Consensus        91 ~r~l~~aD~aILVVDa~~gv~~qt~~~~~~a~~----~~ipiIvviNKiDl~~a  140 (600)
T 2ywe_A           91 SRALAACEGALLLIDASQGIEAQTVANFWKAVE----QDLVIIPVINKIDLPSA  140 (600)
T ss_dssp             HHHHHTCSEEEEEEETTTBCCHHHHHHHHHHHH----TTCEEEEEEECTTSTTC
T ss_pred             HHHHHhCCEEEEEEECCCCccHHHHHHHHHHHH----CCCCEEEEEeccCcccc
Confidence            456789999999999999888888877765442    46899999999999763

>2hjg_A GTP-binding protein ENGA; GTPase ENGA KH-domain, hydrolase; HET: GDP; 2.50A {Bacillus subtilis}

Probab=98.28  E-value=1.2e-06  Score=54.80  Aligned_cols=50  Identities=12%  Similarity=0.027  Sum_probs=36.1

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +..+++++|++++|+|.++..++..  .|+..+.+  ..+.|+++|+||+|+..
T Consensus        76 ~~~~~~~ad~il~vvD~~~~~~~~d--~~~~~~l~--~~~~pvilv~NK~D~~~  125 (436)
T 2hjg_A           76 AEIAMDEADVIIFMVNGREGVTAAD--EEVAKILY--RTKKPVVLAVNKLDNTE  125 (436)
T ss_dssp             HHHHHHHCSEEEEEEETTTCSCHHH--HHHHHHHT--TCCSCEEEEEECCCC--
T ss_pred             HHHHHHhCCEEEEEEeCCCCCCHHH--HHHHHHHH--HcCCCEEEEEECccCcc
Confidence            3568899999999999998766554  23333222  25689999999999865

>3cb4_D GTP-binding protein LEPA; GTPase, OB-fold, membrane, nucleotide-binding, translation; 2.80A {Escherichia coli} PDB: 3deg_C*

Probab=98.28  E-value=2.2e-06  Score=55.81  Aligned_cols=50  Identities=22%  Similarity=0.277  Sum_probs=40.8

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..+++.+|++++|+|.++..++.....|.....    .++|+++++||+|+...
T Consensus        89 ~~~l~~aD~aILVVDa~~gv~~qt~~~~~~~~~----~~ipiIvViNKiDl~~a  138 (599)
T 3cb4_D           89 SRSLAACEGALLVVDAGQGVEAQTLANCYTAME----MDLEVVPVLNKIDLPAA  138 (599)
T ss_dssp             HHHHHHCSEEEEEEETTTCCCTHHHHHHHHHHH----TTCEEEEEEECTTSTTC
T ss_pred             HHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHH----CCCCEEEeeeccCcccc
Confidence            457889999999999999888777777765442    46899999999999764

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=98.27  E-value=3.9e-07  Score=53.62  Aligned_cols=52  Identities=19%  Similarity=0.024  Sum_probs=36.6

Q ss_pred             cchh--hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccC
Q 047889            4 SAYY--RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS   60 (72)
Q Consensus         4 ~~y~--~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v   60 (72)
                      +.|+  .++|++++|+|.++.+   ....|..++.+.  ...|+++++||+|+.+.+.+
T Consensus        74 ~~~~~~~~~d~vi~v~D~~~~~---~~~~~~~~~~~~--~~~p~ilv~NK~Dl~~~~~~  127 (271)
T 3k53_A           74 RNFILDGNADVIVDIVDSTCLM---RNLFLTLELFEM--EVKNIILVLNKFDLLKKKGA  127 (271)
T ss_dssp             HHHHHTTCCSEEEEEEEGGGHH---HHHHHHHHHHHT--TCCSEEEEEECHHHHHHHTC
T ss_pred             HHhhhccCCcEEEEEecCCcch---hhHHHHHHHHhc--CCCCEEEEEEChhcCccccc
Confidence            4556  6899999999998854   334455555443  23899999999998654433

>1mky_A Probable GTP-binding protein ENGA; GTPase, DER, KH-domain, tandem G-domains, ligand binding protein; HET: GDP; 1.90A {Thermotoga maritima} SCOP: c.37.1.8 c.37.1.8 d.52.5.1

Probab=98.25  E-value=3.5e-06  Score=52.69  Aligned_cols=57  Identities=19%  Similarity=0.133  Sum_probs=40.7

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHH
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEY   65 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~   65 (72)
                      .+++.++++++++|.++..++... .+...+..   .+.|+++|+||+|+.+.+..+.++.
T Consensus       259 ~~i~~ad~vllv~d~~~~~~~~~~-~i~~~l~~---~~~~~ilv~NK~Dl~~~~~~~~~~~  315 (439)
T 1mky_A          259 DSIEKADVVVIVLDATQGITRQDQ-RMAGLMER---RGRASVVVFNKWDLVVHREKRYDEF  315 (439)
T ss_dssp             HHHHHCSEEEEEEETTTCCCHHHH-HHHHHHHH---TTCEEEEEEECGGGSTTGGGCHHHH
T ss_pred             HHHhhCCEEEEEEeCCCCCCHHHH-HHHHHHHH---cCCCEEEEEECccCCCchhhHHHHH
Confidence            467889999999999987766542 23333332   4689999999999977655555443

>3sjy_A Translation initiation factor 2 subunit gamma; zinc finger, initiate translation, tRNA binding, mRNA bindin binding; HET: GCP GDP; 2.00A {Sulfolobus solfataricus P2} PDB: 3pen_A* 3sjz_A* 2qn6_A* 2aho_A 2qmu_A* 2plf_A* 3v11_A* 3i1f_A* 3cw2_A 2pmd_A* 3p3m_A* 3qsy_A*

Probab=98.24  E-value=2e-06  Score=53.28  Aligned_cols=52  Identities=15%  Similarity=0.052  Sum_probs=42.2

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..+++++|++++|+|.++..++.+...|+..+....  ..|+++++||+|+.+.
T Consensus        93 ~~~~~~~D~~ilVvda~~~~~~~qt~~~~~~~~~~~--~~~iivviNK~Dl~~~  144 (403)
T 3sjy_A           93 LSGAALMDGAILVVAANEPFPQPQTREHFVALGIIG--VKNLIIVQNKVDVVSK  144 (403)
T ss_dssp             HHHHTTCSEEEEEEETTSCSSCHHHHHHHHHHHHHT--CCCEEEEEECGGGSCH
T ss_pred             HHHHhhCCEEEEEEECCCCCCcHHHHHHHHHHHHcC--CCCEEEEEECccccch
Confidence            356789999999999999887888888877766553  3589999999999653

>2j69_A Bacterial dynamin-like protein; FZO, FZL, GTPase, hydrolase; 3.0A {Nostoc punctiforme} PDB: 2j68_A 2w6d_A*

Probab=98.23  E-value=1.3e-06  Score=57.58  Aligned_cols=53  Identities=11%  Similarity=0.157  Sum_probs=42.0

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      +..|++++|++++|+|.+++.+......|...+..   ...|+++|+||+|+....
T Consensus       194 ~~~~i~~aD~vL~Vvda~~~~s~~e~~~l~~~l~~---~~~~iiiVlNK~Dl~~~~  246 (695)
T 2j69_A          194 SLGYVNNCHAILFVMRASQPCTLGERRYLENYIKG---RGLTVFFLVNAWDQVRES  246 (695)
T ss_dssp             HTHHHHSSSEEEEEEETTSTTCHHHHHHHHHHTTT---SCCCEEEEEECGGGGGGG
T ss_pred             HHHHHHhCCEEEEEEeCCCccchhHHHHHHHHHHh---hCCCEEEEEECccccccc
Confidence            45789999999999999998888877766544432   357899999999996544

>3t34_A Dynamin-related protein 1A, linker, dynamin-relat 1A; dynamin-like protein 1A, GTPase, membrane fission, motor Pro; HET: GDP; 2.40A {Arabidopsis thaliana} PDB: 3t35_A*

Probab=98.21  E-value=9.6e-07  Score=53.86  Aligned_cols=60  Identities=17%  Similarity=0.019  Sum_probs=42.1

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHH
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEE   64 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e   64 (72)
                      ...|++++++++++++..+.....  ..|+..+........|+++|+||+|+........+.
T Consensus       166 ~~~~i~~~d~iilvv~~~~~~~~~--~~~~~l~~~~~~~~~~~i~V~nK~Dl~~~~~~~~~~  225 (360)
T 3t34_A          166 VRSYIEKPNCIILAISPANQDLAT--SDAIKISREVDPSGDRTFGVLTKIDLMDKGTDAVEI  225 (360)
T ss_dssp             HHHHHHSSSEEEEEEEETTSCGGG--CHHHHHHHHSCTTCTTEEEEEECGGGCCTTCCSHHH
T ss_pred             HHHHhhcCCeEEEEeecccCCcCC--HHHHHHHHHhcccCCCEEEEEeCCccCCCcccHHHH
Confidence            467899999999999876544322  345555555554578999999999997655544443

>2xtp_A GTPase IMAP family member 2; immune system, G protein; HET: MSE; 1.50A {Homo sapiens} PDB: 2xto_A* 2xtm_A* 2xtn_A* 3p1j_A

Probab=98.20  E-value=3.8e-06  Score=48.84  Aligned_cols=51  Identities=22%  Similarity=0.259  Sum_probs=30.1

Q ss_pred             hhhCCCEEEEEEECCChhhH-HHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTF-ENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~-~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +++++|++++|+|.++.... ..+..|+..+........++++++||+|+..
T Consensus       102 ~~~~~d~il~V~d~~~~~~~~~~~~~~l~~~~~~~~~~~~i~vv~nK~Dl~~  153 (260)
T 2xtp_A          102 SAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNG  153 (260)
T ss_dssp             HTTCCSEEEEEEETTCCCHHHHHHHHHHHHHHCGGGGGGEEEEEECGGGGTT
T ss_pred             cCCCCcEEEEEEeCCCCCHHHHHHHHHHHHHhCchhhccEEEEEEcccccCC
Confidence            78899999999999863322 2223333332211102345566666999974

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=98.17  E-value=2.3e-06  Score=50.49  Aligned_cols=54  Identities=9%  Similarity=-0.030  Sum_probs=37.8

Q ss_pred             ccchhhCCCEEE-EEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccccc
Q 047889            3 TSAYYRGALGAL-LVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLN   59 (72)
Q Consensus         3 ~~~y~~~a~~~i-~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~   59 (72)
                      ...|++++++++ +|+|.++..+......|...+.   ..+.|+++|+||+|+.+...
T Consensus       155 ~~~~~~~~~~~il~v~d~~~~~~~~~~~~~~~~~~---~~~~~~i~V~NK~Dl~~~~~  209 (299)
T 2aka_B          155 LMQFVTKENCLILAVSPANSDLANSDALKIAKEVD---PQGQRTIGVITKLDLMDEGT  209 (299)
T ss_dssp             HHHHHTSTTEEEEEEEESSSCGGGCHHHHHHHHHC---TTCSSEEEEEECGGGSCTTC
T ss_pred             HHHHHcCCCeEEEEEecCCcchhhhHHHHHHHHhC---CCCCeEEEEEEccccCCCCc
Confidence            346888999887 6899987655444334544443   35689999999999976544

>1n0u_A EF-2, elongation factor 2; G-protein, CIS-proline, translation; HET: SO1; 2.12A {Saccharomyces cerevisiae} SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB: 1n0v_C 1s1h_T 2e1r_A* 2npf_A* 2p8w_T* 3dny_T 3b82_A* 1zm2_A* 1zm3_A* 1zm4_A* 1zm9_A* 2p8x_T* 2p8y_T* 2p8z_T* 2zit_A* 1u2r_A* 3b78_A* 3b8h_A*

Probab=98.16  E-value=3.8e-06  Score=56.42  Aligned_cols=59  Identities=24%  Similarity=0.204  Sum_probs=45.0

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc-cccCCHHHH
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH-LLNSMCEEY   65 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~-~~~v~~~e~   65 (72)
                      ...+++.+|++++|+|.++..++.....|.... .   .++|+++++||+|+.. +...+.+++
T Consensus       115 ~~~~l~~aD~ailVvDa~~g~~~qt~~~~~~~~-~---~~~p~ilviNK~D~~~~e~~~~~~e~  174 (842)
T 1n0u_A          115 VTAALRVTDGALVVVDTIEGVCVQTETVLRQAL-G---ERIKPVVVINKVDRALLELQVSKEDL  174 (842)
T ss_dssp             HHHHHHTCSEEEEEEETTTBSCHHHHHHHHHHH-H---TTCEEEEEEECHHHHHHTSCCCHHHH
T ss_pred             HHHHHHhCCEEEEEEeCCCCCCHHHHHHHHHHH-H---cCCCeEEEEECCCcchhhhccCHHHH
Confidence            356889999999999999998888877675333 2   4689999999999863 345555554

>3tr5_A RF-3, peptide chain release factor 3; protein synthesis, translation; HET: GDP; 2.11A {Coxiella burnetii}

Probab=98.15  E-value=8.1e-06  Score=52.44  Aligned_cols=49  Identities=22%  Similarity=0.099  Sum_probs=39.0

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++..+......|. .+..   .++|+++++||+|+..
T Consensus       100 ~~~l~~aD~allVvDa~~g~~~~t~~~~~-~~~~---~~iPiivviNK~Dl~~  148 (528)
T 3tr5_A          100 YRTLTAVDSALMVIDAAKGVEPRTIKLME-VCRL---RHTPIMTFINKMDRDT  148 (528)
T ss_dssp             HHGGGGCSEEEEEEETTTCSCHHHHHHHH-HHHT---TTCCEEEEEECTTSCC
T ss_pred             HHHHHhCCEEEEEEeCCCCCCHHHHHHHH-HHHH---cCCCEEEEEeCCCCcc
Confidence            46889999999999999987777766663 3332   4689999999999964

>3izq_1 HBS1P, elongation factor 1 alpha-like protein; NO-GO mRNA decay, ribosomal protein,hydrolase; 9.50A {Saccharomyces cerevisiae}

Probab=98.14  E-value=1.4e-06  Score=56.73  Aligned_cols=55  Identities=15%  Similarity=0.010  Sum_probs=33.9

Q ss_pred             cchhhCCCEEEEEEECCChh---hHHHHHHHHHHHHHhcCCC-CeEEEEeeCCCCcccc
Q 047889            4 SAYYRGALGALLVYDVTKST---TFENVSRWLKDLRDHAGSN-IVIMLIGNKSDLKHLL   58 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~---s~~~~~~~~~~~~~~~~~~-~~~vlvgnK~Dl~~~~   58 (72)
                      ..+++++|++|+|+|.++..   +|.....+...+....... .|+++|+||+|+.+.+
T Consensus       263 ~~~~~~aD~~llVVDa~~g~~e~~~~~~~qt~e~l~~~~~lgi~~iIVVvNKiDl~~~~  321 (611)
T 3izq_1          263 IMGISQADMAILCVDCSTNAFESGFDLDGQTKEHMLLASSLGIHNLIIAMNKMDNVDWS  321 (611)
T ss_dssp             TTTSSCCSEEEEEEECSHHHHHTTCCTTSHHHHHHHHHHTTTCCEEEEEEECTTTTTTC
T ss_pred             HHHHhhcCceEEEEECCCCcccccchhhhHHHHHHHHHHHcCCCeEEEEEecccccchh
Confidence            45788999999999998742   2211122222222222223 4599999999997643

>1s0u_A EIF-2-gamma, translation initiation factor 2 gamma subunit; GTPase, EF-1A, tRNA; 2.40A {Methanocaldococcus jannaschii} SCOP: b.43.3.1 b.44.1.1 c.37.1.8

Probab=98.11  E-value=1.4e-05  Score=49.58  Aligned_cols=58  Identities=21%  Similarity=0.085  Sum_probs=38.5

Q ss_pred             hhCCCEEEEEEECCC----hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccccc--CCHHHHHHHHh
Q 047889            7 YRGALGALLVYDVTK----STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLN--SMCEEYLIKSR   70 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~----~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~--v~~~e~~~~a~   70 (72)
                      ...+|++++|+|.++    +.+++.+..|    ...  ...|+++++||+|+.+...  ...++..++++
T Consensus       102 ~~~~D~~ilVvda~~g~~~~qt~e~l~~~----~~l--~~~~iivv~NK~Dl~~~~~~~~~~~~i~~~l~  165 (408)
T 1s0u_A          102 ASLMDGAILVIAANEPCPQPQTKEHLMAL----EIL--GIDKIIIVQNKIDLVDEKQAEENYEQIKEFVK  165 (408)
T ss_dssp             CSCCSEEEEEEETTSCSSCHHHHHHHHHH----HHT--TCCCEEEEEECTTSSCTTTTTTHHHHHHHHHT
T ss_pred             HhhCCEEEEEEECCCCCCCchhHHHHHHH----HHc--CCCeEEEEEEccCCCCHHHHHHHHHHHHHHHh
Confidence            345699999999994    5566655443    222  2347999999999976433  34556666654

>2c78_A Elongation factor TU-A; hydrolase, GTPase, translation elongation factor, protein synthesis, antibiotic, GTP-binding, nucleotide-binding; HET: GNP PUL; 1.4A {Thermus thermophilus} SCOP: b.43.3.1 b.44.1.1 c.37.1.8 PDB: 2y0u_Z* 2y0w_Z* 2y0y_Z* 2y10_Z* 2y12_Z* 2y14_Z* 2y16_Z* 2y18_Z* 2wrn_Z* 2wrq_Z* 2c77_A* 1aip_A 1exm_A* 1ha3_A* 2xqd_Z* 3fic_Z* 4abr_Z* 1b23_P* 1ob5_A* 1ttt_A* ...

