Citrus Sinensis ID: 030407

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------18
Protein Sequence
MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIVS
Secondary Structure (PSIPRED)
cHHHHHHHHccccEEEEEcccccHHHHHHHHHccccccccEEEEEccccccccccccccccHHHHHHHHccccccEEEEEcccccEEEccccccccEEEEEEEccccccccccccccccEEcEEEEEcccccccccccHHHHHHHHHHHcccccEEEEEccccccHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHccEEEEEcccccHHHHHHHHHcccccHHHEEEEcccccccHHHHHHHHHHHHHHHHHHHHccccEEEEEcccccccccccHHHHcEEEEEEEccccccccccccccccHccEEEEEccccccHccccHHHHHHHHHHHcccccEEEEcccccccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MLALCKFLRDKyslaavtndiftkedgeflmrngalpeeriravetggcphaairedisinlgpleelsnlFKADLLLcesggdnlaaNFSRELADYIIYIIDVsggdkiprkggpgitqadlLVINKTDLASAIGADLAVMERDalrmrdggpfifAQVGWVIGIIFTLSITHYIVS
Flexible Loop (DISEMBL)
MLALCKFlrdkyslaavtndiftkedgefLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIVS
Low Complexity Region (SEG)
MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIVS
Disordered region (IsUnstruct)
**ALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV*
Disordered Region (DISOPRED)
MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIVS
Disordered Region (DISEMBL)
MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIVS
Disordered Region (DISPRO)
MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIVS
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHi
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIVS
Positional Conservation
no confident homologs detected

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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	178	2.2.26 [Sep-21-2011]
A7HHN3	236	Urease accessory protein	yes	no	0.932	0.703	0.722	3e-67
Q96WV0	286	Uncharacterized urease ac	yes	no	0.882	0.548	0.719	2e-63
A9GP90	302	Urease accessory protein	yes	no	0.932	0.549	0.704	9e-63
Q11VN1	244	Urease accessory protein	yes	no	0.932	0.680	0.664	1e-58
Q8DMQ4	200	Urease accessory protein	yes	no	0.921	0.82	0.618	3e-55
B1M3X4	205	Urease accessory protein	yes	no	0.898	0.780	0.645	5e-55
B8IJ81	204	Urease accessory protein	yes	no	0.898	0.784	0.658	6e-55
B0UBI3	204	Urease accessory protein	yes	no	0.898	0.784	0.652	1e-54
Q0I662	200	Urease accessory protein	yes	no	0.887	0.79	0.654	2e-54
B1ZHN6	204	Urease accessory protein	yes	no	0.898	0.784	0.633	4e-54

>sp|A7HHN3|UREG_ANADF Urease accessory protein UreG OS=Anaeromyxobacter sp. (strain Fw109-5) GN=ureG PE=3 SV=1

 Score =  254 bits (648), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 120/166 (72%), Positives = 140/166 (84%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           +LALC+ LRD  SL  VTNDIFT+ED EFL+RN ALP ERIRAVETGGCPHAAIRED++ 
Sbjct: 52  VLALCRALRDSRSLGVVTNDIFTREDAEFLVRNDALPAERIRAVETGGCPHAAIREDVTA 111

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
           NL  LEEL+   + ++L CESGGDNLAA+FSRELADY IY+IDV+GGDK+PRKGGPGITQ
Sbjct: 112 NLLALEELTEAHRPEILFCESGGDNLAAHFSRELADYTIYVIDVAGGDKVPRKGGPGITQ 171

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           ADLLV+NKTDLA+A+GADL VM RDA RMR  GP +FAQV   +G+
Sbjct: 172 ADLLVVNKTDLATAVGADLDVMARDAARMRGDGPVVFAQVTRGVGV 217

Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.
Anaeromyxobacter sp. (strain Fw109-5) (taxid: 404589)

>sp|Q96WV0|UREG_SCHPO Uncharacterized urease accessory protein ureG-like OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCPB16A4.05c PE=3 SV=1

 Score =  241 bits (615), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 113/157 (71%), Positives = 137/157 (87%)

Query: 10  DKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELS 69
           +KYS+  VTNDIFT+ED EFL+RN ALPEERIRA+ETGGCPHAAIRED+S NL  LEEL 
Sbjct: 112 EKYSIGVVTNDIFTREDQEFLIRNKALPEERIRAIETGGCPHAAIREDVSGNLVALEELQ 171

Query: 70  NLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKT 129
           + F  +LLL ESGGDNLAAN+SR+LAD+IIY+IDVSGGDKIPRKGGPGIT++DLL+INKT
Sbjct: 172 SEFNTELLLVESGGDNLAANYSRDLADFIIYVIDVSGGDKIPRKGGPGITESDLLIINKT 231

Query: 130 DLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           DLA  +GADL+VM+RDA ++R+ GP +FAQV   +G+
Sbjct: 232 DLAKLVGADLSVMDRDAKKIRENGPIVFAQVKNQVGM 268

Probably facilitates nickel incorporation.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|A9GP90|UREG_SORC5 Urease accessory protein UreG OS=Sorangium cellulosum (strain So ce56) GN=ureG PE=3 SV=1

 Score =  239 bits (609), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 117/166 (70%), Positives = 133/166 (80%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           +LALC+ LRD+  L  VTNDIFT+ED EFL RN ALP ERIRAVETGGCPHAAIREDIS 
Sbjct: 115 VLALCRALRDRMPLGVVTNDIFTQEDAEFLHRNKALPPERIRAVETGGCPHAAIREDISH 174

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
           NL  L++L +     LL+ ESGGDNLAA +SREL DY IY+IDV+GGDK+PRKGGPGITQ
Sbjct: 175 NLVALDDLMDHVAPALLIVESGGDNLAAQYSRELVDYTIYVIDVAGGDKVPRKGGPGITQ 234

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           +DLLVINKTDLA  +GADL VMERDA RMR  GPF+FAQ     G+
Sbjct: 235 SDLLVINKTDLAPHVGADLGVMERDARRMRGDGPFLFAQCNRSQGV 280

Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.

