Psyllid ID: psy5805

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70-----
Protein Sequence
MASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHcccccccEEEEEEEcccHHHHHHHHHHHHHHHHHcccccccEEEEEccccccccEEEccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHccccccccEEEEEEEEEcHHHHHHHHHHHHHHHHcccHccccEEEEEccHHHHHccEEccc
Coil and Loop (DISEMBL)
MASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLErrrqvths
Flexible Loop (DISEMBL)
MASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLwdskyigekAVILVankadlerrrqvths
Low Complexity Region (SEG)
MASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS
Disordered region (IsUnstruct)
*****SCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANK************
Disordered Region (DISOPRED)
*****SC*TNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV***
Disordered Region (DISEMBL)
MASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADL*********
Disordered Region (DISPRO)
****TSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR*****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS
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	75	2.2.26 [Sep-21-2011]
P55042	308	GTP-binding protein RAD O	yes	N/A	0.693	0.168	0.403	0.0001
O88667	308	GTP-binding protein RAD O	yes	N/A	0.693	0.168	0.384	0.0001
Q9WTY2	341	GTP-binding protein REM 2	yes	N/A	0.693	0.152	0.423	0.0002
Q8IYK8	340	GTP-binding protein REM 2	no	N/A	0.693	0.152	0.423	0.0002
Q7SZ59	255	Ras-like protein family m	no	N/A	0.72	0.211	0.392	0.0003
Q8VEL9	341	GTP-binding protein REM 2	no	N/A	0.693	0.152	0.423	0.0005
P55041	295	GTP-binding protein GEM O	no	N/A	0.693	0.176	0.384	0.0008
P55040	296	GTP-binding protein GEM O	no	N/A	0.693	0.175	0.384	0.0008
Q5R541	296	GTP-binding protein GEM O	no	N/A	0.693	0.175	0.384	0.0009

>sp|P55042|RAD_HUMAN GTP-binding protein RAD OS=Homo sapiens GN=RRAD PE=1 SV=2

 Score = 45.4 bits (106), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/52 (40%), Positives = 35/52 (67%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D +VIVYSV ++ +F+KA ++   L  ++   +  +ILV NK+DL R R+V+
Sbjct: 163 DAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVS 214

May play an important role in cardiac antiarrhythmia via the strong suppression of voltage-gated L-type Ca(2+) currents. Regulates voltage-dependent L-type calcium channel subunit alpha-1C trafficking to the cell membrane (By similarity). Inhibits cardiac hypertrophy through the calmodulin-dependent kinase II (CaMKII) pathway. Inhibits phosphorylation and activation of CAMK2D.
Homo sapiens (taxid: 9606)

>sp|O88667|RAD_MOUSE GTP-binding protein RAD OS=Mus musculus GN=Rrad PE=1 SV=1

 Score = 45.4 bits (106), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/52 (38%), Positives = 35/52 (67%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D +VIVYS+ ++ +F+KA ++   L  ++   +  +ILV NK+DL R R+V+
Sbjct: 163 DAYVIVYSITDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVS 214

May play an important role in cardiac antiarrhythmia via the strong suppression of voltage-gated L-type Ca(2+) currents. Regulates voltage-dependent L-type calcium channel subunit alpha-1C trafficking to the cell membrane. Inhibits cardiac hypertrophy through the calmodulin-dependent kinase II (CaMKII) pathway. Inhibits phosphorylation and activation of CAMK2D.

Mus musculus (taxid: 10090)

>sp|Q9WTY2|REM2_RAT GTP-binding protein REM 2 OS=Rattus norvegicus GN=Rem2 PE=1 SV=2

 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/52 (42%), Positives = 33/52 (63%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D F+IV+SV +R++F K  + L  L   +   +  VILV NK+DL R R+V+
Sbjct: 190 DAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVS 241

Binds GTP saturably and exhibits a low intrinsic rate of GTP hydrolysis.

Rattus norvegicus (taxid: 10116)

>sp|Q8IYK8|REM2_HUMAN GTP-binding protein REM 2 OS=Homo sapiens GN=REM2 PE=1 SV=2

 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/52 (42%), Positives = 33/52 (63%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D F+IV+SV +R++F K  + L  L   +   +  VILV NK+DL R R+V+
Sbjct: 189 DAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVS 240

Binds GTP saturably and exhibits a low intrinsic rate of GTP hydrolysis.

Homo sapiens (taxid: 9606)

>sp|Q7SZ59|RASLC_DANRE Ras-like protein family member 12 OS=Danio rerio GN=RASL12 PE=2 SV=1

 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKT--LWDSKYIGEKAVILVANKADLERRRQVTHS 75
           + F+IVYS+  R +F+  +  L+T  L+      E  VIL+ NK D+ER RQV+ +
Sbjct: 95  NAFIIVYSIDNRSSFEVCQQYLETVSLYSKGLQPEAPVILLGNKVDMERYRQVSKA 150

Danio rerio (taxid: 7955)

>sp|Q8VEL9|REM2_MOUSE GTP-binding protein REM 2 OS=Mus musculus GN=Rem2 PE=1 SV=2

 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/52 (42%), Positives = 32/52 (61%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D F+IV+SV +R+ F K  + L  L   +   +  VILV NK+DL R R+V+
Sbjct: 190 DAFLIVFSVTDRRGFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVS 241

Binds GTP saturably and exhibits a low intrinsic rate of GTP hydrolysis.

Mus musculus (taxid: 10090)

>sp|P55041|GEM_MOUSE GTP-binding protein GEM OS=Mus musculus GN=Gem PE=1 SV=2

 Score = 42.4 bits (98), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 35/52 (67%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D ++IVYS+ +R +F+KA ++   L  ++   +  +ILV NK+DL R R+V+
Sbjct: 150 DAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVS 201

Could be a regulatory protein, possibly participating in receptor-mediated signal transduction at the plasma membrane. Has guanine nucleotide-binding activity but undetectable intrinsic GTPase activity.

Mus musculus (taxid: 10090)

>sp|P55040|GEM_HUMAN GTP-binding protein GEM OS=Homo sapiens GN=GEM PE=1 SV=1

 Score = 42.4 bits (98), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 35/52 (67%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D ++IVYS+ +R +F+KA ++   L  ++   +  +ILV NK+DL R R+V+
Sbjct: 151 DAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVS 202

Could be a regulatory protein, possibly participating in receptor-mediated signal transduction at the plasma membrane. Has guanine nucleotide-binding activity but undetectable intrinsic GTPase activity.

Homo sapiens (taxid: 9606)

>sp|Q5R541|GEM_PONAB GTP-binding protein GEM OS=Pongo abelii GN=GEM PE=2 SV=1

 Score = 42.4 bits (98), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 35/52 (67%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D ++IVYS+ +R +F+KA ++   L  ++   +  +ILV NK+DL R R+V+
Sbjct: 151 DAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVS 202

Could be a regulatory protein, possibly participating in receptor-mediated signal transduction at the plasma membrane. Has guanine nucleotide-binding activity but undetectable intrinsic GTPase activity.

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	75
242022806	274	GTP-binding protein REM, putative [Pedic	0.8	0.218	0.516	3e-11
157120243	587	hypothetical protein AaeL_AAEL001571 [Ae	0.853	0.109	0.5	3e-10
195153877	750	GL17084 [Drosophila persimilis] gi|19411	0.826	0.082	0.516	4e-10
170065034	501	conserved hypothetical protein [Culex qu	0.773	0.115	0.551	4e-10
198458177	733	GA13469 [Drosophila pseudoobscura pseudo	0.826	0.084	0.516	4e-10
328722064	432	PREDICTED: hypothetical protein LOC10056	0.733	0.127	0.509	6e-10
312370757	621	hypothetical protein AND_23085 [Anophele	0.826	0.099	0.483	2e-09
194881125	742	GG21907 [Drosophila erecta] gi|190657886	0.826	0.083	0.483	2e-09
170068504	328	conserved hypothetical protein [Culex qu	0.8	0.182	0.5	3e-09
195487424	743	GE11981 [Drosophila yakuba] gi|194178004	0.826	0.083	0.483	3e-09

>gi|242022806|ref|XP_002431829.1| GTP-binding protein REM, putative [Pediculus humanus corporis] gi|212517161|gb|EEB19091.1| GTP-binding protein REM, putative [Pediculus humanus corporis]

 Score = 72.8 bits (177), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 43/60 (71%)

Query: 14  NFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           N + TY P  ++IVYSV++R +F+ AE+ L++LW +  IG KAVILV NK DL R R +T
Sbjct: 113 NCITTYQPQAYIIVYSVVDRSSFQIAEETLQSLWKTDSIGSKAVILVGNKTDLVRSRTIT 172

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157120243|ref|XP_001653567.1| hypothetical protein AaeL_AAEL001571 [Aedes aegypti] gi|108883080|gb|EAT47305.1| AAEL001571-PA [Aedes aegypti]

 Score = 68.9 bits (167), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 32/64 (50%), Positives = 43/64 (67%)

Query: 12  VVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ 71
           V N + TY P   V+VYS+++R TF+ AE++L  LW  KY  EKAVI+ ANK+DL R R 
Sbjct: 438 VENSLSTYEPHACVVVYSIVDRNTFRVAEEILNYLWSEKYTKEKAVIIAANKSDLARSRV 497

Query: 72  VTHS 75
           +  S
Sbjct: 498 INTS 501

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195153877|ref|XP_002017850.1| GL17084 [Drosophila persimilis] gi|194113646|gb|EDW35689.1| GL17084 [Drosophila persimilis]

 Score = 68.9 bits (167), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 32/62 (51%), Positives = 43/62 (69%)

Query: 12  VVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ 71
           V N + TY P   V+V+SV++R TF+ AE+++  LW  KY  +KAVILV NKADL R R 
Sbjct: 601 VENSLSTYEPHGCVVVFSVVDRGTFRVAEEIINYLWQEKYTKDKAVILVGNKADLARARL 660

Query: 72  VT 73
           +T
Sbjct: 661 IT 662

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170065034|ref|XP_001867775.1| conserved hypothetical protein [Culex quinquefasciatus] gi|167882178|gb|EDS45561.1| conserved hypothetical protein [Culex quinquefasciatus]

 Score = 68.9 bits (167), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 32/58 (55%), Positives = 43/58 (74%)

Query: 15  FVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV 72
           F  TYH D+FV+VYSV++R +FKKAE +L  L D + +  + VILV NK DLER+R+V
Sbjct: 171 FCSTYHIDIFVVVYSVVDRGSFKKAEKILHFLRDGEMLLTRGVILVGNKTDLERQREV 228

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198458177|ref|XP_001360942.2| GA13469 [Drosophila pseudoobscura pseudoobscura] gi|198136248|gb|EAL25517.2| GA13469 [Drosophila pseudoobscura pseudoobscura]

 Score = 68.9 bits (167), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 32/62 (51%), Positives = 43/62 (69%)

Query: 12  VVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ 71
           V N + TY P   V+V+SV++R TF+ AE+++  LW  KY  +KAVILV NKADL R R 
Sbjct: 584 VENSLSTYEPHGCVVVFSVVDRGTFRVAEEIINYLWQEKYTKDKAVILVGNKADLARARL 643

Query: 72  VT 73
           +T
Sbjct: 644 IT 645

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328722064|ref|XP_003247471.1| PREDICTED: hypothetical protein LOC100569464 [Acyrthosiphon pisum]

 Score = 68.2 bits (165), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 28/55 (50%), Positives = 42/55 (76%)

Query: 18  TYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV 72
           TY+P+VF+++YSV++ ++F  AE ML  LW  +YI  + VILV NK+DLER R++
Sbjct: 298 TYNPNVFIVMYSVVDERSFDMAEQMLLFLWKGEYIHTRGVILVGNKSDLERTRKI 352

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312370757|gb|EFR19085.1| hypothetical protein AND_23085 [Anopheles darlingi]

 Score = 66.6 bits (161), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/62 (48%), Positives = 42/62 (67%)

Query: 12  VVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ 71
           V N + TY P   V+VYS+++R +F+ AE++L  LW   Y  EKAVI+ ANK+DL R R 
Sbjct: 463 VENSLSTYEPHACVVVYSIVDRNSFRVAEEILNYLWSEHYTKEKAVIIAANKSDLARARV 522

Query: 72  VT 73
           +T
Sbjct: 523 IT 524

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194881125|ref|XP_001974699.1| GG21907 [Drosophila erecta] gi|190657886|gb|EDV55099.1| GG21907 [Drosophila erecta]

 Score = 66.2 bits (160), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/62 (48%), Positives = 42/62 (67%)

Query: 12  VVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ 71
           V N + TY P   V+V+SV++R +F+ AE+++  LW   Y  +KAVILV NKADL R R 
Sbjct: 593 VENSLSTYEPHGCVVVFSVVDRSSFRVAEEIINYLWQENYTKDKAVILVGNKADLARARL 652

Query: 72  VT 73
           +T
Sbjct: 653 IT 654

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170068504|ref|XP_001868893.1| conserved hypothetical protein [Culex quinquefasciatus] gi|167864507|gb|EDS27890.1| conserved hypothetical protein [Culex quinquefasciatus]

 Score = 65.9 bits (159), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/60 (50%), Positives = 43/60 (71%)

Query: 14  NFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           N + +Y P  + ++YS  +R +F+ AE++L+ LW S+ I +KAVILVANKADL R R VT
Sbjct: 110 NCMSSYDPHGYCVIYSSSDRSSFQIAEEILQVLWTSENIAQKAVILVANKADLARSRMVT 169

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195487424|ref|XP_002091903.1| GE11981 [Drosophila yakuba] gi|194178004|gb|EDW91615.1| GE11981 [Drosophila yakuba]

 Score = 65.9 bits (159), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/62 (48%), Positives = 42/62 (67%)

Query: 12  VVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ 71
           V N + TY P   V+V+SV++R +F+ AE+++  LW   Y  +KAVILV NKADL R R 
Sbjct: 594 VENSLSTYEPHGCVVVFSVVDRSSFRVAEEIINYLWQENYTKDKAVILVGNKADLARARL 653

Query: 72  VT 73
           +T
Sbjct: 654 IT 655

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	75
FB|FBgn0085419	740	Rgk2 "Rad, Gem/Kir family memb	0.826	0.083	0.483	3.4e-10
FB|FBgn0260658	1418	CG42541 [Drosophila melanogast	0.786	0.041	0.508	1.5e-08
RGD|1559874	192	Rit1 "Ras-like without CAAX 1"	0.666	0.260	0.32	2.6e-06
ZFIN|ZDB-GENE-050417-352	202	rras2 "related RAS viral (r-ra	0.666	0.247	0.42	1.1e-05
UNIPROTKB|E9PK85	166	RRAS2 "Ras-related protein R-R	0.666	0.301	0.38	1.1e-05
FB|FBgn0085426	449	Rgk3 "Rad, Gem/Kir family memb	0.693	0.115	0.423	1.5e-05
UNIPROTKB|C9J0T6	130	RAB17 "Ras-related protein Rab	0.653	0.376	0.408	2.4e-05
UNIPROTKB|H7C1P7	141	RAB17 "Ras-related protein Rab	0.653	0.347	0.408	2.4e-05
UNIPROTKB|F1N7V2	214	F1N7V2 "Uncharacterized protei	0.653	0.228	0.428	2.6e-05
UNIPROTKB|I3L820	237	RRAD "Uncharacterized protein"	0.693	0.219	0.403	2.6e-05

FB|FBgn0085419 Rgk2 "Rad, Gem/Kir family member 2" [Drosophila melanogaster (taxid:7227)]

 Score = 156 (60.0 bits), Expect = 3.4e-10, P = 3.4e-10
 Identities = 30/62 (48%), Positives = 42/62 (67%)

Query:    12 VVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ 71
             V N + TY P   V+V+SV++R +F+ AE+++  LW   Y  +KAVILV NKADL R R 
Sbjct:   591 VENSLSTYEPHGCVVVFSVVDRSSFRVAEEIINYLWQENYTKDKAVILVGNKADLARARL 650

Query:    72 VT 73
             +T
Sbjct:   651 IT 652

GO:0003924 "GTPase activity" evidence=ISS

GO:0005525 "GTP binding" evidence=ISS

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

GO:0006184 "GTP catabolic process" evidence=IEA

GO:0016020 "membrane" evidence=IEA

FB|FBgn0260658 CG42541 [Drosophila melanogaster (taxid:7227)]

 Score = 144 (55.7 bits), Expect = 1.5e-08, P = 1.5e-08
 Identities = 30/59 (50%), Positives = 42/59 (71%)

Query:    15 FVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
             F  TY+ D+FV+VYSVI+R TF  AE +L+ L +++ +  +  ILVANK DL+R R VT
Sbjct:  1075 FCATYNIDLFVVVYSVIDRNTFAAAERVLQYLKENEMLLSRGAILVANKTDLQRHRVVT 1133

GO:0005525 "GTP binding" evidence=ISS

GO:0003924 "GTPase activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0006184 "GTP catabolic process" evidence=IEA

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

GO:0006911 "phagocytosis, engulfment" evidence=IMP

RGD|1559874 Rit1 "Ras-like without CAAX 1" [Rattus norvegicus (taxid:10116)]

 Score = 91 (37.1 bits), Expect = 2.6e-06, Sum P(2) = 2.6e-06
 Identities = 16/50 (32%), Positives = 33/50 (66%)

Query:    24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
             F+I YS+ +R++F +  +  + ++  +   +  V+LV NK+DL++ RQV+
Sbjct:    69 FIICYSITDRRSFHEVREFKQLIYRVRRTDDTPVVLVGNKSDLKQLRQVS 118

GO:0003924 "GTPase activity" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=IEA;ISO

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

ZFIN|ZDB-GENE-050417-352 rras2 "related RAS viral (r-ras) oncogene homolog 2" [Danio rerio (taxid:7955)]

 Score = 91 (37.1 bits), Expect = 1.1e-05, Sum P(2) = 1.1e-05
 Identities = 21/50 (42%), Positives = 33/50 (66%)

Query:    24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
             F++V+SV +R +F++     + +   K   E  +ILV NKADLE++RQVT
Sbjct:    87 FLLVFSVTDRGSFEEIYKFQRQILRVKDRDEFPMILVGNKADLEQQRQVT 136

GO:0003924 "GTPase activity" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

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

GO:0006184 "GTP catabolic process" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E9PK85 RRAS2 "Ras-related protein R-Ras2" [Homo sapiens (taxid:9606)]

 Score = 86 (35.3 bits), Expect = 1.1e-05, Sum P(2) = 1.1e-05
 Identities = 19/50 (38%), Positives = 32/50 (64%)

Query:    24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
             F++V+SV +R +F++     + +   K   E  +IL+ NKADL+ +RQVT
Sbjct:    70 FLLVFSVTDRGSFEEIYKFQRQILRVKDRDEFPMILIGNKADLDHQRQVT 119

GO:0003924 "GTPase activity" evidence=IEA

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

GO:0016020 "membrane" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

FB|FBgn0085426 Rgk3 "Rad, Gem/Kir family member 3" [Drosophila melanogaster (taxid:7227)]

 Score = 110 (43.8 bits), Expect = 1.5e-05, P = 1.5e-05
 Identities = 22/52 (42%), Positives = 34/52 (65%)

Query:    22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
             D F++VYS I++++F +A+ +L  L D   +  +  ILVANK DL R R V+
Sbjct:   303 DAFLVVYSCIDKESFTRAKQILSRLQDMDLLRHRPTILVANKIDLARSRAVS 354

GO:0005525 "GTP binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0003924 "GTPase activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

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

GO:0006184 "GTP catabolic process" evidence=IEA

UNIPROTKB|C9J0T6 RAB17 "Ras-related protein Rab-17" [Homo sapiens (taxid:9606)]

 Score = 99 (39.9 bits), Expect = 2.4e-05, P = 2.4e-05
 Identities = 20/49 (40%), Positives = 31/49 (63%)

Query:    25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
             ++VY +  + +F KA+  LK L +  + GE  V+LV NK DL + R+VT
Sbjct:    73 LLVYDITRKDSFLKAQQWLKDLEEELHPGEVLVMLVGNKTDLSQEREVT 121

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

GO:0005525 "GTP binding" evidence=IEA

UNIPROTKB|H7C1P7 RAB17 "Ras-related protein Rab-17" [Homo sapiens (taxid:9606)]

 Score = 99 (39.9 bits), Expect = 2.4e-05, P = 2.4e-05
 Identities = 20/49 (40%), Positives = 31/49 (63%)

Query:    25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
             ++VY +  + +F KA+  LK L +  + GE  V+LV NK DL + R+VT
Sbjct:    55 LLVYDITRKDSFLKAQQWLKDLEEELHPGEVLVMLVGNKTDLSQEREVT 103

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

GO:0005525 "GTP binding" evidence=IEA

UNIPROTKB|F1N7V2 F1N7V2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 102 (41.0 bits), Expect = 2.6e-05, P = 2.6e-05
 Identities = 21/49 (42%), Positives = 31/49 (63%)

Query:    25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
             ++VY +  + +F KA+  LK L +  + GE  V+LV NK DLE  R+VT
Sbjct:    96 LLVYDITRKDSFCKAQQWLKDLEEEFHPGEVVVMLVGNKTDLEEEREVT 144

GO:0005622 "intracellular" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

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

UNIPROTKB|I3L820 RRAD "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 103 (41.3 bits), Expect = 2.6e-05, P = 2.6e-05
 Identities = 21/52 (40%), Positives = 35/52 (67%)

Query:    22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
             D +VIVYSV ++ +F+KA ++   L  ++   +  +ILV NK+DL R R+V+
Sbjct:   111 DAYVIVYSVTDKDSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVS 162

GO:0005525 "GTP binding" evidence=IEA

GO:0016020 "membrane" evidence=IEA

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

GO:0003924 "GTPase activity" 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	75
cd04148	219	cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfam	7e-15
cd00876	160	cd00876, Ras, Rat sarcoma (Ras) family of small gu	2e-09
cd04146	166	cd04146, RERG_RasL11_like, Ras-related and Estroge	5e-09
cd04141	172	cd04141, Rit_Rin_Ric, Ras-like protein in all tiss	3e-08
pfam00071	162	pfam00071, Ras, Ras family	6e-08
smart00010	166	smart00010, small_GTPase, Small GTPase of the Ras	5e-07
cd04137	180	cd04137, RheB, Ras Homolog Enriched in Brain (RheB	5e-07
smart00173	164	smart00173, RAS, Ras subfamily of RAS small GTPase	7e-07
cd00154	159	cd00154, Rab, Ras-related in brain (Rab) family of	1e-06
cd04145	164	cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3	1e-06
cd01860	163	cd01860, Rab5_related, Rab-related GTPase family i	1e-05
cd04123	162	cd04123, Rab21, Rab GTPase family 21 (Rab21)	1e-05
cd04176	163	cd04176, Rap2, Rap2 family GTPase consists of Rap2	2e-05
cd04136	164	cd04136, Rap_like, Rap-like family consists of Rap	4e-05
cd04175	164	cd04175, Rap1, Rap1 family GTPase consists of Rap1	8e-05
cd00157	171	cd00157, Rho, Ras homology family (Rho) of small g	8e-05
cd00882	161	cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like s	1e-04
smart00175	164	smart00175, RAB, Rab subfamily of small GTPases	1e-04
cd01861	161	cd01861, Rab6, Rab GTPase family 6 (Rab6)	2e-04
PTZ00369	189	PTZ00369, PTZ00369, Ras-like protein; Provisional	2e-04
cd04109	213	cd04109, Rab28, Rab GTPase family 28 (Rab28)	3e-04
cd04101	167	cd04101, RabL4, Rab GTPase-like family 4 (Rab-like	8e-04
cd01867	167	cd01867, Rab8_Rab10_Rab13_like, Rab GTPase familie	0.001
cd04127	180	cd04127, Rab27A, Rab GTPase family 27a (Rab27a)	0.002
cd04113	161	cd04113, Rab4, Rab GTPase family 4 (Rab4)	0.002

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

 Score = 65.5 bits (160), Expect = 7e-15
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 10/73 (13%)

Query: 1   MASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILV 60
           M    SC              D +VIVYSV +R +F+KA ++   L  ++   +  +ILV
Sbjct: 63  MWLEDSCMQV----------GDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILV 112

Query: 61  ANKADLERRRQVT 73
            NK+DL R R+V+
Sbjct: 113 GNKSDLVRSREVS 125

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

 Score = 50.2 bits (121), Expect = 2e-09
 Identities = 18/55 (32%), Positives = 34/55 (61%), Gaps = 6/55 (10%)

Query: 22  DVFVIVYSVIERKTFKKAE---DMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D F++VYS+  R++F++ +   + +  + D + +    ++LV NK DLE  RQV+
Sbjct: 72  DGFILVYSITSRESFEEIKNIREQILRVKDKEDV---PIVLVGNKCDLENERQVS 123

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

 Score = 49.2 bits (118), Expect = 5e-09
 Identities = 24/53 (45%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSK-YIGEKAVILVANKADLERRRQVT 73
           D FV+VYS+ +R +F     +L+ + + K   GE  VILV NKADL   RQV+
Sbjct: 74  DGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADLLHSRQVS 126

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|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 = 47.2 bits (112), Expect = 3e-08
 Identities = 19/50 (38%), Positives = 33/50 (66%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           F+I YSV +R +F++A +  + +   +   +  ++LV NK DLE++RQVT
Sbjct: 77  FIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKVDLEQQRQVT 126

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|215692 pfam00071, Ras, Ras family

 Score = 46.0 bits (110), Expect = 6e-08
 Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 3/53 (5%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
             F++VY +  R +F+  +  L+ +   ++  E   I LV NK DLE +R V+
Sbjct: 73  QGFLLVYDITSRDSFENVKKWLEEI--LRHADENVPIVLVGNKCDLEDQRVVS 123

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

 Score = 43.7 bits (104), Expect = 5e-07
 Identities = 16/52 (30%), Positives = 31/52 (59%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           + F++VYS+ +R++F++     + +   K   +  ++LV NK DLE  R V+
Sbjct: 75  EGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCDLENERVVS 126

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

 Score = 43.8 bits (104), Expect = 5e-07
 Identities = 20/54 (37%), Positives = 36/54 (66%), Gaps = 8/54 (14%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDS--KYIGEKAV--ILVANKADLERRRQVT 73
           +++VYSV  RK+F    +++K ++D     +G+++V  +LV NK+DL   RQV+
Sbjct: 76  YILVYSVTSRKSF----EVVKVIYDKILDMLGKESVPIVLVGNKSDLHMERQVS 125

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|214541 smart00173, RAS, Ras subfamily of RAS small GTPases

 Score = 43.3 bits (103), Expect = 7e-07
 Identities = 16/52 (30%), Positives = 32/52 (61%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           + F++VYS+ +R++F++ +   + +   K   +  ++LV NK DLE  R V+
Sbjct: 73  EGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLESERVVS 124

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

 Score = 42.8 bits (102), Expect = 1e-06
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 3/53 (5%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
              ++VY V  R++F+  +  L  L   +Y      I LV NK+DLE  RQV+
Sbjct: 74  HGAILVYDVTNRESFENLDKWLNEL--KEYAPPNIPIILVGNKSDLEDERQVS 124

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

 Score = 42.8 bits (101), Expect = 1e-06
 Identities = 20/50 (40%), Positives = 32/50 (64%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           F++V+SV +R +F++ +     +   K   E  +ILV NKADLE +RQV+
Sbjct: 77  FLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEHQRQVS 126

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

 Score = 39.8 bits (94), Expect = 1e-05
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           ++VY +   ++F+KA+  +K L          + L  NKADLE +RQV+
Sbjct: 78  IVVYDITSEESFEKAKSWVKEL-QEHGPPNIVIALAGNKADLESKRQVS 125

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|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21)

 Score = 39.9 bits (94), Expect = 1e-05
 Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 3/52 (5%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEK-AVILVANKADLERRRQVTHS 75
           ++VY + +  +F+K +  +K L      G   ++++V NK DLER+R V+ S
Sbjct: 77  ILVYDITDADSFQKVKKWIKELKQM--RGNNISLVIVGNKIDLERQRVVSKS 126

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

 Score = 39.4 bits (92), Expect = 2e-05
 Identities = 18/49 (36%), Positives = 30/49 (61%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV 72
           F++VYS++ ++TF+  + M   +   K   +  +ILV NK DLE  R+V
Sbjct: 76  FIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESEREV 124

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

 Score = 38.7 bits (90), Expect = 4e-05
 Identities = 17/52 (32%), Positives = 29/52 (55%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
           F +VYS+  +++F   +D+ + +   K   +  +ILV NK DLE  R V+  
Sbjct: 76  FALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVSKE 127

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

 Score = 37.9 bits (88), Expect = 8e-05
 Identities = 19/50 (38%), Positives = 28/50 (56%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           FV+VYS+  + TF   +D+ + +   K   +  +ILV NK DLE  R V 
Sbjct: 76  FVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVG 125

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

 Score = 37.9 bits (89), Expect = 8e-05
 Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 7/50 (14%)

Query: 20  HPDVFVIVYSVIERKTFKKAEDMLKTLWD---SKYIGEKAVILVANKADL 66
             DVF++ +SV    +F+  +      W      Y     +ILV  K DL
Sbjct: 71  QTDVFLLCFSVDSPSSFENVKTK----WYPEIKHYCPNVPIILVGTKIDL 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|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases)

 Score = 37.4 bits (87), Expect = 1e-04
 Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV 72
           D+ ++V    +R++ + A+ ++             +ILV NK DL   R+V
Sbjct: 77  DLILLVVDSTDRESEEDAKLLIL---RRLRKEGIPIILVGNKIDLLEEREV 124

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|197555 smart00175, RAB, Rab subfamily of small GTPases

 Score = 37.5 bits (88), Expect = 1e-04
 Identities = 21/51 (41%), Positives = 32/51 (62%), Gaps = 3/51 (5%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
            ++VY +  R++F+  E+ LK L   +Y     VI LV NK+DLE +RQV+
Sbjct: 76  ALLVYDITNRESFENLENWLKEL--REYASPNVVIMLVGNKSDLEEQRQVS 124

Rab GTPases are implicated in vesicle trafficking. Length = 164

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

 Score = 36.8 bits (86), Expect = 2e-04
 Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 3/52 (5%)

Query: 23  VFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           V V+VY +  R++F   +  +  + D +  G   +I LV NK DL  +RQV+
Sbjct: 75  VAVVVYDITNRQSFDNTDKWIDDVRDER--GNDVIIVLVGNKTDLSDKRQVS 124

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|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional

 Score = 36.8 bits (85), Expect = 2e-04
 Identities = 17/50 (34%), Positives = 27/50 (54%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           F+ VYS+  R +F++     + +   K      +ILV NK DL+  RQV+
Sbjct: 80  FLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDSERQVS 129

Length = 189

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

 Score = 36.7 bits (85), Expect = 3e-04
 Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 2/57 (3%)

Query: 19  YHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEK--AVILVANKADLERRRQVT 73
           Y      +VY +   ++F+  ED L  +       E    ++LV NK DLE  RQVT
Sbjct: 72  YGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTDLEHNRQVT 128

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

 Score = 35.2 bits (81), Expect = 8e-04
 Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 8   FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE 67
           F+++V N  +   P V  +VY V    +F      +  +    +      +LV NK DL 
Sbjct: 66  FSDMVENVWE--QPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCDLT 123

Query: 68  RRRQVT 73
            RR+V 
Sbjct: 124 DRREVD 129

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

 Score = 34.6 bits (80), Expect = 0.001
 Identities = 13/50 (26%), Positives = 30/50 (60%), Gaps = 3/50 (6%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 73
           ++VY + + K+F+  ++ ++ +   ++  E    +LV NK D+E +R V+
Sbjct: 80  ILVYDITDEKSFENIKNWMRNI--DEHASEDVERMLVGNKCDMEEKRVVS 127

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

 Score = 34.4 bits (79), Expect = 0.002
 Identities = 12/52 (23%), Positives = 27/52 (51%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
           F++++ +   ++F    + +  L    Y     ++L+ NKADL  +R+V+  
Sbjct: 90  FLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVLIGNKADLPDQREVSER 141

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|206696 cd04113, Rab4, Rab GTPase family 4 (Rab4)

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 5/52 (9%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEK--AVILVANKADLERRRQVTH 74
           ++VY +  R++F     +   L D++ +      +ILV NK DLE  R+VT 
Sbjct: 77  LLVYDITSRESF---NALTNWLTDARTLASPDIVIILVGNKKDLEDDREVTF 125

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	75
KOG0084|consensus	205		99.93
KOG0078|consensus	207		99.91
KOG0087|consensus	222		99.91
KOG0094|consensus	221		99.9
KOG0092|consensus	200		99.89
KOG0098|consensus	216		99.89
KOG0093|consensus	193		99.87
KOG0080|consensus	209		99.87
KOG0079|consensus	198		99.87
KOG0088|consensus	218		99.86
KOG0081|consensus	219		99.86
KOG0091|consensus	213		99.85
KOG0086|consensus	214		99.83
KOG0095|consensus	213		99.82
cd04120	202	Rab12 Rab12 subfamily. Rab12 was first identified	99.82
KOG0083|consensus	192		99.82
cd04102	202	RabL3 RabL3 (Rab-like3) subfamily. RabL3s are nove	99.81
cd04121	189	Rab40 Rab40 subfamily. This subfamily contains Rab	99.81
cd04133	176	Rop_like Rop subfamily. The Rop (Rho-related prote	99.8
KOG0394|consensus	210		99.79
KOG0395|consensus	196		99.78
cd04172	182	Rnd3_RhoE_Rho8 Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE	99.78
cd01875	191	RhoG RhoG subfamily. RhoG is a GTPase with high se	99.77
cd04131	178	Rnd Rnd subfamily. The Rnd subfamily contains Rnd1	99.76
cd04174	232	Rnd1_Rho6 Rnd1/Rho6 subfamily. Rnd1/Rho6 is a memb	99.76
PTZ00099	176	rab6; Provisional	99.76
cd04141	172	Rit_Rin_Ric Rit/Rin/Ric subfamily. Rit (Ras-like p	99.76
smart00176	200	RAN Ran (Ras-related nuclear proteins) /TC4 subfam	99.75
cd04127	180	Rab27A Rab27a subfamily. The Rab27a subfamily cons	99.74
cd04136	163	Rap_like Rap-like subfamily. The Rap subfamily con	99.73
cd04122	166	Rab14 Rab14 subfamily. Rab14 GTPases are localized	99.73
PLN00023	334	GTP-binding protein; Provisional	99.73
KOG0097|consensus	215		99.72
cd04176	163	Rap2 Rap2 subgroup. The Rap2 subgroup is part of t	99.72
cd04175	164	Rap1 Rap1 subgroup. The Rap1 subgroup is part of t	99.71
cd01874	175	Cdc42 Cdc42 subfamily. Cdc42 is an essential GTPas	99.71
PF00071	162	Ras: Ras family; InterPro: IPR001806 Small GTPases	99.71
cd04126	220	Rab20 Rab20 subfamily. Rab20 is one of several Rab	99.71
cd04107	201	Rab32_Rab38 Rab38/Rab32 subfamily. Rab32 and Rab38	99.71
cd04117	161	Rab15 Rab15 subfamily. Rab15 colocalizes with the	99.71
cd04144	190	Ras2 Ras2 subfamily. The Ras2 subfamily, found exc	99.7
cd04109	215	Rab28 Rab28 subfamily. First identified in maize,	99.69
PTZ00369	189	Ras-like protein; Provisional	99.69
cd04173	222	Rnd2_Rho7 Rnd2/Rho7 subfamily. Rnd2/Rho7 is a memb	99.68
cd04108	170	Rab36_Rab34 Rab34/Rab36 subfamily. Rab34, found pr	99.68
cd04134	189	Rho3 Rho3 subfamily. Rho3 is a member of the Rho f	99.68
cd04111	211	Rab39 Rab39 subfamily. Found in eukaryotes, Rab39	99.67
cd04115	170	Rab33B_Rab33A Rab33B/Rab33A subfamily. Rab33B is u	99.67
PLN03071	219	GTP-binding nuclear protein Ran; Provisional	99.67
cd01871	174	Rac1_like Rac1-like subfamily. The Rac1-like subfa	99.66
cd01865	165	Rab3 Rab3 subfamily. The Rab3 subfamily contains R	99.66
cd04106	162	Rab23_lke Rab23-like subfamily. Rab23 is a member	99.66
cd04140	165	ARHI_like ARHI subfamily. ARHI (A Ras homolog memb	99.66
cd01867	167	Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Yp	99.66
cd04145	164	M_R_Ras_like M-Ras/R-Ras-like subfamily. This subf	99.65
cd04110	199	Rab35 Rab35 subfamily. Rab35 is one of several Rab	99.65
cd01869	166	Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in ev	99.65
cd01873	195	RhoBTB RhoBTB subfamily. Members of the RhoBTB sub	99.65
cd04162	164	Arl9_Arfrp2_like Arl9/Arfrp2-like subfamily. Arl9	99.65
PLN03110	216	Rab GTPase; Provisional	99.65
cd04143	247	Rhes_like Rhes_like subfamily. This subfamily incl	99.64
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	99.64
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	99.64
KOG0393|consensus	198		99.64
cd01868	165	Rab11_like Rab11-like. Rab11a, Rab11b, and Rab25 a	99.63
cd04116	170	Rab9 Rab9 subfamily. Rab9 is found in late endosom	99.63
cd04128	182	Spg1 Spg1p. Spg1p (septum-promoting GTPase) was fi	99.63
cd01864	165	Rab19 Rab19 subfamily. Rab19 proteins are associat	99.63
cd04112	191	Rab26 Rab26 subfamily. First identified in rat pan	99.62
cd01866	168	Rab2 Rab2 subfamily. Rab2 is localized on cis-Golg	99.62
cd04125	188	RabA_like RabA-like subfamily. RabA was first iden	99.62
smart00174	174	RHO Rho (Ras homology) subfamily of Ras-like small	99.62
cd00877	166	Ran Ran (Ras-related nuclear proteins) /TC4 subfam	99.62
KOG4252|consensus	246		99.62
cd04138	162	H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras,	99.62
smart00177	175	ARF ARF-like small GTPases; ARF, ADP-ribosylation	99.62
cd04177	168	RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the	99.61
PLN00223	181	ADP-ribosylation factor; Provisional	99.61
cd04103	158	Centaurin_gamma Centaurin gamma. The centaurins (a	99.61
cd04161	167	Arl2l1_Arl13_like Arl2l1/Arl13 subfamily. Arl2l1 (	99.61
cd04150	159	Arf1_5_like Arf1-Arf5-like subfamily. This subfami	99.61
cd04132	187	Rho4_like Rho4-like subfamily. Rho4 is a GTPase th	99.61
cd04124	161	RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily	99.6
cd04113	161	Rab4 Rab4 subfamily. Rab4 has been implicated in n	99.6
cd04149	168	Arf6 Arf6 subfamily. Arf6 (ADP ribosylation factor	99.6
cd01892	169	Miro2 Miro2 subfamily. Miro (mitochondrial Rho) pr	99.59
cd04101	164	RabL4 RabL4 (Rab-like4) subfamily. RabL4s are nove	99.59
cd04146	165	RERG_RasL11_like RERG/RasL11-like subfamily. RERG	99.59
cd04130	173	Wrch_1 Wrch-1 subfamily. Wrch-1 (Wnt-1 responsive	99.58
PLN03108	210	Rab family protein; Provisional	99.58
PLN03118	211	Rab family protein; Provisional	99.56
cd04158	169	ARD1 ARD1 subfamily. ARD1 (ADP-ribosylation factor	99.56
PTZ00133	182	ADP-ribosylation factor; Provisional	99.56
cd04123	162	Rab21 Rab21 subfamily. The localization and functi	99.55
cd01861	161	Rab6 Rab6 subfamily. Rab6 is involved in microtubu	99.54
cd04118	193	Rab24 Rab24 subfamily. Rab24 is distinct from othe	99.53
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	99.52
cd01860	163	Rab5_related Rab5-related subfamily. This subfamil	99.52
cd04114	169	Rab30 Rab30 subfamily. Rab30 appears to be associa	99.51
cd04147	198	Ras_dva Ras-dva subfamily. Ras-dva (Ras - dorsal-v	99.51
cd04154	173	Arl2 Arl2 subfamily. Arl2 (Arf-like 2) GTPases are	99.51
cd04148	221	RGK RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Ki	99.51
cd01863	161	Rab18 Rab18 subfamily. Mammalian Rab18 is implicat	99.49
cd04142	198	RRP22 RRP22 subfamily. RRP22 (Ras-related protein	99.48
cd04157	162	Arl6 Arl6 subfamily. Arl6 (Arf-like 6) forms a sub	99.48
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	99.47
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	99.47
cd01893	166	Miro1 Miro1 subfamily. Miro (mitochondrial Rho) pr	99.47
cd04152	183	Arl4_Arl7 Arl4/Arl7 subfamily. Arl4 (Arf-like 4) i	99.47
cd04135	174	Tc10 TC10 subfamily. TC10 is a Rho family protein	99.47
cd01870	175	RhoA_like RhoA-like subfamily. The RhoA subfamily	99.45
cd04153	174	Arl5_Arl8 Arl5/Arl8 subfamily. Arl5 (Arf-like 5) a	99.45
cd04129	187	Rho2 Rho2 subfamily. Rho2 is a fungal GTPase that	99.44
cd04156	160	ARLTS1 ARLTS1 subfamily. ARLTS1 (Arf-like tumor su	99.44
cd04137	180	RheB Rheb (Ras Homolog Enriched in Brain) subfamil	99.44
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	99.43
cd00876	160	Ras Ras family. The Ras family of the Ras superfam	99.42
cd04151	158	Arl1 Arl1 subfamily. Arl1 (Arf-like 1) localizes t	99.42
PTZ00132	215	GTP-binding nuclear protein Ran; Provisional	99.41
smart00178	184	SAR Sar1p-like members of the Ras-family of small	99.4
cd00878	158	Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-lik	99.4
TIGR00157	245	ribosome small subunit-dependent GTPase A. The Aqu	99.38
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	99.38
cd00879	190	Sar1 Sar1 subfamily. Sar1 is an essential componen	99.37
KOG3883|consensus	198		99.35
cd00157	171	Rho Rho (Ras homology) family. Members of the Rho	99.35
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	99.33
cd00154	159	Rab Rab family. Rab GTPases form the largest famil	99.32
COG1100	219	GTPase SAR1 and related small G proteins [General	99.32
KOG0070|consensus	181		99.3
PF00025	175	Arf: ADP-ribosylation factor family The prints ent	99.29
KOG0096|consensus	216		99.29
cd01890	179	LepA LepA subfamily. LepA belongs to the GTPase fa	99.16
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	99.15
KOG4423|consensus	229		99.14
KOG0075|consensus	186		99.14
cd01898	170	Obg Obg subfamily. The Obg nucleotide binding prot	99.13
cd04105	203	SR_beta Signal recognition particle receptor, beta	99.07
cd01891	194	TypA_BipA TypA (tyrosine phosphorylated protein A)	99.0
KOG1673|consensus	205		99.0
KOG0073|consensus	185		98.99
KOG0071|consensus	180		98.97
PRK12299	335	obgE GTPase CgtA; Reviewed	98.96
KOG0076|consensus	197		98.88
cd00882	157	Ras_like_GTPase Ras-like GTPase superfamily. The R	98.86
KOG1707|consensus	625		98.86
TIGR03156	351	GTP_HflX GTP-binding protein HflX. This protein fa	98.81
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	98.8
cd01897	168	NOG NOG1 is a nucleolar GTP-binding protein presen	98.78
cd01881	176	Obg_like The Obg-like subfamily consists of five w	98.77
cd04171	164	SelB SelB subfamily. SelB is an elongation factor	98.73
cd01885	222	EF2 EF2 (for archaea and eukarya). Translocation r	98.72
TIGR02729	329	Obg_CgtA Obg family GTPase CgtA. This model descri	98.71
TIGR02528	142	EutP ethanolamine utilization protein, EutP. This	98.69
smart00010	124	small_GTPase Small GTPase of the Ras superfamily;	98.68
TIGR01393	595	lepA GTP-binding protein LepA. LepA (GUF1 in Sacca	98.67
TIGR00491	590	aIF-2 translation initiation factor aIF-2/yIF-2. T	98.64
COG2229	187	Predicted GTPase [General function prediction only	98.64
TIGR00231	161	small_GTP small GTP-binding protein domain. This m	98.63
cd01887	168	IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryo	98.62
PRK11058	426	GTPase HflX; Provisional	98.6
PRK03003	472	GTP-binding protein Der; Reviewed	98.55
cd04167	213	Snu114p Snu114p subfamily. Snu114p is one of sever	98.52
KOG0074|consensus	185		98.48
TIGR00450	442	mnmE_trmE_thdF tRNA modification GTPase TrmE. TrmE	98.48
PRK03003	472	GTP-binding protein Der; Reviewed	98.45
PRK04004	586	translation initiation factor IF-2; Validated	98.44
cd00066	317	G-alpha G protein alpha subunit. The alpha subunit	98.44
PRK12297	424	obgE GTPase CgtA; Reviewed	98.43
smart00275	342	G_alpha G protein alpha subunit. Subunit of G prot	98.43
PRK05433	600	GTP-binding protein LepA; Provisional	98.42
CHL00189	742	infB translation initiation factor 2; Provisional	98.41
cd01854	287	YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtil	98.41
TIGR00487	587	IF-2 translation initiation factor IF-2. This mode	98.41
cd01879	158	FeoB Ferrous iron transport protein B (FeoB) subfa	98.4
PRK05306	787	infB translation initiation factor IF-2; Validated	98.39
cd04168	237	TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), T	98.38
PRK05291	449	trmE tRNA modification GTPase TrmE; Reviewed	98.37
PRK04213	201	GTP-binding protein; Provisional	98.34
cd00881	189	GTP_translation_factor GTP translation factor fami	98.32
PRK12289	352	GTPase RsgA; Reviewed	98.31
TIGR00483	426	EF-1_alpha translation elongation factor EF-1 alph	98.29
TIGR01394	594	TypA_BipA GTP-binding protein TypA/BipA. This bact	98.28
cd04169	267	RF3 RF3 subfamily. Peptide chain release factor 3	98.27
TIGR03597	360	GTPase_YqeH ribosome biogenesis GTPase YqeH. This	98.27
cd01855	190	YqeH YqeH. YqeH is an essential GTP-binding protei	98.27
PRK12288	347	GTPase RsgA; Reviewed	98.24
PRK14845	1049	translation initiation factor IF-2; Provisional	98.21
KOG0077|consensus	193		98.21
PRK15467	158	ethanolamine utilization protein EutP; Provisional	98.21
PRK00098	298	GTPase RsgA; Reviewed	98.21
TIGR00475	581	selB selenocysteine-specific elongation factor Sel	98.19
PRK12296	500	obgE GTPase CgtA; Reviewed	98.18
cd04164	157	trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein	98.15
PRK13351	687	elongation factor G; Reviewed	98.12
PRK15494	339	era GTPase Era; Provisional	98.09
TIGR03594	429	GTPase_EngA ribosome-associated GTPase EngA. EngA	98.04
PRK09518	712	bifunctional cytidylate kinase/GTPase Der; Reviewe	98.04
cd01894	157	EngA1 EngA1 subfamily. This CD represents the firs	98.03
cd01857	141	HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to t	98.03
PRK10218	607	GTP-binding protein; Provisional	97.99
cd01888	203	eIF2_gamma eIF2-gamma (gamma subunit of initiation	97.99
PF09439	181	SRPRB: Signal recognition particle receptor beta s	97.99
PRK00741	526	prfC peptide chain release factor 3; Provisional	97.98
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	97.97
PRK00093	435	GTP-binding protein Der; Reviewed	97.97
cd01895	174	EngA2 EngA2 subfamily. This CD represents the seco	97.95
PRK12317	425	elongation factor 1-alpha; Reviewed	97.94
cd00880	163	Era_like Era (E. coli Ras-like protein)-like. This	97.94
PRK12298	390	obgE GTPase CgtA; Reviewed	97.87
TIGR00437	591	feoB ferrous iron transporter FeoB. FeoB (773 amin	97.86
KOG0072|consensus	182		97.85
TIGR00503	527	prfC peptide chain release factor 3. This translat	97.84
PF00009	188	GTP_EFTU: Elongation factor Tu GTP binding domain;	97.76
TIGR03598	179	GTPase_YsxC ribosome biogenesis GTP-binding protei	97.73
cd01859	156	MJ1464 MJ1464. This family represents archaeal GTP	97.73
TIGR03594	429	GTPase_EngA ribosome-associated GTPase EngA. EngA	97.72
PRK09518	712	bifunctional cytidylate kinase/GTPase Der; Reviewe	97.72
PF06858	58	NOG1: Nucleolar GTP-binding protein 1 (NOG1); Inte	97.71
cd04166	208	CysN_ATPS CysN_ATPS subfamily. CysN, together with	97.7
TIGR03680	406	eif2g_arch translation initiation factor 2 subunit	97.69
PRK00093	435	GTP-binding protein Der; Reviewed	97.67
TIGR00484	689	EF-G translation elongation factor EF-G. After pep	97.62
cd01889	192	SelB_euk SelB subfamily. SelB is an elongation fac	97.61
cd01883	219	EF1_alpha Eukaryotic elongation factor 1 (EF1) alp	97.59
COG2262	411	HflX GTPases [General function prediction only]	97.55
cd04170	268	EF-G_bact Elongation factor G (EF-G) subfamily. Tr	97.53
PLN00043	447	elongation factor 1-alpha; Provisional	97.52
PRK04000	411	translation initiation factor IF-2 subunit gamma;	97.49
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	97.47
PRK10512	614	selenocysteinyl-tRNA-specific translation factor;	97.45
cd01876	170	YihA_EngB The YihA (EngB) subfamily. This subfamil	97.41
PRK12740	668	elongation factor G; Reviewed	97.41
PRK00089	292	era GTPase Era; Reviewed	97.33
cd01886	270	EF-G Elongation factor G (EF-G) subfamily. Translo	97.27
KOG1707|consensus	625		97.19
TIGR00490	720	aEF-2 translation elongation factor aEF-2. This mo	97.16
TIGR00485	394	EF-Tu translation elongation factor TU. This align	97.14
PRK00454	196	engB GTP-binding protein YsxC; Reviewed	97.13
cd01858	157	NGP_1 NGP-1. Autoantigen NGP-1 (Nucleolar G-protei	97.09
COG0532	509	InfB Translation initiation factor 2 (IF-2; GTPase	97.09
cd01849	155	YlqF_related_GTPase YlqF-related GTPases. These pr	97.08
KOG1489|consensus	366		97.07
cd04165	224	GTPBP1_like GTPBP1-like. Mammalian GTP binding pro	96.93
PRK01889	356	GTPase RsgA; Reviewed	96.88
PRK13796	365	GTPase YqeH; Provisional	96.86
KOG0090|consensus	238		96.77
PRK09554	772	feoB ferrous iron transport protein B; Reviewed	96.77
PRK12736	394	elongation factor Tu; Reviewed	96.74
PRK12735	396	elongation factor Tu; Reviewed	96.65
PF04670	232	Gtr1_RagA: Gtr1/RagA G protein conserved region; I	96.63
cd01896	233	DRG The developmentally regulated GTP-binding prot	96.55
KOG1144|consensus	1064		96.48
cd04104	197	p47_IIGP_like p47 (47-kDa) family. The p47 GTPase	96.47
PRK12739	691	elongation factor G; Reviewed	96.47
cd01884	195	EF_Tu EF-Tu subfamily. This subfamily includes ort	96.45
TIGR02034	406	CysN sulfate adenylyltransferase, large subunit. H	96.44
PRK13768	253	GTPase; Provisional	96.43
PRK05124	474	cysN sulfate adenylyltransferase subunit 1; Provis	96.28
PF00503	389	G-alpha: G-protein alpha subunit; InterPro: IPR001	96.27
PLN00116	843	translation elongation factor EF-2 subunit; Provis	96.16
PLN03126	478	Elongation factor Tu; Provisional	96.1
cd01856	171	YlqF YlqF. Proteins of the YlqF family contain all	96.1
KOG1145|consensus	683		96.05
CHL00071	409	tufA elongation factor Tu	95.94
PRK07560	731	elongation factor EF-2; Reviewed	95.85
PRK05506	632	bifunctional sulfate adenylyltransferase subunit 1	95.84
PF02421	156	FeoB_N: Ferrous iron transport protein B; InterPro	95.82
PTZ00327	460	eukaryotic translation initiation factor 2 gamma s	95.81
KOG0082|consensus	354		95.74
PTZ00416	836	elongation factor 2; Provisional	95.74
KOG3886|consensus	295		95.69
PRK00049	396	elongation factor Tu; Reviewed	95.69
TIGR03596	276	GTPase_YlqF ribosome biogenesis GTP-binding protei	95.65
cd01850	276	CDC_Septin CDC/Septin. Septins are a conserved fam	95.52
PRK09563	287	rbgA GTPase YlqF; Reviewed	95.5
COG1084	346	Predicted GTPase [General function prediction only	95.46
PRK00007	693	elongation factor G; Reviewed	95.41
KOG0462|consensus	650		95.33
cd04178	172	Nucleostemin_like Nucleostemin-like. Nucleostemin	95.29
KOG4273|consensus	418		95.28
PLN03127	447	Elongation factor Tu; Provisional	95.27
KOG0468|consensus	971		95.18
PRK09866	741	hypothetical protein; Provisional	95.1
COG0486	454	ThdF Predicted GTPase [General function prediction	94.99
COG1160	444	Predicted GTPases [General function prediction onl	94.76
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	94.56
COG0536	369	Obg Predicted GTPase [General function prediction	94.45
PTZ00141	446	elongation factor 1- alpha; Provisional	93.6
COG0480	697	FusA Translation elongation factors (GTPases) [Tra	92.88
PF00350	168	Dynamin_N: Dynamin family; InterPro: IPR001401 Mem	92.79
KOG0705|consensus	749		92.78
smart00053	240	DYNc Dynamin, GTPase. Large GTPases that mediate v	92.68
COG1162	301	Predicted GTPases [General function prediction onl	92.3
COG0218	200	Predicted GTPase [General function prediction only	91.92
PF14331	266	ImcF-related_N: ImcF-related N-terminal domain	91.44
KOG1424|consensus	562		91.26
COG2895	431	CysN GTPases - Sulfate adenylate transferase subun	91.1
TIGR03348	1169	VI_IcmF type VI secretion protein IcmF. Members of	90.58
COG0481	603	LepA Membrane GTPase LepA [Cell envelope biogenesi	90.47
KOG1490|consensus	620		90.23
KOG3929|consensus	363		90.22
cd01882	225	BMS1 Bms1. Bms1 is an essential, evolutionarily co	90.1
COG1159	298	Era GTPase [General function prediction only]	89.98
COG1160	444	Predicted GTPases [General function prediction onl	89.94
cd03110	179	Fer4_NifH_child This protein family's function is	89.81
COG1161	322	Predicted GTPases [General function prediction onl	89.47
KOG1954|consensus	532		87.85
KOG1423|consensus	379		87.21
KOG0447|consensus	980		86.44
COG4108	528	PrfC Peptide chain release factor RF-3 [Translatio	84.35
cd02067	119	B12-binding B12 binding domain (B12-BD). This doma	84.04
KOG2423|consensus	572		83.88
KOG2484|consensus	435		82.17
TIGR00101	199	ureG urease accessory protein UreG. This model rep	81.46
COG0050	394	TufB GTPases - translation elongation factors [Tra	80.73
TIGR02836	492	spore_IV_A stage IV sporulation protein A. A compa	80.5
KOG1191|consensus	531		80.31

>KOG0084|consensus

Probab=99.93  E-value=2.8e-26  Score=135.85  Aligned_cols=70  Identities=17%  Similarity=0.361  Sum_probs=65.3

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      ..|||||++++.+|||  |++|+|+|||+|+++||+++..|+.++.... ..++|++|||||+|+.+.|.|+.
T Consensus        65 TAGQERFrtit~syYR--~ahGii~vyDiT~~~SF~~v~~Wi~Ei~~~~-~~~v~~lLVGNK~Dl~~~~~v~~  134 (205)
T KOG0084|consen   65 TAGQERFRTITSSYYR--GAHGIIFVYDITKQESFNNVKRWIQEIDRYA-SENVPKLLVGNKCDLTEKRVVST  134 (205)
T ss_pred             ccccHHHhhhhHhhcc--CCCeEEEEEEcccHHHhhhHHHHHHHhhhhc-cCCCCeEEEeeccccHhheecCH
Confidence            3689999999999999  7999999999999999999999999999875 57899999999999999998875

>KOG0078|consensus

Probab=99.91  E-value=1.2e-24  Score=129.93  Aligned_cols=71  Identities=24%  Similarity=0.442  Sum_probs=66.3

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS   75 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~e   75 (75)
                      ..|||+|++++.+||+  +|+++++|||+++..||+++..|++.+.++. ++++|++|||||+||+++|+|+.|
T Consensus        68 taGQerf~ti~~sYyr--gA~gi~LvyDitne~Sfeni~~W~~~I~e~a-~~~v~~~LvGNK~D~~~~R~V~~e  138 (207)
T KOG0078|consen   68 TAGQERFRTITTAYYR--GAMGILLVYDITNEKSFENIRNWIKNIDEHA-SDDVVKILVGNKCDLEEKRQVSKE  138 (207)
T ss_pred             cccchhHHHHHHHHHh--hcCeeEEEEEccchHHHHHHHHHHHHHHhhC-CCCCcEEEeeccccccccccccHH
Confidence            4799999999999999  7999999999999999999999999999875 579999999999999999999754

>KOG0087|consensus

Probab=99.91  E-value=1.4e-24  Score=129.75  Aligned_cols=71  Identities=25%  Similarity=0.408  Sum_probs=66.3

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS   75 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~e   75 (75)
                      ..|||||++++++||+  |+.|+++|||+|.+.||+++.+|+.+++.+. .++++++|||||+||...|.|+.|
T Consensus        70 TAGQERyrAitSaYYr--gAvGAllVYDITr~~Tfenv~rWL~ELRdha-d~nivimLvGNK~DL~~lraV~te  140 (222)
T KOG0087|consen   70 TAGQERYRAITSAYYR--GAVGALLVYDITRRQTFENVERWLKELRDHA-DSNIVIMLVGNKSDLNHLRAVPTE  140 (222)
T ss_pred             ccchhhhccccchhhc--ccceeEEEEechhHHHHHHHHHHHHHHHhcC-CCCeEEEEeecchhhhhccccchh
Confidence            4699999999999999  8999999999999999999999999999975 479999999999999999998764

>KOG0094|consensus

Probab=99.90  E-value=5.3e-24  Score=126.40  Aligned_cols=72  Identities=25%  Similarity=0.500  Sum_probs=66.7

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS   75 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~e   75 (75)
                      ..|||||+++.|+|+|  |+.++|+|||+++.+||++..+|++.+.....+.++-++|||||.||.++|+|+.|
T Consensus        78 TAGQERFrslipsY~R--ds~vaviVyDit~~~Sfe~t~kWi~dv~~e~gs~~viI~LVGnKtDL~dkrqvs~e  149 (221)
T KOG0094|consen   78 TAGQERFRSLIPSYIR--DSSVAVIVYDITDRNSFENTSKWIEDVRRERGSDDVIIFLVGNKTDLSDKRQVSIE  149 (221)
T ss_pred             cccHHHHhhhhhhhcc--CCeEEEEEEeccccchHHHHHHHHHHHHhccCCCceEEEEEcccccccchhhhhHH
Confidence            3699999999999999  79999999999999999999999999998776667899999999999999998754

>KOG0092|consensus

Probab=99.89  E-value=2.1e-23  Score=123.27  Aligned_cols=70  Identities=26%  Similarity=0.442  Sum_probs=65.0

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      ..|||+|.++.|.|||  |++++|+|||+|+.+||..++.|+.++++.. ++++.+.|||||+||.+.|+|..
T Consensus        61 TAGQERy~slapMYyR--gA~AAivvYDit~~~SF~~aK~WvkeL~~~~-~~~~vialvGNK~DL~~~R~V~~  130 (200)
T KOG0092|consen   61 TAGQERYHSLAPMYYR--GANAAIVVYDITDEESFEKAKNWVKELQRQA-SPNIVIALVGNKADLLERREVEF  130 (200)
T ss_pred             cCCcccccccccceec--CCcEEEEEEecccHHHHHHHHHHHHHHHhhC-CCCeEEEEecchhhhhhcccccH
Confidence            3699999999999999  8999999999999999999999999999865 48899999999999999898864

>KOG0098|consensus

Probab=99.89  E-value=2.6e-23  Score=122.83  Aligned_cols=71  Identities=21%  Similarity=0.424  Sum_probs=66.4

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS   75 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~e   75 (75)
                      ..|||+|++++.+||+  ++.|+|||||+++++||.++..|+.+++++. .+++.++|+|||+||...|.|+.|
T Consensus        62 taGqe~frsv~~syYr--~a~GalLVydit~r~sF~hL~~wL~D~rq~~-~~NmvImLiGNKsDL~~rR~Vs~E  132 (216)
T KOG0098|consen   62 TAGQESFRSVTRSYYR--GAAGALLVYDITRRESFNHLTSWLEDARQHS-NENMVIMLIGNKSDLEARREVSKE  132 (216)
T ss_pred             cCCcHHHHHHHHHHhc--cCcceEEEEEccchhhHHHHHHHHHHHHHhc-CCCcEEEEEcchhhhhccccccHH
Confidence            3699999999999999  7999999999999999999999999999974 589999999999999999999865

>KOG0093|consensus

Probab=99.87  E-value=1.7e-22  Score=116.01  Aligned_cols=71  Identities=18%  Similarity=0.441  Sum_probs=65.4

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS   75 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~e   75 (75)
                      ..|+|+|+.++..|||  +++|+|++||+++.+||..++.|...++... -.++|+|||||||||.++|.|+.|
T Consensus        77 TagqEryrtiTTayyR--gamgfiLmyDitNeeSf~svqdw~tqIktys-w~naqvilvgnKCDmd~eRvis~e  147 (193)
T KOG0093|consen   77 TAGQERYRTITTAYYR--GAMGFILMYDITNEESFNSVQDWITQIKTYS-WDNAQVILVGNKCDMDSERVISHE  147 (193)
T ss_pred             cccchhhhHHHHHHhh--ccceEEEEEecCCHHHHHHHHHHHHHheeee-ccCceEEEEecccCCccceeeeHH
Confidence            3589999999999999  7999999999999999999999999998764 478999999999999999998864

>KOG0080|consensus

Probab=99.87  E-value=3.9e-23  Score=120.07  Aligned_cols=72  Identities=28%  Similarity=0.316  Sum_probs=66.6

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS   75 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~e   75 (75)
                      ..|||+|++++++|||  |++|+|+|||+|.++||.++..|++++......+++.+++||||+|-+.+|.|+.|
T Consensus        67 TAGqErFRtLTpSyyR--gaqGiIlVYDVT~Rdtf~kLd~W~~Eld~Ystn~diikmlVgNKiDkes~R~V~re  138 (209)
T KOG0080|consen   67 TAGQERFRTLTPSYYR--GAQGIILVYDVTSRDTFVKLDIWLKELDLYSTNPDIIKMLVGNKIDKESERVVDRE  138 (209)
T ss_pred             ccchHhhhccCHhHhc--cCceeEEEEEccchhhHHhHHHHHHHHHhhcCCccHhHhhhcccccchhcccccHH
Confidence            3699999999999999  89999999999999999999999999998777788999999999999888998754

>KOG0079|consensus

Probab=99.87  E-value=2.9e-22  Score=115.21  Aligned_cols=69  Identities=20%  Similarity=0.359  Sum_probs=63.6

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +.|+|+|+.++..||+  +.+++++|||+|+.+||.++++|++++++  .++.+|.+|||||+|+.+.|.|..
T Consensus        64 tAGqErFrtitstyyr--gthgv~vVYDVTn~ESF~Nv~rWLeei~~--ncdsv~~vLVGNK~d~~~RrvV~t  132 (198)
T KOG0079|consen   64 TAGQERFRTITSTYYR--GTHGVIVVYDVTNGESFNNVKRWLEEIRN--NCDSVPKVLVGNKNDDPERRVVDT  132 (198)
T ss_pred             cccHHHHHHHHHHHcc--CCceEEEEEECcchhhhHhHHHHHHHHHh--cCccccceecccCCCCccceeeeh
Confidence            4699999999999999  79999999999999999999999999998  568999999999999998777643

>KOG0088|consensus

Probab=99.86  E-value=1.9e-22  Score=117.15  Aligned_cols=70  Identities=27%  Similarity=0.406  Sum_probs=64.4

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      ..|||+|..+.|-||+  +++|+++||||||++||+.+++|..+++... ...+.+++||||+||+++|+|+.
T Consensus        69 TAGQErfHALGPIYYR--gSnGalLVyDITDrdSFqKVKnWV~Elr~ml-Gnei~l~IVGNKiDLEeeR~Vt~  138 (218)
T KOG0088|consen   69 TAGQERFHALGPIYYR--GSNGALLVYDITDRDSFQKVKNWVLELRTML-GNEIELLIVGNKIDLEEERQVTR  138 (218)
T ss_pred             ccchHhhhccCceEEe--CCCceEEEEeccchHHHHHHHHHHHHHHHHh-CCeeEEEEecCcccHHHhhhhhH
Confidence            3689999999999999  7999999999999999999999999999864 36788999999999999999974

>KOG0081|consensus

Probab=99.86  E-value=4.1e-22  Score=115.80  Aligned_cols=71  Identities=24%  Similarity=0.463  Sum_probs=66.9

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      ..|||+|++++..|++  +|.|+++.||+|+++||.++++|+.+++.+..+.+.-||++|||+||++.|.|++
T Consensus        74 TAGQERFRSLTTAFfR--DAMGFlLiFDlT~eqSFLnvrnWlSQL~~hAYcE~PDivlcGNK~DL~~~R~Vs~  144 (219)
T KOG0081|consen   74 TAGQERFRSLTTAFFR--DAMGFLLIFDLTSEQSFLNVRNWLSQLQTHAYCENPDIVLCGNKADLEDQRVVSE  144 (219)
T ss_pred             cccHHHHHHHHHHHHH--hhccceEEEeccchHHHHHHHHHHHHHHHhhccCCCCEEEEcCccchhhhhhhhH
Confidence            3689999999999999  5999999999999999999999999999988889999999999999999998875

>KOG0091|consensus

Probab=99.85  E-value=1.4e-21  Score=113.88  Aligned_cols=72  Identities=22%  Similarity=0.393  Sum_probs=64.3

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC-CCCCeEEEEeeCCCCcCCCcccCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY-IGEKAVILVANKADLERRRQVTHS   75 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~ilvgnK~Dl~~~r~v~~e   75 (75)
                      ..|||+|++++.+||+  |+-|+++|||++|++||++++.|+++...... +.++...|||.|+||...|+|+.|
T Consensus        65 tagqerfrsitksyyr--nsvgvllvyditnr~sfehv~~w~~ea~m~~q~P~k~VFlLVGhKsDL~SqRqVt~E  137 (213)
T KOG0091|consen   65 TAGQERFRSITKSYYR--NSVGVLLVYDITNRESFEHVENWVKEAAMATQGPDKVVFLLVGHKSDLQSQRQVTAE  137 (213)
T ss_pred             ccchHHHHHHHHHHhh--cccceEEEEeccchhhHHHHHHHHHHHHHhcCCCCeeEEEEeccccchhhhccccHH
Confidence            3699999999999999  79999999999999999999999999877654 445667899999999999999854

>KOG0086|consensus

Probab=99.83  E-value=7.6e-21  Score=110.02  Aligned_cols=70  Identities=23%  Similarity=0.356  Sum_probs=64.9

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      ..|||+|++.+.+||+  |+.|.++|||+++++||+.+.+|+.+++... ++++.++++|||.||.++|+|+.
T Consensus        65 TAGQErFRSVtRsYYR--GAAGAlLVYD~TsrdsfnaLtnWL~DaR~lA-s~nIvviL~GnKkDL~~~R~Vtf  134 (214)
T KOG0086|consen   65 TAGQERFRSVTRSYYR--GAAGALLVYDITSRDSFNALTNWLTDARTLA-SPNIVVILCGNKKDLDPEREVTF  134 (214)
T ss_pred             cccHHHHHHHHHHHhc--cccceEEEEeccchhhHHHHHHHHHHHHhhC-CCcEEEEEeCChhhcChhhhhhH
Confidence            3689999999999999  8999999999999999999999999998764 68999999999999999999874

>KOG0095|consensus

Probab=99.82  E-value=1e-20  Score=109.18  Aligned_cols=70  Identities=21%  Similarity=0.382  Sum_probs=64.6

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      ..|||+|++++.+||+  .++++|++||++-+.||+.+..|+.++.+.. ..++..|+||||.|+.+.|+|+.
T Consensus        63 tagqerfrsitqsyyr--sahalilvydiscqpsfdclpewlreie~ya-n~kvlkilvgnk~d~~drrevp~  132 (213)
T KOG0095|consen   63 TAGQERFRSITQSYYR--SAHALILVYDISCQPSFDCLPEWLREIEQYA-NNKVLKILVGNKIDLADRREVPQ  132 (213)
T ss_pred             ccchHHHHHHHHHHhh--hcceEEEEEecccCcchhhhHHHHHHHHHHh-hcceEEEeeccccchhhhhhhhH
Confidence            3689999999999999  5999999999999999999999999999975 47889999999999999988864

>cd04120 Rab12 Rab12 subfamily

Probab=99.82  E-value=5e-20  Score=110.59  Aligned_cols=68  Identities=19%  Similarity=0.402  Sum_probs=61.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+|+|+++++.|++  +++++|+|||+++++||+++..|+..+.+.. ..++|+++||||+||...++|+
T Consensus        57 aGqe~~~~l~~~y~~--~ad~iIlVfDvtd~~Sf~~l~~w~~~i~~~~-~~~~piilVgNK~DL~~~~~v~  124 (202)
T cd04120          57 AGQERFNSITSAYYR--SAKGIILVYDITKKETFDDLPKWMKMIDKYA-SEDAELLLVGNKLDCETDREIS  124 (202)
T ss_pred             CCchhhHHHHHHHhc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCcEEEEEECcccccccccC
Confidence            689999999999999  6999999999999999999999999887643 4679999999999998777765

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

>KOG0083|consensus

Probab=99.82  E-value=5.9e-21  Score=108.50  Aligned_cols=71  Identities=18%  Similarity=0.428  Sum_probs=64.4

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS   75 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~e   75 (75)
                      ..|||+|++.+.+||+  ++|+++++||++++.||++++.|+.++.+.. ...+.+.++|||+|+..+|.|..+
T Consensus        54 tagqerfrsvt~ayyr--da~allllydiankasfdn~~~wlsei~ey~-k~~v~l~llgnk~d~a~er~v~~d  124 (192)
T KOG0083|consen   54 TAGQERFRSVTHAYYR--DADALLLLYDIANKASFDNCQAWLSEIHEYA-KEAVALMLLGNKCDLAHERAVKRD  124 (192)
T ss_pred             ccchHHHhhhhHhhhc--ccceeeeeeecccchhHHHHHHHHHHHHHHH-HhhHhHhhhccccccchhhccccc
Confidence            3689999999999999  5999999999999999999999999999875 367889999999999988988653

>cd04102 RabL3 RabL3 (Rab-like3) subfamily

Probab=99.81  E-value=8.4e-20  Score=109.69  Aligned_cols=69  Identities=9%  Similarity=0.129  Sum_probs=60.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhc------------------CCCCCeEEEEeeCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSK------------------YIGEKAVILVANKA   64 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~------------------~~~~~~~ilvgnK~   64 (75)
                      +|+|+|+.+++.||+  +++++|+|||+++++||+++..|+.++.+..                  ...++|++|||||+
T Consensus        62 aG~e~~~~l~~~~yr--~ad~iIlVyDvtn~~Sf~~l~~W~~ei~~~~~~~~~~~~~~~~~~~~~~~~~~~PiilVGnK~  139 (202)
T cd04102          62 GGSESVKSTRAVFYN--QVNGIILVHDLTNRKSSQNLQRWSLEALNKDTFPTGLLVTNGDYDSEQFGGNQIPLLVIGTKL  139 (202)
T ss_pred             CCchhHHHHHHHHhC--cCCEEEEEEECcChHHHHHHHHHHHHHHHhhccccccccccccccccccCCCCceEEEEEECc
Confidence            689999999999999  6999999999999999999999999987631                  12478999999999


Q ss_pred             CCcCCCccc
Q psy5805          65 DLERRRQVT   73 (75)
Q Consensus        65 Dl~~~r~v~   73 (75)
                      ||.++|.++
T Consensus       140 Dl~~~r~~~  148 (202)
T cd04102         140 DQIPEKESS  148 (202)
T ss_pred             cchhhcccc
Confidence            998777554

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.

>cd04121 Rab40 Rab40 subfamily

Probab=99.81  E-value=6e-20  Score=109.24  Aligned_cols=68  Identities=22%  Similarity=0.364  Sum_probs=61.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +|+++|+.+++.|++  +++++|+|||++++.||+++..|+.++...  .+++|++|||||+||.+.|.|+.
T Consensus        63 ~G~~~~~~l~~~~~~--~ad~illVfD~t~~~Sf~~~~~w~~~i~~~--~~~~piilVGNK~DL~~~~~v~~  130 (189)
T cd04121          63 SGQGRFCTIFRSYSR--GAQGIILVYDITNRWSFDGIDRWIKEIDEH--APGVPKILVGNRLHLAFKRQVAT  130 (189)
T ss_pred             CCcHHHHHHHHHHhc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHh--CCCCCEEEEEECccchhccCCCH
Confidence            689999999999999  699999999999999999999999999764  36899999999999988777753

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=99.80  E-value=1.4e-19  Score=106.64  Aligned_cols=65  Identities=22%  Similarity=0.376  Sum_probs=58.2

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .+|+|+|+.+++.|++  +++++|+|||+++++||+++ +.|+.++.+..  +++|++|||||+||.+++
T Consensus        56 t~G~~~~~~~~~~~~~--~a~~~ilvyd~~~~~Sf~~~~~~w~~~i~~~~--~~~piilvgnK~Dl~~~~  121 (176)
T cd04133          56 TAGQEDYNRLRPLSYR--GADVFVLAFSLISRASYENVLKKWVPELRHYA--PNVPIVLVGTKLDLRDDK  121 (176)
T ss_pred             CCCCccccccchhhcC--CCcEEEEEEEcCCHHHHHHHHHHHHHHHHHhC--CCCCEEEEEeChhhccCh
Confidence            3789999999999999  69999999999999999998 78999998743  679999999999997654

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,

>KOG0394|consensus

Probab=99.79  E-value=1.5e-19  Score=106.78  Aligned_cols=71  Identities=27%  Similarity=0.383  Sum_probs=62.1

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC---CCCCeEEEEeeCCCCcC--CCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY---IGEKAVILVANKADLER--RRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~~ilvgnK~Dl~~--~r~v~~   74 (75)
                      ..|||||+++.-.+||  |+|++++|||+++++||+++..|.+++.....   +...|.||+|||.|+.+  .|+|+.
T Consensus        65 TAGQERFqsLg~aFYR--gaDcCvlvydv~~~~Sfe~L~~Wr~EFl~qa~~~~Pe~FPFVilGNKiD~~~~~~r~VS~  140 (210)
T KOG0394|consen   65 TAGQERFQSLGVAFYR--GADCCVLVYDVNNPKSFENLENWRKEFLIQASPQDPETFPFVILGNKIDVDGGKSRQVSE  140 (210)
T ss_pred             cccHHHhhhcccceec--CCceEEEEeecCChhhhccHHHHHHHHHHhcCCCCCCcccEEEEcccccCCCCccceeeH
Confidence            4699999999999999  89999999999999999999999999876532   34679999999999976  278764

>KOG0395|consensus

Probab=99.78  E-value=6.8e-19  Score=105.40  Aligned_cols=71  Identities=31%  Similarity=0.541  Sum_probs=64.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS   75 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~e   75 (75)
                      .|++.|..++..|.+  +++|+++||+++++.||+.+..++..+.+......+|+++||||+||...|+|+.+
T Consensus        59 ~g~~~~~~~~~~~~~--~~~gF~lVysitd~~SF~~~~~l~~~I~r~~~~~~~PivlVGNK~Dl~~~R~V~~e  129 (196)
T KOG0395|consen   59 AGQEEFSAMRDLYIR--NGDGFLLVYSITDRSSFEEAKQLREQILRVKGRDDVPIILVGNKCDLERERQVSEE  129 (196)
T ss_pred             CCcccChHHHHHhhc--cCcEEEEEEECCCHHHHHHHHHHHHHHHHhhCcCCCCEEEEEEcccchhccccCHH
Confidence            568999999999999  69999999999999999999999999976666678999999999999998998753

>cd04172 Rnd3_RhoE_Rho8 Rnd3/RhoE/Rho8 subfamily

Probab=99.78  E-value=5.2e-19  Score=104.61  Aligned_cols=62  Identities=16%  Similarity=0.247  Sum_probs=56.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+|+|+.+++.|++  +++++++|||+++++||+++ ..|++++.+.  .+++|++|||||+||.+
T Consensus        61 aG~e~~~~~~~~~~~--~ad~~ilvyDit~~~Sf~~~~~~w~~~i~~~--~~~~piilVgNK~DL~~  123 (182)
T cd04172          61 SGSPYYDNVRPLSYP--DSDAVLICFDISRPETLDSVLKKWKGEIQEF--CPNTKMLLVGCKSDLRT  123 (182)
T ss_pred             CCchhhHhhhhhhcC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHHH--CCCCCEEEEeEChhhhc
Confidence            689999999999999  69999999999999999998 8999999874  36799999999999964

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

>cd01875 RhoG RhoG subfamily

Probab=99.77  E-value=2.1e-18  Score=102.32  Aligned_cols=64  Identities=16%  Similarity=0.305  Sum_probs=56.8

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .+|+|+|+.+++.|++  +++++|+|||+++++||+++. .|..++...  .+++|++|||||+||.+.
T Consensus        58 t~G~e~~~~l~~~~~~--~a~~~ilvydit~~~Sf~~~~~~w~~~i~~~--~~~~piilvgNK~DL~~~  122 (191)
T cd01875          58 TAGQEEYDRLRTLSYP--QTNVFIICFSIASPSSYENVRHKWHPEVCHH--CPNVPILLVGTKKDLRND  122 (191)
T ss_pred             CCCchhhhhhhhhhcc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhh--CCCCCEEEEEeChhhhcC
Confidence            3799999999999999  699999999999999999996 698888763  367999999999999754

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

>cd04131 Rnd Rnd subfamily

Probab=99.76  E-value=1.4e-18  Score=102.33  Aligned_cols=62  Identities=18%  Similarity=0.265  Sum_probs=56.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+|+|..+++.|++  +++++|+|||+++++||+++ ..|..++++.  .+++|++|||||+||.+
T Consensus        57 ~G~~~~~~~~~~~~~--~a~~~ilvfdit~~~Sf~~~~~~w~~~i~~~--~~~~~iilVgnK~DL~~  119 (178)
T cd04131          57 SGSPYYDNVRPLCYP--DSDAVLICFDISRPETLDSVLKKWRGEIQEF--CPNTKVLLVGCKTDLRT  119 (178)
T ss_pred             CCchhhhhcchhhcC--CCCEEEEEEECCChhhHHHHHHHHHHHHHHH--CCCCCEEEEEEChhhhc
Confidence            689999999999999  69999999999999999996 8999999874  36899999999999964

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.

>cd04174 Rnd1_Rho6 Rnd1/Rho6 subfamily

Probab=99.76  E-value=3e-18  Score=104.84  Aligned_cols=62  Identities=16%  Similarity=0.283  Sum_probs=56.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+|+|+.+++.||+  +++++++|||+++++||+++ ..|+.++...  .+++|++|||||+||.+
T Consensus        69 aG~e~~~~~~~~~~~--~ad~vIlVyDit~~~Sf~~~~~~w~~~i~~~--~~~~piilVgNK~DL~~  131 (232)
T cd04174          69 SGSPYYDNVRPLCYS--DSDAVLLCFDISRPETVDSALKKWKAEIMDY--CPSTRILLIGCKTDLRT  131 (232)
T ss_pred             CCchhhHHHHHHHcC--CCcEEEEEEECCChHHHHHHHHHHHHHHHHh--CCCCCEEEEEECccccc
Confidence            689999999999999  69999999999999999985 8999999874  36789999999999964

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.

>PTZ00099 rab6; Provisional

Probab=99.76  E-value=3.2e-18  Score=100.80  Aligned_cols=68  Identities=22%  Similarity=0.488  Sum_probs=60.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|+.+++.|++  +++++|+|||+++++||+.+..|+..+.... .+++|++|||||+||.+.+.|+
T Consensus        37 ~G~e~~~~~~~~~~~--~ad~~ilv~D~t~~~sf~~~~~w~~~i~~~~-~~~~piilVgNK~DL~~~~~v~  104 (176)
T PTZ00099         37 AGQERFRSLIPSYIR--DSAAAIVVYDITNRQSFENTTKWIQDILNER-GKDVIIALVGNKTDLGDLRKVT  104 (176)
T ss_pred             CChHHhhhccHHHhC--CCcEEEEEEECCCHHHHHHHHHHHHHHHHhc-CCCCeEEEEEECcccccccCCC
Confidence            689999999999999  7999999999999999999999999887643 3678999999999997666554

>cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily

Probab=99.76  E-value=3.2e-18  Score=100.06  Aligned_cols=70  Identities=31%  Similarity=0.526  Sum_probs=61.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +|+++|+.+++.|++  +++++++|||++++.||+.+..|...+.+....+++|+++||||+|+.+.++++.
T Consensus        58 ~G~~~~~~l~~~~~~--~~d~~ilv~d~~~~~Sf~~~~~~~~~i~~~~~~~~~piilvgNK~Dl~~~~~v~~  127 (172)
T cd04141          58 AGQAEFTAMRDQYMR--CGEGFIICYSVTDRHSFQEASEFKKLITRVRLTEDIPLVLVGNKVDLESQRQVTT  127 (172)
T ss_pred             CCchhhHHHhHHHhh--cCCEEEEEEECCchhHHHHHHHHHHHHHHhcCCCCCCEEEEEEChhhhhcCccCH
Confidence            688999999999999  6999999999999999999999988887654446799999999999987777653

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

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

Probab=99.75  E-value=4.9e-18  Score=101.83  Aligned_cols=63  Identities=19%  Similarity=0.319  Sum_probs=57.6

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+|+|+|+.+++.|++  +++++|+|||++++.||+++..|+.++.+.  .+++|++|||||+||..
T Consensus        51 t~G~e~~~~l~~~~~~--~ad~~ilV~D~t~~~S~~~i~~w~~~i~~~--~~~~piilvgNK~Dl~~  113 (200)
T smart00176       51 TAGQEKFGGLRDGYYI--QGQCAIIMFDVTARVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDVKD  113 (200)
T ss_pred             CCCchhhhhhhHHHhc--CCCEEEEEEECCChHHHHHHHHHHHHHHHh--CCCCCEEEEEECccccc
Confidence            3789999999999999  699999999999999999999999999874  36899999999999964

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

>cd04127 Rab27A Rab27a subfamily

Probab=99.74  E-value=9e-18  Score=97.91  Aligned_cols=69  Identities=25%  Similarity=0.489  Sum_probs=61.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..+++  +++++++|||+++++||.++..|+.++......+++|+++||||+|+.+.+.++
T Consensus        71 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piiiv~nK~Dl~~~~~v~  139 (180)
T cd04127          71 AGQERFRSLTTAFFR--DAMGFLLIFDLTNEQSFLNVRNWMSQLQTHAYCENPDIVLCGNKADLEDQRQVS  139 (180)
T ss_pred             CChHHHHHHHHHHhC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEeCccchhcCccC
Confidence            688999999999999  699999999999999999999999998875445678999999999997766654

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

>cd04136 Rap_like Rap-like subfamily

Probab=99.73  E-value=1.7e-17  Score=95.06  Aligned_cols=69  Identities=29%  Similarity=0.479  Sum_probs=60.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|+.+++.|++  +++++++|||+++++||+.+..|...+.......++|+++||||+|+.+.+.++
T Consensus        57 ~G~~~~~~~~~~~~~--~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~  125 (163)
T cd04136          57 AGTEQFTAMRDLYIK--NGQGFVLVYSITSQSSFNDLQDLREQILRVKDTENVPMVLVGNKCDLEDERVVS  125 (163)
T ss_pred             CCccccchHHHHHhh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccceec
Confidence            688999999999999  699999999999999999999999988875445689999999999997655543

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.