Probab=98.10  E-value=4.1e-06  Score=51.85  Aligned_cols=49  Identities=18%  Similarity=0.162  Sum_probs=36.5

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++... .....|+..+...   ++| +++++||+|+..
T Consensus        93 ~~~~~~aD~~ilVvda~~g~~-~qt~~~l~~~~~~---~ip~iivviNK~Dl~~  142 (405)
T 2c78_A           93 ITGAAQMDGAILVVSAADGPM-PQTREHILLARQV---GVPYIVVFMNKVDMVD  142 (405)
T ss_dssp             HHHHTTCSSEEEEEETTTCCC-HHHHHHHHHHHHT---TCCCEEEEEECGGGCC
T ss_pred             HHHHHHCCEEEEEEECCCCCc-HHHHHHHHHHHHc---CCCEEEEEEECccccC
Confidence            456789999999999988654 3445555555443   577 899999999974

>3izy_P Translation initiation factor IF-2, mitochondrial; E coli, RNA, ribosomal; 10.80A {Bos taurus}

Probab=98.09  E-value=2.1e-06  Score=55.33  Aligned_cols=51  Identities=16%  Similarity=0.103  Sum_probs=37.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++..+++.+|++++|+|.++.........|    ......++|+++++||+|+.+
T Consensus        68 ~~~~~~~~aD~vILVVDa~dg~~~qt~e~l----~~~~~~~vPiIVViNKiDl~~  118 (537)
T 3izy_P           68 MRARGTQVTDIVILVVAADDGVMKQTVESI----QHAKDAHVPIVLAINKCDKAE  118 (537)
T ss_dssp             SBBSSSBSBSSCEEECBSSSCCCHHHHHHH----HHHHTTTCCEEECCBSGGGTT
T ss_pred             HHHHHHccCCEEEEEEECCCCccHHHHHHH----HHHHHcCCcEEEEEecccccc
Confidence            456788999999999999986554443333    222235689999999999965

>1d2e_A Elongation factor TU (EF-TU); G-protein, beta-barrel, RNA binding protein; HET: GDP; 1.94A {Bos taurus} SCOP: b.43.3.1 b.44.1.1 c.37.1.8 PDB: 1xb2_A* 2hcj_A* 2hdn_A*

Probab=98.08  E-value=6.8e-06  Score=50.84  Aligned_cols=49  Identities=14%  Similarity=0.074  Sum_probs=34.7

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++........+| ..+..   .++| +++++||+|+..
T Consensus        84 ~~~~~~aD~~ilVvda~~g~~~qt~e~l-~~~~~---~~vp~iivviNK~Dl~~  133 (397)
T 1d2e_A           84 ITGTAPLDGCILVVAANDGPMPQTREHL-LLARQ---IGVEHVVVYVNKADAVQ  133 (397)
T ss_dssp             HHTSSCCSEEEEEEETTTCSCHHHHHHH-HHHHH---TTCCCEEEEEECGGGCS
T ss_pred             HhhHhhCCEEEEEEECCCCCCHHHHHHH-HHHHH---cCCCeEEEEEECcccCC
Confidence            4567899999999999985443333333 33433   3577 789999999974

>2qpt_A EH domain-containing protein-2; protein-nucleotide complex, membrane protein, endocytosis; HET: ANP; 3.10A {Mus musculus}

Probab=98.07  E-value=1.1e-06  Score=56.59  Aligned_cols=51  Identities=20%  Similarity=0.192  Sum_probs=39.7

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..+++.+|++++|+|.++.........|++.+..   ...|+++|+||+|+...
T Consensus       183 ~~~l~~aD~il~VvDa~~~~~~~~~~~~l~~l~~---~~~pvilVlNK~Dl~~~  233 (550)
T 2qpt_A          183 RWFAERVDLIILLFDAHKLEISDEFSEAIGALRG---HEDKIRVVLNKADMVET  233 (550)
T ss_dssp             HHHHHHCSEEEEEEETTSCCCCHHHHHHHHHTTT---CGGGEEEEEECGGGSCH
T ss_pred             HHHHHhCCEEEEEEeCCcCCCCHHHHHHHHHHHh---cCCCEEEEEECCCccCH
Confidence            3577889999999999886666666677666643   35789999999998653

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=98.05  E-value=8.1e-06  Score=48.90  Aligned_cols=61  Identities=11%  Similarity=0.038  Sum_probs=38.8

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      ..+++.+|++++|+|.++   +.....|+-...  .....|+++++||+|+...+....+...+++
T Consensus        83 ~~~l~~~D~vl~Vvd~~~---~~~~~~~i~~~l--~~~~~P~ilvlNK~D~~~~~~~~~~~l~~l~  143 (301)
T 1ega_A           83 SSSIGDVELVIFVVEGTR---WTPDDEMVLNKL--REGKAPVILAVNKVDNVQEKADLLPHLQFLA  143 (301)
T ss_dssp             TSCCCCEEEEEEEEETTC---CCHHHHHHHHHH--HSSSSCEEEEEESTTTCCCHHHHHHHHHHHH
T ss_pred             HHHHhcCCEEEEEEeCCC---CCHHHHHHHHHH--HhcCCCEEEEEECcccCccHHHHHHHHHHHH
Confidence            467789999999999876   333333433322  2256899999999999753232233344443

>3j2k_7 ERF3, eukaryotic polypeptide chain release factor 3; rabbit 80S ribosome, ribosome-translation complex; 17.00A {Oryctolagus cuniculus}

Probab=98.01  E-value=5.2e-06  Score=52.08  Aligned_cols=52  Identities=19%  Similarity=0.065  Sum_probs=33.0

Q ss_pred             cchhhCCCEEEEEEECCChh---hHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCc
Q 047889            4 SAYYRGALGALLVYDVTKST---TFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLK   55 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~---s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~   55 (72)
                      ..+++++|++++|+|.++..   +|+...++.+.+.......+| +++++||+|+.
T Consensus       113 ~~~~~~aD~~ilVVDa~~g~~e~~~~~~~qt~e~l~~~~~~~v~~iIvviNK~Dl~  168 (439)
T 3j2k_7          113 IGGASQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDP  168 (439)
T ss_pred             HhhHhhCCEEEEEEECCCCccccccCCCchHHHHHHHHHHcCCCeEEEEeecCCCc
Confidence            45678899999999998753   232222222222222223466 99999999985

>2elf_A Protein translation elongation factor 1A; tRNA, pyrrolysine, structural genomics, NPPSFA; HET: CIT; 1.70A {Methanosarcina mazei}

Probab=98.01  E-value=5.3e-06  Score=51.12  Aligned_cols=59  Identities=7%  Similarity=-0.089  Sum_probs=39.1

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeE-EEEee-CCCCcccccCCH--HHHHHHH
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVI-MLIGN-KSDLKHLLNSMC--EEYLIKS   69 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-vlvgn-K~Dl~~~~~v~~--~e~~~~a   69 (72)
                      .+++.+|++++|+|  +...+.+.+.|+..+...   .+|. +++.| |+|+ +...+..  ++..+++
T Consensus        79 ~~~~~aD~ailVvd--~~g~~~qt~e~~~~~~~~---~i~~~ivvvNNK~Dl-~~~~~~~~~~~i~~~l  141 (370)
T 2elf_A           79 TALNISDIAVLCIP--PQGLDAHTGECIIALDLL---GFKHGIIALTRSDST-HMHAIDELKAKLKVIT  141 (370)
T ss_dssp             HHHHTCSEEEEEEC--TTCCCHHHHHHHHHHHHT---TCCEEEEEECCGGGS-CHHHHHHHHHHHHHHT
T ss_pred             HHHHHCCEEEEEEc--CCCCcHHHHHHHHHHHHc---CCCeEEEEEEeccCC-CHHHHHHHHHHHHHHH
Confidence            45688999999999  455566666676666543   3565 77888 9999 5332222  4555544

>1zo1_I IF2, translation initiation factor 2; E. coli, ribosome, initiation of protein synthesis, cryo-eletron microscopy, translation/RNA complex; 13.80A {Escherichia coli}

Probab=98.00  E-value=1.8e-05  Score=50.68  Aligned_cols=48  Identities=15%  Similarity=0.171  Sum_probs=35.1

Q ss_pred             cccchhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++..+++.+|++++|+|.++   +.+++.+.    .+..   .++|+++++||+|+.+
T Consensus        67 ~~~~~~~~aD~aILVVda~~g~~~qT~e~l~----~~~~---~~vPiIVviNKiDl~~  117 (501)
T 1zo1_I           67 MRARGAQATDIVVLVVAADDGVMPQTIEAIQ----HAKA---AQVPVVVAVNKIDKPE  117 (501)
T ss_dssp             SBCSSSBSCSSEEEEEETTTBSCTTTHHHHH----HHHH---TTCCEEEEEECSSSST
T ss_pred             HHHHHHhhCCEEEEEeecccCccHHHHHHHH----HHHh---cCceEEEEEEeccccc
Confidence            34567788999999999988   45554432    2222   4689999999999964

>1zun_B Sulfate adenylate transferase, subunit 1/adenylylsulfate kinase; beta barrel, switch domain, heterodimer, pyrophosphate, G protein; HET: GDP AGS; 2.70A {Pseudomonas syringae PV} SCOP: b.43.3.1 b.44.1.1 c.37.1.8

Probab=97.99  E-value=2.3e-05  Score=49.01  Aligned_cols=50  Identities=16%  Similarity=-0.023  Sum_probs=34.7

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++... .....|+..+...  ...|+++|+||+|+.+
T Consensus       122 ~~~~~~aD~~ilVvDa~~g~~-~qt~~~l~~~~~~--~~~~iIvviNK~Dl~~  171 (434)
T 1zun_B          122 ATGASTCDLAIILVDARYGVQ-TQTRRHSYIASLL--GIKHIVVAINKMDLNG  171 (434)
T ss_dssp             HHHHTTCSEEEEEEETTTCSC-HHHHHHHHHHHHT--TCCEEEEEEECTTTTT
T ss_pred             HHHHhhCCEEEEEEECCCCCc-HHHHHHHHHHHHc--CCCeEEEEEEcCcCCc
Confidence            346889999999999988542 2334444444432  2236999999999975

>1f60_A Elongation factor EEF1A; protein-protein complex, translation; 1.67A {Saccharomyces cerevisiae} SCOP: b.43.3.1 b.44.1.1 c.37.1.8 PDB: 1g7c_A* 1ije_A* 1ijf_A* 2b7b_A* 2b7c_A

Probab=97.97  E-value=3e-06  Score=53.42  Aligned_cols=50  Identities=12%  Similarity=-0.049  Sum_probs=33.3

Q ss_pred             cchhhCCCEEEEEEECCCh---hhHH---HHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKS---TTFE---NVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~---~s~~---~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++.   .+|+   ....++..+..   ..+| +++++||+|+.+
T Consensus       103 ~~~~~~aD~~ilVvda~~g~~~~sf~~~~qt~~~~~~~~~---~~v~~iivviNK~Dl~~  159 (458)
T 1f60_A          103 ITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFT---LGVRQLIVAVNKMDSVK  159 (458)
T ss_dssp             HHSSSCCSEEEEEEECSHHHHHHHTCTTSHHHHHHHHHHH---TTCCEEEEEEECGGGGT
T ss_pred             HhhhhhCCEEEEEEeCCcCccccccCcchhHHHHHHHHHH---cCCCeEEEEEEcccccc
Confidence            3567899999999999875   2442   22222223332   3455 999999999973

>4dcu_A GTP-binding protein ENGA; GTPase, GDP, protein binding, hydrolase; HET: GDP; 2.00A {Bacillus subtilis} PDB: 4dct_A* 4dcs_A* 4dcv_A* 2hjg_A*

Probab=97.93  E-value=8.4e-06  Score=51.20  Aligned_cols=50  Identities=12%  Similarity=0.030  Sum_probs=32.2

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ...+++++|++++|+|..+..+  ....|+..+..  ..+.|+++|+||+|+..
T Consensus        96 ~~~~~~~ad~il~VvD~~~~~~--~~d~~l~~~l~--~~~~pvilV~NK~D~~~  145 (456)
T 4dcu_A           96 AEIAMDEADVIIFMVNGREGVT--AADEEVAKILY--RTKKPVVLAVNKLDNTE  145 (456)
T ss_dssp             HHHHHHHCSEEEEEEESSSCSC--HHHHHHHHHHT--TCCSCEEEEEECC----
T ss_pred             HHhhHhhCCEEEEEEeCCCCCC--hHHHHHHHHHH--HcCCCEEEEEECccchh
Confidence            4568899999999999765332  33334333322  25789999999999864

>1dar_A EF-G, elongation factor G; ribosomal translocase, translational GTPase; HET: GDP; 2.40A {Thermus thermophilus} SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 PDB: 1elo_A 1ktv_A 2om7_L* 2wri_Y* 2wrk_Y* 2xsy_Y* 2xuy_Y* 2j7k_A* 2efg_A* 1jqm_B 1efg_A* 1fnm_A* 1pn6_A 2bm1_A* 2bm0_A* 2bv3_A* 3izp_E 1zn0_B 1jqs_C 2bcw_C ...

Probab=97.93  E-value=2e-05  Score=51.97  Aligned_cols=49  Identities=18%  Similarity=0.273  Sum_probs=39.9

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++..++.....|.. +..   .++|+++++||+|+..
T Consensus        95 ~~~l~~aD~~ilVvDa~~g~~~~t~~~~~~-~~~---~~~p~ivviNKiD~~~  143 (691)
T 1dar_A           95 ERSMRVLDGAIVVFDSSQGVEPQSETVWRQ-AEK---YKVPRIAFANKMDKTG  143 (691)
T ss_dssp             HHHHHHCSEEEEEEETTTCSCHHHHHHHHH-HHH---TTCCEEEEEECTTSTT
T ss_pred             HHHHHHCCEEEEEEECCCCcchhhHHHHHH-HHH---cCCCEEEEEECCCccc
Confidence            467889999999999999888887777753 333   3689999999999975

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=97.92  E-value=9.7e-06  Score=50.84  Aligned_cols=64  Identities=11%  Similarity=0.123  Sum_probs=41.7

Q ss_pred             cccchhhCCCEEEEEEECCCh-hhHHHHH-HHHHHHHHhcCCCCeEEEEeeCCCCcccccCCH--HHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKS-TTFENVS-RWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMC--EEYLIKS   69 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~-~s~~~~~-~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~--~e~~~~a   69 (72)
                      +.+.+++++++.+++|..+.. .+|..+. .|+..+.    ..+|+++|+||+|+...+.+..  +++.+++
T Consensus       129 IaRal~~d~~~~vlL~ldePt~~~L~~~d~~~lk~L~----~~v~iIlVinK~Dll~~~ev~~~k~~i~~~~  196 (418)
T 2qag_C          129 VNRRQMPDNRVQCCLYFIAPSGHGLKPLDIEFMKRLH----EKVNIIPLIAKADTLTPEECQQFKKQIMKEI  196 (418)
T ss_dssp             -CCCCCCCC-CCEEEEECCC-CCSCCHHHHHHHHHHT----TTSEEEEEEESTTSSCHHHHHHHHHHHHHHH
T ss_pred             HHHHhccCCCeeEEEEEecCcccCCCHHHHHHHHHHh----ccCcEEEEEEcccCccHHHHHHHHHHHHHHH
Confidence            345677888887777777654 4676663 5766663    3689999999999876555443  4444443

>1wb1_A Translation elongation factor SELB; selenocysteine, protein synthesis, selenium, ribosome; HET: GDP DXC; 3.0A {Methanococcus maripaludis} SCOP: b.43.3.1 b.43.3.1 b.44.1.1 c.37.1.8 PDB: 1wb2_A* 1wb3_A*

Probab=97.90  E-value=2.5e-05  Score=49.56  Aligned_cols=46  Identities=28%  Similarity=0.137  Sum_probs=34.3

Q ss_pred             cchhhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++   +.+++.+.    .+..   ..+|+++++||+|+.+
T Consensus        91 ~~~~~~aD~~ilVvda~~g~~~qt~e~l~----~~~~---~~ip~IvviNK~Dl~~  139 (482)
T 1wb1_A           91 VSAADIIDLALIVVDAKEGPKTQTGEHML----ILDH---FNIPIIVVITKSDNAG  139 (482)
T ss_dssp             HHHTTSCCEEEEEEETTTCSCHHHHHHHH----HHHH---TTCCBCEEEECTTSSC
T ss_pred             HHHHhhCCEEEEEEecCCCccHHHHHHHH----HHHH---cCCCEEEEEECCCccc
Confidence            356789999999999988   55655543    2222   3578899999999975

>1kk1_A EIF2gamma; initiation of translation; HET: GNP; 1.80A {Pyrococcus abyssi} SCOP: b.43.3.1 b.44.1.1 c.37.1.8 PDB: 1kjz_A* 1kk2_A* 1kk3_A* 1kk0_A* 2d74_A 2dcu_A*

Probab=97.85  E-value=4.5e-05  Score=47.28  Aligned_cols=57  Identities=18%  Similarity=0.046  Sum_probs=36.2

Q ss_pred             hhCCCEEEEEEECCC----hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccccc--CCHHHHHHHH
Q 047889            7 YRGALGALLVYDVTK----STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLN--SMCEEYLIKS   69 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~----~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~--v~~~e~~~~a   69 (72)
                      ...+|++++|+|.++    +.+++.+..|    ...  ...|+++++||+|+.+...  ...++..+++
T Consensus       104 ~~~~D~~ilVvda~~g~~~~qt~e~l~~~----~~~--~~~~iivviNK~Dl~~~~~~~~~~~~i~~~l  166 (410)
T 1kk1_A          104 ASLMDGAILVIAANEPCPRPQTREHLMAL----QII--GQKNIIIAQNKIELVDKEKALENYRQIKEFI  166 (410)
T ss_dssp             GGGCSEEEEEEETTSCSSCHHHHHHHHHH----HHH--TCCCEEEEEECGGGSCHHHHHHHHHHHHHHH
T ss_pred             hhhCCEEEEEEECCCCCCChhHHHHHHHH----HHc--CCCcEEEEEECccCCCHHHHHHHHHHHHHHH
Confidence            345699999999984    4566655433    222  2357999999999975332  2234445544

>2xex_A Elongation factor G; GTPase, translation, biosynthetic protein; 1.90A {Staphylococcus aureus}

Probab=97.84  E-value=3.2e-05  Score=51.03  Aligned_cols=49  Identities=18%  Similarity=0.167  Sum_probs=39.3

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++++|+|.++..++.....|.. +..   .++|+++++||+|+..
T Consensus        93 ~~~l~~aD~~llVvDa~~g~~~~~~~~~~~-~~~---~~~p~ilviNK~Dl~~  141 (693)
T 2xex_A           93 ERSLRVLDGAVTVLDAQSGVEPQTETVWRQ-ATT---YGVPRIVFVNKMDKLG  141 (693)
T ss_dssp             HHHHHHCSEEEEEEETTTBSCHHHHHHHHH-HHH---TTCCEEEEEECTTSTT
T ss_pred             HHHHHHCCEEEEEECCCCCCcHHHHHHHHH-HHH---cCCCEEEEEECCCccc
Confidence            457889999999999999877777666643 433   3689999999999975

>1jwy_B Dynamin A GTPase domain; dynamin, GTPase, GDP, myosin, fusion-protein, hydrolase; HET: BGC ADP GDP; 2.30A {Dictyostelium discoideum} SCOP: c.37.1.8 PDB: 1jx2_B*

Probab=97.84  E-value=2.1e-05  Score=46.73  Aligned_cols=53  Identities=11%  Similarity=0.059  Sum_probs=34.1

Q ss_pred             cchhhCCCEEEEEEECCChhhH-HHHHHHHHHHHHhcCCCCeEEEEeeCCCCccccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTF-ENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLN   59 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~-~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~   59 (72)
                      ..|++++|++++|+|.++.... .....+...+   .....|+++|+||+|+.....
T Consensus       162 ~~~~~~~d~iilvvd~~~~~~~~~~~~~i~~~~---~~~~~~~i~v~NK~Dl~~~~~  215 (315)
T 1jwy_B          162 MAYIKKQNAIIVAVTPANTDLANSDALQLAKEV---DPEGKRTIGVITKLDLMDKGT  215 (315)
T ss_dssp             HHHHHSTTEEEEEEEESSSCSTTCSHHHHHHHH---CSSCSSEEEEEECTTSSCSSC
T ss_pred             HHHHcCCCeEEEEEEecCcchhhhHHHHHHHHh---CCCCCcEEEEEcCcccCCcch
Confidence            4688999999999997543211 1111222222   235689999999999975443

>3avx_A Elongation factor TS, elongation factor TU, linke replicase; RNA polymerase, translation, transferase-RNA complex; HET: GH3; 2.41A {Escherichia coli O157} PDB: 3agq_A 3agp_A* 3avu_A 3avv_A 3avt_A* 3avw_A* 3avy_A* 3mmp_A* 3mmp_G* 1efu_B

Probab=97.78  E-value=3.1e-05  Score=54.08  Aligned_cols=49  Identities=20%  Similarity=0.133  Sum_probs=35.3

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++|+|+|.++.... +...|+..+...   ++| +++++||+|+.+
T Consensus       377 i~gas~AD~aILVVDAtdGv~~-QTrEhL~ll~~l---gIP~IIVVINKiDLv~  426 (1289)
T 3avx_A          377 ITGAAQMDGAILVVAATDGPMP-QTREHILLGRQV---GVPYIIVFLNKCDMVD  426 (1289)
T ss_dssp             HHTSCCCSEEEEEEETTTCSCT-THHHHHHHHHHH---TCSCEEEEEECCTTCC
T ss_pred             HHHHhhCCEEEEEEcCCccCcH-HHHHHHHHHHHc---CCCeEEEEEeeccccc
Confidence            3567899999999999986432 333444455443   477 799999999975

>2rdo_7 EF-G, elongation factor G; elongation factor G, EF-G, RRF, GDPNP, 50S subunit, cryo-EM, REAL-space refinement, ribonucleoprotein; 9.10A {Escherichia coli} PDB: 3j0e_H

Probab=97.76  E-value=7.5e-05  Score=49.41  Aligned_cols=50  Identities=18%  Similarity=0.165  Sum_probs=38.0

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..+++.+|++++|+|.++..+......|. .+..   .++|+++++||+|+...
T Consensus       100 ~~~l~~aD~aIlVvDa~~gv~~qt~~~~~-~~~~---~~ip~ilviNKiD~~~~  149 (704)
T 2rdo_7          100 ERSMRVLDGAVMVYCAVGGVQPQSETVWR-QANK---YKVPRIAFVNKMDRMGA  149 (704)
T ss_pred             HHHHHHCCEEEEEEeCCCCCcHHHHHHHH-HHHH---cCCCEEEEEeCCCcccc
Confidence            46788999999999999876665555553 2322   46899999999998653

>2h5e_A Peptide chain release factor RF-3; beta barrel, translation; HET: GDP; 2.80A {Escherichia coli} PDB: 2o0f_A 3sfs_W* 3zvo_Y* 3uoq_W*

Probab=97.75  E-value=8.7e-05  Score=47.71  Aligned_cols=50  Identities=16%  Similarity=0.052  Sum_probs=34.7