Sorangium cellulosum (strain So ce56) (taxid: 448385)

>sp|Q11VN1|UREG_CYTH3 Urease accessory protein UreG OS=Cytophaga hutchinsonii (strain ATCC 33406 / NCIMB 9469) GN=ureG PE=3 SV=1

 Score =  225 bits (574), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 111/167 (66%), Positives = 132/167 (79%), Gaps = 1/167 (0%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           ++ +CK LRDK ++A VTNDIFT ED EFL+RN AL ++RI  VETGGCPHAAIRED+S 
Sbjct: 52  LMQICKALRDKMNIAVVTNDIFTSEDAEFLIRNEALSKDRIIGVETGGCPHAAIREDVSQ 111

Query: 61  NLGPLEELSNLFK-ADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGIT 119
           N+  LEEL   F   +LL  ESGGDNLAA+FS+EL DY +Y+IDVSGGDKIPRKGGPGIT
Sbjct: 112 NMYALEELMKRFPDVELLFVESGGDNLAAHFSKELVDYSVYVIDVSGGDKIPRKGGPGIT 171

Query: 120 QADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           QADLLVINK DLA  + ADL+VMERD+ +MR  GPF+FA+     GI
Sbjct: 172 QADLLVINKIDLAHLVNADLSVMERDSKKMRGDGPFLFARAKDCFGI 218

Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.

Cytophaga hutchinsonii (strain ATCC 33406 / NCIMB 9469) (taxid: 269798)

>sp|Q8DMQ4|UREG_THEEB Urease accessory protein UreG OS=Thermosynechococcus elongatus (strain BP-1) GN=ureG PE=3 SV=1

 Score =  214 bits (544), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 102/165 (61%), Positives = 126/165 (76%), Gaps = 1/165 (0%)

Query: 3   ALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINL 62
           ALCK LRD+Y LA VTNDI+T+ED +FL+R+ ALP ERI  VETGGCPH AIRED S+NL
Sbjct: 23  ALCKALRDRYRLAVVTNDIYTQEDAQFLVRSQALPPERILGVETGGCPHTAIREDASLNL 82

Query: 63  GPLEELSNLFKA-DLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQA 121
             +++L   F+  DL+  ESGGDNLAA FS EL D  IY+IDV+ GDKIPRKGGPGIT++
Sbjct: 83  AAIQQLETAFRPLDLIFVESGGDNLAATFSPELVDLTIYVIDVAAGDKIPRKGGPGITKS 142

Query: 122 DLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           DLLVINK DLA  +GADL VM+RD L+MR   P++   +   +G+
Sbjct: 143 DLLVINKIDLAPYVGADLEVMKRDTLKMRGDRPYVMTNLKTGLGL 187

Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.

Thermosynechococcus elongatus (strain BP-1) (taxid: 197221)

>sp|B1M3X4|UREG1_METRJ Urease accessory protein UreG 1 OS=Methylobacterium radiotolerans (strain ATCC 27329 / DSM 1819 / JCM 2831) GN=ureG1 PE=3 SV=1

 Score =  213 bits (542), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 104/161 (64%), Positives = 124/161 (77%), Gaps = 1/161 (0%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           M  LCK  RD+Y + A+TNDI+TKED   L   GALPEERI  VETGGCPH AIRED SI
Sbjct: 24  MEQLCKRFRDRYEICAITNDIYTKEDARILTVAGALPEERILGVETGGCPHTAIREDASI 83

Query: 61  NLGPLEELSNLF-KADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGIT 119
           NL  + E+S  F K DL+L ESGGDNLAA FS ELAD  +Y+IDV+GG+KIPRKGGPGIT
Sbjct: 84  NLAAVAEMSRRFPKLDLVLIESGGDNLAATFSPELADITLYVIDVAGGEKIPRKGGPGIT 143

Query: 120 QADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQV 160
           ++DLL++NKTDLA  +GADL+VME D  RMR   P++FA +
Sbjct: 144 RSDLLIVNKTDLAPLVGADLSVMESDTQRMRGTRPYVFASL 184

Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.

Methylobacterium radiotolerans (strain ATCC 27329 / DSM 1819 / JCM 2831) (taxid: 426355)

>sp|B8IJ81|UREG_METNO Urease accessory protein UreG OS=Methylobacterium nodulans (strain ORS2060 / LMG 21967) GN=ureG PE=3 SV=1

 Score =  213 bits (542), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 106/161 (65%), Positives = 122/161 (75%), Gaps = 1/161 (0%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           M  LCK LR +Y L A+TNDI+TKED   L   GALPEERI  VETGGCPH AIRED SI
Sbjct: 25  MEGLCKALRARYDLCAITNDIYTKEDARLLTVAGALPEERIMGVETGGCPHTAIREDASI 84

Query: 61  NLGPLEELSNLFKA-DLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGIT 119
           NL  + E+   F A DL+L ESGGDNLAA FS ELAD  +Y+IDV+GG+KIPRKGGPGIT
Sbjct: 85  NLAAVAEMRRRFPALDLILIESGGDNLAATFSPELADLTLYVIDVAGGEKIPRKGGPGIT 144

Query: 120 QADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQV 160
           ++DLLVINKTDLA  +GADLAVME D  RMR   P++F  +
Sbjct: 145 RSDLLVINKTDLAPLVGADLAVMEADTRRMRGSRPYVFTSL 185

Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.

Methylobacterium nodulans (strain ORS2060 / LMG 21967) (taxid: 460265)

>sp|B0UBI3|UREG_METS4 Urease accessory protein UreG OS=Methylobacterium sp. (strain 4-46) GN=ureG PE=3 SV=1

 Score =  212 bits (539), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 105/161 (65%), Positives = 123/161 (76%), Gaps = 1/161 (0%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           M  LCK LR ++ L A+TNDI+TKED   L   GALPEERI  VETGGCPH AIRED SI
Sbjct: 25  MEGLCKALRGRFDLCAITNDIYTKEDARLLTVAGALPEERIMGVETGGCPHTAIREDASI 84

Query: 61  NLGPLEELSNLFKA-DLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGIT 119
           NL  + E+   F + DL+L ESGGDNLAA FS ELAD  +Y+IDV+GG+KIPRKGGPGIT
Sbjct: 85  NLAAVAEMRRRFPSLDLILIESGGDNLAATFSPELADLTLYVIDVAGGEKIPRKGGPGIT 144

Query: 120 QADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQV 160
           ++DLLVINKTDLA  +GADLAVME D  RMR G P++F  +
Sbjct: 145 RSDLLVINKTDLAPLVGADLAVMEADTQRMRGGRPYVFTSL 185

Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.