>cd04122 Rab14 Rab14 subfamily

Probab=99.73  E-value=1.7e-17  Score=95.84  Aligned_cols=69  Identities=23%  Similarity=0.386  Sum_probs=60.7

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .+|+++|+.++..+++  +++++|+|||+++++||+.+..|+.++.... .++.|+++||||+|+.+.+.++
T Consensus        58 t~G~~~~~~~~~~~~~--~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~iiiv~nK~Dl~~~~~~~  126 (166)
T cd04122          58 TAGQERFRAVTRSYYR--GAAGALMVYDITRRSTYNHLSSWLTDARNLT-NPNTVIFLIGNKADLEAQRDVT  126 (166)
T ss_pred             CCCcHHHHHHHHHHhc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCeEEEEEECcccccccCcC
Confidence            3689999999999998  6999999999999999999999999887653 3678999999999998777654

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

>PLN00023 GTP-binding protein; Provisional

Probab=99.73  E-value=1.9e-17  Score=105.30  Aligned_cols=65  Identities=15%  Similarity=0.147  Sum_probs=57.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC-----------CCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY-----------IGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-----------~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+|+|+.+++.|++  +++++|+|||+++++||+++..|+.++.....           ..++|++|||||+||..+
T Consensus        91 AGqErfrsL~~~yyr--~AdgiILVyDITdr~SFenL~kWl~eI~~~~~~s~p~~s~~~~~~~ipIILVGNK~DL~~~  166 (334)
T PLN00023         91 SGHERYKDCRSLFYS--QINGVIFVHDLSQRRTKTSLQKWASEVAATGTFSAPLGSGGPGGLPVPYIVIGNKADIAPK  166 (334)
T ss_pred             CCChhhhhhhHHhcc--CCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcccccccccccccCCCCcEEEEEECcccccc
Confidence            789999999999999  69999999999999999999999999987521           135899999999999764

>KOG0097|consensus

Probab=99.72  E-value=5.4e-18  Score=97.37  Aligned_cols=70  Identities=23%  Similarity=0.372  Sum_probs=64.3

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      ..|||+|+..+.+||+  |+.+.++|||++.+.+++++..|+...++.. .++..++++|||.||+.+|.|+-
T Consensus        67 tagqerfravtrsyyr--gaagalmvyditrrstynhlsswl~dar~lt-npnt~i~lignkadle~qrdv~y  136 (215)
T KOG0097|consen   67 TAGQERFRAVTRSYYR--GAAGALMVYDITRRSTYNHLSSWLTDARNLT-NPNTVIFLIGNKADLESQRDVTY  136 (215)
T ss_pred             cccHHHHHHHHHHHhc--cccceeEEEEehhhhhhhhHHHHHhhhhccC-CCceEEEEecchhhhhhcccCcH
Confidence            3689999999999999  8999999999999999999999999988764 47889999999999999998874

>cd04176 Rap2 Rap2 subgroup

Probab=99.72  E-value=2.9e-17  Score=94.40  Aligned_cols=68  Identities=29%  Similarity=0.494  Sum_probs=59.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+|+|..+++.|++  +++++++|||+++++||+++..|...+.+.....++|+++||||+|+...+.+
T Consensus        57 ~G~~~~~~~~~~~~~--~ad~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piviv~nK~Dl~~~~~~  124 (163)
T cd04176          57 AGTEQFASMRDLYIK--NGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESEREV  124 (163)
T ss_pred             CCcccccchHHHHHh--hCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccchhcCcc
Confidence            688999999999999  69999999999999999999999988887544468999999999999665544

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=4e-17  Score=93.96  Aligned_cols=70  Identities=31%  Similarity=0.472  Sum_probs=61.2

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .+|+++|+.+++.|++  +++++++|||++++.||+.+..|...+.......++|+++||||+|+...+.++
T Consensus        56 t~G~~~~~~~~~~~~~--~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~  125 (164)
T cd04175          56 TAGTEQFTAMRDLYMK--NGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVG  125 (164)
T ss_pred             CCCcccchhHHHHHHh--hCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCcchhccEEc
Confidence            3689999999999999  699999999999999999999999988765445789999999999997655543

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

>cd01874 Cdc42 Cdc42 subfamily

Probab=99.71  E-value=2.7e-17  Score=96.39  Aligned_cols=64  Identities=17%  Similarity=0.324  Sum_probs=56.2

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .+|+++|+.+++.|++  +++++|+|||+++++||+++. .|..++...  .+++|+++||||+|+...
T Consensus        56 t~G~~~~~~~~~~~~~--~a~~~ilv~d~~~~~s~~~~~~~w~~~i~~~--~~~~piilvgnK~Dl~~~  120 (175)
T cd01874          56 TAGQEDYDRLRPLSYP--QTDVFLVCFSVVSPSSFENVKEKWVPEITHH--CPKTPFLLVGTQIDLRDD  120 (175)
T ss_pred             CCCccchhhhhhhhcc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEECHhhhhC
Confidence            3789999999999998  699999999999999999996 598888763  367999999999999653

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

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

Probab=99.71  E-value=3.1e-17  Score=94.10  Aligned_cols=68  Identities=28%  Similarity=0.474  Sum_probs=61.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..+++.+++  +++++|+|||+++++||+++..|+..+..... .++|+++||||+|+.+.++|+
T Consensus        56 ~g~~~~~~~~~~~~~--~~~~~ii~fd~~~~~S~~~~~~~~~~i~~~~~-~~~~iivvg~K~D~~~~~~v~  123 (162)
T PF00071_consen   56 SGQERFDSLRDIFYR--NSDAIIIVFDVTDEESFENLKKWLEEIQKYKP-EDIPIIVVGNKSDLSDEREVS  123 (162)
T ss_dssp             TTSGGGHHHHHHHHT--TESEEEEEEETTBHHHHHTHHHHHHHHHHHST-TTSEEEEEEETTTGGGGSSSC
T ss_pred             ccccccccccccccc--cccccccccccccccccccccccccccccccc-ccccceeeeccccccccccch
Confidence            689999999999998  59999999999999999999999999988642 579999999999998877765

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 ....

>cd04126 Rab20 Rab20 subfamily

Probab=99.71  E-value=4.6e-17  Score=98.93  Aligned_cols=64  Identities=20%  Similarity=0.292  Sum_probs=56.5

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+|+++|+.+++.|++  +++++|+|||+++++||+++..|+..+.+.. ..++|++|||||+||.+
T Consensus        51 t~G~e~~~~l~~~~~~--~ad~~IlV~Dvt~~~Sf~~l~~~~~~l~~~~-~~~~piIlVgNK~DL~~  114 (220)
T cd04126          51 TAGREQFHGLGSMYCR--GAAAVILTYDVSNVQSLEELEDRFLGLTDTA-NEDCLFAVVGNKLDLTE  114 (220)
T ss_pred             CCCcccchhhHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhc-CCCCcEEEEEECccccc
Confidence            3689999999999999  6999999999999999999998887776643 46799999999999965

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

>cd04107 Rab32_Rab38 Rab38/Rab32 subfamily

Probab=99.71  E-value=4.9e-17  Score=96.87  Aligned_cols=69  Identities=20%  Similarity=0.207  Sum_probs=58.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhc---CCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSK---YIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~---~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|+.+++.|++  +++++|+|||+++++||+.+..|+.++....   ...++|+++||||+|+...+.++
T Consensus        58 ~G~~~~~~~~~~~~~--~a~~~ilv~D~t~~~s~~~~~~~~~~i~~~~~~~~~~~~piilv~NK~Dl~~~~~~~  129 (201)
T cd04107          58 AGQERFGGMTRVYYR--GAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPCLLLANKCDLKKRLAKD  129 (201)
T ss_pred             CCchhhhhhHHHHhC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhhcccCCCCCcEEEEEECCCcccccccC
Confidence            688999999999999  6999999999999999999999998887532   13578999999999997545443

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.

>cd04117 Rab15 Rab15 subfamily

Probab=99.71  E-value=5.3e-17  Score=93.75  Aligned_cols=68  Identities=18%  Similarity=0.328  Sum_probs=60.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..+++.|++  +++++++|||+++++||+.+..|+.++.... ..++|+++||||.|+.+.+.++
T Consensus        57 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~sf~~~~~~~~~~~~~~-~~~~~iilvgnK~Dl~~~~~v~  124 (161)
T cd04117          57 AGQERYQTITKQYYR--RAQGIFLVYDISSERSYQHIMKWVSDVDEYA-PEGVQKILIGNKADEEQKRQVG  124 (161)
T ss_pred             CCcHhHHhhHHHHhc--CCcEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCeEEEEEECcccccccCCC
Confidence            678999999999998  6999999999999999999999999887653 3579999999999998777664

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

>cd04144 Ras2 Ras2 subfamily

Probab=99.70  E-value=7e-17  Score=95.49  Aligned_cols=69  Identities=25%  Similarity=0.448  Sum_probs=59.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC--CCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY--IGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..|++  +++++|+|||+++++||+.+..|+..+.....  ..++|+++||||+|+...+.++
T Consensus        55 ~G~~~~~~~~~~~~~--~ad~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilvgNK~Dl~~~~~v~  125 (190)
T cd04144          55 AGQEEYTALRDQWIR--EGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVYEREVS  125 (190)
T ss_pred             CCchhhHHHHHHHHH--hCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcccCCCCCEEEEEEChhccccCccC
Confidence            688999999999999  69999999999999999999999988876532  2578999999999997666654

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.

>cd04109 Rab28 Rab28 subfamily

Probab=99.69  E-value=1.1e-16  Score=96.36  Aligned_cols=69  Identities=25%  Similarity=0.360  Sum_probs=59.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC--CCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY--IGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|++.|..+.+.|++  ++|++|+|||+++++||+++..|...+.+...  ..++|+++||||+||.+.+.++
T Consensus        58 ~G~~~~~~l~~~~~~--~ad~iilV~D~t~~~s~~~~~~w~~~l~~~~~~~~~~~piilVgNK~DL~~~~~v~  128 (215)
T cd04109          58 GGQSIGGKMLDKYIY--GAHAVFLVYDVTNSQSFENLEDWYSMVRKVLKSSETQPLVVLVGNKTDLEHNRTVK  128 (215)
T ss_pred             CCcHHHHHHHHHHhh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhccccCCCceEEEEEECcccccccccC
Confidence            578999999999999  69999999999999999999999999887532  2457899999999998767654

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

>PTZ00369 Ras-like protein; Provisional

Probab=99.69  E-value=2.1e-16  Score=93.39  Aligned_cols=69  Identities=25%  Similarity=0.431  Sum_probs=60.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..+++.|++  +++++++|||+++++||+++..|...+.+....+++|+++||||+|+.+.+.++
T Consensus        61 ~G~~~~~~l~~~~~~--~~d~iilv~D~s~~~s~~~~~~~~~~i~~~~~~~~~piiiv~nK~Dl~~~~~i~  129 (189)
T PTZ00369         61 AGQEEYSAMRDQYMR--TGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDSERQVS  129 (189)
T ss_pred             CCCccchhhHHHHhh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccC
Confidence            688999999999999  699999999999999999999999988765444689999999999997666554

>cd04173 Rnd2_Rho7 Rnd2/Rho7 subfamily

Probab=99.68  E-value=1.6e-16  Score=96.69  Aligned_cols=62  Identities=18%  Similarity=0.273  Sum_probs=55.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.|..+++.+|+  ++|++++|||+++++||+++ ..|..++..  ..+++|++|||||+||.+
T Consensus        57 ~G~e~~~~l~~~~~~--~~d~illvfdis~~~Sf~~i~~~w~~~~~~--~~~~~piiLVgnK~DL~~  119 (222)
T cd04173          57 SGSSYYDNVRPLAYP--DSDAVLICFDISRPETLDSVLKKWQGETQE--FCPNAKVVLVGCKLDMRT  119 (222)
T ss_pred             CCcHHHHHHhHHhcc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHh--hCCCCCEEEEEECccccc
Confidence            689999999999999  69999999999999999999 568877765  347899999999999965

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

>cd04108 Rab36_Rab34 Rab34/Rab36 subfamily

Probab=99.68  E-value=2.5e-16  Score=91.88  Aligned_cols=67  Identities=15%  Similarity=0.285  Sum_probs=58.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      +|+++|..++..+++  +++++++|||+++++||+.+..|+.++.+.....++|+++||||+|+...+.
T Consensus        57 ~G~~~~~~~~~~~~~--~ad~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~iilVgnK~Dl~~~~~  123 (170)
T cd04108          57 AGQERFKCIASTYYR--GAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDLSSPAQ  123 (170)
T ss_pred             CChHHHHhhHHHHhc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEChhcCcccc
Confidence            688999999999999  6999999999999999999999999887644345688999999999965443

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

>cd04134 Rho3 Rho3 subfamily

Probab=99.68  E-value=1.5e-16  Score=94.03  Aligned_cols=64  Identities=23%  Similarity=0.303  Sum_probs=56.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +|++.|+.+++.|++  +++++++|||+++++||+.+. .|+..+...  .+++|+++||||+||.+.+
T Consensus        56 ~G~~~~~~l~~~~~~--~a~~~ilv~dv~~~~sf~~~~~~~~~~i~~~--~~~~piilvgNK~Dl~~~~  120 (189)
T cd04134          56 AGQEEFDRLRSLSYA--DTDVIMLCFSVDSPDSLENVESKWLGEIREH--CPGVKLVLVALKCDLREAR  120 (189)
T ss_pred             CCChhcccccccccc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEEChhhccCh
Confidence            688999999999998  699999999999999999996 699888763  4689999999999997654

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.

>cd04111 Rab39 Rab39 subfamily

Probab=99.67  E-value=2.3e-16  Score=95.02  Aligned_cols=69  Identities=25%  Similarity=0.409  Sum_probs=60.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..|++  +++++++|||+++++||+++..|+.++.+......+|+++||||+|+...+.++
T Consensus        60 ~G~~~~~~~~~~~~~--~~d~iilv~D~~~~~Sf~~l~~~~~~i~~~~~~~~~~iilvgNK~Dl~~~~~v~  128 (211)
T cd04111          60 AGQERFRSITRSYYR--NSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCDLESQRQVT  128 (211)
T ss_pred             CcchhHHHHHHHHhc--CCcEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEccccccccccC
Confidence            688999999999998  699999999999999999999999998765444568899999999998766654

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.

>cd04115 Rab33B_Rab33A Rab33B/Rab33A subfamily

Probab=99.67  E-value=2e-16  Score=91.84  Aligned_cols=69  Identities=25%  Similarity=0.354  Sum_probs=59.6

Q ss_pred             cccccch-hhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFT-NLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~-~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|+ .+.+.|++  ++|++++|||+++++||+.+..|..++.......++|+++||||+|+...++++
T Consensus        59 ~G~~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~~~~~  128 (170)
T cd04115          59 AGQERFRKSMVQHYYR--NVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQIQVP  128 (170)
T ss_pred             CChHHHHHhhHHHhhc--CCCEEEEEEECCCHHHHHhHHHHHHHHHHhcCCCCCCEEEEEECccchhhcCCC
Confidence            6788887 57888888  699999999999999999999999988875444689999999999998777654

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

>PLN03071 GTP-binding nuclear protein Ran; Provisional

Probab=99.67  E-value=2.5e-16  Score=95.33  Aligned_cols=63  Identities=21%  Similarity=0.342  Sum_probs=57.2

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+|+++|+.+++.|++  +++++|+|||+++++||+++..|+.++...  .+++|+++||||+|+..
T Consensus        69 t~G~~~~~~~~~~~~~--~~~~~ilvfD~~~~~s~~~i~~w~~~i~~~--~~~~piilvgNK~Dl~~  131 (219)
T PLN03071         69 TAGQEKFGGLRDGYYI--HGQCAIIMFDVTARLTYKNVPTWHRDLCRV--CENIPIVLCGNKVDVKN  131 (219)
T ss_pred             CCCchhhhhhhHHHcc--cccEEEEEEeCCCHHHHHHHHHHHHHHHHh--CCCCcEEEEEEchhhhh
Confidence            3789999999999999  699999999999999999999999999874  46899999999999963

>cd01871 Rac1_like Rac1-like subfamily

Probab=99.66  E-value=3.6e-16  Score=91.56  Aligned_cols=62  Identities=21%  Similarity=0.345  Sum_probs=55.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|..+++.|++  +++++|+|||+++++||+++. .|+..+...  .+++|+++||||+||.+
T Consensus        57 ~G~~~~~~~~~~~~~--~~d~~ilv~d~~~~~sf~~~~~~~~~~~~~~--~~~~piilvgnK~Dl~~  119 (174)
T cd01871          57 AGQEDYDRLRPLSYP--QTDVFLICFSLVSPASFENVRAKWYPEVRHH--CPNTPIILVGTKLDLRD  119 (174)
T ss_pred             CCchhhhhhhhhhcC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEeeChhhcc
Confidence            688999999999998  699999999999999999995 698888763  36899999999999964

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

>cd01865 Rab3 Rab3 subfamily

Probab=99.66  E-value=4.1e-16  Score=90.10  Aligned_cols=67  Identities=21%  Similarity=0.404  Sum_probs=59.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+++|..++..+++  +++++++|||+++++||+.+..|+.++.+.. ..++|+++||||+|+.+.+.+
T Consensus        58 ~g~~~~~~~~~~~~~--~~~~~l~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~piivv~nK~Dl~~~~~~  124 (165)
T cd01865          58 AGQERYRTITTAYYR--GAMGFILMYDITNEESFNAVQDWSTQIKTYS-WDNAQVILVGNKCDMEDERVV  124 (165)
T ss_pred             CChHHHHHHHHHHcc--CCcEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCCEEEEEECcccCccccc
Confidence            578899999999999  6999999999999999999999999987643 357899999999999776654

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

>cd04106 Rab23_lke Rab23-like subfamily

Probab=99.66  E-value=3.5e-16  Score=89.59  Aligned_cols=67  Identities=19%  Similarity=0.370  Sum_probs=59.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..+++.|++  +++++++|||+++++||+.+..|+..+...  ..++|+++||||+|+..++.++
T Consensus        59 ~G~~~~~~~~~~~~~--~~~~~v~v~d~~~~~s~~~l~~~~~~~~~~--~~~~p~iiv~nK~Dl~~~~~v~  125 (162)
T cd04106          59 AGQEEFDAITKAYYR--GAQACILVFSTTDRESFEAIESWKEKVEAE--CGDIPMVLVQTKIDLLDQAVIT  125 (162)
T ss_pred             CchHHHHHhHHHHhc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHh--CCCCCEEEEEEChhcccccCCC
Confidence            588999999999998  699999999999999999999999988763  4689999999999997666554

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

>cd04140 ARHI_like ARHI subfamily

Probab=99.66  E-value=5.7e-16  Score=89.48  Aligned_cols=70  Identities=21%  Similarity=0.413  Sum_probs=59.2

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC--CCCCeEEEEeeCCCCcCCCccc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY--IGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .+|+++|..++..+++  +++++++|||+++++||+++..|+..+.+...  .+++|+++||||+|+...+.+.
T Consensus        56 t~G~~~~~~~~~~~~~--~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~v~  127 (165)
T cd04140          56 TTGSHQFPAMQRLSIS--KGHAFILVYSVTSKQSLEELKPIYELICEIKGNNIEKIPIMLVGNKCDESHKREVS  127 (165)
T ss_pred             CCCCCcchHHHHHHhh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCCEEEEEECccccccCeec
Confidence            3688999999998888  59999999999999999999999887776432  2578999999999997666553

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

>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2

Probab=99.66  E-value=5.5e-16  Score=89.71  Aligned_cols=68  Identities=19%  Similarity=0.432  Sum_probs=59.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..+++  +++++++|||+++++||+.+..|+..+.+.. ..++|+++||||+|+.+.+.++
T Consensus        60 ~g~~~~~~~~~~~~~--~ad~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~p~iiv~nK~Dl~~~~~~~  127 (167)
T cd01867          60 AGQERFRTITTAYYR--GAMGIILVYDITDEKSFENIRNWMRNIEEHA-SEDVERMLVGNKCDMEEKRVVS  127 (167)
T ss_pred             CchHHHHHHHHHHhC--CCCEEEEEEECcCHHHHHhHHHHHHHHHHhC-CCCCcEEEEEECcccccccCCC
Confidence            578899999999888  6999999999999999999999999988753 4679999999999998766554

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

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

Probab=99.65  E-value=7.8e-16  Score=88.21  Aligned_cols=69  Identities=29%  Similarity=0.504  Sum_probs=60.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..+++.+++  +++++++|||++++.+|+.+..|...+.+.....++|++++|||+|+...+.++
T Consensus        58 ~G~~~~~~~~~~~~~--~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~piiiv~NK~Dl~~~~~~~  126 (164)
T cd04145          58 AGQEEFSAMREQYMR--TGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEHQRKVS  126 (164)
T ss_pred             CCCcchhHHHHHHHh--hCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCCEEEEeeCccccccceec
Confidence            688999999999998  699999999999999999999999888765445689999999999997655443

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

>cd04110 Rab35 Rab35 subfamily

Probab=99.65  E-value=6.2e-16  Score=92.14  Aligned_cols=68  Identities=19%  Similarity=0.350  Sum_probs=59.5

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .+|+++|+.++..|++  +++++++|||+++++||+.+..|+..+...  .+.+|+++||||+|+...+.++
T Consensus        62 ~~G~~~~~~~~~~~~~--~a~~iilv~D~~~~~s~~~~~~~~~~i~~~--~~~~piivVgNK~Dl~~~~~~~  129 (199)
T cd04110          62 TAGQERFRTITSTYYR--GTHGVIVVYDVTNGESFVNVKRWLQEIEQN--CDDVCKVLVGNKNDDPERKVVE  129 (199)
T ss_pred             CCCchhHHHHHHHHhC--CCcEEEEEEECCCHHHHHHHHHHHHHHHHh--CCCCCEEEEEECcccccccccC
Confidence            3688999999999999  699999999999999999999999988763  4678999999999997655543

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

>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily

Probab=99.65  E-value=7.3e-16  Score=88.86  Aligned_cols=68  Identities=22%  Similarity=0.392  Sum_probs=59.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..+++  +++++++|||+++++||..+..|+..+.... .++.|+++||||+|+...+.++
T Consensus        59 ~G~~~~~~~~~~~~~--~~~~ii~v~d~~~~~s~~~l~~~~~~~~~~~-~~~~~~iiv~nK~Dl~~~~~~~  126 (166)
T cd01869          59 AGQERFRTITSSYYR--GAHGIIIVYDVTDQESFNNVKQWLQEIDRYA-SENVNKLLVGNKCDLTDKRVVD  126 (166)
T ss_pred             CCcHhHHHHHHHHhC--cCCEEEEEEECcCHHHHHhHHHHHHHHHHhC-CCCCcEEEEEEChhcccccCCC
Confidence            688999999999999  6999999999999999999999999988753 3678999999999997665543

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

>cd01873 RhoBTB RhoBTB subfamily

Probab=99.65  E-value=5.4e-16  Score=92.60  Aligned_cols=60  Identities=17%  Similarity=0.130  Sum_probs=49.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.  .+++.|++  +++++|+|||+++++||+++. .|..++...  .+++|+++||||+||.+
T Consensus        74 aG~~~--~~~~~~~~--~ad~iilv~d~t~~~Sf~~~~~~w~~~i~~~--~~~~piilvgNK~DL~~  134 (195)
T cd01873          74 FGDHD--KDRRFAYG--RSDVVLLCFSIASPNSLRNVKTMWYPEIRHF--CPRVPVILVGCKLDLRY  134 (195)
T ss_pred             CCChh--hhhcccCC--CCCEEEEEEECCChhHHHHHHHHHHHHHHHh--CCCCCEEEEEEchhccc
Confidence            35554  35667787  699999999999999999996 699888764  36789999999999964

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.

>cd04162 Arl9_Arfrp2_like Arl9/Arfrp2-like subfamily

Probab=99.65  E-value=1.1e-15  Score=88.60  Aligned_cols=66  Identities=17%  Similarity=0.262  Sum_probs=58.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+++|+.+++.|++  +++++++|||.+++.+|..++.|+.++...  .+++|+++||||+|+...+.+
T Consensus        52 ~G~~~~~~~~~~~~~--~ad~ii~V~D~t~~~s~~~~~~~l~~~~~~--~~~~piilv~NK~Dl~~~~~~  117 (164)
T cd04162          52 GGSQNLRKYWKRYLS--GSQGLIFVVDSADSERLPLARQELHQLLQH--PPDLPLVVLANKQDLPAARSV  117 (164)
T ss_pred             CCCcchhHHHHHHHh--hCCEEEEEEECCCHHHHHHHHHHHHHHHhC--CCCCcEEEEEeCcCCcCCCCH
Confidence            688999999999999  699999999999999999999998888653  368999999999999876654

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.

>PLN03110 Rab GTPase; Provisional

Probab=99.65  E-value=6.5e-16  Score=93.25  Aligned_cols=68  Identities=21%  Similarity=0.394  Sum_probs=60.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|.++++.+++  +++++++|||++++.||+++..|+..+.... ..++|+++||||+|+...+.++
T Consensus        69 ~G~~~~~~~~~~~~~--~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~piiiv~nK~Dl~~~~~~~  136 (216)
T PLN03110         69 AGQERYRAITSAYYR--GAVGALLVYDITKRQTFDNVQRWLRELRDHA-DSNIVIMMAGNKSDLNHLRSVA  136 (216)
T ss_pred             CCcHHHHHHHHHHhC--CCCEEEEEEECCChHHHHHHHHHHHHHHHhC-CCCCeEEEEEEChhcccccCCC
Confidence            688999999999999  6999999999999999999999999888753 3679999999999998777664

>cd04143 Rhes_like Rhes_like subfamily

Probab=99.64  E-value=8.4e-16  Score=94.69  Aligned_cols=69  Identities=23%  Similarity=0.350  Sum_probs=58.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhc--------CCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSK--------YIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~--------~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|++.|..++..++.  ++|++|+|||+++++||+++..|+.++....        ...++|+++||||+|+..++++.
T Consensus        56 ~G~~~~~~~~~~~~~--~ad~iIlVfdv~~~~Sf~~i~~~~~~I~~~k~~~~~~~~~~~~~piIivgNK~Dl~~~~~v~  132 (247)
T cd04143          56 SGNHPFPAMRRLSIL--TGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKADRDFPREVQ  132 (247)
T ss_pred             CCChhhhHHHHHHhc--cCCEEEEEEeCCCHHHHHHHHHHHHHHHHhhcccccccccCCCCcEEEEEECccchhccccC
Confidence            678999999998888  5999999999999999999999998887542        23578999999999997655553

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

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=99.64  E-value=1.1e-15  Score=87.69  Aligned_cols=69  Identities=25%  Similarity=0.489  Sum_probs=59.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..+++.+++  +++++++|||+++++||+.+..|...+.+.....+.|+++||||+|+...+.++
T Consensus        56 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~pii~v~nK~Dl~~~~~~~  124 (164)
T smart00173       56 AGQEEFSAMRDQYMR--TGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLESERVVS  124 (164)
T ss_pred             CCcccchHHHHHHHh--hCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccceEc
Confidence            688999999999999  599999999999999999999999888765444578999999999997665543

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

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=99.64  E-value=1e-15  Score=87.72  Aligned_cols=68  Identities=25%  Similarity=0.393  Sum_probs=58.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCC----CCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYI----GEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~----~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+++|..+++.+++  +++++|+|||+++++||+.+..|+.++......    .+.|+++||||+|+.+++.+
T Consensus        57 ~G~~~~~~~~~~~~~--~~d~~ilv~D~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~  128 (168)
T cd04119          57 SGHPEYLEVRNEFYK--DTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLTKHRAV  128 (168)
T ss_pred             CccHHHHHHHHHHhc--cCCEEEEEEECCCHHHHHhHHHHHHHHHHhccccccCCCceEEEEEEchhccccccc
Confidence            678899999999998  699999999999999999999999998875322    56899999999999754443

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.

>KOG0393|consensus

Probab=99.64  E-value=4.2e-16  Score=93.23  Aligned_cols=63  Identities=22%  Similarity=0.367  Sum_probs=57.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|||.|..+++..|.  ++|.+++||++.+++||+++ .+|+.+++.+  ++++|+||||+|.||.+.
T Consensus        61 AGqedYDrlRplsY~--~tdvfl~cfsv~~p~S~~nv~~kW~pEi~~~--cp~vpiiLVGtk~DLr~d  124 (198)
T KOG0393|consen   61 AGQEDYDRLRPLSYP--QTDVFLLCFSVVSPESFENVKSKWIPEIKHH--CPNVPIILVGTKADLRDD  124 (198)
T ss_pred             CCCcccccccccCCC--CCCEEEEEEEcCChhhHHHHHhhhhHHHHhh--CCCCCEEEEeehHHhhhC
Confidence            499999999999888  59999999999999999998 6899999984  599999999999999843

>cd01868 Rab11_like Rab11-like

Probab=99.63  E-value=1.4e-15  Score=87.44  Aligned_cols=68  Identities=25%  Similarity=0.415  Sum_probs=59.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..+++.+++  +++++++|||++++.||+++..|+.++.+.. ..++|+++||||+|+...+.++
T Consensus        60 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~pi~vv~nK~Dl~~~~~~~  127 (165)
T cd01868          60 AGQERYRAITSAYYR--GAVGALLVYDITKKQTFENVERWLKELRDHA-DSNIVIMLVGNKSDLRHLRAVP  127 (165)
T ss_pred             CChHHHHHHHHHHHC--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCeEEEEEECccccccccCC
Confidence            578899999999998  5999999999999999999999999988753 3468999999999997666543

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

>cd04116 Rab9 Rab9 subfamily

Probab=99.63  E-value=1.4e-15  Score=88.02  Aligned_cols=67  Identities=19%  Similarity=0.309  Sum_probs=57.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC---CCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY---IGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+++|+.++..+++  +++++++|||+++++||+.+..|..++.....   ..++|+++||||+|+. .+.+
T Consensus        62 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~-~~~~  131 (170)
T cd04116          62 AGQERFRSLRTPFYR--GSDCCLLTFAVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVVLGNKNDIP-ERQV  131 (170)
T ss_pred             CChHHHHHhHHHHhc--CCCEEEEEEECCCHHHHHhHHHHHHHHHHhcccccCCCCcEEEEEECcccc-cccc
Confidence            689999999999999  69999999999999999999999988765432   2568999999999996 3443

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

>cd04128 Spg1 Spg1p

Probab=99.63  E-value=1.5e-15  Score=89.62  Aligned_cols=61  Identities=15%  Similarity=0.215  Sum_probs=53.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      +|+++|+.+++.|++  +++++++|||+++++||+++..|+.++.+.. ...+| ++||||+||.
T Consensus        57 ~G~~~~~~~~~~~~~--~a~~iilv~D~t~~~s~~~i~~~~~~~~~~~-~~~~p-ilVgnK~Dl~  117 (182)
T cd04128          57 GGQREFINMLPLVCN--DAVAILFMFDLTRKSTLNSIKEWYRQARGFN-KTAIP-ILVGTKYDLF  117 (182)
T ss_pred             CCchhHHHhhHHHCc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCE-EEEEEchhcc
Confidence            689999999999999  6999999999999999999999999987753 34567 6899999994

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

>cd01864 Rab19 Rab19 subfamily

Probab=99.63  E-value=1.7e-15  Score=87.31  Aligned_cols=67  Identities=19%  Similarity=0.416  Sum_probs=58.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+++|..++..+++  +++++++|||++++.||+.+..|+..+.... ..++|+++||||+|+...+.+
T Consensus        60 ~G~~~~~~~~~~~~~--~~d~~llv~d~~~~~s~~~~~~~~~~i~~~~-~~~~p~ivv~nK~Dl~~~~~~  126 (165)
T cd01864          60 AGQERFRTITQSYYR--SANGAIIAYDITRRSSFESVPHWIEEVEKYG-ASNVVLLLIGNKCDLEEQREV  126 (165)
T ss_pred             CChHHHHHHHHHHhc--cCCEEEEEEECcCHHHHHhHHHHHHHHHHhC-CCCCcEEEEEECccccccccc
Confidence            678999999999998  5999999999999999999999999987643 467999999999999766544

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=99.62  E-value=1.7e-15  Score=89.65  Aligned_cols=68  Identities=16%  Similarity=0.392  Sum_probs=59.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..+++  +++++|+|||+++++||+++..|+..+.... ..++|+++||||+|+..++.++
T Consensus        58 ~G~~~~~~~~~~~~~--~ad~~i~v~D~~~~~s~~~~~~~~~~i~~~~-~~~~piiiv~NK~Dl~~~~~~~  125 (191)
T cd04112          58 AGQERFRSVTHAYYR--DAHALLLLYDITNKASFDNIRAWLTEIKEYA-QEDVVIMLLGNKADMSGERVVK  125 (191)
T ss_pred             CCcHHHHHhhHHHcc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCcEEEEEEcccchhccccC
Confidence            578999999999988  6999999999999999999999999988753 3578999999999997666543

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.

>cd01866 Rab2 Rab2 subfamily

Probab=99.62  E-value=2.1e-15  Score=87.38  Aligned_cols=68  Identities=24%  Similarity=0.453  Sum_probs=59.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..+++  +++++++|||+++++||+.+..|+.+++... .+++|+++||||.|+...+.++
T Consensus        61 ~G~~~~~~~~~~~~~--~~d~il~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~pvivv~nK~Dl~~~~~~~  128 (168)
T cd01866          61 AGQESFRSITRSYYR--GAAGALLVYDITRRETFNHLTSWLEDARQHS-NSNMTIMLIGNKCDLESRREVS  128 (168)
T ss_pred             CCcHHHHHHHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCcEEEEEECcccccccCCC
Confidence            688999999999998  5999999999999999999999999988753 4689999999999997655543

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

>cd04125 RabA_like RabA-like subfamily

Probab=99.62  E-value=2.1e-15  Score=88.83  Aligned_cols=68  Identities=19%  Similarity=0.333  Sum_probs=59.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..+++.+++  +++++++|||+++++||+.+..|+.++.... ..++|+++||||+|+.+.+.++
T Consensus        57 ~g~~~~~~~~~~~~~--~~d~iilv~d~~~~~s~~~i~~~~~~i~~~~-~~~~~~ivv~nK~Dl~~~~~v~  124 (188)
T cd04125          57 NGQERFRSLNNSYYR--GAHGYLLVYDVTDQESFENLKFWINEINRYA-RENVIKVIVANKSDLVNNKVVD  124 (188)
T ss_pred             CCcHHHHhhHHHHcc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCeEEEEEECCCCcccccCC
Confidence            578889999999998  6999999999999999999999999988753 3568999999999998666553

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.

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

Probab=99.62  E-value=1.8e-15  Score=87.63  Aligned_cols=63  Identities=22%  Similarity=0.290  Sum_probs=55.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+++|..+++.+++  +++++|+|||+++++||+.+. .|+..+...  .+++|+++||||+|+...
T Consensus        54 ~G~~~~~~~~~~~~~--~~d~~ilv~d~~~~~s~~~~~~~~~~~i~~~--~~~~piilv~nK~Dl~~~  117 (174)
T smart00174       54 AGQEDYDRLRPLSYP--DTDVFLICFSVDSPASFENVKEKWYPEVKHF--CPNTPIILVGTKLDLRED  117 (174)
T ss_pred             CCCcccchhchhhcC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhh--CCCCCEEEEecChhhhhC
Confidence            688999999999988  699999999999999999995 699988764  368999999999999653

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

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

Probab=99.62  E-value=2e-15  Score=87.65  Aligned_cols=62  Identities=21%  Similarity=0.349  Sum_probs=56.3

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .+|++.|..+++.+++  ++|++|+|||+++++||++++.|+.++....  .++|+++||||+|+.
T Consensus        56 t~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~--~~~piiiv~nK~Dl~  117 (166)
T cd00877          56 TAGQEKFGGLRDGYYI--GGQCAIIMFDVTSRVTYKNVPNWHRDLVRVC--GNIPIVLCGNKVDIK  117 (166)
T ss_pred             CCCChhhccccHHHhc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhC--CCCcEEEEEEchhcc
Confidence            4688999999999998  6999999999999999999999999998753  489999999999996

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

>KOG4252|consensus

Probab=99.62  E-value=7.8e-16  Score=91.21  Aligned_cols=68  Identities=18%  Similarity=0.290  Sum_probs=61.9

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      ..|||.|..++..||+  |+++.++||+.+|+.||+.+..|..+++.  .+.++|.++|-||+||.+..+++
T Consensus        76 tagqeEfDaItkAyyr--gaqa~vLVFSTTDr~SFea~~~w~~kv~~--e~~~IPtV~vqNKIDlveds~~~  143 (246)
T KOG4252|consen   76 TAGQEEFDAITKAYYR--GAQASVLVFSTTDRYSFEATLEWYNKVQK--ETERIPTVFVQNKIDLVEDSQMD  143 (246)
T ss_pred             hccchhHHHHHHHHhc--cccceEEEEecccHHHHHHHHHHHHHHHH--HhccCCeEEeeccchhhHhhhcc
Confidence            3689999999999999  89999999999999999999999999987  46899999999999998765554

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

Probab=99.62  E-value=4.3e-15  Score=84.64  Aligned_cols=64  Identities=19%  Similarity=0.358  Sum_probs=57.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.+++.|++  +++++++|||++++.+|+.+..|+..+.+.....++|+++||||+|+..
T Consensus        57 ~G~~~~~~l~~~~~~--~~~~~i~v~~~~~~~s~~~~~~~~~~i~~~~~~~~~piivv~nK~Dl~~  120 (162)
T cd04138          57 AGQEEYSAMRDQYMR--TGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAA  120 (162)
T ss_pred             CCCcchHHHHHHHHh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccc
Confidence            688999999999999  6999999999999999999999998888754446889999999999964

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.

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

Probab=99.62  E-value=3e-15  Score=87.64  Aligned_cols=65  Identities=15%  Similarity=0.282  Sum_probs=55.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+++|+.+++.|++  +++++|+|||++++++|+.+..|+..+.+.....++|+++||||+||.+.
T Consensus        65 ~G~~~~~~~~~~~~~--~ad~ii~v~D~t~~~s~~~~~~~l~~~~~~~~~~~~piilv~NK~Dl~~~  129 (175)
T smart00177       65 GGQDKIRPLWRHYYT--NTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDA  129 (175)
T ss_pred             CCChhhHHHHHHHhC--CCCEEEEEEECCCHHHHHHHHHHHHHHhhCHhhcCCcEEEEEeCcCcccC
Confidence            688999999999999  69999999999999999999888877754322357899999999999653

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).

>cd04177 RSR1 RSR1 subgroup

Probab=99.61  E-value=2.8e-15  Score=86.78  Aligned_cols=68  Identities=29%  Similarity=0.436  Sum_probs=60.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+++|..+++.+++  +++++++|||++++++|+.+..|...+.+.....+.|++++|||.|+.+.+.+
T Consensus        57 ~G~~~~~~~~~~~~~--~~~~~vlv~~~~~~~s~~~~~~~~~~i~~~~~~~~~piiiv~nK~D~~~~~~~  124 (168)
T cd04177          57 AGTEQFTAMRELYIK--SGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLEDDRQV  124 (168)
T ss_pred             CCcccchhhhHHHHh--hCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCCEEEEEEChhccccCcc
Confidence            689999999999999  69999999999999999999999998876544568999999999999766654

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

>PLN00223 ADP-ribosylation factor; Provisional

Probab=99.61  E-value=3e-15  Score=88.22  Aligned_cols=65  Identities=18%  Similarity=0.293  Sum_probs=55.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+++|+.+++.|++  +++++|+|||++++++|..+..|+..+.+....+++|+++||||+|+...
T Consensus        69 ~Gq~~~~~~~~~~~~--~a~~iI~V~D~s~~~s~~~~~~~l~~~l~~~~~~~~piilv~NK~Dl~~~  133 (181)
T PLN00223         69 GGQDKIRPLWRHYFQ--NTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNA  133 (181)
T ss_pred             CCCHHHHHHHHHHhc--cCCEEEEEEeCCcHHHHHHHHHHHHHHhcCHhhCCCCEEEEEECCCCCCC
Confidence            689999999999999  69999999999999999999888777654323467999999999999653

>cd04103 Centaurin_gamma Centaurin gamma

Probab=99.61  E-value=1.9e-15  Score=87.44  Aligned_cols=58  Identities=21%  Similarity=0.397  Sum_probs=48.7

Q ss_pred             hhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC--CCccc
Q psy5805          14 NFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER--RRQVT   73 (75)
Q Consensus        14 ~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~--~r~v~   73 (75)
                      .|++  +++++++|||+++++||+++..|++++......+++|+++||||.||..  .+.|+
T Consensus        61 ~~~~--~~~~~ilv~d~~~~~sf~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~~~~~v~  120 (158)
T cd04103          61 QFAS--WVDAVIFVFSLENEASFQTVYNLYHQLSSYRNISEIPLILVGTQDAISESNPRVID  120 (158)
T ss_pred             hHHh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEeeHHHhhhcCCcccC
Confidence            4556  6999999999999999999999999998765446799999999999853  45554

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.

>cd04161 Arl2l1_Arl13_like Arl2l1/Arl13 subfamily

Probab=99.61  E-value=3.9e-15  Score=86.52  Aligned_cols=66  Identities=18%  Similarity=0.338  Sum_probs=58.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +|+++|+.++..|++  +++++++|||.+++.+|+.+..|+..+.+.....++|+++|+||+|+.+.+
T Consensus        51 ~G~~~~~~~~~~~~~--~a~~ii~V~D~s~~~s~~~~~~~l~~l~~~~~~~~~piliv~NK~Dl~~~~  116 (167)
T cd04161          51 GGGANFRGIWVNYYA--EAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNAL  116 (167)
T ss_pred             CCcHHHHHHHHHHHc--CCCEEEEEEECCchhHHHHHHHHHHHHHcCccccCCcEEEEEeCCCCcCCC
Confidence            688899999999998  699999999999999999999999888764334578999999999997655

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.

>cd04150 Arf1_5_like Arf1-Arf5-like subfamily

Probab=99.61  E-value=4.1e-15  Score=85.84  Aligned_cols=64  Identities=17%  Similarity=0.306  Sum_probs=54.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.+++.|++  +++++++|||.+++.||+.+..|+..+.......++|++++|||+|+..
T Consensus        52 ~G~~~~~~~~~~~~~--~ad~~i~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~  115 (159)
T cd04150          52 GGQDKIRPLWRHYFQ--NTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPN  115 (159)
T ss_pred             CCCHhHHHHHHHHhc--CCCEEEEEEeCCCHHHHHHHHHHHHHHHhcHHhcCCCEEEEEECCCCCC
Confidence            688999999999999  6999999999999999999988877765432235689999999999964

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

>cd04132 Rho4_like Rho4-like subfamily

Probab=99.61  E-value=3.8e-15  Score=87.41  Aligned_cols=63  Identities=19%  Similarity=0.249  Sum_probs=55.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+++|..+++.+++  +++++++|||+++++||+++. .|+..+...  .+++|+++||||+|+...
T Consensus        57 ~G~~~~~~~~~~~~~--~ad~ii~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~piilv~nK~Dl~~~  120 (187)
T cd04132          57 AGQEEYDRLRPLSYP--DVDVLLICYAVDNPTSLDNVEDKWFPEVNHF--CPGTPIMLVGLKTDLRKD  120 (187)
T ss_pred             CCchhHHHHHHHhCC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEeChhhhhC
Confidence            688999999999998  699999999999999999995 698887753  468999999999999653

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.

>cd04124 RabL2 RabL2 subfamily

Probab=99.60  E-value=5.1e-15  Score=85.37  Aligned_cols=61  Identities=23%  Similarity=0.402  Sum_probs=55.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      +|+++|..+++.|++  +++++++|||++++.+|+++..|+..+++.  .+++|+++||||+|+.
T Consensus        57 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~--~~~~p~ivv~nK~Dl~  117 (161)
T cd04124          57 AGQERFQTMHASYYH--KAHACILVFDVTRKITYKNLSKWYEELREY--RPEIPCIVVANKIDLD  117 (161)
T ss_pred             CCchhhhhhhHHHhC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHh--CCCCcEEEEEECccCc
Confidence            689999999999999  699999999999999999999999998763  3679999999999985

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

>cd04113 Rab4 Rab4 subfamily

Probab=99.60  E-value=4.5e-15  Score=85.10  Aligned_cols=67  Identities=24%  Similarity=0.366  Sum_probs=58.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+++|..+++.+++  +++++++|||++++.+|.++..|+.+++... .+++|+++||||.|+...+.+
T Consensus        57 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~iivv~nK~D~~~~~~~  123 (161)
T cd04113          57 AGQERFRSVTRSYYR--GAAGALLVYDITNRTSFEALPTWLSDARALA-SPNIVVILVGNKSDLADQREV  123 (161)
T ss_pred             cchHHHHHhHHHHhc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCeEEEEEEchhcchhccC
Confidence            688899999999998  6999999999999999999999999887653 478999999999999765554

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

>cd04149 Arf6 Arf6 subfamily

Probab=99.60  E-value=4.1e-15  Score=86.60  Aligned_cols=64  Identities=16%  Similarity=0.269  Sum_probs=54.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.+++.|++  +++++++|||++++.+|+++..|+.++.......++|++|||||+|+.+
T Consensus        61 ~G~~~~~~~~~~~~~--~a~~ii~v~D~t~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~  124 (168)
T cd04149          61 GGQDKIRPLWRHYYT--GTQGLIFVVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPD  124 (168)
T ss_pred             CCCHHHHHHHHHHhc--cCCEEEEEEeCCchhhHHHHHHHHHHHhcCHhhcCCcEEEEEECcCCcc
Confidence            789999999999999  6999999999999999999988877765432235789999999999964

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

>cd01892 Miro2 Miro2 subfamily

Probab=99.59  E-value=6.6e-15  Score=85.75  Aligned_cols=66  Identities=26%  Similarity=0.344  Sum_probs=56.2

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .+|++.|+.+++.|++  ++|++++|||++++.||+.+..|+..+..   ..++|+++||||+|+.+.+++
T Consensus        61 ~~g~~~~~~~~~~~~~--~~d~~llv~d~~~~~s~~~~~~~~~~~~~---~~~~p~iiv~NK~Dl~~~~~~  126 (169)
T cd01892          61 VGEDEVAILLNDAELA--ACDVACLVYDSSDPKSFSYCAEVYKKYFM---LGEIPCLFVAAKADLDEQQQR  126 (169)
T ss_pred             cCCcccccccchhhhh--cCCEEEEEEeCCCHHHHHHHHHHHHHhcc---CCCCeEEEEEEcccccccccc
Confidence            4688899999999998  69999999999999999999999887643   247999999999999655543

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.

>cd04101 RabL4 RabL4 (Rab-like4) subfamily

Probab=99.59  E-value=8.8e-15  Score=84.01  Aligned_cols=67  Identities=25%  Similarity=0.527  Sum_probs=58.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|++.|..+.+.+++  ++|++++|||+++++||+.+..|+..+....  .++|+++||||+|+...+++.
T Consensus        60 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~--~~~p~ilv~nK~Dl~~~~~~~  126 (164)
T cd04101          60 AGQELYSDMVSNYWE--SPSVFILVYDVSNKASFENCSRWVNKVRTAS--KHMPGVLVGNKMDLADKAEVT  126 (164)
T ss_pred             CCHHHHHHHHHHHhC--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhC--CCCCEEEEEECcccccccCCC
Confidence            588999999999998  5999999999999999999999999888642  578999999999997665543

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.

>cd04146 RERG_RasL11_like RERG/RasL11-like subfamily

Probab=99.59  E-value=6.4e-15  Score=84.91  Aligned_cols=69  Identities=33%  Similarity=0.426  Sum_probs=55.5

Q ss_pred             ccccc-chhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC-CCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSC-FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY-IGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~-f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++ +......+++  ++|++++|||+++++||+.+..|+..+..... ..++|+++||||+|+...+.++
T Consensus        55 ~g~~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~v~  125 (165)
T cd04146          55 AGQQQADTEQLERSIR--WADGFVLVYSITDRSSFDEISQLKQLIREIKKRDREIPVILVGNKADLLHYRQVS  125 (165)
T ss_pred             CCCcccccchHHHHHH--hCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCchHHhCccC
Confidence            46665 3455667777  59999999999999999999999988876532 4579999999999997666554

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

>cd04130 Wrch_1 Wrch-1 subfamily

Probab=99.58  E-value=6e-15  Score=85.85  Aligned_cols=62  Identities=24%  Similarity=0.411  Sum_probs=54.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|..+++.+++  +++++++|||+++++||+.+ ..|+..+...  .+++|+++||||+|+..
T Consensus        56 ~G~~~~~~~~~~~~~--~a~~~i~v~d~~~~~sf~~~~~~~~~~~~~~--~~~~piilv~nK~Dl~~  118 (173)
T cd04130          56 AGQDEFDKLRPLCYP--DTDVFLLCFSVVNPSSFQNISEKWIPEIRKH--NPKAPIILVGTQADLRT  118 (173)
T ss_pred             CCChhhccccccccC--CCcEEEEEEECCCHHHHHHHHHHHHHHHHhh--CCCCCEEEEeeChhhcc
Confidence            688999999999888  69999999999999999998 4799888753  35789999999999963

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,

>PLN03108 Rab family protein; Provisional

Probab=99.58  E-value=1e-14  Score=87.65  Aligned_cols=68  Identities=22%  Similarity=0.429  Sum_probs=59.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..+++  +++++++|||++++.||+.+..|+..+.... .+++|+++||||+|+...+.++
T Consensus        63 ~G~~~~~~~~~~~~~--~ad~~vlv~D~~~~~s~~~l~~~~~~~~~~~-~~~~piiiv~nK~Dl~~~~~~~  130 (210)
T PLN03108         63 AGQESFRSITRSYYR--GAAGALLVYDITRRETFNHLASWLEDARQHA-NANMTIMLIGNKCDLAHRRAVS  130 (210)
T ss_pred             CCcHHHHHHHHHHhc--cCCEEEEEEECCcHHHHHHHHHHHHHHHHhc-CCCCcEEEEEECccCccccCCC
Confidence            578899999999998  6999999999999999999999998877643 3679999999999998766654

>PLN03118 Rab family protein; Provisional

Probab=99.56  E-value=1.8e-14  Score=86.44  Aligned_cols=69  Identities=26%  Similarity=0.349  Sum_probs=57.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHH-HHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAED-MLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~-~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..|++  +++++++|||+++++||+.+.. |...+.......+.|+++||||+|+...+.++
T Consensus        70 ~G~~~~~~~~~~~~~--~~d~~vlv~D~~~~~sf~~~~~~~~~~~~~~~~~~~~~~ilv~NK~Dl~~~~~i~  139 (211)
T PLN03118         70 AGQERFRTLTSSYYR--NAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVDRESERDVS  139 (211)
T ss_pred             CCchhhHHHHHHHHh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccCccC
Confidence            688999999999999  6999999999999999999965 76666544333568999999999997666553

>cd04158 ARD1 ARD1 subfamily

Probab=99.56  E-value=2.1e-14  Score=83.44  Aligned_cols=64  Identities=19%  Similarity=0.254  Sum_probs=55.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.++..+++  +++++++|||.+++++|+.+..|+..+.+.....+.|+++||||+|+.+
T Consensus        51 ~G~~~~~~~~~~~~~--~ad~ii~V~D~s~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~  114 (169)
T cd04158          51 GGKHKLRPLWKHYYL--NTQAVVFVVDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAG  114 (169)
T ss_pred             CCChhcchHHHHHhc--cCCEEEEEEeCCcHHHHHHHHHHHHHHhcChhhCCCCEEEEEeCcCccc
Confidence            578899999999998  6999999999999999999999998887543345689999999999964

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

>PTZ00133 ADP-ribosylation factor; Provisional

Probab=99.56  E-value=2.3e-14  Score=84.46  Aligned_cols=64  Identities=17%  Similarity=0.298  Sum_probs=54.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.+++.|++  +++++|+|||++++++|+.+..|+.++.......++|+++||||.|+.+
T Consensus        69 ~G~~~~~~~~~~~~~--~ad~iI~v~D~t~~~s~~~~~~~l~~~~~~~~~~~~piilv~NK~Dl~~  132 (182)
T PTZ00133         69 GGQDKLRPLWRHYYQ--NTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPN  132 (182)
T ss_pred             CCCHhHHHHHHHHhc--CCCEEEEEEeCCCHHHHHHHHHHHHHHHhCHhhcCCCEEEEEeCCCCCC
Confidence            688999999999999  6999999999999999999988777665432235789999999999964

>cd04123 Rab21 Rab21 subfamily

Probab=99.55  E-value=2.7e-14  Score=81.36  Aligned_cols=67  Identities=25%  Similarity=0.439  Sum_probs=58.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|++.|..+++.+++  +++++++|||++++++|+.+..|..++.... ..++|+++|+||+|+...+++
T Consensus        57 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~piiiv~nK~D~~~~~~~  123 (162)
T cd04123          57 AGQERYHALGPIYYR--DADGAILVYDITDADSFQKVKKWIKELKQMR-GNNISLVIVGNKIDLERQRVV  123 (162)
T ss_pred             CchHHHHHhhHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCeEEEEEECcccccccCC
Confidence            678899999999988  6999999999999999999999999988754 247999999999999765554

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

>cd01861 Rab6 Rab6 subfamily

Probab=99.54  E-value=3.4e-14  Score=81.27  Aligned_cols=68  Identities=26%  Similarity=0.570  Sum_probs=58.0

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .+|+++|..+.+.+++  +++++++|||+++++||+.+..|+..+.... ..++|+++||||+|+.+.+.+
T Consensus        56 ~~G~~~~~~~~~~~~~--~~~~ii~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~iilv~nK~D~~~~~~~  123 (161)
T cd01861          56 TAGQERFRSLIPSYIR--DSSVAVVVYDITNRQSFDNTDKWIDDVRDER-GNDVIIVLVGNKTDLSDKRQV  123 (161)
T ss_pred             CCCcHHHHHHHHHHhc--cCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCEEEEEEEChhccccCcc
Confidence            3688999999999998  5999999999999999999999999887643 347999999999999655543

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

>cd04118 Rab24 Rab24 subfamily

Probab=99.53  E-value=6e-14  Score=82.77  Aligned_cols=62  Identities=15%  Similarity=0.275  Sum_probs=55.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|..++..+++  +++++++|||++++.||+++..|+..+...  .+++|+++||||+|+..
T Consensus        58 ~G~~~~~~~~~~~~~--~~d~iilv~d~~~~~s~~~~~~~~~~i~~~--~~~~piilv~nK~Dl~~  119 (193)
T cd04118          58 AGSERYEAMSRIYYR--GAKAAIVCYDLTDSSSFERAKFWVKELQNL--EEHCKIYLCGTKSDLIE  119 (193)
T ss_pred             CCchhhhhhhHhhcC--CCCEEEEEEECCCHHHHHHHHHHHHHHHhc--CCCCCEEEEEEcccccc
Confidence            578899999999888  699999999999999999999999998764  35799999999999853

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

>smart00175 RAB Rab subfamily of small GTPases

Probab=99.52  E-value=5.4e-14  Score=80.44  Aligned_cols=67  Identities=27%  Similarity=0.456  Sum_probs=58.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+++|..++..+++  ++|++++|||++++.+|+.+..|+..+.... .+++|+++|+||+|+...+++
T Consensus        57 ~G~~~~~~~~~~~~~--~~d~~ilv~d~~~~~s~~~~~~~l~~~~~~~-~~~~pivvv~nK~D~~~~~~~  123 (164)
T smart00175       57 AGQERFRSITSSYYR--GAVGALLVYDITNRESFENLKNWLKELREYA-DPNVVIMLVGNKSDLEDQRQV  123 (164)
T ss_pred             CChHHHHHHHHHHhC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCeEEEEEEchhcccccCC
Confidence            678889999999998  6999999999999999999999999887754 368999999999999765443

Rab GTPases are implicated in vesicle trafficking.

>cd01860 Rab5_related Rab5-related subfamily

Probab=99.52  E-value=6.9e-14  Score=80.12  Aligned_cols=68  Identities=28%  Similarity=0.447  Sum_probs=58.7

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .+|+++|...++.+++  +++++++|||.+++++|+.+..|+..+.... .+.+|+++++||+|+...+.+
T Consensus        57 ~~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~iivv~nK~D~~~~~~~  124 (163)
T cd01860          57 TAGQERYRSLAPMYYR--GAAAAIVVYDITSEESFEKAKSWVKELQRNA-SPNIIIALVGNKADLESKRQV  124 (163)
T ss_pred             CCchHHHHHHHHHHhc--cCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCeEEEEEECccccccCcC
Confidence            3678899999998888  6999999999999999999999999988754 367999999999999755443

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

>cd04114 Rab30 Rab30 subfamily

Probab=99.51  E-value=8.2e-14  Score=80.30  Aligned_cols=68  Identities=21%  Similarity=0.417  Sum_probs=58.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|++.|...+..+++  +++++++|||+++++||+.+..|+.++.... ..++|+++||||+|+...+++.
T Consensus        64 ~g~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~l~~~~-~~~~~~i~v~NK~D~~~~~~i~  131 (169)
T cd04114          64 AGQERFRSITQSYYR--SANALILTYDITCEESFRCLPEWLREIEQYA-NNKVITILVGNKIDLAERREVS  131 (169)
T ss_pred             CCcHHHHHHHHHHhc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCeEEEEEECcccccccccC
Confidence            578889988888888  5999999999999999999999998887653 3579999999999997666543

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.

>cd04147 Ras_dva Ras-dva subfamily

Probab=99.51  E-value=1.3e-13  Score=82.07  Aligned_cols=64  Identities=25%  Similarity=0.364  Sum_probs=56.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.|..++..+++  +++++++|||++++.+|+.+..|+..+.......++|+++|+||.|+..
T Consensus        55 ~G~~~~~~~~~~~~~--~ad~vilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~NK~Dl~~  118 (198)
T cd04147          55 SGSYSFPAMRKLSIQ--NSDAFALVYAVDDPESFEEVERLREEILEVKEDKFVPIVVVGNKADSLE  118 (198)
T ss_pred             CCchhhhHHHHHHhh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEEcccccc
Confidence            578899999999888  6999999999999999999999998887764446799999999999954

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.

>cd04154 Arl2 Arl2 subfamily

Probab=99.51  E-value=1.1e-13  Score=80.50  Aligned_cols=65  Identities=18%  Similarity=0.310  Sum_probs=55.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|++.|+.++..|++  +++++++|||.+++.+|..+..|+..+.......++|+++||||+|+.+.
T Consensus        66 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~  130 (173)
T cd04154          66 GGQKTLRPYWRNYFE--STDALIWVVDSSDRLRLDDCKRELKELLQEERLAGATLLILANKQDLPGA  130 (173)
T ss_pred             CCCHHHHHHHHHHhC--CCCEEEEEEECCCHHHHHHHHHHHHHHHhChhhcCCCEEEEEECcccccC
Confidence            588899999999988  69999999999999999999888877754333467999999999999643

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.

>cd04148 RGK RGK subfamily

Probab=99.51  E-value=8.8e-14  Score=84.33  Aligned_cols=62  Identities=35%  Similarity=0.611  Sum_probs=50.9

Q ss_pred             hhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805          11 LVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus        11 ~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +...++++ ++|++++|||++++.||+.+..|+..+.+.....++|+++||||+|+...+.|+
T Consensus        64 ~~~~~~~~-~ad~iilV~d~td~~S~~~~~~~~~~l~~~~~~~~~piilV~NK~Dl~~~~~v~  125 (221)
T cd04148          64 TEDSCMQY-QGDAFVVVYSVTDRSSFERASELRIQLRRNRQLEDRPIILVGNKSDLARSREVS  125 (221)
T ss_pred             HHhHHhhc-CCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEChhccccceec
Confidence            44455542 599999999999999999999999988775444689999999999997777664

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

>cd01863 Rab18 Rab18 subfamily

Probab=99.49  E-value=1.9e-13  Score=78.26  Aligned_cols=63  Identities=27%  Similarity=0.368  Sum_probs=56.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      +|++.|..+...+++  +++++++|||++++.||+.+..|+..+.......++|+++||||+|+.
T Consensus        57 ~g~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~iv~nK~D~~  119 (161)
T cd01863          57 AGQERFRTLTSSYYR--GAQGVILVYDVTRRDTFTNLETWLNELETYSTNNDIVKMLVGNKIDKE  119 (161)
T ss_pred             CCchhhhhhhHHHhC--CCCEEEEEEECCCHHHHHhHHHHHHHHHHhCCCCCCcEEEEEECCccc
Confidence            578888888888888  699999999999999999999999988876555789999999999996

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

>cd04142 RRP22 RRP22 subfamily

Probab=99.48  E-value=1.6e-13  Score=82.05  Aligned_cols=54  Identities=20%  Similarity=0.429  Sum_probs=46.2

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhc--CCCCCeEEEEeeCCCCcCCCccc
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSK--YIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~--~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      ++|++++|||+++++||+.+..|+..+.+..  ...++|+++||||+|+...+.++
T Consensus        80 ~ad~iilv~D~~~~~S~~~~~~~~~~i~~~~~~~~~~~piiivgNK~Dl~~~~~~~  135 (198)
T cd04142          80 NSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQRHRFAP  135 (198)
T ss_pred             cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcccCCCCCCEEEEEECcccccccccc
Confidence            6999999999999999999999998887653  24679999999999997665543

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.

>cd04157 Arl6 Arl6 subfamily

Probab=99.48  E-value=3.4e-13  Score=77.07  Aligned_cols=65  Identities=18%  Similarity=0.234  Sum_probs=55.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC--CCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY--IGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+++|+.+++.|++  +++++++|+|.+++.+|..+..|+..+.+...  ..++|+++|+||+|+.+.
T Consensus        53 ~G~~~~~~~~~~~~~--~~d~ii~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~iiv~NK~Dl~~~  119 (162)
T cd04157          53 SGQGKYRGLWEHYYK--NIQGIIFVIDSSDRLRLVVVKDELELLLNHPDIKHRRVPILFFANKMDLPDA  119 (162)
T ss_pred             CCCHhhHHHHHHHHc--cCCEEEEEEeCCcHHHHHHHHHHHHHHHcCcccccCCCCEEEEEeCccccCC
Confidence            688999999999998  69999999999999999999999888765321  247999999999999653

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

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=99.47  E-value=3e-13  Score=77.24  Aligned_cols=66  Identities=21%  Similarity=0.415  Sum_probs=57.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .|++.|..+++.+++  ++++++++||+++++||+++..|...+.......++|+++|+||+|+...+
T Consensus        56 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piiiv~NK~D~~~~~  121 (164)
T cd04139          56 AGQEDYAAIRDNYHR--SGEGFLLVFSITDMESFTATAEFREQILRVKDDDNVPLLLVGNKCDLEDKR  121 (164)
T ss_pred             CChhhhhHHHHHHhh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEcccccccc
Confidence            578899999999998  699999999999999999999999888875444689999999999996533

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

>cd01862 Rab7 Rab7 subfamily

Probab=99.47  E-value=2.9e-13  Score=77.98  Aligned_cols=66  Identities=26%  Similarity=0.387  Sum_probs=55.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC---CCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY---IGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +|++.|..++..+++  +++++|++||++++.+|+++..|...+.....   ..++|+++||||+|+...+
T Consensus        57 ~g~~~~~~~~~~~~~--~~d~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~  125 (172)
T cd01862          57 AGQERFQSLGVAFYR--GADCCVLVYDVTNPKSFESLDSWRDEFLIQASPSDPENFPFVVLGNKIDLEEKR  125 (172)
T ss_pred             CChHHHHhHHHHHhc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCccCCCCceEEEEEECccccccc
Confidence            578899999999998  69999999999999999999999887655322   2378999999999997433

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-

>cd01893 Miro1 Miro1 subfamily

Probab=99.47  E-value=3.6e-13  Score=77.91  Aligned_cols=65  Identities=23%  Similarity=0.249  Sum_probs=53.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      +|++.++.....+++  +++++++|||+++++||+.+. .|...++..  ..++|+++||||+|+.+.+.
T Consensus        55 ~G~~~~~~~~~~~~~--~ad~~ilv~d~~~~~s~~~~~~~~~~~i~~~--~~~~pviiv~nK~Dl~~~~~  120 (166)
T cd01893          55 SSRPQDRANLAAEIR--KANVICLVYSVDRPSTLERIRTKWLPLIRRL--GVKVPIILVGNKSDLRDGSS  120 (166)
T ss_pred             CCchhhhHHHhhhcc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEEchhcccccc
Confidence            567777777677776  699999999999999999985 688888764  35799999999999976543

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.

>cd04152 Arl4_Arl7 Arl4/Arl7 subfamily

Probab=99.47  E-value=3.4e-13  Score=79.36  Aligned_cols=64  Identities=19%  Similarity=0.223  Sum_probs=55.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.+++.+++  +++++++|||.+++++++.+..|+.++.......+.|+++|+||+|+..
T Consensus        60 ~G~~~~~~~~~~~~~--~~d~ii~v~D~~~~~~~~~~~~~~~~i~~~~~~~~~p~iiv~NK~D~~~  123 (183)
T cd04152          60 GGQEKLRPLWKSYTR--CTDGIVFVVDSVDVERMEEAKTELHKITRFSENQGVPVLVLANKQDLPN  123 (183)
T ss_pred             CCcHhHHHHHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHhhhhcCCCcEEEEEECcCccc
Confidence            688999999999998  6999999999999999999999988877643345789999999999864

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.

>cd04135 Tc10 TC10 subfamily

Probab=99.47  E-value=2.5e-13  Score=78.67  Aligned_cols=62  Identities=21%  Similarity=0.333  Sum_probs=54.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.|..+++.+++  +++++++|||+++++||+.+. .|...+...  .+++|+++||||+|+.+
T Consensus        56 ~G~~~~~~~~~~~~~--~~~~~ilv~~~~~~~s~~~~~~~~~~~l~~~--~~~~piivv~nK~Dl~~  118 (174)
T cd04135          56 AGQEDYDRLRPLSYP--MTDVFLICFSVVNPASFQNVKEEWVPELKEY--APNVPYLLVGTQIDLRD  118 (174)
T ss_pred             CCcccccccccccCC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhh--CCCCCEEEEeEchhhhc
Confidence            688899999999888  699999999999999999995 788888764  47899999999999854

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

>cd01870 RhoA_like RhoA-like subfamily

Probab=99.45  E-value=3.5e-13  Score=78.09  Aligned_cols=62  Identities=18%  Similarity=0.224  Sum_probs=53.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.|+.+++.+++  +++++++|||+++++||+++. .|...+...  .+++|+++||||+|+..
T Consensus        57 ~G~~~~~~~~~~~~~--~~d~~i~v~~~~~~~s~~~~~~~~~~~~~~~--~~~~piilv~nK~Dl~~  119 (175)
T cd01870          57 AGQEDYDRLRPLSYP--DTDVILMCFSIDSPDSLENIPEKWTPEVKHF--CPNVPIILVGNKKDLRN  119 (175)
T ss_pred             CCchhhhhccccccC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhh--CCCCCEEEEeeChhccc
Confidence            688889888888887  699999999999999999995 688888763  36899999999999864

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

>cd04153 Arl5_Arl8 Arl5/Arl8 subfamily

Probab=99.45  E-value=5.8e-13  Score=77.73  Aligned_cols=64  Identities=14%  Similarity=0.288  Sum_probs=54.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.+++.+++  +++++++|+|.+++++|..+..|+..+.+.....++|+++++||+|+.+
T Consensus        67 ~G~~~~~~~~~~~~~--~~d~vi~V~D~s~~~~~~~~~~~l~~~~~~~~~~~~p~viv~NK~Dl~~  130 (174)
T cd04153          67 GGQESLRSSWNTYYT--NTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKG  130 (174)
T ss_pred             CCCHHHHHHHHHHhh--cCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhcCCCEEEEEECCCCCC
Confidence            688899999999888  6999999999999999999988777765533345789999999999864

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.

>cd04129 Rho2 Rho2 subfamily

Probab=99.44  E-value=3.6e-13  Score=79.45  Aligned_cols=62  Identities=18%  Similarity=0.214  Sum_probs=52.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|++.|..+.+.+++  ++++++++||+++++||+.+. .|+..+...  .+++|+++||||+|+..
T Consensus        57 ~g~~~~~~~~~~~~~--~a~~~llv~~i~~~~s~~~~~~~~~~~i~~~--~~~~piilvgnK~Dl~~  119 (187)
T cd04129          57 AGQEEYERLRPLSYS--KAHVILIGFAVDTPDSLENVRTKWIEEVRRY--CPNVPVILVGLKKDLRQ  119 (187)
T ss_pred             CCChhccccchhhcC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEeeChhhhh
Confidence            467788777777777  699999999999999999996 699988764  35799999999999853

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).

>cd04156 ARLTS1 ARLTS1 subfamily

Probab=99.44  E-value=7.8e-13  Score=75.62  Aligned_cols=64  Identities=20%  Similarity=0.297  Sum_probs=54.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.|..++..+++  +++++++|+|.+++.+|..+..|+.++.......+.|+++|+||+|+..
T Consensus        52 ~G~~~~~~~~~~~~~--~~~~iv~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~  115 (160)
T cd04156          52 GGQEKMRTVWKCYLE--NTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPG  115 (160)
T ss_pred             CCCHhHHHHHHHHhc--cCCEEEEEEECCcHHHHHHHHHHHHHHHhchhhcCCCEEEEEECccccc
Confidence            578888888888888  6999999999999999999998888776543336799999999999853

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

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

Probab=99.44  E-value=5.4e-13  Score=77.77  Aligned_cols=68  Identities=26%  Similarity=0.401  Sum_probs=57.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+++|+.+.+.++.  ++++++++||+++..+|+.+..|+..+.+.....+.|+++|+||+|+...+.+
T Consensus        57 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~NK~Dl~~~~~~  124 (180)
T cd04137          57 AGQDEYSILPQKYSI--GIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHTQRQV  124 (180)
T ss_pred             CChHhhHHHHHHHHh--hCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEchhhhhcCcc
Confidence            578889989888888  59999999999999999999998887776433457899999999999755443

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

>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=99.43  E-value=5.9e-13  Score=73.12  Aligned_cols=59  Identities=22%  Similarity=0.362  Sum_probs=44.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHH---HHHHHHhhcCCCCCeEEEEeeCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAED---MLKTLWDSKYIGEKAVILVANKAD   65 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~---~~~~~~~~~~~~~~~~ilvgnK~D   65 (75)
                      +|++.+......+..  +++++++|||++++.||+.+.+   |+..+...  .+++|+++||||.|
T Consensus        58 ~g~~~~~~~~~~~~~--~~d~~ilv~D~s~~~s~~~~~~~~~~l~~~~~~--~~~~piilv~nK~D  119 (119)
T PF08477_consen   58 GGQEEFYSQHQFFLK--KADAVILVYDLSDPESLEYLSQLLKWLKNIRKR--DKNIPIILVGNKSD  119 (119)
T ss_dssp             SSSHCHHCTSHHHHH--HSCEEEEEEECCGHHHHHHHHHHHHHHHHHHHH--SSCSEEEEEEE-TC
T ss_pred             Cccceecccccchhh--cCcEEEEEEcCCChHHHHHHHHHHHHHHHHHcc--CCCCCEEEEEeccC
Confidence            355666665555566  4999999999999999999855   55555542  46799999999998

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.

>cd00876 Ras Ras family

Probab=99.42  E-value=1.1e-12  Score=74.57  Aligned_cols=68  Identities=28%  Similarity=0.499  Sum_probs=57.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|++.+..++..+++  +++++++|||++++++++++..|...+.+......+|+++|+||+|+...+.+
T Consensus        55 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~~~~~  122 (160)
T cd00876          55 AGQEEFSAMRDLYIR--QGDGFILVYSITDRESFEEIKGYREQILRVKDDEDIPIVLVGNKCDLENERQV  122 (160)
T ss_pred             CChHHHHHHHHHHHh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECCccccccee
Confidence            577888888888888  69999999999999999999999888877543358999999999999764443

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

>cd04151 Arl1 Arl1 subfamily

Probab=99.42  E-value=1.5e-12  Score=74.59  Aligned_cols=64  Identities=14%  Similarity=0.280  Sum_probs=52.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.|+.++..|++  +++++++|+|.+++.++.....|+..+.+.....+.|+++|+||+|+.+
T Consensus        51 ~G~~~~~~~~~~~~~--~~~~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~piiiv~nK~Dl~~  114 (158)
T cd04151          51 GGQTSIRPYWRCYYS--NTDAIIYVVDSTDRDRLGTAKEELHAMLEEEELKGAVLLVFANKQDMPG  114 (158)
T ss_pred             CCCHHHHHHHHHHhc--CCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhcCCcEEEEEeCCCCCC
Confidence            688899999999998  6999999999999999988766665543322235789999999999964

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.

>PTZ00132 GTP-binding nuclear protein Ran; Provisional

Probab=99.41  E-value=1.7e-12  Score=78.02  Aligned_cols=62  Identities=19%  Similarity=0.328  Sum_probs=55.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|..++..|++  +++++++|||++++.||..+..|+..+...  .+++|++++|||+|+.+
T Consensus        66 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~--~~~~~i~lv~nK~Dl~~  127 (215)
T PTZ00132         66 AGQEKFGGLRDGYYI--KGQCAIIMFDVTSRITYKNVPNWHRDIVRV--CENIPIVLVGNKVDVKD  127 (215)
T ss_pred             CCchhhhhhhHHHhc--cCCEEEEEEECcCHHHHHHHHHHHHHHHHh--CCCCCEEEEEECccCcc
Confidence            578899999999988  599999999999999999999999988864  36799999999999864

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

Probab=99.40  E-value=1.4e-12  Score=76.93  Aligned_cols=64  Identities=13%  Similarity=0.224  Sum_probs=54.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++++.++..|+.  +++++++|+|.+++++|.....|+.++.+.....++|+++|+||+|+..
T Consensus        69 ~G~~~~~~~~~~~~~--~ad~ii~vvD~~~~~~~~~~~~~l~~l~~~~~~~~~piliv~NK~Dl~~  132 (184)
T smart00178       69 GGHQQARRLWKDYFP--EVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPY  132 (184)
T ss_pred             CCCHHHHHHHHHHhC--CCCEEEEEEECCcHHHHHHHHHHHHHHHcChhhcCCCEEEEEeCccccC
Confidence            688889999999998  6999999999999999999988887776432336789999999999864

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

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

Probab=99.40  E-value=2.5e-12  Score=73.49  Aligned_cols=66  Identities=17%  Similarity=0.277  Sum_probs=56.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +|++.|..++..+++  +++++++|||++++++|..+..|+..+.......+.|+++|+||+|+...+
T Consensus        51 ~G~~~~~~~~~~~~~--~~~~~i~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~piiiv~nK~D~~~~~  116 (158)
T cd00878          51 GGQDKIRPLWKHYYE--NTNGIIFVVDSSDRERIEEAKEELHKLLNEEELKGVPLLIFANKQDLPGAL  116 (158)
T ss_pred             CCChhhHHHHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHhCcccCCCcEEEEeeccCCcccc
Confidence            578889989998888  599999999999999999998888877654334688999999999997533

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

>TIGR00157 ribosome small subunit-dependent GTPase A

Probab=99.38  E-value=5.3e-13  Score=82.24  Aligned_cols=62  Identities=23%  Similarity=0.223  Sum_probs=53.6

Q ss_pred             cccchhhhhhhhhccCCcEEEEEEECCChh-HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           5 TSCFTNLVVNFVQTYHPDVFVIVYSVIERK-TFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .|+|..+.+.|++  |+|++++|||++++. ||+.+.+|+..+..    .++|+++|+||+||.+.+++
T Consensus        23 ~eR~~~L~r~~~~--n~D~viiV~d~~~p~~s~~~l~r~l~~~~~----~~i~~vIV~NK~DL~~~~~~   85 (245)
T TIGR00157        23 AERKNELTRPIVA--NIDQIVIVSSAVLPELSLNQLDRFLVVAEA----QNIEPIIVLNKIDLLDDEDM   85 (245)
T ss_pred             ecccceEECcccc--cCCEEEEEEECCCCCCCHHHHHHHHHHHHH----CCCCEEEEEECcccCCCHHH
Confidence            4889999999999  799999999999988 99999999976653    56899999999999765544

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

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=99.38  E-value=3e-12  Score=73.61  Aligned_cols=64  Identities=16%  Similarity=0.316  Sum_probs=55.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|++.|..++..+++  +++++++|+|.++++++..+..|+..+.+.....++|+++++||+|+..
T Consensus        58 ~G~~~~~~~~~~~~~--~~~~~v~vvd~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~NK~D~~~  121 (167)
T cd04160          58 GGQESLRSLWDKYYA--ECHAIIYVIDSTDRERFEESKSALEKVLRNEALEGVPLLILANKQDLPD  121 (167)
T ss_pred             CCChhhHHHHHHHhC--CCCEEEEEEECchHHHHHHHHHHHHHHHhChhhcCCCEEEEEEcccccc
Confidence            588899999888888  6999999999999999999998988876643346799999999999864

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.

>cd00879 Sar1 Sar1 subfamily

Probab=99.37  E-value=3.8e-12  Score=74.84  Aligned_cols=64  Identities=16%  Similarity=0.293  Sum_probs=54.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.++..|++  +++++++|+|.+++.+|.....|+.++.+.....+.|+++++||+|+..
T Consensus        71 ~G~~~~~~~~~~~~~--~ad~iilV~D~~~~~s~~~~~~~~~~i~~~~~~~~~pvivv~NK~Dl~~  134 (190)
T cd00879          71 GGHEQARRLWKDYFP--EVDGIVFLVDAADPERFQESKEELDSLLSDEELANVPFLILGNKIDLPG  134 (190)
T ss_pred             CCCHHHHHHHHHHhc--cCCEEEEEEECCcHHHHHHHHHHHHHHHcCccccCCCEEEEEeCCCCCC
Confidence            578888888888888  6999999999999999999988888876543345789999999999863

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.

>KOG3883|consensus

Probab=99.35  E-value=3.3e-12  Score=74.21  Aligned_cols=63  Identities=30%  Similarity=0.463  Sum_probs=51.6

Q ss_pred             hhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           9 TNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         9 ~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      ..+...|++.  +||+++|||..|++||+.+.-..+++....+...+||++.|||+|+.+.++|.
T Consensus        75 ~eLprhy~q~--aDafVLVYs~~d~eSf~rv~llKk~Idk~KdKKEvpiVVLaN~rdr~~p~~vd  137 (198)
T KOG3883|consen   75 QELPRHYFQF--ADAFVLVYSPMDPESFQRVELLKKEIDKHKDKKEVPIVVLANKRDRAEPREVD  137 (198)
T ss_pred             hhhhHhHhcc--CceEEEEecCCCHHHHHHHHHHHHHHhhccccccccEEEEechhhcccchhcC
Confidence            4566778885  99999999999999999876655555555556789999999999998887764

>cd00157 Rho Rho (Ras homology) family

Probab=99.35  E-value=3.5e-12  Score=73.41  Aligned_cols=64  Identities=22%  Similarity=0.312  Sum_probs=53.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +|++.|..+++.+++  +++++++|||++++.||... ..|+..+...  ..+.|+++||||+|+...+
T Consensus        56 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~p~ivv~nK~Dl~~~~  120 (171)
T cd00157          56 AGQEEYDRLRPLSYP--NTDVFLICFSVDSPSSFENVKTKWIPEIRHY--CPNVPIILVGTKIDLRDDE  120 (171)
T ss_pred             CCcccccccchhhcC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhh--CCCCCEEEEEccHHhhhch
Confidence            578888888888888  59999999999999999987 5688877763  3589999999999996544

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

>cd04159 Arl10_like Arl10-like subfamily

Probab=99.33  E-value=1.1e-11  Score=70.01  Aligned_cols=66  Identities=17%  Similarity=0.292  Sum_probs=55.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +|++.|+.++..+++  +++++++|+|++++.++.....|+..+.......++|+++|+||+|+.+..
T Consensus        52 ~g~~~~~~~~~~~~~--~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~p~iiv~nK~D~~~~~  117 (159)
T cd04159          52 GGQPRFRSMWERYCR--GVNAIVYVVDAADRTALEAAKNELHDLLEKPSLEGIPLLVLGNKNDLPGAL  117 (159)
T ss_pred             CCCHhHHHHHHHHHh--cCCEEEEEEECCCHHHHHHHHHHHHHHHcChhhcCCCEEEEEeCccccCCc
Confidence            578889999899888  599999999999999999988887776653334578999999999986543

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.

>cd00154 Rab Rab family

Probab=99.32  E-value=9.4e-12  Score=70.12  Aligned_cols=62  Identities=26%  Similarity=0.445  Sum_probs=54.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      +|++.|..+...+++  +++++++|||++++++++.+..|+..+.... ..+.|+++++||+|+.
T Consensus        57 ~g~~~~~~~~~~~~~--~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~-~~~~p~ivv~nK~D~~  118 (159)
T cd00154          57 AGQERFRSITPSYYR--GAHGAILVYDITNRESFENLDKWLKELKEYA-PENIPIILVGNKIDLE  118 (159)
T ss_pred             CChHHHHHHHHHHhc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCcEEEEEEccccc
Confidence            577888888888888  6999999999999999999999999888743 3678999999999996

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

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

Probab=99.32  E-value=7.1e-12  Score=74.99  Aligned_cols=65  Identities=20%  Similarity=0.294  Sum_probs=55.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC-hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE-RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~-~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .|+++|+.+++.|++  ++++++++||.++ ..+++....|..++.... ....|+++||||+||...+
T Consensus        62 ~gq~~~~~~~~~y~~--~~~~~l~~~d~~~~~~~~~~~~~~~~~l~~~~-~~~~~iilv~nK~Dl~~~~  127 (219)
T COG1100          62 AGQEEYRSLRPEYYR--GANGILIVYDSTLRESSDELTEEWLEELRELA-PDDVPILLVGNKIDLFDEQ  127 (219)
T ss_pred             CCHHHHHHHHHHHhc--CCCEEEEEEecccchhhhHHHHHHHHHHHHhC-CCCceEEEEecccccccch
Confidence            589999999999999  7999999999999 555566689999988753 2579999999999998764

>KOG0070|consensus

Probab=99.30  E-value=1.1e-11  Score=73.22  Aligned_cols=67  Identities=16%  Similarity=0.268  Sum_probs=59.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      +||++++.+++.||+  +.+++|+|.|-+|++.+...+.-+..+......+++|+++.+||.|+.+...
T Consensus        69 GGq~k~R~lW~~Y~~--~t~~lIfVvDS~Dr~Ri~eak~eL~~~l~~~~l~~~~llv~aNKqD~~~als  135 (181)
T KOG0070|consen   69 GGQEKLRPLWKHYFQ--NTQGLIFVVDSSDRERIEEAKEELHRMLAEPELRNAPLLVFANKQDLPGALS  135 (181)
T ss_pred             CCCcccccchhhhcc--CCcEEEEEEeCCcHHHHHHHHHHHHHHHcCcccCCceEEEEechhhccccCC
Confidence            799999999999999  6999999999999999999988777777665567999999999999986554

>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=99.29  E-value=2.7e-11  Score=71.15  Aligned_cols=64  Identities=22%  Similarity=0.386  Sum_probs=56.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.++.+++.|++  +++++|+|.|.++++.+......+..+.......++|+++++||+|+.+
T Consensus        66 gG~~~~~~~w~~y~~--~~~~iIfVvDssd~~~l~e~~~~L~~ll~~~~~~~~piLIl~NK~D~~~  129 (175)
T PF00025_consen   66 GGQESFRPLWKSYFQ--NADGIIFVVDSSDPERLQEAKEELKELLNDPELKDIPILILANKQDLPD  129 (175)
T ss_dssp             SSSGGGGGGGGGGHT--TESEEEEEEETTGGGGHHHHHHHHHHHHTSGGGTTSEEEEEEESTTSTT
T ss_pred             cccccccccceeecc--ccceeEEEEecccceeecccccchhhhcchhhcccceEEEEeccccccC
Confidence            688999999999999  6999999999999999999988887777654456899999999999875

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 ....