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..+++.+|++++|+|.++...-. ...++..+   ...++|+++++||+|+...
T Consensus       100 ~~~l~~aD~~IlVvDa~~g~~~~-t~~~~~~~---~~~~ipiivviNK~Dl~~~  149 (529)
T 2h5e_A          100 YRTLTAVDCCLMVIDAAKGVEDR-TRKLMEVT---RLRDTPILTFMNKLDRDIR  149 (529)
T ss_dssp             HHGGGGCSEEEEEEETTTCSCHH-HHHHHHHH---TTTTCCEEEEEECTTSCCS
T ss_pred             HHHHHHCCEEEEEEeCCccchHH-HHHHHHHH---HHcCCCEEEEEcCcCCccc
Confidence            46789999999999998754322 12222222   2256899999999999753

>1puj_A YLQF, conserved hypothetical protein YLQF; structural genomics, nysgxrc T18, GTPase, PSI, protein structure initiative; HET: GNP; 2.00A {Bacillus subtilis} SCOP: c.37.1.8

Probab=97.57  E-value=6.4e-05  Score=44.79  Aligned_cols=44  Identities=14%  Similarity=0.012  Sum_probs=34.9

Q ss_pred             chhhCCCEEEEEEECCChhhHH--HHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFE--NVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~--~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+..+|+++.|+|..++.+..  .+..|+        .+.|.++|.||+||.+
T Consensus        19 ~~l~~aDvVl~VvDAr~p~~~~~~~l~~~l--------~~kp~ilVlNK~DL~~   64 (282)
T 1puj_A           19 EKLKLIDIVYELVDARIPMSSRNPMIEDIL--------KNKPRIMLLNKADKAD   64 (282)
T ss_dssp             HHGGGCSEEEEEEETTSTTTTSCHHHHHHC--------SSSCEEEEEECGGGSC
T ss_pred             HHHhhCCEEEEEEeCCCCCccCCHHHHHHH--------CCCCEEEEEECcccCC
Confidence            3577899999999999998765  334332        4689999999999965

>1udx_A The GTP-binding protein OBG; TGS domain, riken structural genomics/proteomics initiative, RSGI, structural genomics; 2.07A {Thermus thermophilus} SCOP: b.117.1.1 c.37.1.8 d.242.1.1

Probab=97.50  E-value=0.00023  Score=44.64  Aligned_cols=48  Identities=17%  Similarity=0.107  Sum_probs=38.7

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~   56 (72)
                      ..++.++.++|++ ..++..+..|..++.....  ...|.++++||+|+..
T Consensus       234 era~~lL~vvDls-~~~~~~ls~g~~el~~la~aL~~~P~ILVlNKlDl~~  283 (416)
T 1udx_A          234 ARTRVLLYVLDAA-DEPLKTLETLRKEVGAYDPALLRRPSLVALNKVDLLE  283 (416)
T ss_dssp             TSSSEEEEEEETT-SCHHHHHHHHHHHHHHHCHHHHHSCEEEEEECCTTSC
T ss_pred             HHHHhhhEEeCCc-cCCHHHHHHHHHHHHHHhHHhhcCCEEEEEECCChhh
Confidence            3689999999998 7788888888888766532  3578899999999975

>2dy1_A Elongation factor G; translocation, GTP complex, structural genomics, NPPSFA; HET: GTP; 1.60A {Thermus thermophilus} SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB: 1wdt_A*

Probab=97.47  E-value=0.00027  Score=46.50  Aligned_cols=48  Identities=15%  Similarity=0.058  Sum_probs=35.3

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      ..+++.+|++++|+|.++.-.... ..++..+..   .++|+++++||+|+.
T Consensus        92 ~~~l~~ad~~ilVvD~~~g~~~qt-~~~~~~~~~---~~ip~ilv~NKiD~~  139 (665)
T 2dy1_A           92 RGALEAADAALVAVSAEAGVQVGT-ERAWTVAER---LGLPRMVVVTKLDKG  139 (665)
T ss_dssp             HHHHHHCSEEEEEEETTTCSCHHH-HHHHHHHHH---TTCCEEEEEECGGGC
T ss_pred             HHHHhhcCcEEEEEcCCcccchhH-HHHHHHHHH---ccCCEEEEecCCchh
Confidence            467889999999999877544333 344444443   358999999999986

>1wxq_A GTP-binding protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; 2.60A {Pyrococcus horikoshii} SCOP: c.37.1.8 d.15.10.2

Probab=97.37  E-value=0.00018  Score=44.72  Aligned_cols=18  Identities=28%  Similarity=0.135  Sum_probs=15.8

Q ss_pred             chhhCCCEEEEEEECCCh
Q 047889            5 AYYRGALGALLVYDVTKS   22 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~   22 (72)
                      .+++++|++++|+|.++.
T Consensus        97 ~~i~~aD~il~VvD~~~~  114 (397)
T 1wxq_A           97 DDLRMASALIHVVDATGK  114 (397)
T ss_dssp             CSSTTCSEEEEEEETTCC
T ss_pred             HHHhcCCEEEEEEecccc
Confidence            457999999999999885

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=97.26  E-value=0.00059  Score=38.01  Aligned_cols=43  Identities=21%  Similarity=0.378  Sum_probs=31.0

Q ss_pred             hCCCEEEEEEECCChhhHHH--HHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKSTTFEN--VSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +.++++++++|++++.++..  +..|+   ..   ...|+++++||+|+..
T Consensus       107 ~~~~~~~~v~d~~~~~~~~~~~~~~~~---~~---~~~~~~~v~nK~D~~s  151 (210)
T 1pui_A          107 QSLQGLVVLMDIRHPLKDLDQQMIEWA---VD---SNIAVLVLLTKADKLA  151 (210)
T ss_dssp             TTEEEEEEEEETTSCCCHHHHHHHHHH---HH---TTCCEEEEEECGGGSC
T ss_pred             hcccEEEEEEECCCCCchhHHHHHHHH---HH---cCCCeEEEEecccCCC
Confidence            47899999999998766542  23332   21   4588999999999854

>3mca_A HBS1, elongation factor 1 alpha-like protein; protein protein complex, translation regulation; 2.74A {Schizosaccharomyces pombe}

Probab=97.24  E-value=1.1e-05  Score=52.31  Aligned_cols=46  Identities=35%  Similarity=0.205  Sum_probs=25.0

Q ss_pred             cchhhCCCEEEEEEECCCh----------hhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            4 SAYYRGALGALLVYDVTKS----------TTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~----------~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      ..+++.+|++|+|+|.++.          .+.+.+    ..+..   ..+| +++|+||+|+..
T Consensus       273 ~~~~~~aD~alLVVDa~~g~~e~gi~~~~qt~e~l----~~~~~---lgip~iIvviNKiDl~~  329 (592)
T 3mca_A          273 IAGASSADFAVLVVDSSQNNFERGFLENGQTREHA----YLLRA---LGISEIVVSVNKLDLMS  329 (592)
T ss_dssp             CC-------CCSEEEEEECCSSTTSCSCSSHHHHH----HHHHH---SSCCCEEEEEECGGGGT
T ss_pred             HHHHhhCCEEEEEEECCCCccccccccchHHHHHH----HHHHH---cCCCeEEEEEecccccc
Confidence            4577899999999999853          232222    22222   2355 899999999964

>2x2e_A Dynamin-1; nitration, hydrolase, membrane fission, nucleotide-binding, endocytosis, motor protein; HET: GDP; 2.00A {Homo sapiens} PDB: 2x2f_A* 3zyc_A* 3zys_A

Probab=97.16  E-value=0.00041  Score=42.22  Aligned_cols=53  Identities=15%  Similarity=0.043  Sum_probs=31.8

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ...|+++++++++++...+. .+... .|...+........|+++|+||+|+.+.
T Consensus       160 ~~~~~~~~~~iiL~v~~a~~-~~~~~-~~~~i~~~~~~~~~~~i~V~NK~Dl~~~  212 (353)
T 2x2e_A          160 LMQFVTKENCLILAVSPANS-DLANS-DALKVAKEVDPQGQRTIGVITKLDLMDE  212 (353)
T ss_dssp             HHHHHTSTTEEEEEEEETTS-CGGGC-HHHHHHHHHCTTCTTEEEEEECGGGSCT
T ss_pred             HHHHHcCCCeEEEEEecCCC-ccchh-HHHHHHHHhCcCCCceEEEeccccccCc
Confidence            34678888877776643332 12211 1222333333457899999999999654

>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8

Probab=97.08  E-value=0.0016  Score=39.37  Aligned_cols=49  Identities=18%  Similarity=0.179  Sum_probs=35.3

Q ss_pred             hhhCCCEEEEEEECCChh-hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            6 YYRGALGALLVYDVTKST-TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      -..++|.+++|+|..+|. +...+..++-.+.   ..++|.++|.||+||.++
T Consensus        83 ~~anvD~v~~V~~~~~p~~~~~~i~r~L~~~~---~~~~~~vivlnK~DL~~~  132 (307)
T 1t9h_A           83 PICNVDQAVLVFSAVQPSFSTALLDRFLVLVE---ANDIQPIICITKMDLIED  132 (307)
T ss_dssp             TEECCCEEEEEEESTTTTCCHHHHHHHHHHHH---TTTCEEEEEEECGGGCCC
T ss_pred             HHHhCCEEEEEEeCCCCCCCHHHHHHHHHHHH---HCCCCEEEEEECCccCch
Confidence            356899999999998765 4554555543332   256888999999999753

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=97.05  E-value=0.00049  Score=38.73  Aligned_cols=54  Identities=15%  Similarity=0.124  Sum_probs=33.8

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHH
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKS   69 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a   69 (72)
                      ...+++++|+|.++...  ....+.   ..   ...|+++|+||+|+...+....++..+.+
T Consensus       128 ~~~~~~i~vvd~~~~~~--~~~~~~---~~---~~~~~iiv~NK~Dl~~~~~~~~~~~~~~~  181 (221)
T 2wsm_A          128 LGENYRVVMVSVTEGDD--VVEKHP---EI---FRVADLIVINKVALAEAVGADVEKMKADA  181 (221)
T ss_dssp             CSCSEEEEEEEGGGCTT--HHHHCH---HH---HHTCSEEEEECGGGHHHHTCCHHHHHHHH
T ss_pred             cccCcEEEEEeCCCcch--hhhhhh---hh---hhcCCEEEEecccCCcchhhHHHHHHHHH
Confidence            46788899999876532  111111   11   13688999999999764445566655544

>3t5d_A Septin-7; GTP-binding protein, cytoskeleton, signaling protein; HET: GDP; 3.30A {Homo sapiens} PDB: 3tw4_A*

Probab=96.97  E-value=0.00081  Score=39.49  Aligned_cols=43  Identities=14%  Similarity=0.086  Sum_probs=27.9

Q ss_pred             CCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889           10 ALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus        10 a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +|+++++.+.++......-..+++.+..    .+|+++|+||+|+..
T Consensus       116 ~~~~l~~i~~~~~~~~~~d~~~l~~l~~----~~pvi~V~nK~D~~~  158 (274)
T 3t5d_A          116 VQCCLYFIAPSGHGLKPLDIEFMKRLHE----KVNIIPLIAKADTLT  158 (274)
T ss_dssp             CCEEEEEECSCCSSCCHHHHHHHHHHTT----TSCEEEEESSGGGSC
T ss_pred             eeEEEEEecCCCCCCCHHHHHHHHHHhc----cCCEEEEEeccCCCC
Confidence            6788888876653222222334444433    699999999999854

>3cnl_A YLQF, putative uncharacterized protein; circular permutation, GNP, signaling protein; HET: GNP; 2.00A {Thermotoga maritima} PDB: 3cnn_A* 3cno_A*

Probab=96.69  E-value=0.00043  Score=40.82  Aligned_cols=42  Identities=17%  Similarity=0.152  Sum_probs=32.8

Q ss_pred             chhhCCCEEEEEEECCChhhHHH--HHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFEN--VSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ....++|.++.|.|..++.+..+  +. +       .  +.|.++|.||+||.+
T Consensus        17 ~~l~~~D~vl~VvDar~P~~~~~~~l~-l-------l--~k~~iivlNK~DL~~   60 (262)
T 3cnl_A           17 DLLRLVNTVVEVRDARAPFATSAYGVD-F-------S--RKETIILLNKVDIAD   60 (262)
T ss_dssp             HHHTTCSEEEEEEETTSTTTTSCTTSC-C-------T--TSEEEEEEECGGGSC
T ss_pred             HHHhhCCEEEEEeeCCCCCcCcChHHH-h-------c--CCCcEEEEECccCCC
Confidence            35678999999999999876543  12 2       1  689999999999965

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=96.35  E-value=0.011  Score=36.53  Aligned_cols=47  Identities=15%  Similarity=0.186  Sum_probs=32.1

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..++|.+++|.+..-..+...+..++-....   .++|.+||.||+||.+
T Consensus       128 ~anvD~v~iv~a~~P~~~~~~i~r~L~~a~~---~~~~~iivlNK~DL~~  174 (358)
T 2rcn_A          128 AANIDQIVIVSAILPELSLNIIDRYLVGCET---LQVEPLIVLNKIDLLD  174 (358)
T ss_dssp             EECCCEEEEEEESTTTCCHHHHHHHHHHHHH---HTCEEEEEEECGGGCC
T ss_pred             HhcCCEEEEEEeCCCCCCHHHHHHHHHHHHh---cCCCEEEEEECccCCC
Confidence            3678999999887533355555555544333   3477799999999965

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=96.21  E-value=0.00092  Score=40.04  Aligned_cols=44  Identities=11%  Similarity=0.092  Sum_probs=27.0

Q ss_pred             hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccccc--CCHHHHHHHHh
Q 047889           24 TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLN--SMCEEYLIKSR   70 (72)
Q Consensus        24 s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~--v~~~e~~~~a~   70 (72)
                      +|+.+..  +.++... ..+|+++|+||.|+...++  +..+++.++++
T Consensus       140 ~Ld~~~~--~~l~~l~-~~~~iilV~~K~Dl~~~~e~~~~~~~~~~~~~  185 (301)
T 2qnr_A          140 GLKPLDV--AFMKAIH-NKVNIVPVIAKADTLTLKERERLKKRILDEIE  185 (301)
T ss_dssp             SCCHHHH--HHHHHHT-TTSCEEEEECCGGGSCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHH--HHHHHHH-hcCCEEEEEEeCCCCCHHHHHHHHHHHHHHHH
Confidence            4555431  3333333 5689999999999976443  33456666654

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=96.02  E-value=0.0076  Score=34.66  Aligned_cols=48  Identities=13%  Similarity=-0.060  Sum_probs=26.0

Q ss_pred             hhCCCEEEEEEECCC---hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            7 YRGALGALLVYDVTK---STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      +.+ +.++++.|...   +..+.....+....  ....+.|+++|+||+|+...
T Consensus       136 ~~~-~~iv~vvD~~~~~~~~~~~~~~~~~~~~--~~~~~~p~~iv~NK~D~~~~  186 (262)
T 1yrb_A          136 LPY-PLVVYISDPEILKKPNDYCFVRFFALLI--DLRLGATTIPALNKVDLLSE  186 (262)
T ss_dssp             SSS-CEEEEEECGGGCCSHHHHHHHHHHHHHH--HHHHTSCEEEEECCGGGCCH
T ss_pred             Hhh-ceEEeccchhhhcCHHHHHHHHHHHHHH--hcccCCCeEEEEeccccccc
Confidence            344 56666666543   33333322221111  11235899999999998754

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=95.92  E-value=0.0027  Score=35.76  Aligned_cols=28  Identities=14%  Similarity=0.153  Sum_probs=20.6

Q ss_pred             CeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889           43 IVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus        43 ~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      .|.++|+||+|+.+.+.+..+++.++++
T Consensus       165 ~~~iiv~NK~Dl~~~~~~~~~~~~~~~~  192 (226)
T 2hf9_A          165 TADLIVINKIDLADAVGADIKKMENDAK  192 (226)
T ss_dssp             TCSEEEEECGGGHHHHTCCHHHHHHHHH
T ss_pred             cCCEEEEeccccCchhHHHHHHHHHHHH
Confidence            4559999999997655566777666554

>1jal_A YCHF protein; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; 2.40A {Haemophilus influenzae} SCOP: c.37.1.8 d.15.10.2

Probab=95.69  E-value=0.11  Score=32.18  Aligned_cols=16  Identities=13%  Similarity=-0.147  Sum_probs=14.6

Q ss_pred             hhhCCCEEEEEEECCC
Q 047889            6 YYRGALGALLVYDVTK   21 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~   21 (72)
                      +++++|++++|+|.++
T Consensus        93 ~ir~ad~il~VvD~~~  108 (363)
T 1jal_A           93 NIRETDAIGHVVRCFE  108 (363)
T ss_dssp             HHHTCSEEEEEEECSC
T ss_pred             HHHhcCeEEEEEecCC
Confidence            5799999999999986

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=95.18  E-value=0.0024  Score=38.93  Aligned_cols=42  Identities=12%  Similarity=0.079  Sum_probs=29.0

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ...+|.+++|+|....+.+..+..+        -...|+++|.||+|+..
T Consensus       190 ~~~aD~vl~V~d~~~~~~~~~l~~~--------~~~~p~ivVlNK~Dl~~  231 (355)
T 3p32_A          190 ANMVDTFVLLTLARTGDQLQGIKKG--------VLELADIVVVNKADGEH  231 (355)
T ss_dssp             HTTCSEEEEEEESSTTCTTTTCCTT--------SGGGCSEEEEECCCGGG
T ss_pred             HHhCCEEEEEECCCCCccHHHHHHh--------HhhcCCEEEEECCCCcC
Confidence            4789999999997765544322210        12368999999999864

>3vqt_A RF-3, peptide chain release factor 3; translation, GTPase; HET: GDP; 1.80A {Desulfovibrio vulgaris} PDB: 3vr1_A*

Probab=95.16  E-value=0.088  Score=34.10  Aligned_cols=46  Identities=22%  Similarity=0.137  Sum_probs=32.2

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++-+|++++|+|-..----.....| .++.+   .++|.+++-||+|...
T Consensus       121 L~~~DgAvlVvda~~GV~~qT~~v~-~~a~~---~~lp~i~fINK~Dr~~  166 (548)
T 3vqt_A          121 LTAVDSALVVIDAAKGVEAQTRKLM-DVCRM---RATPVMTFVNKMDREA  166 (548)
T ss_dssp             HHSCSEEEEEEETTTBSCHHHHHHH-HHHHH---TTCCEEEEEECTTSCC
T ss_pred             HHhcCceEEEeecCCCcccccHHHH-HHHHH---hCCceEEEEecccchh
Confidence            4678999999998764333333344 34443   4599999999999865

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=94.73  E-value=0.0068  Score=36.79  Aligned_cols=43  Identities=12%  Similarity=0.093  Sum_probs=25.6

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+.+|++++|+|.+....+..+..   ..     .+.|.++|.||+|+..
T Consensus       166 ~~~~aD~vl~Vvd~~~~~~~~~l~~---~~-----~~~p~ivv~NK~Dl~~  208 (341)
T 2p67_A          166 VARMVDCFISLQIAGGGDDLQGIKK---GL-----MEVADLIVINKDDGDN  208 (341)
T ss_dssp             HHTTCSEEEEEECC------CCCCH---HH-----HHHCSEEEECCCCTTC
T ss_pred             HHHhCCEEEEEEeCCccHHHHHHHH---hh-----hcccCEEEEECCCCCC
Confidence            3468999999999876543221111   00     1367899999999865

>3zvr_A Dynamin-1; hydrolase, DRP1, DRP, endocytosis, mitochondrial fission, GT stalk, PH, BSE, membrane fission; HET: 1PE; 3.10A {Rattus norvegicus} PDB: 3snh_A

Probab=94.52  E-value=0.063  Score=36.34  Aligned_cols=47  Identities=13%  Similarity=0.010  Sum_probs=30.8

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..+|.+++|.|.+....-.....+...+   .....|+++|.||+|+...
T Consensus       186 ~~aDlIL~VVDAs~~~~~~d~l~ll~~L---~~~g~pvIlVlNKiDlv~~  232 (772)
T 3zvr_A          186 KENCLILAVSPANSDLANSDALKIAKEV---DPQGQRTIGVITKLDLMDE  232 (772)
T ss_dssp             STTEEEEEEEETTSCSSSCHHHHHHHHH---CTTCSSEEEEEECTTSSCT
T ss_pred             cCCcEEEEEEcCCCCcchhHHHHHHHHH---HhcCCCEEEEEeCcccCCc
Confidence            4678999999987643322222233333   3356899999999998653

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=94.31  E-value=0.045  Score=33.36  Aligned_cols=43  Identities=12%  Similarity=0.050  Sum_probs=24.9