Methylobacterium sp. (strain 4-46) (taxid: 426117)

>sp|Q0I662|UREG_SYNS3 Urease accessory protein UreG OS=Synechococcus sp. (strain CC9311) GN=ureG PE=3 SV=1

 Score =  211 bits (537), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 104/159 (65%), Positives = 123/159 (77%), Gaps = 1/159 (0%)

Query: 3   ALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINL 62
           ALC+ LRD+  LA VTNDI+T+ED +FL R+GAL  ERIR VETGGCPH AIRED SIN 
Sbjct: 23  ALCRRLRDRLQLAVVTNDIYTQEDAQFLTRSGALEPERIRGVETGGCPHTAIREDCSINR 82

Query: 63  GPLEELSNLFKA-DLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQA 121
             + EL + F   DL++ ESGGDNLAA+FS EL D  IY+IDV+ GDKIPRKGGPGIT++
Sbjct: 83  AAVSELEHQFPGLDLVMVESGGDNLAASFSPELVDLCIYVIDVAAGDKIPRKGGPGITRS 142

Query: 122 DLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQV 160
           DLLVINK DLAS +GADL VME+D LRMR   P+ F  +
Sbjct: 143 DLLVINKIDLASFVGADLGVMEQDTLRMRRNRPWCFTNL 181

Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.

Synechococcus sp. (strain CC9311) (taxid: 64471)

>sp|B1ZHN6|UREG1_METPB Urease accessory protein UreG 1 OS=Methylobacterium populi (strain ATCC BAA-705 / NCIMB 13946 / BJ001) GN=ureG1 PE=3 SV=1

 Score =  210 bits (534), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 102/161 (63%), Positives = 123/161 (76%), Gaps = 1/161 (0%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           M  LC+  RD+Y + A+TNDI+TKED   L   GALPEERI  VETGGCPH AIRED SI
Sbjct: 24  MEQLCRRFRDRYEICAITNDIYTKEDARILTVAGALPEERILGVETGGCPHTAIREDASI 83

Query: 61  NLGPLEELSNLF-KADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGIT 119
           NL  + E+   F K DL+L ESGGDNLAA FS ELAD  +Y+IDV+GG+KIPRKGGPGIT
Sbjct: 84  NLAAVAEMRRRFPKLDLVLIESGGDNLAATFSPELADITLYVIDVAGGEKIPRKGGPGIT 143

Query: 120 QADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQV 160
           ++DLL++NKTDLA  +GADL+VME D  RMR   P++FA +
Sbjct: 144 RSDLLIVNKTDLAPLVGADLSVMESDTQRMRGTRPYVFASL 184

Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.

Methylobacterium populi (strain ATCC BAA-705 / NCIMB 13946 / BJ001) (taxid: 441620)

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	178
222143562	279	urease accessory protein ureG [Morus alb	0.932	0.594	0.933	1e-84
297826907	278	predicted protein [Arabidopsis lyrata su	0.932	0.597	0.921	3e-84
222424894	191	AT2G34470 [Arabidopsis thaliana]	0.932	0.869	0.915	4e-84
79324312	276	urease accessory protein [Arabidopsis th	0.932	0.601	0.915	5e-84
15226754	275	urease accessory protein [Arabidopsis th	0.932	0.603	0.915	5e-84
255557339	275	Urease accessory protein ureG, putative	0.932	0.603	0.909	1e-83
224069802	280	predicted protein [Populus trichocarpa]	0.932	0.592	0.921	2e-83
242088853	276	hypothetical protein SORBIDRAFT_09g02862	0.932	0.601	0.915	2e-83
449500609	287	PREDICTED: uncharacterized urease access	0.932	0.578	0.903	3e-83
449459358	277	PREDICTED: uncharacterized urease access	0.932	0.599	0.903	3e-83

>gi|222143562|dbj|BAH19310.1| urease accessory protein ureG [Morus alba]

 Score =  317 bits (812), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 155/166 (93%), Positives = 161/166 (96%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           MLALCKFLRDKYSLAAVTNDIFTKEDGEFL++NGALPEERIRAVETGGCPHAAIREDISI
Sbjct: 94  MLALCKFLRDKYSLAAVTNDIFTKEDGEFLVKNGALPEERIRAVETGGCPHAAIREDISI 153

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
           NLGPLEELSNLFKAD+LLCESGGDNLAANFSRELADYIIYIIDVS GDKIPRKGGPGITQ
Sbjct: 154 NLGPLEELSNLFKADILLCESGGDNLAANFSRELADYIIYIIDVSAGDKIPRKGGPGITQ 213

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           ADLLVINKTDLA A+GADLAVMERDALRMRDGGPF+FAQV   +GI
Sbjct: 214 ADLLVINKTDLAPAVGADLAVMERDALRMRDGGPFVFAQVKHGVGI 259

Source: Morus alba

Species: Morus alba

Genus: Morus

Family: Moraceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297826907|ref|XP_002881336.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297327175|gb|EFH57595.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  316 bits (809), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 153/166 (92%), Positives = 162/166 (97%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           MLALC+FLRDKYSLAAVTNDIFTKEDGEFL++NGALPEERIRAVETGGCPHAAIREDISI
Sbjct: 93  MLALCRFLRDKYSLAAVTNDIFTKEDGEFLVKNGALPEERIRAVETGGCPHAAIREDISI 152

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
           NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVS GDKIPRKGGPGITQ
Sbjct: 153 NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSAGDKIPRKGGPGITQ 212

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           ADLLVINKTDLA+A+GADL+VMERDALRMRDGGPF+FAQV   +G+
Sbjct: 213 ADLLVINKTDLAAAVGADLSVMERDALRMRDGGPFVFAQVKHGLGV 258

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222424894|dbj|BAH20398.1| AT2G34470 [Arabidopsis thaliana]

 Score =  315 bits (808), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 152/166 (91%), Positives = 162/166 (97%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           MLALC+FLRDKYSLAAVTNDIFTKEDGEFL++NGALPEERIRAVETGGCPHAAIREDISI
Sbjct: 6   MLALCRFLRDKYSLAAVTNDIFTKEDGEFLVKNGALPEERIRAVETGGCPHAAIREDISI 65

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
           NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVS GDKIPRKGGPGITQ
Sbjct: 66  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSAGDKIPRKGGPGITQ 125

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           ADLLVINKTDLA+A+GADL+VMERD+LRMRDGGPF+FAQV   +G+
Sbjct: 126 ADLLVINKTDLAAAVGADLSVMERDSLRMRDGGPFVFAQVKHGLGV 171

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79324312|ref|NP_001031481.1| urease accessory protein [Arabidopsis thaliana] gi|330253885|gb|AEC08979.1| urease accessory protein [Arabidopsis thaliana]

 Score =  315 bits (806), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 152/166 (91%), Positives = 162/166 (97%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           MLALC+FLRDKYSLAAVTNDIFTKEDGEFL++NGALPEERIRAVETGGCPHAAIREDISI
Sbjct: 91  MLALCRFLRDKYSLAAVTNDIFTKEDGEFLVKNGALPEERIRAVETGGCPHAAIREDISI 150

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
           NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVS GDKIPRKGGPGITQ
Sbjct: 151 NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSAGDKIPRKGGPGITQ 210

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           ADLLVINKTDLA+A+GADL+VMERD+LRMRDGGPF+FAQV   +G+
Sbjct: 211 ADLLVINKTDLAAAVGADLSVMERDSLRMRDGGPFVFAQVKHGLGV 256

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15226754|ref|NP_180994.1| urease accessory protein [Arabidopsis thaliana] gi|3128220|gb|AAC26700.1| putative urease accessory protein [Arabidopsis thaliana] gi|20197163|gb|AAM14950.1| putative urease accessory protein [Arabidopsis thaliana] gi|21553947|gb|AAM63028.1| putative urease accessory protein [Arabidopsis thaliana] gi|26453270|dbj|BAC43708.1| putative urease accessory protein [Arabidopsis thaliana] gi|28950833|gb|AAO63340.1| At2g34470 [Arabidopsis thaliana] gi|330253884|gb|AEC08978.1| urease accessory protein [Arabidopsis thaliana]

 Score =  315 bits (806), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 152/166 (91%), Positives = 162/166 (97%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           MLALC+FLRDKYSLAAVTNDIFTKEDGEFL++NGALPEERIRAVETGGCPHAAIREDISI
Sbjct: 90  MLALCRFLRDKYSLAAVTNDIFTKEDGEFLVKNGALPEERIRAVETGGCPHAAIREDISI 149

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
           NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVS GDKIPRKGGPGITQ
Sbjct: 150 NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSAGDKIPRKGGPGITQ 209

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           ADLLVINKTDLA+A+GADL+VMERD+LRMRDGGPF+FAQV   +G+
Sbjct: 210 ADLLVINKTDLAAAVGADLSVMERDSLRMRDGGPFVFAQVKHGLGV 255

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255557339|ref|XP_002519700.1| Urease accessory protein ureG, putative [Ricinus communis] gi|223541117|gb|EEF42673.1| Urease accessory protein ureG, putative [Ricinus communis]

 Score =  314 bits (804), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 151/166 (90%), Positives = 160/166 (96%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           MLA+CKFLRDKYSLAAVTNDIFTKEDGEFL++NGALPEERIRAVETGGCPHAAIREDISI
Sbjct: 90  MLAICKFLRDKYSLAAVTNDIFTKEDGEFLIKNGALPEERIRAVETGGCPHAAIREDISI 149

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
           NLGPLEELS LFK D+LLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ
Sbjct: 150 NLGPLEELSKLFKTDILLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 209

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           ADLLVINKTDLASA+GADL VMERDA+RMRDGGPF+FAQV   +G+
Sbjct: 210 ADLLVINKTDLASAVGADLTVMERDAVRMRDGGPFVFAQVKHGVGV 255

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224069802|ref|XP_002303043.1| predicted protein [Populus trichocarpa] gi|222844769|gb|EEE82316.1| predicted protein [Populus trichocarpa]

 Score =  313 bits (801), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 153/166 (92%), Positives = 160/166 (96%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           ML+LCK LRDKYSLAAVTNDIFTKEDGEFL+++GALPEERIRAVETGGCPHAAIREDISI
Sbjct: 95  MLSLCKLLRDKYSLAAVTNDIFTKEDGEFLIKHGALPEERIRAVETGGCPHAAIREDISI 154

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
           NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ
Sbjct: 155 NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 214

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           ADLLVINKTDLA A+GADL VMERDALRMRDGGPF+FAQV   +GI
Sbjct: 215 ADLLVINKTDLAPAVGADLVVMERDALRMRDGGPFVFAQVKHGLGI 260

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242088853|ref|XP_002440259.1| hypothetical protein SORBIDRAFT_09g028620 [Sorghum bicolor] gi|241945544|gb|EES18689.1| hypothetical protein SORBIDRAFT_09g028620 [Sorghum bicolor]

 Score =  313 bits (801), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 152/166 (91%), Positives = 162/166 (97%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           MLALC+FLRDKYSLAAVTNDIFTKEDGEFL+++GALPEERIRAVETGGCPHAAIREDISI
Sbjct: 91  MLALCRFLRDKYSLAAVTNDIFTKEDGEFLIKHGALPEERIRAVETGGCPHAAIREDISI 150

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
           NLGPLEELSNL+KADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ
Sbjct: 151 NLGPLEELSNLYKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 210