>KOG0096|consensus

Probab=99.29  E-value=2.6e-12  Score=76.55  Aligned_cols=62  Identities=18%  Similarity=0.242  Sum_probs=56.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+|.|..++.-||-  ++.+.|++||++.+-++.++.+|..++...  +.++||+++|||.|...
T Consensus        67 agqEk~gglrdgyyI--~~qcAiimFdVtsr~t~~n~~rwhrd~~rv--~~NiPiv~cGNKvDi~~  128 (216)
T KOG0096|consen   67 AGQEKKGGLRDGYYI--QGQCAIIMFDVTSRFTYKNVPRWHRDLVRV--RENIPIVLCGNKVDIKA  128 (216)
T ss_pred             ccceeecccccccEE--ecceeEEEeeeeehhhhhcchHHHHHHHHH--hcCCCeeeeccceeccc
Confidence            589999999999998  499999999999999999999999999874  57899999999999864

>cd01890 LepA LepA subfamily

Probab=99.16  E-value=1.9e-10  Score=66.78  Aligned_cols=59  Identities=15%  Similarity=0.110  Sum_probs=48.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|++.|..+...+++  ++|++|+|||.++..++..+..|.....     .++|+++|+||+|+.+
T Consensus        75 ~G~~~~~~~~~~~~~--~ad~~i~v~D~~~~~~~~~~~~~~~~~~-----~~~~iiiv~NK~Dl~~  133 (179)
T cd01890          75 PGHVDFSYEVSRSLA--ACEGALLLVDATQGVEAQTLANFYLALE-----NNLEIIPVINKIDLPS  133 (179)
T ss_pred             CCChhhHHHHHHHHH--hcCeEEEEEECCCCccHhhHHHHHHHHH-----cCCCEEEEEECCCCCc
Confidence            578899999888888  6999999999999888877777753321     4579999999999864

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.

>cd04155 Arl3 Arl3 subfamily

Probab=99.15  E-value=3.2e-10  Score=65.57  Aligned_cols=64  Identities=20%  Similarity=0.335  Sum_probs=52.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.|...+..+++  +++++++|+|.++..+|.....|+..+.......++|+++++||+|+.+
T Consensus        66 ~G~~~~~~~~~~~~~--~~~~ii~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~  129 (173)
T cd04155          66 GGQRAIRPYWRNYFE--NTDCLIYVIDSADKKRLEEAGAELVELLEEEKLAGVPVLVFANKQDLAT  129 (173)
T ss_pred             CCCHHHHHHHHHHhc--CCCEEEEEEeCCCHHHHHHHHHHHHHHHhChhhcCCCEEEEEECCCCcc
Confidence            567778888888887  6999999999999999999887776665433335799999999999864

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.

>KOG4423|consensus

Probab=99.14  E-value=1.4e-11  Score=73.45  Aligned_cols=64  Identities=22%  Similarity=0.256  Sum_probs=56.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhh---cCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDS---KYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~---~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|||+|..|+..||+  .+++.++|||+++.-+|+.+..|..++...   ....++|+++.+||||++.
T Consensus        83 agQerfg~mtrVyyk--ea~~~~iVfdvt~s~tfe~~skwkqdldsk~qLpng~Pv~~vllankCd~e~  149 (229)
T KOG4423|consen   83 AGQERFGNMTRVYYK--EAHGAFIVFDVTRSLTFEPVSKWKQDLDSKLQLPNGTPVPCVLLANKCDQEK  149 (229)
T ss_pred             hhhhhhcceEEEEec--CCcceEEEEEccccccccHHHHHHHhccCcccCCCCCcchheeccchhccCh
Confidence            489999999999999  599999999999999999999999887643   2335788999999999863

>KOG0075|consensus

Probab=99.14  E-value=1.3e-10  Score=67.23  Aligned_cols=64  Identities=16%  Similarity=0.264  Sum_probs=56.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +||.+|+++++.|++  +.+++++|.|..+++.+...+.-+..+........+|+++.|||.|+.+
T Consensus        73 gGq~rfrsmWerycR--~v~aivY~VDaad~~k~~~sr~EL~~LL~k~~l~gip~LVLGnK~d~~~  136 (186)
T KOG0075|consen   73 GGQPRFRSMWERYCR--GVSAIVYVVDAADPDKLEASRSELHDLLDKPSLTGIPLLVLGNKIDLPG  136 (186)
T ss_pred             CCCccHHHHHHHHhh--cCcEEEEEeecCCcccchhhHHHHHHHhcchhhcCCcEEEecccccCcc
Confidence            689999999999999  7999999999999999988877666666545567899999999999975

>cd01898 Obg Obg subfamily

Probab=99.13  E-value=2.1e-10  Score=65.99  Aligned_cols=64  Identities=19%  Similarity=0.154  Sum_probs=48.5

Q ss_pred             chhhhhhhhhcc-CCcEEEEEEECCCh-hHHHHHHHHHHHHHhhcC-CCCCeEEEEeeCCCCcCCCc
Q psy5805           8 FTNLVVNFVQTY-HPDVFVIVYSVIER-KTFKKAEDMLKTLWDSKY-IGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         8 f~~~~~~~~~~~-~~~~~ilv~d~~~~-~s~~~~~~~~~~~~~~~~-~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      ++.+...+++.+ +++++++|+|.+++ ++++++..|.+++..... ....|+++|+||+|+.....
T Consensus        65 ~~~~~~~~~~~~~~~d~vi~v~D~~~~~~~~~~~~~~~~~l~~~~~~~~~~p~ivv~NK~Dl~~~~~  131 (170)
T cd01898          65 GKGLGHRFLRHIERTRLLLHVIDLSGDDDPVEDYKTIRNELELYNPELLEKPRIVVLNKIDLLDEEE  131 (170)
T ss_pred             cCCchHHHHHHHHhCCEEEEEEecCCCCCHHHHHHHHHHHHHHhCccccccccEEEEEchhcCCchh
Confidence            334555555533 59999999999999 899999999988876421 24689999999999965433

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.

>cd04105 SR_beta Signal recognition particle receptor, beta subunit (SR-beta)

Probab=99.07  E-value=5.9e-10  Score=66.92  Aligned_cols=65  Identities=15%  Similarity=0.203  Sum_probs=51.9

Q ss_pred             cccccchhhhhhhhhccCC-cEEEEEEECCCh-hHHHHHHHHHHHHHhhc--CCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHP-DVFVIVYSVIER-KTFKKAEDMLKTLWDSK--YIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~-~~~ilv~d~~~~-~s~~~~~~~~~~~~~~~--~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .||++|+.....+++  ++ +++|+|+|.++. +++..+..|+..+....  ..+.+|+++++||+|+...
T Consensus        56 pG~~~~~~~~~~~~~--~~~~~vV~VvD~~~~~~~~~~~~~~l~~il~~~~~~~~~~pvliv~NK~Dl~~a  124 (203)
T cd04105          56 PGHPKLRDKLLETLK--NSAKGIVFVVDSATFQKNLKDVAEFLYDILTDLEKVKNKIPVLIACNKQDLFTA  124 (203)
T ss_pred             CCCHHHHHHHHHHHh--ccCCEEEEEEECccchhHHHHHHHHHHHHHHHHhhccCCCCEEEEecchhhccc
Confidence            589999988888888  58 999999999998 78888877765543321  1257999999999998653

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

>cd01891 TypA_BipA TypA (tyrosine phosphorylated protein A)/BipA subfamily

Probab=99.00  E-value=1.8e-09  Score=63.98  Aligned_cols=60  Identities=18%  Similarity=0.138  Sum_probs=45.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|..+...+++  ++|++++|+|.++. .+.....|+..+..    .++|+++|+||+|+...
T Consensus        73 pG~~~~~~~~~~~~~--~~d~~ilV~d~~~~-~~~~~~~~~~~~~~----~~~p~iiv~NK~Dl~~~  132 (194)
T cd01891          73 PGHADFGGEVERVLS--MVDGVLLLVDASEG-PMPQTRFVLKKALE----LGLKPIVVINKIDRPDA  132 (194)
T ss_pred             CCcHHHHHHHHHHHH--hcCEEEEEEECCCC-ccHHHHHHHHHHHH----cCCCEEEEEECCCCCCC
Confidence            589999999999998  69999999999874 23444444444432    46899999999999643

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

>KOG1673|consensus

Probab=99.00  E-value=7.7e-10  Score=64.63  Aligned_cols=60  Identities=17%  Similarity=0.248  Sum_probs=51.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADL   66 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl   66 (75)
                      +|+++|..+.|.-+.  ++-+++++||++.+.++.++..|+.+.+... ...+| |+||+|.|+
T Consensus        77 gG~~~~~n~lPiac~--dsvaIlFmFDLt~r~TLnSi~~WY~QAr~~N-ktAiP-ilvGTKyD~  136 (205)
T KOG1673|consen   77 GGQREFINMLPIACK--DSVAILFMFDLTRRSTLNSIKEWYRQARGLN-KTAIP-ILVGTKYDL  136 (205)
T ss_pred             CCcHhhhccCceeec--CcEEEEEEEecCchHHHHHHHHHHHHHhccC-Cccce-EEeccchHh
Confidence            689999999999999  6999999999999999999999998887642 13344 679999996

>KOG0073|consensus

Probab=98.99  E-value=2.7e-09  Score=62.55  Aligned_cols=64  Identities=17%  Similarity=0.294  Sum_probs=53.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +||-.+++.++.||..  +||+|+|+|.+|+..|+.+..-+.++.........|+++++||.|+..
T Consensus        68 GGq~~lr~~W~nYfes--tdglIwvvDssD~~r~~e~~~~L~~lL~eerlaG~~~Lvlank~dl~~  131 (185)
T KOG0073|consen   68 GGQKTLRSYWKNYFES--TDGLIWVVDSSDRMRMQECKQELTELLVEERLAGAPLLVLANKQDLPG  131 (185)
T ss_pred             CCcchhHHHHHHhhhc--cCeEEEEEECchHHHHHHHHHHHHHHHhhhhhcCCceEEEEecCcCcc
Confidence            6888899999999994  999999999999999999877666655433345689999999999974

>KOG0071|consensus

Probab=98.97  E-value=2.8e-09  Score=61.35  Aligned_cols=68  Identities=15%  Similarity=0.272  Sum_probs=57.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+++.+.++..||.  |+.|+|+|.|..+++..+..++-+..+.+.+...++|+++.+||.|+.+.+.+
T Consensus        69 GGqd~iRplWrhYy~--gtqglIFV~Dsa~~dr~eeAr~ELh~ii~~~em~~~~~LvlANkQDlp~A~~p  136 (180)
T KOG0071|consen   69 GGQDKIRPLWRHYYT--GTQGLIFVVDSADRDRIEEARNELHRIINDREMRDAIILILANKQDLPDAMKP  136 (180)
T ss_pred             cCchhhhHHHHhhcc--CCceEEEEEeccchhhHHHHHHHHHHHhCCHhhhcceEEEEecCcccccccCH
Confidence            688888888888888  89999999999999999988777666666555678999999999999876654

>PRK12299 obgE GTPase CgtA; Reviewed

Probab=98.96  E-value=2e-09  Score=69.08  Aligned_cols=63  Identities=17%  Similarity=0.190  Sum_probs=49.3

Q ss_pred             chhhhhhhhhcc-CCcEEEEEEECCChhHHHHHHHHHHHHHhhcC-CCCCeEEEEeeCCCCcCCC
Q psy5805           8 FTNLVVNFVQTY-HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY-IGEKAVILVANKADLERRR   70 (75)
Q Consensus         8 f~~~~~~~~~~~-~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~ilvgnK~Dl~~~r   70 (75)
                      ...+...|++.+ .++++++|+|+++.++++.+..|..++..... ..+.|+++|+||+|+.+..
T Consensus       223 ~~gLg~~flrhie~a~vlI~ViD~s~~~s~e~~~~~~~EL~~~~~~L~~kp~IIV~NKiDL~~~~  287 (335)
T PRK12299        223 GAGLGHRFLKHIERTRLLLHLVDIEAVDPVEDYKTIRNELEKYSPELADKPRILVLNKIDLLDEE  287 (335)
T ss_pred             cccHHHHHHHHhhhcCEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhcccCCeEEEEECcccCCch
Confidence            344555655543 69999999999998899999999999987531 2468999999999996544

>KOG0076|consensus

Probab=98.88  E-value=1.4e-09  Score=64.23  Aligned_cols=67  Identities=15%  Similarity=0.306  Sum_probs=57.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      +|||.-++++..||..  ++++|+++|.++++-|+....-++.+.......++|+++.+||.|+.+..+
T Consensus        77 gGQe~lrSlw~~yY~~--~H~ii~viDa~~~eR~~~~~t~~~~v~~~E~leg~p~L~lankqd~q~~~~  143 (197)
T KOG0076|consen   77 GGQESLRSLWKKYYWL--AHGIIYVIDATDRERFEESKTAFEKVVENEKLEGAPVLVLANKQDLQNAME  143 (197)
T ss_pred             CChHHHHHHHHHHHHH--hceeEEeecCCCHHHHHHHHHHHHHHHHHHHhcCCchhhhcchhhhhhhhh
Confidence            6899999999999995  999999999999999999877776666555567899999999999976543

>cd00882 Ras_like_GTPase Ras-like GTPase superfamily

Probab=98.86  E-value=2.5e-08  Score=54.96  Aligned_cols=65  Identities=26%  Similarity=0.393  Sum_probs=48.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|++.+......+.+  +++++++|+|.+++.++.....|............+|+++++||+|+...
T Consensus        53 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivv~nk~D~~~~  117 (157)
T cd00882          53 AGQERFRSLRRLYYR--GADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGNKIDLPEE  117 (157)
T ss_pred             CChHHHHhHHHHHhc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhhccCCCcEEEEEeccccccc
Confidence            455556555566666  59999999999999999999888433332224578999999999998643

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

>KOG1707|consensus

Probab=98.86  E-value=9.2e-09  Score=69.58  Aligned_cols=58  Identities=28%  Similarity=0.306  Sum_probs=47.4

Q ss_pred             hhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcC-CCCCeEEEEeeCCCCcCCC
Q psy5805          10 NLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKY-IGEKAVILVANKADLERRR   70 (75)
Q Consensus        10 ~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~-~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .++....+   |+++.++|+.+++.|++.+ ..|++.+++... ..++|+||||||+|+.+..
T Consensus        72 ~l~~Eirk---A~vi~lvyavd~~~T~D~ist~WLPlir~~~~~~~~~PVILvGNK~d~~~~~  131 (625)
T KOG1707|consen   72 CLRKEIRK---ADVICLVYAVDDESTVDRISTKWLPLIRQLFGDYHETPVILVGNKSDNGDNE  131 (625)
T ss_pred             HHHHHHhh---cCEEEEEEecCChHHhhhhhhhhhhhhhcccCCCccCCEEEEeeccCCcccc
Confidence            34555555   9999999999999999999 689999987531 2589999999999997543

>TIGR03156 GTP_HflX GTP-binding protein HflX

Probab=98.81  E-value=1.6e-08  Score=65.36  Aligned_cols=60  Identities=22%  Similarity=0.252  Sum_probs=45.5

Q ss_pred             ccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           6 SCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         6 e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      |.|++..+. ++  ++|++++|+|.+++.+++++..|...+.... ..+.|+++|+||+|+...
T Consensus       257 e~f~~tle~-~~--~ADlil~VvD~s~~~~~~~~~~~~~~L~~l~-~~~~piIlV~NK~Dl~~~  316 (351)
T TIGR03156       257 AAFRATLEE-VR--EADLLLHVVDASDPDREEQIEAVEKVLEELG-AEDIPQLLVYNKIDLLDE  316 (351)
T ss_pred             HHHHHHHHH-HH--hCCEEEEEEECCCCchHHHHHHHHHHHHHhc-cCCCCEEEEEEeecCCCh
Confidence            345544433 34  5999999999999999998888877666543 357899999999999653

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).

>cd01878 HflX HflX subfamily

Probab=98.80  E-value=2e-08  Score=59.70  Aligned_cols=49  Identities=24%  Similarity=0.250  Sum_probs=41.3

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +++++++|+|.+++.++..+..|...+.... ..+.|+++|+||+|+...
T Consensus       120 ~~d~ii~v~D~~~~~~~~~~~~~~~~l~~~~-~~~~~viiV~NK~Dl~~~  168 (204)
T cd01878         120 EADLLLHVVDASDPDYEEQIETVEKVLKELG-AEDIPMILVLNKIDLLDD  168 (204)
T ss_pred             cCCeEEEEEECCCCChhhHHHHHHHHHHHcC-cCCCCEEEEEEccccCCh
Confidence            5999999999999999999888887776543 356899999999998654

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.

>cd01897 NOG NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans

Probab=98.78  E-value=1.8e-08  Score=57.84  Aligned_cols=50  Identities=18%  Similarity=0.268  Sum_probs=39.3

Q ss_pred             CcEEEEEEECCChhHH--HHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805          21 PDVFVIVYSVIERKTF--KKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus        21 ~~~~ilv~d~~~~~s~--~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      ++++++|+|.+++.++  +....|+..++..  ..+.|+++|+||+|+...+.+
T Consensus        80 ~d~~l~v~d~~~~~~~~~~~~~~~~~~l~~~--~~~~pvilv~NK~Dl~~~~~~  131 (168)
T cd01897          80 RAAVLFLFDPSETCGYSLEEQLSLFEEIKPL--FKNKPVIVVLNKIDLLTFEDL  131 (168)
T ss_pred             cCcEEEEEeCCcccccchHHHHHHHHHHHhh--cCcCCeEEEEEccccCchhhH
Confidence            6899999999988764  6667788887653  257899999999999755443

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.

>cd01881 Obg_like The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1

Probab=98.77  E-value=2.1e-08  Score=57.78  Aligned_cols=52  Identities=25%  Similarity=0.227  Sum_probs=41.8

Q ss_pred             CCcEEEEEEECCCh------hHHHHHHHHHHHHHhhcCC------CCCeEEEEeeCCCCcCCCc
Q psy5805          20 HPDVFVIVYSVIER------KTFKKAEDMLKTLWDSKYI------GEKAVILVANKADLERRRQ   71 (75)
Q Consensus        20 ~~~~~ilv~d~~~~------~s~~~~~~~~~~~~~~~~~------~~~~~ilvgnK~Dl~~~r~   71 (75)
                      +++++++|+|.++.      .+++....|..++......      .+.|+++|+||+|+...+.
T Consensus        74 ~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ivv~NK~Dl~~~~~  137 (176)
T cd01881          74 RADAILHVVDASEDDDIGGVDPLEDYEILNAELKLYDLETILGLLTAKPVIYVLNKIDLDDAEE  137 (176)
T ss_pred             ccCEEEEEEeccCCccccccCHHHHHHHHHHHHHHhhhhhHHHHHhhCCeEEEEEchhcCchhH
Confidence            69999999999998      6888888888887654321      4689999999999965443

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

>cd04171 SelB SelB subfamily

Probab=98.73  E-value=3.9e-08  Score=55.96  Aligned_cols=58  Identities=24%  Similarity=0.193  Sum_probs=40.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|......+++  ++|++++|+|.++   +++++.+.    .+..   .+..|+++|+||+|+...
T Consensus        59 pG~~~~~~~~~~~~~--~ad~ii~V~d~~~~~~~~~~~~~~----~~~~---~~~~~~ilv~NK~Dl~~~  119 (164)
T cd04171          59 PGHEKFIKNMLAGAG--GIDLVLLVVAADEGIMPQTREHLE----ILEL---LGIKRGLVVLTKADLVDE  119 (164)
T ss_pred             CChHHHHHHHHhhhh--cCCEEEEEEECCCCccHhHHHHHH----HHHH---hCCCcEEEEEECccccCH
Confidence            578888766666666  6999999999987   55555443    1222   122489999999999653

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

>cd01885 EF2 EF2 (for archaea and eukarya)

Probab=98.72  E-value=4.4e-08  Score=59.83  Aligned_cols=58  Identities=17%  Similarity=0.118  Sum_probs=44.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .||+.|......+++  ++|++++|+|.++..+.+....|. ....    .++|+++|+||+|+.
T Consensus        81 PG~~~f~~~~~~~l~--~aD~~ilVvD~~~g~~~~t~~~l~-~~~~----~~~p~ilviNKiD~~  138 (222)
T cd01885          81 PGHVDFSSEVTAALR--LCDGALVVVDAVEGVCVQTETVLR-QALK----ERVKPVLVINKIDRL  138 (222)
T ss_pred             CCccccHHHHHHHHH--hcCeeEEEEECCCCCCHHHHHHHH-HHHH----cCCCEEEEEECCCcc
Confidence            588999998888888  599999999999876655433332 2221    357999999999975

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

>TIGR02729 Obg_CgtA Obg family GTPase CgtA

Probab=98.71  E-value=3.9e-08  Score=63.05  Aligned_cols=61  Identities=21%  Similarity=0.231  Sum_probs=47.1

Q ss_pred             hhhhhhhhhcc-CCcEEEEEEECCCh---hHHHHHHHHHHHHHhhc-CCCCCeEEEEeeCCCCcCC
Q psy5805           9 TNLVVNFVQTY-HPDVFVIVYSVIER---KTFKKAEDMLKTLWDSK-YIGEKAVILVANKADLERR   69 (75)
Q Consensus         9 ~~~~~~~~~~~-~~~~~ilv~d~~~~---~s~~~~~~~~~~~~~~~-~~~~~~~ilvgnK~Dl~~~   69 (75)
                      ..+...|++.+ .++++++|+|+++.   ++++.+..|..++.... ...+.|+++|+||+|+.+.
T Consensus       223 ~gLg~~flrhierad~ll~VvD~s~~~~~~~~e~l~~l~~EL~~~~~~l~~kp~IIV~NK~DL~~~  288 (329)
T TIGR02729       223 AGLGHRFLKHIERTRVLLHLIDISPLDGRDPIEDYEIIRNELKKYSPELAEKPRIVVLNKIDLLDE  288 (329)
T ss_pred             ccHHHHHHHHHHhhCEEEEEEcCccccccCHHHHHHHHHHHHHHhhhhhccCCEEEEEeCccCCCh
Confidence            34566666533 59999999999987   78889989988887642 1246899999999999654

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.

>TIGR02528 EutP ethanolamine utilization protein, EutP

Probab=98.69  E-value=1.2e-08  Score=57.43  Aligned_cols=52  Identities=23%  Similarity=0.307  Sum_probs=37.8

Q ss_pred             ccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           6 SCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         6 e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +.|+.+.+. ++  ++|++++|||++++.|+.. ..|...+      . .|+++|+||+|+.+
T Consensus        51 ~~~~~~~~~-~~--~ad~vilv~d~~~~~s~~~-~~~~~~~------~-~p~ilv~NK~Dl~~  102 (142)
T TIGR02528        51 RLYSALIVT-AA--DADVIALVQSATDPESRFP-PGFASIF------V-KPVIGLVTKIDLAE  102 (142)
T ss_pred             HHHHHHHHH-hh--cCCEEEEEecCCCCCcCCC-hhHHHhc------c-CCeEEEEEeeccCC
Confidence            345666553 55  6999999999999999865 3453321      1 39999999999964

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.

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

Probab=98.68  E-value=5.2e-08  Score=53.28  Aligned_cols=56  Identities=18%  Similarity=0.205  Sum_probs=43.7

Q ss_pred             hhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805          12 VVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus        12 ~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      ...+++  +++++++||+.++++|++.+  |...+.... ..++|.+++|||.|+.+++++
T Consensus        40 ~~~~~~--s~~~~~~v~~~~~~~s~~~~--~~~~i~~~~-k~dl~~~~~~nk~dl~~~~~~   95 (124)
T smart00010       40 DPTSYE--SFDVVLQCWRVDDRDSADNK--NVPEVLVGN-KSDLPILVGGNRDVLEEERQV   95 (124)
T ss_pred             cccccC--CCCEEEEEEEccCHHHHHHH--hHHHHHhcC-CCCCcEEEEeechhhHhhCcC
Confidence            455666  69999999999999999877  887776532 356889999999999655443

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.

>TIGR01393 lepA GTP-binding protein LepA

Probab=98.67  E-value=6.9e-08  Score=66.01  Aligned_cols=59  Identities=15%  Similarity=0.116  Sum_probs=48.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|......+++  ++|++|+|+|.++..+++....|...+.     .++|+++|+||+|+.+
T Consensus        78 PG~~dF~~~v~~~l~--~aD~aILVvDat~g~~~qt~~~~~~~~~-----~~ipiIiViNKiDl~~  136 (595)
T TIGR01393        78 PGHVDFSYEVSRSLA--ACEGALLLVDAAQGIEAQTLANVYLALE-----NDLEIIPVINKIDLPS  136 (595)
T ss_pred             CCcHHHHHHHHHHHH--hCCEEEEEecCCCCCCHhHHHHHHHHHH-----cCCCEEEEEECcCCCc
Confidence            689999988888888  5999999999999877777777754432     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.

>TIGR00491 aIF-2 translation initiation factor aIF-2/yIF-2

Probab=98.64  E-value=8.8e-08  Score=65.47  Aligned_cols=56  Identities=20%  Similarity=0.154  Sum_probs=45.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|..++..+++  ++|++++|+|.++   +++++.+..+    ..    .++|+++++||+|+..
T Consensus        77 pG~e~f~~l~~~~~~--~aD~~IlVvD~~~g~~~qt~e~i~~l----~~----~~vpiIVv~NK~Dl~~  135 (590)
T TIGR00491        77 PGHEAFTNLRKRGGA--LADLAILIVDINEGFKPQTQEALNIL----RM----YKTPFVVAANKIDRIP  135 (590)
T ss_pred             CCcHhHHHHHHHHHh--hCCEEEEEEECCcCCCHhHHHHHHHH----HH----cCCCEEEEEECCCccc
Confidence            589999999999888  5999999999997   6777765432    21    3579999999999953

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.

>COG2229 Predicted GTPase [General function prediction only]

Probab=98.64  E-value=1e-07  Score=56.65  Aligned_cols=63  Identities=17%  Similarity=0.155  Sum_probs=50.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      -||+||.-+++.+.+  |+.++|++.|-+.+..| ....-+..+...   ..+|+++..||.||...+.
T Consensus        76 PGq~RF~fm~~~l~~--ga~gaivlVDss~~~~~-~a~~ii~f~~~~---~~ip~vVa~NK~DL~~a~p  138 (187)
T COG2229          76 PGQERFKFMWEILSR--GAVGAIVLVDSSRPITF-HAEEIIDFLTSR---NPIPVVVAINKQDLFDALP  138 (187)
T ss_pred             CCcHHHHHHHHHHhC--CcceEEEEEecCCCcch-HHHHHHHHHhhc---cCCCEEEEeeccccCCCCC
Confidence            489999999999999  89999999999999999 444444444431   2299999999999986543

>TIGR00231 small_GTP small GTP-binding protein domain

Probab=98.63  E-value=1.7e-07  Score=52.23  Aligned_cols=63  Identities=14%  Similarity=0.188  Sum_probs=51.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCCh-hHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIER-KTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~-~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|++.|..+...+.+  ++++++.++|+... .++.... .|...+..... .+.|+++++||+|+..
T Consensus        58 ~G~~~~~~~~~~~~~--~~~~~i~~~d~~~~v~~~~~~~~~~~~~~~~~~~-~~~p~ivv~nK~D~~~  122 (161)
T TIGR00231        58 AGQEDYRAIRRLYYR--AVESSLRVFDIVILVLDVEEILEKQTKEIIHHAE-SNVPIILVGNKIDLRD  122 (161)
T ss_pred             CCcccchHHHHHHHh--hhhEEEEEEEEeeeehhhhhHhHHHHHHHHHhcc-cCCcEEEEEEcccCCc
Confidence            467888888888888  49999999999998 8888775 78777766432 2889999999999965

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.

>cd01887 IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily

Probab=98.62  E-value=2.3e-07  Score=53.11  Aligned_cols=56  Identities=18%  Similarity=0.203  Sum_probs=41.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCCh---hHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIER---KTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~---~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|++.|..++..+++  .+|++++|+|.++.   +++..+.    .+..    .++|+++|+||+|+.+
T Consensus        58 pG~~~~~~~~~~~~~--~~d~il~v~d~~~~~~~~~~~~~~----~~~~----~~~p~ivv~NK~Dl~~  116 (168)
T cd01887          58 PGHEAFTNMRARGAS--LTDIAILVVAADDGVMPQTIEAIK----LAKA----ANVPFIVALNKIDKPN  116 (168)
T ss_pred             CCcHHHHHHHHHHHh--hcCEEEEEEECCCCccHHHHHHHH----HHHH----cCCCEEEEEEceeccc
Confidence            578888888888777  59999999999984   4444332    2222    4579999999999864

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.

>PRK11058 GTPase HflX; Provisional

Probab=98.60  E-value=1.7e-07  Score=61.97  Aligned_cols=48  Identities=19%  Similarity=0.223  Sum_probs=38.9

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|++++|+|.+++.+++++..|...+.... ..++|+++|+||+|+..
T Consensus       276 ~ADlIL~VvDaS~~~~~e~l~~v~~iL~el~-~~~~pvIiV~NKiDL~~  323 (426)
T PRK11058        276 QATLLLHVVDAADVRVQENIEAVNTVLEEID-AHEIPTLLVMNKIDMLD  323 (426)
T ss_pred             cCCEEEEEEeCCCccHHHHHHHHHHHHHHhc-cCCCCEEEEEEcccCCC
Confidence            5999999999999999998876655555432 25789999999999854

>PRK03003 GTP-binding protein Der; Reviewed

Probab=98.55  E-value=2.4e-07  Score=61.76  Aligned_cols=58  Identities=19%  Similarity=0.289  Sum_probs=43.7

Q ss_pred             ccccchhhhhh-hhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           4 RTSCFTNLVVN-FVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         4 ~~e~f~~~~~~-~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|.|..++.. +++  +++++++|+|.++..++..+. ++..+..    .+.|+++|+||+||.+
T Consensus       278 ~~e~~~~~~~~~~i~--~ad~vilV~Da~~~~s~~~~~-~~~~~~~----~~~piIiV~NK~Dl~~  336 (472)
T PRK03003        278 GHEYYASLRTHAAIE--AAEVAVVLIDASEPISEQDQR-VLSMVIE----AGRALVLAFNKWDLVD  336 (472)
T ss_pred             hHHHHHHHHHHHHHh--cCCEEEEEEeCCCCCCHHHHH-HHHHHHH----cCCCEEEEEECcccCC
Confidence            35677766543 455  599999999999998988774 3444432    4689999999999964

>cd04167 Snu114p Snu114p subfamily

Probab=98.52  E-value=5.1e-07  Score=54.36  Aligned_cols=58  Identities=24%  Similarity=0.248  Sum_probs=44.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .|++.|......+++  .+|++++|+|.++..++.. ..|+.....    .+.|+++|+||+|+.
T Consensus        79 pG~~~f~~~~~~~~~--~aD~~llVvD~~~~~~~~~-~~~~~~~~~----~~~p~iiviNK~D~~  136 (213)
T cd04167          79 PGHVNFMDEVAAALR--LSDGVVLVVDVVEGVTSNT-ERLIRHAIL----EGLPIVLVINKIDRL  136 (213)
T ss_pred             CCCcchHHHHHHHHH--hCCEEEEEEECCCCCCHHH-HHHHHHHHH----cCCCEEEEEECcccC
Confidence            578889888888887  4999999999988776643 344444432    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.

>KOG0074|consensus

Probab=98.48  E-value=2.4e-07  Score=53.56  Aligned_cols=64  Identities=22%  Similarity=0.326  Sum_probs=51.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +||-..+..+..||.  +.|++|+|-|.+|+.-|+.+..-+.++.+......+|+.+.+||.|+.-
T Consensus        70 GGqr~IRpyWsNYye--nvd~lIyVIDS~D~krfeE~~~el~ELleeeKl~~vpvlIfankQdllt  133 (185)
T KOG0074|consen   70 GGQRGIRPYWSNYYE--NVDGLIYVIDSTDEKRFEEISEELVELLEEEKLAEVPVLIFANKQDLLT  133 (185)
T ss_pred             CCccccchhhhhhhh--ccceEEEEEeCCchHhHHHHHHHHHHHhhhhhhhccceeehhhhhHHHh
Confidence            466566677777777  7999999999999999999976666665555567899999999999853

>TIGR00450 mnmE_trmE_thdF tRNA modification GTPase TrmE

Probab=98.48  E-value=4.7e-07  Score=60.14  Aligned_cols=47  Identities=26%  Similarity=0.327  Sum_probs=37.8

Q ss_pred             hhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          14 NFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        14 ~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+++  ++|++++|||.+++.+++..  |+..+..    .+.|+++|+||+|+..
T Consensus       278 ~~~~--~aD~il~V~D~s~~~s~~~~--~l~~~~~----~~~piIlV~NK~Dl~~  324 (442)
T TIGR00450       278 KAIK--QADLVIYVLDASQPLTKDDF--LIIDLNK----SKKPFILVLNKIDLKI  324 (442)
T ss_pred             HHHh--hCCEEEEEEECCCCCChhHH--HHHHHhh----CCCCEEEEEECccCCC
Confidence            4555  69999999999999988876  7666542    4679999999999854

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.

>PRK03003 GTP-binding protein Der; Reviewed

Probab=98.45  E-value=4.8e-07  Score=60.35  Aligned_cols=54  Identities=28%  Similarity=0.285  Sum_probs=38.9

Q ss_pred             chhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           8 FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         8 f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +......+++  ++|++++|+|.++..++.. ..|...++.    .+.|+++|+||+|+..
T Consensus       107 ~~~~~~~~~~--~aD~il~VvD~~~~~s~~~-~~i~~~l~~----~~~piilV~NK~Dl~~  160 (472)
T PRK03003        107 VAEQAEVAMR--TADAVLFVVDATVGATATD-EAVARVLRR----SGKPVILAANKVDDER  160 (472)
T ss_pred             HHHHHHHHHH--hCCEEEEEEECCCCCCHHH-HHHHHHHHH----cCCCEEEEEECccCCc
Confidence            4445556666  5999999999998866543 334444442    4689999999999853

>PRK04004 translation initiation factor IF-2; Validated

Probab=98.44  E-value=5.8e-07  Score=61.48  Aligned_cols=55  Identities=22%  Similarity=0.219  Sum_probs=45.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .||+.|..++...++  .+|++++|+|.++   +++++.+..+    ..    .++|+++++||+|+.
T Consensus        79 PG~e~f~~~~~~~~~--~aD~~IlVvDa~~g~~~qt~e~i~~~----~~----~~vpiIvviNK~D~~  136 (586)
T PRK04004         79 PGHEAFTNLRKRGGA--LADIAILVVDINEGFQPQTIEAINIL----KR----RKTPFVVAANKIDRI  136 (586)
T ss_pred             CChHHHHHHHHHhHh--hCCEEEEEEECCCCCCHhHHHHHHHH----HH----cCCCEEEEEECcCCc
Confidence            589999999988887  5999999999997   7788776432    21    468999999999985

>cd00066 G-alpha G protein alpha subunit

Probab=98.44  E-value=7.3e-07  Score=56.94  Aligned_cols=63  Identities=14%  Similarity=0.297  Sum_probs=49.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCCh----------hHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIER----------KTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~----------~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      |||...+..+..|+.  +++++|+|.|+++.          +.+......++.+.+.....++|++|++||.|+-
T Consensus       169 gGq~~~R~kW~~~f~--~v~~iifvv~lsd~d~~~~e~~~~nrl~esl~~f~~i~~~~~~~~~pill~~NK~D~f  241 (317)
T cd00066         169 GGQRSERKKWIHCFE--DVTAIIFVVALSEYDQVLFEDESTNRMQESLNLFDSICNSRWFANTSIILFLNKKDLF  241 (317)
T ss_pred             CCCcccchhHHHHhC--CCCEEEEEEEchhcccccccCCcchHHHHHHHHHHHHHhCccccCCCEEEEccChHHH
Confidence            788888888888888  79999999999974          4555555555555544334689999999999974

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.

>PRK12297 obgE GTPase CgtA; Reviewed

Probab=98.43  E-value=9.4e-07  Score=58.51  Aligned_cols=61  Identities=26%  Similarity=0.231  Sum_probs=45.8

Q ss_pred             chhhhhhhhhcc-CCcEEEEEEECCCh---hHHHHHHHHHHHHHhhcC-CCCCeEEEEeeCCCCcC
Q psy5805           8 FTNLVVNFVQTY-HPDVFVIVYSVIER---KTFKKAEDMLKTLWDSKY-IGEKAVILVANKADLER   68 (75)
Q Consensus         8 f~~~~~~~~~~~-~~~~~ilv~d~~~~---~s~~~~~~~~~~~~~~~~-~~~~~~ilvgnK~Dl~~   68 (75)
                      ...+...|++.+ .++++++|+|+++.   ++++....|..++..... ..+.|+++|+||+||.+
T Consensus       223 ~~gLg~~fLrhier~~llI~VID~s~~~~~dp~e~~~~i~~EL~~y~~~L~~kP~IVV~NK~DL~~  288 (424)
T PRK12297        223 GVGLGHQFLRHIERTRVIVHVIDMSGSEGRDPIEDYEKINKELKLYNPRLLERPQIVVANKMDLPE  288 (424)
T ss_pred             cchHHHHHHHHHhhCCEEEEEEeCCccccCChHHHHHHHHHHHhhhchhccCCcEEEEEeCCCCcC
Confidence            344556665533 58999999999865   788888888888876421 24689999999999853

>smart00275 G_alpha G protein alpha subunit

Probab=98.43  E-value=9.4e-07  Score=57.03  Aligned_cols=63  Identities=13%  Similarity=0.280  Sum_probs=49.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCCh----------hHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIER----------KTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~----------~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      |||..++..+..|+.  +++++|+|.|+++.          ..+......++.+.+.....++|++|+.||.|+-
T Consensus       192 gGqr~~R~kW~~~f~--~v~~IiFvvdlSd~d~~~~Ed~~~nrl~esl~~f~~l~~~~~~~~~piil~~NK~D~~  264 (342)
T smart00275      192 GGQRSERKKWIHCFD--NVTAIIFCVALSEYDQVLEEDESTNRMQESLNLFESICNSRWFANTSIILFLNKIDLF  264 (342)
T ss_pred             CCchhhhhhHHHHhC--CCCEEEEEEECcccccchhccCcchHHHHHHHHHHHHHcCccccCCcEEEEEecHHhH
Confidence            788888999999888  79999999999973          4565555555555554444689999999999984

Subunit of G proteins that contains the guanine nucleotide binding site

>PRK05433 GTP-binding protein LepA; Provisional

Probab=98.42  E-value=9.8e-07  Score=60.52  Aligned_cols=59  Identities=17%  Similarity=0.117  Sum_probs=46.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|......+++  ++|++|+|+|.++....+....|.....     .++|+++|+||+|+..
T Consensus        82 PGh~dF~~~v~~sl~--~aD~aILVVDas~gv~~qt~~~~~~~~~-----~~lpiIvViNKiDl~~  140 (600)
T PRK05433         82 PGHVDFSYEVSRSLA--ACEGALLVVDASQGVEAQTLANVYLALE-----NDLEIIPVLNKIDLPA  140 (600)
T ss_pred             CCcHHHHHHHHHHHH--HCCEEEEEEECCCCCCHHHHHHHHHHHH-----CCCCEEEEEECCCCCc
Confidence            689999988888888  5999999999998766666666643321     3579999999999864

>CHL00189 infB translation initiation factor 2; Provisional

Probab=98.41  E-value=7e-07  Score=62.48  Aligned_cols=56  Identities=13%  Similarity=0.214  Sum_probs=44.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|..++..+++  .+|++|+|+|.++   +.+++.+..    +.    ..++|+++++||+|+..
T Consensus       303 PGhe~F~~mr~rg~~--~aDiaILVVDA~dGv~~QT~E~I~~----~k----~~~iPiIVViNKiDl~~  361 (742)
T CHL00189        303 PGHEAFSSMRSRGAN--VTDIAILIIAADDGVKPQTIEAINY----IQ----AANVPIIVAINKIDKAN  361 (742)
T ss_pred             CcHHHHHHHHHHHHH--HCCEEEEEEECcCCCChhhHHHHHH----HH----hcCceEEEEEECCCccc
Confidence            589999999998888  4999999999987   455554432    22    24689999999999864

>cd01854 YjeQ_engC YjeQ/EngC

Probab=98.41  E-value=6.6e-07  Score=56.42  Aligned_cols=45  Identities=27%  Similarity=0.194  Sum_probs=39.4

Q ss_pred             CCcEEEEEEECCChh-HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERK-TFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |+|.+++|+|++++. ++..+.+|+..+..    .++|+++|.||+||..
T Consensus        78 nvD~vllV~d~~~p~~s~~~ldr~L~~~~~----~~ip~iIVlNK~DL~~  123 (287)
T cd01854          78 NVDQLVIVVSLNEPFFNPRLLDRYLVAAEA----AGIEPVIVLTKADLLD  123 (287)
T ss_pred             eCCEEEEEEEcCCCCCCHHHHHHHHHHHHH----cCCCEEEEEEHHHCCC
Confidence            799999999999998 88999999887764    4589999999999954

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.

>TIGR00487 IF-2 translation initiation factor IF-2

Probab=98.41  E-value=9.4e-07  Score=60.51  Aligned_cols=56  Identities=18%  Similarity=0.227  Sum_probs=43.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|..++..+++  .+|++++|+|.++   +++++.+.    ...    ..++|+++++||+|+.+
T Consensus       143 PGhe~F~~~r~rga~--~aDiaILVVda~dgv~~qT~e~i~----~~~----~~~vPiIVviNKiDl~~  201 (587)
T TIGR00487       143 PGHEAFTSMRARGAK--VTDIVVLVVAADDGVMPQTIEAIS----HAK----AANVPIIVAINKIDKPE  201 (587)
T ss_pred             CCCcchhhHHHhhhc--cCCEEEEEEECCCCCCHhHHHHHH----HHH----HcCCCEEEEEECccccc
Confidence            689999999988887  5999999999986   45554432    122    24689999999999853

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.

>cd01879 FeoB Ferrous iron transport protein B (FeoB) subfamily

Probab=98.40  E-value=1.4e-06  Score=49.26  Aligned_cols=61  Identities=18%  Similarity=0.188  Sum_probs=40.0

Q ss_pred             ccccchh------hhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           4 RTSCFTN------LVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         4 ~~e~f~~------~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      |++.|..      ++..++..-+++++++|+|.+++++..   .|...+..    .++|+++|+||+|+...+.
T Consensus        52 G~~~~~~~~~~~~~~~~~~~~~~~d~vi~v~d~~~~~~~~---~~~~~~~~----~~~~~iiv~NK~Dl~~~~~  118 (158)
T cd01879          52 GTYSLSPYSEDEKVARDFLLGEKPDLIVNVVDATNLERNL---YLTLQLLE----LGLPVVVALNMIDEAEKRG  118 (158)
T ss_pred             CccccCCCChhHHHHHHHhcCCCCcEEEEEeeCCcchhHH---HHHHHHHH----cCCCEEEEEehhhhccccc
Confidence            5555543      345555301599999999999865533   34444443    3579999999999965443

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.

>PRK05306 infB translation initiation factor IF-2; Validated

Probab=98.39  E-value=1.1e-06  Score=61.89  Aligned_cols=56  Identities=20%  Similarity=0.217  Sum_probs=43.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|..++..+.+  .+|++|+|+|.++   +++++.+..    +.    ..++|+++++||+|+.+
T Consensus       345 PGhe~F~~m~~rga~--~aDiaILVVdAddGv~~qT~e~i~~----a~----~~~vPiIVviNKiDl~~  403 (787)
T PRK05306        345 PGHEAFTAMRARGAQ--VTDIVVLVVAADDGVMPQTIEAINH----AK----AAGVPIIVAINKIDKPG  403 (787)
T ss_pred             CCCccchhHHHhhhh--hCCEEEEEEECCCCCCHhHHHHHHH----HH----hcCCcEEEEEECccccc
Confidence            589999999988887  4999999999987   455554321    11    24689999999999954

>cd04168 TetM_like Tet(M)-like subfamily

Probab=98.38  E-value=2e-06  Score=52.97  Aligned_cols=59  Identities=19%  Similarity=0.119  Sum_probs=45.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|++.|......+++  .+|++++|+|.++.... ....|+..+..    .++|+++++||+|+..
T Consensus        72 PG~~~f~~~~~~~l~--~aD~~IlVvd~~~g~~~-~~~~~~~~~~~----~~~P~iivvNK~D~~~  130 (237)
T cd04168          72 PGHMDFIAEVERSLS--VLDGAILVISAVEGVQA-QTRILWRLLRK----LNIPTIIFVNKIDRAG  130 (237)
T ss_pred             CCccchHHHHHHHHH--HhCeEEEEEeCCCCCCH-HHHHHHHHHHH----cCCCEEEEEECccccC
Confidence            578889888888888  59999999999986543 34455555543    3579999999999864

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.

>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed

Probab=98.37  E-value=8.9e-07  Score=58.88  Aligned_cols=47  Identities=30%  Similarity=0.374  Sum_probs=37.2

Q ss_pred             hhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805          15 FVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus        15 ~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +++  ++|++++|+|.+++.+++....|..       ..+.|+++|+||+|+....
T Consensus       291 ~~~--~aD~il~VvD~s~~~s~~~~~~l~~-------~~~~piiiV~NK~DL~~~~  337 (449)
T PRK05291        291 AIE--EADLVLLVLDASEPLTEEDDEILEE-------LKDKPVIVVLNKADLTGEI  337 (449)
T ss_pred             HHH--hCCEEEEEecCCCCCChhHHHHHHh-------cCCCCcEEEEEhhhccccc
Confidence            445  6999999999999998887655543       2568999999999996543

>PRK04213 GTP-binding protein; Provisional

Probab=98.34  E-value=2.2e-07  Score=55.07  Aligned_cols=62  Identities=18%  Similarity=0.148  Sum_probs=35.8

Q ss_pred             cccchhhhhhhhhcc--CCcEEEEEEECCChhHHHHH-HHHHH--------HHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           5 TSCFTNLVVNFVQTY--HPDVFVIVYSVIERKTFKKA-EDMLK--------TLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~--~~~~~ilv~d~~~~~s~~~~-~~~~~--------~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+|+.++..|++..  .++++++|.|.   .++.++ ..|..        ++.......++|+++|+||+|+.+.
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~vi~v~d~---~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~p~iiv~NK~Dl~~~  145 (201)
T PRK04213         73 QEKIKDEIVRYIEDNADRILAAVLVVDG---KSFIEIIERWEGRGEIPIDVEMFDFLRELGIPPIVAVNKMDKIKN  145 (201)
T ss_pred             HHHHHHHHHHHHHhhhhhheEEEEEEeC---ccccccccccccCCCcHHHHHHHHHHHHcCCCeEEEEECccccCc
Confidence            678888888887631  23455555554   444333 33421        1111111246899999999999643

>cd00881 GTP_translation_factor GTP translation factor family

Probab=98.32  E-value=3.2e-06  Score=49.02  Aligned_cols=59  Identities=19%  Similarity=0.196  Sum_probs=44.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|++.|......+++  ++|++++|+|.++..+... ..++..+..    .+.|+++|+||+|+..
T Consensus        70 pG~~~~~~~~~~~~~--~~d~~i~v~d~~~~~~~~~-~~~~~~~~~----~~~~i~iv~nK~D~~~  128 (189)
T cd00881          70 PGHEDFSSEVIRGLS--VSDGAILVVDANEGVQPQT-REHLRIARE----GGLPIIVAINKIDRVG  128 (189)
T ss_pred             CCcHHHHHHHHHHHH--hcCEEEEEEECCCCCcHHH-HHHHHHHHH----CCCCeEEEEECCCCcc
Confidence            467788888888888  5999999999987665443 233333332    5689999999999964

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.

>PRK12289 GTPase RsgA; Reviewed

Probab=98.31  E-value=1.8e-06  Score=56.02  Aligned_cols=45  Identities=22%  Similarity=0.268  Sum_probs=36.8

Q ss_pred             CCcEEEEEEECCChh-HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERK-TFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |+|.+++|+|++++. +...+.+|+..+..    .++|+++|.||+||..
T Consensus        89 NvD~vLlV~d~~~p~~~~~~LdR~L~~a~~----~~ip~ILVlNK~DLv~  134 (352)
T PRK12289         89 NADQILLVFALAEPPLDPWQLSRFLVKAES----TGLEIVLCLNKADLVS  134 (352)
T ss_pred             cCCEEEEEEECCCCCCCHHHHHHHHHHHHH----CCCCEEEEEEchhcCC
Confidence            799999999999876 55577888766632    5689999999999964

>TIGR00483 EF-1_alpha translation elongation factor EF-1 alpha

Probab=98.29  E-value=9.3e-07  Score=58.23  Aligned_cols=62  Identities=18%  Similarity=0.134  Sum_probs=40.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHH-HHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAED-MLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~-~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||++|.......++  ++|++++|+|.++.+++...+. +...+..  ..+..++++++||+|+.+
T Consensus        93 pGh~~f~~~~~~~~~--~aD~~ilVvDa~~~~~~~~~~t~~~~~~~~--~~~~~~iIVviNK~Dl~~  155 (426)
T TIGR00483        93 PGHRDFIKNMITGAS--QADAAVLVVAVGDGEFEVQPQTREHAFLAR--TLGINQLIVAINKMDSVN  155 (426)
T ss_pred             CCHHHHHHHHHhhhh--hCCEEEEEEECCCCCcccCCchHHHHHHHH--HcCCCeEEEEEEChhccC
Confidence            578888655555555  5999999999998865422211 1112222  123457999999999963

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.

>TIGR01394 TypA_BipA GTP-binding protein TypA/BipA

Probab=98.28  E-value=3.2e-06  Score=58.01  Aligned_cols=61  Identities=20%  Similarity=0.156  Sum_probs=47.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .||+.|......+++  .+|++++|+|.++. ...+.+.|+..+..    .++|+++|.||+|+.+.+
T Consensus        72 PGh~DF~~ev~~~l~--~aD~alLVVDa~~G-~~~qT~~~l~~a~~----~~ip~IVviNKiD~~~a~  132 (594)
T TIGR01394        72 PGHADFGGEVERVLG--MVDGVLLLVDASEG-PMPQTRFVLKKALE----LGLKPIVVINKIDRPSAR  132 (594)
T ss_pred             CCHHHHHHHHHHHHH--hCCEEEEEEeCCCC-CcHHHHHHHHHHHH----CCCCEEEEEECCCCCCcC
Confidence            589999988888888  49999999999763 34555666666654    457899999999986543

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.

>cd04169 RF3 RF3 subfamily

Probab=98.27  E-value=4.5e-06  Score=52.22  Aligned_cols=59  Identities=15%  Similarity=0.113  Sum_probs=41.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+++|......+++  ++|++++|+|.++.-. .....++.....    .++|+++++||+|+..
T Consensus        79 PG~~df~~~~~~~l~--~aD~~IlVvda~~g~~-~~~~~i~~~~~~----~~~P~iivvNK~D~~~  137 (267)
T cd04169          79 PGHEDFSEDTYRTLT--AVDSAVMVIDAAKGVE-PQTRKLFEVCRL----RGIPIITFINKLDREG  137 (267)
T ss_pred             CCchHHHHHHHHHHH--HCCEEEEEEECCCCcc-HHHHHHHHHHHh----cCCCEEEEEECCccCC
Confidence            578888876666777  5999999999987532 222334333332    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.

>TIGR03597 GTPase_YqeH ribosome biogenesis GTPase YqeH

Probab=98.27  E-value=6.1e-07  Score=58.16  Aligned_cols=55  Identities=25%  Similarity=0.335  Sum_probs=42.9

Q ss_pred             cccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           5 TSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|.|+.+.+.+++  +++++++|+|+.+..     ..|.+++.+..  .+.|+++|+||+||..
T Consensus        50 ~e~f~~~l~~~~~--~~~~Il~VvD~~d~~-----~s~~~~l~~~~--~~~piilV~NK~DLl~  104 (360)
T TIGR03597        50 DDDFLNLLNSLGD--SNALIVYVVDIFDFE-----GSLIPELKRFV--GGNPVLLVGNKIDLLP  104 (360)
T ss_pred             HHHHHHHHhhccc--CCcEEEEEEECcCCC-----CCccHHHHHHh--CCCCEEEEEEchhhCC
Confidence            4678889898888  599999999997654     34666666542  4679999999999854

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=98.27  E-value=1.3e-06  Score=51.63  Aligned_cols=52  Identities=27%  Similarity=0.309  Sum_probs=37.7

Q ss_pred             chhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           8 FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         8 f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |+++.+.|++  +++++++|+|++++..     .|...+...  ..+.|+++|+||+|+..
T Consensus        24 ~~~~l~~~~~--~ad~il~VvD~~~~~~-----~~~~~l~~~--~~~~~~ilV~NK~Dl~~   75 (190)
T cd01855          24 ILNLLSSISP--KKALVVHVVDIFDFPG-----SLIPRLRLF--GGNNPVILVGNKIDLLP   75 (190)
T ss_pred             HHHHHHhccc--CCcEEEEEEECccCCC-----ccchhHHHh--cCCCcEEEEEEchhcCC
Confidence            5777788887  5999999999987642     233333221  24679999999999853

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.

>PRK12288 GTPase RsgA; Reviewed

Probab=98.24  E-value=3.2e-06  Score=54.77  Aligned_cols=45  Identities=24%  Similarity=0.209  Sum_probs=38.9

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |.|.+++|++++...++..+..|+..+..    .++|.++|.||+||..
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            79999999999988999999999875542    4589999999999964

>PRK14845 translation initiation factor IF-2; Provisional

Probab=98.21  E-value=4.4e-06  Score=60.32  Aligned_cols=56  Identities=25%  Similarity=0.233  Sum_probs=44.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|.+++...++  .+|++++|+|.++   +++++.+..    +..    .++|+++|+||+|+..
T Consensus       534 PGhe~F~~lr~~g~~--~aDivlLVVDa~~Gi~~qT~e~I~~----lk~----~~iPiIVViNKiDL~~  592 (1049)
T PRK14845        534 PGHEAFTSLRKRGGS--LADLAVLVVDINEGFKPQTIEAINI----LRQ----YKTPFVVAANKIDLIP  592 (1049)
T ss_pred             CCcHHHHHHHHhhcc--cCCEEEEEEECcccCCHhHHHHHHH----HHH----cCCCEEEEEECCCCcc
Confidence            589999999888777  5999999999986   677776643    222    3579999999999953

>KOG0077|consensus

Probab=98.21  E-value=3.2e-06  Score=50.00  Aligned_cols=64  Identities=13%  Similarity=0.252  Sum_probs=52.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +||-.-+..+..|+..  ++++++.+|.-|.+.|...+.-++.+.......++|+++.|||+|...
T Consensus        72 GGH~qArr~wkdyf~~--v~~iv~lvda~d~er~~es~~eld~ll~~e~la~vp~lilgnKId~p~  135 (193)
T KOG0077|consen   72 GGHLQARRVWKDYFPQ--VDAIVYLVDAYDQERFAESKKELDALLSDESLATVPFLILGNKIDIPY  135 (193)
T ss_pred             ccHHHHHHHHHHHHhh--hceeEeeeehhhHHHhHHHHHHHHHHHhHHHHhcCcceeecccccCCC
Confidence            5676677777788874  999999999999999999887776666544457899999999999864

>PRK15467 ethanolamine utilization protein EutP; Provisional

Probab=98.21  E-value=2.8e-06  Score=49.16  Aligned_cols=42  Identities=19%  Similarity=0.146  Sum_probs=32.5

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|++++|+|.++..++.  ..|+..+     ..+.|+++++||+|+.+
T Consensus        64 ~ad~il~v~d~~~~~s~~--~~~~~~~-----~~~~~ii~v~nK~Dl~~  105 (158)
T PRK15467         64 DVDMLIYVHGANDPESRL--PAGLLDI-----GVSKRQIAVISKTDMPD  105 (158)
T ss_pred             cCCEEEEEEeCCCccccc--CHHHHhc-----cCCCCeEEEEEccccCc
Confidence            599999999999998763  3454443     13568999999999854

>PRK00098 GTPase RsgA; Reviewed

Probab=98.21  E-value=2.6e-06  Score=54.00  Aligned_cols=45  Identities=24%  Similarity=0.202  Sum_probs=36.9

Q ss_pred             CCcEEEEEEECCChhHHHH-HHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKK-AEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~-~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |+|.+++|+|++++.++.. +.+|+..+..    .++|+++|.||+||.+
T Consensus        80 niD~vllV~d~~~p~~~~~~idr~L~~~~~----~~ip~iIVlNK~DL~~  125 (298)
T PRK00098         80 NVDQAVLVFAAKEPDFSTDLLDRFLVLAEA----NGIKPIIVLNKIDLLD  125 (298)
T ss_pred             cCCEEEEEEECCCCCCCHHHHHHHHHHHHH----CCCCEEEEEEhHHcCC
Confidence            7999999999999877655 4788776653    4689999999999963

>TIGR00475 selB selenocysteine-specific elongation factor SelB

Probab=98.19  E-value=3e-06  Score=58.01  Aligned_cols=57  Identities=19%  Similarity=0.019  Sum_probs=43.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~~   69 (75)
                      .||++|......++.  ++|++++|+|.++   +++++++.    .+..    .++| +++|+||+|+.+.
T Consensus        58 PGhe~f~~~~~~g~~--~aD~aILVVDa~~G~~~qT~ehl~----il~~----lgi~~iIVVlNK~Dlv~~  118 (581)
T TIGR00475        58 PGHEKFISNAIAGGG--GIDAALLVVDADEGVMTQTGEHLA----VLDL----LGIPHTIVVITKADRVNE  118 (581)
T ss_pred             CCHHHHHHHHHhhhc--cCCEEEEEEECCCCCcHHHHHHHH----HHHH----cCCCeEEEEEECCCCCCH
Confidence            588999877777777  6999999999998   66766653    1222    3466 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.

>PRK12296 obgE GTPase CgtA; Reviewed

Probab=98.18  E-value=3.5e-06  Score=56.84  Aligned_cols=62  Identities=21%  Similarity=0.297  Sum_probs=42.2

Q ss_pred             hhhhhhhhhcc-CCcEEEEEEECCC----hhHHHHHHHHHHHHHhhc----------CCCCCeEEEEeeCCCCcCCC
Q psy5805           9 TNLVVNFVQTY-HPDVFVIVYSVIE----RKTFKKAEDMLKTLWDSK----------YIGEKAVILVANKADLERRR   70 (75)
Q Consensus         9 ~~~~~~~~~~~-~~~~~ilv~d~~~----~~s~~~~~~~~~~~~~~~----------~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      ..+...+++.+ .++++++|+|+++    ++.++.+..|..++....          ...+.|+++|+||+|+.+.+
T Consensus       224 ~gLg~~fLrhieradvLv~VVD~s~~e~~rdp~~d~~~i~~EL~~y~~~l~~~~~~~~l~~kP~IVVlNKiDL~da~  300 (500)
T PRK12296        224 KGLGLDFLRHIERCAVLVHVVDCATLEPGRDPLSDIDALEAELAAYAPALDGDLGLGDLAERPRLVVLNKIDVPDAR  300 (500)
T ss_pred             hHHHHHHHHHHHhcCEEEEEECCcccccccCchhhHHHHHHHHHHhhhcccccchhhhhcCCCEEEEEECccchhhH
Confidence            34444444433 6999999999986    346666666666665432          12468999999999996543

>cd04164 trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes

Probab=98.15  E-value=6.3e-06  Score=46.34  Aligned_cols=43  Identities=23%  Similarity=0.244  Sum_probs=34.9

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +++++++|+|.+++.+......|..       ....|+++|+||+|+.+.
T Consensus        80 ~~~~~v~v~d~~~~~~~~~~~~~~~-------~~~~~vi~v~nK~D~~~~  122 (157)
T cd04164          80 EADLVLFVIDASRGLDEEDLEILEL-------PADKPIIVVLNKSDLLPD  122 (157)
T ss_pred             hCCEEEEEEECCCCCCHHHHHHHHh-------hcCCCEEEEEEchhcCCc
Confidence            5999999999999888877655532       256899999999998653

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.

>PRK13351 elongation factor G; Reviewed

Probab=98.12  E-value=1.2e-05  Score=55.87  Aligned_cols=59  Identities=15%  Similarity=0.010  Sum_probs=46.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+..|......+++  .+|++++|+|.++..+......|. .+..    .++|+++++||+|+..
T Consensus        81 PG~~df~~~~~~~l~--~aD~~ilVvd~~~~~~~~~~~~~~-~~~~----~~~p~iiviNK~D~~~  139 (687)
T PRK13351         81 PGHIDFTGEVERSLR--VLDGAVVVFDAVTGVQPQTETVWR-QADR----YGIPRLIFINKMDRVG  139 (687)
T ss_pred             CCcHHHHHHHHHHHH--hCCEEEEEEeCCCCCCHHHHHHHH-HHHh----cCCCEEEEEECCCCCC
Confidence            578889888888888  599999999999887777665563 3332    4689999999999875

>PRK15494 era GTPase Era; Provisional

Probab=98.09  E-value=1.1e-05  Score=52.04  Aligned_cols=43  Identities=23%  Similarity=0.438  Sum_probs=30.6

Q ss_pred             CCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|++++|+|.+  ++|.... .|+..+..    .+.|.++|+||+|+..
T Consensus       131 ~aDvil~VvD~~--~s~~~~~~~il~~l~~----~~~p~IlViNKiDl~~  174 (339)
T PRK15494        131 SADLVLLIIDSL--KSFDDITHNILDKLRS----LNIVPIFLLNKIDIES  174 (339)
T ss_pred             hCCEEEEEEECC--CCCCHHHHHHHHHHHh----cCCCEEEEEEhhcCcc
Confidence            799999999854  4666664 45555543    2356678999999864

>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA

Probab=98.04  E-value=1.6e-05  Score=52.18  Aligned_cols=46  Identities=26%  Similarity=0.320  Sum_probs=34.6

Q ss_pred             hhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805          15 FVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus        15 ~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      +++  ++|++++|+|.++..+.....- ...+..    .+.|+++|+||+|+.
T Consensus       251 ~~~--~ad~~ilV~D~~~~~~~~~~~~-~~~~~~----~~~~iiiv~NK~Dl~  296 (429)
T TIGR03594       251 AIE--RADVVLLVLDATEGITEQDLRI-AGLILE----AGKALVIVVNKWDLV  296 (429)
T ss_pred             HHH--hCCEEEEEEECCCCccHHHHHH-HHHHHH----cCCcEEEEEECcccC
Confidence            455  5999999999998877766532 233332    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.

>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed

Probab=98.04  E-value=1.4e-05  Score=55.85  Aligned_cols=57  Identities=18%  Similarity=0.290  Sum_probs=41.0

Q ss_pred             cccchhhhhh-hhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           5 TSCFTNLVVN-FVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         5 ~e~f~~~~~~-~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|.|..++.. +++  ++|++++|+|.++..++..+.-| ..+..    .+.|+++|+||+||.+
T Consensus       518 ~e~~~~~r~~~~i~--~advvilViDat~~~s~~~~~i~-~~~~~----~~~piIiV~NK~DL~~  575 (712)
T PRK09518        518 AEYYSSLRTQAAIE--RSELALFLFDASQPISEQDLKVM-SMAVD----AGRALVLVFNKWDLMD  575 (712)
T ss_pred             HHHHHHHHHHHHhh--cCCEEEEEEECCCCCCHHHHHHH-HHHHH----cCCCEEEEEEchhcCC
Confidence            3455554433 345  59999999999999888877544 33332    4589999999999964

>cd01894 EngA1 EngA1 subfamily

Probab=98.03  E-value=1.8e-05  Score=44.56  Aligned_cols=45  Identities=36%  Similarity=0.352  Sum_probs=31.2

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      ++|++++|+|..+..+..... ....++.    .+.|+++|+||+|+.+.
T Consensus        76 ~~d~ii~v~d~~~~~~~~~~~-~~~~~~~----~~~piiiv~nK~D~~~~  120 (157)
T cd01894          76 EADVILFVVDGREGLTPADEE-IAKYLRK----SKKPVILVVNKVDNIKE  120 (157)
T ss_pred             hCCEEEEEEeccccCCccHHH-HHHHHHh----cCCCEEEEEECcccCCh
Confidence            699999999998765544321 1122222    34899999999998653

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.

>cd01857 HSR1_MMR1 HSR1/MMR1

Probab=98.03  E-value=7.7e-06  Score=46.42  Aligned_cols=44  Identities=30%  Similarity=0.352  Sum_probs=32.9

Q ss_pred             CCcEEEEEEECCChhHHH--HHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFK--KAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~--~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|++++|+|..++.+..  .+..|+...    . .+.|+++|.||+|+..
T Consensus        11 ~aD~vl~ViD~~~p~~~~~~~l~~~l~~~----~-~~k~~iivlNK~DL~~   56 (141)
T cd01857          11 RSDIVVQIVDARNPLLFRPPDLERYVKEV----D-PRKKNILLLNKADLLT   56 (141)
T ss_pred             hCCEEEEEEEccCCcccCCHHHHHHHHhc----c-CCCcEEEEEechhcCC
Confidence            499999999999887654  445554432    1 4579999999999954

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.

>PRK10218 GTP-binding protein; Provisional

Probab=97.99  E-value=3.5e-05  Score=53.16  Aligned_cols=60  Identities=17%  Similarity=0.117  Sum_probs=44.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .||+.|......+++  ++|++++|+|.++.... +.+.++..+..    .++|.+++.||+|+...
T Consensus        76 PG~~df~~~v~~~l~--~aDg~ILVVDa~~G~~~-qt~~~l~~a~~----~gip~IVviNKiD~~~a  135 (607)
T PRK10218         76 PGHADFGGEVERVMS--MVDSVLLVVDAFDGPMP-QTRFVTKKAFA----YGLKPIVVINKVDRPGA  135 (607)
T ss_pred             CCcchhHHHHHHHHH--hCCEEEEEEecccCccH-HHHHHHHHHHH----cCCCEEEEEECcCCCCC
Confidence            589999999898888  59999999999875322 22333333332    45788999999998653

>cd01888 eIF2_gamma eIF2-gamma (gamma subunit of initiation factor 2)

Probab=97.99  E-value=1.9e-05  Score=47.27  Aligned_cols=57  Identities=19%  Similarity=0.190  Sum_probs=37.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCCh----hHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIER----KTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~----~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||++|.........  ++|++++|+|.+++    .+++.+..|    ..   ....|+++|.||+|+..
T Consensus        91 PG~~~~~~~~~~~~~--~~D~~llVvd~~~~~~~~~t~~~l~~~----~~---~~~~~iiivvNK~Dl~~  151 (203)
T cd01888          91 PGHEILMATMLSGAA--VMDGALLLIAANEPCPQPQTSEHLAAL----EI---MGLKHIIIVQNKIDLVK  151 (203)
T ss_pred             CChHHHHHHHHHhhh--cCCEEEEEEECCCCCCCcchHHHHHHH----HH---cCCCcEEEEEEchhccC
Confidence            356666554444444  58999999999873    455544433    21   12247899999999964

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

>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=97.99  E-value=2.8e-05  Score=46.42  Aligned_cols=65  Identities=11%  Similarity=0.236  Sum_probs=39.8

Q ss_pred             ccccchhhhhhh---hhccCCcEEEEEEECC-ChhHHHHHHHHHHHHHhhc--CCCCCeEEEEeeCCCCcCCC
Q psy5805           4 RTSCFTNLVVNF---VQTYHPDVFVIVYSVI-ERKTFKKAEDMLKTLWDSK--YIGEKAVILVANKADLERRR   70 (75)
Q Consensus         4 ~~e~f~~~~~~~---~~~~~~~~~ilv~d~~-~~~s~~~~~~~~~~~~~~~--~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      ||++.+.....+   ..  ++.|+|+|.|.+ .+..+..+..++-.+....  ....+|+++++||.|+...+
T Consensus        58 GH~rlr~~~~~~~~~~~--~~k~IIfvvDSs~~~~~~~~~Ae~Ly~iL~~~~~~~~~~piLIacNK~Dl~~A~  128 (181)
T PF09439_consen   58 GHPRLRSKLLDELKYLS--NAKGIIFVVDSSTDQKELRDVAEYLYDILSDTEVQKNKPPILIACNKQDLFTAK  128 (181)
T ss_dssp             T-HCCCHHHHHHHHHHG--GEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHCCTT--EEEEEEE-TTSTT--
T ss_pred             CcHHHHHHHHHhhhchh--hCCEEEEEEeCccchhhHHHHHHHHHHHHHhhhhccCCCCEEEEEeCccccccC
Confidence            777776533333   44  599999999987 4556666655554443321  23678999999999996543

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.

>PRK00741 prfC peptide chain release factor 3; Provisional

Probab=97.98  E-value=1.6e-05  Score=54.02  Aligned_cols=59  Identities=10%  Similarity=0.157  Sum_probs=42.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|......+++  .+|++|+|+|.++.-. .....++....    ..++|++++.||+|+..
T Consensus        87 PG~~df~~~~~~~l~--~aD~aIlVvDa~~gv~-~~t~~l~~~~~----~~~iPiiv~iNK~D~~~  145 (526)
T PRK00741         87 PGHEDFSEDTYRTLT--AVDSALMVIDAAKGVE-PQTRKLMEVCR----LRDTPIFTFINKLDRDG  145 (526)
T ss_pred             CCchhhHHHHHHHHH--HCCEEEEEEecCCCCC-HHHHHHHHHHH----hcCCCEEEEEECCcccc
Confidence            578889877777777  5999999999987421 12333333332    25689999999999864

>TIGR00436 era GTP-binding protein Era

Probab=97.97  E-value=2e-05  Score=49.19  Aligned_cols=43  Identities=23%  Similarity=0.179  Sum_probs=33.4

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|++++|+|.++..+.+  ..+...+..    .+.|+++|+||+|+..
T Consensus        79 ~aDvvl~VvD~~~~~~~~--~~i~~~l~~----~~~p~ilV~NK~Dl~~  121 (270)
T TIGR00436        79 GVDLILFVVDSDQWNGDG--EFVLTKLQN----LKRPVVLTRNKLDNKF  121 (270)
T ss_pred             hCCEEEEEEECCCCCchH--HHHHHHHHh----cCCCEEEEEECeeCCC
Confidence            699999999999887775  344444443    4579999999999864

Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.

>PRK00093 GTP-binding protein Der; Reviewed

Probab=97.97  E-value=4e-05  Score=50.46  Aligned_cols=48  Identities=27%  Similarity=0.273  Sum_probs=33.3

Q ss_pred             hhhhhhccCCcEEEEEEECCChhHHH--HHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          12 VVNFVQTYHPDVFVIVYSVIERKTFK--KAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        12 ~~~~~~~~~~~~~ilv~d~~~~~s~~--~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ...+++  ++|++++|+|.++..+..  .+..|+..       .+.|+++|+||+|+.+
T Consensus        74 ~~~~~~--~ad~il~vvd~~~~~~~~~~~~~~~l~~-------~~~piilv~NK~D~~~  123 (435)
T PRK00093         74 AELAIE--EADVILFVVDGRAGLTPADEEIAKILRK-------SNKPVILVVNKVDGPD  123 (435)
T ss_pred             HHHHHH--hCCEEEEEEECCCCCCHHHHHHHHHHHH-------cCCcEEEEEECccCcc
Confidence            344555  699999999998754432  33444332       2579999999999753

>cd01895 EngA2 EngA2 subfamily

Probab=97.95  E-value=4e-05  Score=43.54  Aligned_cols=45  Identities=27%  Similarity=0.364  Sum_probs=33.7

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      ++|++++|+|.+++.+..... +...+..    .+.|+++++||+|+...
T Consensus        84 ~~d~vi~v~d~~~~~~~~~~~-~~~~~~~----~~~~~iiv~nK~Dl~~~  128 (174)
T cd01895          84 RADVVLLVIDATEGITEQDLR-IAGLILE----EGKALVIVVNKWDLVEK  128 (174)
T ss_pred             hcCeEEEEEeCCCCcchhHHH-HHHHHHh----cCCCEEEEEeccccCCc
Confidence            599999999999988766543 3333332    35799999999999654

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.

>PRK12317 elongation factor 1-alpha; Reviewed

Probab=97.94  E-value=1.8e-05  Score=52.22  Aligned_cols=61  Identities=15%  Similarity=0.150  Sum_probs=37.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|........+  ++|++++|+|.+++.++... ..+...+..   .+..|+++++||+|+.+
T Consensus        92 pG~~~~~~~~~~~~~--~aD~~ilVvDa~~~~~~~~~~~~~~~~~~~---~~~~~iivviNK~Dl~~  153 (425)
T PRK12317         92 PGHRDFVKNMITGAS--QADAAVLVVAADDAGGVMPQTREHVFLART---LGINQLIVAINKMDAVN  153 (425)
T ss_pred             CCcccchhhHhhchh--cCCEEEEEEEcccCCCCCcchHHHHHHHHH---cCCCeEEEEEEcccccc
Confidence            578888654434444  59999999999874233222 222222222   23346899999999964

>cd00880 Era_like Era (E

Probab=97.94  E-value=5.3e-05  Score=42.02  Aligned_cols=50  Identities=26%  Similarity=0.321  Sum_probs=37.5

Q ss_pred             hhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805          14 NFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus        14 ~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .+.+  +++++++++|.++..+..... |.....    ..+.|+++|.||+|+....
T Consensus        71 ~~~~--~~d~il~v~~~~~~~~~~~~~-~~~~~~----~~~~~~ivv~nK~D~~~~~  120 (163)
T cd00880          71 RVLE--RADLILFVVDADLRADEEEEK-LLELLR----ERGKPVLLVLNKIDLLPEE  120 (163)
T ss_pred             HHHH--hCCEEEEEEeCCCCCCHHHHH-HHHHHH----hcCCeEEEEEEccccCChh
Confidence            3455  599999999999998877665 433333    2578999999999986543

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

>PRK12298 obgE GTPase CgtA; Reviewed

Probab=97.87  E-value=3.6e-05  Score=50.58  Aligned_cols=50  Identities=22%  Similarity=0.222  Sum_probs=39.6

Q ss_pred             CCcEEEEEEECC---ChhHHHHHHHHHHHHHhhc-CCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVI---ERKTFKKAEDMLKTLWDSK-YIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~---~~~s~~~~~~~~~~~~~~~-~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .++++++|+|++   +.+.++.+..|..++.... ...+.|+++|.||+|+...
T Consensus       237 radvlL~VVD~s~~~~~d~~e~~~~l~~eL~~~~~~L~~kP~IlVlNKiDl~~~  290 (390)
T PRK12298        237 RCRVLLHLIDIAPIDGSDPVENARIIINELEKYSPKLAEKPRWLVFNKIDLLDE  290 (390)
T ss_pred             hCCEEEEEeccCcccccChHHHHHHHHHHHHhhhhhhcCCCEEEEEeCCccCCh
Confidence            599999999998   5678888888888887642 1236799999999999643

>TIGR00437 feoB ferrous iron transporter FeoB

Probab=97.86  E-value=2.8e-05  Score=53.44  Aligned_cols=62  Identities=16%  Similarity=0.180  Sum_probs=38.5

Q ss_pred             cccccchhh------hhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           3 SRTSCFTNL------VVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         3 s~~e~f~~~------~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      .|+++|.+.      ...|+...++|+++.|+|.++.+.   ...+..++.+    .++|+++|+||+|+.+++.
T Consensus        49 PG~~~~~~~s~~e~v~~~~l~~~~aDvvI~VvDat~ler---~l~l~~ql~~----~~~PiIIVlNK~Dl~~~~~  116 (591)
T TIGR00437        49 PGIYSLTTFSLEEEVARDYLLNEKPDLVVNVVDASNLER---NLYLTLQLLE----LGIPMILALNLVDEAEKKG  116 (591)
T ss_pred             CCccccCccchHHHHHHHHHhhcCCCEEEEEecCCcchh---hHHHHHHHHh----cCCCEEEEEehhHHHHhCC
Confidence            356666543      333433115899999999987432   2233333332    4689999999999965444

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.

>KOG0072|consensus

Probab=97.85  E-value=5.5e-05  Score=44.04  Aligned_cols=60  Identities=17%  Similarity=0.226  Sum_probs=39.6

Q ss_pred             hhhhhhhhcc-CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          10 NLVVNFVQTY-HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        10 ~~~~~~~~~~-~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +++|.+..+| +.+++|+|.|.+|++-..-...-+..+.+........+++++||.|....
T Consensus        74 SirPyWRcYy~dt~avIyVVDssd~dris~a~~el~~mL~E~eLq~a~llv~anKqD~~~~  134 (182)
T KOG0072|consen   74 SIRPYWRCYYADTDAVIYVVDSSDRDRISIAGVELYSMLQEEELQHAKLLVFANKQDYSGA  134 (182)
T ss_pred             cccHHHHHHhcccceEEEEEeccchhhhhhhHHHHHHHhccHhhcCceEEEEeccccchhh
Confidence            3444333333 89999999999999876655433323322223456788999999998653

>TIGR00503 prfC peptide chain release factor 3

Probab=97.84  E-value=6.9e-05  Score=50.97  Aligned_cols=59  Identities=10%  Similarity=0.151  Sum_probs=41.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|......+++  .+|++|+|+|.++. -......++....    ..++|+++++||+|+..
T Consensus        88 PG~~df~~~~~~~l~--~aD~aIlVvDa~~g-v~~~t~~l~~~~~----~~~~PiivviNKiD~~~  146 (527)
T TIGR00503        88 PGHEDFSEDTYRTLT--AVDNCLMVIDAAKG-VETRTRKLMEVTR----LRDTPIFTFMNKLDRDI  146 (527)
T ss_pred             CChhhHHHHHHHHHH--hCCEEEEEEECCCC-CCHHHHHHHHHHH----hcCCCEEEEEECccccC
Confidence            578888776666677  59999999999863 1122334443332    25689999999999853

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.

>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=97.76  E-value=0.00016  Score=42.63  Aligned_cols=58  Identities=22%  Similarity=0.267  Sum_probs=39.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .||+.|......-.+  .+|++|+|.|..+.-.-..... +..+..    .++|+++|.||+|+.
T Consensus        78 PG~~~f~~~~~~~~~--~~D~ailvVda~~g~~~~~~~~-l~~~~~----~~~p~ivvlNK~D~~  135 (188)
T PF00009_consen   78 PGHEDFIKEMIRGLR--QADIAILVVDANDGIQPQTEEH-LKILRE----LGIPIIVVLNKMDLI  135 (188)
T ss_dssp             SSSHHHHHHHHHHHT--TSSEEEEEEETTTBSTHHHHHH-HHHHHH----TT-SEEEEEETCTSS
T ss_pred             ccccceeecccceec--ccccceeeeecccccccccccc-cccccc----cccceEEeeeeccch
Confidence            478888777777676  4999999999986533322222 233332    457899999999986

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 ....

>TIGR03598 GTPase_YsxC ribosome biogenesis GTP-binding protein YsxC/EngB

Probab=97.73  E-value=0.00011  Score=42.90  Aligned_cols=58  Identities=17%  Similarity=0.200  Sum_probs=38.4

Q ss_pred             ccchhhhhhhhhcc-CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           6 SCFTNLVVNFVQTY-HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         6 e~f~~~~~~~~~~~-~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +.|..+...|++.. +++++++|+|.+++-+...... +..+..    .+.|+++++||+|+..
T Consensus        85 ~~~~~~~~~~l~~~~~~~~ii~vvd~~~~~~~~~~~~-~~~~~~----~~~pviiv~nK~D~~~  143 (179)
T TIGR03598        85 EKWQKLIEEYLEKRENLKGVVLLMDIRHPLKELDLEM-LEWLRE----RGIPVLIVLTKADKLK  143 (179)
T ss_pred             HHHHHHHHHHHHhChhhcEEEEEecCCCCCCHHHHHH-HHHHHH----cCCCEEEEEECcccCC
Confidence            34555566666532 3579999999988655555432 223332    4589999999999854

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.

>cd01859 MJ1464 MJ1464

Probab=97.73  E-value=6e-05  Score=43.19  Aligned_cols=52  Identities=23%  Similarity=0.304  Sum_probs=33.7

Q ss_pred             hhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           9 TNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         9 ~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      +.+.....+  ++|.+++|+|.+++.+... ..+...+.    ..+.|+++|.||+|+.
T Consensus         3 ~~~~~~i~~--~aD~vl~V~D~~~~~~~~~-~~l~~~~~----~~~~p~iiv~NK~Dl~   54 (156)
T cd01859           3 KRLVRRIIK--ESDVVLEVLDARDPELTRS-RKLERYVL----ELGKKLLIVLNKADLV   54 (156)
T ss_pred             HHHHHHHHh--hCCEEEEEeeCCCCcccCC-HHHHHHHH----hCCCcEEEEEEhHHhC
Confidence            344555555  5999999999987653322 11211222    2357999999999985

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.

>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA

Probab=97.72  E-value=0.00013  Score=47.98  Aligned_cols=55  Identities=27%  Similarity=0.238  Sum_probs=37.4

Q ss_pred             ccchhhhhhhhhccCCcEEEEEEECCChhHHHH--HHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           6 SCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKK--AEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         6 e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +.+......+++  ++|++++|+|.++.-+...  +..|+   +.    .+.|+++|+||+|+...
T Consensus        66 ~~~~~~~~~~~~--~ad~vl~vvD~~~~~~~~d~~i~~~l---~~----~~~piilVvNK~D~~~~  122 (429)
T TIGR03594        66 KQIREQAEIAIE--EADVILFVVDGREGLTPEDEEIAKWL---RK----SGKPVILVANKIDGKKE  122 (429)
T ss_pred             HHHHHHHHHHHh--hCCEEEEEEeCCCCCCHHHHHHHHHH---HH----hCCCEEEEEECccCCcc
Confidence            445555566666  6999999999987544332  33343   22    35799999999998653

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.

>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed

Probab=97.72  E-value=0.0001  Score=51.61  Aligned_cols=53  Identities=23%  Similarity=0.234  Sum_probs=36.0

Q ss_pred             chhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           8 FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         8 f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |......+++  ++|++++|+|.++.  +... ..|...++.    .+.|+++|+||+|+..
T Consensus       344 ~~~~~~~~~~--~aD~iL~VvDa~~~--~~~~d~~i~~~Lr~----~~~pvIlV~NK~D~~~  397 (712)
T PRK09518        344 IASQAQIAVS--LADAVVFVVDGQVG--LTSTDERIVRMLRR----AGKPVVLAVNKIDDQA  397 (712)
T ss_pred             HHHHHHHHHH--hCCEEEEEEECCCC--CCHHHHHHHHHHHh----cCCCEEEEEECccccc
Confidence            3444455566  59999999999763  2222 235444543    5689999999999854

>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=97.71  E-value=0.00031  Score=34.65  Aligned_cols=43  Identities=23%  Similarity=0.316  Sum_probs=26.9

Q ss_pred             CcEEEEEEECCChhHH--HHHHHHHHHHHhhcCCCCCeEEEEeeCCC
Q psy5805          21 PDVFVIVYSVIERKTF--KKAEDMLKTLWDSKYIGEKAVILVANKAD   65 (75)
Q Consensus        21 ~~~~ilv~d~~~~~s~--~~~~~~~~~~~~~~~~~~~~~ilvgnK~D   65 (75)
                      ++++++++|++....+  +.=...+++++...  ++.|+++|.||+|
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            7899999999988655  33234456666643  5789999999998

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.

>cd04166 CysN_ATPS CysN_ATPS subfamily

Probab=97.70  E-value=0.00018  Score=43.24  Aligned_cols=60  Identities=17%  Similarity=0.182  Sum_probs=36.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+++|........+  ++|++++|+|.++... .........+..   ....++++|.||+|+..
T Consensus        85 pG~~~~~~~~~~~~~--~ad~~llVvD~~~~~~-~~~~~~~~~~~~---~~~~~iIvviNK~D~~~  144 (208)
T cd04166          85 PGHEQYTRNMVTGAS--TADLAILLVDARKGVL-EQTRRHSYILSL---LGIRHVVVAVNKMDLVD  144 (208)
T ss_pred             CcHHHHHHHHHHhhh--hCCEEEEEEECCCCcc-HhHHHHHHHHHH---cCCCcEEEEEEchhccc
Confidence            467777654455555  5999999999987532 111222222222   12235788999999864

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.

>TIGR03680 eif2g_arch translation initiation factor 2 subunit gamma

Probab=97.69  E-value=0.00012  Score=48.15  Aligned_cols=57  Identities=23%  Similarity=0.191  Sum_probs=38.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCCh----hHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIER----KTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~----~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||++|....-....  ++|++++|+|.++.    ++.+.+.    .+..   ..-.|++++.||+|+.+
T Consensus        88 PGh~~f~~~~~~g~~--~aD~aIlVVDa~~g~~~~qt~e~l~----~l~~---~gi~~iIVvvNK~Dl~~  148 (406)
T TIGR03680        88 PGHETLMATMLSGAA--LMDGALLVIAANEPCPQPQTKEHLM----ALEI---IGIKNIVIVQNKIDLVS  148 (406)
T ss_pred             CCHHHHHHHHHHHHH--HCCEEEEEEECCCCccccchHHHHH----HHHH---cCCCeEEEEEEccccCC
Confidence            478888666555555  48999999999953    3444433    2222   12346899999999964

eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA.