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ....+|.+++|+|.++......+..   .+     -..|.++|.||+|+.+
T Consensus       184 l~~~~d~vl~V~d~~~~~~~~~i~~---~i-----l~~~~ivVlNK~Dl~~  226 (349)
T 2www_A          184 VADMVDMFVLLLPPAGGDELQGIKR---GI-----IEMADLVAVTKSDGDL  226 (349)
T ss_dssp             HHTTCSEEEEEECCC--------------------CCSCSEEEECCCSGGG
T ss_pred             HHhhCCEEEEEEcCCcchhHHHhHH---HH-----HhcCCEEEEeeecCCC
Confidence            3467899999999886543322211   11     2357899999999864

>4fn5_A EF-G 1, elongation factor G 1; translation, translation-antibiotic compl; HET: 0UO; 2.90A {Pseudomonas aeruginosa}

Probab=93.51  E-value=0.2  Score=33.32  Aligned_cols=46  Identities=20%  Similarity=0.242  Sum_probs=30.3

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++-+||+++|.|...=-.-....-| .++.+.   ++|.+++-||+|...
T Consensus       106 Lr~~DgavlvVDaveGV~~qT~~v~-~~a~~~---~lp~i~~iNKiDr~~  151 (709)
T 4fn5_A          106 LRVLDGAVVVFCGTSGVEPQSETVW-RQANKY---GVPRIVYVNKMDRQG  151 (709)
T ss_dssp             HHHCSEEEEEEETTTCSCHHHHHHH-HHHHHH---TCCEEEEEECSSSTT
T ss_pred             HHHhCeEEEEEECCCCCchhHHHHH-HHHHHc---CCCeEEEEccccccC
Confidence            4558999999998753222222233 334333   589999999999754

>3j25_A Tetracycline resistance protein TETM; antibiotic resistance, translation; HET: GCP; 7.20A {Enterococcus faecalis}

Probab=90.53  E-value=0.26  Score=32.43  Aligned_cols=46  Identities=20%  Similarity=0.192  Sum_probs=30.3

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+-+|++++|.|...=-.-.....| .++.+.   ++|.+++-||+|...
T Consensus        88 L~~~DgavlVVDa~~GV~~qT~~v~-~~a~~~---~lp~i~~INKmDr~~  133 (638)
T 3j25_A           88 LSVLDGAILLISAKDGVQAQTRILF-HALRKM---GIPTIFFINKIDQNG  133 (638)
T ss_dssp             HTTCSEEECCEESSCTTCSHHHHHH-HHHHHH---TCSCEECCEECCSSS
T ss_pred             HHHhCEEEEEEeCCCCCcHHHHHHH-HHHHHc---CCCeEEEEecccccc
Confidence            4668999999998753222222333 344443   478899999999754

>4a9a_A Ribosome-interacting GTPase 1; DRG-DFRP complex, ribosome binding GTPase; 2.67A {Saccharomyces cerevisiae}

Probab=90.34  E-value=0.65  Score=28.85  Aligned_cols=48  Identities=15%  Similarity=0.046  Sum_probs=30.9

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc--CCCCeEEEEeeCCCCc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA--GSNIVIMLIGNKSDLK   55 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~~~vlvgnK~Dl~   55 (72)
                      ..+.+|++++|.|.+++..  .......++....  -...|..++.||.|..
T Consensus       146 ~i~~ad~il~vvD~~~p~~--~~~~i~~EL~~~~~~l~~k~~~i~~nK~d~~  195 (376)
T 4a9a_A          146 VARTCNLLFIILDVNKPLH--HKQIIEKELEGVGIRLNKTPPDILIKKKEKG  195 (376)
T ss_dssp             HHHHCSEEEEEEETTSHHH--HHHHHHHHHHHTTEEETCCCCCEEEEECSSS
T ss_pred             HHHhcCccccccccCccHH--HHHHHHHHHHHhhHhhccCChhhhhhHhhhh
Confidence            3578999999999998743  2222223333322  1456778889999964

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=87.86  E-value=0.088  Score=33.20  Aligned_cols=34  Identities=18%  Similarity=0.186  Sum_probs=26.7

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHh
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDH   38 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~   38 (72)
                      ..|+..+.|.++|+|.++. +++....|.+.+++.
T Consensus       115 ~~~l~~~~G~~vV~D~tn~-~~~~R~~~~~~~~~~  148 (469)
T 1bif_A          115 RKFLSEEGGHVAVFDATNT-TRERRAMIFNFGEQN  148 (469)
T ss_dssp             HHHHHTTCCSEEEEESCCC-SHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCCEEEEeCCCC-CHHHHHHHHHHHHhc
Confidence            4567778899999999988 677777887777664

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=86.26  E-value=0.52  Score=28.59  Aligned_cols=41  Identities=12%  Similarity=-0.006  Sum_probs=22.2

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      ...+|.+++++|.........+..+   +.     ..|.+++.||.|+.
T Consensus       166 ~~~~d~vl~v~d~~~~~~~~~i~~~---i~-----~~~~ivvlNK~Dl~  206 (337)
T 2qm8_A          166 ADLTDFFLVLMLPGAGDELQGIKKG---IF-----ELADMIAVNKADDG  206 (337)
T ss_dssp             HTTSSEEEEEECSCC------CCTT---HH-----HHCSEEEEECCSTT
T ss_pred             HhhCCEEEEEEcCCCcccHHHHHHH---Hh-----ccccEEEEEchhcc
Confidence            3578999999987644322211111   11     23556667999974

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=83.72  E-value=3.7  Score=22.27  Aligned_cols=47  Identities=0%  Similarity=-0.154  Sum_probs=32.8

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc--CCCCeEEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHA--GSNIVIMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~~~vlvgnK~Dl~   55 (72)
                      +..+|.++++...+. .+ ..+....+.+.+..  .+..++.+|.|+.+-.
T Consensus        95 l~~ad~viiv~~~~~-~~-~~~~~~~~~l~~~~~~~~~~~~~vv~N~~~~~  143 (206)
T 4dzz_A           95 VMVSDLVIIPVTPSP-LD-FSAAGSVVTVLEAQAYSRKVEARFLITRKIEM  143 (206)
T ss_dssp             HHHCSEEEEEECSCT-TT-HHHHHHHHHHHTTSCGGGCCEEEEEECSBCTT
T ss_pred             HHHCCEEEEEecCCH-HH-HHHHHHHHHHHHHHHhCCCCcEEEEEeccCCC
Confidence            455888888887654 44 67777777776543  2456779999999854

>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH, niaid, borellia burgdorferi, plasmid partition protein, iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A

Probab=80.59  E-value=6  Score=22.56  Aligned_cols=46  Identities=11%  Similarity=-0.019  Sum_probs=33.3

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCC
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSD   53 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~D   53 (72)
                      -+..+|.++++... +..++..+....+.+.... .+.++.+|.|+..
T Consensus       163 ~l~~aD~vivv~~~-~~~s~~~~~~~~~~l~~~~-~~~~~~vv~N~~~  208 (267)
T 3k9g_A          163 ALLCSDYVIIPMTA-EKWAVESLDLFNFFVRKLN-LFLPIFLIITRFK  208 (267)
T ss_dssp             HHTTCSEEEEEEES-CTTHHHHHHHHHHHHHTTT-CCCCEEEEEEEEC
T ss_pred             HHHHCCeEEEEeCC-ChHHHHHHHHHHHHHHHHh-ccCCEEEEEeccc
Confidence            34568999999876 5667777777777776653 4567778889984

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	72
d2f9la1	175	c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [T	1e-09
d2a5ja1	173	c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [Ta	1e-08
d2bcgy1	194	c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Sac	6e-08
d1z0fa1	166	c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [Ta	8e-08
d2fu5c1	173	c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [Ta	3e-07
d1g16a_	166	c.37.1.8 (A:) Rab-related protein Sec4 {Baker's ye	1e-06
d1m7ba_	179	c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [T	2e-06
d1u8za_	168	c.37.1.8 (A:) Ras-related protein RalA {Cotton-top	2e-05
d1kaoa_	167	c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId:	2e-05
d2ngra_	191	c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId:	2e-05
d3raba_	169	c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxI	2e-05
d1mh1a_	183	c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 96	3e-05
d2g6ba1	170	c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [T	1e-04
d1r2qa_	170	c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId:	2e-04
d1ctqa_	166	c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapi	2e-04
d1z08a1	167	c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [T	2e-04
d1z0ja1	167	c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [	5e-04
d2ew1a1	171	c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [Ta	8e-04
d2atxa1	185	c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [Tax	0.001
d1e0sa_	173	c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo	0.001
d2f7sa1	186	c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [T	0.004
d2bmea1	174	c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [Ta	0.004

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]} Length = 175

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (116), Expect = 1e-09
 Identities = 46/64 (71%), Positives = 53/64 (82%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
            ITSAYYRGA+GALLVYD+ K  T+ENV RWLK+LRDHA SNIVIML+GNKSDL+HL   
Sbjct: 68  RITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAV 127

Query: 61  MCEE 64
             +E
Sbjct: 128 PTDE 131

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]} Length = 173

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.4 bits (109), Expect = 1e-08
 Identities = 36/63 (57%), Positives = 48/63 (76%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           +IT +YYRGA GALLVYD+T+  TF +++ WL+D R H+ SN+VIMLIGNKSDL+   + 
Sbjct: 67  SITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESRRDV 126

Query: 61  MCE 63
             E
Sbjct: 127 KRE 129

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 194

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.9 bits (105), Expect = 6e-08
 Identities = 26/65 (40%), Positives = 40/65 (61%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
            ITS+YYRG+ G ++VYDVT   +F  V  WL+++  +A S ++ +L+GNK DLK     
Sbjct: 70  TITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYATSTVLKLLVGNKCDLKDKRVV 129

Query: 61  MCEEY 65
             +  
Sbjct: 130 EYDVA 134

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]} Length = 166

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.1 bits (103), Expect = 8e-08
 Identities = 32/64 (50%), Positives = 46/64 (71%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           A+T +YYRGA GAL+VYD+T+ +T+ ++S WL D R+    N VI+LIGNK+DL+   + 
Sbjct: 68  AVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIILIGNKADLEAQRDV 127

Query: 61  MCEE 64
             EE
Sbjct: 128 TYEE 131

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]} Length = 173

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.8 bits (100), Expect = 3e-07
 Identities = 25/64 (39%), Positives = 43/64 (67%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
            IT+AYYRGA+G +LVYD+T   +F+N+  W++++ +HA +++  M++GNK D+      
Sbjct: 70  TITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQV 129

Query: 61  MCEE 64
             E 
Sbjct: 130 SKER 133

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 166

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.9 bits (95), Expect = 1e-06
 Identities = 27/56 (48%), Positives = 40/56 (71%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
            IT+AYYRGA+G +LVYD+T   TF N+ +W K + +HA     ++L+GNKSD++ 
Sbjct: 66  TITTAYYRGAMGIILVYDITDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMET 121

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]} Length = 179

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.4 bits (93), Expect = 2e-06
 Identities = 14/68 (20%), Positives = 32/68 (47%)

Query: 3   TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMC 62
               Y  +   L+ +D+++  T ++V +  K        N  ++L+G KSDL+  ++++ 
Sbjct: 67  RPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDLRTDVSTLV 126

Query: 63  EEYLIKSR 70
           E    +  
Sbjct: 127 ELSNHRQT 134

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]} Length = 168

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

 Score = 38.0 bits (87), Expect = 2e-05
 Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKD-LRDHAGSNIVIMLIGNKSDLKHLLN 59
           AI   Y+R   G L V+ +T+  +F   + + +  LR     N+  +L+GNKSDL+    
Sbjct: 67  AIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQ 126

Query: 60  SMCEEY 65
              EE 
Sbjct: 127 VSVEEA 132

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]} Length = 167

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.0 bits (87), Expect = 2e-05
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 3   TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRD-HAGSNIVIMLIGNKSDLKHLLNSM 61
              Y +   G +LVY +    +F+++      +        + ++L+GNK DL+      
Sbjct: 68  RDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRYEKVPVILVGNKVDLESEREVS 127

Query: 62  CEE 64
             E
Sbjct: 128 SSE 130

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]} Length = 191

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (87), Expect = 2e-05
 Identities = 12/51 (23%), Positives = 20/51 (39%)

Query: 6   YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
            Y      L+ + V   ++FENV         H       +L+G + DL+ 
Sbjct: 71  SYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRD 121

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 169

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 37.5 bits (86), Expect = 2e-05
 Identities = 23/65 (35%), Positives = 38/65 (58%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
            IT+AYYRGA+G +L+YD+T   +F  V  W   ++ ++  N  ++L+GNK D++     
Sbjct: 69  TITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDMEDERVV 128

Query: 61  MCEEY 65
             E  
Sbjct: 129 SSERG 133

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (85), Expect = 3e-05
 Identities = 14/54 (25%), Positives = 22/54 (40%)

Query: 3   TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
               Y     +L+ + +    +FENV         H   N  I+L+G K DL+ 
Sbjct: 70  RPLSYPQTDVSLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRD 123

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]} Length = 170

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.6 bits (81), Expect = 1e-04
 Identities = 25/64 (39%), Positives = 40/64 (62%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNS 60
           ++T AYYR A   LL+YDVT   +F+N+  WL ++ ++A  ++ +ML+GNK D  H    
Sbjct: 71  SVTHAYYRDAHALLLLYDVTNKASFDNIQAWLTEIHEYAQHDVALMLLGNKVDSAHERVV 130

Query: 61  MCEE 64
             E+
Sbjct: 131 KRED 134

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]} Length = 170

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (79), Expect = 2e-04
 Identities = 26/64 (40%), Positives = 37/64 (57%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSM 61
           +   YYRGA  A++VYD+T   +F     W+K+L+  A  NIVI L GNK+DL +     
Sbjct: 71  LAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVD 130

Query: 62  CEEY 65
            +E 
Sbjct: 131 FQEA 134

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]} Length = 166

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (79), Expect = 2e-04
 Identities = 13/64 (20%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 3   TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSM 61
              Y R   G L V+ +  + +FE++ ++ + ++      ++ ++L+GNK DL       
Sbjct: 68  RDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVES 127

Query: 62  CEEY 65
            +  
Sbjct: 128 RQAQ 131

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]} Length = 167

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.9 bits (79), Expect = 2e-04
 Identities = 23/55 (41%), Positives = 36/55 (65%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           +   YYR + GA+LVYD+T   +F+ V  W+K+LR   G+ I + ++GNK DL+ 
Sbjct: 68  LGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEK 122

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]} Length = 167

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.8 bits (76), Expect = 5e-04
 Identities = 24/64 (37%), Positives = 38/64 (59%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSM 61
           +   YYRG+  A++VYD+TK  TF  +  W+++LR H   +IV+ + GNK DL  +   M
Sbjct: 69  LAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQHGPPSIVVAIAGNKCDLTDVREVM 128

Query: 62  CEEY 65
             + 
Sbjct: 129 ERDA 132

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]} Length = 171

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.2 bits (75), Expect = 8e-04
 Identities = 20/56 (35%), Positives = 35/56 (62%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH 56
           +IT +YYR A   +L YD+T   +F  +  WL+++  +A + ++ +L+GNK DL  
Sbjct: 69  SITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYASNKVITVLVGNKIDLAE 124

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]} Length = 185

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.7 bits (73), Expect = 0.001
 Identities = 12/61 (19%), Positives = 22/61 (36%)

Query: 3   TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMC 62
               Y      L+ + V    +F+NV             N+  +LIG + DL+    ++ 
Sbjct: 74  RPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKTLA 133

Query: 63  E 63
            
Sbjct: 134 R 134

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]} Length = 173

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

 Score = 32.6 bits (73), Expect = 0.001
 Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 1/65 (1%)

Query: 2   ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDL-RDHAGSNIVIMLIGNKSDLKHLLNS 60
           +   YY G  G + V D       +   + L  +  D    + +I++  NK DL   +  
Sbjct: 72  LWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKP 131

Query: 61  MCEEY 65
              + 
Sbjct: 132 HEIQE 136

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]} Length = 186

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 31.4 bits (70), Expect = 0.004
 Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSN-IVIMLIGNKSDLKHLLN 59
           ++T+A++R A+G LL++D+T   +F NV  W+  L+ +A      I+LIGNK+DL     
Sbjct: 79  SLTTAFFRDAMGFLLMFDLTSQQSFLNVRNWMSQLQANAYCENPDIVLIGNKADLPDQRE 138

Query: 60  SMCEE 64
               +
Sbjct: 139 VNERQ 143

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]} Length = 174

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 31.4 bits (70), Expect = 0.004
 Identities = 27/50 (54%), Positives = 35/50 (70%)

Query: 1   AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGN 50
           ++T +YYRGA GALLVYD+T   T+  ++ WL D R  A  NIVI+L GN
Sbjct: 69  SVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGN 118

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	72
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	99.85
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	99.84
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	99.83
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	99.82
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	99.82
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	99.81
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	99.79
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	99.79
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	99.79
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	99.79
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	99.78
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	99.78
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	99.78
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	99.78
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	99.77
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	99.77
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	99.76
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	99.76
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	99.75
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	99.75
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	99.75
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	99.74
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	99.73
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	99.73
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	99.71
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	99.7
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	99.69
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	99.69
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	99.69
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	99.69
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	99.68
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	99.66
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	99.66
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	99.65
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	99.57
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	99.51
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	99.47
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	99.46
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	99.42
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	99.41
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	99.39
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	99.35
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	99.03
d2fh5b1	207	Signal recognition particle receptor beta-subunit	98.99
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	98.99
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	98.9
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	98.83
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	98.78
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	98.78
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	98.74
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	98.67
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	98.67
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	98.43
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	98.41
d1nrjb_	209	Signal recognition particle receptor beta-subunit	97.95
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	97.93
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	97.89
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	97.64
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	97.63
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	97.54
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	97.31
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	97.13
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	97.12
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	97.03
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	97.01
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	96.49
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	96.34
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	95.55
d2qn6a3	205	Initiation factor eIF2 gamma subunit, N-terminal (	95.54
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	95.43
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	95.24
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	95.2
d1d2ea3	196	Elongation factor Tu (EF-Tu), N-terminal (G) domai	94.99
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	94.58
d1kk1a3	195	Initiation factor eIF2 gamma subunit, N-terminal (	94.26
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	93.13
d1zunb3	222	Sulfate adenylate transferase subunit cysN/C, EF-T	92.6
d1f60a3	239	Elongation factor eEF-1alpha, N-terminal (G) domai	90.79
d1jnya3	224	Elongation factor eEF-1alpha, N-terminal (G) domai	88.84
d1r5ba3	245	Eukaryotic peptide chain release factor ERF2, G do	87.43
d2akab1	299	Dynamin G domain {Rat (Rattus norvegicus) [TaxId:	86.32
d1jwyb_	306	Dynamin G domain {Dictyostelium discoideum [TaxId:	84.88
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	84.31
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	80.34

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=5.4e-21  Score=105.01  Aligned_cols=70  Identities=26%  Similarity=0.296  Sum_probs=63.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||+++|++++|||++++.||+.+..|+.++..... ..+|+++||||+|+.++++++.+++.+++++
T Consensus        64 ~~~~~~~~~d~~ilv~d~t~~~s~~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~~~v~~~~~~~~~~~  134 (168)
T d2gjsa1          64 LPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVSVDEGRACAVV  134 (168)
T ss_dssp             CHHHHHTSCSEEEEEEETTCHHHHHHHHHHHHHHHHHCC--CCCEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             ecccchhhhhhhceeccccccccccccccccchhhcccccccceEEEeecccchhhhcchhHHHHHHHHHh
Confidence            568899999999999999999999999999999877654 6789999999999999999999999998864

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=7.4e-21  Score=103.80  Aligned_cols=70  Identities=24%  Similarity=0.542  Sum_probs=63.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      .++.||+++|++++|||+++++||+.+..|+.++.+.. .+++|++|||||+||.+++.++.++++++|++
T Consensus        68 ~~~~~~~~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~pi~lvgnK~Dl~~~~~v~~~~~~~~~~~  138 (165)
T d1z06a1          68 MVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRILVGNKCDLRSAIQVPTDLAQKFADT  138 (165)
T ss_dssp             THHHHHTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHCCCSCCCEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             cceeeecCCCceEEEEEeehhhhhhhhhhhhHHHHhhccCCCCeEEEEeccccchhccchhHHHHHHHHHH
Confidence            35679999999999999999999999999999987765 36899999999999999999999999999874