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           ADLLVINKTDLA A+GADLAVMERDALRMR+GGPF+FAQV   +G+
Sbjct: 211 ADLLVINKTDLAPAVGADLAVMERDALRMREGGPFVFAQVKHGVGV 256

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449500609|ref|XP_004161145.1| PREDICTED: uncharacterized urease accessory protein ureG-like [Cucumis sativus]

 Score =  312 bits (800), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 150/166 (90%), Positives = 161/166 (96%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           MLALC FLRDKYSLAAVTNDIFTKEDGEFL+++GALPEERIRAVETGGCPHAAIREDISI
Sbjct: 102 MLALCTFLRDKYSLAAVTNDIFTKEDGEFLVKHGALPEERIRAVETGGCPHAAIREDISI 161

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
           NLGPLEELSNL+K D+LLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ
Sbjct: 162 NLGPLEELSNLYKTDILLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 221

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           ADLLVINKTDLA+A+GADLAVMERDAL+MRDGGPF+FAQV   +G+
Sbjct: 222 ADLLVINKTDLATAVGADLAVMERDALKMRDGGPFVFAQVKHGVGV 267

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449459358|ref|XP_004147413.1| PREDICTED: uncharacterized urease accessory protein ureG-like [Cucumis sativus]

 Score =  312 bits (800), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 150/166 (90%), Positives = 161/166 (96%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           MLALC FLRDKYSLAAVTNDIFTKEDGEFL+++GALPEERIRAVETGGCPHAAIREDISI
Sbjct: 92  MLALCTFLRDKYSLAAVTNDIFTKEDGEFLVKHGALPEERIRAVETGGCPHAAIREDISI 151

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
           NLGPLEELSNL+K D+LLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ
Sbjct: 152 NLGPLEELSNLYKTDILLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 211

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
           ADLLVINKTDLA+A+GADLAVMERDAL+MRDGGPF+FAQV   +G+
Sbjct: 212 ADLLVINKTDLATAVGADLAVMERDALKMRDGGPFVFAQVKHGVGV 257

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	178
TAIR|locus:2040894	276	UREG "AT2G34470" [Arabidopsis	0.932	0.601	0.915	2.3e-78
UNIPROTKB|G4NCH0	277	MGG_01086 "Uncharacterized pro	0.932	0.599	0.748	1.8e-62
POMBASE|SPCPB16A4.05c	286	SPCPB16A4.05c "urease accessor	0.932	0.580	0.704	9e-61
ASPGD|ASPL0000062920	266	ureD [Emericella nidulans (tax	0.898	0.601	0.725	3.9e-60
UNIPROTKB|Q48DC7	205	ureG "Urease accessory protein	0.882	0.765	0.626	1.1e-48
UNIPROTKB|P0A664	224	ureG "Urease accessory protein	0.865	0.687	0.606	3e-46
TIGR_CMR|SPO_1717	215	SPO_1717 "urease accessory pro	0.887	0.734	0.584	1e-45
UNIPROTKB|P18319	205	ureG "Urease accessory protein	0.887	0.770	0.616	1.3e-45

TAIR|locus:2040894 UREG "AT2G34470" [Arabidopsis thaliana (taxid:3702)]

 Score = 788 (282.4 bits), Expect = 2.3e-78, P = 2.3e-78
 Identities = 152/166 (91%), Positives = 162/166 (97%)

Query:     1 MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
             MLALC+FLRDKYSLAAVTNDIFTKEDGEFL++NGALPEERIRAVETGGCPHAAIREDISI
Sbjct:    91 MLALCRFLRDKYSLAAVTNDIFTKEDGEFLVKNGALPEERIRAVETGGCPHAAIREDISI 150

Query:    61 NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
             NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVS GDKIPRKGGPGITQ
Sbjct:   151 NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSAGDKIPRKGGPGITQ 210

Query:   121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
             ADLLVINKTDLA+A+GADL+VMERD+LRMRDGGPF+FAQV   +G+
Sbjct:   211 ADLLVINKTDLAAAVGADLSVMERDSLRMRDGGPFVFAQVKHGLGV 256

GO:0000166 "nucleotide binding" evidence=ISS

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM;IEA

GO:0016151 "nickel cation binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=ISS

GO:0006807 "nitrogen compound metabolic process" evidence=IMP

GO:0048554 "positive regulation of metalloenzyme activity" evidence=IMP

GO:0016020 "membrane" evidence=IDA

UNIPROTKB|G4NCH0 MGG_01086 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 638 (229.6 bits), Expect = 1.8e-62, P = 1.8e-62
 Identities = 125/167 (74%), Positives = 141/167 (84%)

Query:     1 MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
             MLALC  LRD +SLAAVTNDIFT+ED EFL RN ALP  RIRA+ETGGCPHAA+REDIS 
Sbjct:    74 MLALCLALRDTHSLAAVTNDIFTREDAEFLTRNKALPPSRIRAIETGGCPHAAVREDISA 133

Query:    61 NLGPLEELSNLFKA-DLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGIT 119
             NL  LE+L   F   DLLL ESGGDNLAAN+SRELAD+IIY+IDVSGGDKIPRKGGPGIT
Sbjct:   134 NLACLEDLHRTFNGVDLLLIESGGDNLAANYSRELADFIIYVIDVSGGDKIPRKGGPGIT 193

Query:   120 QADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
             Q+DLLV+NKTDLA  +GADL VMERDA +MR+GGP +FAQV   +G+
Sbjct:   194 QSDLLVVNKTDLAEIVGADLGVMERDARKMREGGPTVFAQVKKSVGV 240

GO:0005575 "cellular_component" evidence=ND

POMBASE|SPCPB16A4.05c SPCPB16A4.05c "urease accessory protein UREG (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 622 (224.0 bits), Expect = 9.0e-61, P = 9.0e-61
 Identities = 117/166 (70%), Positives = 143/166 (86%)

Query:     1 MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
             +L LC+ L +KYS+  VTNDIFT+ED EFL+RN ALPEERIRA+ETGGCPHAAIRED+S 
Sbjct:   103 LLQLCRLLGEKYSIGVVTNDIFTREDQEFLIRNKALPEERIRAIETGGCPHAAIREDVSG 162