>PRK00093 GTP-binding protein Der; Reviewed

Probab=97.67  E-value=0.00013  Score=48.00  Aligned_cols=57  Identities=19%  Similarity=0.247  Sum_probs=38.3

Q ss_pred             cccchhhhh-hhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           5 TSCFTNLVV-NFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         5 ~e~f~~~~~-~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|.|...+. .+++  .+|++++|+|.++..+.....- ...+.+    ...|+++|+||+|+.+
T Consensus       241 ~e~~~~~~~~~~~~--~ad~~ilViD~~~~~~~~~~~i-~~~~~~----~~~~~ivv~NK~Dl~~  298 (435)
T PRK00093        241 VEKYSVIRTLKAIE--RADVVLLVIDATEGITEQDLRI-AGLALE----AGRALVIVVNKWDLVD  298 (435)
T ss_pred             HHHHHHHHHHHHHH--HCCEEEEEEeCCCCCCHHHHHH-HHHHHH----cCCcEEEEEECccCCC
Confidence            344443333 2455  4999999999998877766532 233332    3579999999999863

>TIGR00484 EF-G translation elongation factor EF-G

Probab=97.62  E-value=0.00027  Score=49.33  Aligned_cols=59  Identities=19%  Similarity=-0.019  Sum_probs=42.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+..|......+++  .+|++++|+|.++........-|. .+..    .++|+++++||+|+..
T Consensus        83 PG~~~~~~~~~~~l~--~~D~~ilVvda~~g~~~~~~~~~~-~~~~----~~~p~ivviNK~D~~~  141 (689)
T TIGR00484        83 PGHVDFTVEVERSLR--VLDGAVAVLDAVGGVQPQSETVWR-QANR----YEVPRIAFVNKMDKTG  141 (689)
T ss_pred             CCCcchhHHHHHHHH--HhCEEEEEEeCCCCCChhHHHHHH-HHHH----cCCCEEEEEECCCCCC
Confidence            477788777777777  599999999998765544433332 3332    3579999999999864

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.

>cd01889 SelB_euk SelB subfamily

Probab=97.61  E-value=0.00033  Score=41.39  Aligned_cols=43  Identities=26%  Similarity=0.251  Sum_probs=29.2

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .+|++++|+|.++..+......|.  +...   .+.|+++|+||+|+.
T Consensus        91 ~~d~vi~VvD~~~~~~~~~~~~~~--~~~~---~~~~~iiv~NK~Dl~  133 (192)
T cd01889          91 IIDLMLLVVDATKGIQTQTAECLV--IGEI---LCKKLIVVLNKIDLI  133 (192)
T ss_pred             hCCEEEEEEECCCCccHHHHHHHH--HHHH---cCCCEEEEEECcccC
Confidence            578999999998754443333332  1111   246999999999985

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

>cd01883 EF1_alpha Eukaryotic elongation factor 1 (EF1) alpha subfamily

Probab=97.59  E-value=0.00024  Score=43.05  Aligned_cols=59  Identities=24%  Similarity=0.267  Sum_probs=36.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhH---H----HHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKT---F----KKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s---~----~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .|+..|........+  .++++++|.|.++...   |    +....|. ....   ....|++++.||+|+.
T Consensus        85 pG~~~~~~~~~~~~~--~~d~~i~VvDa~~~~~~~~~~~~~~~~~~~~-~~~~---~~~~~iiivvNK~Dl~  150 (219)
T cd01883          85 PGHRDFVPNMITGAS--QADVAVLVVDARKGEFEAGFEKGGQTREHAL-LART---LGVKQLIVAVNKMDDV  150 (219)
T ss_pred             CChHHHHHHHHHHhh--hCCEEEEEEECCCCccccccccccchHHHHH-HHHH---cCCCeEEEEEEccccc
Confidence            466666544444444  5999999999998421   1    1122232 2221   2335899999999996

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

>COG2262 HflX GTPases [General function prediction only]

Probab=97.55  E-value=0.00048  Score=45.60  Aligned_cols=56  Identities=25%  Similarity=0.315  Sum_probs=42.7

Q ss_pred             chhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           8 FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         8 f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      |++-.+.-.   .+|.++.|.|.+++...+++..-..-+.+.. ..++|+++|-||+|+.
T Consensus       262 FksTLEE~~---~aDlllhVVDaSdp~~~~~~~~v~~vL~el~-~~~~p~i~v~NKiD~~  317 (411)
T COG2262         262 FKSTLEEVK---EADLLLHVVDASDPEILEKLEAVEDVLAEIG-ADEIPIILVLNKIDLL  317 (411)
T ss_pred             HHHHHHHhh---cCCEEEEEeecCChhHHHHHHHHHHHHHHcC-CCCCCEEEEEeccccc
Confidence            444444433   4999999999999988888877666666643 4679999999999964

>cd04170 EF-G_bact Elongation factor G (EF-G) subfamily

Probab=97.53  E-value=0.00046  Score=42.96  Aligned_cols=58  Identities=17%  Similarity=0.066  Sum_probs=41.4

Q ss_pred             ccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           4 RTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         4 ~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |+..|......+++  .+|++++|+|.++.........|. .+..    .++|.+++.||+|+..
T Consensus        73 G~~~f~~~~~~~l~--~aD~~i~Vvd~~~g~~~~~~~~~~-~~~~----~~~p~iivvNK~D~~~  130 (268)
T cd04170          73 GYADFVGETRAALR--AADAALVVVSAQSGVEVGTEKLWE-FADE----AGIPRIIFINKMDRER  130 (268)
T ss_pred             CHHHHHHHHHHHHH--HCCEEEEEEeCCCCCCHHHHHHHH-HHHH----cCCCEEEEEECCccCC
Confidence            55667666667777  499999999999876554444442 2322    4579999999999864

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

>PLN00043 elongation factor 1-alpha; Provisional

Probab=97.52  E-value=0.00028  Score=47.17  Aligned_cols=58  Identities=14%  Similarity=0.153  Sum_probs=40.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHH-------HHHHHHHHHHhhcCCCCC-eEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFK-------KAEDMLKTLWDSKYIGEK-AVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~-------~~~~~~~~~~~~~~~~~~-~~ilvgnK~Dl~   67 (75)
                      -||+.|........+  .+|++|+|+|.++ .+|+       +.+..+..+..    ..+ +++++.||+|+.
T Consensus        93 PGh~df~~~~~~g~~--~aD~aIlVVda~~-G~~e~g~~~~~qT~eh~~~~~~----~gi~~iIV~vNKmD~~  158 (447)
T PLN00043         93 PGHRDFIKNMITGTS--QADCAVLIIDSTT-GGFEAGISKDGQTREHALLAFT----LGVKQMICCCNKMDAT  158 (447)
T ss_pred             CCHHHHHHHHHhhhh--hccEEEEEEEccc-CceecccCCCchHHHHHHHHHH----cCCCcEEEEEEcccCC
Confidence            589999877777777  4999999999986 4443       33222222222    345 478899999975

>PRK04000 translation initiation factor IF-2 subunit gamma; Validated

Probab=97.49  E-value=0.00047  Score=45.61  Aligned_cols=56  Identities=21%  Similarity=0.203  Sum_probs=34.4

Q ss_pred             cccccchhhhhhhhhcc-CCcEEEEEEECCC----hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTY-HPDVFVIVYSVIE----RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~-~~~~~ilv~d~~~----~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|..   .++... ++|++++|+|.++    ..+.+.+..+    ..   ....|+++|+||+|+.+
T Consensus        93 PG~~~f~~---~~~~~~~~~D~~llVVDa~~~~~~~~t~~~l~~l----~~---~~i~~iiVVlNK~Dl~~  153 (411)
T PRK04000         93 PGHETLMA---TMLSGAALMDGAILVIAANEPCPQPQTKEHLMAL----DI---IGIKNIVIVQNKIDLVS  153 (411)
T ss_pred             CCHHHHHH---HHHHHHhhCCEEEEEEECCCCCCChhHHHHHHHH----HH---cCCCcEEEEEEeecccc
Confidence            35666543   233311 4799999999994    4455544332    21   12236899999999864

>cd04163 Era Era subfamily

Probab=97.47  E-value=0.00026  Score=39.74  Aligned_cols=43  Identities=30%  Similarity=0.440  Sum_probs=30.1

Q ss_pred             CCcEEEEEEECCChhHHHHHHHH-HHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDM-LKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~-~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +++++++|+|.+++  +.....| ...+..    .+.|+++|+||+|+..
T Consensus        82 ~~d~i~~v~d~~~~--~~~~~~~~~~~~~~----~~~~~iiv~nK~Dl~~  125 (168)
T cd04163          82 DVDLVLFVVDASEP--IGEGDEFILELLKK----SKTPVILVLNKIDLVK  125 (168)
T ss_pred             hCCEEEEEEECCCc--cCchHHHHHHHHHH----hCCCEEEEEEchhccc
Confidence            59999999999987  2222222 233332    2579999999999873

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.

>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional

Probab=97.45  E-value=0.00061  Score=47.25  Aligned_cols=56  Identities=16%  Similarity=0.054  Sum_probs=39.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      .|||+|.........  ++|++++|+|.++   +++.+.+.    .+..    .++| +++|.||+|+.+
T Consensus        59 PGhe~fi~~m~~g~~--~~D~~lLVVda~eg~~~qT~ehl~----il~~----lgi~~iIVVlNKiDlv~  118 (614)
T PRK10512         59 PGHEKFLSNMLAGVG--GIDHALLVVACDDGVMAQTREHLA----ILQL----TGNPMLTVALTKADRVD  118 (614)
T ss_pred             CCHHHHHHHHHHHhh--cCCEEEEEEECCCCCcHHHHHHHH----HHHH----cCCCeEEEEEECCccCC
Confidence            588999655555566  5999999999987   55655542    2222    2244 679999999964

>cd01876 YihA_EngB The YihA (EngB) subfamily

Probab=97.41  E-value=0.00043  Score=38.99  Aligned_cols=56  Identities=14%  Similarity=0.113  Sum_probs=36.3

Q ss_pred             cccchhhhhhhhhcc-CCcEEEEEEECCChh--HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           5 TSCFTNLVVNFVQTY-HPDVFVIVYSVIERK--TFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~-~~~~~ilv~d~~~~~--s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .+.|..+...|+... +.+++++++|.+...  ....+..|+..       ...|+++|+||+|+.
T Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~v~d~~~~~~~~~~~~~~~l~~-------~~~~vi~v~nK~D~~  123 (170)
T cd01876          65 KEKWGKLIEEYLENRENLKGVVLLIDSRHGPTEIDLEMLDWLEE-------LGIPFLVVLTKADKL  123 (170)
T ss_pred             HHHHHHHHHHHHHhChhhhEEEEEEEcCcCCCHhHHHHHHHHHH-------cCCCEEEEEEchhcC
Confidence            344566666666542 457888999988663  22334455433       237999999999984

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.

>PRK12740 elongation factor G; Reviewed

Probab=97.41  E-value=0.00077  Score=46.88  Aligned_cols=59  Identities=17%  Similarity=0.010  Sum_probs=43.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+..|......+++  .+|++++|+|.+...+......|. .+..    .++|+++|.||+|+..
T Consensus        68 PG~~~~~~~~~~~l~--~aD~vllvvd~~~~~~~~~~~~~~-~~~~----~~~p~iiv~NK~D~~~  126 (668)
T PRK12740         68 PGHVDFTGEVERALR--VLDGAVVVVCAVGGVEPQTETVWR-QAEK----YGVPRIIFVNKMDRAG  126 (668)
T ss_pred             CCcHHHHHHHHHHHH--HhCeEEEEEeCCCCcCHHHHHHHH-HHHH----cCCCEEEEEECCCCCC
Confidence            467777766677777  499999999999876665554443 3332    4579999999999864

>PRK00089 era GTPase Era; Reviewed

Probab=97.33  E-value=0.00059  Score=42.85  Aligned_cols=42  Identities=29%  Similarity=0.379  Sum_probs=29.1

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHH-HHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDML-KTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~-~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      ++|++++|+|.++.  +.....++ ..+.    ..+.|+++|+||+|+.
T Consensus        84 ~~D~il~vvd~~~~--~~~~~~~i~~~l~----~~~~pvilVlNKiDl~  126 (292)
T PRK00089         84 DVDLVLFVVDADEK--IGPGDEFILEKLK----KVKTPVILVLNKIDLV  126 (292)
T ss_pred             cCCEEEEEEeCCCC--CChhHHHHHHHHh----hcCCCEEEEEECCcCC
Confidence            69999999999982  22222222 2222    2468999999999996

>cd01886 EF-G Elongation factor G (EF-G) subfamily

Probab=97.27  E-value=0.0019  Score=40.66  Aligned_cols=59  Identities=19%  Similarity=0.064  Sum_probs=39.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+..|......+++  .+|++++|.|.++.-.-. ....+..+..    .++|++++.||+|+.+
T Consensus        72 PG~~df~~~~~~~l~--~aD~ailVVDa~~g~~~~-t~~~~~~~~~----~~~p~ivviNK~D~~~  130 (270)
T cd01886          72 PGHVDFTIEVERSLR--VLDGAVAVFDAVAGVEPQ-TETVWRQADR----YNVPRIAFVNKMDRTG  130 (270)
T ss_pred             CCcHHHHHHHHHHHH--HcCEEEEEEECCCCCCHH-HHHHHHHHHH----cCCCEEEEEECCCCCC
Confidence            467777777777777  499999999987642211 1222233332    4579999999999864

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

>KOG1707|consensus

Probab=97.19  E-value=0.0011  Score=45.73  Aligned_cols=49  Identities=27%  Similarity=0.433  Sum_probs=40.2

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      .+|.+.++||.+++.||..+.........   ....|+++|+.|+||.+..+
T Consensus       495 ~cDv~~~~YDsS~p~sf~~~a~v~~~~~~---~~~~Pc~~va~K~dlDe~~Q  543 (625)
T KOG1707|consen  495 ACDVACLVYDSSNPRSFEYLAEVYNKYFD---LYKIPCLMVATKADLDEVPQ  543 (625)
T ss_pred             eeeeEEEecccCCchHHHHHHHHHHHhhh---ccCCceEEEeeccccchhhh
Confidence            38999999999999999998776555443   36799999999999976553

>TIGR00490 aEF-2 translation elongation factor aEF-2

Probab=97.16  E-value=0.0013  Score=46.35  Aligned_cols=58  Identities=16%  Similarity=0.081  Sum_probs=39.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .|++.|.......++  .+|++++|+|..+--.-+....|. .+..    .+.|++++.||+|..
T Consensus        94 PG~~~f~~~~~~al~--~aD~~llVvda~~g~~~~t~~~~~-~~~~----~~~p~ivviNKiD~~  151 (720)
T TIGR00490        94 PGHVDFGGDVTRAMR--AVDGAIVVVCAVEGVMPQTETVLR-QALK----ENVKPVLFINKVDRL  151 (720)
T ss_pred             CCccccHHHHHHHHH--hcCEEEEEEecCCCCCccHHHHHH-HHHH----cCCCEEEEEEChhcc
Confidence            578888877777777  499999999987632222222232 1221    346778999999985

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.

>TIGR00485 EF-Tu translation elongation factor TU

Probab=97.14  E-value=0.0024  Score=41.97  Aligned_cols=56  Identities=13%  Similarity=0.093  Sum_probs=34.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeE-EEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~-ilvgnK~Dl~~   68 (75)
                      .||++|....-.-..  ++|++++|+|.++   +++.+.+.    .+..    .++|. +++.||+|+.+
T Consensus        83 pGh~~f~~~~~~~~~--~~D~~ilVvda~~g~~~qt~e~l~----~~~~----~gi~~iIvvvNK~Dl~~  142 (394)
T TIGR00485        83 PGHADYVKNMITGAA--QMDGAILVVSATDGPMPQTREHIL----LARQ----VGVPYIVVFLNKCDMVD  142 (394)
T ss_pred             CchHHHHHHHHHHHh--hCCEEEEEEECCCCCcHHHHHHHH----HHHH----cCCCEEEEEEEecccCC
Confidence            478887533333233  5899999999987   33433222    2322    24564 57899999864

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.

>PRK00454 engB GTP-binding protein YsxC; Reviewed

Probab=97.13  E-value=0.0019  Score=37.87  Aligned_cols=59  Identities=17%  Similarity=0.175  Sum_probs=36.4

Q ss_pred             cccchhhhhhhhhcc-CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           5 TSCFTNLVVNFVQTY-HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~-~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +++|..+...|++.. +.+++++++|.+++.+.... .....+..    .+.|+++++||+|+..
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~v~d~~~~~~~~~~-~i~~~l~~----~~~~~iiv~nK~Dl~~  149 (196)
T PRK00454         90 KEKWQKLIEEYLRTRENLKGVVLLIDSRHPLKELDL-QMIEWLKE----YGIPVLIVLTKADKLK  149 (196)
T ss_pred             HHHHHHHHHHHHHhCccceEEEEEEecCCCCCHHHH-HHHHHHHH----cCCcEEEEEECcccCC
Confidence            455666667777632 34678888888776544321 11122221    3578999999999854

>cd01858 NGP_1 NGP-1

Probab=97.09  E-value=0.0011  Score=38.07  Aligned_cols=44  Identities=30%  Similarity=0.308  Sum_probs=30.3

Q ss_pred             CCcEEEEEEECCChhH--HHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKT--FKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s--~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|.+++|.|..++.+  -..+..++   ..  ...+.|+++|.||+|+..
T Consensus         8 ~aD~il~VvD~~~p~~~~~~~i~~~l---~~--~~~~~p~ilVlNKiDl~~   53 (157)
T cd01858           8 SSDVVIQVLDARDPMGTRCKHVEEYL---KK--EKPHKHLIFVLNKCDLVP   53 (157)
T ss_pred             hCCEEEEEEECCCCccccCHHHHHHH---Hh--ccCCCCEEEEEEchhcCC
Confidence            5999999999988742  22333332   22  124579999999999954

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.

>COG0532 InfB Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]

Probab=97.09  E-value=0.0013  Score=44.65  Aligned_cols=56  Identities=14%  Similarity=0.201  Sum_probs=44.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      -|||.|.+|+..=...  +|.+|||.++++   +++.+.+.+    ++    ..++|+++..||+|..+
T Consensus        63 PGHeAFt~mRaRGa~v--tDIaILVVa~dDGv~pQTiEAI~h----ak----~a~vP~iVAiNKiDk~~  121 (509)
T COG0532          63 PGHEAFTAMRARGASV--TDIAILVVAADDGVMPQTIEAINH----AK----AAGVPIVVAINKIDKPE  121 (509)
T ss_pred             CcHHHHHHHHhcCCcc--ccEEEEEEEccCCcchhHHHHHHH----HH----HCCCCEEEEEecccCCC
Confidence            4899999999987776  999999999986   356555432    22    36799999999999863

>cd01849 YlqF_related_GTPase YlqF-related GTPases

Probab=97.08  E-value=0.00087  Score=38.45  Aligned_cols=43  Identities=28%  Similarity=0.189  Sum_probs=29.1

Q ss_pred             cEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        22 ~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |.+++|.|..++.+...  .|+.. ... ...+.|+++|.||+|+..
T Consensus         1 Dvvl~VvD~~~p~~~~~--~~i~~-~~~-~~~~~p~IiVlNK~Dl~~   43 (155)
T cd01849           1 DVILEVLDARDPLGTRS--PDIER-VLI-KEKGKKLILVLNKADLVP   43 (155)
T ss_pred             CEEEEEEeccCCccccC--HHHHH-HHH-hcCCCCEEEEEechhcCC
Confidence            57899999988866542  23331 111 125689999999999953

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.

>KOG1489|consensus

Probab=97.07  E-value=0.0021  Score=41.75  Aligned_cols=47  Identities=17%  Similarity=0.287  Sum_probs=37.7

Q ss_pred             CcEEEEEEECCCh---hHHHHHHHHHHHHHhhc-CCCCCeEEEEeeCCCCc
Q psy5805          21 PDVFVIVYSVIER---KTFKKAEDMLKTLWDSK-YIGEKAVILVANKADLE   67 (75)
Q Consensus        21 ~~~~ilv~d~~~~---~s~~~~~~~~~~~~~~~-~~~~~~~ilvgnK~Dl~   67 (75)
                      +..+++|.|++..   .-+++++....++..+. ...+-|.++|+||+|+.
T Consensus       275 ~~~l~fVvD~s~~~~~~p~~~~~lL~~ELe~yek~L~~rp~liVaNKiD~~  325 (366)
T KOG1489|consen  275 CKGLLFVVDLSGKQLRNPWQQLQLLIEELELYEKGLADRPALIVANKIDLP  325 (366)
T ss_pred             hceEEEEEECCCcccCCHHHHHHHHHHHHHHHhhhhccCceEEEEeccCch
Confidence            8899999999999   77787777666665542 34577999999999994

>cd04165 GTPBP1_like GTPBP1-like

Probab=96.93  E-value=0.0049  Score=37.73  Aligned_cols=61  Identities=16%  Similarity=0.154  Sum_probs=36.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||++|..-.-.-.....+|++++|.|.+...+ .....++..+..    .++|+++|.||+|+..
T Consensus        92 pG~~~~~~~~~~~~~~~~~D~~llVvda~~g~~-~~d~~~l~~l~~----~~ip~ivvvNK~D~~~  152 (224)
T cd04165          92 AGHERYLKTTLFGLTGYAPDYAMLVVAANAGII-GMTKEHLGLALA----LNIPVFVVVTKIDLAP  152 (224)
T ss_pred             CCcHHHHHHHHHhhcccCCCEEEEEEECCCCCc-HHHHHHHHHHHH----cCCCEEEEEECccccC
Confidence            477777543322221003899999999875432 222333333433    3478999999999853

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

>PRK01889 GTPase RsgA; Reviewed

Probab=96.88  E-value=0.004  Score=40.59  Aligned_cols=46  Identities=26%  Similarity=0.398  Sum_probs=34.7

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      |.|.+++|.+++..-+...+.+++..+..    .+++.++|.||+||.+.
T Consensus       112 NvD~vliV~s~~p~~~~~~ldr~L~~a~~----~~i~piIVLNK~DL~~~  157 (356)
T PRK01889        112 NVDTVFIVCSLNHDFNLRRIERYLALAWE----SGAEPVIVLTKADLCED  157 (356)
T ss_pred             eCCEEEEEEecCCCCChhHHHHHHHHHHH----cCCCEEEEEEChhcCCC
Confidence            78999999999755555566777666554    45677889999999643

>PRK13796 GTPase YqeH; Provisional

Probab=96.86  E-value=0.0017  Score=42.39  Aligned_cols=52  Identities=29%  Similarity=0.360  Sum_probs=33.8

Q ss_pred             cchhhhhhhhhccCCc-EEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           7 CFTNLVVNFVQTYHPD-VFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         7 ~f~~~~~~~~~~~~~~-~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|..+......   .+ .+++|.|+.+..     ..|...+.+..  .+.|+++|+||+||..
T Consensus        58 ~~~~~l~~i~~---~~~lIv~VVD~~D~~-----~s~~~~L~~~~--~~kpviLViNK~DLl~  110 (365)
T PRK13796         58 DFLKLLNGIGD---SDALVVNVVDIFDFN-----GSWIPGLHRFV--GNNPVLLVGNKADLLP  110 (365)
T ss_pred             HHHHHHHhhcc---cCcEEEEEEECccCC-----CchhHHHHHHh--CCCCEEEEEEchhhCC
Confidence            34444333333   44 788899987743     33566666532  4678999999999953

>KOG0090|consensus

Probab=96.77  E-value=0.0072  Score=37.32  Aligned_cols=64  Identities=20%  Similarity=0.336  Sum_probs=38.2

Q ss_pred             ccccchhhhhhhhh-ccCCcEEEEEEECC-ChhHHHHHHHHHHHH-Hhhc-CCCCCeEEEEeeCCCCc
Q psy5805           4 RTSCFTNLVVNFVQ-TYHPDVFVIVYSVI-ERKTFKKAEDMLKTL-WDSK-YIGEKAVILVANKADLE   67 (75)
Q Consensus         4 ~~e~f~~~~~~~~~-~~~~~~~ilv~d~~-~~~s~~~~~~~~~~~-~~~~-~~~~~~~ilvgnK~Dl~   67 (75)
                      ||++-+.-...|+. .|.+-++++|.|.. ...-...+..++-.+ .... ....+|++++.||.|+.
T Consensus        91 GH~rlR~kl~e~~~~~~~akaiVFVVDSa~f~k~vrdvaefLydil~~~~~~~~~~~vLIaCNKqDl~  158 (238)
T KOG0090|consen   91 GHSRLRRKLLEYLKHNYSAKAIVFVVDSATFLKNVRDVAEFLYDILLDSRVKKNKPPVLIACNKQDLF  158 (238)
T ss_pred             CcHHHHHHHHHHccccccceeEEEEEeccccchhhHHHHHHHHHHHHhhccccCCCCEEEEecchhhh
Confidence            67777644444443 33588888887754 333444444443333 3221 23578899999999985

>PRK09554 feoB ferrous iron transport protein B; Reviewed

Probab=96.77  E-value=0.0038  Score=44.48  Aligned_cols=46  Identities=13%  Similarity=0.160  Sum_probs=33.4

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .+|++++|.|.++.+.-   ..|..++.+    .++|++++.||+|+.+++.+
T Consensus        85 ~aD~vI~VvDat~ler~---l~l~~ql~e----~giPvIvVlNK~Dl~~~~~i  130 (772)
T PRK09554         85 DADLLINVVDASNLERN---LYLTLQLLE----LGIPCIVALNMLDIAEKQNI  130 (772)
T ss_pred             CCCEEEEEecCCcchhh---HHHHHHHHH----cCCCEEEEEEchhhhhccCc
Confidence            59999999999886542   235455544    35899999999998655443

>PRK12736 elongation factor Tu; Reviewed

Probab=96.74  E-value=0.0069  Score=39.90  Aligned_cols=56  Identities=13%  Similarity=0.112  Sum_probs=34.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCCh---hHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIER---KTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~---~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      -||+.|....-.-..  .+|++++|.|.+..   .+.+.+    ..+..    .++| ++++.||+|+.+
T Consensus        83 PGh~~f~~~~~~~~~--~~d~~llVvd~~~g~~~~t~~~~----~~~~~----~g~~~~IvviNK~D~~~  142 (394)
T PRK12736         83 PGHADYVKNMITGAA--QMDGAILVVAATDGPMPQTREHI----LLARQ----VGVPYLVVFLNKVDLVD  142 (394)
T ss_pred             CCHHHHHHHHHHHHh--hCCEEEEEEECCCCCchhHHHHH----HHHHH----cCCCEEEEEEEecCCcc
Confidence            367777543333334  48999999999763   333322    22332    2467 678999999863

>PRK12735 elongation factor Tu; Reviewed

Probab=96.65  E-value=0.0075  Score=39.76  Aligned_cols=59  Identities=12%  Similarity=0.113  Sum_probs=34.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEE-EEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~i-lvgnK~Dl~~   68 (75)
                      -||+.|......-..  ++|++++|+|.++... .+....+..+..    .++|.+ ++.||+|+.+
T Consensus        83 PGh~~f~~~~~~~~~--~aD~~llVvda~~g~~-~qt~e~l~~~~~----~gi~~iivvvNK~Dl~~  142 (396)
T PRK12735         83 PGHADYVKNMITGAA--QMDGAILVVSAADGPM-PQTREHILLARQ----VGVPYIVVFLNKCDMVD  142 (396)
T ss_pred             CCHHHHHHHHHhhhc--cCCEEEEEEECCCCCc-hhHHHHHHHHHH----cCCCeEEEEEEecCCcc
Confidence            367666433333333  5899999999986321 122222233332    346754 6799999953

>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=96.63  E-value=0.011  Score=36.69  Aligned_cols=53  Identities=15%  Similarity=0.177  Sum_probs=35.6

Q ss_pred             hhhhhhhccCCcEEEEEEECCChhHHHHHHH---HHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805          11 LVVNFVQTYHPDVFVIVYSVIERKTFKKAED---MLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus        11 ~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~---~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .++..++  +..++|+|+|+.+.+-.+.+..   .+..+.+  ..+++.+.+.-+|.|+.
T Consensus        69 ~~~~if~--~v~~LIyV~D~qs~~~~~~l~~~~~~i~~l~~--~sp~~~v~vfiHK~D~l  124 (232)
T PF04670_consen   69 QREEIFS--NVGVLIYVFDAQSDDYDEDLAYLSDCIEALRQ--YSPNIKVFVFIHKMDLL  124 (232)
T ss_dssp             CHHHHHC--TESEEEEEEETT-STCHHHHHHHHHHHHHHHH--HSTT-EEEEEEE-CCCS
T ss_pred             cHHHHHh--ccCEEEEEEEcccccHHHHHHHHHHHHHHHHH--hCCCCeEEEEEeecccC
Confidence            4566666  6999999999996654444444   4444444  35889999999999984

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.

>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=96.55  E-value=0.015  Score=35.78  Aligned_cols=24  Identities=8%  Similarity=0.176  Sum_probs=17.5

Q ss_pred             hhhhccCCcEEEEEEECCChh-HHHHH
Q psy5805          14 NFVQTYHPDVFVIVYSVIERK-TFKKA   39 (75)
Q Consensus        14 ~~~~~~~~~~~ilv~d~~~~~-s~~~~   39 (75)
                      .+++  +++++++|+|.++++ ..+.+
T Consensus        73 ~~~~--~ad~il~V~D~t~~~~~~~~~   97 (233)
T cd01896          73 AVAR--TADLILMVLDATKPEGHREIL   97 (233)
T ss_pred             Hhhc--cCCEEEEEecCCcchhHHHHH
Confidence            3455  699999999998876 44433

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.

>KOG1144|consensus

Probab=96.48  E-value=0.0041  Score=44.46  Aligned_cols=54  Identities=24%  Similarity=0.303  Sum_probs=42.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECC---ChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVI---ERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADL   66 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~---~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl   66 (75)
                      -|||.|..++......  ++.+|+|.||.   .+++.+++.    .++    ..+.|+|+.-||+|.
T Consensus       548 pghEsFtnlRsrgssl--C~~aIlvvdImhGlepqtiESi~----lLR----~rktpFivALNKiDR  604 (1064)
T KOG1144|consen  548 PGHESFTNLRSRGSSL--CDLAILVVDIMHGLEPQTIESIN----LLR----MRKTPFIVALNKIDR  604 (1064)
T ss_pred             CCchhhhhhhhccccc--cceEEEEeehhccCCcchhHHHH----HHH----hcCCCeEEeehhhhh
Confidence            4899999999998884  99999999996   344554432    222    367899999999995

>cd04104 p47_IIGP_like p47 (47-kDa) family

Probab=96.47  E-value=0.0067  Score=36.15  Aligned_cols=40  Identities=25%  Similarity=0.344  Sum_probs=27.2

Q ss_pred             CCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805          20 HPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      ++|.++++-+    .+|... ..|++.++..    ..|+++|+||+|+.
T Consensus        80 ~~d~~l~v~~----~~~~~~d~~~~~~l~~~----~~~~ilV~nK~D~~  120 (197)
T cd04104          80 EYDFFIIISS----TRFSSNDVKLAKAIQCM----GKKFYFVRTKVDRD  120 (197)
T ss_pred             CcCEEEEEeC----CCCCHHHHHHHHHHHHh----CCCEEEEEecccch
Confidence            5888888732    345555 4566666542    46899999999983

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

>PRK12739 elongation factor G; Reviewed

Probab=96.47  E-value=0.014  Score=41.04  Aligned_cols=59  Identities=17%  Similarity=0.012  Sum_probs=39.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+..|........+  .+|++++|.|.++.-.-....-| ..+..    .++|++++.||+|+..
T Consensus        81 PG~~~f~~e~~~al~--~~D~~ilVvDa~~g~~~qt~~i~-~~~~~----~~~p~iv~iNK~D~~~  139 (691)
T PRK12739         81 PGHVDFTIEVERSLR--VLDGAVAVFDAVSGVEPQSETVW-RQADK----YGVPRIVFVNKMDRIG  139 (691)
T ss_pred             CCHHHHHHHHHHHHH--HhCeEEEEEeCCCCCCHHHHHHH-HHHHH----cCCCEEEEEECCCCCC
Confidence            366667666666666  49999999998765332222222 22322    4578899999999864

>cd01884 EF_Tu EF-Tu subfamily

Probab=96.45  E-value=0.017  Score=34.69  Aligned_cols=57  Identities=14%  Similarity=0.132  Sum_probs=33.5

Q ss_pred             ccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCc
Q psy5805           4 RTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLE   67 (75)
Q Consensus         4 ~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~   67 (75)
                      |+..|......-..  .+|++++|.|.+..-.- .....+..+..    .++| ++++.||.|+.
T Consensus        74 G~~~~~~~~~~~~~--~~D~~ilVvda~~g~~~-~~~~~~~~~~~----~~~~~iIvviNK~D~~  131 (195)
T cd01884          74 GHADYIKNMITGAA--QMDGAILVVSATDGPMP-QTREHLLLARQ----VGVPYIVVFLNKADMV  131 (195)
T ss_pred             CHHHHHHHHHHHhh--hCCEEEEEEECCCCCcH-HHHHHHHHHHH----cCCCcEEEEEeCCCCC
Confidence            55555433333344  59999999998764221 12222233332    3355 77899999985

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.

>TIGR02034 CysN sulfate adenylyltransferase, large subunit

Probab=96.44  E-value=0.0086  Score=39.62  Aligned_cols=60  Identities=17%  Similarity=0.141  Sum_probs=35.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      -||+.|......-..  .+|++++|.|.+..-.-+..+.|. .+..   .+..+++++.||+|+.+
T Consensus        88 PGh~~f~~~~~~~~~--~aD~allVVda~~G~~~qt~~~~~-~~~~---~~~~~iivviNK~D~~~  147 (406)
T TIGR02034        88 PGHEQYTRNMATGAS--TADLAVLLVDARKGVLEQTRRHSY-IASL---LGIRHVVLAVNKMDLVD  147 (406)
T ss_pred             CCHHHHHHHHHHHHh--hCCEEEEEEECCCCCccccHHHHH-HHHH---cCCCcEEEEEEeccccc
Confidence            478888543334344  499999999986542211112222 2222   12236889999999853

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).

>PRK13768 GTPase; Provisional

Probab=96.43  E-value=0.0055  Score=38.14  Aligned_cols=59  Identities=22%  Similarity=0.094  Sum_probs=35.0

Q ss_pred             hhhhhhhhhcc---CCcEEEEEEECCChhHHHHH--HHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           9 TNLVVNFVQTY---HPDVFVIVYSVIERKTFKKA--EDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         9 ~~~~~~~~~~~---~~~~~ilv~d~~~~~s~~~~--~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +...+.+.+.+   ++++++++.|.....+-...  ..|+.......  .+.|+++|.||+|+...
T Consensus       114 ~~~~~~~~~~l~~~~~~~ii~liD~~~~~~~~d~~~~~~l~~~~~~~--~~~~~i~v~nK~D~~~~  177 (253)
T PRK13768        114 RESGRKLVERLSGSSKSVVVFLIDAVLAKTPSDFVSLLLLALSVQLR--LGLPQIPVLNKADLLSE  177 (253)
T ss_pred             hHHHHHHHHHHHhcCCeEEEEEechHHhCCHHHHHHHHHHHHHHHHH--cCCCEEEEEEhHhhcCc
Confidence            44444444432   27899999999654333222  23333333222  46899999999998643

>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional

Probab=96.28  E-value=0.013  Score=39.58  Aligned_cols=60  Identities=13%  Similarity=0.112  Sum_probs=34.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|......-..  .+|++++|.|.+..-.=.....|. .+..   .+..+++++.||+|+.+
T Consensus       115 PGh~~f~~~~~~~l~--~aD~allVVDa~~G~~~qt~~~~~-l~~~---lg~~~iIvvvNKiD~~~  174 (474)
T PRK05124        115 PGHEQYTRNMATGAS--TCDLAILLIDARKGVLDQTRRHSF-IATL---LGIKHLVVAVNKMDLVD  174 (474)
T ss_pred             CCcHHHHHHHHHHHh--hCCEEEEEEECCCCccccchHHHH-HHHH---hCCCceEEEEEeecccc
Confidence            468888533333334  599999999987532111111221 1221   12237889999999863

>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=96.27  E-value=0.015  Score=38.13  Aligned_cols=63  Identities=14%  Similarity=0.258  Sum_probs=39.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChh----------HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERK----------TFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~----------s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      |||-.-+.-+..++.  +.+++|+|.++++-+          .+...-..++.+.+.....+.|++|+-||.|+-
T Consensus       244 GGqr~eRkKW~~~F~--~v~~vif~vsls~ydq~~~ed~~~nrl~esl~lF~~i~~~~~~~~~~iil~lnK~D~f  316 (389)
T PF00503_consen  244 GGQRSERKKWIHCFE--DVTAVIFVVSLSEYDQTLYEDPNTNRLHESLNLFESICNNPWFKNTPIILFLNKIDLF  316 (389)
T ss_dssp             TSSGGGGGGGGGGGT--TESEEEEEEEGGGGGSBESSSTTSBHHHHHHHHHHHHHTSGGGTTSEEEEEEE-HHHH
T ss_pred             CCCchhhhhHHHHhc--cccEEEEeecccchhhhhcccchHHHHHHHHHHHHHHHhCcccccCceEEeeecHHHH
Confidence            566444444555555  799999999986432          243333344455443334689999999999983

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 ....

>PLN00116 translation elongation factor EF-2 subunit; Provisional

Probab=96.16  E-value=0.016  Score=41.67  Aligned_cols=58  Identities=17%  Similarity=0.092  Sum_probs=39.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      -||..|..-...-.+  .+|++|+|.|...--......-|. .+.    ..++|++++.||.|..
T Consensus       106 PGh~dF~~e~~~al~--~~D~ailVvda~~Gv~~~t~~~~~-~~~----~~~~p~i~~iNK~D~~  163 (843)
T PLN00116        106 PGHVDFSSEVTAALR--ITDGALVVVDCIEGVCVQTETVLR-QAL----GERIRPVLTVNKMDRC  163 (843)
T ss_pred             CCHHHHHHHHHHHHh--hcCEEEEEEECCCCCcccHHHHHH-HHH----HCCCCEEEEEECCccc
Confidence            477788666666566  499999999988653333333343 222    2568999999999985

>PLN03126 Elongation factor Tu; Provisional

Probab=96.10  E-value=0.025  Score=38.41  Aligned_cols=59  Identities=10%  Similarity=0.069  Sum_probs=36.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      -||+.|-.....-..  .+|++++|.|.++-.. .+.+.++..+..    .++| ++++.||+|+.+
T Consensus       152 PGh~~f~~~~~~g~~--~aD~ailVVda~~G~~-~qt~e~~~~~~~----~gi~~iIvvvNK~Dl~~  211 (478)
T PLN03126        152 PGHADYVKNMITGAA--QMDGAILVVSGADGPM-PQTKEHILLAKQ----VGVPNMVVFLNKQDQVD  211 (478)
T ss_pred             CCHHHHHHHHHHHHh--hCCEEEEEEECCCCCc-HHHHHHHHHHHH----cCCCeEEEEEecccccC
Confidence            467777544433344  4999999999875422 222333333332    3467 788999999854

>cd01856 YlqF YlqF

Probab=96.10  E-value=0.0054  Score=35.74  Aligned_cols=42  Identities=29%  Similarity=0.296  Sum_probs=28.3

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|.+++|+|..++.+-... .+...      ..+.|+++|.||+|+..
T Consensus        19 ~aD~il~v~D~~~~~~~~~~-~i~~~------~~~k~~ilVlNK~Dl~~   60 (171)
T cd01856          19 LVDLVIEVRDARIPLSSRNP-LLEKI------LGNKPRIIVLNKADLAD   60 (171)
T ss_pred             hCCEEEEEeeccCccCcCCh-hhHhH------hcCCCEEEEEehhhcCC
Confidence            69999999999876432211 11111      13468999999999964

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.

>KOG1145|consensus

Probab=96.05  E-value=0.019  Score=39.92  Aligned_cols=56  Identities=14%  Similarity=0.219  Sum_probs=43.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      -||..|.+||..=-.  .+|.+++|...+|   +++.+.+++    .    ...++|+|+.-||+|-.+
T Consensus       209 PGHaAF~aMRaRGA~--vtDIvVLVVAadDGVmpQT~EaIkh----A----k~A~VpiVvAinKiDkp~  267 (683)
T KOG1145|consen  209 PGHAAFSAMRARGAN--VTDIVVLVVAADDGVMPQTLEAIKH----A----KSANVPIVVAINKIDKPG  267 (683)
T ss_pred             CcHHHHHHHHhccCc--cccEEEEEEEccCCccHhHHHHHHH----H----HhcCCCEEEEEeccCCCC
Confidence            489999999988777  4999999998876   356555432    1    247899999999999754

>CHL00071 tufA elongation factor Tu

Probab=95.94  E-value=0.037  Score=36.66  Aligned_cols=58  Identities=10%  Similarity=0.097  Sum_probs=34.6

Q ss_pred             ccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           4 RTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         4 ~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      ||+.|-.....-..  .+|++++|.|.+..-. .+....+..+..    .++| ++++.||.|+.+
T Consensus        84 Gh~~~~~~~~~~~~--~~D~~ilVvda~~g~~-~qt~~~~~~~~~----~g~~~iIvvvNK~D~~~  142 (409)
T CHL00071         84 GHADYVKNMITGAA--QMDGAILVVSAADGPM-PQTKEHILLAKQ----VGVPNIVVFLNKEDQVD  142 (409)
T ss_pred             ChHHHHHHHHHHHH--hCCEEEEEEECCCCCc-HHHHHHHHHHHH----cCCCEEEEEEEccCCCC
Confidence            56666433333334  4999999999875321 222222233332    3467 778999999864

>PRK07560 elongation factor EF-2; Reviewed

Probab=95.85  E-value=0.025  Score=40.10  Aligned_cols=58  Identities=16%  Similarity=0.084  Sum_probs=38.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      -||..|........+  .+|++++|.|...--.-.....|.. ...    .+.|.+++.||+|+.
T Consensus        95 PG~~df~~~~~~~l~--~~D~avlVvda~~g~~~~t~~~~~~-~~~----~~~~~iv~iNK~D~~  152 (731)
T PRK07560         95 PGHVDFGGDVTRAMR--AVDGAIVVVDAVEGVMPQTETVLRQ-ALR----ERVKPVLFINKVDRL  152 (731)
T ss_pred             CCccChHHHHHHHHH--hcCEEEEEEECCCCCCccHHHHHHH-HHH----cCCCeEEEEECchhh
Confidence            377778776677677  4999999999876433222233432 222    235778999999975

>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional

Probab=95.84  E-value=0.024  Score=39.53  Aligned_cols=60  Identities=18%  Similarity=0.156  Sum_probs=35.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|......-..  .+|++++|.|.+..-.-+....+ ..+..   .+..+++++.||+|+.+
T Consensus       112 PG~~~f~~~~~~~~~--~aD~~llVvda~~g~~~~t~e~~-~~~~~---~~~~~iivvvNK~D~~~  171 (632)
T PRK05506        112 PGHEQYTRNMVTGAS--TADLAIILVDARKGVLTQTRRHS-FIASL---LGIRHVVLAVNKMDLVD  171 (632)
T ss_pred             CChHHHHHHHHHHHH--hCCEEEEEEECCCCccccCHHHH-HHHHH---hCCCeEEEEEEeccccc
Confidence            467777543333344  59999999998654211111112 12222   13357889999999863

>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=95.82  E-value=0.012  Score=34.36  Aligned_cols=44  Identities=23%  Similarity=0.316  Sum_probs=31.0

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      ..|+++.|.|.++.+.-..   ...++.+    -++|+++|.||+|....+
T Consensus        78 ~~D~ii~VvDa~~l~r~l~---l~~ql~e----~g~P~vvvlN~~D~a~~~  121 (156)
T PF02421_consen   78 KPDLIIVVVDATNLERNLY---LTLQLLE----LGIPVVVVLNKMDEAERK  121 (156)
T ss_dssp             SSSEEEEEEEGGGHHHHHH---HHHHHHH----TTSSEEEEEETHHHHHHT
T ss_pred             CCCEEEEECCCCCHHHHHH---HHHHHHH----cCCCEEEEEeCHHHHHHc
Confidence            5999999999987543222   2333443    358999999999986443

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 ....

>PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional

Probab=95.81  E-value=0.034  Score=37.63  Aligned_cols=60  Identities=17%  Similarity=0.173  Sum_probs=34.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChh-HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERK-TFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      -||+.|-.-.-.-..  ++|++++|.|.+..- .-+..+.+ ..+..   .+-.++++|-||+|+.+
T Consensus       125 PGH~~fi~~m~~g~~--~~D~alLVVda~~g~~~~qT~ehl-~i~~~---lgi~~iIVvlNKiDlv~  185 (460)
T PTZ00327        125 PGHDILMATMLNGAA--VMDAALLLIAANESCPQPQTSEHL-AAVEI---MKLKHIIILQNKIDLVK  185 (460)
T ss_pred             CCHHHHHHHHHHHHh--hCCEEEEEEECCCCccchhhHHHH-HHHHH---cCCCcEEEEEecccccC
Confidence            367777433223233  499999999998631 11111222 22221   12246899999999864

>KOG0082|consensus

Probab=95.74  E-value=0.043  Score=36.07  Aligned_cols=60  Identities=15%  Similarity=0.332  Sum_probs=37.3

Q ss_pred             hhhhhhhhhcc-CCcEEEEEEECCChhHH--HH--------HHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           9 TNLVVNFVQTY-HPDVFVIVYSVIERKTF--KK--------AEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         9 ~~~~~~~~~~~-~~~~~ilv~d~~~~~s~--~~--------~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++-+..+.+.+ |++++|+|.++++-+-.  +.        ..+.++.+.+...-.+.++||.-||.||-+
T Consensus       206 RseRrKWihcFe~v~aviF~vslSeYdq~l~ED~~~NRM~eS~~LF~sI~n~~~F~~tsiiLFLNK~DLFe  276 (354)
T KOG0082|consen  206 RSERKKWIHCFEDVTAVIFCVSLSEYDQVLEEDETTNRMHESLKLFESICNNKWFANTSIILFLNKKDLFE  276 (354)
T ss_pred             HHHhhhHHHhhcCCCEEEEEEehhhhhhhcccccchhHHHHHHHHHHHHhcCcccccCcEEEEeecHHHHH
Confidence            34444555555 89999999999865321  11        122333333333235789999999999954

>PTZ00416 elongation factor 2; Provisional

Probab=95.74  E-value=0.028  Score=40.51  Aligned_cols=58  Identities=16%  Similarity=0.165  Sum_probs=37.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      -||..|..-...-.+  .+|++|+|.|.++--.-..-.-| ..+..    .++|++++.||+|+.
T Consensus       100 PG~~~f~~~~~~al~--~~D~ailVvda~~g~~~~t~~~~-~~~~~----~~~p~iv~iNK~D~~  157 (836)
T PTZ00416        100 PGHVDFSSEVTAALR--VTDGALVVVDCVEGVCVQTETVL-RQALQ----ERIRPVLFINKVDRA  157 (836)
T ss_pred             CCHHhHHHHHHHHHh--cCCeEEEEEECCCCcCccHHHHH-HHHHH----cCCCEEEEEEChhhh
Confidence            366667555555556  49999999998764322222233 23332    457999999999985

>KOG3886|consensus

Probab=95.69  E-value=0.056  Score=34.11  Aligned_cols=64  Identities=20%  Similarity=0.196  Sum_probs=42.3

Q ss_pred             cccccc-----hhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhh-cCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCF-----TNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDS-KYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f-----~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~-~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|||.|     ++.....++  +.+++|.|||+...+--..+..+.+-++.. +.++...+.+.-.|.||..
T Consensus        61 Ggqe~fmen~~~~q~d~iF~--nV~vli~vFDves~e~~~D~~~yqk~Le~ll~~SP~AkiF~l~hKmDLv~  130 (295)
T KOG3886|consen   61 GGQEEFMENYLSSQEDNIFR--NVQVLIYVFDVESREMEKDFHYYQKCLEALLQNSPEAKIFCLLHKMDLVQ  130 (295)
T ss_pred             CCcHHHHHHHHhhcchhhhe--eheeeeeeeeccchhhhhhHHHHHHHHHHHHhcCCcceEEEEEeechhcc
Confidence            466644     223334445  799999999999887665555554433222 1457778899999999954

>PRK00049 elongation factor Tu; Reviewed

Probab=95.69  E-value=0.044  Score=36.20  Aligned_cols=58  Identities=12%  Similarity=0.112  Sum_probs=34.6

Q ss_pred             ccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEE-EEeeCCCCcC
Q psy5805           4 RTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLER   68 (75)
Q Consensus         4 ~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~i-lvgnK~Dl~~   68 (75)
                      ||++|......-..  .+|++++|.|.+..-. ......+..+..    .++|.+ ++.||.|+..
T Consensus        84 G~~~f~~~~~~~~~--~aD~~llVVDa~~g~~-~qt~~~~~~~~~----~g~p~iiVvvNK~D~~~  142 (396)
T PRK00049         84 GHADYVKNMITGAA--QMDGAILVVSAADGPM-PQTREHILLARQ----VGVPYIVVFLNKCDMVD  142 (396)
T ss_pred             CHHHHHHHHHhhhc--cCCEEEEEEECCCCCc-hHHHHHHHHHHH----cCCCEEEEEEeecCCcc
Confidence            56666433333344  5999999999876422 222223333332    346865 6899999863

>TIGR03596 GTPase_YlqF ribosome biogenesis GTP-binding protein YlqF

Probab=95.65  E-value=0.024  Score=35.65  Aligned_cols=42  Identities=29%  Similarity=0.363  Sum_probs=28.8

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|.+++|.|...+.+..+  .++.+..     .+.|+++|.||+||..
T Consensus        21 ~aDvVl~V~Dar~p~~~~~--~~i~~~l-----~~kp~IiVlNK~DL~~   62 (276)
T TIGR03596        21 LVDVVIEVLDARIPLSSRN--PMIDEIR-----GNKPRLIVLNKADLAD   62 (276)
T ss_pred             hCCEEEEEEeCCCCCCCCC--hhHHHHH-----CCCCEEEEEEccccCC
Confidence            5999999999987654332  1122221     2469999999999953

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.

>cd01850 CDC_Septin CDC/Septin

Probab=95.52  E-value=0.013  Score=36.94  Aligned_cols=15  Identities=33%  Similarity=0.257  Sum_probs=13.0

Q ss_pred             CCeEEEEeeCCCCcC
Q psy5805          54 EKAVILVANKADLER   68 (75)
Q Consensus        54 ~~~~ilvgnK~Dl~~   68 (75)
                      .+|+++|+||+|+..
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.

>PRK09563 rbgA GTPase YlqF; Reviewed

Probab=95.50  E-value=0.022  Score=36.05  Aligned_cols=42  Identities=26%  Similarity=0.348  Sum_probs=29.2

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+|.+++|.|...+.+..+  .++.+..     .+.|+++|.||+||.+
T Consensus        24 ~aDvIL~VvDar~p~~~~~--~~l~~~~-----~~kp~iiVlNK~DL~~   65 (287)
T PRK09563         24 LVDVVIEVLDARIPLSSEN--PMIDKII-----GNKPRLLILNKSDLAD   65 (287)
T ss_pred             hCCEEEEEEECCCCCCCCC--hhHHHHh-----CCCCEEEEEEchhcCC
Confidence            5999999999977654332  1222222     2578999999999953

>COG1084 Predicted GTPase [General function prediction only]

Probab=95.46  E-value=0.045  Score=35.73  Aligned_cols=46  Identities=15%  Similarity=0.335  Sum_probs=33.2

Q ss_pred             CcEEEEEEECCChhHH--HHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          21 PDVFVIVYSVIERKTF--KKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        21 ~~~~ilv~d~~~~~s~--~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +++++++||.+....|  +.=.+.+++++...   +.|+++|.||.|+.+.
T Consensus       248 ~~~IlF~~D~Se~cgy~lE~Q~~L~~eIk~~f---~~p~v~V~nK~D~~~~  295 (346)
T COG1084         248 AGVILFLFDPSETCGYSLEEQISLLEEIKELF---KAPIVVVINKIDIADE  295 (346)
T ss_pred             cCeEEEEEcCccccCCCHHHHHHHHHHHHHhc---CCCeEEEEecccccch
Confidence            6889999999877643  33344556666533   3899999999998743

>PRK00007 elongation factor G; Reviewed

Probab=95.41  E-value=0.094  Score=37.08  Aligned_cols=58  Identities=17%  Similarity=-0.015  Sum_probs=36.1

Q ss_pred             ccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           4 RTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         4 ~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |+..|..-...-.+  .+|++++|.|...--.-+...-|. .+..    .+.|.+++.||.|+..
T Consensus        84 G~~~f~~ev~~al~--~~D~~vlVvda~~g~~~qt~~~~~-~~~~----~~~p~iv~vNK~D~~~  141 (693)
T PRK00007         84 GHVDFTIEVERSLR--VLDGAVAVFDAVGGVEPQSETVWR-QADK----YKVPRIAFVNKMDRTG  141 (693)
T ss_pred             CcHHHHHHHHHHHH--HcCEEEEEEECCCCcchhhHHHHH-HHHH----cCCCEEEEEECCCCCC
Confidence            55566543444445  499999999976543333333332 2332    3478899999999864

>KOG0462|consensus

Probab=95.33  E-value=0.086  Score=36.76  Aligned_cols=61  Identities=18%  Similarity=0.131  Sum_probs=39.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      -||-.|+.-....+..  ++|+++|.|.+.---=+.+.+++..+.     .+..+|.|-||+|+...+
T Consensus       133 PGHvDFs~EVsRslaa--c~G~lLvVDA~qGvqAQT~anf~lAfe-----~~L~iIpVlNKIDlp~ad  193 (650)
T KOG0462|consen  133 PGHVDFSGEVSRSLAA--CDGALLVVDASQGVQAQTVANFYLAFE-----AGLAIIPVLNKIDLPSAD  193 (650)
T ss_pred             CCcccccceehehhhh--cCceEEEEEcCcCchHHHHHHHHHHHH-----cCCeEEEeeeccCCCCCC
Confidence            4777887555555553  999999999874322222333332222     457889999999997643

>cd04178 Nucleostemin_like Nucleostemin-like

Probab=95.29  E-value=0.022  Score=33.61  Aligned_cols=44  Identities=25%  Similarity=0.279  Sum_probs=27.0

Q ss_pred             cEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        22 ~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |+++++.|..++.+-.+ ....+.+. . ...+.|+++|.||+||..
T Consensus         1 DvVl~VvDar~p~~~~~-~~i~~~~~-l-~~~~kp~IlVlNK~DL~~   44 (172)
T cd04178           1 DVILEVLDARDPLGCRC-PQVEEAVL-Q-AGGNKKLVLVLNKIDLVP   44 (172)
T ss_pred             CEEEEEEECCCCCCCCC-HHHHHHHH-h-ccCCCCEEEEEehhhcCC
Confidence            67899999887633221 11222211 1 124579999999999964

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

>KOG4273|consensus

Probab=95.28  E-value=0.013  Score=37.37  Aligned_cols=43  Identities=23%  Similarity=0.344  Sum_probs=32.5

Q ss_pred             CcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCc
Q psy5805          21 PDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLE   67 (75)
Q Consensus        21 ~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~   67 (75)
                      ..+++++||++....+..++.|+..-.    ....- .+.+|||.|..
T Consensus        79 l~a~vmvfdlse~s~l~alqdwl~htd----insfdillcignkvdrv  122 (418)
T KOG4273|consen   79 LQAFVMVFDLSEKSGLDALQDWLPHTD----INSFDILLCIGNKVDRV  122 (418)
T ss_pred             eeeEEEEEeccchhhhHHHHhhccccc----cccchhheecccccccc
Confidence            468999999999999999999975432    12233 35689999963

>PLN03127 Elongation factor Tu; Provisional

Probab=95.27  E-value=0.085  Score=35.57  Aligned_cols=59  Identities=10%  Similarity=0.094  Sum_probs=33.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      -||+.|-.....-..  .+|++++|.|.++.-. .+....+..+..    .++| ++++.||+|+.+
T Consensus       132 PGh~~f~~~~~~g~~--~aD~allVVda~~g~~-~qt~e~l~~~~~----~gip~iIvviNKiDlv~  191 (447)
T PLN03127        132 PGHADYVKNMITGAA--QMDGGILVVSAPDGPM-PQTKEHILLARQ----VGVPSLVVFLNKVDVVD  191 (447)
T ss_pred             CCccchHHHHHHHHh--hCCEEEEEEECCCCCc-hhHHHHHHHHHH----cCCCeEEEEEEeeccCC
Confidence            366666433333333  4999999999875321 111222222332    3467 578899999864

>KOG0468|consensus

Probab=95.18  E-value=0.047  Score=39.00  Aligned_cols=58  Identities=21%  Similarity=0.267  Sum_probs=41.6

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADL   66 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl   66 (75)
                      +.||-.|..-...-++.  +|++++++|.-.--+++. .+.++...    ..+.|+++|-||.|.
T Consensus       204 TPGHVnF~DE~ta~l~~--sDgvVlvvDv~EGVmlnt-Er~ikhai----q~~~~i~vviNKiDR  261 (971)
T KOG0468|consen  204 TPGHVNFSDETTASLRL--SDGVVLVVDVAEGVMLNT-ERIIKHAI----QNRLPIVVVINKVDR  261 (971)
T ss_pred             CCCcccchHHHHHHhhh--cceEEEEEEcccCceeeH-HHHHHHHH----hccCcEEEEEehhHH
Confidence            46888887777777775  999999999976655543 22222222    256899999999996

>PRK09866 hypothetical protein; Provisional

Probab=95.10  E-value=0.083  Score=37.61  Aligned_cols=46  Identities=11%  Similarity=0.166  Sum_probs=30.5

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|++++|.|.+...+...- ...+.++..  ....|+++|.||+|+.+
T Consensus       258 eADvVLFVVDat~~~s~~De-eIlk~Lkk~--~K~~PVILVVNKIDl~d  303 (741)
T PRK09866        258 RASAVLAVLDYTQLKSISDE-EVREAILAV--GQSVPLYVLVNKFDQQD  303 (741)
T ss_pred             hCCEEEEEEeCCCCCChhHH-HHHHHHHhc--CCCCCEEEEEEcccCCC
Confidence            59999999999875443331 122333331  12369999999999853

>COG0486 ThdF Predicted GTPase [General function prediction only]

Probab=94.99  E-value=0.062  Score=36.39  Aligned_cols=43  Identities=26%  Similarity=0.220  Sum_probs=30.4

Q ss_pred             CCcEEEEEEECCChh-HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIERK-TFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .||.+++|+|.+.+. ..+...-|       ....+.|+++|.||.||..+
T Consensus       296 ~ADlvL~v~D~~~~~~~~d~~~~~-------~~~~~~~~i~v~NK~DL~~~  339 (454)
T COG0486         296 EADLVLFVLDASQPLDKEDLALIE-------LLPKKKPIIVVLNKADLVSK  339 (454)
T ss_pred             hCCEEEEEEeCCCCCchhhHHHHH-------hcccCCCEEEEEechhcccc
Confidence            499999999999862 22221111       12467899999999999764

>COG1160 Predicted GTPases [General function prediction only]

Probab=94.76  E-value=0.13  Score=34.79  Aligned_cols=41  Identities=32%  Similarity=0.355  Sum_probs=28.5

Q ss_pred             CCcEEEEEEECCCh-hHHH-HHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805          20 HPDVFVIVYSVIER-KTFK-KAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus        20 ~~~~~ilv~d~~~~-~s~~-~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .||++|+|.|...- ...+ .+.+|+.       ..+.|+++|.||+|-.
T Consensus        83 eADvilfvVD~~~Git~~D~~ia~~Lr-------~~~kpviLvvNK~D~~  125 (444)
T COG1160          83 EADVILFVVDGREGITPADEEIAKILR-------RSKKPVILVVNKIDNL  125 (444)
T ss_pred             hCCEEEEEEeCCCCCCHHHHHHHHHHH-------hcCCCEEEEEEcccCc
Confidence            59999999998652 2222 3344432       1457999999999975

>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=94.56  E-value=0.19  Score=27.06  Aligned_cols=36  Identities=28%  Similarity=0.304  Sum_probs=25.5

Q ss_pred             CCcEEEEEEECCCh--hHHHHHHHHHHHHHhhcCCCCCeEEEEeeC
Q psy5805          20 HPDVFVIVYSVIER--KTFKKAEDMLKTLWDSKYIGEKAVILVANK   63 (75)
Q Consensus        20 ~~~~~ilv~d~~~~--~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK   63 (75)
                      .+|++++|+|.+++  ++..++.+|+   +     .+.|+++|-||
T Consensus        79 ~~d~ii~vv~~~~~~~~~~~~~~~~l---~-----~~~~~i~v~NK  116 (116)
T PF01926_consen   79 KSDLIIYVVDASNPITEDDKNILREL---K-----NKKPIILVLNK  116 (116)
T ss_dssp             TESEEEEEEETTSHSHHHHHHHHHHH---H-----TTSEEEEEEES
T ss_pred             HCCEEEEEEECCCCCCHHHHHHHHHH---h-----cCCCEEEEEcC
Confidence            59999999998774  2344443333   2     45799999998

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 ....

>COG0536 Obg Predicted GTPase [General function prediction only]

Probab=94.45  E-value=0.13  Score=33.90  Aligned_cols=47  Identities=23%  Similarity=0.249  Sum_probs=33.0

Q ss_pred             CcEEEEEEECCChhH---HHHHHHHHHHHHhhc-CCCCCeEEEEeeCCCCc
Q psy5805          21 PDVFVIVYSVIERKT---FKKAEDMLKTLWDSK-YIGEKAVILVANKADLE   67 (75)
Q Consensus        21 ~~~~ilv~d~~~~~s---~~~~~~~~~~~~~~~-~~~~~~~ilvgnK~Dl~   67 (75)
                      +..++.|.|++..+-   .+..+....++..+. ...+.|.++|.||+|+.
T Consensus       238 t~vL~hviD~s~~~~~dp~~~~~~i~~EL~~Y~~~L~~K~~ivv~NKiD~~  288 (369)
T COG0536         238 TRVLLHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKPRIVVLNKIDLP  288 (369)
T ss_pred             hheeEEEEecCcccCCCHHHHHHHHHHHHHHhhHHhccCceEEEEeccCCC
Confidence            778899999986653   555555555555542 34577999999999953

>PTZ00141 elongation factor 1- alpha; Provisional

Probab=93.60  E-value=0.21  Score=33.63  Aligned_cols=57  Identities=18%  Similarity=0.183  Sum_probs=34.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChh---HH---HHH-HHHHHHHHhhcCCCCCe-EEEEeeCCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERK---TF---KKA-EDMLKTLWDSKYIGEKA-VILVANKADL   66 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~---s~---~~~-~~~~~~~~~~~~~~~~~-~ilvgnK~Dl   66 (75)
                      -||++|-.....-..  .+|++++|.|.+.-.   .|   .+. +.|. .+..    -.+| +|++-||.|+
T Consensus        93 PGh~~f~~~~~~g~~--~aD~ailVVda~~G~~e~~~~~~~qT~eh~~-~~~~----~gi~~iiv~vNKmD~  157 (446)
T PTZ00141         93 PGHRDFIKNMITGTS--QADVAILVVASTAGEFEAGISKDGQTREHAL-LAFT----LGVKQMIVCINKMDD  157 (446)
T ss_pred             CChHHHHHHHHHhhh--hcCEEEEEEEcCCCceecccCCCccHHHHHH-HHHH----cCCCeEEEEEEcccc
Confidence            478888554444445  499999999987531   11   122 2332 2322    3455 6789999994

>COG0480 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]

Probab=92.88  E-value=0.28  Score=34.99  Aligned_cols=58  Identities=21%  Similarity=0.004  Sum_probs=41.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      -||-.|..-...-.+.  .|++++|+|...--..+.-.-|. +..    ..++|.+++-||.|..
T Consensus        84 PGHVDFt~EV~rslrv--lDgavvVvdaveGV~~QTEtv~r-qa~----~~~vp~i~fiNKmDR~  141 (697)
T COG0480          84 PGHVDFTIEVERSLRV--LDGAVVVVDAVEGVEPQTETVWR-QAD----KYGVPRILFVNKMDRL  141 (697)
T ss_pred             CCccccHHHHHHHHHh--hcceEEEEECCCCeeecHHHHHH-HHh----hcCCCeEEEEECcccc
Confidence            4788888777777775  99999999987553333333343 222    2568999999999974

>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=92.79  E-value=0.78  Score=26.08  Aligned_cols=54  Identities=24%  Similarity=0.247  Sum_probs=35.4

Q ss_pred             cccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCC
Q psy5805           5 TSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKA   64 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~   64 (75)
                      ......+...|..  .+|++|+|.+.+..-+-.....+......    .....++|-||.
T Consensus       115 ~~~~~~~~~~~~~--~~d~vi~V~~~~~~~~~~~~~~l~~~~~~----~~~~~i~V~nk~  168 (168)
T PF00350_consen  115 NSEHTEITEEYLP--KADVVIFVVDANQDLTESDMEFLKQMLDP----DKSRTIFVLNKA  168 (168)
T ss_dssp             HTTTSHHHHHHHS--TTEEEEEEEETTSTGGGHHHHHHHHHHTT----TCSSEEEEEE-G
T ss_pred             hhhhHHHHHHhhc--cCCEEEEEeccCcccchHHHHHHHHHhcC----CCCeEEEEEcCC
Confidence            3444567777887  59999999999886554555555544443    223488888884

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 ....

>KOG0705|consensus

Probab=92.78  E-value=0.079  Score=37.10  Aligned_cols=53  Identities=23%  Similarity=0.441  Sum_probs=41.6

Q ss_pred             hhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805          13 VNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus        13 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      ..|..  ..|++|+||.+.+..+|+.+......+........+|++++|++.-..
T Consensus        90 aQft~--wvdavIfvf~~~d~~s~q~v~~l~~~l~~~r~r~~i~l~lvgtqd~iS  142 (749)
T KOG0705|consen   90 AQFCQ--WVDAVVFVFSVEDEQSFQAVQALAHEMSSYRNISDLPLILVGTQDHIS  142 (749)
T ss_pred             hhhhh--hccceEEEEEeccccCHHHHHHHHhhcccccccccchHHhhcCcchhh
Confidence            34555  599999999999999999998887777655445678899998875443

>smart00053 DYNc Dynamin, GTPase

Probab=92.68  E-value=0.66  Score=28.94  Aligned_cols=55  Identities=16%  Similarity=0.128  Sum_probs=31.1

Q ss_pred             chhhhhhhhhccCCcEEEEEEECCC-hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           8 FTNLVVNFVQTYHPDVFVIVYSVIE-RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         8 f~~~~~~~~~~~~~~~~ilv~d~~~-~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ...+...|.+. ..+.+++|.|.+. ....+ .......+.    ....++++|.||.|..+
T Consensus       151 i~~lv~~yi~~-~~~IIL~Vvda~~d~~~~d-~l~ia~~ld----~~~~rti~ViTK~D~~~  206 (240)
T smart00053      151 IKDMIKQFISK-EECLILAVTPANVDLANSD-ALKLAKEVD----PQGERTIGVITKLDLMD  206 (240)
T ss_pred             HHHHHHHHHhC-ccCeEEEEEECCCCCCchh-HHHHHHHHH----HcCCcEEEEEECCCCCC
Confidence            44566677763 2346777876643 22211 111122222    24679999999999864

Large GTPases that mediate vesicle trafficking. Dynamin participates in the endocytic uptake of receptors, associated ligands, and plasma membrane following an exocytic event.

>COG1162 Predicted GTPases [General function prediction only]

Probab=92.30  E-value=0.73  Score=29.84  Aligned_cols=46  Identities=24%  Similarity=0.253  Sum_probs=32.8

Q ss_pred             CCcEEEEEEECCChh-HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIERK-TFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      |.+-.+++++..+++ +...+.+++-....    .++.-++|-||+||.+.
T Consensus        79 n~d~~iiIvs~~~P~~~~~~ldR~Lv~ae~----~gi~pvIvlnK~DL~~~  125 (301)
T COG1162          79 NNDQAIIVVSLVDPDFNTNLLDRYLVLAEA----GGIEPVIVLNKIDLLDD  125 (301)
T ss_pred             ccceEEEEEeccCCCCCHHHHHHHHHHHHH----cCCcEEEEEEccccCcc
Confidence            567777777777776 66667777655543    55777778999999653

>COG0218 Predicted GTPase [General function prediction only]

Probab=91.92  E-value=0.77  Score=28.08  Aligned_cols=59  Identities=17%  Similarity=0.210  Sum_probs=35.4

Q ss_pred             cccchhhhhhhhhcc-CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           5 TSCFTNLVVNFVQTY-HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~-~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|....+...|.... +-.+++++.|..-.-.=... .-++-+..    .++|++++.||+|-..
T Consensus        90 ~e~w~~~i~~YL~~R~~L~~vvlliD~r~~~~~~D~-em~~~l~~----~~i~~~vv~tK~DKi~  149 (200)
T COG0218          90 KEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDR-EMIEFLLE----LGIPVIVVLTKADKLK  149 (200)
T ss_pred             HHHHHHHHHHHHhhchhheEEEEEEECCCCCcHHHH-HHHHHHHH----cCCCeEEEEEccccCC
Confidence            345566777777653 56677777776544322111 11222222    5689999999999643

>PF14331 ImcF-related_N: ImcF-related N-terminal domain

Probab=91.44  E-value=0.32  Score=30.64  Aligned_cols=47  Identities=19%  Similarity=0.104  Sum_probs=30.7

Q ss_pred             CCcEEEEEEECCChhH-------HHH----HHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805          20 HPDVFVIVYSVIERKT-------FKK----AEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s-------~~~----~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      ..+|+|++.|+.+.-.       +..    ++.-+.++.+.- .-.+|+++|-+|+|+.
T Consensus        25 PlnGvil~vs~~~Ll~~~~~~r~l~~~a~~lR~rL~el~~~l-g~~~PVYvv~Tk~D~l   82 (266)
T PF14331_consen   25 PLNGVILTVSVDDLLNADEAERELEALARALRQRLEELQRTL-GVRLPVYVVFTKCDLL   82 (266)
T ss_pred             CCCEEEEEEEHHHHhcCChhhhHHHHHHHHHHHHHHHHHHHh-CCCCCeEeeeECCCcc
Confidence            5699999999875422       222    222333444422 3589999999999984

>KOG1424|consensus

Probab=91.26  E-value=0.25  Score=34.19  Aligned_cols=55  Identities=29%  Similarity=0.317  Sum_probs=37.2

Q ss_pred             hhhhhhhhhccCCcEEEEEEECCChhHHH--HHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           9 TNLVVNFVQTYHPDVFVIVYSVIERKTFK--KAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         9 ~~~~~~~~~~~~~~~~ilv~d~~~~~s~~--~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      +.++...-+   +|.++.+.|.-++--|.  .+..+.++..     +..-.+|+.||+||....+
T Consensus       166 RQLWRVlEr---SDivvqIVDARnPllfr~~dLe~Yvke~d-----~~K~~~LLvNKaDLl~~~q  222 (562)
T KOG1424|consen  166 RQLWRVLER---SDIVVQIVDARNPLLFRSPDLEDYVKEVD-----PSKANVLLVNKADLLPPEQ  222 (562)
T ss_pred             HHHHHHHhh---cceEEEEeecCCccccCChhHHHHHhccc-----cccceEEEEehhhcCCHHH
Confidence            344444444   99999999999987764  3455544432     3456789999999965433

>COG2895 CysN GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]

Probab=91.10  E-value=0.99  Score=30.26  Aligned_cols=62  Identities=15%  Similarity=0.220  Sum_probs=35.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      -|||+|....-.=-..  ++.+|++.|. ...-+++.++.. .+...  .+=-.+++..||+||.+..
T Consensus        94 PGHeQYTRNMaTGAST--adlAIlLVDA-R~Gvl~QTrRHs-~I~sL--LGIrhvvvAVNKmDLvdy~  155 (431)
T COG2895          94 PGHEQYTRNMATGAST--ADLAILLVDA-RKGVLEQTRRHS-FIASL--LGIRHVVVAVNKMDLVDYS  155 (431)
T ss_pred             CcHHHHhhhhhccccc--ccEEEEEEec-chhhHHHhHHHH-HHHHH--hCCcEEEEEEeeecccccC
Confidence            4788885333333332  8999999887 233444443321 12221  1223578889999997643

>TIGR03348 VI_IcmF type VI secretion protein IcmF

Probab=90.58  E-value=0.58  Score=35.16  Aligned_cols=47  Identities=26%  Similarity=0.192  Sum_probs=34.4

Q ss_pred             CCcEEEEEEECCChhHH---------HHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805          20 HPDVFVIVYSVIERKTF---------KKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~---------~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      ..+|+|++.|+.+.-+-         ..++..+.++.+.- .-.+|+.++-+|+|+.
T Consensus       201 plnGvil~vs~~~Ll~~~~~~~~~~a~~lR~rl~el~~~l-g~~~PVYvv~Tk~Dll  256 (1169)
T TIGR03348       201 PLNGVVVTVSLADLLTADPAERKAHARAIRQRLQELREQL-GARFPVYLVLTKADLL  256 (1169)
T ss_pred             CCCeEEEEEEHHHHhCCCHHHHHHHHHHHHHHHHHHHHHh-CCCCCEEEEEecchhh
Confidence            68999999998765321         24455666666643 3589999999999975

Members of this protein family are IcmF homologs and tend to be associated with type VI secretion systems.

>COG0481 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]

Probab=90.47  E-value=1.1  Score=31.13  Aligned_cols=58  Identities=17%  Similarity=0.107  Sum_probs=36.3

Q ss_pred             ccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           4 RTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         4 ~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ||-.|.--......  -+.|++++.|.+.---=+.+.+.+-.+.     .+..++-|-||+||..
T Consensus        85 GHVDFsYEVSRSLA--ACEGalLvVDAsQGveAQTlAN~YlAle-----~~LeIiPViNKIDLP~  142 (603)
T COG0481          85 GHVDFSYEVSRSLA--ACEGALLVVDASQGVEAQTLANVYLALE-----NNLEIIPVLNKIDLPA  142 (603)
T ss_pred             CccceEEEehhhHh--hCCCcEEEEECccchHHHHHHHHHHHHH-----cCcEEEEeeecccCCC
Confidence            56666532233333  2899999999886533333433333332     4578899999999964

>KOG1490|consensus

Probab=90.23  E-value=0.62  Score=32.48  Aligned_cols=48  Identities=19%  Similarity=0.192  Sum_probs=31.7

Q ss_pred             CcEEEEEEECCChhHHH--HHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805          21 PDVFVIVYSVIERKTFK--KAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus        21 ~~~~ilv~d~~~~~s~~--~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      ..+++++-|++..-.+.  .=-..+..++...  .+.|.|+|.||+|+-...
T Consensus       248 raaVLYfmDLSe~CGySva~QvkLfhsIKpLF--aNK~~IlvlNK~D~m~~e  297 (620)
T KOG1490|consen  248 RSAVLYFMDLSEMCGYSVAAQVKLYHSIKPLF--ANKVTILVLNKIDAMRPE  297 (620)
T ss_pred             hhhheeeeechhhhCCCHHHHHHHHHHhHHHh--cCCceEEEeecccccCcc
Confidence            35788888998875443  2223344555432  578999999999986433

>KOG3929|consensus

Probab=90.22  E-value=0.7  Score=29.86  Aligned_cols=13  Identities=31%  Similarity=0.506  Sum_probs=11.7

Q ss_pred             CCeEEEEeeCCCC
Q psy5805          54 EKAVILVANKADL   66 (75)
Q Consensus        54 ~~~~ilvgnK~Dl   66 (75)
                      ++|+++||.|.|.
T Consensus       190 P~PV~IVgsKYDv  202 (363)
T KOG3929|consen  190 PVPVVIVGSKYDV  202 (363)
T ss_pred             CCceEEeccchhh
Confidence            6789999999996

>cd01882 BMS1 Bms1

Probab=90.10  E-value=1.3  Score=27.02  Aligned_cols=43  Identities=16%  Similarity=0.081  Sum_probs=26.1

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCc
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLE   67 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~   67 (75)
                      .+|.++++.|.+....... ...+..+..    .+.| +++|.||.|+.
T Consensus       103 ~aDvVllviDa~~~~~~~~-~~i~~~l~~----~g~p~vi~VvnK~D~~  146 (225)
T cd01882         103 VADLVLLLIDASFGFEMET-FEFLNILQV----HGFPRVMGVLTHLDLF  146 (225)
T ss_pred             hcCEEEEEEecCcCCCHHH-HHHHHHHHH----cCCCeEEEEEeccccC
Confidence            4999999999875432222 122222322    2356 45599999985

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.

>COG1159 Era GTPase [General function prediction only]

Probab=89.98  E-value=1.6  Score=28.32  Aligned_cols=42  Identities=26%  Similarity=0.313  Sum_probs=28.7

Q ss_pred             CCcEEEEEEECCCh-hHHHHHHHHH-HHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIER-KTFKKAEDML-KTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~-~s~~~~~~~~-~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|.+++|-|.+.. ...+   +|. +.++.    .+.|++++.||.|...
T Consensus        85 dvDlilfvvd~~~~~~~~d---~~il~~lk~----~~~pvil~iNKID~~~  128 (298)
T COG1159          85 DVDLILFVVDADEGWGPGD---EFILEQLKK----TKTPVILVVNKIDKVK  128 (298)
T ss_pred             cCcEEEEEEeccccCCccH---HHHHHHHhh----cCCCeEEEEEccccCC
Confidence            79999999998873 2222   232 22322    4579999999999754

>COG1160 Predicted GTPases [General function prediction only]

Probab=89.94  E-value=1.4  Score=30.08  Aligned_cols=59  Identities=15%  Similarity=0.193  Sum_probs=38.1

Q ss_pred             ccccchhhhhh-hhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           4 RTSCFTNLVVN-FVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         4 ~~e~f~~~~~~-~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      ++|.|...+.. -..  -++.+++|.|.+..-+-+..+- ...+.+    ...++++|-||-|+.++
T Consensus       245 ~~E~~Sv~rt~~aI~--~a~vvllviDa~~~~~~qD~~i-a~~i~~----~g~~~vIvvNKWDl~~~  304 (444)
T COG1160         245 SVEKYSVARTLKAIE--RADVVLLVIDATEGISEQDLRI-AGLIEE----AGRGIVIVVNKWDLVEE  304 (444)
T ss_pred             ceEEEeehhhHhHHh--hcCEEEEEEECCCCchHHHHHH-HHHHHH----cCCCeEEEEEccccCCc
Confidence            46777655443 223  3999999999998765443321 112222    45689999999998654

>cd03110 Fer4_NifH_child This protein family's function is unkown

Probab=89.81  E-value=2.1  Score=24.82  Aligned_cols=43  Identities=21%  Similarity=0.176  Sum_probs=32.4

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .+|.++++...+ ..+...+..+.+.++..    +.|+.+|.||+|..
T Consensus       114 ~aD~vliv~~~~-~~~~~~~~~~~~~l~~~----~~~~~vV~N~~~~~  156 (179)
T cd03110         114 GADAALLVTEPT-PSGLHDLERAVELVRHF----GIPVGVVINKYDLN  156 (179)
T ss_pred             cCCEEEEEecCC-cccHHHHHHHHHHHHHc----CCCEEEEEeCCCCC
Confidence            499999998776 55777777777666642    35678999999975

It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.

>COG1161 Predicted GTPases [General function prediction only]

Probab=89.47  E-value=0.43  Score=30.89  Aligned_cols=42  Identities=33%  Similarity=0.302  Sum_probs=29.8

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ..|.++.|.|.-++.+..+     ..+.+.  ..+.|.++|.||+||..
T Consensus        34 ~~d~vvevvDar~P~~s~~-----~~l~~~--v~~k~~i~vlNK~DL~~   75 (322)
T COG1161          34 SVDVVVEVVDARDPLGTRN-----PELERI--VKEKPKLLVLNKADLAP   75 (322)
T ss_pred             cCCEEEEEEeccccccccC-----ccHHHH--HccCCcEEEEehhhcCC
Confidence            4999999999999976543     222222  13445599999999975

>KOG1954|consensus

Probab=87.85  E-value=1.4  Score=29.84  Aligned_cols=56  Identities=20%  Similarity=0.277  Sum_probs=38.0

Q ss_pred             cchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           7 CFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         7 ~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|....+.|...  +|.+|++||.-..+--+....-+..++.    ..-.+-+|-||+|..+
T Consensus       170 dF~~v~~WFaeR--~D~IiLlfD~hKLDIsdEf~~vi~aLkG----~EdkiRVVLNKADqVd  225 (532)
T KOG1954|consen  170 DFTGVLEWFAER--VDRIILLFDAHKLDISDEFKRVIDALKG----HEDKIRVVLNKADQVD  225 (532)
T ss_pred             ChHHHHHHHHHh--ccEEEEEechhhccccHHHHHHHHHhhC----CcceeEEEeccccccC
Confidence            466666666663  9999999997766555555555555553    3335667889999764

>KOG1423|consensus

Probab=87.21  E-value=1.2  Score=29.45  Aligned_cols=45  Identities=27%  Similarity=0.282  Sum_probs=30.7

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +||++++++|.++....-+. +.+..+..+   ..+|-++|-||.|+..
T Consensus       155 ~AD~vvVv~Das~tr~~l~p-~vl~~l~~y---s~ips~lvmnkid~~k  199 (379)
T KOG1423|consen  155 NADCVVVVVDASATRTPLHP-RVLHMLEEY---SKIPSILVMNKIDKLK  199 (379)
T ss_pred             hCCEEEEEEeccCCcCccCh-HHHHHHHHH---hcCCceeeccchhcch
Confidence            69999999999975443321 223333332   5689999999999754

>KOG0447|consensus

Probab=86.44  E-value=2.1  Score=30.56  Aligned_cols=58  Identities=14%  Similarity=0.277  Sum_probs=36.8

Q ss_pred             cchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           7 CFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         7 ~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      ...++...|..  |++++|+|..=   -|.+.=+.-...+....++..-..|+|-+|.||.++
T Consensus       437 ~I~~msKayM~--NPNAIILCIQD---GSVDAERSnVTDLVsq~DP~GrRTIfVLTKVDlAEk  494 (980)
T KOG0447|consen  437 TIFSISKAYMQ--NPNAIILCIQD---GSVDAERSIVTDLVSQMDPHGRRTIFVLTKVDLAEK  494 (980)
T ss_pred             HHHHHHHHHhc--CCCeEEEEecc---CCcchhhhhHHHHHHhcCCCCCeeEEEEeecchhhh
Confidence            34578888888  79999999532   233322222223333234456678999999999764

>COG4108 PrfC Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]

Probab=84.35  E-value=2.7  Score=29.05  Aligned_cols=59  Identities=17%  Similarity=0.148  Sum_probs=36.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      -|||.|+.=+-.-.-  -+|.+++|.|...-     ++.--..+-+.....++||+-.-||.|-..
T Consensus        89 PGHeDFSEDTYRtLt--AvDsAvMVIDaAKG-----iE~qT~KLfeVcrlR~iPI~TFiNKlDR~~  147 (528)
T COG4108          89 PGHEDFSEDTYRTLT--AVDSAVMVIDAAKG-----IEPQTLKLFEVCRLRDIPIFTFINKLDREG  147 (528)
T ss_pred             CCccccchhHHHHHH--hhheeeEEEecccC-----ccHHHHHHHHHHhhcCCceEEEeecccccc
Confidence            478888643332223  48999999886532     211111222223358899999999999754

>cd02067 B12-binding B12 binding domain (B12-BD)

Probab=84.04  E-value=4.5  Score=21.96  Aligned_cols=40  Identities=10%  Similarity=0.208  Sum_probs=26.5

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEee
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVAN   62 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgn   62 (75)
                      +++.+.+  +.++...+..+.++.+.+++.. .+++++++-|+
T Consensus        50 ~pdvV~i--S~~~~~~~~~~~~~i~~l~~~~-~~~~~i~vGG~   89 (119)
T cd02067          50 DADAIGL--SGLLTTHMTLMKEVIEELKEAG-LDDIPVLVGGA   89 (119)
T ss_pred             CCCEEEE--eccccccHHHHHHHHHHHHHcC-CCCCeEEEECC
Confidence            4564444  5667778889999999998742 22566665554

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.