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=7e-21  Score=104.73  Aligned_cols=70  Identities=27%  Similarity=0.402  Sum_probs=63.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||++++++++|||+++++||++++.|+..+.+.. ..++|++++|||+|+...+.++.+++.++|++
T Consensus        68 ~~~~~~~~~~~~llv~d~~d~~Sf~~~~~~~~~i~~~~~~~~~p~ilvgnK~Dl~~~~~v~~e~~~~~~~~  138 (169)
T d1x1ra1          68 MREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTRDQGKEMATK  138 (169)
T ss_dssp             SHHHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTSSCCCEEEEEECTTCSTTCCSCHHHHHHHHHH
T ss_pred             chhhhhhhccEEEEecccccchhhhccchhhHHHHhhccccCccEEEEecccchhhhceeehhhHHHHHHH
Confidence            56789999999999999999999999999999987664 36899999999999999999999999999874

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.1e-20  Score=102.28  Aligned_cols=71  Identities=32%  Similarity=0.326  Sum_probs=64.4

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++..|++++|++++|||+++++||+.+..|+.++.+.. ..++|++|||||+|+..+|.|+.+++.++|++
T Consensus        67 ~~~~~~~~~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~r~v~~~~~~~~a~~  138 (167)
T d1xtqa1          67 IFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES  138 (167)
T ss_dssp             CCCGGGTSSCCEEEEEEETTCHHHHHHHHHHHHHHHHHHCSSCCCEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             cccchhhhhhhhhhhhcccchhhhhhhhhhhhhhhhhcccccccceeeeccccccccccchhHHHHHHHHHH
Confidence            357889999999999999999999999999999987765 46899999999999999999999999999874

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=2.2e-20  Score=102.96  Aligned_cols=69  Identities=28%  Similarity=0.304  Sum_probs=62.1

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++.|++++|++++|||+++++||+.+..|...+.... .+++|+++||||+|+.+.|.++.++++++|+.
T Consensus        71 ~~~~~~~~~~~ilvfd~t~~~s~~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~~~v~~~~~~~~a~~  140 (172)
T d2g3ya1          71 HDHCMQVGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVSVSEGRACAVV  140 (172)
T ss_dssp             HHCCCCCCSEEEEEEETTCHHHHHHHHHHHHHHHTSGGGTTSCEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             ccccccccceeeeeecccccchhhhhhhhhhhhhhccccCCceEEEEeccccccccccccHHHHHHHHHH
Confidence            4678999999999999999999999999999887654 36899999999999999999999999998864

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.9e-20  Score=102.57  Aligned_cols=70  Identities=36%  Similarity=0.650  Sum_probs=63.4

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||++++++++|||+++++||+.+..|+..+........|++|+|||+|+..+|.|+.+|++++|++
T Consensus        68 ~~~~~~~~~~~~i~v~d~~~~~Sf~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~~~v~~~e~~~~a~~  137 (167)
T d1z08a1          68 LGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEKERHVSIQEAESYAES  137 (167)
T ss_dssp             --CCSSTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHHGGGSEEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             cchhhccCCceeEEEEeCCchhHHHhhhhhhhhcccccccccceeeeccccccccccccchHHHHHHHHH
Confidence            5788999999999999999999999999999988777667889999999999999999999999999874

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=6.5e-20  Score=100.17  Aligned_cols=69  Identities=33%  Similarity=0.455  Sum_probs=63.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||+++++||+++..|++++.+.. +++|+++||||+|+.++|.++.++++++|++
T Consensus        67 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~iilVgnK~Dl~~~~~v~~~~~~~~~~~  135 (164)
T d1z2aa1          67 ITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAEV-GDIPTALVQNKIDLLDDSCIKNEEAEGLAKR  135 (164)
T ss_dssp             CCHHHHTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHH-CSCCEEEEEECGGGGGGCSSCHHHHHHHHHH
T ss_pred             hhhhhhccCceEEEEEeccchhhhhhcccccccccccC-CCceEEEeeccCCcccceeeeehhhHHHHHH
Confidence            56789999999999999999999999999999998766 6799999999999999999999999999874

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=2.3e-19  Score=98.22  Aligned_cols=70  Identities=36%  Similarity=0.687  Sum_probs=65.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||+++++||+.+..|+..+.....+..|+++||||+|+.++|.++.++++++|++
T Consensus        69 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilvgnK~Dl~~~~~v~~~~~~~~~~~  138 (167)
T d1z0ja1          69 LAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQHGPPSIVVAIAGNKCDLTDVREVMERDAKDYADS  138 (167)
T ss_dssp             GTHHHHTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTSEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHHhhccceEEEeeechhhhhhhHHHhhhhhhhccCCcceEEEecccchhccccchhHHHHHHHHHH
Confidence            5678999999999999999999999999999988887778899999999999999999999999999874

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=99.79  E-value=1.3e-19  Score=99.51  Aligned_cols=70  Identities=26%  Similarity=0.436  Sum_probs=63.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||++++.||+.+..|++++.+.. .+++|+++||||+|+.+++.++.+++++++++
T Consensus        68 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piiivgnK~Dl~~~~~v~~~~~~~~~~~  138 (168)
T d1u8za_          68 IRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRADQ  138 (168)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHCCTTSCEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             hhhhcccccceeEEEeeccchhhhhhHHHHHHHHHHhhCCCCCcEEEEeccccccccccccHHHHHHHHHH
Confidence            45789999999999999999999999999999987764 46899999999999999999999999999864

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=8e-20  Score=100.19  Aligned_cols=70  Identities=23%  Similarity=0.315  Sum_probs=62.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC--CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG--SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|+++++++++|||+++++||+.+..|+..+.+...  .++|++|||||+|+.++|.++.++++++|++
T Consensus        66 ~~~~~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~piilVgnK~Dl~~~~~v~~~e~~~~~~~  137 (171)
T d2erxa1          66 MQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIKGDVESIPIMLVGNKCDESPSREVQSSEAEALART  137 (171)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHTTHHHHHHHHHHHC---CCCEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             cccccccceeEEEEEeecccccchhcccchhhhhhhhhccCCCCcEEEEeecccccccccccHHHHHHHHHH
Confidence            356799999999999999999999999999988876543  6799999999999999999999999999874

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.2e-19  Score=98.23  Aligned_cols=70  Identities=23%  Similarity=0.350  Sum_probs=63.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||++++++++|||++++.||+.+..|+..+.+.. .+++|++|||||+|+...+.++.+++..++++
T Consensus        67 ~~~~~~~~~~~~ilv~d~~~~~sf~~~~~~~~~~~~~~~~~~~p~ilvgnK~Dl~~~~~~~~~~~~~~~~~  137 (167)
T d1c1ya_          67 MRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQ  137 (167)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSCCCEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             cccccccccceeEEeeeccchhhhHhHHHHHHHHHHhcCCCCCeEEEEEEecCcccccccchhHHHHHHHH
Confidence            56789999999999999999999999999999887654 46899999999999999999999999988864

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.9e-19  Score=98.72  Aligned_cols=69  Identities=30%  Similarity=0.377  Sum_probs=61.0

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      .+.|+++++++++|||+++++||..+..|......... .+.|+++||||+|+.++|.|+.+++.++|++
T Consensus        66 ~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilvgnK~Dl~~~r~V~~~e~~~~a~~  135 (168)
T d2atva1          66 REGHMRWGEGFVLVYDITDRGSFEEVLPLKNILDEIKKPKNVTLILVGNKADLDHSRQVSTEEGEKLATE  135 (168)
T ss_dssp             HHHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTTSCCCEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             chhhhcccccceeecccCCccchhhhhhhcccccccccccCcceeeeccchhhhhhccCcHHHHHHHHHH
Confidence            35689999999999999999999999998777655443 6899999999999999999999999999874

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=9e-19  Score=96.31  Aligned_cols=71  Identities=54%  Similarity=0.833  Sum_probs=65.1

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++++.+++++|++++|||++++.||+.+..|+..+.+....++|++|||||+|+...+.+..+++..+|++
T Consensus        67 ~~~~~~~~~~d~~ilv~d~~~~~sf~~~~~~~~~~~~~~~~~~piilv~nK~D~~~~~~~~~~~~~~~a~~  137 (173)
T d2a5ja1          67 SITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESRRDVKREEGEAFARE  137 (173)
T ss_dssp             CCCHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             hHHHHHhhccCEEEEEEeecChHHHHhHHHHHHHHHHhCCCCCeEEEEecCCchhhhhhhHHHHHHHHHHH
Confidence            36788999999999999999999999999999999887778899999999999999999999999999864

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4.3e-19  Score=97.69  Aligned_cols=70  Identities=23%  Similarity=0.386  Sum_probs=63.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||++++.||+.+..|+..+.+.. ..++|++|||||+|+.+++.++.+++..+|++
T Consensus        70 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~p~ilvgnK~Dl~~~~~~~~~~~~~~~~~  140 (173)
T d2fn4a1          70 MREQYMRAGHGFLLVFAINDRQSFNEVGKLFTQILRVKDRDDFPVVLVGNKADLESQRQVPRSEASAFGAS  140 (173)
T ss_dssp             CHHHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHTSSCCCEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             ccchhhccceeeeeecccccccccchhhhhhHHHHHHhccCCCceEEEEEeechhhccccchhhhhHHHHh
Confidence            56789999999999999999999999999999886654 47899999999999999999999999999874

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=6.6e-19  Score=95.94  Aligned_cols=70  Identities=34%  Similarity=0.676  Sum_probs=64.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||++++.||+.+..|+..+.....+++|+++||||+|+.+.+.+..+++.+++++
T Consensus        65 ~~~~~~~~~~~~ilv~d~~~~~s~~~i~~~~~~~~~~~~~~~~iilvgnK~Dl~~~~~~~~~~~~~~~~~  134 (164)
T d1yzqa1          65 LIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQVSIEEGERKAKE  134 (164)
T ss_dssp             GHHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTTSSEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             chHHHhhccceEEEeeccccccchhhhHhhHHHHHHhcCCCceEEEEecccchhhhhhhhHHHHHHHHHH
Confidence            4578999999999999999999999999999998887778899999999999999999999999999874

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=6.9e-19  Score=96.47  Aligned_cols=70  Identities=37%  Similarity=0.629  Sum_probs=64.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||++++++++|||++++++|+.+..|...+.+...+++|++|||||+|+.+++.++.+++.++++.
T Consensus        71 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilvgnK~Dl~~~~~v~~e~~~~~~~~  140 (170)
T d1r2qa_          71 LAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADD  140 (170)
T ss_dssp             GHHHHHTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             hHHHHhhCcceEEEEeccchhhHHHHHHHHhhhhhhccCCCceEEeecccccccccccccHHHHHHHHHh
Confidence            5678999999999999999999999999999998877778899999999999999999999999998864

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=5.4e-19  Score=96.61  Aligned_cols=70  Identities=19%  Similarity=0.350  Sum_probs=62.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..|+++++++++|||+++++||..+..|+..+..... +++|++|||||+|+.+.+.+..+++..++++
T Consensus        67 ~~~~~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilvgnK~Dl~~~~~~~~~~~~~~~~~  137 (167)
T d1kaoa_          67 MRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRYEKVPVILVGNKVDLESEREVSSSEGRALAEE  137 (167)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTTSCCCEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             chHHHhhcccceeeeeeecchhhhhhhhchhhhhhhhccCCCCCEEEEEEccchhhcccchHHHHHHHHHH
Confidence            356799999999999999999999999999998876543 6799999999999999999999999988864

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.4e-18  Score=96.58  Aligned_cols=69  Identities=22%  Similarity=0.400  Sum_probs=58.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHH-HHHHHHHhcCCCCeEEEEeeCCCCcc------------cccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSR-WLKDLRDHAGSNIVIMLIGNKSDLKH------------LLNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~-~~~~~~~~~~~~~~~vlvgnK~Dl~~------------~~~v~~~e~~~~   68 (72)
                      ++..||+++|++++|||+++++||+++.. |...++.. .+++|+++||||+||.+            +|.|+.+++.++
T Consensus        73 ~~~~~~~~a~~~ilv~d~t~~~Sf~~~~~~~~~~~~~~-~~~~~~ilvgnK~Dl~~~~~~~~~~~~~~~r~v~~~~~~~~  151 (185)
T d2atxa1          73 LRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEY-APNVPFLLIGTQIDLRDDPKTLARLNDMKEKPICVEQGQKL  151 (185)
T ss_dssp             TGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHH-STTCCEEEEEECTTSTTCHHHHHHHTTTTCCCCCHHHHHHH
T ss_pred             hhhhcccccceeeeccccchHHHHHHHHHHHHHHHHhc-CCCCCeeEeeeccccccchhhhhhhhhcccccccHHHHHHH
Confidence            67889999999999999999999999865 44445544 47899999999999864            478999999998


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      |++
T Consensus       152 a~~  154 (185)
T d2atxa1         152 AKE  154 (185)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            864

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=1.8e-18  Score=95.78  Aligned_cols=70  Identities=19%  Similarity=0.287  Sum_probs=58.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc------------cccCCHHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH------------LLNSMCEEYLIKS   69 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~------------~~~v~~~e~~~~a   69 (72)
                      +++.||+++|++++|||+++++||+.+..|+........+++|++|||||+|+..            .+.|+.+++.++|
T Consensus        66 ~~~~~~~~~~~~ilv~d~~~~~Sf~~~~~~~~~~~~~~~~~~~iilVgnK~Dl~~~~~~~~~~~~~~~~~V~~~e~~~~a  145 (179)
T d1m7ba_          66 VRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDLRTDVSTLVELSNHRQTPVSYDQGANMA  145 (179)
T ss_dssp             TGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHCTTCEEEEEEECGGGGGCHHHHHHHHTTTCCCCCHHHHHHHH
T ss_pred             cccchhhhhhhhheeeecccCCCHHHHHHHHHHHHhccCCcceEEEEEecccccccchhhHHHhhhhcCcchHHHHHHHH
Confidence            5678999999999999999999999997655554344447899999999999864            4679999999988


Q ss_pred             hc
Q 047889           70 RS   71 (72)
Q Consensus        70 ~~   71 (72)
                      ++
T Consensus       146 ~~  147 (179)
T d1m7ba_         146 KQ  147 (179)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2.5e-18  Score=94.71  Aligned_cols=70  Identities=21%  Similarity=0.249  Sum_probs=57.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIKS   69 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~a   69 (72)
                      +++.||++++++++|||+++++||+++..|+........+++|++|||||+|+.+.            +.++.+++.++|
T Consensus        66 ~~~~~~~~~~~~ilv~d~~~~~Sf~~~~~~~~~~~~~~~~~~piilvgnK~Dl~~~~~~~~~~~~~~~~~v~~~e~~~~a  145 (177)
T d1kmqa_          66 LRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMA  145 (177)
T ss_dssp             TGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHSTTSCEEEEEECGGGTTCHHHHHHHHHTTCCCCCHHHHHHHH
T ss_pred             cchhhcccchhhhhhcccchhHHHHHHHHHHHHHHHHhCCCCceEEeeecccccchhhHHHHHHHhhcccccHHHHHHHH
Confidence            57889999999999999999999999976554443444478999999999999643            468899999888


Q ss_pred             hc
Q 047889           70 RS   71 (72)
Q Consensus        70 ~~   71 (72)
                      ++
T Consensus       146 ~~  147 (177)
T d1kmqa_         146 NR  147 (177)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=6.7e-19  Score=97.60  Aligned_cols=70  Identities=34%  Similarity=0.551  Sum_probs=62.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||++++.+|+.+..|+..+.... ...+|+++||||.|+...+.++.+++.+++++
T Consensus        80 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~iilv~nK~Dl~~~~~v~~~e~~~~~~~  150 (186)
T d2f7sa1          80 LTTAFFRDAMGFLLMFDLTSQQSFLNVRNWMSQLQANAYCENPDIVLIGNKADLPDQREVNERQARELADK  150 (186)
T ss_dssp             HHHHHHTTCCEEEEEEETTCHHHHHHHHHHHHTCCCCCTTTCCEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHHhcCCEEEEEEeccccccceeeeeccchhhhhccCCCceEEEEeeeccchhhhcchHHHHHHHHHH
Confidence            46779999999999999999999999999998876554 36789999999999999999999999999875

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=4.3e-18  Score=94.85  Aligned_cols=71  Identities=20%  Similarity=0.204  Sum_probs=58.8

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc------------cccCCHHHHHHH
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH------------LLNSMCEEYLIK   68 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~------------~~~v~~~e~~~~   68 (72)
                      ++++.||+++|++++|||+++++||+++..|+........+++|+++||||+||.+            .+.++.+++.++
T Consensus        66 ~~~~~~~~~~~~~ilv~d~~~~~Sf~~~~~~~~~~~~~~~~~~~i~lvgnK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~  145 (191)
T d2ngra_          66 RLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKL  145 (191)
T ss_dssp             TTGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHCTTCCEEEEEECGGGGGCHHHHHHHHTTTCCCCCHHHHHHH
T ss_pred             hhhhhcccccceeecccccchHHHHHHHHHHHHHHHhhcCCCCceEEEeccccccccchhhhhhhhcccccccHHHHHHH
Confidence            36789999999999999999999999997655454444457899999999999864            346999999999


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      |++
T Consensus       146 ~~~  148 (191)
T d2ngra_         146 ARD  148 (191)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            864

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.1e-18  Score=94.60  Aligned_cols=70  Identities=30%  Similarity=0.463  Sum_probs=62.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||+++++||+.+..|+.++.+.. ....|+++||||+|+..++.++.+++.+++++
T Consensus        69 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilvgnK~Dl~~~~~v~~~~~~~~~~~  139 (171)
T d2erya1          69 MREQYMRTGEGFLLVFSVTDRGSFEEIYKFQRQILRVKDRDEFPMILIGNKADLDHQRQVTQEEGQQLARQ  139 (171)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTSSCCSEEEEEECTTCTTSCSSCHHHHHHHHHH
T ss_pred             cccccccccceEEEeeccccccchhhHHHHhHHHHhhcccCCCCEEEEEeccchhhhccchHHHHHHHHHH
Confidence            35678999999999999999999999999998876654 36799999999999999999999999999874

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=3.6e-18  Score=93.26  Aligned_cols=70  Identities=44%  Similarity=0.753  Sum_probs=64.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++..+++++|++++|||+++++||+.+..|+..+.+......|++++|||+|+...+.+..+++++++++
T Consensus        69 ~~~~~~~~~d~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilvgnK~Dl~~~~~~~~~~~~~~~~~  138 (166)
T d1z0fa1          69 VTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIILIGNKADLEAQRDVTYEEAKQFAEE  138 (166)
T ss_dssp             HHHHHHHTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHhcCCcEEEEEeccCchHHHHHHHHHHHHHHhhccccceEEEEcccccchhhcccHHHHHHHHHHH
Confidence            4678999999999999999999999999999998877778899999999999999999999999999874

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=7.7e-18  Score=92.29  Aligned_cols=70  Identities=30%  Similarity=0.526  Sum_probs=64.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.||++++++++|||++++.+|..+..|+..+.+.....+|++|||||+|+.+.+.++.+++.++++.
T Consensus        70 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~ilvgnK~D~~~~~~v~~~~~~~~~~~  139 (171)
T d2ew1a1          70 ITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYASNKVITVLVGNKIDLAERREVSQQRAEEFSEA  139 (171)
T ss_dssp             HHGGGSTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCSSCHHHHHHHHHH
T ss_pred             HHHHHHhccceEEEeeecccchhhhhhhhhhhhhcccccccccEEEEEeecccccccchhhhHHHHHHHh
Confidence            4688999999999999999999999999999998777667899999999999999899999999998863

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.73  E-value=1.2e-17  Score=91.52  Aligned_cols=70  Identities=33%  Similarity=0.585  Sum_probs=63.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|++++|++|+|||++++++|..+..|+..+.....+..|++++|||+|+.+.+.++.++++++|++
T Consensus        70 ~~~~~~~~ad~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~iivv~nK~D~~~~~~v~~~~~~~~~~~  139 (169)
T d3raba_          70 ITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDMEDERVVSSERGRQLADH  139 (169)
T ss_dssp             HHHTTTTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHCCSCCEEEEEEECTTCGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHHhcCCEEEEEEECccchhhhhhhhhhhhhhcccCCcceEEEEEeecccccccccchhhhHHHHHH
Confidence            4678999999999999999999999999998888777667899999999999999999999999998864