Query:    61 NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
             NL  LEEL + F  +LLL ESGGDNLAAN+SR+LAD+IIY+IDVSGGDKIPRKGGPGIT+
Sbjct:   163 NLVALEELQSEFNTELLLVESGGDNLAANYSRDLADFIIYVIDVSGGDKIPRKGGPGITE 222

Query:   121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI 166
             +DLL+INKTDLA  +GADL+VM+RDA ++R+ GP +FAQV   +G+
Sbjct:   223 SDLLIINKTDLAKLVGADLSVMDRDAKKIRENGPIVFAQVKNQVGM 268

GO:0003924 "GTPase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0006184 "GTP catabolic process" evidence=IEA

GO:0016151 "nickel cation binding" evidence=IEA

GO:0016530 "metallochaperone activity" evidence=IEA

GO:0019627 "urea metabolic process" evidence=ISM

GO:0042803 "protein homodimerization activity" evidence=IEA

ASPGD|ASPL0000062920 ureD [Emericella nidulans (taxid:162425)]

 Score = 616 (221.9 bits), Expect = 3.9e-60, P = 3.9e-60
 Identities = 116/160 (72%), Positives = 139/160 (86%)

Query:     1 MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
             MLALC+ LRD+Y++AAVTNDIFT+ED EFL RN AL  +RIRA+ETGGCPHAA+REDIS 
Sbjct:    64 MLALCRALRDEYNIAAVTNDIFTREDAEFLTRNKALSPDRIRAIETGGCPHAAVREDISA 123

Query:    61 NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
             NL  L+ L   F+ DLLL ESGGDNLAAN+SRELAD+IIY+IDV+GGDK+PRKGGPGIT 
Sbjct:   124 NLLALQNLHRQFQTDLLLIESGGDNLAANYSRELADFIIYVIDVAGGDKVPRKGGPGITG 183

Query:   121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQV 160
             +DLLV+NK DLA A+GAD++VMERDA +MR+GGP +FA V
Sbjct:   184 SDLLVVNKIDLAEAVGADISVMERDAAKMREGGPTVFAVV 223

GO:0043419 "urea catabolic process" evidence=IMP

GO:0009039 "urease activity" evidence=IMP

GO:0005634 "nucleus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016151 "nickel cation binding" evidence=IEA

UNIPROTKB|Q48DC7 ureG "Urease accessory protein UreG" [Pseudomonas syringae pv. phaseolicola 1448A (taxid:264730)]

 Score = 508 (183.9 bits), Expect = 1.1e-48, P = 1.1e-48
 Identities = 99/158 (62%), Positives = 123/158 (77%)

Query:     2 LALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISIN 61
             LALC  LRD+Y+LA VTNDI+T+ED +FL+RN AL  ERI  VETGGCPH AIRED SIN
Sbjct:    23 LALCLALRDRYNLAVVTNDIYTREDADFLVRNEALAPERIIGVETGGCPHTAIREDASIN 82

Query:    62 LGPLEELSNLFKA-DLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
             L  +++L+  F+  DL++ ESGGDNL+A FS EL+D  IY+IDVS GDK+PRKGGPGI +
Sbjct:    83 LEAVDQLNRRFEGLDLIIVESGGDNLSATFSPELSDLTIYVIDVSAGDKLPRKGGPGICK 142

Query:   121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFA 158
             +DLLVINK DLA  +GA L +M+ D  RMR   PF+F+
Sbjct:   143 SDLLVINKIDLAPLVGASLEMMDSDTRRMRGEKPFVFS 180

GO:0016530 "metallochaperone activity" evidence=ISS

UNIPROTKB|P0A664 ureG "Urease accessory protein UreG" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 485 (175.8 bits), Expect = 3.0e-46, P = 3.0e-46
 Identities = 94/155 (60%), Positives = 119/155 (76%)

Query:     3 ALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINL 62
             ALC+ LR + SLA +TNDI+T ED +FL  +  LP++RI AV+TGGCPH AIR+DI+ NL
Sbjct:    44 ALCRQLRGELSLAVLTNDIYTTEDADFLRTHAVLPDDRIAAVQTGGCPHTAIRDDITANL 103

Query:    63 GPLEELSNLFKA-DLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQA 121
               ++EL     A DL+L ESGGDNL A FS  L D  I++IDV+GGDK+PRKGGPG+T +
Sbjct:   104 DAIDELMAAHDALDLILVESGGDNLTATFSSGLVDAQIFVIDVAGGDKVPRKGGPGVTYS 163

Query:   122 DLLVINKTDLASAIGADLAVMERDALRMRDGGPFI 156
             DLLV+NKTDLA+ +GADLAVM RDA  +RDG P +
Sbjct:   164 DLLVVNKTDLAALVGADLAVMARDADAVRDGRPTV 198

GO:0003924 "GTPase activity" evidence=IDA

GO:0006184 "GTP catabolic process" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IPI

TIGR_CMR|SPO_1717 SPO_1717 "urease accessory protein UreG" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 480 (174.0 bits), Expect = 1.0e-45, P = 1.0e-45
 Identities = 93/159 (58%), Positives = 120/159 (75%)

Query:     3 ALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINL 62
             AL + LRD +S+  +TNDI+T+ED E LMR   LP++RI  VETGGCPH AIRED SINL
Sbjct:    26 ALSEALRDSHSIGVITNDIYTREDAEALMRLQILPQDRIIGVETGGCPHTAIREDASINL 85

Query:    63 GPLEELSNLFKA-DLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQA 121
               + E+       +++L ESGGDNL+A FS ELAD  +Y+IDV+ G++IPRKGGP IT++
Sbjct:    86 AAVAEMERRHPGIEIILIESGGDNLSATFSPELADVTLYVIDVAAGEEIPRKGGPAITKS 145

Query:   122 DLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQV 160
             D+L+INKTDLA  +GA L VMERDA RMR G PF+F+ +
Sbjct:   146 DILIINKTDLAPHVGASLEVMERDAGRMRCGRPFVFSSL 184