>KOG2423|consensus

Probab=83.88  E-value=3.9  Score=28.09  Aligned_cols=52  Identities=27%  Similarity=0.260  Sum_probs=33.5

Q ss_pred             hhhhhhhcc-CCcEEEEEEECCChhHH--HHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805          11 LVVNFVQTY-HPDVFVIVYSVIERKTF--KKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus        11 ~~~~~~~~~-~~~~~ilv~d~~~~~s~--~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      ++...|+-. .+|++|-|.|.-|+-.-  ..+..++   +..  .+-...|+|-||+||.
T Consensus       203 IW~ELyKViDSSDVvvqVlDARDPmGTrc~~ve~yl---kke--~phKHli~vLNKvDLV  257 (572)
T KOG2423|consen  203 IWGELYKVIDSSDVVVQVLDARDPMGTRCKHVEEYL---KKE--KPHKHLIYVLNKVDLV  257 (572)
T ss_pred             HHHHHHHhhcccceeEEeeeccCCcccccHHHHHHH---hhc--CCcceeEEEeeccccc
Confidence            334444433 68999999999988532  3344443   221  2445689999999995

>KOG2484|consensus

Probab=82.17  E-value=2.6  Score=28.60  Aligned_cols=44  Identities=30%  Similarity=0.323  Sum_probs=32.4

Q ss_pred             CCcEEEEEEECCChhHHHH--HHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKK--AEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+|++|-|.|.-||.+-.+  +..|.   .+  ..++.-.|+|-||.||..
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            5999999999999976543  44553   22  225577899999999963

>TIGR00101 ureG urease accessory protein UreG

Probab=81.46  E-value=1.3  Score=26.64  Aligned_cols=37  Identities=24%  Similarity=0.248  Sum_probs=24.6

Q ss_pred             CcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeE--EEEeeCCCCcC
Q psy5805          21 PDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV--ILVANKADLER   68 (75)
Q Consensus        21 ~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~--ilvgnK~Dl~~   68 (75)
                      ++++|.|+|.++-++...  .+.         ..+..  +++.||+|+.+
T Consensus       113 ~~~~i~vvD~~~~~~~~~--~~~---------~qi~~ad~~~~~k~d~~~  151 (199)
T TIGR00101       113 ADLTIFVIDVAAGDKIPR--KGG---------PGITRSDLLVINKIDLAP  151 (199)
T ss_pred             hCcEEEEEEcchhhhhhh--hhH---------hHhhhccEEEEEhhhccc
Confidence            677999999987666321  111         12333  88999999963

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.

>COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]

Probab=80.73  E-value=1.6  Score=28.79  Aligned_cols=56  Identities=16%  Similarity=0.195  Sum_probs=32.8

Q ss_pred             ccccc-hhhhhhhhhccCCcEEEEEEECCCh---hHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcCCC
Q psy5805           4 RTSCF-TNLVVNFVQTYHPDVFVIVYSVIER---KTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLERRR   70 (75)
Q Consensus         4 ~~e~f-~~~~~~~~~~~~~~~~ilv~d~~~~---~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~~r   70 (75)
                      ||-.| .+|...-.+   .|+.|||.+.++-   ++-+++     .+.+  . -.+| ++++-||+|+.+.+
T Consensus        84 GHaDYvKNMItgAaq---mDgAILVVsA~dGpmPqTrEHi-----Llar--q-vGvp~ivvflnK~Dmvdd~  144 (394)
T COG0050          84 GHADYVKNMITGAAQ---MDGAILVVAATDGPMPQTREHI-----LLAR--Q-VGVPYIVVFLNKVDMVDDE  144 (394)
T ss_pred             ChHHHHHHHhhhHHh---cCccEEEEEcCCCCCCcchhhh-----hhhh--h-cCCcEEEEEEecccccCcH
Confidence            34334 344444444   8999999998864   343332     1111  1 2355 67788999997643

>TIGR02836 spore_IV_A stage IV sporulation protein A

Probab=80.50  E-value=8.9  Score=26.56  Aligned_cols=42  Identities=24%  Similarity=0.364  Sum_probs=29.6

Q ss_pred             CCcEEEEEE-ECC----ChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCC
Q psy5805          20 HPDVFVIVY-SVI----ERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKAD   65 (75)
Q Consensus        20 ~~~~~ilv~-d~~----~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~D   65 (75)
                      .++..++|. |-+    .++.+... .+|..++++    .+.|++++-||.|
T Consensus       144 hstIgivVtTDgsi~dI~Re~y~~aEe~~i~eLk~----~~kPfiivlN~~d  191 (492)
T TIGR02836       144 HSTIGVVVTTDGTITDIPREDYVEAEERVIEELKE----LNKPFIILLNSTH  191 (492)
T ss_pred             cCcEEEEEEcCCCccccccccchHHHHHHHHHHHh----cCCCEEEEEECcC
Confidence            378888876 442    12345444 578888876    5689999999999

A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis.

>KOG1191|consensus

Probab=80.31  E-value=2.7  Score=29.21  Aligned_cols=49  Identities=29%  Similarity=0.365  Sum_probs=31.3

Q ss_pred             CcEEEEEEEC--CChhHHHHHHHHHHHHHhh-----cCCCCCeEEEEeeCCCCcCC
Q psy5805          21 PDVFVIVYSV--IERKTFKKAEDMLKTLWDS-----KYIGEKAVILVANKADLERR   69 (75)
Q Consensus        21 ~~~~ilv~d~--~~~~s~~~~~~~~~~~~~~-----~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|.+++|+|.  ++-++-..+.+-+.....-     .....-+++++.||.|+...
T Consensus       349 advi~~vvda~~~~t~sd~~i~~~l~~~~~g~~~~~~~~~~~~~i~~~nk~D~~s~  404 (531)
T KOG1191|consen  349 ADVILLVVDAEESDTESDLKIARILETEGVGLVVIVNKMEKQRIILVANKSDLVSK  404 (531)
T ss_pred             cCEEEEEecccccccccchHHHHHHHHhccceEEEeccccccceEEEechhhccCc
Confidence            9999999999  4444444444433333211     01134689999999999654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	75
3cbq_A	195	Crystal Structure Of The Human Rem2 Gtpase With Bou		2e-05
2gjs_A	176	The Crystal Structure Of Human Rrad In Complex With		2e-05
3q85_A	169	Crystal Structure Of Rem2 G-Domain -Gtp Analog Comp		2e-05
2dpx_A	174	Crystal Structure Of Human Rad Gtpase Length = 174		2e-05
4aii_A	180	Crystal Structure Of The Rat Rem2 Gtpase - G Domain		2e-05
3q72_A	166	Crystal Structure Of Rad G-Domain-Gtp Analog Comple		2e-05
2cjw_A	192	Crystal Structure Of The Small Gtpase Gem (Gemdndca		6e-05
2cjw_B	192	Crystal Structure Of The Small Gtpase Gem (Gemdndca		6e-05
2g3y_A	211	Crystal Structure Of The Human Small Gtpase Gem Len		6e-05
2ht6_A	174	Crystal Structure Of Human Gem G-Domain Bound To Gd		6e-05
2nzj_A	175	The Crystal Structure Of Rem1 In Complex With Gdp L		4e-04

>pdb|3CBQ|A Chain A, Crystal Structure Of The Human Rem2 Gtpase With Bound Gdp Length = 195

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%)
Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D F+IV+SV +R++F K  + L  L   +   +  VILV NK+DL R R+V+
Sbjct: 98  DAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVS 149

>pdb|2GJS|A Chain A, The Crystal Structure Of Human Rrad In Complex With Gdp Length = 176

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 35/52 (67%)
Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D +VIVYSV ++ +F+KA ++   L  ++   +  +ILV NK+DL R R+V+
Sbjct: 79  DAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVS 130

>pdb|3Q85|A Chain A, Crystal Structure Of Rem2 G-Domain -Gtp Analog Complex Length = 169

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%)
Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D F+IV+SV +R++F K  + L  L   +   +  VILV NK+DL R R+V+
Sbjct: 77  DAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVS 128

>pdb|2DPX|A Chain A, Crystal Structure Of Human Rad Gtpase Length = 174

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 35/52 (67%)
Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D +VIVYSV ++ +F+KA ++   L  ++   +  +ILV NK+DL R R+V+
Sbjct: 79  DAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVS 130

>pdb|4AII|A Chain A, Crystal Structure Of The Rat Rem2 Gtpase - G Domain Bound To Gdp Length = 180

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 33/52 (63%)
Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D F+IV+SV +R++F K  + L  L   +   +  VILV NK+DL R R+V+
Sbjct: 87  DAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVS 138

>pdb|3Q72|A Chain A, Crystal Structure Of Rad G-Domain-Gtp Analog Complex Length = 166

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 35/52 (67%)
Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D +VIVYSV ++ +F+KA ++   L  ++   +  +ILV NK+DL R R+V+
Sbjct: 74  DAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVS 125

>pdb|2CJW|A Chain A, Crystal Structure Of The Small Gtpase Gem (Gemdndcam) In Complex To Mg.Gdp Length = 192

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 36/55 (65%)
Query: 21  PDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
            D ++IVYS+ +R +F+KA ++   L  ++   +  +ILV NK+DL R R+V+ S
Sbjct: 81  GDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRXREVSVS 135

>pdb|2CJW|B Chain B, Crystal Structure Of The Small Gtpase Gem (Gemdndcam) In Complex To Mg.Gdp Length = 192

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 36/55 (65%)
Query: 21  PDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
            D ++IVYS+ +R +F+KA ++   L  ++   +  +ILV NK+DL R R+V+ S
Sbjct: 81  GDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRXREVSVS 135

>pdb|2G3Y|A Chain A, Crystal Structure Of The Human Small Gtpase Gem Length = 211

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 36/55 (65%)
Query: 21  PDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
            D ++IVYS+ +R +F+KA ++   L  ++   +  +ILV NK+DL R R+V+ S
Sbjct: 112 GDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVSVS 166

>pdb|2HT6|A Chain A, Crystal Structure Of Human Gem G-Domain Bound To Gdp Length = 174

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 36/55 (65%)
Query: 21  PDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
            D ++IVYS+ +R +F+KA ++   L  ++   +  +ILV NK+DL R R+V+ S
Sbjct: 81  GDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVSVS 135

>pdb|2NZJ|A Chain A, The Crystal Structure Of Rem1 In Complex With Gdp Length = 175

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 31/50 (62%)
Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           +VIVYS+ +R +F+ A ++   L  +       +ILV NKADL R R+V+
Sbjct: 81  YVIVYSIADRGSFESASELRIQLRRTHQADHVPIILVGNKADLARCREVS 130

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	75
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	5e-12
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	2e-11
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	7e-11
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	7e-11
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	2e-10
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	2e-10
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	4e-10
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	5e-10
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	7e-10
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	2e-09
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	2e-09
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	2e-09
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	3e-09
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	3e-09
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	3e-09
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	4e-09
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	5e-09
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	5e-09
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	7e-08
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	2e-07
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	2e-07
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	3e-07
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	7e-07
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	7e-07
3bbp_A	211	RAB-6, RAS-related protein RAB-6A; golgi complex,	2e-06
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	2e-06
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	2e-06
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	2e-06
3c5h_A	255	Glucocorticoid receptor DNA-binding factor 1; RAS,	2e-06
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	3e-06
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	4e-06
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	4e-06
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	4e-06
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	5e-06
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	6e-06
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	6e-06
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	6e-06
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	6e-06
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	7e-06
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	7e-06
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	8e-06
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	8e-06
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	9e-06
4djt_A	218	GTP-binding nuclear protein GSP1; structural genom	1e-05
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	1e-05
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	1e-05
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	1e-05
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	1e-05
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	1e-05
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	2e-05
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	2e-05
3l0i_B	199	RAS-related protein RAB-1A; GEF-GDF-RAB complex, G	2e-05
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	3e-05
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	3e-05
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	3e-05
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	3e-05
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	4e-05
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	4e-05
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	5e-05
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	6e-05
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	7e-05
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	8e-05
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	1e-04
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	4e-04
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	5e-04
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	6e-04

>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 = 57.3 bits (139), Expect = 5e-12
 Identities = 20/52 (38%), Positives = 35/52 (67%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D ++IVYS+ +R +F+KA ++   L  ++   +  +ILV NK+DL R R+V+
Sbjct: 113 DAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVS 164

>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 = 54.9 bits (133), Expect = 2e-11
 Identities = 20/50 (40%), Positives = 31/50 (62%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           +VIVYS+ +R +F+ A ++   L  +       +ILV NKADL R R+V+
Sbjct: 81  YVIVYSIADRGSFESASELRIQLRRTHQADHVPIILVGNKADLARCREVS 130

>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 = 53.8 bits (130), Expect = 7e-11
 Identities = 21/50 (42%), Positives = 32/50 (64%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           F+IV+SV +R++F K  + L  L   +   +  VILV NK+DL R R+V+
Sbjct: 100 FLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVS 149

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} Length = 169

 Score = 53.7 bits (130), Expect = 7e-11
 Identities = 22/52 (42%), Positives = 33/52 (63%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D F+IV+SV +R++F K  + L  L   +   +  VILV NK+DL R R+V+
Sbjct: 77  DAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVS 128

>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 = 52.5 bits (127), Expect = 2e-10
 Identities = 21/52 (40%), Positives = 35/52 (67%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D +VIVYSV ++ +F+KA ++   L  ++   +  +ILV NK+DL R R+V+
Sbjct: 74  DAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVS 125

>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 = 52.6 bits (127), Expect = 2e-10
 Identities = 19/50 (38%), Positives = 30/50 (60%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           FV+VY + +R +F++   +   L + K      +ILV NKADL+  RQV+
Sbjct: 102 FVLVYDITDRGSFEEVLPLKNILDEIKKPKNVTLILVGNKADLDHSRQVS 151

>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 = 51.9 bits (125), Expect = 4e-10
 Identities = 20/52 (38%), Positives = 35/52 (67%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D ++IVYS+ +R +F+KA ++   L  ++   +  +ILV NK+DL R R+V+
Sbjct: 82  DAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRXREVS 133

>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 = 51.4 bits (124), Expect = 5e-10
 Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 2/52 (3%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV--ILVANKADLERRRQVT 73
           F++VYSV  R++F  +   L+ L       ++++  +L+ NK D+ + RQVT
Sbjct: 95  FLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQYRQVT 146

>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 = 51.0 bits (123), Expect = 7e-10
 Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLERRRQVTHS 75
             F++VYS+  R++ ++ + + + + + K   E   ++LV NK D    R+V  S
Sbjct: 76  HAFILVYSITSRQSLEELKPIYEQICEIKGDVESIPIMLVGNKCDESPSREVQSS 130

>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 = 49.9 bits (120), Expect = 2e-09
 Identities = 19/52 (36%), Positives = 29/52 (55%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
           F+IVYSV ++ +F+  +   + +   K      +ILVANK DL   R+VT  
Sbjct: 93  FLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTRD 144

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens} Length = 201

 Score = 49.9 bits (120), Expect = 2e-09
 Identities = 18/50 (36%), Positives = 27/50 (54%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           +V+VYSV    +F+  E + + L +        V+LV NKADL   R+V 
Sbjct: 99  YVLVYSVTSLHSFQVIESLYQKLHEGHGKTRVPVVLVGNKADLSPEREVQ 148

>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 = 49.8 bits (120), Expect = 2e-09
 Identities = 15/52 (28%), Positives = 28/52 (53%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
           +++VYSV   K+F+  + +   L D     +  ++LV NK DL   R +++ 
Sbjct: 81  YILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYE 132

>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 = 49.5 bits (119), Expect = 3e-09
 Identities = 17/50 (34%), Positives = 28/50 (56%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           F+ V+S+ E ++F    D  + +   K       +LV NK+DLE +RQV+
Sbjct: 93  FLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVS 142

>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 = 49.5 bits (119), Expect = 3e-09
 Identities = 17/50 (34%), Positives = 28/50 (56%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           F+ V+S+ E ++F    D  + +   K       +LV NK+DLE +RQV+
Sbjct: 89  FLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVS 138

>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 = 49.0 bits (118), Expect = 3e-09
 Identities = 18/52 (34%), Positives = 27/52 (51%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
           F +VYS+  + TF   +D+ + +   K   +  +ILV NK DLE  R V   
Sbjct: 78  FALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKE 129

>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 = 48.6 bits (117), Expect = 4e-09
 Identities = 17/50 (34%), Positives = 28/50 (56%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           F+ V+S+ E ++F    D  + +   K       +LV NK+DLE +RQV+
Sbjct: 79  FLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVS 128

>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 = 48.6 bits (117), Expect = 5e-09
 Identities = 18/50 (36%), Positives = 31/50 (62%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           F++VYS++ +++F+  + M   +   K   +  VILV NK DLE  R+V+
Sbjct: 78  FILVYSLVNQQSFQDIKPMRDQIIRVKRYEKVPVILVGNKVDLESEREVS 127

>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 = 48.7 bits (117), Expect = 5e-09
 Identities = 18/52 (34%), Positives = 32/52 (61%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
           F++V+++ +R++F +   +   +   K   +  V+LV NKADLE +RQV  S
Sbjct: 84  FLLVFAINDRQSFNEVGKLFTQILRVKDRDDFPVVLVGNKADLESQRQVPRS 135

>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 = 45.7 bits (109), Expect = 7e-08
 Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLERRRQVT 73
           F++V+SV  +++ ++   + K +   K   E   V+LV NK D   +R+V 
Sbjct: 83  FILVFSVTSKQSLEELGPIYKLIVQIKGSVEDIPVMLVGNKCDET-QREVD 132

>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 = 44.0 bits (105), Expect = 2e-07
 Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
           F+ V+++   K+F+      + +   K   +  ++LV NK+DL   R V   
Sbjct: 78  FLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKSDLA-ARTVESR 128

>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 = 44.5 bits (106), Expect = 2e-07
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
           F+ V+++   K+F       + +   K   +  ++LV NK DL   R V   
Sbjct: 96  FLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLP-TRTVDTK 146

>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 = 44.1 bits (105), Expect = 3e-07
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
           F+ V+++   K+F+      + +   K   +  ++LV NK DL   R V   
Sbjct: 79  FLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLP-SRTVDTK 129

>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 = 43.0 bits (102), Expect = 7e-07
 Identities = 8/56 (14%), Positives = 20/56 (35%), Gaps = 4/56 (7%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV----ILVANKADLERRRQVT 73
           D  + V+S+ +  +F+    +   L   +  G   +    +   ++      R V 
Sbjct: 74  DAVIFVFSLEDENSFQAVSRLHGQLSSLRGEGRGGLALALVGTQDRISASSPRVVG 129

>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 = 42.9 bits (102), Expect = 7e-07
 Identities = 9/52 (17%), Positives = 21/52 (40%), Gaps = 2/52 (3%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADL--ERRRQVT 73
            V V+S+ +  +F+   +    L   +   E  ++LV  +  +     R + 
Sbjct: 89  VVFVFSLEDEISFQTVYNYFLRLCSFRNASEVPMVLVGTQDAISAANPRVID 140

>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 = 42.3 bits (100), Expect = 2e-06
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 23  VFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           V V+VY +    +F++    +  +      G   +I LV NK DL  +RQV+
Sbjct: 91  VAVVVYDITNVNSFQQTTKWIDDV--RTERGSDVIIMLVGNKTDLADKRQVS 140

>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 = 42.1 bits (100), Expect = 2e-06
 Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 2/52 (3%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
              V+V+S  +R++F+      + +     +G+    LV NK DL     + 
Sbjct: 79  QACVLVFSTTDRESFEAISSWREKV--VAEVGDIPTALVQNKIDLLDDSCIK 128

>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 = 42.1 bits (100), Expect = 2e-06
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           +IV+ V  + +F++A+  ++ L          V+ L  NK+DL   R+VT
Sbjct: 89  IIVFDVTNQASFERAKKWVQEL--QAQGNPNMVMALAGNKSDLLDARKVT 136

>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 = 41.7 bits (99), Expect = 2e-06
 Identities = 16/50 (32%), Positives = 31/50 (62%), Gaps = 3/50 (6%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           ++VY + +  +F+K ++ +K L   K +G +  + +V NK DLE+ R V+
Sbjct: 83  ILVYDITDEDSFQKVKNWVKEL--RKMLGNEICLCIVGNKIDLEKERHVS 130

>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 = 41.9 bits (98), Expect = 2e-06
 Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 2/54 (3%)

Query: 22  DVFVIVYSV--IERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           D F++   V     + F      +  L++     +K +++V  K D    R + 
Sbjct: 164 DGFLLGIDVSRGMNRNFDDQLKFVSNLYNQLAKTKKPIVVVLTKCDEGVERYIR 217

>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 = 41.4 bits (98), Expect = 3e-06
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 23  VFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           V V+VY +    +F +    +  +      G   +I LV NK DL  +RQV+
Sbjct: 89  VAVVVYDITNTNSFHQTSKWIDDV--RTERGSDVIIMLVGNKTDLSDKRQVS 138

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 40.7 bits (94), Expect = 4e-06
 Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 6/36 (16%)

Query: 32 ERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE 67
          E++  KK +  LK      Y  + A  L A KA +E
Sbjct: 18 EKQALKKLQASLK-----LYADDSAPAL-AIKATME 47

>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 = 41.1 bits (97), Expect = 4e-06
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           VIVY + ++ +F   +  +K L   ++  E  V+ +  NK DL   R+V 
Sbjct: 100 VIVYDITKQDSFYTLKKWVKEL--KEHGPENIVMAIAGNKCDLSDIREVP 147

>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 = 40.6 bits (96), Expect = 4e-06
 Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           +IVY + + +TF   ++ ++ L   ++     V+ +  NK DL   R+V 
Sbjct: 83  IIVYDITKEETFSTLKNWVREL--RQHGPPSIVVAIAGNKCDLTDVREVM 130

>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 = 40.8 bits (96), Expect = 5e-06
 Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           +IVY + +  +++     L  L   +   +   + L+ NK+DL   R V 
Sbjct: 90  LIVYDISKSSSYENCNHWLSEL--RENADDNVAVGLIGNKSDLAHLRAVP 137

>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 = 40.6 bits (96), Expect = 6e-06
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           ++VY +   ++F +A++ +K L   +      VI L  NKADL  +R V 
Sbjct: 83  IVVYDITNEESFARAKNWVKEL--QRQASPNIVIALSGNKADLANKRAVD 130

>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 = 40.7 bits (96), Expect = 6e-06
 Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 3/51 (5%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 73
            +IVY V ++++F   +  L+ +   +Y     + +LV NK DL+ +R V 
Sbjct: 84  IIIVYDVTDQESFNGVKMWLQEI--DRYATSTVLKLLVGNKCDLKDKRVVE 132

>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 = 40.7 bits (96), Expect = 6e-06
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVTH 74
           ++VY + +  T++  E  LK L    +     VI LV NK+DL   R V  
Sbjct: 106 LLVYDIAKHLTYENVERWLKEL--RDHADSNIVIMLVGNKSDLRHLRAVPT 154

>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 = 40.3 bits (95), Expect = 6e-06
 Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 3/51 (5%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVTH 74
           ++VY +  R T+      L             VI L+ NKADLE +R VT+
Sbjct: 92  LMVYDITRRSTYNHLSSWLTDA--RNLTNPNTVIILIGNKADLEAQRDVTY 140

>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 = 40.3 bits (95), Expect = 7e-06
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVTH 74
           ++VY +  R+TF      L+     ++     VI L+ NK+DLE RR V  
Sbjct: 98  LLVYDITRRETFNHLTSWLEDA--RQHSSSNMVIMLIGNKSDLESRRDVKR 146

>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 = 40.3 bits (95), Expect = 7e-06
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 3/51 (5%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVTH 74
           ++V+ + + +T+   E  LK L    +     V+ LV NK+DL + R+V  
Sbjct: 102 LLVFDLTKHQTYAVVERWLKEL--YDHAEATIVVMLVGNKSDLSQAREVPT 150

>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 = 40.3 bits (95), Expect = 8e-06
 Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 3/50 (6%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           ++VY + +  T++  E  LK L    +     VI LV NK+DL   R V 
Sbjct: 82  LLVYDIAKHLTYENVERWLKEL--RDHADSNIVIMLVGNKSDLRHLRAVP 129

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens} Length = 196

 Score = 40.3 bits (95), Expect = 8e-06
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
            ++VY V ++++F   +  L+ +   +Y  E     LV NK DL  ++ V 
Sbjct: 92  IIVVYDVTDQESFNNVKQWLQEI--DRYASENVNKLLVGNKCDLTTKKVVD 140

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens} Length = 181

 Score = 39.8 bits (94), Expect = 9e-06
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
            ++VY V   ++F   +  L  +  ++   +   ILV NK D   R+ V 
Sbjct: 85  VIVVYDVTSAESFVNVKRWLHEI--NQNCDDVCRILVGNKNDDPERKVVE 132

>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 = 40.0 bits (94), Expect = 1e-05
 Identities = 12/50 (24%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           ++ + V  R T +     +K       +G +A I + ANK D++ R++++
Sbjct: 89  ILFFDVTSRITCQNLARWVKEF--QAVVGNEAPIVVCANKIDIKNRQKIS 136

>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 = 40.0 bits (94), Expect = 1e-05
 Identities = 12/50 (24%), Positives = 28/50 (56%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           F++++ +  +++F    + +  L  + Y     ++L+ NKADL  +R+V 
Sbjct: 111 FLLMFDLTSQQSFLNVRNWMSQLQANAYCENPDIVLIGNKADLPDQREVN 160

>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 = 39.8 bits (94), Expect = 1e-05
 Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 2/51 (3%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV--ILVANKADLERRRQVT 73
           ++VY +   ++F+  ED    +       E      LV NK DLE  R + 
Sbjct: 84  LLVYDITNYQSFENLEDWYTVVKKVSEESETQPLVALVGNKIDLEHMRTIK 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 = 39.9 bits (94), Expect = 1e-05
 Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 3/51 (5%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVTH 74
           ++ Y + +R +F      ++ +   KY G   V +L+ NK+DL   R+V+ 
Sbjct: 106 ILAYDITKRSSFLSVPHWIEDV--RKYAGSNIVQLLIGNKSDLSELREVSL 154

>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 = 39.5 bits (93), Expect = 1e-05
 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 3/50 (6%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           ++VY +  R+T+      L             V+ L  NK DL+  R+VT
Sbjct: 102 LLVYDITSRETYNSLAAWLTDA--RTLASPNIVVILCGNKKDLDPEREVT 149

>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 = 39.6 bits (93), Expect = 1e-05
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 73
           F+++Y +   ++F   +D    +    Y  + A  +LV NK D+E  R V+
Sbjct: 84  FILMYDITNEESFNAVQDWSTQI--KTYSWDNAQVLLVGNKCDMEDERVVS 132

>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 = 39.1 bits (92), Expect = 2e-05
 Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 4/52 (7%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV--ILVANKADLERRRQVTH 74
           V VY +    +F      ++     +++    +  ILV NK DL    QV  
Sbjct: 98  VFVYDMTNMASFHSLPAWIEEC--KQHLLANDIPRILVGNKCDLRSAIQVPT 147

>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 = 38.7 bits (91), Expect = 2e-05
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 73
           F+++Y +  +++F   +D    +    Y  + A  ILV NK DLE  R V 
Sbjct: 98  FLLMYDIANQESFAAVQDWATQI--KTYSWDNAQVILVGNKCDLEDERVVP 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 = 38.8 bits (91), Expect = 2e-05
 Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 3/51 (5%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 73
            ++VY V ++++F   +  L+ +   +Y  E    +LV NK DL  ++ V 
Sbjct: 109 IIVVYDVTDQESFNNVKQWLQEI--DRYASENVNKLLVGNKCDLTTKKVVD 157

>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 = 38.8 bits (91), Expect = 3e-05
 Identities = 12/50 (24%), Positives = 25/50 (50%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           F++++ +   ++F    + +  L    Y     ++L  NK+DLE +R V 
Sbjct: 97  FLLLFDLTNEQSFLNVRNWISQLQMHAYSENPDIVLCGNKSDLEDQRAVK 146

>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 = 38.8 bits (91), Expect = 3e-05
 Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 3/52 (5%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVTHS 75
           ++ Y +   ++F+   + L+ +   +Y   K + +LV NK DL  RR+V+  
Sbjct: 103 ILTYDITCEESFRCLPEWLREI--EQYASNKVITVLVGNKIDLAERREVSQQ 152

>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 = 38.7 bits (91), Expect = 3e-05
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
           ++VY +  R+T+    + L          +  VI L  NK DL+  R+VT
Sbjct: 87  LLVYDITSRETYNALTNWLTDA--RMLASQNIVIILCGNKKDLDADREVT 134

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C Length = 208

 Score = 38.4 bits (90), Expect = 3e-05
 Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 3/52 (5%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV--ILVANKADLE-RRRQVT 73
           ++V+ V   ++F+  +   + L  ++   E+ +  +LVANK DL  +R QV 
Sbjct: 101 ILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANKTDLPPQRHQVR 152

>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 = 38.4 bits (90), Expect = 4e-05
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 3/51 (5%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 73
            ++VY + +++TF      +K +   KY  E A  +LV NK D E  R++T
Sbjct: 102 IILVYDITKKETFDDLPKWMKMI--DKYASEDAELLLVGNKLDCETDREIT 150

>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 = 37.9 bits (89), Expect = 4e-05
 Identities = 10/51 (19%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 73
            ++VY +   K+F    + ++ +   ++       +++ NK D+  +RQV+
Sbjct: 84  IMLVYDITNEKSFDNIRNWIRNI--EEHASADVEKMILGNKCDVNDKRQVS 132

>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 = 38.0 bits (89), Expect = 5e-05
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 73
           F+++Y +   ++F   +D    +    Y  + A  ILV NK D+E  R V 
Sbjct: 99  FILMYDITNEESFNAVQDWATQI--KTYSWDNAQVILVGNKCDMEEERVVP 147

>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 = 37.9 bits (89), Expect = 6e-05
 Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 3/51 (5%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 73
            +++Y V  + +F   +  L  +   +Y       +L+ NK D    R V 
Sbjct: 87  LLLLYDVTNKASFDNIQAWLTEI--HEYAQHDVALMLLGNKVDSAHERVVK 135

>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 = 37.6 bits (88), Expect = 7e-05
 Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 3/55 (5%)

Query: 22  DVFVIVYSVIERKTFKKAEDMLKTLWD--SKYIGEKAVI-LVANKADLERRRQVT 73
           D  V+V+ V    TFK  +          S    E     ++ NK DLE R+  T
Sbjct: 82  DCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVAT 136

>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 = 37.7 bits (88), Expect = 8e-05
 Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 2/49 (4%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           +I++ V  R T+K   +  + L   +      ++L  NK D++ R+   
Sbjct: 92  IIMFDVTSRVTYKNVPNWHRDL--VRVCENIPIVLCGNKVDIKDRKVKA 138

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum} Length = 208

 Score = 36.7 bits (85), Expect = 1e-04
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 25  VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
           ++V+ +    T  +A+  +  L  S       +ILVANK D   + QV 
Sbjct: 121 IVVFDISNSNTLDRAKTWVNQLKISSNY---IIILVANKIDKN-KFQVD 165

>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 = 35.7 bits (83), Expect = 4e-04
 Identities = 16/46 (34%), Positives = 22/46 (47%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR 69
            ++VY V  R TF K ++ L  L       +   +LV NK D E R
Sbjct: 91  VILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKENR 136

>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 = 35.4 bits (82), Expect = 5e-04
 Identities = 15/47 (31%), Positives = 29/47 (61%), Gaps = 3/47 (6%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERR 69
            ++VY V + +TF   +   KT+  +++  ++A + LV NK+D+E R
Sbjct: 96  IILVYDVTDERTFTNIKQWFKTV--NEHANDEAQLLLVGNKSDMETR 140

>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 = 34.8 bits (81), Expect = 6e-04
 Identities = 14/47 (29%), Positives = 29/47 (61%), Gaps = 3/47 (6%)

Query: 24  FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERR 69
            ++VY + + +TF   +   KT+  +++  ++A  +LV NK+D+E R
Sbjct: 79  IILVYDITDERTFTNIKQWFKTV--NEHANDEAQLLLVGNKSDMETR 123

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	75
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	99.85
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	99.68
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	99.68
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	99.67
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	99.67
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	99.66
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	99.66
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	99.66
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	99.64
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	99.64
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	99.63
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	99.63
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	99.63
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	99.62
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	99.62
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	99.62
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	99.62
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	99.62
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	99.62
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	99.61
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	99.61
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	99.61
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	99.61
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	99.61
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	99.61
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	99.61
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	99.61
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	99.61
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	99.6
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	99.6
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	99.6
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	99.6
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	99.6
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	99.6
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	99.6
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	99.6
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	99.6
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	99.6
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	99.6
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	99.6
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	99.59
1azs_C	402	GS-alpha; complex (lyase/hydrolase), hydrolase, si	99.59
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	99.59
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	99.59
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	99.59
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	99.59
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	99.59
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	99.59
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	99.59
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	99.58
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	99.58
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	99.58
3l0i_B	199	RAS-related protein RAB-1A; GEF-GDF-RAB complex, G	99.58
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	99.58
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	99.57
2xtz_A	354	Guanine nucleotide-binding protein alpha-1 subuni;	99.57
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	99.57
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	99.57
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	99.57
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	99.57
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	99.57
3c5h_A	255	Glucocorticoid receptor DNA-binding factor 1; RAS,	99.57
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	99.57
3r7w_B	331	Gtpase2, GTP-binding protein GTR2; RAG gtpases, GT	99.56
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	99.56
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	99.56
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	99.56
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	99.56
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	99.56
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	99.56
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	99.56
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	99.56
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	99.55
4fid_A	340	G protein alpha subunit; RAS-like domain, all-heli	99.55
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	99.55
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	99.55
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	99.55
4djt_A	218	GTP-binding nuclear protein GSP1; structural genom	99.55
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	99.55
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	99.54
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	99.54
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	99.54
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	99.54
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	99.54
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	99.53
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	99.53
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	99.53
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	99.53
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	99.52
1cip_A	353	Protein (guanine nucleotide-binding protein alpha-	99.52
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	99.52
3ohm_A	327	Guanine nucleotide-binding protein G(Q) subunit A;	99.51
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	99.51
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	99.51
3llu_A	196	RAS-related GTP-binding protein C; structural geno	99.51
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	99.51
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	99.51
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	99.51
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	99.5
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	99.5
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	99.49
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	99.49
3o47_A	329	ADP-ribosylation factor GTPase-activating protein	99.46
3lvq_E	497	ARF-GAP with SH3 domain, ANK repeat and PH domain	99.46
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	99.46
1zcb_A	362	G alpha I/13; GTP-binding, lipoprotein, membrane,	99.45
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	99.45
3r7w_A	307	Gtpase1, GTP-binding protein GTR1; RAG gtpases, GT	99.41
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	99.41
2ged_A	193	SR-beta, signal recognition particle receptor beta	99.38
1nrj_B	218	SR-beta, signal recognition particle receptor beta	99.38
3th5_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	99.07
2fh5_B	214	SR-beta, signal recognition particle receptor beta	99.34
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	99.33
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	99.26
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	99.26
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	99.07
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	99.06
3dpu_A	535	RAB family protein; roccor, G-domain, COR, GTP-bin	99.06
2wji_A	165	Ferrous iron transport protein B homolog; membrane	99.05
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	99.05
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	98.99
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	98.94
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	98.85
1lnz_A	342	SPO0B-associated GTP-binding protein; GTPase, OBG,	98.8
3l82_B	227	F-box only protein 4; TRFH domain, helix, GTPase d	98.79
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	98.78
2hjg_A	436	GTP-binding protein ENGA; GTPase ENGA KH-domain, h	98.74
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	98.72
1g7s_A	594	Translation initiation factor IF2/EIF5B; translati	98.71
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	98.7
1jny_A	435	EF-1-alpha, elongation factor 1-alpha, EF-TU, TUF-	98.69
3cb4_D	599	GTP-binding protein LEPA; GTPase, OB-fold, membran	98.67
2ywe_A	600	GTP-binding protein LEPA; G domain, beta-barrel, f	98.67
3sjy_A	403	Translation initiation factor 2 subunit gamma; zin	98.67
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	98.66
3h2y_A	368	GTPase family protein; GTP-binding protein YQEH, p	98.65
3gee_A	476	MNME, tRNA modification GTPase MNME; G protein, cy	98.63
3a1s_A	258	Iron(II) transport protein B; FEOB, iron transport	98.62
3p26_A	483	Elongation factor 1 alpha-like protein; GTP/GDP bi	98.61
1r5b_A	467	Eukaryotic peptide chain release factor GTP-bindi	98.6
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	98.6
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	98.6
4dcu_A	456	GTP-binding protein ENGA; GTPase, GDP, protein bin	98.58
3l2o_B	312	F-box only protein 4; small G protein fold, UBL co	98.57
3i8s_A	274	Ferrous iron transport protein B; GTPase, GPCR, ir	98.51
1n0u_A	842	EF-2, elongation factor 2; G-protein, CIS-proline,	98.5
3izy_P	537	Translation initiation factor IF-2, mitochondrial;	98.5
3qq5_A	423	Small GTP-binding protein; hydrogenase, H-cluster,	98.5
1zun_B	434	Sulfate adenylate transferase, subunit 1/adenylyls	98.49
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	98.48
2c78_A	405	Elongation factor TU-A; hydrolase, GTPase, transla	98.48
3tr5_A	528	RF-3, peptide chain release factor 3; protein synt	98.46
3ec1_A	369	YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase	98.46
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	98.46
1zo1_I	501	IF2, translation initiation factor 2; E. coli, rib	98.44
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	98.44
2hjg_A	436	GTP-binding protein ENGA; GTPase ENGA KH-domain, h	98.43
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	98.41
1d2e_A	397	Elongation factor TU (EF-TU); G-protein, beta-barr	98.41
3izq_1	611	HBS1P, elongation factor 1 alpha-like protein; NO-	98.4
1f60_A	458	Elongation factor EEF1A; protein-protein complex,	98.39
2h5e_A	529	Peptide chain release factor RF-3; beta barrel, tr	98.38
1s0u_A	408	EIF-2-gamma, translation initiation factor 2 gamma	98.37
1dar_A	691	EF-G, elongation factor G; ribosomal translocase,	98.35
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	98.32
3j2k_7	439	ERF3, eukaryotic polypeptide chain release factor	98.3
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	98.29
2rdo_7	704	EF-G, elongation factor G; elongation factor G, EF	98.28
1wb1_A	482	Translation elongation factor SELB; selenocysteine	98.25
4dcu_A	456	GTP-binding protein ENGA; GTPase, GDP, protein bin	98.24
2xex_A	693	Elongation factor G; GTPase, translation, biosynth	98.22
1kk1_A	410	EIF2gamma; initiation of translation; HET: GNP; 1.	98.21
3geh_A	462	MNME, tRNA modification GTPase MNME; G protein, U3	98.19
2elf_A	370	Protein translation elongation factor 1A; tRNA, py	98.18
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	98.16
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	98.15
1xzp_A	482	Probable tRNA modification GTPase TRME; GTP-bindin	98.13
2qpt_A	550	EH domain-containing protein-2; protein-nucleotide	98.11
3avx_A	1289	Elongation factor TS, elongation factor TU, linke	98.1
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	98.05
2qag_A	361	Septin-2, protein NEDD5; cell cycle, cell division	98.04
2j69_A	695	Bacterial dynamin-like protein; FZO, FZL, GTPase,	97.96
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	97.94
3t34_A	360	Dynamin-related protein 1A, linker, dynamin-relat	97.94
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	97.92
2dy1_A	665	Elongation factor G; translocation, GTP complex, s	97.87
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	97.86
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	97.74
3mca_A	592	HBS1, elongation factor 1 alpha-like protein; prot	97.68
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	97.66
1puj_A	282	YLQF, conserved hypothetical protein YLQF; structu	97.55
2x2e_A	353	Dynamin-1; nitration, hydrolase, membrane fission,	97.28
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	97.27
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	97.16
1udx_A	416	The GTP-binding protein OBG; TGS domain, riken str	97.12
1wxq_A	397	GTP-binding protein; structural genomics, riken st	97.12
3t5d_A	274	Septin-7; GTP-binding protein, cytoskeleton, signa	96.97
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	96.87
3cnl_A	262	YLQF, putative uncharacterized protein; circular p	96.67
3vqt_A	548	RF-3, peptide chain release factor 3; translation,	96.54
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	96.37
4fn5_A	709	EF-G 1, elongation factor G 1; translation, transl	96.07
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	95.96
3j25_A	638	Tetracycline resistance protein TETM; antibiotic r	95.69
3zvr_A	772	Dynamin-1; hydrolase, DRP1, DRP, endocytosis, mito	95.5
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	94.86
1jal_A	363	YCHF protein; nucleotide-binding fold, structural	94.61
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	94.33
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	93.79
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	93.44
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	92.97
2dby_A	368	GTP-binding protein; GDP, structural genomics, NPP	88.34
2hf9_A	226	Probable hydrogenase nickel incorporation protein	86.42
4a9a_A	376	Ribosome-interacting GTPase 1; DRG-DFRP complex, r	83.44

>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=99.85  E-value=3.1e-21  Score=115.63  Aligned_cols=70  Identities=21%  Similarity=0.458  Sum_probs=64.1

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      .+|+|+|+++++.|++  +++++++|||+++++||+++..|+..+.... .+++|++|||||+||.++|+|+.
T Consensus        69 taGqe~~~~l~~~~~~--~a~~~ilv~di~~~~Sf~~i~~~~~~i~~~~-~~~~piilVgNK~Dl~~~r~V~~  138 (216)
T 4dkx_A           69 TAGLERFRSLIPSYIR--DSAAAVVVYDITNVNSFQQTTKWIDDVRTER-GSDVIIMLVGNKTDLADKRQVSI  138 (216)
T ss_dssp             CSCTTTCGGGHHHHHT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHH-TTSSEEEEEEECTTCGGGCCSCH
T ss_pred             CCCchhhhhHHHHHhc--cccEEEEEeecchhHHHHHHHHHHHHHHHhc-CCCCeEEEEeeccchHhcCcccH
Confidence            3689999999999999  6999999999999999999999999988764 47899999999999998888864

>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=99.68  E-value=1.2e-16  Score=90.39  Aligned_cols=69  Identities=32%  Similarity=0.436  Sum_probs=45.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|++.|+.+++.|++  +++++++|||+++++||+.+..|+..+.......++|+++||||+|+.+.+.++
T Consensus        57 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~  125 (166)
T 3q72_A           57 WEQDGGRWLPGHCMA--MGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVS  125 (166)
T ss_dssp             C-----------------CCEEEEEEETTCHHHHHHHHHHHHHHHHCC---CCCEEEEEECTTCCSSCCSC
T ss_pred             CCCccchhhhhhhhh--hCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeccccccccccC
Confidence            588999999999998  599999999999999999999999988875445689999999999998777654

>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=99.68  E-value=1.3e-16  Score=93.37  Aligned_cols=69  Identities=35%  Similarity=0.470  Sum_probs=58.5

Q ss_pred             cccccchh-hhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTN-LVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~-~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|.. +++.|++  +++++|+|||++++.||+.+..|+.++.......++|+++||||+|+.+.+.++
T Consensus        80 ~g~~~~~~~~~~~~~~--~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~v~  149 (195)
T 3cbq_A           80 WEQGDAGGWLRDHCLQ--TGDAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVS  149 (195)
T ss_dssp             CCCSGGGHHHHHHHHH--HCSEEEEEEETTCHHHHHTHHHHHHHHHHHSTTSCCCEEEEEECTTCTTTCCSC
T ss_pred             CCCccchhhhHHHhhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEeechhccccCCcC
Confidence            57777765 8888888  599999999999999999999999988775433579999999999998777664

>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=99.67  E-value=1.1e-16  Score=95.50  Aligned_cols=68  Identities=32%  Similarity=0.467  Sum_probs=55.8

Q ss_pred             cccc-chhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           4 RTSC-FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         4 ~~e~-f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      |++. ++.+++.|++  +++++|+|||+++++||+.+..|...+.......++|++|||||+||.+.|+|+
T Consensus        96 g~~~~~~~l~~~~~~--~a~~~ilVydvt~~~sf~~~~~~~~~l~~~~~~~~~piilVgNK~DL~~~r~v~  164 (211)
T 2g3y_A           96 ENKGENEWLHDHCMQ--VGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVS  164 (211)
T ss_dssp             TTTHHHHHHHHCCCC--CCSEEEEEEETTCHHHHHHHHHHHHHHHTSGGGTTSCEEEEEECTTCGGGCCSC
T ss_pred             CCcchhhhHHHHHHh--hCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCcEEEEEEChHHhcCceEe
Confidence            4444 5667778888  699999999999999999999999888764333579999999999998766664

>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=99.67  E-value=1.9e-16  Score=90.91  Aligned_cols=69  Identities=30%  Similarity=0.457  Sum_probs=61.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..++..|++  +++++++|||++++.||+.+..|+..+.......++|+++||||+|+.+.+.++
T Consensus        74 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~v~  142 (183)
T 3kkq_A           74 AGQEEFSAMREQYMR--TGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVT  142 (183)
T ss_dssp             CSCGGGCSSHHHHHH--HCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTSSCCCEEEEEECTTCSTTCCSC
T ss_pred             CCchhhHHHHHHHHh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECCCchhccCcC
Confidence            578999999999999  599999999999999999999999988765555789999999999998777664

>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=99.66  E-value=2.7e-16  Score=90.16  Aligned_cols=69  Identities=22%  Similarity=0.310  Sum_probs=58.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|+.+...|++  +++++++|||++++++|+.+..|+.++.......++|+++||||+|+.+.+.++
T Consensus        62 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~  130 (181)
T 3t5g_A           62 AGQDEYSIFPQTYSI--DINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVIS  130 (181)
T ss_dssp             CCCCTTCCCCGGGTT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHC----CCEEEEEECTTCTTTCCSC
T ss_pred             CCchhhhHHHHHHHh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccchhcceec
Confidence            588999999999998  599999999999999999999999988765444689999999999998777664

>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=99.66  E-value=3e-16  Score=92.06  Aligned_cols=68  Identities=16%  Similarity=0.348  Sum_probs=60.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|+.++..|++  +++++|+|||++++.+|+.+..|+..+.... ..++|+++||||+|+.+.+.++
T Consensus        86 ~G~~~~~~~~~~~~~--~~d~iilv~D~~~~~s~~~~~~~~~~i~~~~-~~~~piilv~NK~Dl~~~~~v~  153 (201)
T 2hup_A           86 AGQERFRTITQSYYR--SANGAILAYDITKRSSFLSVPHWIEDVRKYA-GSNIVQLLIGNKSDLSELREVS  153 (201)
T ss_dssp             TTCGGGHHHHHHHHT--TCSEEEEEEETTBHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECTTCGGGCCSC
T ss_pred             CCcHhHHHHHHHHHh--hCCEEEEEEECCCHHHHHHHHHHHHHHHHhc-CCCCCEEEEEECCccccccccC
Confidence            688999999999999  6999999999999999999999999988754 4679999999999998766654

>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=99.66  E-value=3.3e-16  Score=89.92  Aligned_cols=68  Identities=16%  Similarity=0.406  Sum_probs=50.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|+.++..+++  +++++++|||++++.||+.+..|+..+.... ..++|+++||||+|+.+.+.++
T Consensus        65 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~piilv~nK~Dl~~~~~v~  132 (183)
T 2fu5_C           65 AGQERFRTITTAYYR--GAMGIMLVYDITNEKSFDNIRNWIRNIEEHA-SADVEKMILGNKCDVNDKRQVS  132 (183)
T ss_dssp             ---------CCTTTT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHS-CTTCEEEEEEEC--CCSCCCSC
T ss_pred             CCChhhhhhHHHHHh--cCCEEEEEEECcCHHHHHHHHHHHHHHHHhc-CCCCCEEEEEECccCCccCcCC
Confidence            578999999999998  6999999999999999999999999988753 4679999999999998776654

>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=99.64  E-value=4.5e-16  Score=92.23  Aligned_cols=62  Identities=16%  Similarity=0.269  Sum_probs=56.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHH-HHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKK-AEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~-~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.+++.|++  +++++|+|||++++.||+. +..|+..+...  .+++|+++||||+|+.+
T Consensus        83 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~i~~~--~~~~piilv~nK~Dl~~  145 (214)
T 3q3j_B           83 SGSPYYDNVRPLCYS--DSDAVLLCFDISRPETVDSALKKWRTEILDY--CPSTRVLLIGCKTDLRT  145 (214)
T ss_dssp             CCSGGGTTTGGGGCT--TCSEEEEEEETTCTHHHHHHHTHHHHHHHHH--CTTSEEEEEEECGGGGG
T ss_pred             CCCHhHHHHHHHHcC--CCeEEEEEEECcCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEEChhhcc
Confidence            689999999999999  6999999999999999999 69999999875  36899999999999975

>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=99.64  E-value=3.6e-16  Score=88.61  Aligned_cols=69  Identities=35%  Similarity=0.472  Sum_probs=53.2

Q ss_pred             cccccchh-hhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTN-LVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~-~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|.. +++.+++  +++++++|||+++++||+.+..|+.++.......++|+++||||+|+.+.+.++
T Consensus        59 ~g~~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~  128 (169)
T 3q85_A           59 WEQGDAGGWLQDHCLQ--TGDAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVS  128 (169)
T ss_dssp             CCC--------CHHHH--HCSEEEEEEETTCHHHHHTHHHHHHHHHHHSTTSCCCEEEEEECTTCGGGCCSC
T ss_pred             CCccccchhhhhhhhc--cCCEEEEEEECCChHHHHHHHHHHHHHHhcccCCCCCEEEEeeCcchhhcccCC
Confidence            57788876 7777888  499999999999999999999999998875444589999999999998766654

>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=99.63  E-value=7.3e-16  Score=90.82  Aligned_cols=68  Identities=19%  Similarity=0.417  Sum_probs=59.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|+.++..|++  +++++|+|||++++.||+.+..|+.++.... ..++|+++||||+|+.+.++++
T Consensus        83 ~G~~~~~~~~~~~~~--~~d~~i~v~D~~~~~s~~~~~~~~~~i~~~~-~~~~piilv~NK~Dl~~~~~v~  150 (201)
T 2ew1_A           83 AGQERFRSITQSYYR--SANALILTYDITCEESFRCLPEWLREIEQYA-SNKVITVLVGNKIDLAERREVS  150 (201)
T ss_dssp             CCSGGGHHHHGGGST--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECGGGGGGCSSC
T ss_pred             CCcHHHHHHHHHHHh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhc-CCCCCEEEEEECCCCccccccC
Confidence            578999999999998  6999999999999999999999999988753 4679999999999998666654

>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=99.63  E-value=5.5e-16  Score=87.43  Aligned_cols=69  Identities=30%  Similarity=0.460  Sum_probs=60.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..++..|++  +++++++|||++++.||+.+..|+..+.......++|+++|+||+|+.+.+.++
T Consensus        59 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~  127 (167)
T 1c1y_A           59 AGTEQFTAMRDLYMK--NGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVG  127 (167)
T ss_dssp             CSSCSSTTHHHHHHH--HCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSCCCEEEEEECTTCGGGCCSC
T ss_pred             CChHHHHHHHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCcCCCcEEEEEECccccccccCC
Confidence            578999999999998  499999999999999999999999888775445689999999999997766553

>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=99.63  E-value=9.9e-16  Score=87.06  Aligned_cols=69  Identities=30%  Similarity=0.398  Sum_probs=52.6

Q ss_pred             ccccc--chhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSC--FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~--f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|++.  +..+...+++  +++++++|||++++.||+.+..|+..+.......++|+++||||+|+.+.++++
T Consensus        60 ~g~~~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~l~~~~~~~~~piilv~NK~Dl~~~~~v~  130 (175)
T 2nzj_A           60 WEAEKLDKSWSQESCLQ--GGSAYVIVYSIADRGSFESASELRIQLRRTHQADHVPIILVGNKADLARCREVS  130 (175)
T ss_dssp             C-------CHHHHHTTT--SCSEEEEEEETTCHHHHHHHHHHHHHHHHCC----CCEEEEEECTTCTTTCCSC
T ss_pred             CCCCccchhhhHHhhcc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhhccCCCCEEEEEEChhhccccccC
Confidence            46666  6778888888  599999999999999999999999888775334579999999999998777664

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=99.62  E-value=1.5e-15  Score=88.83  Aligned_cols=69  Identities=29%  Similarity=0.428  Sum_probs=58.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..|++  +++++++|||++++++|+.+..|+..+.......++|+++||||+|+...+.++
T Consensus        80 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~v~  148 (201)
T 3oes_A           80 AGQDEYSILPYSFII--GVHGYVLVYSVTSLHSFQVIESLYQKLHEGHGKTRVPVVLVGNKADLSPEREVQ  148 (201)
T ss_dssp             CCCCTTCCCCGGGTT--TCCEEEEEEETTCHHHHHHHHHHHHHHHC-----CCCEEEEEECTTCGGGCCSC
T ss_pred             CCccchHHHHHHHHh--cCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccCccccccC
Confidence            578999999999999  699999999999999999999999998875444678999999999998766654

>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=99.62  E-value=1.2e-15  Score=88.32  Aligned_cols=69  Identities=22%  Similarity=0.324  Sum_probs=60.0

Q ss_pred             cccccch-hhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFT-NLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~-~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|+ .+...|++  +++++|+|||++++.||+.+..|+.++.......++|+++|+||+|+.+.++++
T Consensus        77 ~G~~~~~~~~~~~~~~--~~d~iilv~D~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~v~  146 (189)
T 1z06_A           77 AGQERFRKSMVQHYYR--NVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRILVGNKCDLRSAIQVP  146 (189)
T ss_dssp             CCSHHHHTTTHHHHHT--TCCEEEEEEETTCHHHHHTHHHHHHHHHHHCCCSCCCEEEEEECTTCGGGCCSC
T ss_pred             CCchhhhhhhhHHHhc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccceeC
Confidence            5788888 88899998  599999999999999999999999998876445689999999999997766554

>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=99.62  E-value=2.3e-15  Score=85.00  Aligned_cols=68  Identities=22%  Similarity=0.401  Sum_probs=59.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..++..+++  +++++++|||++++.+|+.+..|+..+.... .+++|+++||||+|+.+.+.++
T Consensus        63 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~iilv~nK~Dl~~~~~~~  130 (170)
T 1r2q_A           63 AGQERYHSLAPMYYR--GAQAAIVVYDITNEESFARAKNWVKELQRQA-SPNIVIALSGNKADLANKRAVD  130 (170)
T ss_dssp             CCSGGGGGGHHHHHT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHS-CTTCEEEEEEECGGGGGGCCSC
T ss_pred             CCcHHhhhhhHHhcc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhc-CCCCcEEEEEECccCccccccC
Confidence            578999999999998  5999999999999999999999999888753 4689999999999997655543

>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=99.62  E-value=8.2e-16  Score=89.20  Aligned_cols=68  Identities=21%  Similarity=0.407  Sum_probs=59.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..+++  +++++++|||++++.+|+.+..|+..+.... ..++|+++||||+|+.+.+.++
T Consensus        80 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~piilv~nK~Dl~~~~~~~  147 (191)
T 3dz8_A           80 AGQERYRTITTAYYR--GAMGFILMYDITNEESFNAVQDWATQIKTYS-WDNAQVILVGNKCDMEEERVVP  147 (191)
T ss_dssp             HHHHHCHHHHHHHHT--TCCEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECTTCGGGCCSC
T ss_pred             CChHHHHHHHHHHHc--cCCEEEEEEECcCHHHHHHHHHHHHHHHHhc-CCCCCEEEEEECCCCccccccC
Confidence            578899999999999  6999999999999999999999999998753 4689999999999997766553

>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=99.62  E-value=7.1e-16  Score=89.51  Aligned_cols=68  Identities=26%  Similarity=0.366  Sum_probs=54.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC--CCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY--IGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|+.+ ..|++  +++++++|||+++++||+.+..|+.++.....  ..++|+++||||+|+.+.++++
T Consensus        77 ~G~~~~~~~-~~~~~--~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~v~  146 (187)
T 3c5c_A           77 ADLDTPRNC-ERYLN--WAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQYRQVT  146 (187)
T ss_dssp             CC---CCCT-HHHHT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECGGGGGGCSSC
T ss_pred             CCCCcchhH-HHHHh--hCCEEEEEEECCCHHHHHHHHHHHHHHHHHhhccCCCCCEEEEEECcchhhcCccC
Confidence            678889886 56777  59999999999999999999999998876421  2578999999999998766664

>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=99.62  E-value=1.2e-15  Score=85.84  Aligned_cols=69  Identities=26%  Similarity=0.427  Sum_probs=57.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..++..|++  +++++++|||++++++|+.+..|+..+.......++|+++|+||+|+.+.++++
T Consensus        60 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~  128 (168)
T 1u8z_A           60 AGQEDYAAIRDNYFR--SGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVS  128 (168)
T ss_dssp             CC---CHHHHHHHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHHCCTTSCEEEEEECGGGGGGCCSC
T ss_pred             CCcchhHHHHHHHhh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECccccccCccC
Confidence            578899999999998  499999999999999999999999998876544589999999999997766553

>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=99.61  E-value=1.6e-15  Score=87.55  Aligned_cols=62  Identities=16%  Similarity=0.247  Sum_probs=55.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.+++.+++  +++++++|||++++.||+.+ ..|+..+...  .+++|+++||||+|+.+
T Consensus        63 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~i~~~--~~~~piilv~nK~Dl~~  125 (184)
T 1m7b_A           63 SGSPYYDNVRPLSYP--DSDAVLICFDISRPETLDSVLKKWKGEIQEF--CPNTKMLLVGCKSDLRT  125 (184)
T ss_dssp             CCSGGGTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH--CTTCEEEEEEECGGGGG
T ss_pred             CCChhhhhhHHhhcC--CCcEEEEEEECCCHHHHHHHHHHHHHHHHHH--CCCCCEEEEEEcchhhc
Confidence            688999999999998  69999999999999999999 7899888764  36899999999999974

>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=99.61  E-value=4.8e-15  Score=83.55  Aligned_cols=65  Identities=17%  Similarity=0.276  Sum_probs=56.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+++|+.++..+++  +++++++|||+++++||+.+..|+..+.......++|+++||||+|+.+.
T Consensus        52 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~  116 (164)
T 1r8s_A           52 GGQDKIRPLWRHYFQ--NTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNA  116 (164)
T ss_dssp             CCCGGGHHHHHHHTT--TCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC
T ss_pred             CCChhhHHHHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhcCCeEEEEEECcCCcCC
Confidence            688999999999998  69999999999999999999999988876433468999999999999754

>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=99.61  E-value=4.5e-15  Score=84.83  Aligned_cols=68  Identities=22%  Similarity=0.351  Sum_probs=60.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|+.++..+++  +++++++|||++++.+|+.+..|+..+.... .+++|+++|+||+|+.+.+.++
T Consensus        69 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~p~i~v~nK~Dl~~~~~~~  136 (181)
T 2efe_B           69 AGQERYHSLAPMYYR--GAAAAIIVFDVTNQASFERAKKWVQELQAQG-NPNMVMALAGNKSDLLDARKVT  136 (181)
T ss_dssp             CCSGGGGGGTHHHHT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHS-CTTCEEEEEEECTTCTTTCCSC
T ss_pred             CCChhhhhhhHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhc-CCCCcEEEEEECCcccccccCC
Confidence            578999999999998  5999999999999999999999999988753 3689999999999997766653

>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=99.61  E-value=1.2e-15  Score=86.97  Aligned_cols=69  Identities=26%  Similarity=0.474  Sum_probs=59.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..|++  +++++++|||++++.+|+.+..|+.++.......++|+++|+||+|+.+.++++
T Consensus        65 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~v~  133 (181)
T 2fn4_A           65 AGQEEFGAMREQYMR--AGHGFLLVFAINDRQSFNEVGKLFTQILRVKDRDDFPVVLVGNKADLESQRQVP  133 (181)
T ss_dssp             CCTTTTSCCHHHHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHHTSSCCCEEEEEECGGGGGGCCSC
T ss_pred             CCchhhHHHHHHHHh--hCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccC
Confidence            578899999999998  499999999999999999999999888554445689999999999998766653

>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=99.61  E-value=3.4e-15  Score=86.22  Aligned_cols=66  Identities=20%  Similarity=0.324  Sum_probs=57.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +|+++|+.++..|++  +++++++|||++++++|+.+..|+.++.......++|+++||||+|+.+.+
T Consensus        68 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~~  133 (181)
T 1fzq_A           68 GGQRKIRPYWRSYFE--NTDILIYVIDSADRKRFEETGQELTELLEEEKLSCVPVLIFANKQDLLTAA  133 (181)
T ss_dssp             SSCGGGHHHHHHHHT--TCSEEEEEEETTCGGGHHHHHHHHHHHTTCGGGTTCCEEEEEECTTSTTCC
T ss_pred             CCCHHHHHHHHHHhC--CCCEEEEEEECcCHHHHHHHHHHHHHHHhChhhcCCCEEEEEECcCcccCC
Confidence            689999999999998  699999999999999999999998887653334678999999999997654

>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=99.61  E-value=1.7e-15  Score=87.84  Aligned_cols=68  Identities=24%  Similarity=0.448  Sum_probs=59.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|+.++..+++  +++++|+|||++++.+|+.+..|+..+.... ..++|+++|+||+|+.+.++++
T Consensus        78 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~l~~i~~~~-~~~~piilv~nK~Dl~~~~~v~  145 (191)
T 2a5j_A           78 AGQESFRSITRSYYR--GAAGALLVYDITRRETFNHLTSWLEDARQHS-SSNMVIMLIGNKSDLESRRDVK  145 (191)
T ss_dssp             TTGGGTSCCCHHHHT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECTTCGGGCCSC
T ss_pred             CCchhhhhhHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhc-CCCCCEEEEEECcccCCccccC
Confidence            688999999999999  6999999999999999999999999988753 4689999999999997666553

>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=2.6e-15  Score=87.91  Aligned_cols=64  Identities=13%  Similarity=0.225  Sum_probs=53.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.+++.|++  +++++++|||+++++||+.+..|+.++.+.....++|+++||||+|+..
T Consensus        77 ~G~~~~~~~~~~~~~--~~d~~i~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~  140 (198)
T 1f6b_A           77 GGHIQARRVWKNYLP--AINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPE  140 (198)
T ss_dssp             CC----CCGGGGGGG--GCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTSCEEEEEECTTSTT
T ss_pred             CCcHhhHHHHHHHHh--cCCEEEEEEECCCHHHHHHHHHHHHHHHhCcccCCCcEEEEEECCCccc
Confidence            589999999999999  5999999999999999999999998887643346899999999999964

>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=99.61  E-value=2.8e-15  Score=87.51  Aligned_cols=68  Identities=32%  Similarity=0.476  Sum_probs=53.9

Q ss_pred             cccc-chhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           4 RTSC-FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         4 ~~e~-f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      |++. ++.+++.|++  +++++++|||+++++||+.+..|...+.......++|+++||||+|+...|.++
T Consensus        65 ~~~~~~~~~~~~~~~--~~~~~i~v~dv~~~~s~~~~~~~~~~l~~~~~~~~~piilV~NK~Dl~~~r~v~  133 (192)
T 2cjw_A           65 ENKGENEWLHDHCMQ--VGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRXREVS  133 (192)
T ss_dssp             CC----CTTGGGHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTTSCCCEEEEEECTTCGGGCCSC
T ss_pred             cCcchhhhHHHhhcc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCeEEEEEechhhhcccccc
Confidence            3443 5667888888  499999999999999999999998888765334679999999999997666553

>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=99.61  E-value=4.1e-15  Score=84.04  Aligned_cols=68  Identities=22%  Similarity=0.344  Sum_probs=59.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..+...+++  +++++++|||++++.+|+.+..|+..+.... .+.+|+++||||+|+.+.+++.
T Consensus        63 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~l~~~~-~~~~~iilv~nK~Dl~~~~~v~  130 (170)
T 1z0j_A           63 AGLERFRALAPMYYR--GSAAAIIVYDITKEETFSTLKNWVRELRQHG-PPSIVVAIAGNKCDLTDVREVM  130 (170)
T ss_dssp             CCSGGGGGGTHHHHT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHS-CTTSEEEEEEECTTCGGGCCSC
T ss_pred             CCchhhhcccHhhCc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCcEEEEEECCccccccccC
Confidence            578899999999998  5999999999999999999999999988753 4789999999999997666553

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=99.60  E-value=5.9e-15  Score=85.34  Aligned_cols=68  Identities=19%  Similarity=0.378  Sum_probs=60.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|+.+...|++  +++++++|||++++.+|+.+..|+..+.... ..++|+++|+||+|+...+.++
T Consensus        73 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~p~ilv~nK~Dl~~~~~~~  140 (196)
T 3tkl_A           73 AGQERFRTITSSYYR--GAHGIIVVYDVTDQESFNNVKQWLQEIDRYA-SENVNKLLVGNKCDLTTKKVVD  140 (196)
T ss_dssp             CCSGGGCTTHHHHHT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECTTCTTTCCSC
T ss_pred             CCcHhhhhhHHHHHh--hCCEEEEEEECcCHHHHHHHHHHHHHHHHhc-CCCCCEEEEEECcccccccccC
Confidence            578999999999999  5999999999999999999999999988754 4689999999999998776654

>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=99.60  E-value=2.7e-15  Score=86.23  Aligned_cols=69  Identities=22%  Similarity=0.432  Sum_probs=60.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|+.+...+++  +++++|+|||++++.+++.+..|+..+.......++|+++|+||+|+.+.+.++
T Consensus        78 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~  146 (195)
T 3bc1_A           78 AGLERFRSLTTAFFR--DAMGFLLLFDLTNEQSFLNVRNWISQLQMHAYSENPDIVLCGNKSDLEDQRAVK  146 (195)
T ss_dssp             CCSGGGHHHHHHTTT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHSSSSSCCEEEEEECTTCGGGCCSC
T ss_pred             CCcHHHHHHHHHHHc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccC
Confidence            578999999999998  699999999999999999999999998876444689999999999997765553

>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=99.60  E-value=2.4e-15  Score=87.59  Aligned_cols=69  Identities=26%  Similarity=0.427  Sum_probs=60.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..|++  +++++++|||++++.+|+.+..|+..+.......++|+++|+||+|+.+.++++
T Consensus        70 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~  138 (206)
T 2bov_A           70 AGQEDYAAIRDNYFR--SGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVS  138 (206)
T ss_dssp             CCTTCCHHHHHHHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTCSCCCEEEEEECTTCGGGCCSC
T ss_pred             CChhhhHHHHHHHHh--hCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeccCcccccccc
Confidence            688999999999998  499999999999999999999999998876544589999999999998766553

>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=99.60  E-value=4.3e-15  Score=86.62  Aligned_cols=68  Identities=19%  Similarity=0.393  Sum_probs=59.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|+.++..+++  +++++|+|||++++.+|+.+..|+..+.... ..++|+++||||+|+.+.+.++
T Consensus        65 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~piilv~nK~Dl~~~~~~~  132 (203)
T 1zbd_A           65 AGLERYRTITTAYYR--GAMGFILMYDITNEESFNAVQDWSTQIKTYS-WDNAQVLLVGNKCDMEDERVVS  132 (203)
T ss_dssp             CCSGGGHHHHHTTGG--GCSEEEEEEETTCHHHHHHHHHHHHHHHHHS-CSSCEEEEEEECTTCTTSCCSC
T ss_pred             CCchhhcchHHHhhc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhc-CCCCCEEEEEECcccCcccccC
Confidence            578999999999998  5999999999999999999999999988753 4678999999999998766553

>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=99.60  E-value=2.3e-15  Score=84.64  Aligned_cols=69  Identities=29%  Similarity=0.504  Sum_probs=59.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..++..+++  +++++++|||++++.+|+.+..|..++.......++|+++|+||+|+...++++
T Consensus        59 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~  127 (167)
T 1kao_A           59 AGTEQFASMRDLYIK--NGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRYEKVPVILVGNKVDLESEREVS  127 (167)
T ss_dssp             CCTTCCHHHHHHHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTTSCCCEEEEEECGGGGGGCCSC
T ss_pred             CCchhhHHHHHHHhc--cCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCcccccccCC
Confidence            578999999999998  499999999999999999999999888775444689999999999997666553

>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=99.60  E-value=4.4e-15  Score=86.88  Aligned_cols=68  Identities=22%  Similarity=0.372  Sum_probs=60.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|+.++..+++  +++++|+|||++++.+|+.+..|+..+.... ..++|+++||||+|+.+.+.++
T Consensus        65 ~G~~~~~~~~~~~~~--~~d~vilv~d~~~~~s~~~~~~~~~~i~~~~-~~~~piilv~nK~Dl~~~~~~~  132 (206)
T 2bcg_Y           65 AGQERFRTITSSYYR--GSHGIIIVYDVTDQESFNGVKMWLQEIDRYA-TSTVLKLLVGNKCDLKDKRVVE  132 (206)
T ss_dssp             TTTTTTTCCCGGGGT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHS-CTTCEEEEEEECTTCTTTCCSC
T ss_pred             CChHHHHHHHHHhcc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhc-CCCCCEEEEEECCCCccccccC
Confidence            578999999999998  6999999999999999999999999988754 4679999999999998766653

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C

Probab=99.60  E-value=2.5e-15  Score=87.49  Aligned_cols=69  Identities=20%  Similarity=0.310  Sum_probs=55.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC--CCCCeEEEEeeCCCCcC-CCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY--IGEKAVILVANKADLER-RRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~~ilvgnK~Dl~~-~r~v~   73 (75)
                      +|+++|..++..|++  +++++|+|||++++.||+.+..|+..+.....  ..++|+++||||+|+.+ .+.++
T Consensus        81 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~~v~  152 (208)
T 2yc2_C           81 AGSDLYKEQISQYWN--GVYYAILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANKTDLPPQRHQVR  152 (208)
T ss_dssp             TTTHHHHHHHSTTCC--CCCEEEEEEETTCHHHHHHHHHHHHHHHHHCSCTTSCCEEEEEEECC-------CCC
T ss_pred             CCcHHHHHHHHHHHh--hCcEEEEEEECCCHHHHHHHHHHHHHHHHhhcccccCCcEEEEEECcccchhhccCC
Confidence            688899999999998  69999999999999999999999999987542  15899999999999987 66654

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=99.60  E-value=2e-15  Score=87.82  Aligned_cols=68  Identities=21%  Similarity=0.407  Sum_probs=59.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..++..+++  +++++|+|||++++.+|+.+..|+..+.... ..++|+++||||+|+.+.++++
T Consensus        83 ~G~~~~~~~~~~~~~--~~d~iilV~D~~~~~s~~~~~~~~~~i~~~~-~~~~piilV~NK~Dl~~~~~v~  150 (192)
T 2il1_A           83 AGQERFNSITSAYYR--SAKGIILVYDITKKETFDDLPKWMKMIDKYA-SEDAELLLVGNKLDCETDREIT  150 (192)
T ss_dssp             CCSGGGHHHHHHHHH--HCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECGGGGGGCCSC
T ss_pred             CCcHHHHHHHHHHhc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhc-CCCCcEEEEEECcccccccccC
Confidence            578999999999998  5999999999999999999999998887753 4679999999999998766654

>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=99.60  E-value=4e-15  Score=86.45  Aligned_cols=68  Identities=22%  Similarity=0.338  Sum_probs=59.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..++..+++  +++++++|||++++.+|+.+..|+..+.... ..++|+++|+||+|+.+.+.++
T Consensus        80 ~G~~~~~~~~~~~~~--~~d~iilV~d~~~~~s~~~~~~~~~~i~~~~-~~~~piiiv~NK~Dl~~~~~v~  147 (192)
T 2fg5_A           80 AGQERFHSLAPMYYR--GSAAAVIVYDITKQDSFYTLKKWVKELKEHG-PENIVMAIAGNKCDLSDIREVP  147 (192)
T ss_dssp             CCSGGGGGGTHHHHT--TCSEEEEEEETTCTHHHHHHHHHHHHHHHHS-CTTCEEEEEEECGGGGGGCCSC
T ss_pred             CCchhhHhhhHHhhc--cCCEEEEEEeCCCHHHHHHHHHHHHHHHHhC-CCCCcEEEEEECcccccccccC
Confidence            578999999999999  5999999999999999999999999988753 4679999999999997655553

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=99.60  E-value=5.3e-15  Score=84.29  Aligned_cols=67  Identities=21%  Similarity=0.353  Sum_probs=59.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|++.|..+...+++  +++++++|||++++.+|+.+..|+..+...  .+++|+++|+||+|+.+.+.+.
T Consensus        66 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~--~~~~p~ilv~nK~Dl~~~~~~~  132 (181)
T 3tw8_B           66 AGQERFRTITSTYYR--GTHGVIVVYDVTSAESFVNVKRWLHEINQN--CDDVCRILVGNKNDDPERKVVE  132 (181)
T ss_dssp             TTGGGCSSCCGGGGT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHH--CTTSEEEEEEECTTCGGGCCSC
T ss_pred             CCchhhhhhHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHh--CCCCCEEEEEECCCCchhcccC
Confidence            578899999999998  699999999999999999999999998774  4689999999999997766543

>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=99.60  E-value=4.8e-15  Score=85.12  Aligned_cols=68  Identities=22%  Similarity=0.348  Sum_probs=59.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|+.++..+++  +++++|+|||++++.+|+.+..|+..+.... ..++|+++|+||+|+...+.++
T Consensus        67 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~piilv~nK~Dl~~~~~~~  134 (186)
T 2bme_A           67 AGQERFRSVTRSYYR--GAAGALLVYDITSRETYNALTNWLTDARMLA-SQNIVIILCGNKKDLDADREVT  134 (186)
T ss_dssp             CCSGGGHHHHHTTST--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECGGGGGGCCSC
T ss_pred             CCcHHHHHHHHHHHh--cCCEEEEEEECcCHHHHHHHHHHHHHHHHhc-CCCCcEEEEEECcccccccccC
Confidence            578999999999998  6999999999999999999999998887753 3689999999999997666553

>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=99.60  E-value=3.3e-15  Score=86.72  Aligned_cols=63  Identities=19%  Similarity=0.269  Sum_probs=56.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+++|..++..|++  +++++++|||++++.||+.+ ..|...+...  .+++|+++||||+|+.+.
T Consensus        79 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~p~ilv~nK~Dl~~~  142 (194)
T 3reg_A           79 AGQEEYDRLRPLSYA--DSDVVLLCFAVNNRTSFDNISTKWEPEIKHY--IDTAKTVLVGLKVDLRKD  142 (194)
T ss_dssp             CCSGGGTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH--CTTSEEEEEEECGGGCCT
T ss_pred             CCcHHHHHHhHhhcc--CCcEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEEChhhccC
Confidence            588999999999999  69999999999999999998 7898888764  478999999999999753

>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=6.2e-15  Score=85.78  Aligned_cols=64  Identities=14%  Similarity=0.227  Sum_probs=56.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+++|+.+++.|++  +++++++|||+++++||+.+..|+.++.......++|+++||||+|+..
T Consensus        75 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~  138 (190)
T 1m2o_B           75 GGHIQARRLWKDYFP--EVNGIVFLVDAADPERFDEARVELDALFNIAELKDVPFVILGNKIDAPN  138 (190)
T ss_dssp             CCSGGGTTSGGGGCT--TCCEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCCEEEEEECTTSTT
T ss_pred             CCCHHHHHHHHHHHh--cCCEEEEEEECCChHHHHHHHHHHHHHHcchhhcCCCEEEEEECCCCcC
Confidence            688999999999998  6999999999999999999999998887643346799999999999975

>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=99.59  E-value=1.9e-15  Score=97.61  Aligned_cols=66  Identities=17%  Similarity=0.332  Sum_probs=59.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC----------hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE----------RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~----------~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +||++|+++++.||+  +++++|+|||+++          .++|+.+..|+..+.+.....++|++|||||+||.+++
T Consensus       225 aGQe~~r~~w~~yf~--~a~~iIfV~dis~ydq~l~ed~~~ns~~e~~~~~~~i~~~~~~~~~piiLvgNK~DL~~~k  300 (402)
T 1azs_C          225 GGQRDERRKWIQCFN--DVTAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEK  300 (402)
T ss_dssp             CCSGGGGGGGGGGTT--TCCEEEEEEETTGGGCBCTTTSCSBHHHHHHHHHHHHHTCTTCSSCCEEEEEECHHHHHHH
T ss_pred             chhhhhhhhhHhhcc--CCCEEEEEEECcccccccccccccchHHHHHHHHHHHHhcccCCCCeEEEEEEChhhhhhh
Confidence            799999999999999  7999999999999          89999999999998875445789999999999996544

>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=99.59  E-value=4.6e-15  Score=84.91  Aligned_cols=69  Identities=26%  Similarity=0.427  Sum_probs=60.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..++..|++  +++++++|||++++.+|+.+..|+.++.......++|+++|+||+|+.+.++++
T Consensus        74 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~  142 (187)
T 2a9k_A           74 AGQEDYAAIRDNYFR--SGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVS  142 (187)
T ss_dssp             CCTTCCHHHHHHHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHHCCTTCCEEEEEECGGGGGGCCSC
T ss_pred             CCCcccHHHHHHHhc--cCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccCccC
Confidence            578899999999998  499999999999999999999999998876544589999999999997766543

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=99.59  E-value=2.2e-15  Score=89.47  Aligned_cols=68  Identities=21%  Similarity=0.328  Sum_probs=57.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..++..|++  +++++|+|||++++.+|+.+..|+.++.... ..++|+++|+||+|+...++++
T Consensus        70 ~G~~~~~~~~~~~~~--~~d~vilV~D~~~~~s~~~~~~~l~~i~~~~-~~~~piilv~nK~Dl~~~~~v~  137 (223)
T 3cpj_B           70 AGQERYRAITSAYYR--GAVGALIVYDISKSSSYENCNHWLSELRENA-DDNVAVGLIGNKSDLAHLRAVP  137 (223)
T ss_dssp             TTTTTTTCCCGGGTT--TCCEEEEEEC-CCHHHHHHHHHHHHHHHHHC-C--CEEEEEECCGGGGGGCCSC
T ss_pred             CCccchhhhHHHHhc--cCCEEEEEEeCCCHHHHHHHHHHHHHHHHhC-CCCCeEEEEEECcccccccccC
Confidence            578999999999999  6999999999999999999999999988753 4678999999999997766654

>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=99.59  E-value=5.1e-15  Score=84.25  Aligned_cols=68  Identities=25%  Similarity=0.403  Sum_probs=59.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..+...+++  +++++++|||++++.+|+.+..|+..+.... ..++|+++|+||+|+.+.+.++
T Consensus        72 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~piilv~nK~Dl~~~~~~~  139 (179)
T 1z0f_A           72 AGQERFRAVTRSYYR--GAAGALMVYDITRRSTYNHLSSWLTDARNLT-NPNTVIILIGNKADLEAQRDVT  139 (179)
T ss_dssp             TTGGGTCHHHHHHHH--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECTTCGGGCCSC
T ss_pred             CCChHhhhhHHHHhc--cCCEEEEEEeCcCHHHHHHHHHHHHHHHHhc-CCCCcEEEEEECcccccccccC
Confidence            578999999999998  5999999999999999999999999888754 3689999999999997666553

>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=99.59  E-value=4e-15  Score=84.95  Aligned_cols=68  Identities=18%  Similarity=0.387  Sum_probs=52.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|+.++..+++  +++++++|||++++.+|+.+..|+..+.... ..++|+++|+||+|+...+.++
T Consensus        68 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~piilv~nK~Dl~~~~~~~  135 (180)
T 2g6b_A           68 AGQERFRSVTHAYYR--DAHALLLLYDVTNKASFDNIQAWLTEIHEYA-QHDVALMLLGNKVDSAHERVVK  135 (180)
T ss_dssp             CCC--------CCGG--GCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECCSTTSCCCSC
T ss_pred             CCcHHHHHHHHHHcc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCcEEEEEECcccCcccccC
Confidence            578899999999998  5999999999999999999999999988754 3689999999999998766554

>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=99.59  E-value=3.8e-15  Score=87.87  Aligned_cols=62  Identities=16%  Similarity=0.247  Sum_probs=55.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.++..+++  +++++|+|||++++.||+.+ ..|+..+...  .+++|+++||||+|+..
T Consensus        84 ~G~~~~~~~~~~~~~--~~d~~ilv~D~~~~~s~~~~~~~~~~~i~~~--~~~~piilv~nK~Dl~~  146 (205)
T 1gwn_A           84 SGSPYYDNVRPLSYP--DSDAVLICFDISRPETLDSVLKKWKGEIQEF--CPNTKMLLVGCKSDLRT  146 (205)
T ss_dssp             CCSGGGTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH--CTTCEEEEEEECGGGGG
T ss_pred             CCcHhhhHHHHhhcc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHHH--CCCCCEEEEEechhhcc
Confidence            588999999999998  69999999999999999999 7899888774  36899999999999974

>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=99.59  E-value=5e-15  Score=85.67  Aligned_cols=68  Identities=22%  Similarity=0.401  Sum_probs=59.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|+.++..+++  +++++++|||++++.+|+.+..|+..+.... ..++|+++|+||+|+.+.+.++
T Consensus        79 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~piilv~nK~Dl~~~~~~~  146 (189)
T 2gf9_A           79 AGQERYRTITTAYYR--GAMGFLLMYDIANQESFAAVQDWATQIKTYS-WDNAQVILVGNKCDLEDERVVP  146 (189)
T ss_dssp             CSCCSSCCSGGGGGT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECTTCGGGCCSC
T ss_pred             CCcHHHhhhHHHhcc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhc-CCCCCEEEEEECcccccccCCC
Confidence            578999999999998  5999999999999999999999999988753 4689999999999997766553

>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=99.59  E-value=8.9e-15  Score=82.52  Aligned_cols=64  Identities=23%  Similarity=0.390  Sum_probs=57.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|..++..+++  +++++++|||++++.+|+.+..|+..+.... ..++|+++|+||+|+...
T Consensus        60 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~piilv~nK~Dl~~~  123 (170)
T 1ek0_A           60 AGQERFASLAPXYYR--NAQAALVVYDVTKPQSFIKARHWVKELHEQA-SKDIIIALVGNKIDXLQE  123 (170)
T ss_dssp             CCSGGGGGGHHHHHT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHS-CTTCEEEEEEECGGGGGS
T ss_pred             CCChhhhhhhhhhhc--cCcEEEEEEecCChHHHHHHHHHHHHHHHhc-CCCCcEEEEEECCCcccc
Confidence            578999999999998  5999999999999999999999999888753 468999999999999654

>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=99.58  E-value=2.5e-15  Score=87.19  Aligned_cols=64  Identities=17%  Similarity=0.309  Sum_probs=52.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc--CCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE--RRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~--~~r~v~   73 (75)
                      +|+++|+     |++  +++++++|||++++.||+.+..|+.++.......++|+++||||+|+.  ..+.++
T Consensus        75 ~G~~~~~-----~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~v~  140 (184)
T 3ihw_A           75 GGPPELQ-----FAA--WVDAVVFVFSLEDEISFQTVYNYFLRLCSFRNASEVPMVLVGTQDAISAANPRVID  140 (184)
T ss_dssp             SSSCCHH-----HHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHTTSCGGGSCEEEEEECTTCBTTBCCCSC
T ss_pred             CCChhhh-----eec--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccccC
Confidence            5677776     666  499999999999999999999999999875434679999999999994  445553

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=99.58  E-value=3.4e-15  Score=85.11  Aligned_cols=69  Identities=20%  Similarity=0.306  Sum_probs=57.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC--CCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY--IGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..++..|++  +++++++|||++++.||+.+..|+..+.....  ....|+++||||+|+.+.+.++
T Consensus        64 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~iilv~nK~Dl~~~~~~~  134 (178)
T 2hxs_A           64 GGQTIGGKMLDKYIY--GAQGVLLVYDITNYQSFENLEDWYTVVKKVSEESETQPLVALVGNKIDLEHMRTIK  134 (178)
T ss_dssp             TTCCTTCTTHHHHHT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHHHHHTCCCEEEEEEECGGGGGGCSSC
T ss_pred             CCCccccchhhHHHh--hCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcccCCCCeEEEEEEccccccccccC
Confidence            578999999999998  69999999999999999999999988876421  1334489999999998766554