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=2e-17  Score=91.01  Aligned_cols=69  Identities=67%  Similarity=1.007  Sum_probs=61.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++..++++++++++|||+++++||..+..|+..+.+...+++|+++||||+|+.+.+....+++..+++
T Consensus        69 ~~~~~~~~~~~~i~v~d~~~~~S~~~~~~~~~~i~~~~~~~~piilvgnK~Dl~~~~~~~~~~~~~~~~  137 (175)
T d2f9la1          69 ITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAE  137 (175)
T ss_dssp             CCHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHHHHHHHHH
T ss_pred             HHHHHhhccCeEEEEEECCCcccchhHHHHHHHHHHhcCCCCcEEEEEeeecccccccchHHHHHHhhc
Confidence            467889999999999999999999999999999988877889999999999999888888777766654

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.71  E-value=4.2e-17  Score=89.34  Aligned_cols=70  Identities=31%  Similarity=0.498  Sum_probs=58.3

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc----CCCCeEEEEeeCCCCcccc-cCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA----GSNIVIMLIGNKSDLKHLL-NSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~----~~~~~~vlvgnK~Dl~~~~-~v~~~e~~~~a~~   71 (72)
                      ++..|++.++++++|||++++.||+.+..|++++....    ...+|++++|||+|+.+.+ .++.+++.+++++
T Consensus        68 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~piilv~nK~Dl~~~~~~v~~~~~~~~~~~  142 (175)
T d1ky3a_          68 LGVAFYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEESKKIVSEKSAQELAKS  142 (175)
T ss_dssp             ---CCSTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSCTTTCCEEEEEECTTSCGGGCCSCHHHHHHHHHH
T ss_pred             HHHHHhhccceEEEEeecccccccchhhhcchhhhhhhhhcccccCcEEEEecccchhhhhcchhHHHHHHHHHH
Confidence            46789999999999999999999999999999987643    2578999999999998754 5788899988864

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=2.4e-17  Score=90.43  Aligned_cols=67  Identities=34%  Similarity=0.571  Sum_probs=56.0

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      ++++.|+++++++++|||+++++||+.+..|+..+.+.. +++|+++||||+|+...+...  ++..+++
T Consensus        67 ~~~~~~~~~~~~~ilv~d~~~~~Sf~~~~~~~~~~~~~~-~~~piilvgnK~Dl~~~~~~~--~~~~~~~  133 (170)
T d1i2ma_          67 GLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKDRKVKA--KSIVFHR  133 (170)
T ss_dssp             SCGGGGTTTCCEEEEEEETTSGGGGTTHHHHHHHHHHHH-CSCCEEEEEECCCCSCSCCTT--TSHHHHS
T ss_pred             eecchhcccccchhhccccccccccchhHHHHHHHhhcc-CCCceeeecchhhhhhhhhhh--HHHHHHH
Confidence            367889999999999999999999999999999987765 689999999999998765443  3444443

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=4.4e-17  Score=88.85  Aligned_cols=69  Identities=22%  Similarity=0.437  Sum_probs=60.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      .++.++++++++++|||++++.||+.+..|+..+.+... .++|+++||||+|+.. +.++.+++.+++++
T Consensus        67 ~~~~~~~~~~~~iiv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~-~~~~~~~~~~~~~~  136 (166)
T d1ctqa_          67 MRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAA-RTVESRQAQDLARS  136 (166)
T ss_dssp             HHHHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTCSSCCEEEEEECTTCSC-CCSCHHHHHHHHHH
T ss_pred             chhhhhhcccccceeecccccccHHHHHHHHHHHHHhcCCCCCeEEEEeccccccc-ccccHHHHHHHHHH
Confidence            356789999999999999999999999999999877654 6799999999999964 67889999998864

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.69  E-value=2.3e-16  Score=87.96  Aligned_cols=71  Identities=37%  Similarity=0.608  Sum_probs=64.4

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      ++++.||++++++++|||++++++|..+..|+..+.+.....+|+++||||+|+.+.+.+..+++..+++.
T Consensus        70 ~~~~~~~~~a~~~i~v~d~t~~~s~~~~~~~~~~~~~~~~~~~~iilv~nK~D~~~~~~~~~~~~~~~~~~  140 (194)
T d2bcgy1          70 TITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYATSTVLKLLVGNKCDLKDKRVVEYDVAKEFADA  140 (194)
T ss_dssp             CCCGGGGTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECTTCTTTCCSCHHHHHHHHHH
T ss_pred             HHHHHHhccCCEEEEEEeCcchhhhhhHhhhhhhhhhcccCCceEEEEEeccccccccchhHHHHhhhhhc
Confidence            36789999999999999999999999999998888777778899999999999999999999998887753

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.6e-16  Score=87.78  Aligned_cols=69  Identities=13%  Similarity=0.175  Sum_probs=58.4

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc---CCCCeEEEEeeCCCCc--ccccCCHHHHHHHHhc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA---GSNIVIMLIGNKSDLK--HLLNSMCEEYLIKSRS   71 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~---~~~~~~vlvgnK~Dl~--~~~~v~~~e~~~~a~~   71 (72)
                      ...||+++|++++|||+++++||+++..|++.+....   ...+|+++||||.|+.  ..+.++.+++.+++++
T Consensus        64 ~~~~~~~ad~~ilVfd~~~~~Sf~~~~~~~~~i~~~~~~~~~~~pi~lV~~k~d~d~~~~~~v~~~~~~~~~~~  137 (175)
T d2bmja1          64 DAKFSGWADAVIFVFSLEDENSFQAVSRLHGQLSSLRGEGRGGLALALVGTQDRISASSPRVVGDARARALCAD  137 (175)
T ss_dssp             CHHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHCC--CCCCEEEEEEECTTCCSSSCCCSCHHHHHHHHHT
T ss_pred             ccccccccceeEEEeecccchhhhhhHHHHHHHHHHhhcccCCccEEEEeeecCcchhhhcchhHHHHHHHHHH
Confidence            4579999999999999999999999999999886543   3678999999988874  4578999999988653

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=2e-16  Score=86.81  Aligned_cols=69  Identities=36%  Similarity=0.721  Sum_probs=60.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.|+++++++|+|||++++.||+.+..|...+......+.|+++||||.|+...+....+++.++++
T Consensus        71 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilv~~k~D~~~~~~~~~~~~~~~~~  139 (173)
T d2fu5c1          71 ITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLAL  139 (173)
T ss_dssp             -CCTTTTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEEC--CCSCCCSCHHHHHHHHH
T ss_pred             HHHHhccCCCEEEEEEECCChhhHHHHHHHHHHhhhhccCCceEEEEEecccchhhcccHHHHHHHHHH
Confidence            578899999999999999999999999999999987777889999999999999988998888888775

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=6.3e-17  Score=88.74  Aligned_cols=70  Identities=44%  Similarity=0.657  Sum_probs=64.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||.+++++|..+..|+..+......++|+++||||+|+..++.+..+++.+++++
T Consensus        70 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piivv~nK~D~~~~~~~~~~~~~~~~~~  139 (174)
T d2bmea1          70 VTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGNKKDLDADREVTFLEASRFAQE  139 (174)
T ss_dssp             HHHTTSTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHHHHHHHHHH
T ss_pred             hHHHHhhhCCEEEEEEecccchhHHHHhhhhcccccccCCceEEEEEEecccccchhchhhhHHHHHHHh
Confidence            4678999999999999999999999999999998887778899999999999999999999999888764

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=6.4e-17  Score=89.45  Aligned_cols=69  Identities=25%  Similarity=0.438  Sum_probs=55.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHH-HHHHHHHhcCCCCeEEEEeeCCCCccc------------ccCCHHHHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSR-WLKDLRDHAGSNIVIMLIGNKSDLKHL------------LNSMCEEYLIK   68 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~-~~~~~~~~~~~~~~~vlvgnK~Dl~~~------------~~v~~~e~~~~   68 (72)
                      +++.||++++++++|||+++++||+++.. |...++.. ..++|++|||||+|+.+.            +.+...++..+
T Consensus        69 ~~~~~~~~~~~~ilv~d~~~~~sf~~i~~~~~~~~~~~-~~~~piilvgnK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (183)
T d1mh1a_          69 LRPLSYPQTDVSLICFSLVSPASFENVRAKWYPEVRHH-CPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAM  147 (183)
T ss_dssp             TGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHH-STTSCEEEEEECHHHHTCHHHHHHHHHTTCCCCCHHHHHHH
T ss_pred             hhhhcccccceeeeeeccchHHHHHHHHHHHHHHHHHh-CCCCcEEEEeecccchhhhhhhhhhhhccccchhhHHHHHH
Confidence            57889999999999999999999999976 55445544 478999999999998654            34566677777


Q ss_pred             Hhc
Q 047889           69 SRS   71 (72)
Q Consensus        69 a~~   71 (72)
                      |++
T Consensus       148 a~~  150 (183)
T d1mh1a_         148 AKE  150 (183)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            653

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.66  E-value=3.4e-16  Score=85.49  Aligned_cols=70  Identities=37%  Similarity=0.605  Sum_probs=62.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc---cccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH---LLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~---~~~v~~~e~~~~a~~   71 (72)
                      +++.|++++|++++|||++++.||+++..|+..+........|++++|||+|+.+   .+.++.+++.+++++
T Consensus        68 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~v~nk~d~~~~~~~~~v~~~~~~~~~~~  140 (170)
T d1ek0a_          68 LAPMYYRNAQAALVVYDVTKPQSFIKARHWVKELHEQASKDIIIALVGNKIDMLQEGGERKVAREEGEKLAEE  140 (170)
T ss_dssp             GHHHHHTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECGGGGGSSCCCCSCHHHHHHHHHH
T ss_pred             HHHHHHhccceEEEEEeCCcccchhhhhhhhhhhccccccccceeeeecccccccccchhhhhHHHHHHHHHH
Confidence            4578999999999999999999999999999888777667899999999999855   478999999999874

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=4.9e-16  Score=84.89  Aligned_cols=70  Identities=36%  Similarity=0.615  Sum_probs=62.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|++++|++++|||+++++||..+..|+..+........|+++||||+|+..++.++.+++.+++++
T Consensus        72 ~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilv~~k~d~~~~~~v~~~~~~~~~~~  141 (170)
T d2g6ba1          72 VTHAYYRDAHALLLLYDVTNKASFDNIQAWLTEIHEYAQHDVALMLLGNKVDSAHERVVKREDGEKLAKE  141 (170)
T ss_dssp             ---CCGGGCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECCSTTSCCCSCHHHHHHHHHH
T ss_pred             HHHHhhcCCceeEEEecCCcccchhhhhhhhhhhhhccCCCceEEEEEeeechhhcccccHHHHHHHHHH
Confidence            5778999999999999999999999999998888777767899999999999999999999999998864

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=5.8e-16  Score=84.88  Aligned_cols=68  Identities=29%  Similarity=0.496  Sum_probs=59.7

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc----CCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA----GSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~----~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      .+.++..+++++++||++++.||+.+..|++++....    ..++|++|||||+|+.+ +.++.+++.+++++
T Consensus        72 ~~~~~~~~~~~i~~~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~piilVgnK~Dl~~-~~v~~~~~~~~~~~  143 (174)
T d1wmsa_          72 RTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDISE-RQVSTEEAQAWCRD  143 (174)
T ss_dssp             HGGGGTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTCSCTTTSCEEEEEECTTCSS-CSSCHHHHHHHHHH
T ss_pred             hhhhhhccceEEEEEeeecccccchhhhHHHHHHHHhccccCCCceEEEeccccchhh-ccCcHHHHHHHHHH
Confidence            4678899999999999999999999999999886643    25699999999999965 78999999999874

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.57  E-value=8.5e-15  Score=80.74  Aligned_cols=68  Identities=29%  Similarity=0.489  Sum_probs=57.7

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC----CCCeEEEEeeCCCCcccccCCHHHHHHHHh
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG----SNIVIMLIGNKSDLKHLLNSMCEEYLIKSR   70 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~----~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~   70 (72)
                      +++.++.++++++++||++++.+|..+..|++++.....    .++|+++||||+|+.+ +.+..+++.+++.
T Consensus        67 ~~~~~~~~~~~~i~~~d~~~~~~~~~~~~~~~~i~~~~~~~~~~~ip~ilv~nK~Dl~~-~~~~~~~~~~~~~  138 (184)
T d1vg8a_          67 LGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLEN-RQVATKRAQAWCY  138 (184)
T ss_dssp             SCCGGGTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSSGGGSCEEEEEECTTSSC-CCSCHHHHHHHHH
T ss_pred             cccccccCccEEEEeecccchhhhhcchhhHHHHHHHhccccccCCCEEEEEEeecccc-cchhHHHHHHHHH
Confidence            467899999999999999999999999999998876532    4689999999999976 6677777777764

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=5.2e-14  Score=77.19  Aligned_cols=69  Identities=42%  Similarity=0.677  Sum_probs=60.6

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcC-CCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAG-SNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||++++.+|+.+..|+.++.+... ...|+++++||.|... +.+..+++++++++
T Consensus        72 ~~~~~~~~~~~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~i~~~~nk~d~~~-~~v~~~~~~~~~~~  141 (177)
T d1x3sa1          72 LTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKEN-REVDRNEGLKFARK  141 (177)
T ss_dssp             SHHHHHTTCCEEEEEEETTCHHHHHTHHHHHHHHTTCCSCSCCEEEEEEECTTSSS-CCSCHHHHHHHHHH
T ss_pred             HHHHHHhcCCEEEEEEECCCccccccchhhhhhhcccccccceeeEEEeecccccc-ccccHHHHHHHHHH
Confidence            567899999999999999999999999999999876553 5789999999999754 78999999998864

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.47  E-value=2.5e-13  Score=73.62  Aligned_cols=69  Identities=39%  Similarity=0.759  Sum_probs=60.9

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHHHHHHhc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEYLIKSRS   71 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~~~~a~~   71 (72)
                      +++.|+++++++++|||.++++||+.+..|............|+++++||.|+.. +.+..+++.+++++
T Consensus        67 ~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~i~~~~k~d~~~-~~~~~~~~~~~~~~  135 (166)
T d1g16a_          67 ITTAYYRGAMGIILVYDITDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMET-RVVTADQGEALAKE  135 (166)
T ss_dssp             CCHHHHTTEEEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCTT-CCSCHHHHHHHHHH
T ss_pred             HHHHHHhcCCEEEEEEECCCccCHHHHHhhhhhhhccccCcceeeeecchhhhhh-hhhhHHHHHHHHHh
Confidence            5688999999999999999999999999998888877778899999999999864 67888888888763

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=99.46  E-value=2.2e-13  Score=74.76  Aligned_cols=55  Identities=18%  Similarity=0.274  Sum_probs=47.2

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~   56 (72)
                      +++.|+++++++++|||++++.+|.....|+....... ..+.|++++|||+|+.+
T Consensus        77 ~~~~~~~~~~~ii~v~d~~d~~s~~~~~~~l~~~~~~~~~~~~piliv~NK~Dl~~  132 (182)
T d1moza_          77 YWRCYYADTAAVIFVVDSTDKDRMSTASKELHLMLQEEELQDAALLVFANKQDQPG  132 (182)
T ss_dssp             TGGGTTTTEEEEEEEEETTCTTTHHHHHHHHHHHTTSSTTSSCEEEEEEECTTSTT
T ss_pred             hHHhhhccceeEEEEeeecccccchhHHHHHHHHHHhhccCCcceEEEEEeecccc
Confidence            57889999999999999999999999988876654433 36799999999999965

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=99.42  E-value=2.5e-13  Score=73.95  Aligned_cols=56  Identities=21%  Similarity=0.310  Sum_probs=47.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCccc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~   57 (72)
                      +++.|+++++++++|||++++.+|..+..|+..+.... ..++|++++|||+|+.+.
T Consensus        76 ~~~~~~~~~~~ii~v~d~~d~~s~~~~~~~~~~~~~~~~~~~~pillv~nK~Dl~~~  132 (176)
T d1fzqa_          76 YWRSYFENTDILIYVIDSADRKRFEETGQELTELLEEEKLSCVPVLIFANKQDLLTA  132 (176)
T ss_dssp             HHHHHHTTCSEEEEEEETTCGGGHHHHHHHHHHHTTCGGGTTCCEEEEEECTTSTTC
T ss_pred             HHHHHhhccceeEEeeccccccchhhhhhhhhhhhhhhccCCCeEEEEEEecccccc
Confidence            35689999999999999999999999988877765443 367999999999999753

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=99.41  E-value=8.7e-13  Score=71.37  Aligned_cols=55  Identities=25%  Similarity=0.401  Sum_probs=47.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~   56 (72)
                      .+..|+.+++++++|||++++++|..+..|+..+.+.. .+++|++|||||.|+.+
T Consensus        63 ~~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~pi~lv~nK~Dl~~  118 (164)
T d1zd9a1          63 MWERYCRGVSAIVYMVDAADQEKIEASKNELHNLLDKPQLQGIPVLVLGNKRDLPG  118 (164)
T ss_dssp             THHHHHTTCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCCEEEEEECTTSTT
T ss_pred             cccccccccchhhcccccccccccchhhhhhhhhhhhhcccCCcEEEEEeccccch
Confidence            45778999999999999999999999988887775543 37899999999999975

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=99.39  E-value=1.6e-12  Score=70.86  Aligned_cols=55  Identities=22%  Similarity=0.448  Sum_probs=46.8

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHh-cCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDH-AGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~-~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+..|+++++++++|||++++++|..+..|+....+. ...+.|++++|||+|+.+
T Consensus        72 ~~~~~~~~~~~ii~v~D~s~~~~~~~~~~~l~~~~~~~~~~~~piiiv~NK~Dl~~  127 (173)
T d1e0sa_          72 LWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPD  127 (173)
T ss_dssp             HHGGGTTTCCEEEEEEETTCGGGHHHHHHHHHHHHTSGGGTTCEEEEEEECTTSTT
T ss_pred             HHHhhhcccceEEEEEecccchhHHHHHHHHHHHhhhcccccceeeeeeecccccc
Confidence            3567999999999999999999999998877765443 346799999999999975

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=99.35  E-value=2.9e-12  Score=69.09  Aligned_cols=59  Identities=20%  Similarity=0.342  Sum_probs=47.1

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHH-HHhcCCCCeEEEEeeCCCCcccccC
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDL-RDHAGSNIVIMLIGNKSDLKHLLNS   60 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~-~~~~~~~~~~vlvgnK~Dl~~~~~v   60 (72)
                      +++.+++++++++++||.+++.+|.....|+... ......++|+++||||+|+.+.+.+
T Consensus        62 ~~~~~~~~~~~~i~v~d~~d~~~~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~~~~  121 (165)
T d1ksha_          62 YWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGALSC  121 (165)
T ss_dssp             TGGGGCTTCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTCCCH
T ss_pred             HHHhhhhhhhcceeeeecccchhHHHHHHhhhhhhhhcccCCCceEEEEeccccccccCH
Confidence            4678999999999999999999999986665544 3333477999999999999764433

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=99.03  E-value=1.4e-10  Score=61.49  Aligned_cols=54  Identities=19%  Similarity=0.324  Sum_probs=46.2

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~   56 (72)
                      +..|++++++++++||++++.++..+..|..++.... ...+|++++|||.|+..
T Consensus        61 ~~~~~~~~~~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~k~d~~~  115 (160)
T d1r8sa_          61 WRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPN  115 (160)
T ss_dssp             HHHHTTTCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTT
T ss_pred             hhhhhccceeEEEEEEecChHHHHHHHHHHHHHHHhhcccCceEEEEeecccccc
Confidence            4678999999999999999999999988877765543 36789999999999875

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.99  E-value=1.8e-09  Score=59.77  Aligned_cols=56  Identities=16%  Similarity=0.213  Sum_probs=41.0

Q ss_pred             ccchhhCCCEEEEEEECCChhhH-HHHHHHHHHH-HHh--cCCCCeEEEEeeCCCCcccc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTF-ENVSRWLKDL-RDH--AGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~-~~~~~~~~~~-~~~--~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      +..|++.++++++|+|.++..++ .....|+..+ ...  ....+|+++++||+|+...+
T Consensus        65 ~~~~~~~~~~~i~v~D~~d~~~~~~~~~~~l~~~l~~~~~~~~~~pilvv~NK~Dl~~a~  124 (207)
T d2fh5b1          65 LDRFKSSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAK  124 (207)
T ss_dssp             HHHHGGGEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHTSTTCCEEEEEEECTTSTTCC
T ss_pred             hhhhhhhccccceEEEcccccccHHHHHHHHHHHHHhHHHhhcCCcEEEEEECcccCCCC
Confidence            45688999999999999998764 5555554443 222  23568999999999997643

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.99  E-value=8.2e-11  Score=64.22  Aligned_cols=56  Identities=13%  Similarity=0.086  Sum_probs=44.1