GO:0019627 "urea metabolic process" evidence=ISS

GO:0046872 "metal ion binding" evidence=ISS

UNIPROTKB|P18319 ureG "Urease accessory protein UreG" [Enterobacter aerogenes (taxid:548)]

 Score = 479 (173.7 bits), Expect = 1.3e-45, P = 1.3e-45
 Identities = 98/159 (61%), Positives = 113/159 (71%)

Query:     3 ALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINL 62
             ALCK +RD + LA VTNDI+TKED   L   GAL  ERI  VETGGCPH AIRED S+NL
Sbjct:    26 ALCKAMRDTWQLAVVTNDIYTKEDQRILTEAGALAPERIVGVETGGCPHTAIREDASMNL 85

Query:    63 GPLEELSNLF-KADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQA 121
               +E LS  F   DL+  ESGGDNL+A FS ELAD  IY+IDV+ G+KIPRKGGPGIT++
Sbjct:    86 AAVEALSEKFGNLDLIFVESGGDNLSATFSPELADLTIYVIDVAEGEKIPRKGGPGITKS 145

Query:   122 DLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQV 160
             D LVINKTDLA  +GA L VM  D  RMR   P+ F  +
Sbjct:   146 DFLVINKTDLAPYVGASLEVMASDTQRMRGDRPWTFTNL 184


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.322   0.142   0.414    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      178       178   0.00086  109 3  11 22  0.39    32
                                                     31  0.39    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  8
  No. of states in DFA:  573 (61 KB)
  Total size of DFA:  133 KB (2083 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  15.49u 0.08s 15.57t   Elapsed:  00:00:03
  Total cpu time:  15.49u 0.08s 15.57t   Elapsed:  00:00:03
  Start:  Sat May 11 00:01:23 2013   End:  Sat May 11 00:01:26 2013

GO:0005515 "protein binding" evidence=IPI

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q02FC5	UREG_PSEAB	No assigned EC number	0.6415	0.8876	0.7745	yes	no
B1ZHN6	UREG1_METPB	No assigned EC number	0.6335	0.8988	0.7843	yes	no
B8EPU6	UREG_METSB	No assigned EC number	0.6036	0.9157	0.7912	yes	no
Q6FD79	UREG_ACIAD	No assigned EC number	0.6187	0.8932	0.7794	yes	no
Q0I662	UREG_SYNS3	No assigned EC number	0.6540	0.8876	0.79	yes	no
B0V9P2	UREG_ACIBY	No assigned EC number	0.6024	0.9269	0.8088	yes	no
Q0AC95	UREG_ALHEH	No assigned EC number	0.6289	0.8876	0.7488	yes	no
B6JPH1	UREG_HELP2	No assigned EC number	0.6037	0.8876	0.7939	yes	no
A3M3F5	UREG_ACIBT	No assigned EC number	0.6024	0.9269	0.8088	yes	no
Q4QN12	UREG_HAEI8	No assigned EC number	0.5730	0.8988	0.7111	yes	no
Q1LPS6	UREG_RALME	No assigned EC number	0.6265	0.8820	0.7584	yes	no
Q8DMQ4	UREG_THEEB	No assigned EC number	0.6181	0.9213	0.82	yes	no
A6SZ10	UREG_JANMA	No assigned EC number	0.6265	0.8820	0.7440	yes	no
Q2SDP8	UREG_HAHCH	No assigned EC number	0.6075	0.8820	0.7696	yes	no
A4VQW0	UREG_PSEU5	No assigned EC number	0.6455	0.8820	0.7696	yes	no
Q7V3V8	UREG_PROMM	No assigned EC number	0.5932	0.9719	0.8564	yes	no
A1KBB1	UREG_AZOSB	No assigned EC number	0.6312	0.8932	0.7681	yes	no
A2CDZ5	UREG_PROM3	No assigned EC number	0.6477	0.8876	0.7783	yes	no
A9W6X0	UREG1_METEP	No assigned EC number	0.6335	0.8988	0.7843	yes	no
Q96WV0	UREG_SCHPO	No assigned EC number	0.7197	0.8820	0.5489	yes	no
Q3AGD6	UREG_SYNSC	No assigned EC number	0.6477	0.8876	0.7860	yes	no
P44396	UREG_HAEIN	No assigned EC number	0.5789	0.8988	0.7111	yes	no
Q11VN1	UREG_CYTH3	No assigned EC number	0.6646	0.9325	0.6803	yes	no
B8IJ81	UREG_METNO	No assigned EC number	0.6583	0.8988	0.7843	yes	no
B2HVS4	UREG_ACIBC	No assigned EC number	0.6024	0.9269	0.8088	yes	no
B7V1V6	UREG_PSEA8	No assigned EC number	0.6415	0.8876	0.7745	yes	no
Q473Q6	UREG_CUPPJ	No assigned EC number	0.6455	0.8820	0.7511	yes	no
B0VSB5	UREG_ACIBS	No assigned EC number	0.6024	0.9269	0.8088	yes	no
P72955	UREG_SYNY3	No assigned EC number	0.5738	0.9775	0.8446	N/A	no
B0UBI3	UREG_METS4	No assigned EC number	0.6521	0.8988	0.7843	yes	no
A7HHN3	UREG_ANADF	No assigned EC number	0.7228	0.9325	0.7033	yes	no
B2JF70	UREG_BURP8	No assigned EC number	0.6158	0.9157	0.7652	yes	no
A3N2R0	UREG_ACTP2	No assigned EC number	0.5847	0.8988	0.7582	yes	no
A6UC29	UREG_SINMW	No assigned EC number	0.6392	0.8820	0.7733	yes	no
Q3J773	UREG_NITOC	No assigned EC number	0.6125	0.8932	0.7832	yes	no
O54424	UREG_ACTPL	No assigned EC number	0.5789	0.8988	0.7582	yes	no
A4XQ16	UREG_PSEMY	No assigned EC number	0.6289	0.8876	0.7745	yes	no
B1M3X4	UREG1_METRJ	No assigned EC number	0.6459	0.8988	0.7804	yes	no
B7I8T8	UREG_ACIB5	No assigned EC number	0.6024	0.9269	0.8088	yes	no
B7GXU0	UREG_ACIB3	No assigned EC number	0.6024	0.9269	0.8088	yes	no
A9GP90	UREG_SORC5	No assigned EC number	0.7048	0.9325	0.5496	yes	no
Q39IW6	UREG_BURS3	No assigned EC number	0.6036	0.9157	0.7581	yes	no
A0L6F5	UREG_MAGSM	No assigned EC number	0.6265	0.8820	0.7772	yes	no
Q0KCP3	UREG_CUPNH	No assigned EC number	0.6329	0.8820	0.7511	yes	no
Q1H0F5	UREG_METFK	No assigned EC number	0.6375	0.8932	0.7832	yes	no
C1DMZ7	UREG_AZOVD	No assigned EC number	0.6477	0.8876	0.7745	yes	no
A6VD02	UREG_PSEA7	No assigned EC number	0.6289	0.8876	0.7745	yes	no
Q9HUS0	UREG_PSEAE	No assigned EC number	0.6415	0.8876	0.7745	yes	no
B3H2K9	UREG_ACTP7	No assigned EC number	0.5789	0.8988	0.7582	yes	no
B0BRT8	UREG_ACTPJ	No assigned EC number	0.6036	0.8595	0.7251	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	178
TIGR00101	199	TIGR00101, ureG, urease accessory protein UreG	2e-76
COG0378	202	COG0378, HypB, Ni2+-binding GTPase involved in reg	3e-57
pfam02492	178	pfam02492, cobW, CobW/HypB/UreG, nucleotide-bindin	3e-32
TIGR00073	208	TIGR00073, hypB, hydrogenase accessory protein Hyp	5e-10