>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=99.58  E-value=5.5e-15  Score=85.69  Aligned_cols=63  Identities=19%  Similarity=0.330  Sum_probs=56.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+++|+.++..|++  +++++++|||+++++||+.+. .|+..+...  .+++|+++||||+|+...
T Consensus        74 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~piilv~nK~Dl~~~  137 (194)
T 2atx_A           74 AGQEDYDRLRPLSYP--MTDVFLICFSVVNPASFQNVKEEWVPELKEY--APNVPFLLIGTQIDLRDD  137 (194)
T ss_dssp             CCSSSSTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH--STTCCEEEEEECTTSTTC
T ss_pred             CCCcchhHHHHHhcC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEEChhhccc
Confidence            688999999999998  699999999999999999997 899888874  358999999999999753

>3l0i_B RAS-related protein RAB-1A; GEF-GDF-RAB complex, GTP-binding, guanine-nucleotide exchang GDI-displacement factor; 2.85A {Homo sapiens}

Probab=99.58  E-value=2.2e-15  Score=87.95  Aligned_cols=68  Identities=19%  Similarity=0.378  Sum_probs=54.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..++..|++  +++++++|||++++.+|+.+..|+..+.... ..++|+++|+||+|+...+.++
T Consensus        90 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~p~ilv~nK~Dl~~~~~v~  157 (199)
T 3l0i_B           90 AGQERFRTITSSYYR--GAHGIIVVYDVTDQESFNNVKQWLQEIDRYA-SENVNKLLVGNKCDLTTKKVVD  157 (199)
T ss_dssp             TTCTTCCCCSCC--C--CCSEEEECC-CCCSHHHHHHHHHHHHHHSCC--CCSEEEEC-CCSSCC--CCCC
T ss_pred             CCcHhHHHHHHHHhh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhc-cCCCCEEEEEECccCCccccCC
Confidence            578899999999998  6999999999999999999999999987643 3589999999999998776654

>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=99.58  E-value=2.6e-15  Score=85.00  Aligned_cols=68  Identities=25%  Similarity=0.417  Sum_probs=52.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..+...+++  +++++++|||++++.||+.+..|+..+.... ..++|+++|+||+|+.+.+.++
T Consensus        63 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~piilv~nK~Dl~~~~~~~  130 (170)
T 1z08_A           63 AGQERFHALGPIYYR--DSNGAILVYDITDEDSFQKVKNWVKELRKML-GNEICLCIVGNKIDLEKERHVS  130 (170)
T ss_dssp             CCC-------CCSST--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHH-GGGSEEEEEEECGGGGGGCCSC
T ss_pred             CCcHhhhhhHHHHhc--cCCEEEEEEECcCHHHHHHHHHHHHHHHHhc-CCCCeEEEEEECcccccccccC
Confidence            578899999999988  6999999999999999999999998887653 3578999999999997766554

>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=99.57  E-value=1.1e-14  Score=83.85  Aligned_cols=66  Identities=17%  Similarity=0.289  Sum_probs=57.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .|+++|+.++..+++  ++|++++|||+++++||+.+..|+.++.......++|+++|+||+|+.+.+
T Consensus        70 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~  135 (186)
T 1ksh_A           70 GGQKSLRSYWRNYFE--STDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGAL  135 (186)
T ss_dssp             CCSHHHHTTGGGGCT--TCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTCC
T ss_pred             CCCHhHHHHHHHHhc--CCCEEEEEEECcCHHHHHHHHHHHHHHHhChhcCCCcEEEEEeCccCCCCC
Confidence            588899999999998  699999999999999999999998888764334679999999999997643

>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=99.57  E-value=1.8e-15  Score=96.34  Aligned_cols=65  Identities=6%  Similarity=0.162  Sum_probs=57.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECC----------ChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVI----------ERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~----------~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|||+|+++++.||+  +++++|+|||++          +.++|+++..|+..+.+.....++|++|||||+||.++
T Consensus       191 aGQe~~r~~~~~y~~--~~~~iI~v~dis~ydq~l~e~~~~~s~~~~~~~~~~i~~~~~~~~~piiLvgNK~DL~~~  265 (354)
T 2xtz_A          191 GGQRNERRKWIHLFE--GVTAVIFCAAISEYDQTLFEDEQKNRMMETKELFDWVLKQPCFEKTSFMLFLNKFDIFEK  265 (354)
T ss_dssp             CCSTTGGGGTGGGCT--TEEEEEEEEEGGGTTCBCSSCTTSBHHHHHHHHHHHHHTCGGGSSCEEEEEEECHHHHHH
T ss_pred             CCchhhhHHHHHHhC--CCCEEEEEEECcccccccccccchhHHHHHHHHHHHHHhccccCCCeEEEEEECcchhhh
Confidence            799999999999999  799999999999          88999999999988876543468999999999999643

>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=99.57  E-value=6.7e-15  Score=83.74  Aligned_cols=68  Identities=24%  Similarity=0.510  Sum_probs=59.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..+...+++  +++++++|||++++.+|+.+..|+..+.... ..++|+++|+||+|+.+.++++
T Consensus        71 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~piilv~nK~Dl~~~~~~~  138 (179)
T 2y8e_A           71 AGQERFRSLIPSYIR--DSTVAVVVYDITNTNSFHQTSKWIDDVRTER-GSDVIIMLVGNKTDLSDKRQVS  138 (179)
T ss_dssp             CCSGGGGGGSHHHHH--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHH-TTSSEEEEEEECGGGGGGCCSC
T ss_pred             CCcHHHHHHHHHHhc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHhc-CCCCcEEEEEECCcccccCcCC
Confidence            578999999999998  6999999999999999999999999887754 3679999999999997666553

>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=99.57  E-value=1.3e-14  Score=84.47  Aligned_cols=65  Identities=15%  Similarity=0.297  Sum_probs=52.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+++|+.++..+++  +++++++|||++++++|+.+..|+..+.......++|+++||||+|+.+.
T Consensus        81 ~G~~~~~~~~~~~~~--~~d~iilv~D~~~~~s~~~~~~~l~~~~~~~~~~~~piilv~NK~Dl~~~  145 (192)
T 2b6h_A           81 GGQDKIRPLWRHYFQ--NTQGLIFVVDSNDRERVQESADELQKMLQEDELRDAVLLVFANKQDMPNA  145 (192)
T ss_dssp             C-----CTTHHHHHH--TCCEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC
T ss_pred             CCCHhHHHHHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHhcccccCCCeEEEEEECCCCCCC
Confidence            688999999999998  69999999999999999999999988775433468999999999999754

>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=99.57  E-value=7.5e-15  Score=84.67  Aligned_cols=63  Identities=13%  Similarity=0.157  Sum_probs=55.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECC------ChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVI------ERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~------~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|+.+++.|++  +++++|+|||++      +.++|..+..|+.++..  ...++|+++||||+|+.+.
T Consensus        82 ~G~~~~~~~~~~~~~--~~d~~i~v~D~~~~~~~~~~~s~~~l~~~l~~~~~--~~~~~piilv~NK~Dl~~~  150 (198)
T 3t1o_A           82 PGQVFYNASRKLILR--GVDGIVFVADSAPNRLRANAESMRNMRENLAEYGL--TLDDVPIVIQVNKRDLPDA  150 (198)
T ss_dssp             CSCCSCSHHHHHHTT--TCCEEEEEEECCGGGHHHHHHHHHHHHHHHHHTTC--CTTSSCEEEEEECTTSTTC
T ss_pred             CChHHHHHHHHHHHh--cCCEEEEEEECCcchhhHhHHHHHHHHHHHHhhcc--ccCCCCEEEEEEchhcccc
Confidence            689999999999999  699999999999      67899999999888853  3578999999999999653

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=99.57  E-value=6.7e-15  Score=85.28  Aligned_cols=65  Identities=15%  Similarity=0.239  Sum_probs=56.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCC-------CCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYI-------GEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~-------~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|+.++..|++  +++++|+|||+++++||+.+..|+..+......       .++|+++||||+|+...
T Consensus        71 ~G~~~~~~~~~~~~~--~~d~ii~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~  142 (199)
T 4bas_A           71 GGAKKFRGLWETYYD--NIDAVIFVVDSSDHLRLCVVKSEIQAMLKHEDIRRELPGGGRVPFLFFANKMDAAGA  142 (199)
T ss_dssp             CCSGGGGGGGGGGCT--TCSEEEEEEETTCGGGHHHHHHHHHHHHTSHHHHSBCTTSCBCCEEEEEECTTSTTC
T ss_pred             CCCHhHHHHHHHHHh--cCCEEEEEEECCcHHHHHHHHHHHHHHHhChhhhhcccccCCCCEEEEEECcCCCCC
Confidence            688999999999998  699999999999999999999998887653111       37899999999999765

>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=99.57  E-value=6.5e-15  Score=86.18  Aligned_cols=68  Identities=24%  Similarity=0.354  Sum_probs=59.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|..++..+++  +++++|+|||++++.+|+.+..|+..+.... ..++|+++||||+|+...+.++
T Consensus        82 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~piilv~nK~Dl~~~~~v~  149 (200)
T 2o52_A           82 AGQERFRSVTRSYYR--GAAGALLVYDITSRETYNSLAAWLTDARTLA-SPNIVVILCGNKKDLDPEREVT  149 (200)
T ss_dssp             TTHHHHSCCCHHHHT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHT-CTTCEEEEEEECGGGGGGCCSC
T ss_pred             CCcHhHHHHHHHHhc--cCCEEEEEEECcCHHHHHHHHHHHHHHHHhc-CCCCcEEEEEECCCcccccccC
Confidence            578889999999998  6999999999999999999999999887754 3689999999999997666553

>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=99.57  E-value=9.7e-16  Score=93.23  Aligned_cols=70  Identities=14%  Similarity=0.193  Sum_probs=55.6

Q ss_pred             cccccchhhhhhhhhc-------------------cCCcEEEEEEECCCh--hHHHHHHHHHHHHHhhcCCCCCeEEEEe
Q psy5805           3 SRTSCFTNLVVNFVQT-------------------YHPDVFVIVYSVIER--KTFKKAEDMLKTLWDSKYIGEKAVILVA   61 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~-------------------~~~~~~ilv~d~~~~--~s~~~~~~~~~~~~~~~~~~~~~~ilvg   61 (75)
                      +|+|+|+++++.|++.                   .+++++|+|||++++  .||+.+..|+.++.......++|+++||
T Consensus       126 ~g~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ad~vilV~D~t~~~~~s~~~~~~~l~~i~~~~~~~~~piilV~  205 (255)
T 3c5h_A          126 AAATKLASAEKLMYFCTDQLGLEQDFEQKQMPDGKLLVDGFLLGIDVSRGMNRNFDDQLKFVSNLYNQLAKTKKPIVVVL  205 (255)
T ss_dssp             HTCSEEECTTCBCCCCGGGTTCGGGSCCCBCGGGEEECCEEEEEEECBC----CHHHHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             chhhhhhhhhhhhhhccccccccccccccccccccccCCEEEEEEECCCCchhhHHHHHHHHHHHHHHhccCCCCEEEEE
Confidence            5788999999998870                   039999999999999  9999999999988764223679999999


Q ss_pred             eCCCCcCCCcc
Q psy5805          62 NKADLERRRQV   72 (75)
Q Consensus        62 nK~Dl~~~r~v   72 (75)
                      ||+||.+.+.+
T Consensus       206 NK~Dl~~~~~v  216 (255)
T 3c5h_A          206 TKCDEGVERYI  216 (255)
T ss_dssp             ECGGGBCHHHH
T ss_pred             EcccccccHHH
Confidence            99999765543

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=99.57  E-value=2.8e-15  Score=88.04  Aligned_cols=66  Identities=18%  Similarity=0.333  Sum_probs=56.0

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      .+|+++|+.+++.|++  +++++|+|||++++.+|+.+. .|+..+...  .+++|+++||||+|+.+.+.
T Consensus        64 t~G~~~~~~~~~~~~~--~~d~~ilv~d~~~~~s~~~~~~~~~~~~~~~--~~~~piilv~nK~Dl~~~~~  130 (212)
T 2j0v_A           64 TAGQEDYSRLRPLSYR--GADIFVLAFSLISKASYENVLKKWMPELRRF--APNVPIVLVGTKLDLRDDKG  130 (212)
T ss_dssp             CCCCCCCCC--CGGGT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH--CTTCCEEEEEECHHHHTCHH
T ss_pred             CCCcHHHHHHHHhhcc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEeCHHhhhCcc
Confidence            3688999999999998  699999999999999999996 899988874  35899999999999976554

>3r7w_B Gtpase2, GTP-binding protein GTR2; RAG gtpases, GTR1P, GTR2P, MTOR, protein transport; HET: GNP; 2.77A {Saccharomyces cerevisiae} PDB: 4arz_B*

Probab=99.56  E-value=2.4e-15  Score=95.10  Aligned_cols=64  Identities=6%  Similarity=0.035  Sum_probs=49.1

Q ss_pred             Ccccccchh---hhhhhhhccCCcEEEEEEECCCh--hHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           2 ASRTSCFTN---LVVNFVQTYHPDVFVIVYSVIER--KTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         2 ~s~~e~f~~---~~~~~~~~~~~~~~ilv~d~~~~--~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .+|||+|+.   +++.||+  +++++|+|||++++  +++..+..|+.++...  .+++|++++|||+||..+
T Consensus        53 TAGQErf~~~~l~~~~yyr--~a~~~IlV~Ditd~~~~~~~~l~~~l~~~~~~--~~~ipillvgNK~DL~~~  121 (331)
T 3r7w_B           53 LPGQLNYFEPSYDSERLFK--SVGALVYVIDSQDEYINAITNLAMIIEYAYKV--NPSINIEVLIHKVDGLSE  121 (331)
T ss_dssp             CCSCSSSCCCSHHHHHHHT--TCSEEEEECCCSSCTTHHHHHHHHHHHHHHHH--CTTCEEEEECCCCCSSCS
T ss_pred             CCCchhccchhhhhhhhcc--CCCEEEEEEECCchHHHHHHHHHHHHHHHhhc--CCCCcEEEEEECcccCch
Confidence            369999975   5789999  79999999999998  3333444445555442  478999999999999754

>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=99.56  E-value=1.7e-14  Score=83.31  Aligned_cols=64  Identities=11%  Similarity=0.267  Sum_probs=53.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+++|+.++..|++  ++|++++|||+++++||+.+..|+.++.......++|+++|+||+|+.+
T Consensus        68 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~  131 (187)
T 1zj6_A           68 GGQESLRSSWNTYYT--NTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKE  131 (187)
T ss_dssp             CC----CGGGHHHHT--TCCEEEEEEETTCTTTHHHHHHHHHHHHTSGGGTTCEEEEEEECTTSTT
T ss_pred             CCCHhHHHHHHHHhc--CCCEEEEEEeCCCHHHHHHHHHHHHHHHhchhhCCCeEEEEEECCCCcC
Confidence            688999999999998  6999999999999999999999998887643346799999999999965

>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=99.56  E-value=2.7e-15  Score=88.39  Aligned_cols=69  Identities=22%  Similarity=0.473  Sum_probs=58.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|+.++..+++  +++++|+|||++++.+|+.+..|+..+.......++|+++|+||+|+.+.+.++
T Consensus        92 ~G~~~~~~~~~~~~~--~~d~iilV~D~~~~~s~~~~~~~l~~i~~~~~~~~~piilV~NK~Dl~~~~~v~  160 (217)
T 2f7s_A           92 AGQERFRSLTTAFFR--DAMGFLLMFDLTSQQSFLNVRNWMSQLQANAYCENPDIVLIGNKADLPDQREVN  160 (217)
T ss_dssp             ESHHHHHHHHHHHHT--TCCEEEEEEETTCHHHHHHHHHHHHTCCCCCTTTCCEEEEEEECTTCGGGCCSC
T ss_pred             CCcHhHHhHHHHHhc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCcCCCCEEEEEECCccccccccC
Confidence            578889999999998  599999999999999999999998887654333679999999999997766553

>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=99.56  E-value=2.1e-14  Score=81.31  Aligned_cols=65  Identities=14%  Similarity=0.254  Sum_probs=56.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|+.++..|++  +++++++|||++++.||..+..|+..+.......++|+++|+||+|+.+.
T Consensus        59 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~  123 (171)
T 1upt_A           59 GGLTSIRPYWRCYYS--NTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQA  123 (171)
T ss_dssp             CCCGGGGGGGGGGCT--TCSEEEEEEETTCCTTHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC
T ss_pred             CCChhhhHHHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhCCCEEEEEEECCCCcCC
Confidence            588999999999998  69999999999999999999999888765433368999999999999765

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=99.56  E-value=7.6e-15  Score=85.48  Aligned_cols=62  Identities=19%  Similarity=0.378  Sum_probs=55.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+.++..|++  +++++++|||++++.+|+.+. .|+..+...  .+++|+++||||+|+..
T Consensus        76 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~p~ilv~nK~Dl~~  138 (201)
T 2q3h_A           76 AGQDEFDKLRPLCYT--NTDIFLLCFSVVSPSSFQNVSEKWVPEIRCH--CPKAPIILVGTQSDLRE  138 (201)
T ss_dssp             CCSTTCSSSGGGGGT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH--CSSSCEEEEEECGGGGG
T ss_pred             CCCHHHHHHhHhhcC--CCcEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEECHhhhh
Confidence            688999999999988  699999999999999999996 799888874  35899999999999975

>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=99.56  E-value=4.6e-15  Score=84.83  Aligned_cols=65  Identities=20%  Similarity=0.354  Sum_probs=56.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      +|+++|+.++..+++  +++++++|||++++.||+.+. .|+..+...  .+++|+++||||+|+.+.+.
T Consensus        64 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~piilv~nK~Dl~~~~~  129 (182)
T 3bwd_D           64 AGQEDYNRLRPLSYR--GADVFILAFSLISKASYENVSKKWIPELKHY--APGVPIVLVGTKLDLRDDKQ  129 (182)
T ss_dssp             CC-CTTTTTGGGGGT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH--CTTCCEEEEEECHHHHTCHH
T ss_pred             CCChhhhhhHHhhcc--CCCEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEechhhhcCcc
Confidence            688999999999998  699999999999999999997 799888874  35899999999999976554

>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=99.56  E-value=2.5e-14  Score=82.27  Aligned_cols=65  Identities=11%  Similarity=0.252  Sum_probs=56.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|+.++..|++  ++|++++|||+++++||+.+..|+..+.......++|+++|+||+|+.+.
T Consensus        73 ~G~~~~~~~~~~~~~--~~d~ii~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~  137 (181)
T 2h17_A           73 GGQESLRSSWNTYYT--NTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKEC  137 (181)
T ss_dssp             SSSGGGTCGGGGGGT--TCCEEEEEEETTCTTTHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC
T ss_pred             CCCHhHHHHHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHhChhhCCCeEEEEEECCCcccC
Confidence            588999999999998  69999999999999999999999888775432467999999999999653

>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=99.56  E-value=6.6e-15  Score=85.66  Aligned_cols=68  Identities=29%  Similarity=0.383  Sum_probs=57.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|++. ..++..+++  +++++++|||+++++||+.+..|+..+.......++|+++||||+|+.+.++++
T Consensus        84 ~G~~~-~~~~~~~~~--~~d~iilv~D~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~NK~Dl~~~~~v~  151 (196)
T 2atv_A           84 AGQED-TIQREGHMR--WGEGFVLVYDITDRGSFEEVLPLKNILDEIKKPKNVTLILVGNKADLDHSRQVS  151 (196)
T ss_dssp             CCCCC-CHHHHHHHH--HCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTTSCCCEEEEEECGGGGGGCCSC
T ss_pred             CCCCc-ccchhhhhc--cCCEEEEEEECcCHHHHHHHHHHHHHHHHhhCCCCCcEEEEEECcccccccccC
Confidence            46666 777888888  499999999999999999999999988876545689999999999998766654

>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=99.56  E-value=8.3e-15  Score=82.62  Aligned_cols=66  Identities=20%  Similarity=0.329  Sum_probs=58.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .|++.|..+...+++  +++++++|||++++.||+.+..|+..+....  .+.|+++|+||+|+.+.+++
T Consensus        62 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~--~~~piilv~nK~Dl~~~~~~  127 (168)
T 1z2a_A           62 AGQEEFDAITKAYYR--GAQACVLVFSTTDRESFEAISSWREKVVAEV--GDIPTALVQNKIDLLDDSCI  127 (168)
T ss_dssp             TTGGGTTCCCHHHHT--TCCEEEEEEETTCHHHHHTHHHHHHHHHHHH--CSCCEEEEEECGGGGGGCSS
T ss_pred             CCcHhHHHHHHHHhc--CCCEEEEEEECcCHHHHHHHHHHHHHHHHhC--CCCCEEEEEECcccCccccc
Confidence            578899999999998  5999999999999999999999999887754  67899999999999766554

>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=99.55  E-value=1.7e-14  Score=85.36  Aligned_cols=64  Identities=20%  Similarity=0.365  Sum_probs=57.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .|+++|..++..|++  +++++++|||++++.||+.+..|+..+...  .+++|+++||||+|+.+.+
T Consensus        72 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~--~~~~p~ilv~nK~Dl~~~~  135 (221)
T 3gj0_A           72 AGQEKFGGLRDGYYI--QAQCAIIMFDVTSRVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKDRK  135 (221)
T ss_dssp             CSGGGTSCCCHHHHT--TCCEEEEEEETTCHHHHHTHHHHHHHHHHH--STTCCEEEEEECTTSSSCS
T ss_pred             CChHHHhHHHHHHHh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHh--CCCCCEEEEEECCcccccc
Confidence            578999999999999  699999999999999999999999999875  3689999999999997543

>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=99.55  E-value=1.7e-15  Score=96.07  Aligned_cols=65  Identities=15%  Similarity=0.245  Sum_probs=58.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECC----------ChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVI----------ERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~----------~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|||+|++++..||+  +++++|+|||++          +.++|.....|+..+.+.....++|++|+|||+||.++
T Consensus       169 aGQe~~R~~w~~yy~--~a~~iIfV~diS~ydq~l~e~~~~nr~~es~~~~~~i~~~~~~~~~piiLv~NK~DL~~e  243 (340)
T 4fid_A          169 GGQRSERKXWVSFFS--DVDCAIFVTSLAEYDMKLYEDGNTSRLTESIAVFKDIMTNEFLKGAVKLIFLNKMDLFEE  243 (340)
T ss_dssp             CSCHHHHHHHHTTSC--SCSEEEEEEEGGGTTCBCC--CCSBHHHHHHHHHHHHHHCGGGTTSEEEEEEECHHHHHH
T ss_pred             CCcccccccHHHHhc--cCCEEEEEEECCccccccccccccchHHHHHHHHHHHhhhhccCCCeEEEEEECchhhhh
Confidence            799999999999999  799999999999          78999999999988876544578999999999999653

>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=99.55  E-value=2e-14  Score=83.24  Aligned_cols=67  Identities=24%  Similarity=0.406  Sum_probs=58.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .|+++|+.++..+++  +++++|+|||++++.+|+.+..|+..+.... ..++|+++|+||+|+...+.+
T Consensus        82 ~G~~~~~~~~~~~~~--~~d~vi~v~D~~~~~s~~~~~~~l~~i~~~~-~~~~piilv~nK~Dl~~~~~~  148 (193)
T 2oil_A           82 AGLERYRAITSAYYR--GAVGALLVFDLTKHQTYAVVERWLKELYDHA-EATIVVMLVGNKSDLSQAREV  148 (193)
T ss_dssp             SCCCTTCTTHHHHHT--TCCEEEEEEETTCHHHHHTHHHHHHHHHTTS-CTTCEEEEEEECGGGGGGCCS
T ss_pred             CCchhhhhhhHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhc-CCCCeEEEEEECCCccccccc
Confidence            578899999999998  6999999999999999999999999887643 367999999999999765554

>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=99.55  E-value=2.7e-14  Score=82.38  Aligned_cols=63  Identities=27%  Similarity=0.358  Sum_probs=56.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .|+++|..++..+++  +++++|+|||++++.+|+.+..|+.++.......++|+++|+||+|+.
T Consensus        72 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~p~ilv~nK~Dl~  134 (195)
T 1x3s_A           72 AGQERFRTLTPSYYR--GAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKE  134 (195)
T ss_dssp             CSSGGGCCSHHHHHT--TCCEEEEEEETTCHHHHHTHHHHHHHHTTCCSCSCCEEEEEEECTTSS
T ss_pred             CCchhhhhhhHHHhc--cCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCcCCCcEEEEEECCcCc
Confidence            578999999999998  599999999999999999999999998765434679999999999995

>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=99.55  E-value=2.2e-14  Score=83.06  Aligned_cols=65  Identities=15%  Similarity=0.284  Sum_probs=56.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|..++..|++  +++++++|||++++++|+.+..|+..+.......++|+++|+||+|+...
T Consensus        75 ~G~~~~~~~~~~~~~--~~d~ii~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~  139 (188)
T 1zd9_A           75 GGQPRFRSMWERYCR--GVSAIVYMVDAADQEKIEASKNELHNLLDKPQLQGIPVLVLGNKRDLPGA  139 (188)
T ss_dssp             CCSHHHHTTHHHHHT--TCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCCEEEEEECTTSTTC
T ss_pred             CCCHhHHHHHHHHHc--cCCEEEEEEECCCHHHHHHHHHHHHHHHhCcccCCCCEEEEEECCCCccC
Confidence            578999999999998  69999999999999999999999888765432467999999999999753

>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=99.55  E-value=1.2e-14  Score=85.64  Aligned_cols=68  Identities=16%  Similarity=0.212  Sum_probs=56.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|++.|..+...+++  +++++|+|||++++.||+.+..|+..+.... ..++|+++||||+|+.+.+.+.
T Consensus        69 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~piilv~nK~Dl~~~~~~~  136 (218)
T 4djt_A           69 AGQEKKAVLKDVYYI--GASGAILFFDVTSRITCQNLARWVKEFQAVV-GNEAPIVVCANKIDIKNRQKIS  136 (218)
T ss_dssp             CSGGGTSCCCHHHHT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHH-CSSSCEEEEEECTTCC----CC
T ss_pred             CCchhhchHHHHHhh--cCCEEEEEEeCCCHHHHHHHHHHHHHHHHhc-CCCCCEEEEEECCCCccccccC
Confidence            578899999999998  6999999999999999999999999988764 3568999999999998765553

>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=99.55  E-value=3e-14  Score=81.11  Aligned_cols=67  Identities=21%  Similarity=0.321  Sum_probs=57.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC---CCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY---IGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .|+++|+.++..+++  +++++++|||++++.+|+.+..|+.++.....   ..++|+++|+||+|+. .+++
T Consensus        64 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~p~i~v~nK~Dl~-~~~~  133 (177)
T 1wms_A           64 AGQERFRSLRTPFYR--GSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDIS-ERQV  133 (177)
T ss_dssp             CCCGGGHHHHGGGGT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTCSCTTTSCEEEEEECTTCS-SCSS
T ss_pred             CCchhhhhhHHHHHh--cCCEEEEEEECcCHHHHHHHHHHHHHHHHHccccccCCCcEEEEEECCccc-cccc
Confidence            578999999999998  59999999999999999999999998876532   2678999999999997 3443

>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=99.54  E-value=1.6e-14  Score=81.55  Aligned_cols=62  Identities=23%  Similarity=0.450  Sum_probs=55.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .|+++|..++..+++  +++++++|||++++.+|+.+..|+..+.... ..++|+++|+||+|+.
T Consensus        60 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~piilv~nK~Dl~  121 (170)
T 1g16_A           60 AGQERFRTITTAYYR--GAMGIILVYDITDERTFTNIKQWFKTVNEHA-NDEAQLLLVGNKSDME  121 (170)
T ss_dssp             TTGGGTSCCCHHHHT--TEEEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECTTCT
T ss_pred             CCChhhhhhHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhc-CCCCcEEEEEECccCC
Confidence            578899999999998  5999999999999999999999999888753 3678999999999994

>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=99.54  E-value=6.1e-14  Score=81.10  Aligned_cols=65  Identities=23%  Similarity=0.322  Sum_probs=56.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCC--CCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYI--GEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~--~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|+.++..+++  +++++++|||++++.||+.+..|+..+......  .++|+++|+||+|+.+.
T Consensus        75 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~  141 (190)
T 2h57_A           75 SGQGRYRNLWEHYYK--EGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKHRRIPILFFANKMDLRDA  141 (190)
T ss_dssp             CCSTTTGGGGGGGGG--GCSEEEEEEETTCHHHHHHHHHHHHHHHHSTTTTTSCCCEEEEEECTTSTTC
T ss_pred             CCCHHHHHHHHHHHh--cCCEEEEEEECCCHHHHHHHHHHHHHHHhChhhccCCCeEEEEEeCcCcccC
Confidence            578999999999998  599999999999999999999999888764322  57899999999999754

>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=99.54  E-value=4.1e-14  Score=81.17  Aligned_cols=64  Identities=17%  Similarity=0.333  Sum_probs=55.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|++.|..++..|++  +++++++|||++++.+|+.+..|...+.......++|+++|+||+|+..
T Consensus        60 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~i~v~nK~Dl~~  123 (189)
T 4dsu_A           60 AGQEEYSAMRDQYMR--TGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPS  123 (189)
T ss_dssp             CCC---CTTHHHHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTCSCCCEEEEEECTTSSS
T ss_pred             CCcHHHHHHHHHHHh--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECccCcc
Confidence            578999999999999  4999999999999999999999999988765557899999999999964

>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=2.3e-15  Score=87.02  Aligned_cols=66  Identities=17%  Similarity=0.263  Sum_probs=56.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCCh-hHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIER-KTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~-~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .|+++|+.+++.|++  +++++++|||++++ .+|+.+..|+.++...  .+++|+++||||+|+.+.+.+
T Consensus        64 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~~s~~~~~~~~~~~~~~--~~~~piilv~nK~Dl~~~~~~  130 (184)
T 2zej_A           64 AGREEFYSTHPHFMT--QRALYLAVYDLSKGQAEVDAMKPWLFNIKAR--ASSSPVILVGTHLDVSDEKQR  130 (184)
T ss_dssp             CSHHHHHTTSHHHHH--HSEEEEEEEEGGGCHHHHHTHHHHHHHHHHH--CTTCEEEEEEECGGGCCHHHH
T ss_pred             CCCHHHHHhhHHHcc--CCcEEEEEEeCCcchhHHHHHHHHHHHHHhh--CCCCcEEEEEECCCcccchhh
Confidence            578899999999998  59999999999997 6899999999988764  357899999999999765543

>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=99.54  E-value=1.2e-14  Score=84.82  Aligned_cols=62  Identities=21%  Similarity=0.407  Sum_probs=53.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .|+++|..++..+++  +++++|+|||++++.+|+.+..|+..+.... ..++|+++|+||+|+.
T Consensus        85 ~G~~~~~~~~~~~~~--~~d~iilv~d~~~~~s~~~~~~~~~~i~~~~-~~~~piilv~NK~Dl~  146 (199)
T 2p5s_A           85 AGQERFRSIAKSYFR--KADGVLLLYDVTCEKSFLNIREWVDMIEDAA-HETVPIMLVGNKADIR  146 (199)
T ss_dssp             TTCTTCHHHHHHHHH--HCSEEEEEEETTCHHHHHTHHHHHHHHHHHC----CCEEEEEECGGGH
T ss_pred             CCCcchhhhHHHHHh--hCCEEEEEEECCChHHHHHHHHHHHHHHHhc-CCCCCEEEEEECcccc
Confidence            578999999999998  4999999999999999999999999887653 3578999999999995

>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=99.53  E-value=1.6e-14  Score=82.37  Aligned_cols=63  Identities=22%  Similarity=0.325  Sum_probs=46.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC---CCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY---IGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~~ilvgnK~Dl~   67 (75)
                      .|+++|+.+...+++  +++++++|||++++.+|+.+..|+.++.....   ..++|+++|+||+|+.
T Consensus        66 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~  131 (182)
T 1ky3_A           66 AGQERFQSLGVAFYR--GADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAE  131 (182)
T ss_dssp             C----------CCST--TCCEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSCTTTCCEEEEEECTTSC
T ss_pred             CCChHhhhhhHHHhh--cCCEEEEEEECCChHHHHHHHHHHHHHHHHhcccCcCCCcEEEEEECCccc
Confidence            578899999999988  69999999999999999999999988876532   2678999999999994

>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=99.53  E-value=3.1e-14  Score=81.35  Aligned_cols=59  Identities=20%  Similarity=0.322  Sum_probs=46.7

Q ss_pred             hhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC--CCCCeEEEEeeCCCCc--CCCccc
Q psy5805          13 VNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY--IGEKAVILVANKADLE--RRRQVT   73 (75)
Q Consensus        13 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~~ilvgnK~Dl~--~~r~v~   73 (75)
                      ..|++  +++++++|||+++++||+.+..|+..+.....  .+++|+++||||+|+.  ..+.++
T Consensus        67 ~~~~~--~~d~~ilv~D~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~~~v~  129 (178)
T 2iwr_A           67 AKFSG--WADAVIFVFSLEDENSFQAVSRLHGQLSSLRGEGRGGLALALVGTQDRISASSPRVVG  129 (178)
T ss_dssp             HHHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHHCSSSCCCEEEEEEECTTCBTTBCCCSC
T ss_pred             hHHHH--hCCEEEEEEECcCHHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccccCcCC
Confidence            45677  59999999999999999999998766655422  3578999999999993  445553

>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=99.53  E-value=3.1e-14  Score=83.24  Aligned_cols=63  Identities=19%  Similarity=0.247  Sum_probs=55.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|..++..+++  +++++++|||++++++|+.+ ..|...+...  .+++|+++|+||+|+...
T Consensus        81 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~piilv~nK~Dl~~~  144 (201)
T 2gco_A           81 AGQEDYDRLRPLSYP--DTDVILMCFSIDSPDSLENIPEKWTPEVKHF--CPNVPIILVGNKKDLRQD  144 (201)
T ss_dssp             CCSGGGTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH--STTCCEEEEEECGGGTTC
T ss_pred             CCchhHHHHHHHhcC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEecHHhhcC
Confidence            578999999999998  69999999999999999999 7898888764  368999999999999754

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=99.53  E-value=3.2e-14  Score=82.16  Aligned_cols=65  Identities=18%  Similarity=0.252  Sum_probs=56.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|+.++..+++  ++|++++|||++++++|+.+..|+..+.......++|+++|+||+|+.+.
T Consensus        74 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~  138 (189)
T 2x77_A           74 GGQTGVRPYWRCYFS--DTDAVIYVVDSTDRDRMGVAKHELYALLDEDELRKSLLLIFANKQDLPDA  138 (189)
T ss_dssp             CCSSSSCCCCSSSST--TCCEEEEEEETTCCTTHHHHHHHHHHHHTCSTTTTCEEEEEEECTTSTTC
T ss_pred             CCCHhHHHHHHHHhh--cCCEEEEEEeCCCHHHHHHHHHHHHHHHhhhhcCCCeEEEEEECCCCcCC
Confidence            578899999999888  69999999999999999999999888766433468999999999999754

>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=99.52  E-value=6.3e-15  Score=91.73  Aligned_cols=61  Identities=20%  Similarity=0.141  Sum_probs=54.1

Q ss_pred             cccchhhhhhhhhccCCcEEEEEEECCChh-HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           5 TSCFTNLVVNFVQTYHPDVFVIVYSVIERK-TFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      ||+|+++++.|++  ++|++|+|||++++. +|+.+..|+.++..    .++|+++||||+||.+.++
T Consensus        71 qer~~~l~~~~~~--~ad~vilV~D~~~~~~s~~~l~~~l~~~~~----~~~piilv~NK~DL~~~~~  132 (301)
T 1u0l_A           71 LHRKNLLTKPHVA--NVDQVILVVTVKMPETSTYIIDKFLVLAEK----NELETVMVINKMDLYDEDD  132 (301)
T ss_dssp             CCCSCEETTTTEE--SCCEEEEEECSSTTCCCHHHHHHHHHHHHH----TTCEEEEEECCGGGCCHHH
T ss_pred             ccccceeeccccc--cCCEEEEEEeCCCCCCCHHHHHHHHHHHHH----CCCCEEEEEeHHHcCCchh
Confidence            7899999999999  799999999999998 79999999988764    4689999999999976544

>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=1.4e-14  Score=92.12  Aligned_cols=64  Identities=11%  Similarity=0.251  Sum_probs=56.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC----------hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE----------RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~----------~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +||++|++++..||+  +++++|+|||+++          .++|.....|+..+.+.....++|++|+|||+||..
T Consensus       201 ~GQe~~r~~w~~yf~--~a~~iIfV~dls~~d~~l~ed~~~nr~~e~~~~~~~i~~~~~~~~~piiLv~NK~DL~~  274 (353)
T 1cip_A          201 GGQRSERKKWIHCFE--GVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFE  274 (353)
T ss_dssp             CCSGGGGGGGGGGCT--TCSEEEEEEEGGGGGCEETTEEEEEHHHHHHHHHHHHHTCGGGTTSEEEEEEECHHHHH
T ss_pred             CCchhhhHHHHHHHh--cCCEEEEEEECccccccccccchhhhHHHHHHHHHHHHcCccccCCcEEEEEECcCchh
Confidence            799999999999999  7999999999999          578999999998887654346899999999999953

>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=99.52  E-value=5.5e-14  Score=78.73  Aligned_cols=64  Identities=17%  Similarity=0.344  Sum_probs=56.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+++|..++..+++  +++++++|||++++.+|+.+..|+..+.......++|+++|+||+|+..
T Consensus        59 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~~~~~~~~~~~~i~~~~~~~~~p~iiv~nK~Dl~~  122 (166)
T 2ce2_X           59 AGQEEYSAMRDQYMR--TGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKSDLAA  122 (166)
T ss_dssp             CCCSSCCHHHHHHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHHTCSCCCEEEEEECTTCSC
T ss_pred             CCchhhhHHHHHhhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEEchhhhh
Confidence            578899999999998  4999999999999999999999999888765445899999999999975

>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=99.51  E-value=5.3e-15  Score=93.42  Aligned_cols=66  Identities=12%  Similarity=0.248  Sum_probs=56.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECC----------ChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVI----------ERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~----------~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +|||+|++++..||+  +++++|+|||++          +.++|.....|+..+.+.....++|++|+|||+||.+++
T Consensus       175 gGQe~~R~~w~~yf~--~~~~iIfV~dls~ydq~l~d~~~~nr~~es~~~~~~i~~~~~~~~~~iiL~~NK~DL~~~k  250 (327)
T 3ohm_A          175 GGQRSERRKWIHCFE--NVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNSSVILFLNKKDLLEEK  250 (327)
T ss_dssp             CCSHHHHTTGGGGCS--SCSEEEEEEEGGGGGCBCSSCTTSBHHHHHHHHHHHHHTSGGGTTCEEEEEEECHHHHHHH
T ss_pred             CCchhHHHHHHHHhC--CCCEEEEEEECccccccccccccHhHHHHHHHHHHHHhhhhccCCceEEEEEECchhhhhh
Confidence            799999999999999  799999999665          778899888888888765444789999999999996543

>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=99.51  E-value=1.9e-14  Score=85.01  Aligned_cols=64  Identities=16%  Similarity=0.267  Sum_probs=43.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +|+++|..++..|++  +++++++|||++++.||+.+. .|+..+...  .+++|+++||||+|+...+
T Consensus        90 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~piilv~nK~Dl~~~~  154 (214)
T 2j1l_A           90 AGQDDYDRLRPLFYP--DASVLLLCFDVTSPNSFDNIFNRWYPEVNHF--CKKVPIIVVGCKTDLRKDK  154 (214)
T ss_dssp             -----------------CEEEEEEEEETTCHHHHHHHHHTHHHHHHHH--CSSCCEEEEEECGGGGSCH
T ss_pred             CCchhhhHHHHHHhc--cCCEEEEEEECcCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEEChhhhccc
Confidence            588999999999998  699999999999999999996 799888764  3679999999999997653

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=99.51  E-value=3.4e-14  Score=80.22  Aligned_cols=69  Identities=20%  Similarity=0.398  Sum_probs=57.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhc-CCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSK-YIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..+...+++  +++++++|||++++.+|+.+..|+..+.+.. ..+++|+++|+||+|+...+++.
T Consensus        59 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~~~~~~~~~~~~i~~~~~~~~~~pii~v~nK~Dl~~~~~v~  128 (172)
T 2erx_A           59 TGSHQFPAMQRLSIS--KGHAFILVYSITSRQSLEELKPIYEQICEIKGDVESIPIMLVGNKCDESPSREVQ  128 (172)
T ss_dssp             CSCSSCHHHHHHHHH--HCSEEEEEEETTCHHHHHTTHHHHHHHHHHHC---CCCEEEEEECGGGGGGCCSC
T ss_pred             CCchhhHHHHHHhcc--cCCEEEEEEECcCHHHHHHHHHHHHHHHHHhCCCCCCCEEEEEEccccccccccC
Confidence            578899999999998  4999999999999999999999988877643 23578999999999997666553

>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=99.51  E-value=5.9e-14  Score=81.78  Aligned_cols=62  Identities=6%  Similarity=0.044  Sum_probs=52.8

Q ss_pred             cccccchhhh---hhhhhccCCcEEEEEEECCCh--hHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLV---VNFVQTYHPDVFVIVYSVIER--KTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~---~~~~~~~~~~~~ilv~d~~~~--~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|..+.   ..|++  +++++|+|||++++  +++..+..|+.++...  .+++|+++||||+||..
T Consensus        77 ~G~~~~~~~~~~~~~~~~--~~~~~i~v~d~~~~~~~~~~~~~~~l~~~~~~--~~~~piilv~nK~Dl~~  143 (196)
T 3llu_A           77 PGQMDFFDPTFDYEMIFR--GTGALIYVIDAQDDYMEALTRLHITVSKAYKV--NPDMNFEVFIHKVDGLS  143 (196)
T ss_dssp             CSSCCTTCTTCCHHHHHH--TCSEEEEEEETTSCCHHHHHHHHHHHHHHHHH--CTTCEEEEEEECGGGSC
T ss_pred             CCCHHHHhhhhhcccccc--cCCEEEEEEECCCchHHHHHHHHHHHHHHHhc--CCCCcEEEEEeccccCc
Confidence            6899998887   88888  69999999999998  7888888888877542  46899999999999753

>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=99.51  E-value=6.6e-14  Score=81.90  Aligned_cols=62  Identities=24%  Similarity=0.452  Sum_probs=55.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .|++.|..++..+++  +++++++|||++++.+|+.+..|+..+.... ..++|+++|+||+|+.
T Consensus        77 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~piilv~nK~Dl~  138 (213)
T 3cph_A           77 AGQERFRTITTAYYR--GAMGIILVYDVTDERTFTNIKQWFKTVNEHA-NDEAQLLLVGNKSDME  138 (213)
T ss_dssp             TTGGGGTCCCHHHHT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHT-TTCSEEEEEEECTTCS
T ss_pred             CCcHHHHHHHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHhc-CCCCCEEEEEECCCCc
Confidence            578899999999998  5999999999999999999999999888753 3579999999999994

>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=99.51  E-value=4.4e-14  Score=80.84  Aligned_cols=63  Identities=19%  Similarity=0.287  Sum_probs=55.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|+.++..+++  +++++++|||++++.||+.+. .|+..+...  .+++|+++||||+|+...
T Consensus        61 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~piilv~nK~Dl~~~  124 (186)
T 1mh1_A           61 AGQEDYDRLRPLSYP--QTDVSLICFSLVSPASFENVRAKWYPEVRHH--CPNTPIILVGTKLDLRDD  124 (186)
T ss_dssp             CCSGGGTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH--STTSCEEEEEECHHHHTC
T ss_pred             CCCHhHHHHHHHhcc--CCcEEEEEEECCChhhHHHHHHHHHHHHHHh--CCCCCEEEEeEccccccc
Confidence            688999999999998  699999999999999999997 799888874  358999999999999653

>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=99.51  E-value=7e-14  Score=80.66  Aligned_cols=64  Identities=17%  Similarity=0.309  Sum_probs=46.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+++|..++..+++  +++++++|||+++..+|+.+..|+..+.......++|+++|+||+|+..
T Consensus        77 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~p~ilv~nK~Dl~~  140 (190)
T 3con_A           77 AGQEEYSAMRDQYMR--TGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPT  140 (190)
T ss_dssp             CC-----------CT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHHTCSCCCEEEEEECTTCSC
T ss_pred             CChHHHHHHHHHhhC--cCCEEEEEEECcCHHHHHHHHHHHHHHHHHhCCCCCeEEEEEECCcCCc
Confidence            578889999999998  5999999999999999999999999888765445799999999999965

>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=99.50  E-value=6.5e-14  Score=80.17  Aligned_cols=65  Identities=12%  Similarity=0.211  Sum_probs=53.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|+.++..+++  +++++++|||++++.+|+.+..|+..+.......++|+++|+||+|+.+.
T Consensus        70 ~G~~~~~~~~~~~~~--~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~  134 (183)
T 1moz_A           70 GGQTSIRPYWRCYYA--DTAAVIFVVDSTDKDRMSTASKELHLMLQEEELQDAALLVFANKQDQPGA  134 (183)
T ss_dssp             C----CCTTGGGTTT--TEEEEEEEEETTCTTTHHHHHHHHHHHTTSSTTSSCEEEEEEECTTSTTC
T ss_pred             CCCHhHHHHHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHcChhhCCCeEEEEEECCCCCCC
Confidence            578889999999888  69999999999999999999999988876433478999999999999653

>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=99.50  E-value=3.1e-14  Score=83.61  Aligned_cols=64  Identities=20%  Similarity=0.340  Sum_probs=56.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .|+++|..++..+++  +++++++|||++++.||+.+. .|+..+...  .+++|+++||||+|+...+
T Consensus        86 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~piilv~nK~Dl~~~~  150 (204)
T 4gzl_A           86 AGLEDYDRLRPLSYP--QTDVFLICFSLVSPASFENVRAKWYPEVRHH--CPNTPIILVGTKLDLRDDK  150 (204)
T ss_dssp             CCSGGGTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH--CSSCCEEEEEECHHHHTCH
T ss_pred             CCchhhHHHHHHHhc--cCCEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEechhhccch
Confidence            588999999999998  699999999999999999996 899888874  3689999999999997643

>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=99.49  E-value=7.2e-14  Score=81.42  Aligned_cols=63  Identities=25%  Similarity=0.348  Sum_probs=55.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC---CCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY---IGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~~ilvgnK~Dl~   67 (75)
                      .|+++|..++..+++  +++++|+|||++++.+|+.+..|+.++.....   ..++|+++|+||+|+.
T Consensus        65 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~  130 (207)
T 1vg8_A           65 AGQERFQSLGVAFYR--GADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLE  130 (207)
T ss_dssp             CSSGGGSCSCCGGGT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSSGGGSCEEEEEECTTSS
T ss_pred             CCcHHHHHhHHHHHh--CCcEEEEEEECCCHHHHHHHHHHHHHHHHhcccccCCCCcEEEEEECCCCc
Confidence            578999999999998  69999999999999999999999988876432   1478999999999997

>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=99.49  E-value=1.3e-13  Score=80.94  Aligned_cols=63  Identities=22%  Similarity=0.266  Sum_probs=55.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|..++..+++  +++++++|||++++++|+.+ ..|+..+...  .+++|+++|+||+|+...
T Consensus        81 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~piilv~nK~Dl~~~  144 (207)
T 2fv8_A           81 AGQEDYDRLRPLSYP--DTDVILMCFSVDSPDSLENIPEKWVPEVKHF--CPNVPIILVANKKDLRSD  144 (207)
T ss_dssp             TTCTTCTTTGGGGCT--TCCEEEEEEETTCHHHHHHHHHTHHHHHHHH--STTCCEEEEEECGGGGGC
T ss_pred             CCcHHHHHHHHhhcC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHHh--CCCCCEEEEEEchhhhcc
Confidence            578999999999998  69999999999999999999 7898888764  368999999999999654

>3o47_A ADP-ribosylation factor GTPase-activating protein ribosylation factor 1; structural genomics consortium, GTPase activation; HET: GDP; 2.80A {Homo sapiens}

Probab=99.46  E-value=9.9e-14  Score=87.20  Aligned_cols=66  Identities=17%  Similarity=0.263  Sum_probs=52.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .|++.|..++..+++  +++++|+|||++++.+|+.+..|+..+.......++|+++||||+|+.+..
T Consensus       217 ~G~~~~~~~~~~~~~--~ad~vilV~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilV~NK~Dl~~~~  282 (329)
T 3o47_A          217 GGQDKIRPLWRHYFQ--NTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAM  282 (329)
T ss_dssp             C-----CCSHHHHHT--TEEEEEEEEETTCSSSHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTCC
T ss_pred             CCCHhHHHHHHHHhc--cCCEEEEEEECCchHHHHHHHHHHHHHHhhhccCCCeEEEEEECccCCccc
Confidence            579999999999999  599999999999999999998888777654334689999999999997643

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=99.46  E-value=5.7e-13  Score=76.76  Aligned_cols=64  Identities=23%  Similarity=0.371  Sum_probs=54.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .|++.|..++..+++  +++++++|||++++.+|+.+..|+..+....   +.|+++|+||+| ...+++
T Consensus       101 ~G~~~~~~~~~~~~~--~~d~~i~v~D~~~~~s~~~~~~~~~~i~~~~---~~piilv~NK~D-~~~~~~  164 (208)
T 3clv_A          101 AGQERYASIVPLYYR--GATCAIVVFDISNSNTLDRAKTWVNQLKISS---NYIIILVANKID-KNKFQV  164 (208)
T ss_dssp             TTGGGCTTTHHHHHT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHS---CCEEEEEEECTT-CC-CCS
T ss_pred             CCcHHHHHHHHHHhc--CCCEEEEEEECCCHHHHHHHHHHHHHHHhhC---CCcEEEEEECCC-cccccC
Confidence            578999999999998  5999999999999999999999999887642   389999999999 444444

>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=99.45  E-value=6.3e-14  Score=89.42  Aligned_cols=64  Identities=14%  Similarity=0.209  Sum_probs=50.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC----------hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE----------RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~----------~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +||++|+.++..|++  +++++|+|||+++          .++|..+..|+..+.+.....++|++|+|||+||.+
T Consensus       209 ~Gq~~~r~~w~~~f~--~~~~iIfv~dls~~dq~l~ed~~~n~~~es~~~~~~i~~~~~~~~~piILv~NK~DL~~  282 (362)
T 1zcb_A          209 GGQRSERKRWFECFD--SVTSILFLVSSSEFDQVLMEDRQTNRLTESLNIFETIVNNRVFSNVSIILFLNKTDLLE  282 (362)
T ss_dssp             CC-------CTTSCT--TCCEEEEEEETTCTTCEETTEEEEEHHHHHHHHHHHHHTCGGGTTSEEEEEEECHHHHH
T ss_pred             cchhhhhhhHHHHhC--CCCEEEEEEECccccccccccccccHHHHHHHHHHHHhcchhhCCCCEEEEEEChhhhh
Confidence            799999999999999  7999999999999          789999999998887654346899999999999964

>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=99.45  E-value=2.4e-13  Score=78.64  Aligned_cols=64  Identities=20%  Similarity=0.351  Sum_probs=55.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC-CCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY-IGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+++|..++..+++  +++++++|||++++.+|+.+..|+..+..... ..++|+++|+||+|+..
T Consensus        64 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~piilv~nK~Dl~~  128 (199)
T 2gf0_A           64 TGSHQFPAMQRLSIS--KGHAFILVFSVTSKQSLEELGPIYKLIVQIKGSVEDIPVMLVGNKCDETQ  128 (199)
T ss_dssp             CGGGSCHHHHHHHHH--HCSEEEEEEETTCHHHHHTTHHHHHHHHHHHSCGGGSCEEEEEECTTCSS
T ss_pred             CChHHhHHHHHHhhc--cCCEEEEEEECcCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccCCc
Confidence            578999999999998  49999999999999999999988877766432 24789999999999964

>3r7w_A Gtpase1, GTP-binding protein GTR1; RAG gtpases, GTR1P, GTR2P, MTOR, protein transport; HET: GNP; 2.77A {Saccharomyces cerevisiae} PDB: 4arz_A*

Probab=99.41  E-value=5.1e-13  Score=83.19  Aligned_cols=64  Identities=22%  Similarity=0.312  Sum_probs=53.1

Q ss_pred             cccccc-----hhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhc-CCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCF-----TNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSK-YIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f-----~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|     ..+++.+++  +++++|+|||+++++||+++..|...+.... ..+++|+++||||+|+.+
T Consensus        60 ~G~~~~~~~~~~~~~~~~~~--~ad~vi~V~D~t~~~s~~~l~~~~~~l~~l~~~~~~~piilv~NK~Dl~~  129 (307)
T 3r7w_A           60 GGQDVFMENYFTKQKDHIFQ--MVQVLIHVFDVESTEVLKDIEIFAKALKQLRKYSPDAKIFVLLHKMDLVQ  129 (307)
T ss_dssp             CCSHHHHHHHHTTTHHHHHT--TCSEEEEEEETTCSCHHHHHHHHHHHHHHHHHHCTTCEEEEEEECGGGSC
T ss_pred             CCcHHHhhhhhhhHHHHHhc--cCCEEEEEEECCChhhHHHHHHHHHHHHHHHHhCCCCeEEEEEecccccc
Confidence            578888     788888888  6999999999999999999988765544321 246799999999999976

>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=99.41  E-value=5e-13  Score=82.62  Aligned_cols=63  Identities=21%  Similarity=0.327  Sum_probs=55.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+++|..++..|++  +++++++|||++++.||+.+. .|+..+...  .+++|+++||||+|+...
T Consensus       211 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~--~~~~p~ilv~nK~Dl~~~  274 (332)
T 2wkq_A          211 AGLEDYDRLRPLSYP--QTDVFLICFSLVSPASFHHVRAKWYPEVRHH--CPNTPIILVGTKLDLRDD  274 (332)
T ss_dssp             CCCGGGTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH--CTTSCEEEEEECHHHHTC
T ss_pred             CCchhhhHHHHHhcc--CCCEEEEEEeCCCHHHHHHHHHHHHHHHHhh--CCCCcEEEEEEchhcccc
Confidence            588999999999998  699999999999999999996 798888764  358999999999999653

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=99.38  E-value=7.9e-13  Score=76.37  Aligned_cols=70  Identities=10%  Similarity=0.183  Sum_probs=56.2

Q ss_pred             cccccchhhhhhhhhcc--CCcEEEEEEECC-ChhHHHHHHHHHHHHHhhc---CCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTY--HPDVFVIVYSVI-ERKTFKKAEDMLKTLWDSK---YIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~--~~~~~ilv~d~~-~~~s~~~~~~~~~~~~~~~---~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .|++.|+.....|++..  .++++++|||++ ++++|..+..|+..+....   ...++|+++|+||+|+.+.+.+
T Consensus        99 ~G~~~~~~~~~~~~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~  174 (193)
T 2ged_A           99 PGHVKLRYKLSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTARPP  174 (193)
T ss_dssp             TTCCBSSCCHHHHHHHHGGGEEEEEEEEETTCCHHHHHHHHHHHHHHHHHHHHHSTTCCCEEEEEECTTSTTCCCH
T ss_pred             CCCchHHHHHHHHHHhhcccCCEEEEEEECCCCchhHHHHHHHHHHHHhhhhhccccCCCEEEEEEchHhcCCCCH
Confidence            57888888888887621  279999999999 9999999999987776532   2357999999999999876654

>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=99.38  E-value=9.8e-13  Score=77.38  Aligned_cols=70  Identities=10%  Similarity=0.183  Sum_probs=57.5

Q ss_pred             cccccchhhhhhhhhcc--CCcEEEEEEECC-ChhHHHHHHHHHHHHHhhc---CCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTY--HPDVFVIVYSVI-ERKTFKKAEDMLKTLWDSK---YIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~--~~~~~ilv~d~~-~~~s~~~~~~~~~~~~~~~---~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .|+++|+.+...|++..  .++++|+|||.+ ++++|..+..|+.++....   ...++|+++|+||+|+...+.+
T Consensus        63 ~G~~~~~~~~~~~~~~~~~~~~~~i~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~  138 (218)
T 1nrj_B           63 PGHVKLRYKLSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTARPP  138 (218)
T ss_dssp             CCCGGGTHHHHHHHHHHGGGEEEEEEEEETTSCTTCCHHHHHHHHHHHHHHHHHSTTCCCEEEEEECTTSTTCCCH
T ss_pred             CCcHHHHHHHHHHHHhccccCCEEEEEEECCCChHHHHHHHHHHHHHHhcccccccCCCCEEEEEEchHhcccCCH
Confidence            68899999988888721  279999999999 9999999999988876542   2367999999999999876654

>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=99.07  E-value=4.3e-14  Score=82.62  Aligned_cols=63  Identities=21%  Similarity=0.338  Sum_probs=55.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|+++|..++..+++  +++++++|||++++.+|+.+. .|+..+...  .+++|+++||||+|+.+.
T Consensus        86 ~G~~~~~~~~~~~~~--~~d~iilv~D~~~~~s~~~~~~~~~~~l~~~--~~~~piilv~NK~Dl~~~  149 (204)
T 3th5_A           86 AGQEDYDRLRPLSYP--QTDVFLICFSLVSPASFENVRAKWYPEVRHH--CPNTPIILVGTKLDLRDD  149 (204)
Confidence            578899999999988  599999999999999999996 898888763  347999999999999754

>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=99.34  E-value=6.5e-12  Score=73.68  Aligned_cols=66  Identities=17%  Similarity=0.258  Sum_probs=50.1

Q ss_pred             cccccchh-hhhhhhhccCCcEEEEEEECCChh-HHHHHHH-HHHHHHhhc-CCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTN-LVVNFVQTYHPDVFVIVYSVIERK-TFKKAED-MLKTLWDSK-YIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~-~~~~~~~~~~~~~~ilv~d~~~~~-s~~~~~~-~~~~~~~~~-~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .|+++|+. +++.|++  +++++++|||+++.. ++..+.. |...+.... ...++|+++||||+|+...+
T Consensus        62 ~G~~~~~~~~~~~~~~--~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~  131 (214)
T 2fh5_B           62 PGHESLRFQLLDRFKS--SARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAK  131 (214)
T ss_dssp             CCCHHHHHHHHHHHGG--GEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHTSTTCCEEEEEEECTTSTTCC
T ss_pred             CCChhHHHHHHHHHHh--hCCEEEEEEECCCcCHHHHHHHHHHHHHHhhhhhcccCCCEEEEEECCCCCCcc
Confidence            68899987 8888888  599999999999964 5766655 444443321 23578999999999997654

>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=99.33  E-value=6.8e-12  Score=73.13  Aligned_cols=67  Identities=24%  Similarity=0.385  Sum_probs=57.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+++|+.+...+++  +++++++|||+++..+|+++..|+..+.... ..+.|+++|+||+|+.+.+.+
T Consensus        62 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~i~~v~nK~Dl~~~~~~  128 (199)
T 2f9l_A           62 AGQERYRRITSAYYR--GAVGALLVYDIAKHLTYENVERWLKELRDHA-DSNIVIMLVGNKSDLRHLRAV  128 (199)
T ss_dssp             SSGGGTTCCCHHHHT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECTTCGGGCCS
T ss_pred             CCchhhhhhhHHHHh--cCCEEEEEEECcCHHHHHHHHHHHHHHHHhc-CCCCeEEEEEECcccccccCc
Confidence            578889988888888  5999999999999999999999998876542 357899999999999765554

>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=99.26  E-value=2.1e-11  Score=70.88  Aligned_cols=67  Identities=24%  Similarity=0.375  Sum_probs=56.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .|+++|..+.+.+++  +++++++|||+++..+|+++..|+..+.... ..+.|+++++||+|+.+.+.+
T Consensus        86 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~i~~v~nK~Dl~~~~~~  152 (191)
T 1oix_A           86 AGLERYRAITSAYYR--GAVGALLVYDIAKHLTYENVERWLKELRDHA-DSNIVIMLVGNKSDLRHLRAV  152 (191)
T ss_dssp             CSCCSSSCCCHHHHT--TCCEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECGGGGGGCCS
T ss_pred             CCCcchhhhhHHHhh--cCCEEEEEEECcCHHHHHHHHHHHHHHHHhc-CCCCcEEEEEECccccccccc
Confidence            467888888899888  5999999999999999999999998876542 357899999999999765544

>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=99.26  E-value=3.3e-12  Score=79.56  Aligned_cols=62  Identities=19%  Similarity=0.072  Sum_probs=53.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChh-HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERK-TFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      ..+|+|+.+...+++  |+|++++|||++++. +++.+.+|+..+..    .++|+++|+||+||.+.+
T Consensus        64 ~i~er~~~l~r~~~~--naD~vliV~d~~~p~~s~~~l~~~l~~~~~----~~~~~ilV~NK~DL~~~~  126 (302)
T 2yv5_A           64 EVEERKNLLIRPKVA--NVDRVIIVETLKMPEFNNYLLDNMLVVYEY----FKVEPVIVFNKIDLLNEE  126 (302)
T ss_dssp             EECCCSCEEETTEEE--SCCEEEEEECSTTTTCCHHHHHHHHHHHHH----TTCEEEEEECCGGGCCHH
T ss_pred             eeCChHHHHhHHHHH--hcCEEEEEEECCCCCCCHHHHHHHHHHHHh----CCCCEEEEEEcccCCCcc
Confidence            358899999999888  799999999999997 99999999987764    568999999999996543

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=99.07  E-value=2.6e-10  Score=64.67  Aligned_cols=56  Identities=18%  Similarity=0.233  Sum_probs=43.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+++|..++..+++  +++++++|||+++   +.+++.+..    +.    ..++|+++|+||+|+..
T Consensus        63 ~G~~~~~~~~~~~~~--~~d~~i~v~d~~~~~~~~~~~~l~~----~~----~~~~p~ilv~nK~Dl~~  121 (178)
T 2lkc_A           63 PGHEAFTTMRARGAQ--VTDIVILVVAADDGVMPQTVEAINH----AK----AANVPIIVAINKMDKPE  121 (178)
T ss_dssp             CSSSSSSCSCCSSCC--CCCEEEEEEETTCCCCHHHHHHHHH----HG----GGSCCEEEEEETTTSSC
T ss_pred             CCCHHHHHHHHHHHh--hCCEEEEEEECCCCCcHHHHHHHHH----HH----hCCCCEEEEEECccCCc
Confidence            578899988888887  6999999999998   555544322    22    24689999999999965

>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=99.06  E-value=4e-10  Score=66.89  Aligned_cols=61  Identities=11%  Similarity=0.222  Sum_probs=42.2

Q ss_pred             chhhhhhhhhccCCcEEEEEEECCChhHHHH--HHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           8 FTNLVVNFVQTYHPDVFVIVYSVIERKTFKK--AEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         8 f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      |..+.. ++.  +++++++|||++++.+|..  ...|+..+...  .+++|+++||||+|+.+.+.++
T Consensus        99 ~~~~~~-~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~l~~~--~~~~piilv~nK~Dl~~~~~~~  161 (228)
T 2qu8_A           99 MTTITA-LAH--INGVILFIIDISEQCGLTIKEQINLFYSIKSV--FSNKSIVIGFNKIDKCNMDSLS  161 (228)
T ss_dssp             HHHHHH-HHT--SSEEEEEEEETTCTTSSCHHHHHHHHHHHHTC--C-CCCEEEEEECGGGCC--CCC
T ss_pred             HHHHHH-hhc--cccEEEEEEecccccCcchHHHHHHHHHHHHh--hcCCcEEEEEeCcccCCchhhH
Confidence            444443 344  5899999999999988862  24566666542  3578999999999998766553

>3dpu_A RAB family protein; roccor, G-domain, COR, GTP-binding, nucleotide-binding, SIGN protein; 2.90A {Chlorobaculum tepidum}

Probab=99.06  E-value=2.2e-10  Score=75.71  Aligned_cols=64  Identities=16%  Similarity=0.219  Sum_probs=53.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|++.|..+...|++  +++++|+|||+++.   +.+..|..++....  ++.|+++||||+|+...+.+.
T Consensus       106 ~G~e~~~~~~~~~l~--~~d~ii~V~D~s~~---~~~~~~~~~l~~~~--~~~pvilV~NK~Dl~~~~~v~  169 (535)
T 3dpu_A          106 GGQEIMHASHQFFMT--RSSVYMLLLDSRTD---SNKHYWLRHIEKYG--GKSPVIVVMNKIDENPSYNIE  169 (535)
T ss_dssp             CSCCTTTTTCHHHHH--SSEEEEEEECGGGG---GGHHHHHHHHHHHS--SSCCEEEEECCTTTCTTCCCC
T ss_pred             CcHHHHHHHHHHHcc--CCcEEEEEEeCCCc---hhHHHHHHHHHHhC--CCCCEEEEEECCCcccccccC
Confidence            579999999999998  59999999999765   55677998888753  578999999999998766653

>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=99.05  E-value=3e-10  Score=64.37  Aligned_cols=64  Identities=16%  Similarity=0.219  Sum_probs=45.9

Q ss_pred             cccccch------hhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFT------NLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~------~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .|+++|.      .+...|++..+++++++|+|.++.++   ...|+.++.+    .++|+++||||+|+...+.++
T Consensus        58 ~G~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~D~~~~~~---~~~~~~~~~~----~~~p~ilv~nK~Dl~~~~~~~  127 (165)
T 2wji_A           58 PGVYSLTANSIDEIIARDYIINEKPDLVVNIVDATALER---NLYLTLQLME----MGANLLLALNKMDLAKSLGIE  127 (165)
T ss_dssp             CCCSCSSSSSHHHHHHHHHHHHHCCSEEEEEEETTCHHH---HHHHHHHHHH----TTCCEEEEEECHHHHHHTTCC
T ss_pred             CCcccCCCcchhHHHHHHHHhcCCCCEEEEEecCCchhH---hHHHHHHHHh----cCCCEEEEEEchHhccccChh
Confidence            4666664      55677774115999999999998654   4557777764    358999999999996555443

>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=99.05  E-value=1.9e-11  Score=70.04  Aligned_cols=64  Identities=14%  Similarity=0.166  Sum_probs=49.8

Q ss_pred             cccchhhhhhhhhccC-CcEEEEEEECCChhHHHHH-HHHHHH--------HHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           5 TSCFTNLVVNFVQTYH-PDVFVIVYSVIERKTFKKA-EDMLKT--------LWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~~-~~~~ilv~d~~~~~s~~~~-~~~~~~--------~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +++|+.+...|++  + +++++++|++.+..+|.++ ..|...        +.......++|+++||||+|+...+
T Consensus        65 ~~~~~~~~~~~~~--~~~~~~~~v~~v~d~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~  138 (190)
T 2cxx_A           65 QERIKDEIVHFIE--DNAKNIDVAVLVVDGKAAPEIIKRWEKRGEIPIDVEFYQFLRELDIPTIVAVNKLDKIKNV  138 (190)
T ss_dssp             HHHHHHHHHHHHH--HHGGGCCEEEEEEETTHHHHHHHHHHHTTCCCHHHHHHHHHHHTTCCEEEEEECGGGCSCH
T ss_pred             HHHHHHHHHHHHH--hhhccCCEEEEEEcchhhhhHHHhhhccCccHHHHHHHHHHHhcCCceEEEeehHhccCcH
Confidence            7889999998888  4 8889999999999999988 778653        2221112578999999999997643

>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=98.99  E-value=2.7e-10  Score=65.21  Aligned_cols=50  Identities=12%  Similarity=0.191  Sum_probs=40.3

Q ss_pred             hhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          15 FVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        15 ~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +++  +++++++|||.+++.|++ ...|+.++.+.. ..++|+++|+||+|+.+
T Consensus        80 ~~~--~ad~~i~v~D~~~~~s~~-~~~~~~~~~~~~-~~~~p~ilv~NK~Dl~~  129 (172)
T 2gj8_A           80 EIE--QADRVLFMVDGTTTDAVD-PAEIWPEFIARL-PAKLPITVVRNKADITG  129 (172)
T ss_dssp             HHH--TCSEEEEEEETTTCCCCS-HHHHCHHHHHHS-CTTCCEEEEEECHHHHC
T ss_pred             HHH--hCCEEEEEEECCCCCCHH-HHHHHHHHHHhc-ccCCCEEEEEECccCCc
Confidence            455  699999999999999987 457777776643 35799999999999954

>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=98.94  E-value=9.9e-10  Score=63.22  Aligned_cols=61  Identities=16%  Similarity=0.204  Sum_probs=46.4

Q ss_pred             cccchhhhhhhhhccCC---cEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           5 TSCFTNLVVNFVQTYHP---DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~~~---~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      ++.|..+...|++.  +   +++++|+|.++..++.... +...+..    .++|+++|+||+|+...+++
T Consensus        89 ~~~~~~~~~~~~~~--~~~~~~~i~v~d~~~~~~~~~~~-~~~~~~~----~~~p~i~v~nK~Dl~~~~~~  152 (195)
T 1svi_A           89 REAWGRMIETYITT--REELKAVVQIVDLRHAPSNDDVQ-MYEFLKY----YGIPVIVIATKADKIPKGKW  152 (195)
T ss_dssp             HHHHHHHHHHHHHH--CTTEEEEEEEEETTSCCCHHHHH-HHHHHHH----TTCCEEEEEECGGGSCGGGH
T ss_pred             HHHHHHHHHHHHhh--hhcCCEEEEEEECCCCCCHHHHH-HHHHHHH----cCCCEEEEEECcccCChHHH
Confidence            77888889998884  6   9999999999988887643 1122222    56899999999999765543

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=98.85  E-value=2.9e-09  Score=60.94  Aligned_cols=63  Identities=16%  Similarity=0.260  Sum_probs=45.9

Q ss_pred             cccccch------hhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFT------NLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~------~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .|++.|.      .+...|++..+++++++|+|.++   ++....|..++..    .++|+++|+||+|+...+.+
T Consensus        62 ~G~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~d~~~---~~~~~~~~~~~~~----~~~piilv~nK~Dl~~~~~~  130 (188)
T 2wjg_A           62 PGVYSLTANSIDEIIARDYIINEKPDLVVNIVDATA---LERNLYLTLQLME----MGANLLLALNKMDLAKSLGI  130 (188)
T ss_dssp             CCCSCCSSSSHHHHHHHHHHHHHCCSEEEEEEEGGG---HHHHHHHHHHHHT----TTCCEEEEEECHHHHHHTTC
T ss_pred             CCcCccccccHHHHHHHHHHhccCCCEEEEEecchh---HHHHHHHHHHHHh----cCCCEEEEEEhhhccccccc
Confidence            4667764      45666664114999999999875   5667778877764    46899999999999755544

>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=98.80  E-value=6.7e-09  Score=65.84  Aligned_cols=62  Identities=23%  Similarity=0.283  Sum_probs=49.5

Q ss_pred             cchhhhhhhhhcc-CCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcC-CCCCeEEEEeeCCCCcC
Q psy5805           7 CFTNLVVNFVQTY-HPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKY-IGEKAVILVANKADLER   68 (75)
Q Consensus         7 ~f~~~~~~~~~~~-~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~-~~~~~~ilvgnK~Dl~~   68 (75)
                      .+..+...|++.. .++++|+|+|+++   +++++.+..|..++..... ..+.|+++|+||+|+..
T Consensus       222 ~~~~l~~~fl~~i~~~d~ll~VvD~s~~~~~~~~~~~~~~~~eL~~~~~~l~~~p~ilV~NK~Dl~~  288 (342)
T 1lnz_A          222 QGVGLGHQFLRHIERTRVIVHVIDMSGLEGRDPYDDYLTINQELSEYNLRLTERPQIIVANKMDMPE  288 (342)
T ss_dssp             CTTTTHHHHHHHHHHCCEEEEEEESSCSSCCCHHHHHHHHHHHHHHSCSSTTTSCBCBEEECTTSTT
T ss_pred             ccchhHHHHHHHHHhccEEEEEEECCcccccChHHHHHHHHHHHHHhhhhhcCCCEEEEEECccCCC
Confidence            4555666666533 4999999999999   8999999999999987531 25789999999999964

>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=98.79  E-value=2e-09  Score=64.88  Aligned_cols=63  Identities=10%  Similarity=0.107  Sum_probs=40.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHH---hhc-CCCCCeEEEEeeCC-CCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLW---DSK-YIGEKAVILVANKA-DLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~---~~~-~~~~~~~ilvgnK~-Dl~~   68 (75)
                      +||++++.++..||.  ++||+|+|.|.+|++-++ .+.-+.++.   ... ...++|+++.+||. |+..
T Consensus       110 GGQ~klRplWr~Yy~--~TdglIfVVDSsD~~R~e-ak~EL~eL~~mL~ee~~L~gapLLVlANKqqDlp~  177 (227)
T 3l82_B          110 GSRYSVIPQIQKVCE--VVDGFIYVANAEAHKRHE-WQDEFSHIMAMTDPAFGSSGRPLLVLSCISQGDVK  177 (227)
T ss_dssp             -------CCHHHHHH--HCSEEEEEEECBTTCCCC-HHHHHHHHHHHSCTTSSCSCSCEEEEEEESSTTSC
T ss_pred             CcHHHHHHHHHHHhc--CCCEEEEEeccccHhHHH-HHHHHHHHHHHhcchhhhCCCeEEEEeCCCcCccC
Confidence            699999999999999  699999999999996554 333332222   111 13679999999995 7754

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=98.78  E-value=1e-08  Score=57.04  Aligned_cols=55  Identities=20%  Similarity=0.154  Sum_probs=36.8

Q ss_pred             chhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           8 FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         8 f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +......+++  +++++++|+|.++..+...  .|+..+...   .++|+++||||+|+.+.
T Consensus        69 ~~~~~~~~~~--~~~~~i~v~d~~~~~~~~~--~~~~~~~~~---~~~p~ilv~nK~Dl~~~  123 (161)
T 2dyk_A           69 IQEKVDRALE--DAEVVLFAVDGRAELTQAD--YEVAEYLRR---KGKPVILVATKVDDPKH  123 (161)
T ss_dssp             HHHHHHHHTT--TCSEEEEEEESSSCCCHHH--HHHHHHHHH---HTCCEEEEEECCCSGGG
T ss_pred             HHHHHHHHHH--hCCEEEEEEECCCcccHhH--HHHHHHHHh---cCCCEEEEEECcccccc
Confidence            3445555666  6999999999998644432  233222221   45799999999999653

>2hjg_A GTP-binding protein ENGA; GTPase ENGA KH-domain, hydrolase; HET: GDP; 2.50A {Bacillus subtilis}

Probab=98.74  E-value=1.9e-08  Score=65.10  Aligned_cols=60  Identities=18%  Similarity=0.186  Sum_probs=47.6

Q ss_pred             ccchhhhhh-hhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           6 SCFTNLVVN-FVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         6 e~f~~~~~~-~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      |+|..++.. +++  ++|++++|+|.++..+++.. .|...+..    .+.|+++|+||+|+.+.+.+
T Consensus       244 e~~~~~~~~~~~~--~ad~~llv~D~~~~~s~~~~-~~~~~~~~----~~~~iiiv~NK~Dl~~~~~~  304 (436)
T 2hjg_A          244 EKYSVLRALKAID--RSEVVAVVLDGEEGIIEQDK-RIAGYAHE----AGKAVVIVVNKWDAVDKDES  304 (436)
T ss_dssp             SHHHHHHHHHHHH--HCSEEEEEEETTTCCCHHHH-HHHHHHHH----TTCEEEEEEECGGGSCCCTT
T ss_pred             HHHHHHHHHHHHH--hCCEEEEEEcCCcCCcHHHH-HHHHHHHH----cCCcEEEEEECccCCCcchH
Confidence            778877663 666  49999999999999888876 57766654    46899999999999765543

>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=98.72  E-value=2.4e-08  Score=62.20  Aligned_cols=54  Identities=20%  Similarity=0.187  Sum_probs=45.3

Q ss_pred             chhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           8 FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         8 f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      +......+++  ++|++++|+|.++..++.....|+..+..    .++|+++|+||+|+.
T Consensus        82 ~~~~~~~~l~--~aD~il~VvD~~~~~~~~~~~~~~~~l~~----~~~pvilV~NK~Dl~  135 (308)
T 3iev_A           82 MVEIAKQSLE--EADVILFMIDATEGWRPRDEEIYQNFIKP----LNKPVIVVINKIDKI  135 (308)
T ss_dssp             HHHHHHHHHH--HCSEEEEEEETTTBSCHHHHHHHHHHTGG----GCCCEEEEEECGGGS
T ss_pred             HHHHHHHHhh--cCCEEEEEEeCCCCCCchhHHHHHHHHHh----cCCCEEEEEECccCC
Confidence            4456667777  59999999999999999998888877765    458999999999996

>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=98.71  E-value=3.1e-08  Score=66.66  Aligned_cols=56  Identities=18%  Similarity=0.138  Sum_probs=46.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|..++..+++  .+|++|+|+|.++   ++|++.+..+    ..    .++|+++++||+|+..
T Consensus        78 PGhe~F~~~~~r~~~--~aD~aILVvDa~~Gv~~qT~e~l~~l----~~----~~vPiIVViNKiDl~~  136 (594)
T 1g7s_A           78 PGHEAFTTLRKRGGA--LADLAILIVDINEGFKPQTQEALNIL----RM----YRTPFVVAANKIDRIH  136 (594)
T ss_dssp             CTTSCCTTSBCSSSB--SCSEEEEEEETTTCCCHHHHHHHHHH----HH----TTCCEEEEEECGGGST
T ss_pred             CCcHHHHHHHHHHHh--hCCEEEEEEECCCCccHhHHHHHHHH----HH----cCCeEEEEeccccccc
Confidence            589999999998888  5999999999999   8888776532    22    4689999999999964

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=98.70  E-value=2.5e-08  Score=57.06  Aligned_cols=57  Identities=11%  Similarity=0.075  Sum_probs=42.0

Q ss_pred             cccchhhhhhhhhcc-CCcEEEEEEECCChhH--HHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           5 TSCFTNLVVNFVQTY-HPDVFVIVYSVIERKT--FKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~-~~~~~ilv~d~~~~~s--~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++.|..+.+.|++.. +++++++|+|.++..+  +..+..|+..       .++|+++|+||+|+..
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~vi~v~d~~~~~~~~~~~~~~~~~~-------~~~p~i~v~nK~Dl~~  147 (195)
T 3pqc_A           88 RMLWKRLVEDYFKNRWSLQMVFLLVDGRIPPQDSDLMMVEWMKS-------LNIPFTIVLTKMDKVK  147 (195)
T ss_dssp             HHHHHHHHHHHHHHCTTEEEEEEEEETTSCCCHHHHHHHHHHHH-------TTCCEEEEEECGGGSC
T ss_pred             HHHHHHHHHHHHhcCcCceEEEEEecCCCCCCHHHHHHHHHHHH-------cCCCEEEEEEChhcCC
Confidence            677888889888842 3399999999987643  3444455433       2589999999999964

>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=98.69  E-value=1.2e-08  Score=66.05  Aligned_cols=64  Identities=17%  Similarity=0.228  Sum_probs=47.8

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhc----CCCCCeEEEEeeCCCCcC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSK----YIGEKAVILVANKADLER   68 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~----~~~~~~~ilvgnK~Dl~~   68 (75)
                      ..||++|......+++  ++|++|+|+|.++ .+|+.+..|..+..++.    ..+-.|+++++||+|+.+
T Consensus        91 tpG~~~f~~~~~~~~~--~aD~~ilVvDa~~-gsfe~~~~~~~qt~~~~~~~~~~~~~~iivviNK~Dl~~  158 (435)
T 1jny_A           91 APGHRDFVKNMITGAS--QADAAILVVSAKK-GEYEAGMSVEGQTREHIILAKTMGLDQLIVAVNKMDLTE  158 (435)
T ss_dssp             CSSSTTHHHHHHHTSS--CCSEEEEEEECST-THHHHHHSTTCHHHHHHHHHHHTTCTTCEEEEECGGGSS
T ss_pred             CCCcHHHHHHHHhhhh--hcCEEEEEEECCC-CccccccccchHHHHHHHHHHHcCCCeEEEEEEcccCCC
Confidence            3689999988888888  5999999999998 88987665544333221    112236899999999975

>3cb4_D GTP-binding protein LEPA; GTPase, OB-fold, membrane, nucleotide-binding, translation; 2.80A {Escherichia coli} PDB: 3deg_C*

Probab=98.67  E-value=6.5e-08  Score=65.20  Aligned_cols=60  Identities=15%  Similarity=0.072  Sum_probs=50.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .||+.|......+++.  +|++|+|+|.++..+++....|.....     .++|+++|+||+|+.+.
T Consensus        79 PGh~dF~~ev~~~l~~--aD~aILVVDa~~gv~~qt~~~~~~~~~-----~~ipiIvViNKiDl~~a  138 (599)
T 3cb4_D           79 PGHVDFSYEVSRSLAA--CEGALLVVDAGQGVEAQTLANCYTAME-----MDLEVVPVLNKIDLPAA  138 (599)
T ss_dssp             CCCGGGHHHHHHHHHH--CSEEEEEEETTTCCCTHHHHHHHHHHH-----TTCEEEEEEECTTSTTC
T ss_pred             CCchHHHHHHHHHHHH--CCEEEEEEECCCCCCHHHHHHHHHHHH-----CCCCEEEeeeccCcccc
Confidence            5899999888888884  999999999999888888888865543     45799999999999754

>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=98.67  E-value=9.6e-08  Score=64.43  Aligned_cols=60  Identities=15%  Similarity=0.124  Sum_probs=50.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .||+.|......+++  .+|++++|+|.++..+++....|.....     .++|+++|+||+|+.+.
T Consensus        81 PGh~dF~~ev~r~l~--~aD~aILVVDa~~gv~~qt~~~~~~a~~-----~~ipiIvviNKiDl~~a  140 (600)
T 2ywe_A           81 PGHVDFSYEVSRALA--ACEGALLLIDASQGIEAQTVANFWKAVE-----QDLVIIPVINKIDLPSA  140 (600)
T ss_dssp             CCSGGGHHHHHHHHH--TCSEEEEEEETTTBCCHHHHHHHHHHHH-----TTCEEEEEEECTTSTTC
T ss_pred             CCcHhHHHHHHHHHH--hCCEEEEEEECCCCccHHHHHHHHHHHH-----CCCCEEEEEeccCcccc
Confidence            589999988888888  5999999999999888888888865443     46899999999999753

>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=98.67  E-value=4.4e-08  Score=62.87  Aligned_cols=62  Identities=18%  Similarity=0.156  Sum_probs=51.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .||++|......+++  ++|++++|+|.++..++.+...|+..+...   ...|+++|+||+|+.+.
T Consensus        83 PGh~~~~~~~~~~~~--~~D~~ilVvda~~~~~~~qt~~~~~~~~~~---~~~~iivviNK~Dl~~~  144 (403)
T 3sjy_A           83 PGHEVLMATMLSGAA--LMDGAILVVAANEPFPQPQTREHFVALGII---GVKNLIIVQNKVDVVSK  144 (403)
T ss_dssp             CCCGGGHHHHHHHHT--TCSEEEEEEETTSCSSCHHHHHHHHHHHHH---TCCCEEEEEECGGGSCH
T ss_pred             CCcHHHHHHHHHHHh--hCCEEEEEEECCCCCCcHHHHHHHHHHHHc---CCCCEEEEEECccccch
Confidence            589999998888888  599999999999988888888887766653   23589999999999653

>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=3.1e-08  Score=60.91  Aligned_cols=63  Identities=10%  Similarity=0.087  Sum_probs=45.1

Q ss_pred             cccccch------hhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFT------NLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~------~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .|++.|.      .+...|+...++|++++|+|.++.+++   ..|..++.+    .++|+++|+||+|+...+.+
T Consensus        57 pG~~~~~~~~~~e~v~~~~~~~~~~d~vi~V~D~t~~e~~---~~~~~~l~~----~~~p~ilv~NK~Dl~~~~~~  125 (272)
T 3b1v_A           57 PGIYSMSPYSPEAKVARDYLLSQRADSILNVVDATNLERN---LYLTTQLIE----TGIPVTIALNMIDVLDGQGK  125 (272)
T ss_dssp             CCCSCSSCSSHHHHHHHHHHHTTCCSEEEEEEEGGGHHHH---HHHHHHHHH----TCSCEEEEEECHHHHHHTTC
T ss_pred             CCcCccCCCChHHHHHHHHHhcCCCCEEEEEecCCchHhH---HHHHHHHHh----cCCCEEEEEEChhhCCcCCc
Confidence            4667765      566667651149999999999987654   346666654    46899999999999654443