Q ss_pred             CcccchhhCCCEEEEEEECCChhhHH-----------HHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            1 AITSAYYRGALGALLVYDVTKSTTFE-----------NVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         1 sl~~~y~~~a~~~i~v~d~~~~~s~~-----------~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++++.||++++++++|||+++..+|.           ....|...+........|++++|||+|+..
T Consensus        57 ~~~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~e~~~~~~~i~~~~~~~~~~~~lv~Nk~d~~~  123 (195)
T d1svsa1          57 KKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFE  123 (195)
T ss_dssp             GGGGGGCTTCSEEEEEEEGGGGGCBCSSCTTSBHHHHHHHHHHHHHTCGGGTTSEEEEEEECHHHHH
T ss_pred             cchhhcccCCceeeeEEeecccchHHHHhhhhHHHHHHHHHHHHHhcccccCCCCEEEEeccchhhh
Confidence            36889999999999999999998873           334555555544457899999999999744

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=98.90  E-value=8.4e-09  Score=55.44  Aligned_cols=55  Identities=20%  Similarity=0.250  Sum_probs=45.1

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCccc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~~   57 (72)
                      +..++..++++++++|.++..++.....+........ ....|+++||||+|+...
T Consensus        76 ~~~~~~~~~~~i~v~d~~d~~~~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~  131 (177)
T d1zj6a1          76 WNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKEC  131 (177)
T ss_dssp             GHHHHTTCCEEEEEEETTCTTTHHHHHHHHHHHHTSGGGTTCEEEEEEECTTSTTC
T ss_pred             hhhhhccceeeeeecccccccchhhhhhhhhhhhhcccccceEEEEEEEccccccc
Confidence            4678889999999999999999999877665554433 368999999999999753

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.83  E-value=9.5e-10  Score=60.07  Aligned_cols=57  Identities=12%  Similarity=0.031  Sum_probs=47.5

Q ss_pred             cccchhhCCCEEEEEEECCChh-----------hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccc
Q 047889            2 ITSAYYRGALGALLVYDVTKST-----------TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~-----------s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      ++..||+++++++++||.++..           .++.+..|...+......++|++++|||.|+.+.+
T Consensus        61 ~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~l~~~~~~~~~~~~v~NK~Dl~~~~  128 (200)
T d2bcjq2          61 KWIHCFENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNSSVILFLNKKDLLEEK  128 (200)
T ss_dssp             GGGGGCSSCSEEEEEEEGGGGGCBCSSCTTSBHHHHHHHHHHHHHHCGGGSSSEEEEEEECHHHHHHH
T ss_pred             cccccccccceeeEeeeccchhhhhhhhccccchHHHHHHHHHHHhhhhccCccEEEecchhhhhhhc
Confidence            5789999999999999998864           46667888888877666889999999999986544

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.78  E-value=2.4e-09  Score=60.27  Aligned_cols=57  Identities=12%  Similarity=0.089  Sum_probs=40.8

Q ss_pred             cccchhhCCCEEEEEEECCChh----------hHHHH-HHHHHHHHHhcCCCCeEEEEeeCCCCcccc
Q 047889            2 ITSAYYRGALGALLVYDVTKST----------TFENV-SRWLKDLRDHAGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~----------s~~~~-~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      .+..||++++++++++|+++..          .+... ..|...+.+....++|++|+|||+|+.+++
T Consensus        63 ~w~~~~~~~~~ii~v~d~s~~~~~~~~~~~~~r~~e~~~~~~~il~~~~~~~~~iil~~NK~Dl~~~k  130 (221)
T d1azta2          63 KWIQCFNDVTAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEK  130 (221)
T ss_dssp             GGGGGCTTCSEEEEEEETTGGGCBCTTTSCSBHHHHHHHHHHHHHTCGGGSSCEEEEEEECHHHHHHH
T ss_pred             chhhhcccccceEEEEEccccccccccccchHHHHHHHHHHHHHhcChhhCCCcEEEEechhhhhhhh
Confidence            4688999999999999998653          23333 334444443333679999999999996543

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=98.78  E-value=6.6e-09  Score=56.35  Aligned_cols=50  Identities=22%  Similarity=0.264  Sum_probs=36.9

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .++++||++++|+|.+++.+... ..|.+.++.. ..+.|+++|+||+|+..
T Consensus        80 ~~~~~ad~il~v~D~~~~~~~~~-~~i~~~l~~~-~~~~piilv~NK~Dl~~  129 (178)
T d1wf3a1          80 EALADVNAVVWVVDLRHPPTPED-ELVARALKPL-VGKVPILLVGNKLDAAK  129 (178)
T ss_dssp             HHTSSCSEEEEEEETTSCCCHHH-HHHHHHHGGG-TTTSCEEEEEECGGGCS
T ss_pred             cccccccceeeeechhhhhcccc-cchhhheecc-ccchhhhhhhccccccc
Confidence            35678999999999988654432 4455555544 36789999999999865

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=98.74  E-value=1.9e-09  Score=57.45  Aligned_cols=53  Identities=17%  Similarity=0.209  Sum_probs=43.7

Q ss_pred             cchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            4 SAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         4 ~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ..+++++|++++++|..+..++.....|...+.... ...|+++|+||+||..+
T Consensus        75 ~~~~~~~d~~i~~~d~~~~~~~~~~~~~~~~~~~~~-~~~~iilv~NK~Dl~~~  127 (161)
T d2gj8a1          75 WQEIEQADRVLFMVDGTTTDAVDPAEIWPEFIARLP-AKLPITVVRNKADITGE  127 (161)
T ss_dssp             HHHHHTCSEEEEEEETTTCCCCSHHHHCHHHHHHSC-TTCCEEEEEECHHHHCC
T ss_pred             HHHHHhccccceeeccccccchhhhhhhhhhhhhcc-cccceeeccchhhhhhh
Confidence            457889999999999999998888887766665543 67999999999998553

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.67  E-value=5e-09  Score=57.33  Aligned_cols=55  Identities=16%  Similarity=0.190  Sum_probs=40.9

Q ss_pred             cccchhhCCCEEEEEEECCChhh----------HHHHHHHHHHHHH-hcCCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTT----------FENVSRWLKDLRD-HAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s----------~~~~~~~~~~~~~-~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .++.||+++++++++|+.++..+          ++....|+..+.+ ....++|++|+|||+|+.+
T Consensus        60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~piilv~NK~Dl~~  125 (200)
T d1zcba2          60 RWFECFDSVTSILFLVSSSEFDQVLMEDRQTNRLTESLNIFETIVNNRVFSNVSIILFLNKTDLLE  125 (200)
T ss_dssp             -CTTSCTTCCEEEEEEETTCTTCEETTEEEEEHHHHHHHHHHHHHTCGGGTTSEEEEEEECHHHHH
T ss_pred             cccccccccceeEEEEEcCCcceeeeecccchhhhHHHHHHHHHhhChhhcCceEEEEeccchhhh
Confidence            46889999999999999998644          4445555555433 3347899999999999854

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.67  E-value=2.4e-07  Score=48.43  Aligned_cols=55  Identities=20%  Similarity=0.357  Sum_probs=46.5

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhc-CCCCeEEEEeeCCCCcc
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHA-GSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~vlvgnK~Dl~~   56 (72)
                      +.+.+++.++++++++|.+++.++.....|.....+.. ..+.|+++++||.|+..
T Consensus        60 ~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~~~k~d~~~  115 (166)
T d2qtvb1          60 LWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIAELKDVPFVILGNKIDAPN  115 (166)
T ss_dssp             GGGGGCTTCSEEEEEEETTCGGGHHHHHHHHHHHHTCTTTTTCCEEEEEECTTSSS
T ss_pred             hHhhhhhheeeeeeeccccchhhhhhhhHHHHhhhhhhccCCceEEEEeccccccc
Confidence            45788999999999999999999999987777765544 36789999999999965

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=98.43  E-value=3.9e-07  Score=47.95  Aligned_cols=55  Identities=15%  Similarity=0.248  Sum_probs=43.8

Q ss_pred             ccchhhCCCEEEEEEECCChhhHHHHHHHHHHH-HHhcCCCCeEEEEeeCCCCccc
Q 047889            3 TSAYYRGALGALLVYDVTKSTTFENVSRWLKDL-RDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~-~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ...+++..+++++++|+++..++.....+.... ........|+++++||.|+...
T Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iv~nk~Dl~~~  121 (169)
T d1upta_          66 WRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQA  121 (169)
T ss_dssp             GGGGCTTCSEEEEEEETTCCTTHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC
T ss_pred             chhhhhhhhhhhhhhhhhhcchhhhccchhhhhhhhhccccceEEEEEeecccccc
Confidence            467788999999999999999998886654444 3333467999999999999763

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=98.41  E-value=2.9e-06  Score=45.08  Aligned_cols=62  Identities=19%  Similarity=0.259  Sum_probs=47.0

Q ss_pred             cccchhhCCCEEEEEEECCChhhHHHHHHHHHHHHH-hcCCCCeEEEEeeCCCCcccccCCHHHH
Q 047889            2 ITSAYYRGALGALLVYDVTKSTTFENVSRWLKDLRD-HAGSNIVIMLIGNKSDLKHLLNSMCEEY   65 (72)
Q Consensus         2 l~~~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~-~~~~~~~~vlvgnK~Dl~~~~~v~~~e~   65 (72)
                      .+..+++..+++++++|.+++..+.....+...... ....+.|+++++||.|++.  .+..++.
T Consensus        73 ~~~~~~~~~~~~~~~~d~~d~~~~~~~~~~~~~~~~~~~~~~~~~li~~~K~D~~~--~~~~~~i  135 (186)
T d1f6ba_          73 VWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPE--AISEERL  135 (186)
T ss_dssp             GGGGGGGGCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTSCEEEEEECTTSTT--CCCHHHH
T ss_pred             HHhhhhcccceeeeeeeccCccchHHHHHHHHHhhcccccCCCceEEEEeccCccc--cCCHHHH
Confidence            356788999999999999999999988665444433 3337899999999999875  3444443

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.95  E-value=6.1e-05  Score=40.74  Aligned_cols=49  Identities=22%  Similarity=0.333  Sum_probs=35.0

Q ss_pred             CCCEEEEEEECC-ChhhHHHHHHHHHHH----HHhcCCCCeEEEEeeCCCCccc
Q 047889            9 GALGALLVYDVT-KSTTFENVSRWLKDL----RDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         9 ~a~~~i~v~d~~-~~~s~~~~~~~~~~~----~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      .++.+++++|.. +..+++.+..|+.++    ......++|+++++||+|+...
T Consensus        73 ~~~~~i~~vd~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~piiiv~NK~D~~~~  126 (209)
T d1nrjb_          73 FVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTA  126 (209)
T ss_dssp             GEEEEEEEEETTSCTTCCHHHHHHHHHHHHHHHHHSTTCCCEEEEEECTTSTTC
T ss_pred             hccccceEEEEecccccHHHHHHHHHHHHHHHHHHHhccCCeEEEEEeeccccc
Confidence            446777777755 567788777776543    3334478999999999999753

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=97.93  E-value=2.1e-05  Score=41.73  Aligned_cols=47  Identities=26%  Similarity=0.243  Sum_probs=33.4

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++..+|.++++.+.+....... ..+.+.++..   +.|+++|+||+|+..
T Consensus        77 ~~~~ad~i~~~~~~~~~~~~~~-~~~~~~l~~~---~~pviiv~NK~Dl~~  123 (171)
T d1mkya1          77 MIREADLVLFVVDGKRGITKED-ESLADFLRKS---TVDTILVANKAENLR  123 (171)
T ss_dssp             HHTTCSEEEEEEETTTCCCHHH-HHHHHHHHHH---TCCEEEEEESCCSHH
T ss_pred             ccccCcEEEEeecccccccccc-cccccccccc---cccccccchhhhhhh
Confidence            4578999999999766544332 4455555543   478999999999864

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=97.89  E-value=3.1e-05  Score=41.45  Aligned_cols=56  Identities=20%  Similarity=0.132  Sum_probs=36.9

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccccCCHHHH
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLLNSMCEEY   65 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~~v~~~e~   65 (72)
                      +.+.+|++++++|...... .....+...+..   ...|+++|+||+|+.........+.
T Consensus        88 ~~~~~dvii~v~d~~~~~~-~~~~~~~~~~~~---~~~~~i~v~nK~D~~~~~~~~~~~~  143 (186)
T d1mkya2          88 SIEKADVVVIVLDATQGIT-RQDQRMAGLMER---RGRASVVVFNKWDLVVHREKRYDEF  143 (186)
T ss_dssp             HHHHCSEEEEEEETTTCCC-HHHHHHHHHHHH---TTCEEEEEEECGGGSTTGGGCHHHH
T ss_pred             HHhcCCEEEEeecccccch-hhHHHHHHHHHH---cCCceeeeccchhhhcchhhhhhhH
Confidence            4578999999999875433 222334444443   3589999999999865554444443

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=97.64  E-value=6e-05  Score=40.08  Aligned_cols=48  Identities=21%  Similarity=0.128  Sum_probs=31.6

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHH----------HHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVS----------RWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~----------~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .++.+|+++++.|...+.......          ...+.+.+   .+.|+++|+||+|+.+
T Consensus        78 ~~~~~d~~~~vvD~~~~~~~~~~~~~~~~~~~d~~~~~~l~~---~~~p~iiv~NK~D~~~  135 (184)
T d2cxxa1          78 NAKNIDVAVLVVDGKAAPEIIKRWEKRGEIPIDVEFYQFLRE---LDIPTIVAVNKLDKIK  135 (184)
T ss_dssp             HGGGCCEEEEEEETTHHHHHHHHHHHTTCCCHHHHHHHHHHH---TTCCEEEEEECGGGCS
T ss_pred             cccccchheeeeeccccchhhhhhhhccccHHHHHHHHHHHH---cCCCEEEEEeeeehhh
Confidence            456789999999987654332221          12222222   4689999999999754

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=97.63  E-value=6.7e-05  Score=40.00  Aligned_cols=51  Identities=18%  Similarity=0.073  Sum_probs=33.6

Q ss_pred             hhhCCCEEEEEEECCCh--hhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            6 YYRGALGALLVYDVTKS--TTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~--~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ++..++.+++++|....  .++.....|+....... .+.|+++|+||+|+..+
T Consensus        76 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~-~~~p~iiv~NK~D~~~~  128 (180)
T d1udxa2          76 HIARTRVLLYVLDAADEPLKTLETLRKEVGAYDPAL-LRRPSLVALNKVDLLEE  128 (180)
T ss_dssp             HHTSSSEEEEEEETTSCHHHHHHHHHHHHHHHCHHH-HHSCEEEEEECCTTSCH
T ss_pred             HHHhhhhhhhhcccccccccchhhhhhhhhcccccc-chhhhhhhhhhhhhhhH
Confidence            46788999999997653  34444444443332221 35799999999999653

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=97.54  E-value=8.3e-05  Score=40.10  Aligned_cols=48  Identities=13%  Similarity=0.141  Sum_probs=31.7

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      .+..+++++++.|...+.. ..-..+++.++.   .+.|+++|+||+|+..+
T Consensus       102 ~~~~~~~vi~viD~~~~~~-~~~~~~~~~l~~---~~~piivv~NK~D~~~~  149 (195)
T d1svia_         102 TREELKAVVQIVDLRHAPS-NDDVQMYEFLKY---YGIPVIVIATKADKIPK  149 (195)
T ss_dssp             HCTTEEEEEEEEETTSCCC-HHHHHHHHHHHH---TTCCEEEEEECGGGSCG
T ss_pred             cccchhhhhhhhhcccccc-cccccccccccc---ccCcceechhhccccCH
Confidence            3456789999999875532 112334444544   35899999999998543

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=97.31  E-value=0.00027  Score=37.76  Aligned_cols=48  Identities=23%  Similarity=0.082  Sum_probs=32.5

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .....+|++++++|..+.........| ..+..   .++|+++|.||+|+..
T Consensus        78 ~~l~~~d~~ilv~d~~~g~~~~~~~~~-~~~~~---~~~p~iiv~NKiD~~~  125 (179)
T d1wb1a4          78 SAADIIDLALIVVDAKEGPKTQTGEHM-LILDH---FNIPIIVVITKSDNAG  125 (179)
T ss_dssp             HHTTSCCEEEEEEETTTCSCHHHHHHH-HHHHH---TTCCBCEEEECTTSSC
T ss_pred             hhhhhccccccccccccccchhhhhhh-hhhhh---cCCcceeccccccccC
Confidence            345678999999999875433322222 22332   4589999999999865

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=97.13  E-value=0.001  Score=36.80  Aligned_cols=48  Identities=23%  Similarity=0.068  Sum_probs=32.1

Q ss_pred             hhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            6 YYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         6 y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ....+|++|+|.|..+.-.-.. ...+..+..   .+.|++++.||+|+...
T Consensus        90 ~~~~~D~~ilVvda~~g~~~~~-~~~~~~~~~---~~~p~iivlNK~D~~~~  137 (227)
T d1g7sa4          90 GGALADLAILIVDINEGFKPQT-QEALNILRM---YRTPFVVAANKIDRIHG  137 (227)
T ss_dssp             SSBSCSEEEEEEETTTCCCHHH-HHHHHHHHH---TTCCEEEEEECGGGSTT
T ss_pred             cccccceEEEEEecccCcccch-hHHHHHhhc---CCCeEEEEEECccCCCc
Confidence            4567999999999876432222 222333333   45899999999998653

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.12  E-value=0.0014  Score=33.82  Aligned_cols=45  Identities=20%  Similarity=0.138  Sum_probs=33.0

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ++++|++++|+|.+++.+.....-+     ... ...++++++||.|+.++
T Consensus        78 ~~~ad~ii~v~d~~~~~~~~~~~~~-----~~~-~~~~~i~~~~k~d~~~~  122 (160)
T d1xzpa2          78 IEKADIVLFVLDASSPLDEEDRKIL-----ERI-KNKRYLVVINKVDVVEK  122 (160)
T ss_dssp             HHHCSEEEEEEETTSCCCHHHHHHH-----HHH-TTSSEEEEEEECSSCCC
T ss_pred             HHhCCEEEEEEeCCCCcchhhhhhh-----hhc-ccccceeeeeeccccch
Confidence            5689999999999998765543322     111 45788999999999763

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.03  E-value=0.00069  Score=38.08  Aligned_cols=47  Identities=17%  Similarity=0.178  Sum_probs=36.5

Q ss_pred             hhCCCEEEEEEECCChh-hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKST-TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+.|.+++|+++.+|. +...+.+|+-.+..   .++|.+||.||+||.+
T Consensus         8 vANiD~vliV~s~~~P~~~~~~ldR~Lv~a~~---~~i~pvIvlnK~DL~~   55 (225)
T d1u0la2           8 VANVDQVILVVTVKMPETSTYIIDKFLVLAEK---NELETVMVINKMDLYD   55 (225)
T ss_dssp             EESCCEEEEEECSSTTCCCHHHHHHHHHHHHH---TTCEEEEEECCGGGCC
T ss_pred             cccCCEEEEEEeCCCCCCCHHHHHHHHHHHHH---cCCCEEEEEeCcccCC
Confidence            45789999999998864 66777777655543   4689999999999965

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=97.01  E-value=0.0011  Score=37.31  Aligned_cols=46  Identities=20%  Similarity=0.242  Sum_probs=35.9

Q ss_pred             hCCCEEEEEEECCChh-hHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKST-TFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .+.|.+++|++..+|. ++..+.+++-.+..   .+++.+||.||+||.+
T Consensus         9 ANiD~~~iV~s~~~P~~~~~~idR~Lv~a~~---~~i~pvIvlnK~DL~~   55 (231)
T d1t9ha2           9 CNVDQAVLVFSAVQPSFSTALLDRFLVLVEA---NDIQPIICITKMDLIE   55 (231)
T ss_dssp             ECCCEEEEEEESTTTTCCHHHHHHHHHHHHT---TTCEEEEEEECGGGCC
T ss_pred             cccCEEEEEEECCCCCCCHHHHHHHHHHHHH---cCCCEEEEEecccccc
Confidence            5789999999998864 67777777555433   5688999999999965

>d1puja_ c.37.1.8 (A:) Probable GTPase YlqF {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase YlqF
species: Bacillus subtilis [TaxId: 1423]

Probab=96.49  E-value=0.0012  Score=37.51  Aligned_cols=46  Identities=15%  Similarity=0.078  Sum_probs=32.9