>3h2y_A GTPase family protein; GTP-binding protein YQEH, possibly involved in replication initiation, csgid, IDP90222; HET: DGI; 1.80A {Bacillus anthracis str}

Probab=98.65  E-value=2.1e-08  Score=63.97  Aligned_cols=55  Identities=24%  Similarity=0.334  Sum_probs=45.3

Q ss_pred             cccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           5 TSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+|+++.+.+++  +++++++|+|++++.     ..|..++.+.  ..+.|+++|+||+||..
T Consensus        56 ~e~f~~~l~~i~~--~~~~il~VvD~~d~~-----~~~~~~l~~~--~~~~p~ilV~NK~DL~~  110 (368)
T 3h2y_A           56 DDDFLRILNGIGK--SDALVVKIVDIFDFN-----GSWLPGLHRF--VGNNKVLLVGNKADLIP  110 (368)
T ss_dssp             CHHHHHHHHHHHH--SCCEEEEEEETTSHH-----HHCCTTHHHH--SSSSCEEEEEECGGGSC
T ss_pred             HHHHHHHHHHHhc--cCcEEEEEEECCCCc-----ccHHHHHHHH--hCCCcEEEEEEChhcCC
Confidence            5789999999998  588999999999864     4576677664  35789999999999964

>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=98.63  E-value=3.8e-08  Score=64.71  Aligned_cols=52  Identities=12%  Similarity=0.096  Sum_probs=39.5

Q ss_pred             hhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805          15 FVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus        15 ~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      +++  ++|++++|+|.+++.+++++..+...+...   .+.|+++|+||+|+...+.
T Consensus       309 ~~~--~aD~vl~VvD~s~~~s~~~~~~~~~~l~~l---~~~piIvV~NK~Dl~~~~~  360 (476)
T 3gee_A          309 KMA--EADLILYLLDLGTERLDDELTEIRELKAAH---PAAKFLTVANKLDRAANAD  360 (476)
T ss_dssp             CCS--SCSEEEEEEETTTCSSGGGHHHHHHHHHHC---TTSEEEEEEECTTSCTTTH
T ss_pred             hcc--cCCEEEEEEECCCCcchhhhHHHHHHHHhc---CCCCEEEEEECcCCCCccc
Confidence            445  699999999999999987655544444432   3689999999999976554

>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=4.7e-08  Score=59.55  Aligned_cols=63  Identities=16%  Similarity=0.238  Sum_probs=44.1

Q ss_pred             cccccchh------hhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTN------LVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~------~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .|++.|..      +...|+..-+++++++|+|.++.++..   .|..++..    .++|+++|+||+|+...+.+
T Consensus        60 pG~~~~~~~~~~e~v~~~~~~~~~~d~ii~V~D~t~~~~~~---~~~~~l~~----~~~pvilv~NK~Dl~~~~~i  128 (258)
T 3a1s_A           60 PGTYSLGYSSIDEKIARDYLLKGDADLVILVADSVNPEQSL---YLLLEILE----MEKKVILAMTAIDEAKKTGM  128 (258)
T ss_dssp             CCCSSCCSSSHHHHHHHHHHHHSCCSEEEEEEETTSCHHHH---HHHHHHHT----TTCCEEEEEECHHHHHHTTC
T ss_pred             CCcCccCCCCHHHHHHHHHHhhcCCCEEEEEeCCCchhhHH---HHHHHHHh----cCCCEEEEEECcCCCCccch
Confidence            46666654      445665311699999999999876543   46666654    36899999999999655544

>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=98.61  E-value=9.1e-08  Score=62.71  Aligned_cols=62  Identities=11%  Similarity=0.080  Sum_probs=41.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHH------HHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKA------EDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~------~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .||++|......+++  ++|++|+|+|.++..++..+      ......+..   .+..|+++|+||+|+.+.
T Consensus       119 PG~~~f~~~~~~~~~--~aD~~llVvDa~~g~~~~~~~~~~qt~e~~~~~~~---~~~~~iIvviNK~Dl~~~  186 (483)
T 3p26_A          119 PGHRDFVPNAIMGIS--QADMAILCVDCSTNAFESGFDLDGQTKEHMLLASS---LGIHNLIIAMNKMDNVDW  186 (483)
T ss_dssp             CCCGGGHHHHHHHHT--TCSEEEEEEECCC------CCCCHHHHHHHHHHHH---TTCCCEEEEEECGGGGTT
T ss_pred             CCcHHHHHHHHHhhh--hCCEEEEEEECCCCccccccchhhhHHHHHHHHHH---cCCCcEEEEEECcCcccc
Confidence            589999999999998  59999999999997665432      111112221   233469999999999764

>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=98.60  E-value=1.7e-08  Score=66.01  Aligned_cols=63  Identities=16%  Similarity=0.170  Sum_probs=36.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCCh---hHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIER---KTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~---~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      .||++|......+++  ++|++|+|+|.++.   .||+...+|.+.+.... ..++| +++|+||+|+..
T Consensus       129 PGh~~f~~~~~~~~~--~aD~~ilVvDa~~g~~e~sf~~~~qt~e~l~~~~-~~~vp~iivviNK~Dl~~  195 (467)
T 1r5b_A          129 PGHKGYVTNMINGAS--QADIGVLVISARRGEFEAGFERGGQTREHAVLAR-TQGINHLVVVINKMDEPS  195 (467)
T ss_dssp             CC-----------TT--SCSEEEEEEECSTTHHHHTTSTTCCHHHHHHHHH-HTTCSSEEEEEECTTSTT
T ss_pred             CCcHHHHHHHHhhcc--cCCEEEEEEeCCcCccccccCCCCcHHHHHHHHH-HcCCCEEEEEEECccCCC
Confidence            589999888888887  59999999999986   46654444444433222 24577 999999999953

>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=98.60  E-value=1.8e-08  Score=61.44  Aligned_cols=52  Identities=17%  Similarity=0.201  Sum_probs=38.9

Q ss_pred             hhhhhh--hccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805          11 LVVNFV--QTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus        11 ~~~~~~--~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      +...|+  +  ++|++++|+|.++.+++..+..|+   ..    .++|+++|+||+|+...+.
T Consensus        74 i~~~~~~~~--~~d~vi~VvDas~~~~~~~l~~~l---~~----~~~pvilv~NK~Dl~~~~~  127 (256)
T 3iby_A           74 IAAQSVIDL--EYDCIINVIDACHLERHLYLTSQL---FE----LGKPVVVALNMMDIAEHRG  127 (256)
T ss_dssp             HHHHHHHHS--CCSEEEEEEEGGGHHHHHHHHHHH---TT----SCSCEEEEEECHHHHHHTT
T ss_pred             HHHHHHhhC--CCCEEEEEeeCCCchhHHHHHHHH---HH----cCCCEEEEEEChhcCCcCC
Confidence            556666  5  699999999999987776654443   22    3689999999999865443

>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=98.60  E-value=1e-07  Score=59.28  Aligned_cols=57  Identities=19%  Similarity=0.289  Sum_probs=41.4

Q ss_pred             chhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHH-HHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           8 FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDML-KTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         8 f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~-~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      |......+++  ++|++++|+|.++..+..  ..|+ +.+...  .+++|+++|+||+|+...+
T Consensus        76 ~~~~~~~~l~--~ad~il~VvD~~~~~~~~--~~~i~~~l~~~--~~~~p~ilV~NK~Dl~~~~  133 (301)
T 1wf3_A           76 MDQEVYEALA--DVNAVVWVVDLRHPPTPE--DELVARALKPL--VGKVPILLVGNKLDAAKYP  133 (301)
T ss_dssp             HHHHHHHHTS--SCSEEEEEEETTSCCCHH--HHHHHHHHGGG--TTTSCEEEEEECGGGCSSH
T ss_pred             HHHHHHHHHh--cCCEEEEEEECCCCCChH--HHHHHHHHHhh--cCCCCEEEEEECcccCCch
Confidence            5566667777  699999999999875544  3454 445442  2578999999999997543

>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=98.58  E-value=1.3e-07  Score=61.44  Aligned_cols=61  Identities=20%  Similarity=0.229  Sum_probs=45.5

Q ss_pred             cccchhhhhh-hhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           5 TSCFTNLVVN-FVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         5 ~e~f~~~~~~-~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+|..++.. +++  +++++++|+|.++.-+ +....|...+..    .+.|+++|+||+|+.+.+++
T Consensus       263 ~e~~~~~~~~~~~~--~ad~~llviD~~~~~~-~~~~~~~~~~~~----~~~~~ilv~NK~Dl~~~~~~  324 (456)
T 4dcu_A          263 TEKYSVLRALKAID--RSEVVAVVLDGEEGII-EQDKRIAGYAHE----AGKAVVIVVNKWDAVDKDES  324 (456)
T ss_dssp             CSHHHHHHHHHHHH--HCSEEEEEEETTTCCC-HHHHHHHHHHHH----TTCEEEEEEECGGGSCCCSS
T ss_pred             HHHHHHHHHHHHHh--hCCEEEEEEeCCCCcC-HHHHHHHHHHHH----cCCCEEEEEEChhcCCCchH
Confidence            7899988876 556  4999999999987533 233455555554    45899999999999866554

>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=98.57  E-value=4.1e-08  Score=61.57  Aligned_cols=63  Identities=8%  Similarity=0.017  Sum_probs=44.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHH----HHhhcCCCCCeEEEEeeC-CCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKT----LWDSKYIGEKAVILVANK-ADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~----~~~~~~~~~~~~ilvgnK-~Dl~~   68 (75)
                      +||++.+.++..||.  ++||+|+|.|.+|++.++ .+.-+.+    +.+.....++|+++.+|| .|+.+
T Consensus       195 GGQ~~lRplWr~Yy~--~tdglIfVVDSsDreRle-ak~EL~eL~~mL~e~~~l~~apLLVfANKkQDlp~  262 (312)
T 3l2o_B          195 GSRYSVIPQIQKVCE--VVDGFIYVANAEAHKRHE-WQDEFSHIMAMTDPAFGSSGRPLLVLSCISQGDVK  262 (312)
T ss_dssp             --CCCCCHHHHHHHH--HCSEEEECCBCBTTCCCC-HHHHHHHHHHHHCHHHHCTTCCEEEEEEESSTTSC
T ss_pred             CCHHHHHHHHHHHhc--CCCEEEEEecCCcHhHHH-HHHHHHHHHHHhcchhhcCCCeEEEEeCCcccccC
Confidence            799999999999999  699999999999997654 3222221    222111367999999997 58864

>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=98.51  E-value=1.1e-07  Score=58.34  Aligned_cols=45  Identities=13%  Similarity=0.109  Sum_probs=33.9

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      ++|++++|+|.++.++...+..|   +.+    .++|+++|+||+|+.+.+.
T Consensus        85 ~~d~ii~VvD~~~~~~~~~~~~~---l~~----~~~p~ivv~NK~Dl~~~~~  129 (274)
T 3i8s_A           85 DADLLINVVDASNLERNLYLTLQ---LLE----LGIPCIVALNMLDIAEKQN  129 (274)
T ss_dssp             CCSEEEEEEEGGGHHHHHHHHHH---HHH----HTCCEEEEEECHHHHHHTT
T ss_pred             CCCEEEEEecCCChHHHHHHHHH---HHh----cCCCEEEEEECccchhhhh
Confidence            69999999999997766554444   333    2589999999999865443

>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=98.50  E-value=1.8e-07  Score=64.96  Aligned_cols=58  Identities=19%  Similarity=0.167  Sum_probs=49.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .||++|......+++  .+|++|+|+|.++..+++....|.....     .++|+++|+||+|+.
T Consensus       106 PG~~df~~~~~~~l~--~aD~ailVvDa~~g~~~qt~~~~~~~~~-----~~~p~ilviNK~D~~  163 (842)
T 1n0u_A          106 PGHVDFSSEVTAALR--VTDGALVVVDTIEGVCVQTETVLRQALG-----ERIKPVVVINKVDRA  163 (842)
T ss_dssp             CCCCSSCHHHHHHHH--TCSEEEEEEETTTBSCHHHHHHHHHHHH-----TTCEEEEEEECHHHH
T ss_pred             cCchhhHHHHHHHHH--hCCEEEEEEeCCCCCCHHHHHHHHHHHH-----cCCCeEEEEECCCcc
Confidence            589999999999998  5999999999999988888777754332     468999999999985

>3izy_P Translation initiation factor IF-2, mitochondrial; E coli, RNA, ribosomal; 10.80A {Bos taurus}

Probab=98.50  E-value=5e-08  Score=65.08  Aligned_cols=59  Identities=15%  Similarity=0.187  Sum_probs=46.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|..++..+++  ++|++++|+|.++....+....|. .+.    ..++|+++|+||+|+.+
T Consensus        60 PGhe~f~~~~~~~~~--~aD~vILVVDa~dg~~~qt~e~l~-~~~----~~~vPiIVViNKiDl~~  118 (537)
T 3izy_P           60 PGHAAFSAMRARGTQ--VTDIVILVVAADDGVMKQTVESIQ-HAK----DAHVPIVLAINKCDKAE  118 (537)
T ss_dssp             SSSCCTTTSBBSSSB--SBSSCEEECBSSSCCCHHHHHHHH-HHH----TTTCCEEECCBSGGGTT
T ss_pred             CChHHHHHHHHHHHc--cCCEEEEEEECCCCccHHHHHHHH-HHH----HcCCcEEEEEecccccc
Confidence            689999999999998  599999999999865554444332 222    25689999999999964

>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation, GTP-binding domain, maturation enzyme, oxidoreductase; 2.99A {Thermotoga neapolitana}

Probab=98.50  E-value=2e-07  Score=60.55  Aligned_cols=60  Identities=15%  Similarity=0.159  Sum_probs=42.1

Q ss_pred             cccccchhhh-------hhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           3 SRTSCFTNLV-------VNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         3 s~~e~f~~~~-------~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      .|++.|..+.       ..+++  ++|++++|+|.+..+.   ...|+..+.+.    ++|+++|+||+|+...+.
T Consensus        91 pG~~d~~~l~~~~~~~~~~~l~--~aD~vllVvD~~~~~~---~~~~l~~l~~~----~~piIvV~NK~Dl~~~~~  157 (423)
T 3qq5_A           91 PGLDDVGELGRLRVEKARRVFY--RADCGILVTDSAPTPY---EDDVVNLFKEM----EIPFVVVVNKIDVLGEKA  157 (423)
T ss_dssp             SSTTCCCTTCCCCHHHHHHHHT--SCSEEEEECSSSCCHH---HHHHHHHHHHT----TCCEEEECCCCTTTTCCC
T ss_pred             cCCCcccchhHHHHHHHHHHHh--cCCEEEEEEeCCChHH---HHHHHHHHHhc----CCCEEEEEeCcCCCCccH
Confidence            4666666552       33555  5999999999943333   35677777652    689999999999976543

>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=98.49  E-value=5.2e-07  Score=58.43  Aligned_cols=60  Identities=15%  Similarity=0.083  Sum_probs=43.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||++|......+++  ++|++|+|+|.++... .+...|+..+...   +-.|+++|+||+|+.+
T Consensus       112 pGh~~f~~~~~~~~~--~aD~~ilVvDa~~g~~-~qt~~~l~~~~~~---~~~~iIvviNK~Dl~~  171 (434)
T 1zun_B          112 PGHEQYTRNMATGAS--TCDLAIILVDARYGVQ-TQTRRHSYIASLL---GIKHIVVAINKMDLNG  171 (434)
T ss_dssp             CCSGGGHHHHHHHHT--TCSEEEEEEETTTCSC-HHHHHHHHHHHHT---TCCEEEEEEECTTTTT
T ss_pred             CChHHHHHHHHHHHh--hCCEEEEEEECCCCCc-HHHHHHHHHHHHc---CCCeEEEEEEcCcCCc
Confidence            589999888888887  5999999999988542 2334444444431   2236999999999975

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=98.48  E-value=9.9e-08  Score=55.93  Aligned_cols=61  Identities=15%  Similarity=0.149  Sum_probs=42.5

Q ss_pred             cccchhhhhhhhhcc-CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           5 TSCFTNLVVNFVQTY-HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~-~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      ++.|..+...|++.. +++++++|+|.++..+.. -..|+..+..    .++|+++|+||+|+...+
T Consensus        99 ~~~~~~~~~~~~~~~~~~d~vi~v~d~~~~~~~~-~~~~~~~l~~----~~~p~i~v~nK~Dl~~~~  160 (223)
T 4dhe_A           99 KAHWEQLLSSYLQTRPQLCGMILMMDARRPLTEL-DRRMIEWFAP----TGKPIHSLLTKCDKLTRQ  160 (223)
T ss_dssp             HHHHHHHHHHHHHHCTTEEEEEEEEETTSCCCHH-HHHHHHHHGG----GCCCEEEEEECGGGSCHH
T ss_pred             HHHHHHHHHHHHhcCcCcCEEEEEEeCCCCCCHH-HHHHHHHHHh----cCCCEEEEEeccccCChh
Confidence            566777887887743 477899999998754322 2345455543    458999999999996543

>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=98.48  E-value=2.6e-07  Score=59.24  Aligned_cols=59  Identities=10%  Similarity=0.129  Sum_probs=45.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      .||++|......+++  ++|++|+|+|.++... .+...|+..+..    .++| +++++||+|+.+
T Consensus        83 pG~~~f~~~~~~~~~--~aD~~ilVvda~~g~~-~qt~~~l~~~~~----~~ip~iivviNK~Dl~~  142 (405)
T 2c78_A           83 PGHADYIKNMITGAA--QMDGAILVVSAADGPM-PQTREHILLARQ----VGVPYIVVFMNKVDMVD  142 (405)
T ss_dssp             CCSGGGHHHHHHHHT--TCSSEEEEEETTTCCC-HHHHHHHHHHHH----TTCCCEEEEEECGGGCC
T ss_pred             CChHHHHHHHHHHHH--HCCEEEEEEECCCCCc-HHHHHHHHHHHH----cCCCEEEEEEECccccC
Confidence            589999888888888  5999999999988653 344555555554    3577 899999999974

>3tr5_A RF-3, peptide chain release factor 3; protein synthesis, translation; HET: GDP; 2.11A {Coxiella burnetii}

Probab=98.46  E-value=6.2e-07  Score=59.64  Aligned_cols=59  Identities=14%  Similarity=0.063  Sum_probs=48.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|......+++  .+|++|+|+|.++..+......|. .+..    .++|+++|+||+|+..
T Consensus        90 PG~~df~~~~~~~l~--~aD~allVvDa~~g~~~~t~~~~~-~~~~----~~iPiivviNK~Dl~~  148 (528)
T 3tr5_A           90 PGHADFTEDTYRTLT--AVDSALMVIDAAKGVEPRTIKLME-VCRL----RHTPIMTFINKMDRDT  148 (528)
T ss_dssp             CCSTTCCHHHHHGGG--GCSEEEEEEETTTCSCHHHHHHHH-HHHT----TTCCEEEEEECTTSCC
T ss_pred             CCchhHHHHHHHHHH--hCCEEEEEEeCCCCCCHHHHHHHH-HHHH----cCCCEEEEEeCCCCcc
Confidence            589999999999998  499999999999987777776663 3332    4689999999999964

>3ec1_A YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase, signaling protein; HET: GDP; 2.36A {Geobacillus stearothermophilus}

Probab=98.46  E-value=4.8e-08  Score=62.29  Aligned_cols=56  Identities=18%  Similarity=0.263  Sum_probs=44.1

Q ss_pred             ccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           4 RTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         4 ~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+|+|++..+.+++  +++++++|+|++++.+     .|..++.+.  ..+.|+++|+||+||..
T Consensus        57 ~~e~f~~~L~~~~~--~~~lil~VvD~~d~~~-----s~~~~l~~~--l~~~piilV~NK~DLl~  112 (369)
T 3ec1_A           57 DDDDFLSMLHRIGE--SKALVVNIVDIFDFNG-----SFIPGLPRF--AADNPILLVGNKADLLP  112 (369)
T ss_dssp             --CHHHHHHHHHHH--HCCEEEEEEETTCSGG-----GCCSSHHHH--CTTSCEEEEEECGGGSC
T ss_pred             CHHHHHHHHHHhhc--cCcEEEEEEECCCCCC-----chhhHHHHH--hCCCCEEEEEEChhcCC
Confidence            47899999999887  4999999999999874     465555553  35789999999999964

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=98.46  E-value=1.5e-07  Score=57.17  Aligned_cols=66  Identities=11%  Similarity=0.003  Sum_probs=44.7

Q ss_pred             cccccchhhhhhhhhc-------cCCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCC--CeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQT-------YHPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGE--KAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~-------~~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~--~~~ilvgnK~Dl~~~r   70 (75)
                      .|++.|..+.+.+++.       .+++++++|++++... +... ..|+..+..... .+  .|+++|+||+|+...+
T Consensus        92 pG~~~~~~~~~~~~~~i~~~l~~~~~~~il~V~~~d~~~-~~~~~~~~~~~l~~~~~-~~~~~~~ivv~nK~Dl~~~~  167 (262)
T 3def_A           92 PGLVEAGYVNHQALELIKGFLVNRTIDVLLYVDRLDVYA-VDELDKQVVIAITQTFG-KEIWCKTLLVLTHAQFSPPD  167 (262)
T ss_dssp             CCSEETTEECHHHHHHHHHHTTTCEECEEEEEEESSCSC-CCHHHHHHHHHHHHHHC-GGGGGGEEEEEECTTCCCST
T ss_pred             CCCCCcccchHHHHHHHHHHHhcCCCCEEEEEEcCCCCC-CCHHHHHHHHHHHHHhc-hhhhcCEEEEEeCcccCCCC
Confidence            4677776655555431       1589999999998765 5444 567777766432 22  4899999999996443

>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=98.44  E-value=1.8e-07  Score=61.99  Aligned_cols=57  Identities=19%  Similarity=0.264  Sum_probs=43.9

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ..||+.|..++..+.+  .+|++++|+|.++   +++++.+.    .+..    .++|+++++||+|+.+
T Consensus        58 TPGhe~f~~~~~~~~~--~aD~aILVVda~~g~~~qT~e~l~----~~~~----~~vPiIVviNKiDl~~  117 (501)
T 1zo1_I           58 TPGHAAFTSMRARGAQ--ATDIVVLVVAADDGVMPQTIEAIQ----HAKA----AQVPVVVAVNKIDKPE  117 (501)
T ss_dssp             CCTTTCCTTSBCSSSB--SCSSEEEEEETTTBSCTTTHHHHH----HHHH----TTCCEEEEEECSSSST
T ss_pred             CCCcHHHHHHHHHHHh--hCCEEEEEeecccCccHHHHHHHH----HHHh----cCceEEEEEEeccccc
Confidence            3589999999888887  5999999999988   45554432    2222    4679999999999964

>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=9.6e-07  Score=56.31  Aligned_cols=59  Identities=14%  Similarity=0.226  Sum_probs=44.4

Q ss_pred             ccchhhhhhhhhccCCcEEEEEEECCChh--HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           6 SCFTNLVVNFVQTYHPDVFVIVYSVIERK--TFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         6 e~f~~~~~~~~~~~~~~~~ilv~d~~~~~--s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |.|++..+. +.  ++|++++|+|++++.  ++..+..|...+.... ..+.|+++|+||+|+.+
T Consensus       246 e~f~~tl~~-~~--~aD~il~VvD~s~~~~~~~~~~~~~~~~L~~l~-~~~~p~ilV~NK~Dl~~  306 (364)
T 2qtf_A          246 DAFFVTLSE-AK--YSDALILVIDSTFSENLLIETLQSSFEILREIG-VSGKPILVTLNKIDKIN  306 (364)
T ss_dssp             HHHHHHHHG-GG--GSSEEEEEEETTSCHHHHHHHHHHHHHHHHHHT-CCSCCEEEEEECGGGCC
T ss_pred             HHHHHHHHH-HH--hCCEEEEEEECCCCcchHHHHHHHHHHHHHHhC-cCCCCEEEEEECCCCCC
Confidence            446555543 34  499999999999987  6777777776666542 36789999999999864

>2hjg_A GTP-binding protein ENGA; GTPase ENGA KH-domain, hydrolase; HET: GDP; 2.50A {Bacillus subtilis}

Probab=98.43  E-value=3.8e-07  Score=59.04  Aligned_cols=56  Identities=18%  Similarity=0.141  Sum_probs=40.4

Q ss_pred             cchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           7 CFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         7 ~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +++.....+++  ++|++++|+|.++..++..  .|+..+..   ..+.|+++|+||+|+...
T Consensus        71 ~~~~~~~~~~~--~ad~il~vvD~~~~~~~~d--~~~~~~l~---~~~~pvilv~NK~D~~~~  126 (436)
T 2hjg_A           71 QIRQQAEIAMD--EADVIIFMVNGREGVTAAD--EEVAKILY---RTKKPVVLAVNKLDNTEM  126 (436)
T ss_dssp             HHHHHHHHHHH--HCSEEEEEEETTTCSCHHH--HHHHHHHT---TCCSCEEEEEECCCC---
T ss_pred             HHHHHHHHHHH--hCCEEEEEEeCCCCCCHHH--HHHHHHHH---HcCCCEEEEEECccCccc
Confidence            67777788888  5999999999998766654  34433332   256899999999998643

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=98.41  E-value=3.5e-07  Score=57.82  Aligned_cols=49  Identities=10%  Similarity=0.251  Sum_probs=41.4

Q ss_pred             CCcEEEEEEECCChh--HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805          20 HPDVFVIVYSVIERK--TFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~--s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .++++++|+|+++..  +++....|+.++....  ++.|+++|+||+|+...+
T Consensus       246 ~ad~illV~D~s~~~~~~~~~~~~~~~~i~~~~--~~~piilV~NK~Dl~~~~  296 (357)
T 2e87_A          246 LGNLIIYIFDPSEHCGFPLEEQIHLFEEVHGEF--KDLPFLVVINKIDVADEE  296 (357)
T ss_dssp             TCSEEEEEECTTCTTSSCHHHHHHHHHHHHHHT--TTSCEEEEECCTTTCCHH
T ss_pred             cCCEEEEEEeCCccccCCHHHHHHHHHHHHHhc--CCCCEEEEEECcccCChH
Confidence            599999999999988  7888889998887643  378999999999997543

>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=98.41  E-value=6.1e-07  Score=57.50  Aligned_cols=59  Identities=14%  Similarity=0.090  Sum_probs=43.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      .||++|......+++  ++|++|+|+|.++....+....| ..+..    .++| +++++||+|+.+
T Consensus        74 pG~~~f~~~~~~~~~--~aD~~ilVvda~~g~~~qt~e~l-~~~~~----~~vp~iivviNK~Dl~~  133 (397)
T 1d2e_A           74 PGHADYVKNMITGTA--PLDGCILVVAANDGPMPQTREHL-LLARQ----IGVEHVVVYVNKADAVQ  133 (397)
T ss_dssp             SSHHHHHHHHHHTSS--CCSEEEEEEETTTCSCHHHHHHH-HHHHH----TTCCCEEEEEECGGGCS
T ss_pred             CChHHHHHHHHhhHh--hCCEEEEEEECCCCCCHHHHHHH-HHHHH----cCCCeEEEEEECcccCC
Confidence            588999888888888  59999999999985433333333 33433    3577 789999999974

>3izq_1 HBS1P, elongation factor 1 alpha-like protein; NO-GO mRNA decay, ribosomal protein,hydrolase; 9.50A {Saccharomyces cerevisiae}

Probab=98.40  E-value=2.2e-07  Score=62.66  Aligned_cols=65  Identities=12%  Similarity=0.133  Sum_probs=42.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChh---HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERK---TFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~---s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .||++|......+++  ++|++|+|+|.++..   +|....++...+......+..|+++|+||+|+.+.
T Consensus       253 PG~e~f~~~~~~~~~--~aD~~llVVDa~~g~~e~~~~~~~qt~e~l~~~~~lgi~~iIVVvNKiDl~~~  320 (611)
T 3izq_1          253 PGHRDFVPNAIMGIS--QADMAILCVDCSTNAFESGFDLDGQTKEHMLLASSLGIHNLIIAMNKMDNVDW  320 (611)
T ss_dssp             CSSSCHHHHHTTTSS--CCSEEEEEEECSHHHHHTTCCTTSHHHHHHHHHHTTTCCEEEEEEECTTTTTT
T ss_pred             CCCcccHHHHHHHHh--hcCceEEEEECCCCcccccchhhhHHHHHHHHHHHcCCCeEEEEEecccccch
Confidence            589999988888888  599999999998742   22111122222221112233469999999999763

>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=98.39  E-value=5.2e-07  Score=58.92  Aligned_cols=60  Identities=10%  Similarity=0.080  Sum_probs=42.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCCh---hHHH---HHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIER---KTFK---KAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~---~s~~---~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      .||++|......+++  ++|++|+|+|.++.   .||+   +...++..+..    .++| +++|+||+|+.+
T Consensus        93 PGh~~f~~~~~~~~~--~aD~~ilVvda~~g~~~~sf~~~~qt~~~~~~~~~----~~v~~iivviNK~Dl~~  159 (458)
T 1f60_A           93 PGHRDFIKNMITGTS--QADCAILIIAGGVGEFEAGISKDGQTREHALLAFT----LGVRQLIVAVNKMDSVK  159 (458)
T ss_dssp             CCCTTHHHHHHHSSS--CCSEEEEEEECSHHHHHHHTCTTSHHHHHHHHHHH----TTCCEEEEEEECGGGGT
T ss_pred             CCcHHHHHHHHhhhh--hCCEEEEEEeCCcCccccccCcchhHHHHHHHHHH----cCCCeEEEEEEcccccc
Confidence            589999988888888  59999999999875   3442   22222223332    3455 899999999963

>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=98.38  E-value=9.1e-07  Score=58.83  Aligned_cols=60  Identities=12%  Similarity=0.179  Sum_probs=43.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .||+.|......+++  .+|++|+|+|.++...-.. ..++..+    ...++|+++++||+|+...
T Consensus        90 PG~~df~~~~~~~l~--~aD~~IlVvDa~~g~~~~t-~~~~~~~----~~~~ipiivviNK~Dl~~~  149 (529)
T 2h5e_A           90 PGHEDFSEDTYRTLT--AVDCCLMVIDAAKGVEDRT-RKLMEVT----RLRDTPILTFMNKLDRDIR  149 (529)
T ss_dssp             CCSTTCCHHHHHGGG--GCSEEEEEEETTTCSCHHH-HHHHHHH----TTTTCCEEEEEECTTSCCS
T ss_pred             CCChhHHHHHHHHHH--HCCEEEEEEeCCccchHHH-HHHHHHH----HHcCCCEEEEEcCcCCccc
Confidence            589999988888888  4999999999987532211 2222222    2357899999999999653

>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=98.37  E-value=1.1e-06  Score=56.38  Aligned_cols=58  Identities=17%  Similarity=0.159  Sum_probs=41.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECC----ChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVI----ERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~----~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .||+.|.........  .+|++|+|+|.+    .+++++++..|    ..   ....|+++|+||+|+.+.
T Consensus        89 PGh~~f~~~~~~~~~--~~D~~ilVvda~~g~~~~qt~e~l~~~----~~---l~~~~iivv~NK~Dl~~~  150 (408)
T 1s0u_A           89 PGHETLMATMLSGAS--LMDGAILVIAANEPCPQPQTKEHLMAL----EI---LGIDKIIIVQNKIDLVDE  150 (408)
T ss_dssp             SSHHHHHHHHHTTCS--CCSEEEEEEETTSCSSCHHHHHHHHHH----HH---TTCCCEEEEEECTTSSCT
T ss_pred             CCHHHHHHHHHHhHh--hCCEEEEEEECCCCCCCchhHHHHHHH----HH---cCCCeEEEEEEccCCCCH
Confidence            578888766555555  489999999999    46677766544    22   123479999999999654

>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=98.35  E-value=1.6e-06  Score=59.22  Aligned_cols=60  Identities=17%  Similarity=0.021  Sum_probs=49.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .||+.|......+++.  +|++|+|+|.++..++.....|.. +..    .++|+++|+||+|+...
T Consensus        85 PG~~df~~~~~~~l~~--aD~~ilVvDa~~g~~~~t~~~~~~-~~~----~~~p~ivviNKiD~~~~  144 (691)
T 1dar_A           85 PGHVDFTIEVERSMRV--LDGAIVVFDSSQGVEPQSETVWRQ-AEK----YKVPRIAFANKMDKTGA  144 (691)
T ss_dssp             CSSTTCHHHHHHHHHH--CSEEEEEEETTTCSCHHHHHHHHH-HHH----TTCCEEEEEECTTSTTC
T ss_pred             cCccchHHHHHHHHHH--CCEEEEEEECCCCcchhhHHHHHH-HHH----cCCCEEEEEECCCcccC
Confidence            5889999999998884  999999999999888887777753 332    36899999999999653

>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=98.32  E-value=5.8e-07  Score=54.72  Aligned_cols=62  Identities=24%  Similarity=0.293  Sum_probs=41.8

Q ss_pred             cccccchh------hhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTN------LVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~------~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .|++.|..      +...|+..-++|++++|+|.++.+   ....|..++..   ...+|+++|+||+|+...+
T Consensus        58 pG~~~~~~~~~~~~~~~~~~~~~~~d~vi~v~D~~~~~---~~~~~~~~~~~---~~~~p~ilv~NK~Dl~~~~  125 (271)
T 3k53_A           58 PGIYSLTAHSIDELIARNFILDGNADVIVDIVDSTCLM---RNLFLTLELFE---MEVKNIILVLNKFDLLKKK  125 (271)
T ss_dssp             CCCSCCCSSCHHHHHHHHHHHTTCCSEEEEEEEGGGHH---HHHHHHHHHHH---TTCCSEEEEEECHHHHHHH
T ss_pred             CCccccccCCHHHHHHHHhhhccCCcEEEEEecCCcch---hhHHHHHHHHh---cCCCCEEEEEEChhcCccc
Confidence            46666665      566666311699999999998864   33344445544   2338999999999986443

>3j2k_7 ERF3, eukaryotic polypeptide chain release factor 3; rabbit 80S ribosome, ribosome-translation complex; 17.00A {Oryctolagus cuniculus}

Probab=98.30  E-value=5.8e-07  Score=58.44  Aligned_cols=62  Identities=19%  Similarity=0.205  Sum_probs=41.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChh---HHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERK---TFKKAEDMLKTLWDSKYIGEKA-VILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~---s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~   67 (75)
                      .||++|......+++  ++|++++|+|.++..   +|+...++.+.+.... ..++| +++|+||+|+.
T Consensus       103 PGh~~f~~~~~~~~~--~aD~~ilVVDa~~g~~e~~~~~~~qt~e~l~~~~-~~~v~~iIvviNK~Dl~  168 (439)
T 3j2k_7          103 PGHKSFVPNMIGGAS--QADLAVLVISARKGEFETGFEKGGQTREHAMLAK-TAGVKHLIVLINKMDDP  168 (439)
T ss_pred             CChHHHHHHHHhhHh--hCCEEEEEEECCCCccccccCCCchHHHHHHHHH-HcCCCeEEEEeecCCCc
Confidence            589999988888888  499999999998753   2321122222222111 13456 89999999984

>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=98.29  E-value=1.4e-06  Score=56.48  Aligned_cols=52  Identities=25%  Similarity=0.318  Sum_probs=37.7

Q ss_pred             cchhhhhhhhhccCCcEEEEEEECCChhHHHH--HHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           7 CFTNLVVNFVQTYHPDVFVIVYSVIERKTFKK--AEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         7 ~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .++.....+++  ++|++++|+|.++..+...  +..|+..       .+.|+++|+||+|+.
T Consensus        70 ~~~~~~~~~~~--~ad~il~V~D~~~~~~~~d~~i~~~l~~-------~~~p~ilv~NK~D~~  123 (439)
T 1mky_A           70 KMKEVTLNMIR--EADLVLFVVDGKRGITKEDESLADFLRK-------STVDTILVANKAENL  123 (439)
T ss_dssp             HHHHHHHHHHT--TCSEEEEEEETTTCCCHHHHHHHHHHHH-------HTCCEEEEEESCCSH
T ss_pred             HHHHHHHHHHH--hCCEEEEEEECCCCCCHHHHHHHHHHHH-------cCCCEEEEEeCCCCc
Confidence            35666777888  6999999999987655432  3334322       257999999999985

>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=98.28  E-value=2.2e-06  Score=58.65  Aligned_cols=59  Identities=19%  Similarity=0.017  Sum_probs=47.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|......+++  .+|++|+|+|.++..+......|. .+..    .++|+++|+||+|+..
T Consensus        90 PG~~df~~~~~~~l~--~aD~aIlVvDa~~gv~~qt~~~~~-~~~~----~~ip~ilviNKiD~~~  148 (704)
T 2rdo_7           90 PGHVDFTIEVERSMR--VLDGAVMVYCAVGGVQPQSETVWR-QANK----YKVPRIAFVNKMDRMG  148 (704)
T ss_pred             CCccchHHHHHHHHH--HCCEEEEEEeCCCCCcHHHHHHHH-HHHH----cCCCEEEEEeCCCccc
Confidence            589999988888888  499999999999877666655553 2222    4689999999999864

>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=98.25  E-value=2.2e-06  Score=56.32  Aligned_cols=56  Identities=21%  Similarity=0.121  Sum_probs=43.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|......+++  ++|++++|+|.++   +++++.+.    .+..    .++|+++|+||+|+.+
T Consensus        81 PGh~~~~~~~~~~~~--~aD~~ilVvda~~g~~~qt~e~l~----~~~~----~~ip~IvviNK~Dl~~  139 (482)
T 1wb1_A           81 PGHADLIRAVVSAAD--IIDLALIVVDAKEGPKTQTGEHML----ILDH----FNIPIIVVITKSDNAG  139 (482)
T ss_dssp             SSHHHHHHHHHHHTT--SCCEEEEEEETTTCSCHHHHHHHH----HHHH----TTCCBCEEEECTTSSC
T ss_pred             CChHHHHHHHHHHHh--hCCEEEEEEecCCCccHHHHHHHH----HHHH----cCCCEEEEEECCCccc
Confidence            588999888888888  5999999999998   66766553    2222    3478899999999964

>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=98.24  E-value=1.4e-06  Score=56.74  Aligned_cols=58  Identities=17%  Similarity=0.172  Sum_probs=39.4

Q ss_pred             cccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           5 TSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +++++.+...+++  ++|++++|+|..+.  +.....|+.++..   ..+.|+++|+||+|+.+.
T Consensus        89 ~~~~~~~~~~~~~--~ad~il~VvD~~~~--~~~~d~~l~~~l~---~~~~pvilV~NK~D~~~~  146 (456)
T 4dcu_A           89 LAQIRQQAEIAMD--EADVIIFMVNGREG--VTAADEEVAKILY---RTKKPVVLAVNKLDNTEM  146 (456)
T ss_dssp             HHHHHHHHHHHHH--HCSEEEEEEESSSC--SCHHHHHHHHHHT---TCCSCEEEEEECC-----
T ss_pred             HHHHHHHHHhhHh--hCCEEEEEEeCCCC--CChHHHHHHHHHH---HcCCCEEEEEECccchhh
Confidence            7788888899998  59999999997653  3333344444433   257899999999998654

>2xex_A Elongation factor G; GTPase, translation, biosynthetic protein; 1.90A {Staphylococcus aureus}

Probab=98.22  E-value=4.7e-06  Score=56.92  Aligned_cols=60  Identities=17%  Similarity=-0.044  Sum_probs=48.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|++.|......+++.  +|++++|+|.++..++.....|.. +..    .++|+++|+||+|+...
T Consensus        83 PG~~df~~~~~~~l~~--aD~~llVvDa~~g~~~~~~~~~~~-~~~----~~~p~ilviNK~Dl~~~  142 (693)
T 2xex_A           83 PGHVDFTVEVERSLRV--LDGAVTVLDAQSGVEPQTETVWRQ-ATT----YGVPRIVFVNKMDKLGA  142 (693)
T ss_dssp             CCCSSCCHHHHHHHHH--CSEEEEEEETTTBSCHHHHHHHHH-HHH----TTCCEEEEEECTTSTTC
T ss_pred             cCCcchHHHHHHHHHH--CCEEEEEECCCCCCcHHHHHHHHH-HHH----cCCCEEEEEECCCcccc
Confidence            5788898888888884  999999999999888877766643 333    36899999999999653

>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=98.21  E-value=5.1e-06  Score=53.35  Aligned_cols=57  Identities=16%  Similarity=0.156  Sum_probs=41.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECC----ChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVI----ERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~----~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .||+.|.........  .+|++++|+|.+    .+++++++..|.    ..   ...|+++|+||+|+.+
T Consensus        91 PGh~~f~~~~~~~~~--~~D~~ilVvda~~g~~~~qt~e~l~~~~----~~---~~~~iivviNK~Dl~~  151 (410)
T 1kk1_A           91 PGHEALMTTMLAGAS--LMDGAILVIAANEPCPRPQTREHLMALQ----II---GQKNIIIAQNKIELVD  151 (410)
T ss_dssp             SSHHHHHHHHHHCGG--GCSEEEEEEETTSCSSCHHHHHHHHHHH----HH---TCCCEEEEEECGGGSC
T ss_pred             CChHHHHHHHHhhhh--hCCEEEEEEECCCCCCChhHHHHHHHHH----Hc---CCCcEEEEEECccCCC
Confidence            478888766655555  489999999999    456777665442    21   2247999999999965

>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=98.19  E-value=2.6e-06  Score=55.90  Aligned_cols=45  Identities=20%  Similarity=0.325  Sum_probs=34.5

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      ++|++++|+|.+++.+... ..|+..+.      +.|+++|+||+|+...+.
T Consensus       303 ~aD~vl~VvD~s~~~~~~~-~~i~~~l~------~~piivV~NK~Dl~~~~~  347 (462)
T 3geh_A          303 TADLVLLTIDAATGWTTGD-QEIYEQVK------HRPLILVMNKIDLVEKQL  347 (462)
T ss_dssp             SCSEEEEEEETTTCSCHHH-HHHHHHHT------TSCEEEEEECTTSSCGGG
T ss_pred             cCCEEEEEeccCCCCCHHH-HHHHHhcc------CCcEEEEEECCCCCcchh
Confidence            6999999999999877655 44544442      369999999999976544

>2elf_A Protein translation elongation factor 1A; tRNA, pyrrolysine, structural genomics, NPPSFA; HET: CIT; 1.70A {Methanosarcina mazei}

Probab=98.18  E-value=2.9e-06  Score=54.16  Aligned_cols=56  Identities=7%  Similarity=-0.045  Sum_probs=42.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeE-EEEee-CCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVAN-KADL   66 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~-ilvgn-K~Dl   66 (75)
                      .||++|......+++  .+|++|+|+|  +...+.+.+.|+..+..    .++|. +++.| |+|+
T Consensus        68 PGh~~f~~~~~~~~~--~aD~ailVvd--~~g~~~qt~e~~~~~~~----~~i~~~ivvvNNK~Dl  125 (370)
T 2elf_A           68 HSYPKTLKSLITALN--ISDIAVLCIP--PQGLDAHTGECIIALDL----LGFKHGIIALTRSDST  125 (370)
T ss_dssp             TTTTTCHHHHHHHHH--TCSEEEEEEC--TTCCCHHHHHHHHHHHH----TTCCEEEEEECCGGGS
T ss_pred             CChHHHHHHHHHHHH--HCCEEEEEEc--CCCCcHHHHHHHHHHHH----cCCCeEEEEEEeccCC
Confidence            589999777777777  5999999999  45566677777666654    23565 78888 9999

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=98.16  E-value=2.4e-06  Score=52.00  Aligned_cols=49  Identities=16%  Similarity=0.091  Sum_probs=35.7

Q ss_pred             CCcEEEEEEECCChhHHHHH-HHHHHHHHhhcCCCC--CeEEEEeeCCCCcCCC
Q psy5805          20 HPDVFVIVYSVIERKTFKKA-EDMLKTLWDSKYIGE--KAVILVANKADLERRR   70 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~--~~~ilvgnK~Dl~~~r   70 (75)
                      ++|++++|+|++.. ++... ..|+..+..... .+  .|+++|+||+|+...+
T Consensus       119 ~~d~il~v~~~d~~-~~~~~~~~~~~~l~~~~~-~~~~~~iivV~nK~Dl~~~~  170 (270)
T 1h65_A          119 TIDVLLYVDRLDAY-RVDNLDKLVAKAITDSFG-KGIWNKAIVALTHAQFSPPD  170 (270)
T ss_dssp             EECEEEEEEESSCC-CCCHHHHHHHHHHHHHHC-GGGGGGEEEEEECCSCCCGG
T ss_pred             CCCEEEEEEeCCCC-cCCHHHHHHHHHHHHHhC-cccccCEEEEEECcccCCcC
Confidence            59999999999764 45544 477777765421 22  6999999999996544

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=98.15  E-value=3.9e-06  Score=51.16  Aligned_cols=58  Identities=17%  Similarity=0.161  Sum_probs=41.4

Q ss_pred             cchhhhhhhhhccCCcEEE-EEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           7 CFTNLVVNFVQTYHPDVFV-IVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         7 ~f~~~~~~~~~~~~~~~~i-lv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .+..+...|++  ++++++ +|+|.++.-+......|...+.    ..+.|+++|+||+|+.+.+
T Consensus       150 ~~~~~~~~~~~--~~~~~il~v~d~~~~~~~~~~~~~~~~~~----~~~~~~i~V~NK~Dl~~~~  208 (299)
T 2aka_B          150 QIRDMLMQFVT--KENCLILAVSPANSDLANSDALKIAKEVD----PQGQRTIGVITKLDLMDEG  208 (299)
T ss_dssp             HHHHHHHHHHT--STTEEEEEEEESSSCGGGCHHHHHHHHHC----TTCSSEEEEEECGGGSCTT
T ss_pred             HHHHHHHHHHc--CCCeEEEEEecCCcchhhhHHHHHHHHhC----CCCCeEEEEEEccccCCCC
Confidence            56778888888  588777 6999987655444444554443    2568999999999996543

>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=98.13  E-value=7.1e-06  Score=54.10  Aligned_cols=47  Identities=15%  Similarity=0.258  Sum_probs=35.7

Q ss_pred             hhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          13 VNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        13 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ..+++  ++|++++|+|.+++.+++...-| +.+      .+.|+++|+||+|+..
T Consensus       318 ~~~~~--~aD~vl~VvD~s~~~s~~~~~il-~~l------~~~piivV~NK~DL~~  364 (482)
T 1xzp_A          318 LQEIE--KADIVLFVLDASSPLDEEDRKIL-ERI------KNKRYLVVINKVDVVE  364 (482)
T ss_dssp             HHHHH--HCSEEEEEEETTSCCCHHHHHHH-HHH------TTSSEEEEEEECSSCC
T ss_pred             HHHhh--cccEEEEEecCCCCCCHHHHHHH-HHh------cCCCEEEEEECccccc
Confidence            34555  49999999999999888764332 222      3679999999999964

>2qpt_A EH domain-containing protein-2; protein-nucleotide complex, membrane protein, endocytosis; HET: ANP; 3.10A {Mus musculus}

Probab=98.11  E-value=1.5e-06  Score=58.01  Aligned_cols=56  Identities=18%  Similarity=0.338  Sum_probs=43.6

Q ss_pred             chhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           8 FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         8 f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      |..+...++.  ++|++++|+|.++.........|+..+..    .+.|+++|+||+|+...
T Consensus       178 f~~~~~~~l~--~aD~il~VvDa~~~~~~~~~~~~l~~l~~----~~~pvilVlNK~Dl~~~  233 (550)
T 2qpt_A          178 FPAVLRWFAE--RVDLIILLFDAHKLEISDEFSEAIGALRG----HEDKIRVVLNKADMVET  233 (550)
T ss_dssp             HHHHHHHHHH--HCSEEEEEEETTSCCCCHHHHHHHHHTTT----CGGGEEEEEECGGGSCH
T ss_pred             HHHHHHHHHH--hCCEEEEEEeCCcCCCCHHHHHHHHHHHh----cCCCEEEEEECCCccCH
Confidence            5667777777  49999999999887666677777766653    35789999999998654

>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=98.10  E-value=2.6e-06  Score=61.38  Aligned_cols=59  Identities=10%  Similarity=0.095  Sum_probs=44.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      .||++|......+++  ++|++|+|+|.++.... +...|+..+..    .++| +++++||+|+.+
T Consensus       367 PGHedF~~~mi~gas--~AD~aILVVDAtdGv~~-QTrEhL~ll~~----lgIP~IIVVINKiDLv~  426 (1289)
T 3avx_A          367 PGHADYVKNMITGAA--QMDGAILVVAATDGPMP-QTREHILLGRQ----VGVPYIIVFLNKCDMVD  426 (1289)
T ss_dssp             CCHHHHHHHHHHTSC--CCSEEEEEEETTTCSCT-THHHHHHHHHH----HTCSCEEEEEECCTTCC
T ss_pred             CChHHHHHHHHHHHh--hCCEEEEEEcCCccCcH-HHHHHHHHHHH----cCCCeEEEEEeeccccc
Confidence            589999888888888  59999999999986433 33344444443    2467 789999999974

>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=98.05  E-value=3.2e-06  Score=50.36  Aligned_cols=61  Identities=8%  Similarity=0.054  Sum_probs=33.3

Q ss_pred             chhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhc-CCCCCeEEEEeeCCCCcCCCcc
Q psy5805           8 FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSK-YIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         8 f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +......+++  +++++++|+|+++...-  ...|+..+.... .....|+++|+||+|+...+.+
T Consensus       102 ~~~~~~~~~~--~~~~~l~v~d~~~~~~~--~~~~l~~~~~~~~~~~~~~~iiv~nK~D~~~~~~~  163 (239)
T 3lxx_A          102 IIRCILLTSP--GPHALLLVVPLGRYTEE--EHKATEKILKMFGERARSFMILIFTRKDDLGDTNL  163 (239)
T ss_dssp             HHHHHHHTTT--CCSEEEEEEETTCCSSH--HHHHHHHHHHHHHHHHGGGEEEEEECGGGC-----
T ss_pred             HHHHHHhcCC--CCcEEEEEeeCCCCCHH--HHHHHHHHHHHhhhhccceEEEEEeCCccCCcccH
Confidence            3333344444  69999999999765432  122333332211 0123589999999998655443

>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=98.04  E-value=3.9e-07  Score=57.92  Aligned_cols=60  Identities=15%  Similarity=0.343  Sum_probs=38.6

Q ss_pred             ccchhhhh-------hhhhccCCcEE-----------EEEEECCC-hhHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCC
Q psy5805           6 SCFTNLVV-------NFVQTYHPDVF-----------VIVYSVIE-RKTFKKAE-DMLKTLWDSKYIGEKAVILVANKAD   65 (75)
Q Consensus         6 e~f~~~~~-------~~~~~~~~~~~-----------ilv~d~~~-~~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~D   65 (75)
                      ++|+.+..       .|++.  ++++           +++|++++ ..+|..+. .|+..+     ..++|+|+|+||+|
T Consensus       113 e~~~~i~~~i~~~~~~yl~~--~~~~~r~~~~d~rv~~~vy~I~~~~~~l~~~d~~~~~~l-----~~~~piIlV~NK~D  185 (361)
T 2qag_A          113 DCFKTIISYIDEQFERYLHD--ESGLNRRHIIDNRVHCCFYFISPFGHGLKPLDVAFMKAI-----HNKVNIVPVIAKAD  185 (361)
T ss_dssp             ---CCTHHHHHHHHHHHHHH--HTCSCCC-CCCCCCCEEEEEECSSSSSCCHHHHHHHHHT-----CS-SCEEEEEECCS
T ss_pred             HHHHHHHHHHHHHHHHHHHH--hhhhccccccCCceEEEEEEEecCCCCcchhHHHHHHHh-----ccCCCEEEEEECCC
Confidence            77888876       67763  5544           47888876 66777664 454433     26789999999999


Q ss_pred             CcCCCcc
Q psy5805          66 LERRRQV   72 (75)
Q Consensus        66 l~~~r~v   72 (75)
                      +...+++
T Consensus       186 l~~~~ev  192 (361)
T 2qag_A          186 TLTLKER  192 (361)
T ss_dssp             SSCHHHH
T ss_pred             CCCHHHH
Confidence            9765443

>2j69_A Bacterial dynamin-like protein; FZO, FZL, GTPase, hydrolase; 3.0A {Nostoc punctiforme} PDB: 2j68_A 2w6d_A*

Probab=97.96  E-value=1.4e-05  Score=54.57  Aligned_cols=55  Identities=15%  Similarity=0.175  Sum_probs=42.3

Q ss_pred             hhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           9 TNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         9 ~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      ......|++  ++|++++|+|.++..+......|...+..    .+.|+++|+||+|+...
T Consensus       191 ~~~~~~~i~--~aD~vL~Vvda~~~~s~~e~~~l~~~l~~----~~~~iiiVlNK~Dl~~~  245 (695)
T 2j69_A          191 NELSLGYVN--NCHAILFVMRASQPCTLGERRYLENYIKG----RGLTVFFLVNAWDQVRE  245 (695)
T ss_dssp             HHHHTHHHH--SSSEEEEEEETTSTTCHHHHHHHHHHTTT----SCCCEEEEEECGGGGGG
T ss_pred             HHHHHHHHH--hCCEEEEEEeCCCccchhHHHHHHHHHHh----hCCCEEEEEECcccccc
Confidence            445566777  69999999999999888887777554432    35689999999998643

>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=97.94  E-value=1.5e-05  Score=50.34  Aligned_cols=57  Identities=18%  Similarity=0.289  Sum_probs=40.2

Q ss_pred             hhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           9 TNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         9 ~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      ..+...|++  +++++|++++.++.+...  ..|...++... ..+.|+++|+||+|+...+
T Consensus       163 ~~~~~~~i~--~~d~iilvv~~~~~~~~~--~~~~~l~~~~~-~~~~~~i~V~nK~Dl~~~~  219 (360)
T 3t34_A          163 ENMVRSYIE--KPNCIILAISPANQDLAT--SDAIKISREVD-PSGDRTFGVLTKIDLMDKG  219 (360)
T ss_dssp             HHHHHHHHH--SSSEEEEEEEETTSCGGG--CHHHHHHHHSC-TTCTTEEEEEECGGGCCTT
T ss_pred             HHHHHHHhh--cCCeEEEEeecccCCcCC--HHHHHHHHHhc-ccCCCEEEEEeCCccCCCc
Confidence            667777887  699999999876554332  34555555432 3567999999999996544

>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=97.92  E-value=3.8e-05  Score=46.13  Aligned_cols=51  Identities=18%  Similarity=0.309  Sum_probs=29.6

Q ss_pred             hhhccCCcEEEEEEECCChhHH-HHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          15 FVQTYHPDVFVIVYSVIERKTF-KKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        15 ~~~~~~~~~~ilv~d~~~~~s~-~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +++  ++|++++|+|.++.... ..+..|+.++.... ....++++++||+|+..
T Consensus       102 ~~~--~~d~il~V~d~~~~~~~~~~~~~~l~~~~~~~-~~~~~i~vv~nK~Dl~~  153 (260)
T 2xtp_A          102 SAP--GPHVLLLVTQLGRYTSQDQQAAQRVKEIFGED-AMGHTIVLFTHKEDLNG  153 (260)
T ss_dssp             HTT--CCSEEEEEEETTCCCHHHHHHHHHHHHHHCGG-GGGGEEEEEECGGGGTT
T ss_pred             cCC--CCcEEEEEEeCCCCCHHHHHHHHHHHHHhCch-hhccEEEEEEcccccCC
Confidence            445  69999999999863322 22334444432211 12234556666999974

>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=97.87  E-value=5.1e-05  Score=51.67  Aligned_cols=58  Identities=12%  Similarity=0.029  Sum_probs=44.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .||+.|......+++.  ++++++|+|.++.-.... ..++..+..    .++|+++|+||+|+.
T Consensus        82 pG~~~f~~~~~~~l~~--ad~~ilVvD~~~g~~~qt-~~~~~~~~~----~~ip~ilv~NKiD~~  139 (665)
T 2dy1_A           82 PGYGDFVGEIRGALEA--ADAALVAVSAEAGVQVGT-ERAWTVAER----LGLPRMVVVTKLDKG  139 (665)
T ss_dssp             CCSGGGHHHHHHHHHH--CSEEEEEEETTTCSCHHH-HHHHHHHHH----TTCCEEEEEECGGGC
T ss_pred             CCccchHHHHHHHHhh--cCcEEEEEcCCcccchhH-HHHHHHHHH----ccCCEEEEecCCchh
Confidence            5899999888888884  999999999877544333 344444443    358999999999986

>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=97.86  E-value=4.7e-05  Score=49.29  Aligned_cols=59  Identities=27%  Similarity=0.313  Sum_probs=39.0

Q ss_pred             ccchhhhh-hhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           6 SCFTNLVV-NFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         6 e~f~~~~~-~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      |.|..++. .+++  .++++++++|.++..++... .+...+..    .+.|+++|+||+|+.+.+.
T Consensus       250 e~~~~~~~~~~i~--~ad~vllv~d~~~~~~~~~~-~i~~~l~~----~~~~~ilv~NK~Dl~~~~~  309 (439)
T 1mky_A          250 EKYSNYRVVDSIE--KADVVVIVLDATQGITRQDQ-RMAGLMER----RGRASVVVFNKWDLVVHRE  309 (439)
T ss_dssp             CCSCCHHHHHHHH--HCSEEEEEEETTTCCCHHHH-HHHHHHHH----TTCEEEEEEECGGGSTTGG
T ss_pred             HHHHHHHHHHHHh--hCCEEEEEEeCCCCCCHHHH-HHHHHHHH----cCCCEEEEEECccCCCchh
Confidence            34443332 3555  49999999999987776543 22233332    4689999999999976543

>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=97.74  E-value=2.6e-05  Score=47.97  Aligned_cols=58  Identities=16%  Similarity=0.203  Sum_probs=37.3

Q ss_pred             cchhhhhhhhhccCCcEEEEEEECCChhHH-HHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           7 CFTNLVVNFVQTYHPDVFVIVYSVIERKTF-KKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         7 ~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~-~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .+..+...|++  ++|++++|+|.++.... .....+...+.    ..+.|+++|+||+|+....
T Consensus       156 ~~~~~~~~~~~--~~d~iilvvd~~~~~~~~~~~~~i~~~~~----~~~~~~i~v~NK~Dl~~~~  214 (315)
T 1jwy_B          156 QIRRMVMAYIK--KQNAIIVAVTPANTDLANSDALQLAKEVD----PEGKRTIGVITKLDLMDKG  214 (315)
T ss_dssp             HHHHHHHHHHH--STTEEEEEEEESSSCSTTCSHHHHHHHHC----SSCSSEEEEEECTTSSCSS
T ss_pred             HHHHHHHHHHc--CCCeEEEEEEecCcchhhhHHHHHHHHhC----CCCCcEEEEEcCcccCCcc
Confidence            36667777777  69999999998544311 11112222222    2568999999999996543

>3mca_A HBS1, elongation factor 1 alpha-like protein; protein protein complex, translation regulation; 2.74A {Schizosaccharomyces pombe}

Probab=97.68  E-value=6e-06  Score=55.58  Aligned_cols=56  Identities=20%  Similarity=0.156  Sum_probs=34.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCCh----------hHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIER----------KTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~----------~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      .||++|......+++  ++|++|+|+|.++.          .+.+.+    ..+..    .++| +|+|+||+|+.+
T Consensus       263 PGh~~f~~~~~~~~~--~aD~alLVVDa~~g~~e~gi~~~~qt~e~l----~~~~~----lgip~iIvviNKiDl~~  329 (592)
T 3mca_A          263 PGHRDFISGMIAGAS--SADFAVLVVDSSQNNFERGFLENGQTREHA----YLLRA----LGISEIVVSVNKLDLMS  329 (592)
T ss_dssp             ESSSEEEEECCC---------CCSEEEEEECCSSTTSCSCSSHHHHH----HHHHH----SSCCCEEEEEECGGGGT
T ss_pred             CChHHHHHHHHHHHh--hCCEEEEEEECCCCccccccccchHHHHHH----HHHHH----cCCCeEEEEEecccccc
Confidence            489999888888887  59999999999853          333332    22222    2355 899999999964

>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=97.66  E-value=6.8e-05  Score=46.48  Aligned_cols=48  Identities=19%  Similarity=0.280  Sum_probs=33.6

Q ss_pred             hhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          13 VNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        13 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ..+++  .+|++++|+|.++   +.....|+.+...   ..+.|+++++||+|+..
T Consensus        83 ~~~l~--~~D~vl~Vvd~~~---~~~~~~~i~~~l~---~~~~P~ilvlNK~D~~~  130 (301)
T 1ega_A           83 SSSIG--DVELVIFVVEGTR---WTPDDEMVLNKLR---EGKAPVILAVNKVDNVQ  130 (301)
T ss_dssp             TSCCC--CEEEEEEEEETTC---CCHHHHHHHHHHH---SSSSCEEEEEESTTTCC
T ss_pred             HHHHh--cCCEEEEEEeCCC---CCHHHHHHHHHHH---hcCCCEEEEEECcccCc
Confidence            44445  6999999999976   4444445443332   24689999999999975

>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=97.55  E-value=9.6e-05  Score=45.58  Aligned_cols=40  Identities=25%  Similarity=0.234  Sum_probs=32.3

Q ss_pred             CCcEEEEEEECCChhHHH--HHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFK--KAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~--~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|+++.|.|..++.+..  .+.+|+         .+.|.++|.||+||.+
T Consensus        23 ~aDvVl~VvDAr~p~~~~~~~l~~~l---------~~kp~ilVlNK~DL~~   64 (282)
T 1puj_A           23 LIDIVYELVDARIPMSSRNPMIEDIL---------KNKPRIMLLNKADKAD   64 (282)
T ss_dssp             GCSEEEEEEETTSTTTTSCHHHHHHC---------SSSCEEEEEECGGGSC
T ss_pred             hCCEEEEEEeCCCCCccCCHHHHHHH---------CCCCEEEEEECcccCC
Confidence            399999999999998775  344442         5689999999999965

>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=97.28  E-value=0.00046  Score=43.49  Aligned_cols=58  Identities=19%  Similarity=0.256  Sum_probs=34.6

Q ss_pred             cchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           7 CFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         7 ~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .++.+...|++  +++.+++++...+. .+... .|...+... ...+.|+++|+||+|+.+.
T Consensus       155 ~~~~~~~~~~~--~~~~iiL~v~~a~~-~~~~~-~~~~i~~~~-~~~~~~~i~V~NK~Dl~~~  212 (353)
T 2x2e_A          155 QIRDMLMQFVT--KENCLILAVSPANS-DLANS-DALKVAKEV-DPQGQRTIGVITKLDLMDE  212 (353)
T ss_dssp             HHHHHHHHHHT--STTEEEEEEEETTS-CGGGC-HHHHHHHHH-CTTCTTEEEEEECGGGSCT
T ss_pred             HHHHHHHHHHc--CCCeEEEEEecCCC-ccchh-HHHHHHHHh-CcCCCceEEEeccccccCc
Confidence            67778888887  47766665543322 22211 122222222 2357899999999999654

>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=97.27  E-value=0.001  Score=41.64  Aligned_cols=46  Identities=20%  Similarity=0.242  Sum_probs=34.6

Q ss_pred             CCcEEEEEEECCChh-HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIERK-TFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      |+|.+++|.|..++. +...+.+++.....    .++|.++|.||+||.+.
T Consensus        86 nvD~v~~V~~~~~p~~~~~~i~r~L~~~~~----~~~~~vivlnK~DL~~~  132 (307)
T 1t9h_A           86 NVDQAVLVFSAVQPSFSTALLDRFLVLVEA----NDIQPIICITKMDLIED  132 (307)
T ss_dssp             CCCEEEEEEESTTTTCCHHHHHHHHHHHHT----TTCEEEEEEECGGGCCC
T ss_pred             hCCEEEEEEeCCCCCCCHHHHHHHHHHHHH----CCCCEEEEEECCccCch
Confidence            899999999999765 44455666544432    56889999999999754

>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=97.16  E-value=0.00085  Score=38.59  Aligned_cols=55  Identities=13%  Similarity=0.121  Sum_probs=36.1

Q ss_pred             cchhhhhhhhhcc-CCcEEEEEEECCChhHHHH--HHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           7 CFTNLVVNFVQTY-HPDVFVIVYSVIERKTFKK--AEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         7 ~f~~~~~~~~~~~-~~~~~ilv~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|+.....|++.. .++++++++|+++..++..  +..|+.   .    ..+|+++|+||+|+..
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~v~d~~~~~~~~~~~~~~~~~---~----~~~~~~~v~nK~D~~s  151 (210)
T 1pui_A           94 KWQRALGEYLEKRQSLQGLVVLMDIRHPLKDLDQQMIEWAV---D----SNIAVLVLLTKADKLA  151 (210)
T ss_dssp             HHHHHHHHHHHHCTTEEEEEEEEETTSCCCHHHHHHHHHHH---H----TTCCEEEEEECGGGSC
T ss_pred             HHHHHHHHHHHhhhcccEEEEEEECCCCCchhHHHHHHHHH---H----cCCCeEEEEecccCCC
Confidence            3444444555321 5899999999998766542  333432   1    4578999999999854

>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=97.12  E-value=0.00056  Score=44.42  Aligned_cols=48  Identities=19%  Similarity=0.232  Sum_probs=37.8

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcC-CCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY-IGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~ilvgnK~Dl~~   68 (75)
                      .++.++.++|++ ++++.++..|..++..... ....|.+++.||+|+..
T Consensus       235 ra~~lL~vvDls-~~~~~~ls~g~~el~~la~aL~~~P~ILVlNKlDl~~  283 (416)
T 1udx_A          235 RTRVLLYVLDAA-DEPLKTLETLRKEVGAYDPALLRRPSLVALNKVDLLE  283 (416)
T ss_dssp             SSSEEEEEEETT-SCHHHHHHHHHHHHHHHCHHHHHSCEEEEEECCTTSC
T ss_pred             HHHhhhEEeCCc-cCCHHHHHHHHHHHHHHhHHhhcCCEEEEEECCChhh
Confidence            489999999998 7788888888877765420 12568899999999864

>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=97.12  E-value=0.00041  Score=44.70  Aligned_cols=26  Identities=12%  Similarity=0.139  Sum_probs=14.6

Q ss_pred             chhhhhhhhhcc-CCcEEEEEEECCCh
Q psy5805           8 FTNLVVNFVQTY-HPDVFVIVYSVIER   33 (75)
Q Consensus         8 f~~~~~~~~~~~-~~~~~ilv~d~~~~   33 (75)
                      ++.+...+...+ ++|++++|+|.++.
T Consensus        88 ~~~l~~~~l~~i~~aD~il~VvD~~~~  114 (397)
T 1wxq_A           88 GRGLGNKFLDDLRMASALIHVVDATGK  114 (397)
T ss_dssp             -------CCCSSTTCSEEEEEEETTCC
T ss_pred             hhhHHHHHHHHHhcCCEEEEEEecccc
Confidence            344444443222 79999999999886

>3t5d_A Septin-7; GTP-binding protein, cytoskeleton, signaling protein; HET: GDP; 3.30A {Homo sapiens} PDB: 3tw4_A*

Probab=96.97  E-value=0.00097  Score=40.51  Aligned_cols=43  Identities=14%  Similarity=0.091  Sum_probs=27.7

Q ss_pred             CcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          21 PDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        21 ~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++++.+.++......-..++..+..     ++|+++|+||+|+..
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            6788888876653222222334444432     689999999999853

>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=96.87  E-value=0.0003  Score=45.69  Aligned_cols=48  Identities=19%  Similarity=0.261  Sum_probs=32.9

Q ss_pred             CCcEEEEEEECCCh-hHHHHHH-HHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805          20 HPDVFVIVYSVIER-KTFKKAE-DMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus        20 ~~~~~ilv~d~~~~-~s~~~~~-~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      ++++.+++|.++.. .+|+.+. .|+..+.     .++|+|+|+||+|+...+++
T Consensus       136 d~~~~vlL~ldePt~~~L~~~d~~~lk~L~-----~~v~iIlVinK~Dll~~~ev  185 (418)
T 2qag_C          136 DNRVQCCLYFIAPSGHGLKPLDIEFMKRLH-----EKVNIIPLIAKADTLTPEEC  185 (418)
T ss_dssp             CC-CCEEEEECCC-CCSCCHHHHHHHHHHT-----TTSEEEEEEESTTSSCHHHH
T ss_pred             CCCeeEEEEEecCcccCCCHHHHHHHHHHh-----ccCcEEEEEEcccCccHHHH
Confidence            57777777777765 5677664 5776653     36899999999998654443

>3cnl_A YLQF, putative uncharacterized protein; circular permutation, GNP, signaling protein; HET: GNP; 2.00A {Thermotoga maritima} PDB: 3cnn_A* 3cno_A*

Probab=96.67  E-value=0.00059  Score=41.65  Aligned_cols=40  Identities=18%  Similarity=0.061  Sum_probs=30.3

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|.++.|.|..++.+..+.     .+. .  . +.|.++|.||+||.+
T Consensus        21 ~~D~vl~VvDar~P~~~~~~-----~l~-l--l-~k~~iivlNK~DL~~   60 (262)
T 3cnl_A           21 LVNTVVEVRDARAPFATSAY-----GVD-F--S-RKETIILLNKVDIAD   60 (262)
T ss_dssp             TCSEEEEEEETTSTTTTSCT-----TSC-C--T-TSEEEEEEECGGGSC
T ss_pred             hCCEEEEEeeCCCCCcCcCh-----HHH-h--c-CCCcEEEEECccCCC
Confidence            49999999999998776531     111 1  1 679999999999965

>3vqt_A RF-3, peptide chain release factor 3; translation, GTPase; HET: GDP; 1.80A {Desulfovibrio vulgaris} PDB: 3vr1_A*

Probab=96.54  E-value=0.013  Score=39.29  Aligned_cols=59  Identities=15%  Similarity=0.085  Sum_probs=42.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      -||..|..=...-.+.  +|++|+|.|...----+...-|. ....    .++|++++-||+|...
T Consensus       108 PGHvDF~~Ev~raL~~--~DgAvlVvda~~GV~~qT~~v~~-~a~~----~~lp~i~fINK~Dr~~  166 (548)
T 3vqt_A          108 PGHQDFSEDTYRVLTA--VDSALVVIDAAKGVEAQTRKLMD-VCRM----RATPVMTFVNKMDREA  166 (548)
T ss_dssp             CCGGGCSHHHHHHHHS--CSEEEEEEETTTBSCHHHHHHHH-HHHH----TTCCEEEEEECTTSCC
T ss_pred             CCcHHHHHHHHHHHHh--cCceEEEeecCCCcccccHHHHH-HHHH----hCCceEEEEecccchh
Confidence            3788888777777775  99999999987653333344453 3332    5689999999999864

>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=96.37  E-value=0.0089  Score=38.21  Aligned_cols=45  Identities=22%  Similarity=0.216  Sum_probs=31.9

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |+|.+++|.+..-.-+...+.+++.....    .++|.+||.||+||.+
T Consensus       130 nvD~v~iv~a~~P~~~~~~i~r~L~~a~~----~~~~~iivlNK~DL~~  174 (358)
T 2rcn_A          130 NIDQIVIVSAILPELSLNIIDRYLVGCET----LQVEPLIVLNKIDLLD  174 (358)
T ss_dssp             CCCEEEEEEESTTTCCHHHHHHHHHHHHH----HTCEEEEEEECGGGCC
T ss_pred             cCCEEEEEEeCCCCCCHHHHHHHHHHHHh----cCCCEEEEEECccCCC
Confidence            89999999887533355555666544433    3467899999999964

>4fn5_A EF-G 1, elongation factor G 1; translation, translation-antibiotic compl; HET: 0UO; 2.90A {Pseudomonas aeruginosa}

Probab=96.07  E-value=0.02  Score=39.33  Aligned_cols=59  Identities=17%  Similarity=0.010  Sum_probs=41.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      -||-.|..=...-.+.  +|++|+|.|...==.-+...-|.. ..+    .++|.+++-||.|...
T Consensus        93 PGHvDF~~Ev~~aLr~--~DgavlvVDaveGV~~qT~~v~~~-a~~----~~lp~i~~iNKiDr~~  151 (709)
T 4fn5_A           93 PGHVDFTIEVERSLRV--LDGAVVVFCGTSGVEPQSETVWRQ-ANK----YGVPRIVYVNKMDRQG  151 (709)
T ss_dssp             CSCTTCHHHHHHHHHH--CSEEEEEEETTTCSCHHHHHHHHH-HHH----HTCCEEEEEECSSSTT
T ss_pred             CCCcccHHHHHHHHHH--hCeEEEEEECCCCCchhHHHHHHH-HHH----cCCCeEEEEccccccC
Confidence            3788888777777776  999999999875432222333432 222    4589999999999753

>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=95.96  E-value=0.0054  Score=36.48  Aligned_cols=45  Identities=13%  Similarity=-0.069  Sum_probs=25.4

Q ss_pred             cEEEEEEECCC---hhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          22 DVFVIVYSVIE---RKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        22 ~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +.++++.|.+.   +..+.....+......   ..+.|+++|+||+|+...
T Consensus       139 ~~iv~vvD~~~~~~~~~~~~~~~~~~~~~~---~~~~p~~iv~NK~D~~~~  186 (262)
T 1yrb_A          139 PLVVYISDPEILKKPNDYCFVRFFALLIDL---RLGATTIPALNKVDLLSE  186 (262)
T ss_dssp             CEEEEEECGGGCCSHHHHHHHHHHHHHHHH---HHTSCEEEEECCGGGCCH
T ss_pred             ceEEeccchhhhcCHHHHHHHHHHHHHHhc---ccCCCeEEEEeccccccc
Confidence            67777776543   3344333222211111   135799999999998653

>3j25_A Tetracycline resistance protein TETM; antibiotic resistance, translation; HET: GCP; 7.20A {Enterococcus faecalis}

Probab=95.69  E-value=0.009  Score=40.59  Aligned_cols=59  Identities=15%  Similarity=0.039  Sum_probs=41.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      -||..|..-...-.+.  +|++|+|.|...=-.-+....|. .+..    .++|.+++-||.|...
T Consensus        75 PGH~DF~~Ev~raL~~--~DgavlVVDa~~GV~~qT~~v~~-~a~~----~~lp~i~~INKmDr~~  133 (638)
T 3j25_A           75 PGHMDFLAEVYRSLSV--LDGAILLISAKDGVQAQTRILFH-ALRK----MGIPTIFFINKIDQNG  133 (638)
T ss_dssp             CCSSSTHHHHHHHHTT--CSEEECCEESSCTTCSHHHHHHH-HHHH----HTCSCEECCEECCSSS
T ss_pred             CCcHHHHHHHHHHHHH--hCEEEEEEeCCCCCcHHHHHHHH-HHHH----cCCCeEEEEecccccc
Confidence            4888998877777775  99999999987542222223343 3332    3478899999999754

>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=95.50  E-value=0.02  Score=40.02  Aligned_cols=57  Identities=18%  Similarity=0.130  Sum_probs=36.7

Q ss_pred             cchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           7 CFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         7 ~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+..+...|... .++.+++|.|.+...+-.........+.    ..+.|+++|.||+|+..
T Consensus       175 ~i~~lv~~yi~~-~aDlIL~VVDAs~~~~~~d~l~ll~~L~----~~g~pvIlVlNKiDlv~  231 (772)
T 3zvr_A          175 QIRDMLMQFVTK-ENCLILAVSPANSDLANSDALKIAKEVD----PQGQRTIGVITKLDLMD  231 (772)
T ss_dssp             HHHHHHHHHHTS-TTEEEEEEEETTSCSSSCHHHHHHHHHC----TTCSSEEEEEECTTSSC
T ss_pred             HHHHHHHHHHhc-CCcEEEEEEcCCCCcchhHHHHHHHHHH----hcCCCEEEEEeCcccCC
Confidence            455566666653 5899999999876432222222233332    24689999999999864

>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=94.86  E-value=0.0044  Score=38.35  Aligned_cols=18  Identities=22%  Similarity=0.230  Sum_probs=14.8

Q ss_pred             CCCeEEEEeeCCCCcCCC
Q psy5805          53 GEKAVILVANKADLERRR   70 (75)
Q Consensus        53 ~~~~~ilvgnK~Dl~~~r   70 (75)
                      .++++++|+||.|+...+
T Consensus       154 ~~~~iilV~~K~Dl~~~~  171 (301)
T 2qnr_A          154 NKVNIVPVIAKADTLTLK  171 (301)
T ss_dssp             TTSCEEEEECCGGGSCHH
T ss_pred             hcCCEEEEEEeCCCCCHH
Confidence            568999999999997543

>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=94.61  E-value=0.18  Score=32.28  Aligned_cols=13  Identities=23%  Similarity=0.194  Sum_probs=12.1

Q ss_pred             CCcEEEEEEECCC
Q psy5805          20 HPDVFVIVYSVIE   32 (75)
Q Consensus        20 ~~~~~ilv~d~~~   32 (75)
                      ++|++++|+|.++
T Consensus        96 ~ad~il~VvD~~~  108 (363)
T 1jal_A           96 ETDAIGHVVRCFE  108 (363)
T ss_dssp             TCSEEEEEEECSC
T ss_pred             hcCeEEEEEecCC
Confidence            6999999999986

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=94.33  E-value=0.028  Score=32.42  Aligned_cols=40  Identities=25%  Similarity=0.167  Sum_probs=25.9

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +.+.+++|+|.++...  ....+..   .    .+.|+++|+||+|+..
T Consensus       129 ~~~~~i~vvd~~~~~~--~~~~~~~---~----~~~~~iiv~NK~Dl~~  168 (221)
T 2wsm_A          129 GENYRVVMVSVTEGDD--VVEKHPE---I----FRVADLIVINKVALAE  168 (221)
T ss_dssp             SCSEEEEEEEGGGCTT--HHHHCHH---H----HHTCSEEEEECGGGHH
T ss_pred             ccCcEEEEEeCCCcch--hhhhhhh---h----hhcCCEEEEecccCCc
Confidence            5788999999876532  1111111   1    1368899999999853

>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=93.79  E-value=0.0057  Score=38.55  Aligned_cols=40  Identities=30%  Similarity=0.267  Sum_probs=27.9

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+|++++|+|.+..+.+..+..         ...+.|+++|.||+|+..
T Consensus       192 ~aD~vl~V~d~~~~~~~~~l~~---------~~~~~p~ivVlNK~Dl~~  231 (355)
T 3p32_A          192 MVDTFVLLTLARTGDQLQGIKK---------GVLELADIVVVNKADGEH  231 (355)
T ss_dssp             TCSEEEEEEESSTTCTTTTCCT---------TSGGGCSEEEEECCCGGG
T ss_pred             hCCEEEEEECCCCCccHHHHHH---------hHhhcCCEEEEECCCCcC
Confidence            5999999999876654432221         112458899999999864

>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=93.44  E-value=0.028  Score=35.24  Aligned_cols=40  Identities=23%  Similarity=0.189  Sum_probs=23.7

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+|++++|+|.+..+.+..+..+   .      .+.|.++|.||+|+..
T Consensus       169 ~aD~vl~Vvd~~~~~~~~~l~~~---~------~~~p~ivv~NK~Dl~~  208 (341)
T 2p67_A          169 MVDCFISLQIAGGGDDLQGIKKG---L------MEVADLIVINKDDGDN  208 (341)
T ss_dssp             TCSEEEEEECC------CCCCHH---H------HHHCSEEEECCCCTTC
T ss_pred             hCCEEEEEEeCCccHHHHHHHHh---h------hcccCEEEEECCCCCC
Confidence            59999999998765443221110   0      1357899999999864

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=92.97  E-value=0.084  Score=33.26  Aligned_cols=40  Identities=18%  Similarity=0.222  Sum_probs=23.1

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+|.+++|+|.+.......+..   .+      -..|.++|.||+|+..
T Consensus       187 ~~d~vl~V~d~~~~~~~~~i~~---~i------l~~~~ivVlNK~Dl~~  226 (349)
T 2www_A          187 MVDMFVLLLPPAGGDELQGIKR---GI------IEMADLVAVTKSDGDL  226 (349)
T ss_dssp             TCSEEEEEECCC---------------------CCSCSEEEECCCSGGG
T ss_pred             hCCEEEEEEcCCcchhHHHhHH---HH------HhcCCEEEEeeecCCC
Confidence            5999999999987543322211   11      2357789999999853

>2dby_A GTP-binding protein; GDP, structural genomics, NPPSFA, natio project on protein structural and functional analyses; HET: GDP; 1.76A {Thermus thermophilus} PDB: 2dwq_A

Probab=88.34  E-value=2.7  Score=26.82  Aligned_cols=13  Identities=8%  Similarity=0.028  Sum_probs=12.0

Q ss_pred             CCcEEEEEEECCC
Q psy5805          20 HPDVFVIVYSVIE   32 (75)
Q Consensus        20 ~~~~~ilv~d~~~   32 (75)
                      ++|++++|+|.++
T Consensus        99 ~ad~ii~VvD~~~  111 (368)
T 2dby_A           99 EVAAIAHVLRCFP  111 (368)
T ss_dssp             TCSEEEEEEECCC
T ss_pred             hCCEEEEEEECCC
Confidence            6999999999986

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=86.42  E-value=0.21  Score=28.77  Aligned_cols=13  Identities=46%  Similarity=0.572  Sum_probs=10.8

Q ss_pred             eEEEEeeCCCCcC
Q psy5805          56 AVILVANKADLER   68 (75)
Q Consensus        56 ~~ilvgnK~Dl~~   68 (75)
                      |.++|+||+|+.+
T Consensus       166 ~~iiv~NK~Dl~~  178 (226)
T 2hf9_A          166 ADLIVINKIDLAD  178 (226)
T ss_dssp             CSEEEEECGGGHH
T ss_pred             CCEEEEeccccCc
Confidence            4599999999864

>4a9a_A Ribosome-interacting GTPase 1; DRG-DFRP complex, ribosome binding GTPase; 2.67A {Saccharomyces cerevisiae}

Probab=83.44  E-value=2  Score=27.59  Aligned_cols=45  Identities=13%  Similarity=0.099  Sum_probs=28.9

Q ss_pred             CCcEEEEEEECCChhH-HHHHHHHHHHHHhhc-CCCCCeEEEEeeCCCCc
Q psy5805          20 HPDVFVIVYSVIERKT-FKKAEDMLKTLWDSK-YIGEKAVILVANKADLE   67 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s-~~~~~~~~~~~~~~~-~~~~~~~ilvgnK~Dl~   67 (75)
                      ++|++++|.|.+++-. ++.+.   .++.... ...+.|.+++.||.|..
T Consensus       149 ~ad~il~vvD~~~p~~~~~~i~---~EL~~~~~~l~~k~~~i~~nK~d~~  195 (376)
T 4a9a_A          149 TCNLLFIILDVNKPLHHKQIIE---KELEGVGIRLNKTPPDILIKKKEKG  195 (376)
T ss_dssp             HCSEEEEEEETTSHHHHHHHHH---HHHHHTTEEETCCCCCEEEEECSSS
T ss_pred             hcCccccccccCccHHHHHHHH---HHHHHhhHhhccCChhhhhhHhhhh
Confidence            4999999999998742 22232   2333221 12456778899999964

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	75
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	99.81
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	99.79
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	99.77
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	99.77
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	99.75
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	99.75
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	99.74
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	99.74
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	99.74
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	99.73
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	99.72
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	99.72
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	99.72
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	99.71
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	99.71
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	99.7
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	99.69
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	99.69
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	99.68
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	99.68
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	99.68
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	99.68
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	99.67
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	99.67
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	99.66
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	99.64
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	99.63
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	99.63
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	99.63
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	99.57
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	99.56
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	99.54
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	99.53
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	99.52
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	99.5
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	99.49
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	99.49
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	99.44
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	99.42
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	99.35
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	99.2
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	99.15
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	99.03
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	99.0
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	98.99
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	98.98
d2fh5b1	207	Signal recognition particle receptor beta-subunit	98.94
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	98.74
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	98.62
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	98.59
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	98.58
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	98.41
d1nrjb_	209	Signal recognition particle receptor beta-subunit	98.3
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	98.13
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	97.78
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	97.57
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	97.57
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	97.57
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	97.42
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	97.28
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	97.21
d2qn6a3	205	Initiation factor eIF2 gamma subunit, N-terminal (	97.11
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	97.1
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	97.09
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	97.07
d1d2ea3	196	Elongation factor Tu (EF-Tu), N-terminal (G) domai	96.94
d1jnya3	224	Elongation factor eEF-1alpha, N-terminal (G) domai	96.79
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	96.73
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	96.64
d1kk1a3	195	Initiation factor eIF2 gamma subunit, N-terminal (	96.52
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	96.48
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	96.38
d1zunb3	222	Sulfate adenylate transferase subunit cysN/C, EF-T	96.33
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	96.29
d1f60a3	239	Elongation factor eEF-1alpha, N-terminal (G) domai	95.42
d1r5ba3	245	Eukaryotic peptide chain release factor ERF2, G do	94.15
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	89.14
d2akab1	299	Dynamin G domain {Rat (Rattus norvegicus) [TaxId:	85.78
d1jwyb_	306	Dynamin G domain {Dictyostelium discoideum [TaxId:	82.21

>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=99.81  E-value=4e-20  Score=105.11  Aligned_cols=70  Identities=31%  Similarity=0.420  Sum_probs=55.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +|+|+|+.+++.|++  +++++|+|||++++.||+++..|+.++........+|+++||||+||.+.++|+.
T Consensus        56 ~g~e~~~~~~~~~~~--~~d~~ilv~d~t~~~s~~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~~~v~~  125 (168)
T d2gjsa1          56 WEQDGGRWLPGHCMA--MGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVSV  125 (168)
T ss_dssp             C-------CHHHHHT--SCSEEEEEEETTCHHHHHHHHHHHHHHHHHCC--CCCEEEEEECTTCGGGCCSCH
T ss_pred             ccccccceecccchh--hhhhhceeccccccccccccccccchhhcccccccceEEEeecccchhhhcchhH
Confidence            689999999999999  6999999999999999999999999988765557899999999999988887753

>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=99.79  E-value=1.3e-19  Score=103.19  Aligned_cols=71  Identities=30%  Similarity=0.450  Sum_probs=63.7

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      .+|++.|..+++.|++  +++++++|||+++++||++++.|+.++.+.....++|+++||||+|+...|+|+.
T Consensus        59 ~~g~~~~~~~~~~~~~--~~~~~llv~d~~d~~Sf~~~~~~~~~i~~~~~~~~~p~ilvgnK~Dl~~~~~v~~  129 (169)
T d1x1ra1          59 TAGQEEFSAMREQYMR--TGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTR  129 (169)
T ss_dssp             CCSCGGGCSSHHHHHH--HCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTSSCCCEEEEEECTTCSTTCCSCH
T ss_pred             cccccccccchhhhhh--hccEEEEecccccchhhhccchhhHHHHhhccccCccEEEEecccchhhhceeeh
Confidence            3689999999999999  5999999999999999999999999987765557899999999999998888764

>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=99.77  E-value=4e-19  Score=100.58  Aligned_cols=71  Identities=21%  Similarity=0.294  Sum_probs=63.1

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      .+|++.|..++..+++  +++++|+|||+++++||+.+..|+.++.+.....++|+++||||+||...|+|+.
T Consensus        59 ~~g~~~~~~~~~~~~~--~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~r~v~~  129 (167)
T d1xtqa1          59 TAGQDEYSIFPQTYSI--DINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISY  129 (167)
T ss_dssp             CCCCCTTCCCCGGGTS--SCCEEEEEEETTCHHHHHHHHHHHHHHHHHHCSSCCCEEEEEECTTCGGGCCSCH
T ss_pred             cccccccccccchhhh--hhhhhhhhcccchhhhhhhhhhhhhhhhhcccccccceeeeccccccccccchhH
Confidence            3578899999999999  6999999999999999999999999987765557899999999999988888764

>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=99.77  E-value=2.7e-19  Score=102.01  Aligned_cols=68  Identities=32%  Similarity=0.498  Sum_probs=58.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +|+|+|  +++.|++  +++++|+|||++++.||+++..|..++......+++|+++||||+||.+.|+|+.
T Consensus        64 ~g~e~~--~~~~~~~--~~~~~ilvfd~t~~~s~~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~~~v~~  131 (172)
T d2g3ya1          64 KGENEW--LHDHCMQ--VGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVSV  131 (172)
T ss_dssp             THHHHH--HHHCCCC--CCSEEEEEEETTCHHHHHHHHHHHHHHHTSGGGTTSCEEEEEECTTCGGGCCSCH
T ss_pred             cccccc--ccccccc--ccceeeeeecccccchhhhhhhhhhhhhhccccCCceEEEEeccccccccccccH
Confidence            467777  6677777  6999999999999999999999999887755557899999999999988887753

>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=99.76  E-value=9.5e-19  Score=98.64  Aligned_cols=68  Identities=21%  Similarity=0.283  Sum_probs=58.0

Q ss_pred             cccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           5 TSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         5 ~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      .+.....++.|++  +++++|+|||+++++||+++..|+.++.+....+++|++|||||+||.++++|+.
T Consensus        62 ~~~~~~~~~~~~~--~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~pi~lvgnK~Dl~~~~~v~~  129 (165)
T d1z06a1          62 ERFRKSMVQHYYR--NVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRILVGNKCDLRSAIQVPT  129 (165)
T ss_dssp             HHHHTTTHHHHHT--TCCEEEEEEETTCHHHHHTHHHHHHHHHHHCCCSCCCEEEEEECTTCGGGCCSCH
T ss_pred             hhhccccceeeec--CCCceEEEEEeehhhhhhhhhhhhHHHHhhccCCCCeEEEEeccccchhccchhH
Confidence            3344566778888  6999999999999999999999999988765567899999999999988887764

>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=99.75  E-value=7.7e-19  Score=99.47  Aligned_cols=69  Identities=30%  Similarity=0.460  Sum_probs=61.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|++.|+++++.|++  +++++|+|||++++.||+++..|+..+.+....+++|++|||||+|+..++.++
T Consensus        59 ~g~~~~~~~~~~~~~--~~~~~ilv~d~~~~~sf~~~~~~~~~~~~~~~~~~~p~ilvgnK~Dl~~~~~~~  127 (167)
T d1c1ya_          59 AGTEQFTAMRDLYMK--NGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVG  127 (167)
T ss_dssp             CSSCSSTTHHHHHHH--HCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSCCCEEEEEECTTCGGGCCSC
T ss_pred             cCccccccccccccc--ccceeEEeeeccchhhhHhHHHHHHHHHHhcCCCCCeEEEEEEecCcccccccc
Confidence            688999999999999  599999999999999999999999988775556789999999999998776654

>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=99.75  E-value=1.1e-18  Score=99.12  Aligned_cols=70  Identities=26%  Similarity=0.412  Sum_probs=60.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +|++++..+++.+++  +++++++|||++++.||+++..|+.++.+.....++|+++||||+|+.+.|+|+.
T Consensus        60 ~g~~~~~~~~~~~~~--~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piiivgnK~Dl~~~~~v~~  129 (168)
T d1u8za_          60 AGQEDYAAIRDNYFR--SGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSV  129 (168)
T ss_dssp             CC---CHHHHHHHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHHCCTTSCEEEEEECGGGGGGCCSCH
T ss_pred             ccccchhhhhhhccc--ccceeEEEeeccchhhhhhHHHHHHHHHHhhCCCCCcEEEEeccccccccccccH
Confidence            578899999999999  5999999999999999999999999988765567899999999999988888764

>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=99.74  E-value=7.8e-19  Score=100.81  Aligned_cols=70  Identities=21%  Similarity=0.469  Sum_probs=62.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +|+|.|+.+++.|++  +++++|+|||++++.||+.+..|+.++........+|+++||||+|+.+.|+|+.
T Consensus        72 ~G~e~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~iilv~nK~Dl~~~~~v~~  141 (186)
T d2f7sa1          72 AGQERFRSLTTAFFR--DAMGFLLMFDLTSQQSFLNVRNWMSQLQANAYCENPDIVLIGNKADLPDQREVNE  141 (186)
T ss_dssp             ESHHHHHHHHHHHHT--TCCEEEEEEETTCHHHHHHHHHHHHTCCCCCTTTCCEEEEEEECTTCGGGCCSCH
T ss_pred             CcchhhHHHHHHHHh--cCCEEEEEEeccccccceeeeeccchhhhhccCCCceEEEEeeeccchhhhcchH
Confidence            689999999999999  6999999999999999999999998877655567889999999999988887753

>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=99.74  E-value=1.8e-18  Score=98.58  Aligned_cols=69  Identities=26%  Similarity=0.474  Sum_probs=61.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..+++.|++  +++++++|||++++.||+.+..|+..+.+.....++|++|||||+|+.+.|+++
T Consensus        62 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~p~ilvgnK~Dl~~~~~~~  130 (173)
T d2fn4a1          62 AGQEEFGAMREQYMR--AGHGFLLVFAINDRQSFNEVGKLFTQILRVKDRDDFPVVLVGNKADLESQRQVP  130 (173)
T ss_dssp             CCTTTTSCCHHHHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHHTSSCCCEEEEEECGGGGGGCCSC
T ss_pred             ccccccccccchhhc--cceeeeeecccccccccchhhhhhHHHHHHhccCCCceEEEEEeechhhccccc
Confidence            688999999999999  599999999999999999999999988766556789999999999998877664

>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=99.74  E-value=2.2e-18  Score=97.35  Aligned_cols=69  Identities=19%  Similarity=0.324  Sum_probs=61.8

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      .+|+++|..+++.+++  +++++++|||+++++||+++..|++++....  +++|+++||||+|+.++|+|+.
T Consensus        58 ~~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~--~~~~iilVgnK~Dl~~~~~v~~  126 (164)
T d1z2aa1          58 TAGQEEFDAITKAYYR--GAQACVLVFSTTDRESFEAISSWREKVVAEV--GDIPTALVQNKIDLLDDSCIKN  126 (164)
T ss_dssp             CTTGGGTTCCCHHHHT--TCCEEEEEEETTCHHHHHTHHHHHHHHHHHH--CSCCEEEEEECGGGGGGCSSCH
T ss_pred             cCCccchhhhhhhhhc--cCceEEEEEeccchhhhhhcccccccccccC--CCceEEEeeccCCcccceeeee
Confidence            3688999999999999  6999999999999999999999999988743  6799999999999988887753

>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=99.73  E-value=2.1e-18  Score=97.74  Aligned_cols=71  Identities=20%  Similarity=0.389  Sum_probs=60.6

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhc-CCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSK-YIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      .+|++.|..++..|++  +++++++|||+++++||+++..|+.++.+.. ...++|++|||||+|+...|+|+.
T Consensus        57 ~~g~~~~~~~~~~~~~--~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~piilVgnK~Dl~~~~~v~~  128 (171)
T d2erxa1          57 TTGSHQFPAMQRLSIS--KGHAFILVYSITSRQSLEELKPIYEQICEIKGDVESIPIMLVGNKCDESPSREVQS  128 (171)
T ss_dssp             CCSCSSCHHHHHHHHH--HCSEEEEEEETTCHHHHHTTHHHHHHHHHHHC---CCCEEEEEECGGGGGGCCSCH
T ss_pred             cccccccccccccccc--ceeEEEEEeecccccchhcccchhhhhhhhhccCCCCcEEEEeecccccccccccH
Confidence            3689999999999999  5999999999999999999999998876643 246789999999999988888753

>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=99.72  E-value=4.8e-18  Score=96.05  Aligned_cols=69  Identities=29%  Similarity=0.504  Sum_probs=61.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|++.+..++..|++  +++++++|||+++++||+++..|..++......+++|++|||||+|+...+.+.
T Consensus        59 ~g~~~~~~~~~~~~~--~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilvgnK~Dl~~~~~~~  127 (167)
T d1kaoa_          59 AGTEQFASMRDLYIK--NGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRYEKVPVILVGNKVDLESEREVS  127 (167)
T ss_dssp             CCTTCCHHHHHHHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTTSCCCEEEEEECGGGGGGCCSC
T ss_pred             CCccccccchHHHhh--cccceeeeeeecchhhhhhhhchhhhhhhhccCCCCCEEEEEEccchhhcccch
Confidence            678999999999999  599999999999999999999999888765555789999999999998777654

>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=99.72  E-value=5.5e-18  Score=96.37  Aligned_cols=67  Identities=19%  Similarity=0.328  Sum_probs=59.5

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      .+|++.|+.+++.|++  +++++++|||+++++||+++..|+.++....  +++|+++||||+||...+..
T Consensus        59 ~~g~~~~~~~~~~~~~--~~~~~ilv~d~~~~~Sf~~~~~~~~~~~~~~--~~~piilvgnK~Dl~~~~~~  125 (170)
T d1i2ma_          59 TAGQEKFGGLRDGYYI--QAQCAIIMFDVTSRVTYKNVPNWHRDLVRVC--ENIPIVLCGNKVDIKDRKVK  125 (170)
T ss_dssp             CTTHHHHSSCGGGGTT--TCCEEEEEEETTSGGGGTTHHHHHHHHHHHH--CSCCEEEEEECCCCSCSCCT
T ss_pred             cccccccceecchhcc--cccchhhccccccccccchhHHHHHHHhhcc--CCCceeeecchhhhhhhhhh
Confidence            3688999999999999  6999999999999999999999999887743  68999999999999876543

>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=99.72  E-value=3.6e-18  Score=96.67  Aligned_cols=70  Identities=24%  Similarity=0.398  Sum_probs=55.0

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      .+|+++++.+++.|++  +++++++|||+++++||+++..|+..+.... ....|+++||||+|+..+|+|+.
T Consensus        59 ~~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~Sf~~~~~~~~~~~~~~-~~~~~~ilvgnK~Dl~~~~~v~~  128 (167)
T d1z08a1          59 TAGQERFHALGPIYYR--DSNGAILVYDITDEDSFQKVKNWVKELRKML-GNEICLCIVGNKIDLEKERHVSI  128 (167)
T ss_dssp             CCCC-------CCSST--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHH-GGGSEEEEEEECGGGGGGCCSCH
T ss_pred             cCCcceecccchhhcc--CCceeEEEEeCCchhHHHhhhhhhhhccccc-ccccceeeeccccccccccccch
Confidence            3688999999999999  6999999999999999999999998876643 46789999999999998888753

>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=99.72  E-value=1.7e-17  Score=93.88  Aligned_cols=69  Identities=22%  Similarity=0.341  Sum_probs=61.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +|+++++.+++.|++  +++++++|||+++++||++++.|+.++.... ..+.|+++||||+|+.++|.++.
T Consensus        61 ~g~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~iilvgnK~Dl~~~~~v~~  129 (167)
T d1z0ja1          61 AGLERFRALAPMYYR--GSAAAIIVYDITKEETFSTLKNWVRELRQHG-PPSIVVAIAGNKCDLTDVREVME  129 (167)
T ss_dssp             CCSGGGGGGTHHHHT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHS-CTTSEEEEEEECTTCGGGCCSCH
T ss_pred             CCchhhhHHHHHHHh--hccceEEEeeechhhhhhhHHHhhhhhhhcc-CCcceEEEecccchhccccchhH
Confidence            689999999999999  5999999999999999999999998877654 57899999999999988887753

>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=99.71  E-value=1.6e-17  Score=94.12  Aligned_cols=69  Identities=22%  Similarity=0.394  Sum_probs=62.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +|++.|..+++.|++  +++++++|||+++++||+++..|...+.+.. .+++|+++||||+|+..+|+|+.
T Consensus        63 ~g~~~~~~~~~~~~~--~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~iilvgnK~Dl~~~~~v~~  131 (170)
T d1r2qa_          63 AGQERYHSLAPMYYR--GAQAAIVVYDITNEESFARAKNWVKELQRQA-SPNIVIALSGNKADLANKRAVDF  131 (170)
T ss_dssp             CCSGGGGGGHHHHHT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHS-CTTCEEEEEEECGGGGGGCCSCH
T ss_pred             CCchhhhhhHHHHhh--CcceEEEEeccchhhHHHHHHHHhhhhhhcc-CCCceEEeecccccccccccccH
Confidence            689999999999999  6999999999999999999999998887643 57899999999999998888764

>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=99.71  E-value=1.9e-17  Score=94.40  Aligned_cols=64  Identities=17%  Similarity=0.203  Sum_probs=54.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|++.|+.+++.|++  +++++|+|||+++++||+++..|+....... .+++|++|||||+|+.+.
T Consensus        58 ~g~~~~~~~~~~~~~--~~~~~ilv~d~~~~~Sf~~~~~~~~~~~~~~-~~~~piilvgnK~Dl~~~  121 (177)
T d1kmqa_          58 AGLEDYDRLRPLSYP--DTDVILMCFSIDSPDSLENIPEKWTPEVKHF-CPNVPIILVGNKKDLRND  121 (177)
T ss_dssp             CCSGGGTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH-STTSCEEEEEECGGGTTC
T ss_pred             Cccchhcccchhhcc--cchhhhhhcccchhHHHHHHHHHHHHHHHHh-CCCCceEEeeecccccch
Confidence            689999999999999  6999999999999999999876554444332 478999999999999654

>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=99.70  E-value=3.9e-17  Score=91.92  Aligned_cols=68  Identities=22%  Similarity=0.486  Sum_probs=61.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|++.|..+++.+++  +++++++|||++++.||+++..|+.++.... .+++|+++||||+|+.+.+.++
T Consensus        57 ~g~~~~~~~~~~~~~--~~~~~ilv~d~~~~~s~~~i~~~~~~~~~~~-~~~~~iilvgnK~Dl~~~~~~~  124 (164)
T d1yzqa1          57 AGQERFRSLIPSYIR--DSAAAVVVYDITNVNSFQQTTKWIDDVRTER-GSDVIIMLVGNKTDLADKRQVS  124 (164)
T ss_dssp             CCSGGGGGGHHHHHT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHH-TTSSEEEEEEECTTCGGGCCSC
T ss_pred             CCcchhccchHHHhh--ccceEEEeeccccccchhhhHhhHHHHHHhc-CCCceEEEEecccchhhhhhhh
Confidence            688999999999999  5999999999999999999999998887754 4789999999999998777664

>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=99.69  E-value=4.1e-17  Score=93.74  Aligned_cols=63  Identities=19%  Similarity=0.335  Sum_probs=53.7

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHH-HHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAED-MLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~-~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+|+|+|+.++..|++  +++++++|||+++++||+++.. |...++..  .+++|+++||||+||.+
T Consensus        64 ~~g~e~~~~~~~~~~~--~a~~~ilv~d~t~~~Sf~~~~~~~~~~~~~~--~~~~~~ilvgnK~Dl~~  127 (185)
T d2atxa1          64 TAGQEDYDRLRPLSYP--MTDVFLICFSVVNPASFQNVKEEWVPELKEY--APNVPFLLIGTQIDLRD  127 (185)
T ss_dssp             CCCSSSSTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHHH--STTCCEEEEEECTTSTT
T ss_pred             ccccchhhhhhhhccc--ccceeeeccccchHHHHHHHHHHHHHHHHhc--CCCCCeeEeeecccccc
Confidence            4789999999999999  5999999999999999998865 54555443  47899999999999965

>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=99.69  E-value=3e-17  Score=93.47  Aligned_cols=67  Identities=24%  Similarity=0.385  Sum_probs=60.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|+|+|..++..+++  +++++++|||+++++||..+..|+.++.+.. .+++|+++||||+|+.+.+.+
T Consensus        61 ~g~e~~~~~~~~~~~--~~~~~i~v~d~~~~~S~~~~~~~~~~i~~~~-~~~~piilvgnK~Dl~~~~~~  127 (175)
T d2f9la1          61 AGQERYRRITSAYYR--GAVGALLVYDIAKHLTYENVERWLKELRDHA-DSNIVIMLVGNKSDLRHLRAV  127 (175)
T ss_dssp             SSGGGTTCCCHHHHT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECTTCGGGCCS
T ss_pred             CCcHHHHHHHHHHhh--ccCeEEEEEECCCcccchhHHHHHHHHHHhc-CCCCcEEEEEeeecccccccc
Confidence            689999999999999  5999999999999999999999999988764 478999999999999876554

>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=99.68  E-value=4.6e-17  Score=92.30  Aligned_cols=70  Identities=29%  Similarity=0.479  Sum_probs=58.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +|++.|..+++.+++  +++++++|||+++++||+.+..|+.++.......+.|+++||||+|+..++.++.
T Consensus        61 ~g~~~~~~~~~~~~~--~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilvgnK~Dl~~~~~v~~  130 (171)
T d2erya1          61 AGQEEFGAMREQYMR--TGEGFLLVFSVTDRGSFEEIYKFQRQILRVKDRDEFPMILIGNKADLDHQRQVTQ  130 (171)
T ss_dssp             C----CCHHHHHHHH--HCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTSSCCSEEEEEECTTCTTSCSSCH
T ss_pred             ccccccccccccccc--ccceEEEeeccccccchhhHHHHhHHHHhhcccCCCCEEEEEeccchhhhccchH
Confidence            578899999999999  4999999999999999999999998877665567899999999999988887753

>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=99.68  E-value=3.9e-17  Score=92.58  Aligned_cols=69  Identities=28%  Similarity=0.364  Sum_probs=57.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +|++.|. .+..|++  +++++++|||+++++||+++..|..........+++|+++||||+||..+|+|+.
T Consensus        58 ~g~~~~~-~~~~~~~--~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilvgnK~Dl~~~r~V~~  126 (168)
T d2atva1          58 AGQEDTI-QREGHMR--WGEGFVLVYDITDRGSFEEVLPLKNILDEIKKPKNVTLILVGNKADLDHSRQVST  126 (168)
T ss_dssp             CCCCCCH-HHHHHHH--HCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTTSCCCEEEEEECGGGGGGCCSCH
T ss_pred             ccccccc-cchhhhc--ccccceeecccCCccchhhhhhhcccccccccccCcceeeeccchhhhhhccCcH
Confidence            5777775 4566777  4999999999999999999999877665554567899999999999998888763

>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=99.68  E-value=6.6e-17  Score=91.59  Aligned_cols=68  Identities=19%  Similarity=0.390  Sum_probs=60.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+|+|..+++.|++  +++++|+|||+++++||..+..|+..+... ..++.|+++||||+|+.+.+.|+
T Consensus        62 ~G~e~~~~~~~~~~~--~ad~~ilv~d~~~~~s~~~~~~~~~~~~~~-~~~~~~iivv~nK~D~~~~~~v~  129 (169)
T d3raba_          62 AGQERYRTITTAYYR--GAMGFILMYDITNEESFNAVQDWSTQIKTY-SWDNAQVLLVGNKCDMEDERVVS  129 (169)
T ss_dssp             CCSGGGHHHHHTTTT--TCCEEEEEEETTCHHHHHTHHHHHHHHHHH-CCSCCEEEEEEECTTCGGGCCSC
T ss_pred             CCchhhHHHHHHHHh--cCCEEEEEEECccchhhhhhhhhhhhhhcc-cCCcceEEEEEeecccccccccc
Confidence            689999999999999  699999999999999999999998877664 35789999999999998887765

>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=99.68  E-value=6e-17  Score=91.84  Aligned_cols=68  Identities=19%  Similarity=0.417  Sum_probs=60.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+|.|+.+++.|++  +++++++|||++++.||+.+..|+..+.+.. ...+|+++||||+|+...++++
T Consensus        62 ~G~e~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~~~ilvgnK~D~~~~~~v~  129 (171)
T d2ew1a1          62 AGQERFRSITQSYYR--SANALILTYDITCEESFRCLPEWLREIEQYA-SNKVITVLVGNKIDLAERREVS  129 (171)
T ss_dssp             CCSGGGHHHHGGGST--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECGGGGGGCSSC
T ss_pred             CCchhhHHHHHHHHh--ccceEEEeeecccchhhhhhhhhhhhhcccc-cccccEEEEEeecccccccchh
Confidence            689999999999999  6999999999999999999999998887643 4679999999999998777764

>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=99.67  E-value=7.4e-17  Score=91.07  Aligned_cols=68  Identities=25%  Similarity=0.403  Sum_probs=60.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+|+|+.+++.+++  +++++++|||+++++||+.+..|+..+.+.. ....|++++|||+|+...+.++
T Consensus        61 ~g~~~~~~~~~~~~~--~~d~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~iilvgnK~Dl~~~~~~~  128 (166)
T d1z0fa1          61 AGQERFRAVTRSYYR--GAAGALMVYDITRRSTYNHLSSWLTDARNLT-NPNTVIILIGNKADLEAQRDVT  128 (166)
T ss_dssp             TTGGGTCHHHHHHHH--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECTTCGGGCCSC
T ss_pred             CCchhHHHHHHHHhc--CCcEEEEEeccCchHHHHHHHHHHHHHHhhc-cccceEEEEcccccchhhcccH
Confidence            689999999999999  5999999999999999999999998887653 5788999999999997766654

>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=99.67  E-value=7.8e-17  Score=92.29  Aligned_cols=63  Identities=17%  Similarity=0.254  Sum_probs=53.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.|..+++.+++  +++++++|||+++++||+.+..|+...... ..+++|+++||||+|+..
T Consensus        58 ~g~~~~~~~~~~~~~--~~~~~ilv~d~~~~~Sf~~~~~~~~~~~~~-~~~~~~iilVgnK~Dl~~  120 (179)
T d1m7ba_          58 SGSPYYDNVRPLSYP--DSDAVLICFDISRPETLDSVLKKWKGEIQE-FCPNTKMLLVGCKSDLRT  120 (179)
T ss_dssp             CCSGGGTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHH-HCTTCEEEEEEECGGGGG
T ss_pred             cccccccccccchhh--hhhhhheeeecccCCCHHHHHHHHHHHHhc-cCCcceEEEEEecccccc
Confidence            689999999999999  699999999999999999997655443332 247899999999999864

>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=99.67  E-value=7.1e-17  Score=93.04  Aligned_cols=64  Identities=17%  Similarity=0.279  Sum_probs=54.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+++|+.+++.|++  +++++++|||+++++||+++..|+.+.... ..+++|+++||||+||.+.
T Consensus        59 ~g~~~~~~~~~~~~~--~~~~~ilv~d~~~~~Sf~~~~~~~~~~~~~-~~~~~~i~lvgnK~Dl~~~  122 (191)
T d2ngra_          59 AGQEDYDRLRPLSYP--QTDVFLVCFSVVSPSSFENVKEKWVPEITH-HCPKTPFLLVGTQIDLRDD  122 (191)
T ss_dssp             CCSGGGTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHH-HCTTCCEEEEEECGGGGGC
T ss_pred             ccchhhhhhhhhccc--ccceeecccccchHHHHHHHHHHHHHHHhh-cCCCCceEEEecccccccc
Confidence            689999999999999  699999999999999999997654444333 2478999999999998643

>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=99.67  E-value=6.9e-17  Score=91.81  Aligned_cols=69  Identities=23%  Similarity=0.444  Sum_probs=60.8

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .+|++.|+.+++.+++  +++++++|||+++++||+.+..|+.++.+.. .+++|++|||||+|+...+.+.
T Consensus        59 ~~g~~~~~~~~~~~~~--~~d~~ilv~d~~~~~sf~~~~~~~~~~~~~~-~~~~piilv~nK~D~~~~~~~~  127 (173)
T d2a5ja1          59 TAGQESFRSITRSYYR--GAAGALLVYDITRRETFNHLTSWLEDARQHS-SSNMVIMLIGNKSDLESRRDVK  127 (173)
T ss_dssp             CTTGGGTSCCCHHHHT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECTTCGGGCCSC
T ss_pred             ccCccchhhHHHHHhh--ccCEEEEEEeecChHHHHhHHHHHHHHHHhC-CCCCeEEEEecCCchhhhhhhH
Confidence            3688999999999999  6999999999999999999999998887753 5789999999999998766654

>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=99.66  E-value=7e-17  Score=92.48  Aligned_cols=66  Identities=18%  Similarity=0.281  Sum_probs=55.9

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHH-HHHHHHhhcCCCCCeEEEEeeCCCCcCCCc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAED-MLKTLWDSKYIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~-~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      .+|++.|..+++.|++  +++++++|||+++++||+++.. |...++.  ...++|++|||||+|+.+.+.
T Consensus        60 ~~g~~~~~~~~~~~~~--~~~~~ilv~d~~~~~sf~~i~~~~~~~~~~--~~~~~piilvgnK~Dl~~~~~  126 (183)
T d1mh1a_          60 TAGQEDYDRLRPLSYP--QTDVSLICFSLVSPASFENVRAKWYPEVRH--HCPNTPIILVGTKLDLRDDKD  126 (183)
T ss_dssp             CCCSGGGTTTGGGGCT--TCSEEEEEEETTCHHHHHHHHHTHHHHHHH--HSTTSCEEEEEECHHHHTCHH
T ss_pred             ccccccchhhhhhccc--ccceeeeeeccchHHHHHHHHHHHHHHHHH--hCCCCcEEEEeecccchhhhh
Confidence            4789999999999999  6999999999999999999976 5555554  247899999999999976543

>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=99.64  E-value=4.8e-16  Score=89.76  Aligned_cols=69  Identities=22%  Similarity=0.348  Sum_probs=61.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +|+|+|+.+++.|++  +++++|+|||++++++|..+..|...+.+. ...++|+++||||+|+.+.+.++.
T Consensus        63 ~G~e~~~~~~~~~~~--~a~~~i~v~d~t~~~s~~~~~~~~~~~~~~-~~~~~~iilv~nK~D~~~~~~~~~  131 (194)
T d2bcgy1          63 AGQERFRTITSSYYR--GSHGIIIVYDVTDQESFNGVKMWLQEIDRY-ATSTVLKLLVGNKCDLKDKRVVEY  131 (194)
T ss_dssp             TTTTTTTCCCGGGGT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHH-SCTTCEEEEEEECTTCTTTCCSCH
T ss_pred             CCchhhHHHHHHHhc--cCCEEEEEEeCcchhhhhhHhhhhhhhhhc-ccCCceEEEEEeccccccccchhH
Confidence            789999999999999  699999999999999999999998887764 357899999999999988776653

>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=99.63  E-value=3.5e-16  Score=88.73  Aligned_cols=68  Identities=22%  Similarity=0.348  Sum_probs=60.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+++|..+++.+++  +++++++|||++++++|.++..|...+.... ..++|+++||||+|+...++++
T Consensus        62 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~piivv~nK~D~~~~~~~~  129 (174)
T d2bmea1          62 AGQERFRSVTRSYYR--GAAGALLVYDITSRETYNALTNWLTDARMLA-SQNIVIILCGNKKDLDADREVT  129 (174)
T ss_dssp             CCSGGGHHHHHTTST--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECGGGGGGCCSC
T ss_pred             CCchhhhhhHHHHhh--hCCEEEEEEecccchhHHHHhhhhccccccc-CCceEEEEEEecccccchhchh
Confidence            689999999999999  6999999999999999999999998887754 4789999999999997766654

>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=99.63  E-value=4.2e-16  Score=87.93  Aligned_cols=64  Identities=17%  Similarity=0.340  Sum_probs=58.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.|...++.+++  +++++++|||++++.||+.+..|+..+.+....+++|+++||||+|+..
T Consensus        59 ~~~~~~~~~~~~~~~--~~~~~iiv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~  122 (166)
T d1ctqa_          59 AGQEEYSAMRDQYMR--TGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAA  122 (166)
T ss_dssp             CCCGGGHHHHHHHHH--HCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTCSSCCEEEEEECTTCSC
T ss_pred             cCccccccchhhhhh--cccccceeecccccccHHHHHHHHHHHHHhcCCCCCeEEEEeccccccc
Confidence            578899999999999  5999999999999999999999999988876667899999999999964

>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=99.63  E-value=4e-16  Score=88.39  Aligned_cols=68  Identities=21%  Similarity=0.323  Sum_probs=49.4

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhc---CCCCCeEEEEeeCCCCcCCCc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSK---YIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~---~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      .+|++++..++..|++  +++++++|||++++.||+.+..|+.++....   ...++|+++||||+|+.+.+.
T Consensus        59 ~~g~~~~~~~~~~~~~--~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~piilv~nK~Dl~~~~~  129 (175)
T d1ky3a_          59 TAGQERFQSLGVAFYR--GADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEESKK  129 (175)
T ss_dssp             CC----------CCST--TCCEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSCTTTCCEEEEEECTTSCGGGC
T ss_pred             cCCchhhhhHHHHHhh--ccceEEEEeecccccccchhhhcchhhhhhhhhcccccCcEEEEecccchhhhhc
Confidence            3688999999999999  5999999999999999999999999887543   235789999999999976544

>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=99.61  E-value=8.9e-16  Score=87.12  Aligned_cols=69  Identities=16%  Similarity=0.403  Sum_probs=50.7

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      .+|+|.|..+++.+++  +++++|+|||++++.||+.+..|...+.... ..+.|+++||||+|+...+.+.
T Consensus        62 ~~G~e~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~iilv~~k~D~~~~~~~~  130 (173)
T d2fu5c1          62 TAGQERFRTITTAYYR--GAMGIMLVYDITNEKSFDNIRNWIRNIEEHA-SADVEKMILGNKCDVNDKRQVS  130 (173)
T ss_dssp             C---------CCTTTT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHS-CTTCEEEEEEEC--CCSCCCSC
T ss_pred             CCCchhhHHHHHHhcc--CCCEEEEEEECCChhhHHHHHHHHHHhhhhc-cCCceEEEEEecccchhhcccH
Confidence            3689999999999999  6999999999999999999999998887653 5789999999999998766553

>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=99.57  E-value=3.6e-15  Score=84.27  Aligned_cols=69  Identities=17%  Similarity=0.384  Sum_probs=53.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcccC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH   74 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~~   74 (75)
                      +|+|+|+.+++.+++  +++++++|||+++++||..+..|+..+.... ....|+++||||+|+...+.|+.
T Consensus        64 ~G~e~~~~~~~~~~~--~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~iilv~~k~d~~~~~~v~~  132 (170)
T d2g6ba1          64 AGQERFRSVTHAYYR--DAHALLLLYDVTNKASFDNIQAWLTEIHEYA-QHDVALMLLGNKVDSAHERVVKR  132 (170)
T ss_dssp             CCC--------CCGG--GCSEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECCSTTSCCCSCH
T ss_pred             CCchhhHHHHHHhhc--CCceeEEEecCCcccchhhhhhhhhhhhhcc-CCCceEEEEEeeechhhcccccH
Confidence            689999999999999  5999999999999999999999988776653 46789999999999988877753

>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=99.56  E-value=8.5e-15  Score=82.77  Aligned_cols=67  Identities=19%  Similarity=0.315  Sum_probs=57.7

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      .+|++.|+..++.+++  +++++++|||++++.||..+..|+.++.......++|+++||||+|+.+..
T Consensus        67 ~~g~~~~~~~~~~~~~--~~~~ii~v~d~~d~~s~~~~~~~~~~~~~~~~~~~~pillv~nK~Dl~~~~  133 (176)
T d1fzqa_          67 IGGQRKIRPYWRSYFE--NTDILIYVIDSADRKRFEETGQELTELLEEEKLSCVPVLIFANKQDLLTAA  133 (176)
T ss_dssp             CSSCGGGHHHHHHHHT--TCSEEEEEEETTCGGGHHHHHHHHHHHTTCGGGTTCCEEEEEECTTSTTCC
T ss_pred             ccccccchhHHHHHhh--ccceeEEeeccccccchhhhhhhhhhhhhhhccCCCeEEEEEEeccccccc
Confidence            3688999999999999  599999999999999999998888777655445689999999999997543

>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=99.54  E-value=1.7e-14  Score=81.38  Aligned_cols=63  Identities=24%  Similarity=0.401  Sum_probs=56.0

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++++..+++.+++  +++++++|||++++.||+++..|+.++.... ....|++++|||+|+.+
T Consensus        60 ~g~~~~~~~~~~~~~--~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~~v~nk~d~~~  122 (170)
T d1ek0a_          60 AGQERFASLAPMYYR--NAQAALVVYDVTKPQSFIKARHWVKELHEQA-SKDIIIALVGNKIDMLQ  122 (170)
T ss_dssp             CCSGGGGGGHHHHHT--TCSEEEEEEETTCHHHHHHHHHHHHHHHHHS-CTTCEEEEEEECGGGGG
T ss_pred             CCchhHHHHHHHHHh--ccceEEEEEeCCcccchhhhhhhhhhhcccc-ccccceeeeeccccccc
Confidence            688999999999999  6999999999999999999999988776643 57789999999999854

>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=99.53  E-value=1.4e-14  Score=82.51  Aligned_cols=64  Identities=13%  Similarity=0.218  Sum_probs=52.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.|+.+++.+++  +++++++|||++++.+|..+..|+.+........+.|+++||||+|+.+
T Consensus        69 ~g~~~~~~~~~~~~~--~~~~ii~v~d~~d~~s~~~~~~~l~~~~~~~~~~~~piliv~NK~Dl~~  132 (182)
T d1moza_          69 GGQTSIRPYWRCYYA--DTAAVIFVVDSTDKDRMSTASKELHLMLQEEELQDAALLVFANKQDQPG  132 (182)
T ss_dssp             C----CCTTGGGTTT--TEEEEEEEEETTCTTTHHHHHHHHHHHTTSSTTSSCEEEEEEECTTSTT
T ss_pred             ccccccchhHHhhhc--cceeEEEEeeecccccchhHHHHHHHHHHhhccCCcceEEEEEeecccc
Confidence            688999999999999  6999999999999999999988887765544456899999999999964

>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=99.52  E-value=2.8e-14  Score=80.12  Aligned_cols=65  Identities=15%  Similarity=0.284  Sum_probs=57.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|++.|...+..|+.  +++++++|||++++++|+.+..|+..+.+....+++|+++||||.|+.+.
T Consensus        55 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~pi~lv~nK~Dl~~~  119 (164)
T d1zd9a1          55 GGQPRFRSMWERYCR--GVSAIVYMVDAADQEKIEASKNELHNLLDKPQLQGIPVLVLGNKRDLPGA  119 (164)
T ss_dssp             CCSHHHHTTHHHHHT--TCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCCEEEEEECTTSTTC
T ss_pred             ccccccccccccccc--ccchhhcccccccccccchhhhhhhhhhhhhcccCCcEEEEEeccccchh
Confidence            588999999999998  69999999999999999999988887766555578999999999999653

>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=99.52  E-value=3.5e-14  Score=80.38  Aligned_cols=68  Identities=21%  Similarity=0.324  Sum_probs=56.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhc---CCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSK---YIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~---~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|++.+....+.++.  ++++++++||++++.||+.+..|++++....   ...++|+++||||+|+.+ |+++
T Consensus        63 ~g~~~~~~~~~~~~~--~~~~~i~~~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~piilVgnK~Dl~~-~~v~  133 (174)
T d1wmsa_          63 AGQERFRSLRTPFYR--GSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDISE-RQVS  133 (174)
T ss_dssp             CCCGGGHHHHGGGGT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTCSCTTTSCEEEEEECTTCSS-CSSC
T ss_pred             cCcceehhhhhhhhh--ccceEEEEEeeecccccchhhhHHHHHHHHhccccCCCceEEEeccccchhh-ccCc
Confidence            467777888888888  5999999999999999999999998876542   235789999999999964 5554

>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=99.50  E-value=7.9e-14  Score=78.83  Aligned_cols=65  Identities=15%  Similarity=0.281  Sum_probs=56.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|++.++..+..+++  +++++++|||+++++++..+..|+....+.....+.|+++||||+|+.+.
T Consensus        64 ~g~~~~~~~~~~~~~--~~~~ii~v~D~s~~~~~~~~~~~l~~~~~~~~~~~~piiiv~NK~Dl~~~  128 (173)
T d1e0sa_          64 GGQDKIRPLWRHYYT--GTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDA  128 (173)
T ss_dssp             SCCGGGHHHHGGGTT--TCCEEEEEEETTCGGGHHHHHHHHHHHHTSGGGTTCEEEEEEECTTSTTC
T ss_pred             CCcchhhhHHHhhhc--ccceEEEEEecccchhHHHHHHHHHHHhhhcccccceeeeeeeccccccc
Confidence            688899999999998  59999999999999999999888877665444568999999999999653

>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=99.49  E-value=6.9e-14  Score=78.31  Aligned_cols=68  Identities=16%  Similarity=0.282  Sum_probs=56.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCcc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV   72 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v   72 (75)
                      +|++.|+...+.+++  ++++++++||+++..+|.....|+..........++|+++||||+|+.+.+.+
T Consensus        54 ~G~~~~~~~~~~~~~--~~~~~i~v~d~~d~~~~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~~~~  121 (165)
T d1ksha_          54 GGQKSLRSYWRNYFE--STDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGALSC  121 (165)
T ss_dssp             CCSHHHHTTGGGGCT--TCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTCCCH
T ss_pred             CcchhhhhHHHhhhh--hhhcceeeeecccchhHHHHHHhhhhhhhhcccCCCceEEEEeccccccccCH
Confidence            688999999999998  69999999999999999998776655544334578999999999999765543

>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=99.49  E-value=2.7e-14  Score=81.45  Aligned_cols=65  Identities=26%  Similarity=0.363  Sum_probs=55.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcC---CCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKY---IGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|++.+..+++.++.  ++++++++||++++.+|+.+..|++++.....   ..++|+++||||+||.+.
T Consensus        59 ~g~~~~~~~~~~~~~--~~~~~i~~~d~~~~~~~~~~~~~~~~i~~~~~~~~~~~ip~ilv~nK~Dl~~~  126 (184)
T d1vg8a_          59 AGQERFQSLGVAFYR--GADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENR  126 (184)
T ss_dssp             CSSGGGSCSCCGGGT--TCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSSGGGSCEEEEEECTTSSCC
T ss_pred             CCccccccccccccc--CccEEEEeecccchhhhhcchhhHHHHHHHhccccccCCCEEEEEEeeccccc
Confidence            677888888888888  59999999999999999999999988876432   346899999999999753

>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=99.44  E-value=2.3e-13  Score=77.58  Aligned_cols=59  Identities=20%  Similarity=0.320  Sum_probs=46.7

Q ss_pred             hhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhc--CCCCCeEEEEeeCCCCcC--CCccc
Q psy5805          13 VNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSK--YIGEKAVILVANKADLER--RRQVT   73 (75)
Q Consensus        13 ~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~--~~~~~~~ilvgnK~Dl~~--~r~v~   73 (75)
                      ..|++  ++|++|+|||+++++||+++..|+.++....  ...++|+++||||.|+..  .+.|+
T Consensus        65 ~~~~~--~ad~~ilVfd~~~~~Sf~~~~~~~~~i~~~~~~~~~~~pi~lV~~k~d~d~~~~~~v~  127 (175)
T d2bmja1          65 AKFSG--WADAVIFVFSLEDENSFQAVSRLHGQLSSLRGEGRGGLALALVGTQDRISASSPRVVG  127 (175)
T ss_dssp             HHHHH--HCSEEEEEEETTCHHHHHHHHHHHHHHHHHCC--CCCCEEEEEEECTTCCSSSCCCSC
T ss_pred             ccccc--ccceeEEEeecccchhhhhhHHHHHHHHHHhhcccCCccEEEEeeecCcchhhhcchh
Confidence            34777  5999999999999999999999998876542  236789999999988743  44444

>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=99.42  E-value=4.8e-13  Score=75.83  Aligned_cols=68  Identities=28%  Similarity=0.381  Sum_probs=58.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCCccc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT   73 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r~v~   73 (75)
                      +|+|+++.+++.+++  +++++++|||++++.+|+.+..|+.++.+.......|+++++||.|.. +++|+
T Consensus        64 ~G~~~~~~~~~~~~~--~~~~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~i~~~~nk~d~~-~~~v~  131 (177)
T d1x3sa1          64 AGQERFRTLTPSYYR--GAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKE-NREVD  131 (177)
T ss_dssp             CSSGGGCCSHHHHHT--TCCEEEEEEETTCHHHHHTHHHHHHHHTTCCSCSCCEEEEEEECTTSS-SCCSC
T ss_pred             CCchhhHHHHHHHHh--cCCEEEEEEECCCccccccchhhhhhhcccccccceeeEEEeeccccc-ccccc
Confidence            689999999999999  599999999999999999999999998775545678999999999975 34443

>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=99.35  E-value=1e-12  Score=73.67  Aligned_cols=65  Identities=23%  Similarity=0.456  Sum_probs=56.8

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .+|+|+|+.+++.+++  +++++++|||+++++||+.+..|........ ....|++++++|.|+...
T Consensus        58 t~G~~~~~~~~~~~~~--~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~i~~~~k~d~~~~  122 (166)
T d1g16a_          58 TAGQERFRTITTAYYR--GAMGIILVYDITDERTFTNIKQWFKTVNEHA-NDEAQLLLVGNKSDMETR  122 (166)
T ss_dssp             CTTGGGTSCCCHHHHT--TEEEEEEEEETTCHHHHHTHHHHHHHHHHHS-CTTCEEEEEEECTTCTTC
T ss_pred             CCCchhhHHHHHHHHh--cCCEEEEEEECCCccCHHHHHhhhhhhhccc-cCcceeeeecchhhhhhh
Confidence            3689999999999999  6999999999999999999999887777653 567899999999998653

>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=99.20  E-value=4.4e-12  Score=71.80  Aligned_cols=63  Identities=10%  Similarity=0.094  Sum_probs=50.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHH-----------HHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFK-----------KAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~-----------~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|+++|+++++.|++  +++++++|||+++..+|.           .+..|...+... ...++|++++|||+|+..
T Consensus        50 ~Gq~~~~~~~~~~~~--~~~~~i~v~d~~~~~~~~~~~~~~~~~~e~~~~~~~i~~~~-~~~~~~~~lv~Nk~d~~~  123 (195)
T d1svsa1          50 GGQRSERKKWIHCFE--GVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNK-WFTDTSIILFLNKKDLFE  123 (195)
T ss_dssp             CCSGGGGGGGGGGCT--TCSEEEEEEEGGGGGCBCSSCTTSBHHHHHHHHHHHHHTCG-GGTTSEEEEEEECHHHHH
T ss_pred             ccccccccchhhccc--CCceeeeEEeecccchHHHHhhhhHHHHHHHHHHHHHhccc-ccCCCCEEEEeccchhhh
Confidence            799999999999999  699999999999998873           334455444433 357889999999999743

>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=99.15  E-value=1.8e-10  Score=63.07  Aligned_cols=64  Identities=17%  Similarity=0.283  Sum_probs=55.5

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.++..+..+++  ++++++++||++++.++..+..|..++........+|+++++||.|+.+
T Consensus        52 ~g~~~~~~~~~~~~~--~~~~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~k~d~~~  115 (160)
T d1r8sa_          52 GGQDKIRPLWRHYFQ--NTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPN  115 (160)
T ss_dssp             CCCGGGHHHHHHHTT--TCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTT
T ss_pred             CCcccchhhhhhhhc--cceeEEEEEEecChHHHHHHHHHHHHHHHhhcccCceEEEEeecccccc
Confidence            577888888888888  5999999999999999999988888877655557889999999999875

>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=99.03  E-value=9.5e-11  Score=68.55  Aligned_cols=66  Identities=17%  Similarity=0.324  Sum_probs=48.7

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChh----------HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERK----------TFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~----------s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      +|++.++..+..|+.  +++++++++|+++.+          .+.....++..+.+.....++|++|+|||+||.+++
T Consensus        55 ~Gq~~~r~~w~~~~~--~~~~ii~v~d~s~~~~~~~~~~~~~r~~e~~~~~~~il~~~~~~~~~iil~~NK~Dl~~~k  130 (221)
T d1azta2          55 GGQRDERRKWIQCFN--DVTAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEK  130 (221)
T ss_dssp             CCSTTTTTGGGGGCT--TCSEEEEEEETTGGGCBCTTTSCSBHHHHHHHHHHHHHTCGGGSSCEEEEEEECHHHHHHH
T ss_pred             Cccceeccchhhhcc--cccceEEEEEccccccccccccchHHHHHHHHHHHHHhcChhhCCCcEEEEechhhhhhhh
Confidence            689999999999999  699999999998753          233332333333333345789999999999996544

>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=99.00  E-value=2.4e-10  Score=64.66  Aligned_cols=64  Identities=13%  Similarity=0.068  Sum_probs=53.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChh-----------HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERK-----------TFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~-----------s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      +|+++|+.++..|++  ++++++++||.++..           +++.+..|...+.... ..++|++++|||.|+.+.
T Consensus        53 ~g~~~~~~~~~~~~~--~~~~~i~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~l~~~~-~~~~~~~~v~NK~Dl~~~  127 (200)
T d2bcjq2          53 GGQRSERRKWIHCFE--NVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPW-FQNSSVILFLNKKDLLEE  127 (200)
T ss_dssp             CCSTTGGGGGGGGCS--SCSEEEEEEEGGGGGCBCSSCTTSBHHHHHHHHHHHHHHCGG-GSSSEEEEEEECHHHHHH
T ss_pred             ccccccccccccccc--ccceeeEeeeccchhhhhhhhccccchHHHHHHHHHHHhhhh-ccCccEEEecchhhhhhh
Confidence            689999999999999  699999999998864           5667788887776543 478999999999998543

>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=98.99  E-value=1.5e-10  Score=65.79  Aligned_cols=64  Identities=14%  Similarity=0.193  Sum_probs=43.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhH----------HHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKT----------FKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s----------~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +|++.++..+..+++  ++++++++|+.++..+          ++....|+..+.+.....++|++|+|||+|+.+
T Consensus        52 ~gq~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~piilv~NK~Dl~~  125 (200)
T d1zcba2          52 GGQRSERKRWFECFD--SVTSILFLVSSSEFDQVLMEDRQTNRLTESLNIFETIVNNRVFSNVSIILFLNKTDLLE  125 (200)
T ss_dssp             CC-------CTTSCT--TCCEEEEEEETTCTTCEETTEEEEEHHHHHHHHHHHHHTCGGGTTSEEEEEEECHHHHH
T ss_pred             cceeeeccccccccc--ccceeEEEEEcCCcceeeeecccchhhhHHHHHHHHHhhChhhcCceEEEEeccchhhh
Confidence            689999999999999  6999999999998654          444555555555444457899999999999853

>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=98.98  E-value=1.7e-09  Score=60.28  Aligned_cols=65  Identities=11%  Similarity=0.252  Sum_probs=50.1

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      ++++.++.....++.  +++++++++|.++..++.....+.............|+++||||+|+...
T Consensus        67 ~~~~~~~~~~~~~~~--~~~~~i~v~d~~d~~~~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~  131 (177)
T d1zj6a1          67 GGQESLRSSWNTYYT--NTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKEC  131 (177)
T ss_dssp             CC----CGGGHHHHT--TCCEEEEEEETTCTTTHHHHHHHHHHHHTSGGGTTCEEEEEEECTTSTTC
T ss_pred             ccccccccchhhhhc--cceeeeeecccccccchhhhhhhhhhhhhcccccceEEEEEEEccccccc
Confidence            466777777788887  59999999999999999998777666655444578999999999999653

>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=98.94  E-value=2.5e-09  Score=61.31  Aligned_cols=67  Identities=16%  Similarity=0.239  Sum_probs=46.3

Q ss_pred             cccccch-hhhhhhhhccCCcEEEEEEECCChhHH-HHHHHHHHHH-Hhhc-CCCCCeEEEEeeCCCCcCCCc
Q psy5805           3 SRTSCFT-NLVVNFVQTYHPDVFVIVYSVIERKTF-KKAEDMLKTL-WDSK-YIGEKAVILVANKADLERRRQ   71 (75)
Q Consensus         3 s~~e~f~-~~~~~~~~~~~~~~~ilv~d~~~~~s~-~~~~~~~~~~-~~~~-~~~~~~~ilvgnK~Dl~~~r~   71 (75)
                      +|+++++ .+...|+.  +++++++|+|.++..++ .....|+..+ .... ...++|+++|+||+|+...+.
T Consensus        55 ~g~~~~~~~~~~~~~~--~~~~~i~v~D~~d~~~~~~~~~~~l~~~l~~~~~~~~~~pilvv~NK~Dl~~a~~  125 (207)
T d2fh5b1          55 PGHESLRFQLLDRFKS--SARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMAKS  125 (207)
T ss_dssp             CCCHHHHHHHHHHHGG--GEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHTSTTCCEEEEEEECTTSTTCCC
T ss_pred             cccccccchhhhhhhh--hccccceEEEcccccccHHHHHHHHHHHHHhHHHhhcCCcEEEEEECcccCCCCC
Confidence            4677775 45566666  59999999999998765 4444444433 2222 235689999999999976443

>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=98.74  E-value=6.5e-08  Score=52.40  Aligned_cols=65  Identities=14%  Similarity=0.220  Sum_probs=54.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .++..+....+.++.  .++++++++|.++..++.....|...........+.|+++++||.|+...
T Consensus        52 ~~~~~~~~~~~~~~~--~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~~~k~d~~~~  116 (166)
T d2qtvb1          52 GGHIQARRLWKDYFP--EVNGIVFLVDAADPERFDEARVELDALFNIAELKDVPFVILGNKIDAPNA  116 (166)
T ss_dssp             CCSGGGGGGGGGGCT--TCSEEEEEEETTCGGGHHHHHHHHHHHHTCTTTTTCCEEEEEECTTSSSC
T ss_pred             ccchhhhhhHhhhhh--heeeeeeeccccchhhhhhhhHHHHhhhhhhccCCceEEEEecccccccc
Confidence            355677778888888  59999999999999999999888777776555678899999999998653

>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=98.62  E-value=2.8e-08  Score=55.64  Aligned_cols=46  Identities=24%  Similarity=0.294  Sum_probs=33.8

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++|++++|+|.++..+... ..|...++..  ..+.|+++|+||+|+..
T Consensus        84 ~ad~il~v~D~~~~~~~~~-~~i~~~l~~~--~~~~piilv~NK~Dl~~  129 (178)
T d1wf3a1          84 DVNAVVWVVDLRHPPTPED-ELVARALKPL--VGKVPILLVGNKLDAAK  129 (178)
T ss_dssp             SCSEEEEEEETTSCCCHHH-HHHHHHHGGG--TTTSCEEEEEECGGGCS
T ss_pred             cccceeeeechhhhhcccc-cchhhheecc--ccchhhhhhhccccccc
Confidence            6999999999987654332 3444555542  35789999999999864

>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=98.59  E-value=1.1e-08  Score=56.26  Aligned_cols=52  Identities=15%  Similarity=0.142  Sum_probs=42.2

Q ss_pred             hhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          14 NFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        14 ~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .++.  +++++++++|.++..+++....|...+...  ..+.|+++|+||+||..+
T Consensus        76 ~~~~--~~d~~i~~~d~~~~~~~~~~~~~~~~~~~~--~~~~~iilv~NK~Dl~~~  127 (161)
T d2gj8a1          76 QEIE--QADRVLFMVDGTTTDAVDPAEIWPEFIARL--PAKLPITVVRNKADITGE  127 (161)
T ss_dssp             HHHH--TCSEEEEEEETTTCCCCSHHHHCHHHHHHS--CTTCCEEEEEECHHHHCC
T ss_pred             HHHH--hccccceeeccccccchhhhhhhhhhhhhc--ccccceeeccchhhhhhh
Confidence            3445  699999999999999988888887666653  367899999999998654

>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=98.58  E-value=2.7e-07  Score=50.22  Aligned_cols=66  Identities=14%  Similarity=0.242  Sum_probs=51.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRR   70 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~r   70 (75)
                      ++++.+......++.  ..+++++++|+++..++.....+.............|+++++||.|+....
T Consensus        57 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iv~nk~Dl~~~~  122 (169)
T d1upta_          57 GGLTSIRPYWRCYYS--NTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAM  122 (169)
T ss_dssp             CCCGGGGGGGGGGCT--TCSEEEEEEETTCCTTHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTCC
T ss_pred             cccccccccchhhhh--hhhhhhhhhhhhhcchhhhccchhhhhhhhhccccceEEEEEeeccccccc
Confidence            456677777777777  599999999999999999887765555443345778999999999997543

>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=1.2e-06  Score=48.20  Aligned_cols=63  Identities=13%  Similarity=0.226  Sum_probs=46.9

Q ss_pred             ccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           4 RTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         4 ~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +++.+......+++  ..+++++++|+++..++.....+...........++|+++++||.|+..
T Consensus        66 ~~~~~~~~~~~~~~--~~~~~~~~~d~~d~~~~~~~~~~~~~~~~~~~~~~~~~li~~~K~D~~~  128 (186)
T d1f6ba_          66 GHIQARRVWKNYLP--AINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPE  128 (186)
T ss_dssp             C----CCGGGGGGG--GCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTSCEEEEEECTTSTT
T ss_pred             chhhhhhHHhhhhc--ccceeeeeeeccCccchHHHHHHHHHhhcccccCCCceEEEEeccCccc
Confidence            45566667777777  4999999999999999998876555554433457899999999999864

>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=98.30  E-value=1.1e-06  Score=49.64  Aligned_cols=67  Identities=10%  Similarity=0.208  Sum_probs=44.1

Q ss_pred             cccccchhhhhhhhhcc--CCcEEEEEEECC-ChhHHHHHHHHHHHHH---hhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTY--HPDVFVIVYSVI-ERKTFKKAEDMLKTLW---DSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~--~~~~~ilv~d~~-~~~s~~~~~~~~~~~~---~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .|++.++.....++...  ..+.++++.|.. +..+++.+..|+.++.   ......++|+++|+||+|+...
T Consensus        54 ~g~~~~~~~~~~~~~~~~~~~~~~i~~vd~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~piiiv~NK~D~~~~  126 (209)
T d1nrjb_          54 PGHVKLRYKLSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTA  126 (209)
T ss_dssp             CCCGGGTHHHHHHHHHHGGGEEEEEEEEETTSCTTCCHHHHHHHHHHHHHHHHHSTTCCCEEEEEECTTSTTC
T ss_pred             ccccchhhHHHHHHHHHhhhccccceEEEEecccccHHHHHHHHHHHHHHHHHHHhccCCeEEEEEeeccccc
Confidence            36676666655554331  357778777755 5677777777764432   1223578999999999999654

>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=98.13  E-value=4.3e-06  Score=48.50  Aligned_cols=60  Identities=18%  Similarity=0.144  Sum_probs=41.2

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .||+.|...+.....  .+|++|+|.|..+--.-.....| ..+..    .++|+++|.||+|+...
T Consensus        78 PGh~~f~~~~~~~~~--~~D~~ilVvda~~g~~~~~~~~~-~~~~~----~~~p~iivlNK~D~~~~  137 (227)
T d1g7sa4          78 PGHEAFTTLRKRGGA--LADLAILIVDINEGFKPQTQEAL-NILRM----YRTPFVVAANKIDRIHG  137 (227)
T ss_dssp             CTTSCCTTSBCSSSB--SCSEEEEEEETTTCCCHHHHHHH-HHHHH----TTCCEEEEEECGGGSTT
T ss_pred             cceecccccchhccc--ccceEEEEEecccCcccchhHHH-HHhhc----CCCeEEEEEECccCCCc
Confidence            578888777776666  59999999998764222222222 22332    45799999999998653

>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=97.78  E-value=2.7e-05  Score=43.29  Aligned_cols=59  Identities=22%  Similarity=0.158  Sum_probs=40.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .|++.|...+.....  .+|++++++|.++....+....| ..+..    .++|+++|.||+|+..
T Consensus        67 ~g~~~~~~~~~~~l~--~~d~~ilv~d~~~g~~~~~~~~~-~~~~~----~~~p~iiv~NKiD~~~  125 (179)
T d1wb1a4          67 PGHADLIRAVVSAAD--IIDLALIVVDAKEGPKTQTGEHM-LILDH----FNIPIIVVITKSDNAG  125 (179)
T ss_dssp             SSHHHHHHHHHHHTT--SCCEEEEEEETTTCSCHHHHHHH-HHHHH----TTCCBCEEEECTTSSC
T ss_pred             ccccccccchhhhhh--hccccccccccccccchhhhhhh-hhhhh----cCCcceeccccccccC
Confidence            467777777777776  49999999999875433322222 22222    4579999999999864

>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=97.57  E-value=0.0001  Score=40.27  Aligned_cols=43  Identities=28%  Similarity=0.242  Sum_probs=30.3

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      .+|+++++.+.+...+... ..|...++.    .++|+++|+||+|+.
T Consensus        80 ~ad~i~~~~~~~~~~~~~~-~~~~~~l~~----~~~pviiv~NK~Dl~  122 (171)
T d1mkya1          80 EADLVLFVVDGKRGITKED-ESLADFLRK----STVDTILVANKAENL  122 (171)
T ss_dssp             TCSEEEEEEETTTCCCHHH-HHHHHHHHH----HTCCEEEEEESCCSH
T ss_pred             cCcEEEEeecccccccccc-ccccccccc----ccccccccchhhhhh
Confidence            5999999999776544432 344444543    346999999999985

>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=97.57  E-value=5.5e-05  Score=41.74  Aligned_cols=48  Identities=17%  Similarity=0.241  Sum_probs=32.3

Q ss_pred             CCcEEEEEEECCCh--hHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIER--KTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~--~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .++.+++++|....  .++.....|+......  ..+.|+++|+||+|+...
T Consensus        79 ~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~--~~~~p~iiv~NK~D~~~~  128 (180)
T d1udxa2          79 RTRVLLYVLDAADEPLKTLETLRKEVGAYDPA--LLRRPSLVALNKVDLLEE  128 (180)
T ss_dssp             SSSEEEEEEETTSCHHHHHHHHHHHHHHHCHH--HHHSCEEEEEECCTTSCH
T ss_pred             hhhhhhhhcccccccccchhhhhhhhhccccc--cchhhhhhhhhhhhhhhH
Confidence            58999999997654  3444445555443321  135799999999999653

>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=97.57  E-value=5.8e-05  Score=42.15  Aligned_cols=45  Identities=20%  Similarity=0.120  Sum_probs=29.8

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      ++++++++.|.+..-.- .-..++..++.    .++|+++|+||+|+...
T Consensus       105 ~~~~vi~viD~~~~~~~-~~~~~~~~l~~----~~~piivv~NK~D~~~~  149 (195)
T d1svia_         105 ELKAVVQIVDLRHAPSN-DDVQMYEFLKY----YGIPVIVIATKADKIPK  149 (195)
T ss_dssp             TEEEEEEEEETTSCCCH-HHHHHHHHHHH----TTCCEEEEEECGGGSCG
T ss_pred             chhhhhhhhhccccccc-ccccccccccc----ccCcceechhhccccCH
Confidence            67999999998754321 11233344443    45799999999998543

>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=97.42  E-value=0.00034  Score=38.43  Aligned_cols=45  Identities=29%  Similarity=0.315  Sum_probs=30.8

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      ++|++++++|.+.... .....+...+..    .+.|+++|+||+|+...
T Consensus        91 ~~dvii~v~d~~~~~~-~~~~~~~~~~~~----~~~~~i~v~nK~D~~~~  135 (186)
T d1mkya2          91 KADVVVIVLDATQGIT-RQDQRMAGLMER----RGRASVVVFNKWDLVVH  135 (186)
T ss_dssp             HCSEEEEEEETTTCCC-HHHHHHHHHHHH----TTCEEEEEEECGGGSTT
T ss_pred             cCCEEEEeecccccch-hhHHHHHHHHHH----cCCceeeeccchhhhcc
Confidence            5999999999975432 222334444443    45799999999998543

>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=97.28  E-value=0.00042  Score=39.41  Aligned_cols=59  Identities=14%  Similarity=0.143  Sum_probs=39.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      -||+.|..-.-.-.+.  +|++|+|.|.++--.-+..+.|. .+..    .++| ++++-||.|+.+
T Consensus        75 PGh~df~~~~~~~~~~--aD~avlVvda~~Gv~~qt~~~~~-~~~~----~gi~~iiv~iNK~D~~~  134 (204)
T d2c78a3          75 PGHADYIKNMITGAAQ--MDGAILVVSAADGPMPQTREHIL-LARQ----VGVPYIVVFMNKVDMVD  134 (204)
T ss_dssp             CCSGGGHHHHHHHHTT--CSSEEEEEETTTCCCHHHHHHHH-HHHH----TTCCCEEEEEECGGGCC
T ss_pred             CCchhhHHHHHHHHHH--CCEEEEEEECCCCCcHHHHHHHH-HHHH----cCCCeEEEEEEecccCC
Confidence            4788887655555553  99999999997654444444453 3332    3455 677789999854

>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=97.21  E-value=0.00023  Score=38.93  Aligned_cols=45  Identities=22%  Similarity=0.176  Sum_probs=29.6

Q ss_pred             CCcEEEEEEECCChhHHHHHHH----------HHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAED----------MLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~----------~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      ++++++++.|.+..........          ....+..    .+.|+++|+||+|+..
T Consensus        81 ~~d~~~~vvD~~~~~~~~~~~~~~~~~~~d~~~~~~l~~----~~~p~iiv~NK~D~~~  135 (184)
T d2cxxa1          81 NIDVAVLVVDGKAAPEIIKRWEKRGEIPIDVEFYQFLRE----LDIPTIVAVNKLDKIK  135 (184)
T ss_dssp             GCCEEEEEEETTHHHHHHHHHHHTTCCCHHHHHHHHHHH----TTCCEEEEEECGGGCS
T ss_pred             ccchheeeeeccccchhhhhhhhccccHHHHHHHHHHHH----cCCCEEEEEeeeehhh
Confidence            5999999999876544333211          1122222    4689999999999754

>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=97.11  E-value=0.00055  Score=38.63  Aligned_cols=61  Identities=20%  Similarity=0.175  Sum_probs=36.9

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      -||+.|...+..-..  .+|++|+|.|..+.-.-...+.-+..+..   .+-.|+|++.||+|+.+
T Consensus        94 PGH~df~~~~~~~~~--~ad~ailvVda~~gi~~~~t~e~~~~~~~---~~i~~iIV~vNK~Dl~~  154 (205)
T d2qn6a3          94 PGHEVLMATMLSGAA--LMDGAILVVAANEPFPQPQTREHFVALGI---IGVKNLIIVQNKVDVVS  154 (205)
T ss_dssp             SCHHHHHHHHHHTSS--CCSEEEEEEETTSCSSCHHHHHHHHHHHH---TTCCCEEEEEECGGGSC
T ss_pred             chHHHHHhhhhccee--ccccccccccccccccchhHHHHHHHHHH---cCCceeeeccccCCCcc
Confidence            367777655555555  49999999998764111122211122222   23348899999999964

>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=97.10  E-value=0.001  Score=38.78  Aligned_cols=45  Identities=20%  Similarity=0.250  Sum_probs=36.2

Q ss_pred             CCcEEEEEEECCChh-HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERK-TFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |.|.+++|.+..+++ ++..+.+++-....    .+++.+||.||+||.+
T Consensus        10 NiD~~~iV~s~~~P~~~~~~idR~Lv~a~~----~~i~pvIvlnK~DL~~   55 (231)
T d1t9ha2          10 NVDQAVLVFSAVQPSFSTALLDRFLVLVEA----NDIQPIICITKMDLIE   55 (231)
T ss_dssp             CCCEEEEEEESTTTTCCHHHHHHHHHHHHT----TTCEEEEEEECGGGCC
T ss_pred             ccCEEEEEEECCCCCCCHHHHHHHHHHHHH----cCCCEEEEEecccccc
Confidence            789999999998764 66777887665543    6789999999999964

>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=97.09  E-value=0.00072  Score=39.35  Aligned_cols=45  Identities=22%  Similarity=0.220  Sum_probs=36.3

Q ss_pred             CCcEEEEEEECCChh-HHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERK-TFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      |.|.+++|+++.+|+ +...+.+|+-....    .+++.+||-||+||.+
T Consensus        10 NiD~vliV~s~~~P~~~~~~ldR~Lv~a~~----~~i~pvIvlnK~DL~~   55 (225)
T d1u0la2          10 NVDQVILVVTVKMPETSTYIIDKFLVLAEK----NELETVMVINKMDLYD   55 (225)
T ss_dssp             SCCEEEEEECSSTTCCCHHHHHHHHHHHHH----TTCEEEEEECCGGGCC
T ss_pred             cCCEEEEEEeCCCCCCCHHHHHHHHHHHHH----cCCCEEEEEeCcccCC
Confidence            789999999998864 66677788766654    5689999999999964

>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=97.07  E-value=0.00069  Score=41.56  Aligned_cols=57  Identities=19%  Similarity=0.181  Sum_probs=43.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADL   66 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl   66 (75)
                      -||..|..-...-.+.  +|++++|.|..+--.....+.|.....     .++|++++-||.|.
T Consensus       104 PGh~dF~~ev~~al~~--~D~allVVda~eGv~~qT~~~~~~a~~-----~~~p~i~viNKiDr  160 (341)
T d1n0ua2         104 PGHVDFSSEVTAALRV--TDGALVVVDTIEGVCVQTETVLRQALG-----ERIKPVVVINKVDR  160 (341)
T ss_dssp             CCCCSSCHHHHHHHHT--CSEEEEEEETTTBSCHHHHHHHHHHHH-----TTCEEEEEEECHHH
T ss_pred             CCcHHHHHHHHHHHhh--cCceEEEEecccCcchhHHHHHHHHHH-----cCCCeEEEEECccc
Confidence            4788888777777774  999999999987655555555543322     45899999999996

>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=96.94  E-value=0.0016  Score=36.83  Aligned_cols=60  Identities=17%  Similarity=0.202  Sum_probs=38.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      -||+.|......-.+.  +|++++|.|..+--. .+.+..+..+..   ....|+|++-||.|+..
T Consensus        74 PGh~~f~~~~~~~~~~--aD~allVVda~~G~~-~QT~~~~~~a~~---~~~~~iIv~iNK~D~~~  133 (196)
T d1d2ea3          74 PGHADYVKNMITGTAP--LDGCILVVAANDGPM-PQTREHLLLARQ---IGVEHVVVYVNKADAVQ  133 (196)
T ss_dssp             SSHHHHHHHHHHTSSC--CSEEEEEEETTTCSC-HHHHHHHHHHHH---TTCCCEEEEEECGGGCS
T ss_pred             cchHHHHHHHHHHHhh--cCeEEEEEEcCCCCc-hhHHHHHHHHHH---hcCCcEEEEEecccccc
Confidence            4788886655555553  999999999986321 222222223332   23457899999999854

>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=96.79  E-value=0.0007  Score=38.81  Aligned_cols=61  Identities=16%  Similarity=0.226  Sum_probs=38.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChh---HH---HHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERK---TF---KKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~---s~---~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      -||+.|...+..-.+.  +|++++|.|..+--   ++   .+...-+...+.   .+-.++|++-||.|+..
T Consensus        89 PGH~df~~~~~~g~~~--~D~allVVda~~G~~~~t~~~~~qt~e~l~~~~~---~~~~~iIv~iNK~D~~~  155 (224)
T d1jnya3          89 PGHRDFVKNMITGASQ--ADAAILVVSAKKGEYEAGMSVEGQTREHIILAKT---MGLDQLIVAVNKMDLTE  155 (224)
T ss_dssp             SSSTTHHHHHHHTSSC--CSEEEEEEECSTTHHHHHHSTTCHHHHHHHHHHH---TTCTTCEEEEECGGGSS
T ss_pred             CCcHHHHHHHHHHHHh--hceEEEEEecccCcccccccccchhHHHHHHHHH---hCCCceEEEEEcccCCC
Confidence            4899998777777774  99999999998631   11   112111111121   23346788999999863

>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=96.73  E-value=0.003  Score=37.38  Aligned_cols=58  Identities=10%  Similarity=0.005  Sum_probs=42.6

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCc
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE   67 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~   67 (75)
                      -||..|..-...-.+.  +|++++|.|..+--.-...+.|. .+.+    .++|.+++.||.|..
T Consensus        75 PGh~dF~~e~~~al~~--~D~avlvvda~~Gv~~~t~~~~~-~~~~----~~~p~~i~iNk~D~~  132 (267)
T d2dy1a2          75 PGYGDFVGEIRGALEA--ADAALVAVSAEAGVQVGTERAWT-VAER----LGLPRMVVVTKLDKG  132 (267)
T ss_dssp             CCSGGGHHHHHHHHHH--CSEEEEEEETTTCSCHHHHHHHH-HHHH----TTCCEEEEEECGGGC
T ss_pred             Cchhhhhhhhhhhhcc--cCceEEEeeccCCccchhHHHHH-hhhh----ccccccccccccccc
Confidence            3788887777777775  99999999998665555555553 3332    458999999999963

>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=96.64  E-value=0.0014  Score=35.90  Aligned_cols=49  Identities=24%  Similarity=0.259  Sum_probs=28.5

Q ss_pred             CcEEEEEEECCChhHHHHHHHHH--HHHHhh--cCCCCCeEEEEeeCCCCcCC
Q psy5805          21 PDVFVIVYSVIERKTFKKAEDML--KTLWDS--KYIGEKAVILVANKADLERR   69 (75)
Q Consensus        21 ~~~~ilv~d~~~~~s~~~~~~~~--~~~~~~--~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      ++.++.+.+............+.  ......  ....+.|+++|+||+|+.+.
T Consensus        80 ~~~i~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kp~ivv~NK~Dl~~~  132 (185)
T d1lnza2          80 TRVIVHVIDMSGLEGRDPYDDYLTINQELSEYNLRLTERPQIIVANKMDMPEA  132 (185)
T ss_dssp             CCEEEEEEESSCSSCCCHHHHHHHHHHHHHHSCSSTTTSCBCBEEECTTSTTH
T ss_pred             hhhhhheeeecccccchhhhhhhhhhhccchhhhhccCCcchhhccccchHhH
Confidence            78888777766554333322211  111111  12346899999999999653

>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=96.52  E-value=0.0024  Score=35.53  Aligned_cols=62  Identities=18%  Similarity=0.184  Sum_probs=38.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      -||+.|......-..  .+|+++++.|..+.-.-.....-+..+...   ...+++++-||.|+.+.
T Consensus        86 PGh~~f~~~~~~~~~--~~d~~ilvvda~~g~~~~~t~e~~~~~~~~---~~~~iiv~inK~D~~d~  147 (195)
T d1kk1a3          86 PGHEALMTTMLAGAS--LMDGAILVIAANEPCPRPQTREHLMALQII---GQKNIIIAQNKIELVDK  147 (195)
T ss_dssp             SSHHHHHHHHHHCGG--GCSEEEEEEETTSCSSCHHHHHHHHHHHHH---TCCCEEEEEECGGGSCH
T ss_pred             chhhhhhHHhhcccc--cccccccccchhhhhhhhhhHHHHHHHHHh---cCccceeeeecccchhh
Confidence            477888766666566  399999999988642222222222233321   23457889999998653

>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=96.48  E-value=0.0062  Score=36.19  Aligned_cols=59  Identities=17%  Similarity=0.002  Sum_probs=43.4

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      -||..|..-...-.+.  +|++|+|.|..+----...+-|. ...    ..++|.+++.||.|...
T Consensus        79 PG~~dF~~e~~~~l~~--~D~avlVvda~~Gv~~~T~~~w~-~a~----~~~lP~i~fINKmDr~~  137 (276)
T d2bv3a2          79 PGHVDFTIEVERSMRV--LDGAIVVFDSSQGVEPQSETVWR-QAE----KYKVPRIAFANKMDKTG  137 (276)
T ss_dssp             CSSSSCSTTHHHHHHH--CCEEEEEEETTTSSCHHHHHHHH-HHH----TTTCCEEEEEECTTSTT
T ss_pred             CchhhhHHHHHHHHHh--hhheEEeccccCCcchhHHHHHH-HHH----HcCCCEEEEEecccccc
Confidence            3788887766666664  99999999988765545455552 233    25799999999999864

>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=96.38  E-value=0.0085  Score=31.65  Aligned_cols=43  Identities=19%  Similarity=0.255  Sum_probs=31.7

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      ++|++++|+|.+++.+.....-+. .      ....+++++.||.|+.+.
T Consensus        80 ~ad~ii~v~d~~~~~~~~~~~~~~-~------~~~~~~i~~~~k~d~~~~  122 (160)
T d1xzpa2          80 KADIVLFVLDASSPLDEEDRKILE-R------IKNKRYLVVINKVDVVEK  122 (160)
T ss_dssp             HCSEEEEEEETTSCCCHHHHHHHH-H------HTTSSEEEEEEECSSCCC
T ss_pred             hCCEEEEEEeCCCCcchhhhhhhh-h------cccccceeeeeeccccch
Confidence            599999999999887765443321 1      144688999999999754

>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=96.33  E-value=0.014  Score=33.34  Aligned_cols=60  Identities=13%  Similarity=0.044  Sum_probs=37.7

Q ss_pred             CcccccchhhhhhhhhccCCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           2 ASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         2 ~s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      +.||+.|......-...  +|++++|.|...--.=+..+.|. .+..    .+++ ++++-||.|+.+
T Consensus        96 ~PGH~dfv~~~~~g~~~--aD~ailVvda~~G~~~Qt~e~~~-~~~~----~gv~~iiv~vNK~D~~~  156 (222)
T d1zunb3          96 TPGHEQYTRNMATGAST--CDLAIILVDARYGVQTQTRRHSY-IASL----LGIKHIVVAINKMDLNG  156 (222)
T ss_dssp             CCCSGGGHHHHHHHHTT--CSEEEEEEETTTCSCHHHHHHHH-HHHH----TTCCEEEEEEECTTTTT
T ss_pred             ccchhhhhhhhcccccc--CceEEEEeccccCcccchHHHHH-HHHH----cCCCEEEEEEEcccccc
Confidence            36899996555554553  99999999987542222222221 2222    3444 788999999965

>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=96.29  E-value=0.0028  Score=37.24  Aligned_cols=42  Identities=19%  Similarity=0.207  Sum_probs=30.3

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      .+|.++.|.|.-++-|..+  ..++++.     .+.|+++|.||+||..
T Consensus        15 ~~DvIl~V~DaR~P~ss~~--~~l~~~~-----~~Kp~IlVlNK~DLv~   56 (273)
T d1puja_          15 LIDIVYELVDARIPMSSRN--PMIEDIL-----KNKPRIMLLNKADKAD   56 (273)
T ss_dssp             GCSEEEEEEETTSTTTTSC--HHHHHHC-----SSSCEEEEEECGGGSC
T ss_pred             hCCEEEEEEECCCCCCCCC--HHHHHHH-----cCCCeEEEEECccCCc
Confidence            3999999999988866543  1222221     3569999999999964

>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=95.42  E-value=0.0066  Score=35.16  Aligned_cols=59  Identities=14%  Similarity=0.126  Sum_probs=36.8

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCChh---HH----HHHHHHHHHHHhhcCCCCCe-EEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIERK---TF----KKAEDMLKTLWDSKYIGEKA-VILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~~---s~----~~~~~~~~~~~~~~~~~~~~-~ilvgnK~Dl~~   68 (75)
                      -||+.|......-.+.  +|++|+|.|.+.-.   .+    +..+.|. ....    -++| +|++-||.|+.+
T Consensus        92 PGH~df~~~~~~g~~~--~D~ailvvda~~G~~e~g~~~~~QT~eh~~-~~~~----~gv~~iiv~iNKmD~~~  158 (239)
T d1f60a3          92 PGHRDFIKNMITGTSQ--ADCAILIIAGGVGEFEAGISKDGQTREHAL-LAFT----LGVRQLIVAVNKMDSVK  158 (239)
T ss_dssp             CCCTTHHHHHHHSSSC--CSEEEEEEECSHHHHHHHTCTTSHHHHHHH-HHHH----TTCCEEEEEEECGGGGT
T ss_pred             CCcHHHHHHHHHHHHH--hCEEEEEEECCCCccccccCchHhHHHHHH-HHHH----cCCCeEEEEEECCCCCC
Confidence            4888887665555553  99999999987421   11    1223332 2222    2354 788999999865

>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=94.15  E-value=0.02  Score=33.07  Aligned_cols=60  Identities=17%  Similarity=0.170  Sum_probs=28.3

Q ss_pred             cccccchhhhhhhhhccCCcEEEEEEECCCh---hHHH---HHHHHHHHHHhhcCCCCC-eEEEEeeCCCCcC
Q psy5805           3 SRTSCFTNLVVNFVQTYHPDVFVIVYSVIER---KTFK---KAEDMLKTLWDSKYIGEK-AVILVANKADLER   68 (75)
Q Consensus         3 s~~e~f~~~~~~~~~~~~~~~~ilv~d~~~~---~s~~---~~~~~~~~~~~~~~~~~~-~~ilvgnK~Dl~~   68 (75)
                      -||+.|....-.-...  +|++++|.|...-   .++.   +...-+..+..    .++ +++++-||.|+..
T Consensus       110 PGH~df~~~~~~g~~~--aD~ailVVda~~G~~~~~~~~~~QT~e~l~l~~~----~~i~~iiv~iNKmD~~~  176 (245)
T d1r5ba3         110 PGHKGYVTNMINGASQ--ADIGVLVISARRGEFEAGFERGGQTREHAVLART----QGINHLVVVINKMDEPS  176 (245)
T ss_dssp             CC-----------TTS--CSEEEEEEECSTTHHHHTTSTTCCHHHHHHHHHH----TTCSSEEEEEECTTSTT
T ss_pred             cccccchhhhhhhhhh--hcceeeEEEcCCCccCCccccccchHHHHHHHHH----cCCCeEEEEEEcCCCCc
Confidence            4788886655555553  9999999999752   1111   11111122222    234 4788899999853

>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=89.14  E-value=0.3  Score=25.68  Aligned_cols=44  Identities=25%  Similarity=0.340  Sum_probs=25.4

Q ss_pred             CCcEEEEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805          20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus        20 ~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      .++.++++.|..+..  .....+...+..    ...|.++|.||.|+...
T Consensus        85 ~~~~~l~~~d~~~~~--~~~~~~~~~l~~----~~~~~i~v~~k~d~~~~  128 (179)
T d1egaa1          85 DVELVIFVVEGTRWT--PDDEMVLNKLRE----GKAPVILAVNKVDNVQE  128 (179)
T ss_dssp             CEEEEEEEEETTCCC--HHHHHHHHHHHS----SSSCEEEEEESTTTCCC
T ss_pred             hcceeEEEEecCccc--hhHHHHHHHhhh----ccCceeeeeeeeeccch
Confidence            456666676665432  222333333332    45678889999987543

>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=85.78  E-value=0.96  Score=25.89  Aligned_cols=55  Identities=18%  Similarity=0.177  Sum_probs=34.0

Q ss_pred             hhhhhhhhhccCCcEE-EEEEECCChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcCC
Q psy5805           9 TNLVVNFVQTYHPDVF-VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR   69 (75)
Q Consensus         9 ~~~~~~~~~~~~~~~~-ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~   69 (75)
                      ..+...|..  +.+.+ ++|.+.+..-+-..+..|.+.+.    ....++++|-||+|+..+
T Consensus       152 ~~~~~~y~~--~~~~~il~v~~a~~~~~~~~~~~~~~~~~----~~~~r~i~Vltk~D~~~~  207 (299)
T d2akab1         152 RDMLMQFVT--KENCLILAVSPANSDLANSDALKIAKEVD----PQGQRTIGVITKLDLMDE  207 (299)
T ss_dssp             HHHHHHHHT--STTEEEEEEEESSSCGGGCHHHHHHHHHC----TTCSSEEEEEECGGGSCT
T ss_pred             HHHHHHHhc--CccceeeeecccccchhhhHHHHHHHHhC----cCCCceeeEEeccccccc
Confidence            355666766  36654 45666655545445555655543    244578899999998653

>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=82.21  E-value=1.4  Score=25.31  Aligned_cols=55  Identities=16%  Similarity=0.190  Sum_probs=32.5

Q ss_pred             chhhhhhhhhccCCcEEEEEEEC-CChhHHHHHHHHHHHHHhhcCCCCCeEEEEeeCCCCcC
Q psy5805           8 FTNLVVNFVQTYHPDVFVIVYSV-IERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLER   68 (75)
Q Consensus         8 f~~~~~~~~~~~~~~~~ilv~d~-~~~~s~~~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~   68 (75)
                      +..+...|..  +++++++++.- +..-.-.....+.+.+.    .....+++|.||+|...
T Consensus       157 ~~~~~~~yi~--~~~~~il~v~~~~~~~~~~~~~~~~~~~~----~~~~r~i~Vitk~D~~~  212 (306)
T d1jwyb_         157 IRRMVMAYIK--KQNAIIVAVTPANTDLANSDALQLAKEVD----PEGKRTIGVITKLDLMD  212 (306)
T ss_dssp             HHHHHHHHHH--STTEEEEEEEESSSCSTTCSHHHHHHHHC----SSCSSEEEEEECTTSSC
T ss_pred             HHHHHHHHHh--CCCceeEEeecccccccccHHHHHHHHhC----cCCCeEEEEEecccccc
Confidence            4466777777  59988877632 22211122233433332    24458999999999853