Q ss_pred             chhhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            5 AYYRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         5 ~y~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .....+|.++.|.|.-+|-+..+  ..++++   . .+.|+++|.||+||.+
T Consensus        11 ~~i~~~DvIl~V~DaR~P~ss~~--~~l~~~---~-~~Kp~IlVlNK~DLv~   56 (273)
T d1puja_          11 EKLKLIDIVYELVDARIPMSSRN--PMIEDI---L-KNKPRIMLLNKADKAD   56 (273)
T ss_dssp             HHGGGCSEEEEEEETTSTTTTSC--HHHHHH---C-SSSCEEEEEECGGGSC
T ss_pred             HHHHhCCEEEEEEECCCCCCCCC--HHHHHH---H-cCCCeEEEEECccCCc
Confidence            35778999999999988766543  112222   2 2568999999999965

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=96.34  E-value=0.0029  Score=33.42  Aligned_cols=51  Identities=10%  Similarity=0.028  Sum_probs=29.4

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHH--HHHHHHHhc---CCCCeEEEEeeCCCCccc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSR--WLKDLRDHA---GSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~--~~~~~~~~~---~~~~~~vlvgnK~Dl~~~   57 (72)
                      +..++.++.+.+............  +........   ..+.|+++|+||+|+.+.
T Consensus        77 ~~~~~~i~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kp~ivv~NK~Dl~~~  132 (185)
T d1lnza2          77 IERTRVIVHVIDMSGLEGRDPYDDYLTINQELSEYNLRLTERPQIIVANKMDMPEA  132 (185)
T ss_dssp             HHHCCEEEEEEESSCSSCCCHHHHHHHHHHHHHHSCSSTTTSCBCBEEECTTSTTH
T ss_pred             HHHhhhhhheeeecccccchhhhhhhhhhhccchhhhhccCCcchhhccccchHhH
Confidence            345777877777665543332221  111111111   246899999999999753

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=95.55  E-value=0.014  Score=31.69  Aligned_cols=46  Identities=20%  Similarity=0.167  Sum_probs=30.2

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      .+.+|++++|.|..+--.-+..+.| ..+..   .++| ++++-||+|+.+
T Consensus        88 ~~~aD~avlVvda~~Gv~~qt~~~~-~~~~~---~gi~~iiv~iNK~D~~~  134 (204)
T d2c78a3          88 AAQMDGAILVVSAADGPMPQTREHI-LLARQ---VGVPYIVVFMNKVDMVD  134 (204)
T ss_dssp             HTTCSSEEEEEETTTCCCHHHHHHH-HHHHH---TTCCCEEEEEECGGGCC
T ss_pred             HHHCCEEEEEEECCCCCcHHHHHHH-HHHHH---cCCCeEEEEEEecccCC
Confidence            3568999999998765444443444 23333   2455 677789999854

>d2qn6a3 c.37.1.8 (A:2-206) Initiation factor eIF2 gamma subunit, N-terminal (G) domain {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor eIF2 gamma subunit, N-terminal (G) domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=95.54  E-value=0.016  Score=31.20  Aligned_cols=47  Identities=17%  Similarity=0.122  Sum_probs=28.7

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ..+|++++|.|..+.-.-...+.-+..+...  .-.|++++-||+|+.+
T Consensus       108 ~~ad~ailvVda~~gi~~~~t~e~~~~~~~~--~i~~iIV~vNK~Dl~~  154 (205)
T d2qn6a3         108 ALMDGAILVVAANEPFPQPQTREHFVALGII--GVKNLIIVQNKVDVVS  154 (205)
T ss_dssp             SCCSEEEEEEETTSCSSCHHHHHHHHHHHHT--TCCCEEEEEECGGGSC
T ss_pred             eccccccccccccccccchhHHHHHHHHHHc--CCceeeeccccCCCcc
Confidence            5689999999987642112222222223322  2347889999999965

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.43  E-value=0.013  Score=34.50  Aligned_cols=57  Identities=21%  Similarity=0.148  Sum_probs=37.9

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc-cccCCHHHHHH
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH-LLNSMCEEYLI   67 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~-~~~v~~~e~~~   67 (72)
                      .+-+|++++|.|..+--.......|.. +.+   .++|++++-||+|... +-..+.+++.+
T Consensus       117 l~~~D~allVVda~eGv~~qT~~~~~~-a~~---~~~p~i~viNKiDr~~~el~~~~~~~~~  174 (341)
T d1n0ua2         117 LRVTDGALVVVDTIEGVCVQTETVLRQ-ALG---ERIKPVVVINKVDRALLELQVSKEDLYQ  174 (341)
T ss_dssp             HHTCSEEEEEEETTTBSCHHHHHHHHH-HHH---TTCEEEEEEECHHHHHHTSCCCHHHHHH
T ss_pred             HhhcCceEEEEecccCcchhHHHHHHH-HHH---cCCCeEEEEECcccccccHHhhHHHHHH
Confidence            456899999999988655555555533 222   4589999999999632 23445555543

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=95.24  E-value=0.011  Score=33.67  Aligned_cols=45  Identities=16%  Similarity=0.146  Sum_probs=31.8

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLK   55 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~   55 (72)
                      .+-+|++++|.|..+--.-...+.|. .+.+   ..+|.+++-||+|..
T Consensus        88 l~~~D~avlvvda~~Gv~~~t~~~~~-~~~~---~~~p~~i~iNk~D~~  132 (267)
T d2dy1a2          88 LEAADAALVAVSAEAGVQVGTERAWT-VAER---LGLPRMVVVTKLDKG  132 (267)
T ss_dssp             HHHCSEEEEEEETTTCSCHHHHHHHH-HHHH---TTCCEEEEEECGGGC
T ss_pred             hcccCceEEEeeccCCccchhHHHHH-hhhh---ccccccccccccccc
Confidence            35689999999988655444445553 3333   358999999999964

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=95.20  E-value=0.065  Score=30.58  Aligned_cols=46  Identities=20%  Similarity=0.338  Sum_probs=32.9

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ++-+|++|+|.|-.+--.-...+.| +..++   .++|.+++-||.|...
T Consensus        92 l~~~D~avlVvda~~Gv~~~T~~~w-~~a~~---~~lP~i~fINKmDr~~  137 (276)
T d2bv3a2          92 MRVLDGAIVVFDSSQGVEPQSETVW-RQAEK---YKVPRIAFANKMDKTG  137 (276)
T ss_dssp             HHHCCEEEEEEETTTSSCHHHHHHH-HHHHT---TTCCEEEEEECTTSTT
T ss_pred             HHhhhheEEeccccCCcchhHHHHH-HHHHH---cCCCEEEEEecccccc
Confidence            3568999999998875444444455 23333   4699999999999864

>d1d2ea3 c.37.1.8 (A:55-250) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Cow (Bos taurus), mitochondrial [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Cow (Bos taurus), mitochondrial [TaxId: 9913]

Probab=94.99  E-value=0.039  Score=29.77  Aligned_cols=46  Identities=17%  Similarity=0.136  Sum_probs=29.5

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +.+|++++|.|..+-- +.+.+..+..+...  ...|++++-||+|+..
T Consensus        88 ~~aD~allVVda~~G~-~~QT~~~~~~a~~~--~~~~iIv~iNK~D~~~  133 (196)
T d1d2ea3          88 APLDGCILVVAANDGP-MPQTREHLLLARQI--GVEHVVVYVNKADAVQ  133 (196)
T ss_dssp             SCCSEEEEEEETTTCS-CHHHHHHHHHHHHT--TCCCEEEEEECGGGCS
T ss_pred             hhcCeEEEEEEcCCCC-chhHHHHHHHHHHh--cCCcEEEEEecccccc
Confidence            5689999999988632 22333333333333  2357888999999854

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.58  E-value=0.037  Score=28.58  Aligned_cols=47  Identities=21%  Similarity=0.145  Sum_probs=27.7

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcccc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHLL   58 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~~   58 (72)
                      ...++.++++.|..+..  .....+...+.+   ...|.+++.||.|+...+
T Consensus        83 ~~~~~~~l~~~d~~~~~--~~~~~~~~~l~~---~~~~~i~v~~k~d~~~~~  129 (179)
T d1egaa1          83 IGDVELVIFVVEGTRWT--PDDEMVLNKLRE---GKAPVILAVNKVDNVQEK  129 (179)
T ss_dssp             CCCEEEEEEEEETTCCC--HHHHHHHHHHHS---SSSCEEEEEESTTTCCCH
T ss_pred             hhhcceeEEEEecCccc--hhHHHHHHHhhh---ccCceeeeeeeeeccchh
Confidence            34567777777766533  222233333332   457789999999986543

>d1kk1a3 c.37.1.8 (A:6-200) Initiation factor eIF2 gamma subunit, N-terminal (G) domain {Archaeon Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor eIF2 gamma subunit, N-terminal (G) domain
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

Probab=94.26  E-value=0.059  Score=28.57  Aligned_cols=49  Identities=20%  Similarity=0.135  Sum_probs=30.0

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ...+|+++++.|..+...-.....-+..+...  ...+++++-||+|+.++
T Consensus        99 ~~~~d~~ilvvda~~g~~~~~t~e~~~~~~~~--~~~~iiv~inK~D~~d~  147 (195)
T d1kk1a3          99 ASLMDGAILVIAANEPCPRPQTREHLMALQII--GQKNIIIAQNKIELVDK  147 (195)
T ss_dssp             GGGCSEEEEEEETTSCSSCHHHHHHHHHHHHH--TCCCEEEEEECGGGSCH
T ss_pred             cccccccccccchhhhhhhhhhHHHHHHHHHh--cCccceeeeecccchhh
Confidence            34689999999988753222332222233332  22457888999998653

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=93.13  E-value=0.16  Score=28.19  Aligned_cols=57  Identities=11%  Similarity=-0.087  Sum_probs=32.3

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCC--CCeEEEEeeCCCCcccccCCHHH
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGS--NIVIMLIGNKSDLKHLLNSMCEE   64 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~--~~~~vlvgnK~Dl~~~~~v~~~e   64 (72)
                      .+.+++++|.+++...--..-...+..+....+.  ..++++|.||.|...+...+.++
T Consensus       111 ~~~~~il~v~~~~~~r~~~~~~~~l~~l~~~fg~~~~~~~ivv~t~~D~~~~~~~~~e~  169 (257)
T d1h65a_         111 KTIDVLLYVDRLDAYRVDNLDKLVAKAITDSFGKGIWNKAIVALTHAQFSPPDGLPYDE  169 (257)
T ss_dssp             CEECEEEEEEESSCCCCCHHHHHHHHHHHHHHCGGGGGGEEEEEECCSCCCGGGCCHHH
T ss_pred             CCCCeEEEEEECCCCCCCHHHHHHHHHHHHHcchhhhhCEEEEEECcccCCcCCCcHHH
Confidence            3568888888876542111112223333333222  24689999999987655555543

>d1zunb3 c.37.1.8 (B:16-237) Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain {Pseudomonas syringae pv. tomato [TaxId: 323]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain
species: Pseudomonas syringae pv. tomato [TaxId: 323]

Probab=92.60  E-value=0.37  Score=26.29  Aligned_cols=46  Identities=17%  Similarity=0.036  Sum_probs=27.8

Q ss_pred             hCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCe-EEEEeeCCCCccc
Q 047889            8 RGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKHL   57 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~~   57 (72)
                      ..+|++++|.|..+--.=+...+| ..+..   ..++ ++++-||.|+.+.
T Consensus       111 ~~aD~ailVvda~~G~~~Qt~e~~-~~~~~---~gv~~iiv~vNK~D~~~~  157 (222)
T d1zunb3         111 STCDLAIILVDARYGVQTQTRRHS-YIASL---LGIKHIVVAINKMDLNGF  157 (222)
T ss_dssp             TTCSEEEEEEETTTCSCHHHHHHH-HHHHH---TTCCEEEEEEECTTTTTS
T ss_pred             ccCceEEEEeccccCcccchHHHH-HHHHH---cCCCEEEEEEEccccccc
Confidence            468999999998763211111222 12222   2344 7888999999763

>d1f60a3 c.37.1.8 (A:2-240) Elongation factor eEF-1alpha, N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor eEF-1alpha, N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.79  E-value=0.076  Score=29.49  Aligned_cols=45  Identities=13%  Similarity=-0.020  Sum_probs=26.8

Q ss_pred             hCCCEEEEEEECCChh---hH----HHHHHHHHHHHHhcCCCCe-EEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKST---TF----ENVSRWLKDLRDHAGSNIV-IMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~---s~----~~~~~~~~~~~~~~~~~~~-~vlvgnK~Dl~~   56 (72)
                      +.+|++++|.|-..-.   .|    +...+| ..+..   -.+| ++++-||+|+.+
T Consensus       106 ~~~D~ailvvda~~G~~e~g~~~~~QT~eh~-~~~~~---~gv~~iiv~iNKmD~~~  158 (239)
T d1f60a3         106 SQADCAILIIAGGVGEFEAGISKDGQTREHA-LLAFT---LGVRQLIVAVNKMDSVK  158 (239)
T ss_dssp             SCCSEEEEEEECSHHHHHHHTCTTSHHHHHH-HHHHH---TTCCEEEEEEECGGGGT
T ss_pred             HHhCEEEEEEECCCCccccccCchHhHHHHH-HHHHH---cCCCeEEEEEECCCCCC
Confidence            4689999999976421   11    112233 22222   2354 788999999865

>d1jnya3 c.37.1.8 (A:4-227) Elongation factor eEF-1alpha, N-terminal (G) domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor eEF-1alpha, N-terminal (G) domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=88.84  E-value=0.36  Score=26.11  Aligned_cols=47  Identities=19%  Similarity=0.144  Sum_probs=27.0

Q ss_pred             hCCCEEEEEEECCChh---hH---HHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKST---TF---ENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~~---s~---~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      +-+|++++|.|..+-.   ++   .+...-+..+...  ...+++++-||+|+..
T Consensus       103 ~~~D~allVVda~~G~~~~t~~~~~qt~e~l~~~~~~--~~~~iIv~iNK~D~~~  155 (224)
T d1jnya3         103 SQADAAILVVSAKKGEYEAGMSVEGQTREHIILAKTM--GLDQLIVAVNKMDLTE  155 (224)
T ss_dssp             SCCSEEEEEEECSTTHHHHHHSTTCHHHHHHHHHHHT--TCTTCEEEEECGGGSS
T ss_pred             HhhceEEEEEecccCcccccccccchhHHHHHHHHHh--CCCceEEEEEcccCCC
Confidence            4589999999998631   11   1121111111111  3346788899999864

>d1r5ba3 c.37.1.8 (A:215-459) Eukaryotic peptide chain release factor ERF2, G domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Eukaryotic peptide chain release factor ERF2, G domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=87.43  E-value=0.56  Score=25.86  Aligned_cols=46  Identities=22%  Similarity=0.191  Sum_probs=26.3

Q ss_pred             hCCCEEEEEEECCCh---hhHH---HHHHHHHHHHHhcCCCC-eEEEEeeCCCCcc
Q 047889            8 RGALGALLVYDVTKS---TTFE---NVSRWLKDLRDHAGSNI-VIMLIGNKSDLKH   56 (72)
Q Consensus         8 ~~a~~~i~v~d~~~~---~s~~---~~~~~~~~~~~~~~~~~-~~vlvgnK~Dl~~   56 (72)
                      ..+|++++|.|..+-   .++.   +...-+..+..   .++ +++++-||+|+..
T Consensus       124 ~~aD~ailVVda~~G~~~~~~~~~~QT~e~l~l~~~---~~i~~iiv~iNKmD~~~  176 (245)
T d1r5ba3         124 SQADIGVLVISARRGEFEAGFERGGQTREHAVLART---QGINHLVVVINKMDEPS  176 (245)
T ss_dssp             TSCSEEEEEEECSTTHHHHTTSTTCCHHHHHHHHHH---TTCSSEEEEEECTTSTT
T ss_pred             hhhcceeeEEEcCCCccCCccccccchHHHHHHHHH---cCCCeEEEEEEcCCCCc
Confidence            458999999998752   1111   12111222222   234 4778889999864

>d2akab1 c.37.1.8 (B:6-304) Dynamin G domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Dynamin G domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=86.32  E-value=0.71  Score=25.64  Aligned_cols=52  Identities=12%  Similarity=0.027  Sum_probs=31.1

Q ss_pred             ccchhhCCCEEEE-EEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCccc
Q 047889            3 TSAYYRGALGALL-VYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKHL   57 (72)
Q Consensus         3 ~~~y~~~a~~~i~-v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~~   57 (72)
                      ...|....+.+++ |.+.+..-+-..+..+.+.+   .+...+++.|-||.|...+
T Consensus       155 ~~~y~~~~~~~il~v~~a~~~~~~~~~~~~~~~~---~~~~~r~i~Vltk~D~~~~  207 (299)
T d2akab1         155 LMQFVTKENCLILAVSPANSDLANSDALKIAKEV---DPQGQRTIGVITKLDLMDE  207 (299)
T ss_dssp             HHHHHTSTTEEEEEEEESSSCGGGCHHHHHHHHH---CTTCSSEEEEEECGGGSCT
T ss_pred             HHHHhcCccceeeeecccccchhhhHHHHHHHHh---CcCCCceeeEEeccccccc
Confidence            3457777776555 55554444434444454443   3344678889999998654

>d1jwyb_ c.37.1.8 (B:) Dynamin G domain {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Dynamin G domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=84.88  E-value=0.42  Score=26.77  Aligned_cols=51  Identities=12%  Similarity=0.092  Sum_probs=30.2

Q ss_pred             ccchhhCCCEEEEEEECCC-hhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889            3 TSAYYRGALGALLVYDVTK-STTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus         3 ~~~y~~~a~~~i~v~d~~~-~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      ...|...++++++++.-.. ...-.....+.+.+   .+....+++|.||+|...
T Consensus       161 ~~~yi~~~~~~il~v~~~~~~~~~~~~~~~~~~~---~~~~~r~i~Vitk~D~~~  212 (306)
T d1jwyb_         161 VMAYIKKQNAIIVAVTPANTDLANSDALQLAKEV---DPEGKRTIGVITKLDLMD  212 (306)
T ss_dssp             HHHHHHSTTEEEEEEEESSSCSTTCSHHHHHHHH---CSSCSSEEEEEECTTSSC
T ss_pred             HHHHHhCCCceeEEeecccccccccHHHHHHHHh---CcCCCeEEEEEecccccc
Confidence            4568889999888763222 11111223333333   334467999999999854

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=84.31  E-value=1.8  Score=22.78  Aligned_cols=45  Identities=16%  Similarity=-0.011  Sum_probs=26.2

Q ss_pred             CCEEEEEEECC---ChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCCcc
Q 047889           10 ALGALLVYDVT---KSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDLKH   56 (72)
Q Consensus        10 a~~~i~v~d~~---~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl~~   56 (72)
                      .++++++.|..   ++..+.........+..  .-..|.+++.||+|+..
T Consensus       124 ~~~~v~vvd~~~~~~~~~~~~~~l~~~~~~~--~~~~~~ivvinK~D~~~  171 (244)
T d1yrba1         124 YPLVVYISDPEILKKPNDYCFVRFFALLIDL--RLGATTIPALNKVDLLS  171 (244)
T ss_dssp             SCEEEEEECGGGCCSHHHHHHHHHHHHHHHH--HHTSCEEEEECCGGGCC
T ss_pred             CceEEEEeccccccCchhHhhHHHHHHHHHH--HhCCCceeeeecccccc
Confidence            45677777754   44444333222212211  13588999999999865

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.34  E-value=1.2  Score=26.26  Aligned_cols=42  Identities=7%  Similarity=-0.013  Sum_probs=25.3

Q ss_pred             hhCCCEEEEEEECCChhhHHHHHHHHHHHHHhcCCCCeEEEEeeCCCC
Q 047889            7 YRGALGALLVYDVTKSTTFENVSRWLKDLRDHAGSNIVIMLIGNKSDL   54 (72)
Q Consensus         7 ~~~a~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~vlvgnK~Dl   54 (72)
                      +..+|.++++.|..-.+  .. ....+.+..   .+.|+++|.||+|.
T Consensus       133 ~~~~d~~l~~~~~~~~~--~d-~~l~~~l~~---~~k~~~~V~nK~D~  174 (400)
T d1tq4a_         133 FYEYDFFIIISATRFKK--ND-IDIAKAISM---MKKEFYFVRTKVDS  174 (400)
T ss_dssp             GGGCSEEEEEESSCCCH--HH-HHHHHHHHH---TTCEEEEEECCHHH
T ss_pred             hhcceEEEEecCCCCCH--HH-HHHHHHHHH---cCCCEEEEEeCccc
Confidence            45677777776532221  11 233344443   35899999999996