>gnl|CDD|129208 TIGR00101, ureG, urease accessory protein UreG

 Score =  226 bits (578), Expect = 2e-76
 Identities = 100/159 (62%), Positives = 121/159 (76%), Gaps = 1/159 (0%)

Query: 3   ALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINL 62
           AL + LR KY LA +TNDI+T+ED EFL++N ALP ERI  VETGGCPH AIRED S+NL
Sbjct: 20  ALTRALRQKYQLAVITNDIYTQEDAEFLVKNSALPPERILGVETGGCPHTAIREDASMNL 79

Query: 63  GPLEELSNLF-KADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQA 121
             + E+   F   +++  ESGGDNL+A FS ELAD  I++IDV+ GDKIPRKGGPGIT++
Sbjct: 80  EAVAEMEARFPPLEMVFIESGGDNLSATFSPELADLTIFVIDVAAGDKIPRKGGPGITRS 139

Query: 122 DLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQV 160
           DLLVINK DLA  +GADL VMERDA +MR   PFIF  +
Sbjct: 140 DLLVINKIDLAPMVGADLGVMERDAKKMRGEKPFIFTNL 178

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 [Central intermediary metabolism, Nitrogen metabolism]. Length = 199

>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]

 Score =  177 bits (452), Expect = 3e-57
 Identities = 79/159 (49%), Positives = 97/159 (61%), Gaps = 12/159 (7%)

Query: 2   LALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETG-GCPHAAIREDISI 60
               + L+D+Y +A +T DI+TKED + L +    P E I  VETG GC H     D S+
Sbjct: 31  EKTLRALKDEYKIAVITGDIYTKEDADRLRKL---PGEPIIGVETGKGC-H----LDASM 82

Query: 61  NLGPLEELSNLF-KADLLLCESGGDNLAANFSRELAD-YIIYIIDVSGGDKIPRKGGPGI 118
           NL  +EEL   F   DLL  ES G NL   FS +L D   + +IDV+ G+ IPRKGGPGI
Sbjct: 83  NLEAIEELVLDFPDLDLLFIESVG-NLVCPFSPDLGDHLRVVVIDVTEGEDIPRKGGPGI 141

Query: 119 TQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIF 157
            +ADLLVINKTDLA  +GADL VM RDA  +    P IF
Sbjct: 142 FKADLLVINKTDLAPYVGADLEVMARDAKEVNPEAPIIF 180

Length = 202

>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain

 Score =  113 bits (285), Expect = 3e-32
 Identities = 56/170 (32%), Positives = 76/170 (44%), Gaps = 21/170 (12%)

Query: 1   MLALCKFLRDKYSLAAVTNDIF-TKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDIS 59
           +  L +  R+   +A + ND   T  D E L   GAL    I  +  G       RED+S
Sbjct: 17  LEHLLEKNREGLKIAVIVNDFGETGIDAELLRETGAL----IVELNNGCICCTL-REDLS 71

Query: 60  INLGPLEELSNLFKADLLLCESGG----------DNLAANFSRELADYIIYIIDVSG--G 107
           + L  L EL    + DLL  E+ G                 S    D ++ ++DV+   G
Sbjct: 72  MVLEALLELKE--RLDLLFIETTGLACPAPVAQTFLSPELRSDLGLDGVVTVVDVAETEG 129

Query: 108 DKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIF 157
           + IP K    I  ADL+VINKTDLA A+ ADL  +E D  R+    P I 
Sbjct: 130 EDIPEKAPDQIAFADLIVINKTDLAPAV-ADLEKLEADLRRLNPEAPIIP 178

This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans. Length = 178

>gnl|CDD|232811 TIGR00073, hypB, hydrogenase accessory protein HypB

 Score = 55.9 bits (135), Expect = 5e-10
 Identities = 49/145 (33%), Positives = 72/145 (49%), Gaps = 13/145 (8%)

Query: 7   FLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLE 66
            L+D+  +A +  D+ TK D E L + GA        + TG   H     D  +    LE
Sbjct: 45  NLKDEVKIAVIEGDVITKFDAERLRKYGAPAI----QINTGKECHL----DAHMVAHALE 96

Query: 67  ELSNLFKADLLLCESGGDNLAANFSREL-ADYIIYIIDVSGGDKIPRKGGPGITQ-ADLL 124
           +L      DLL  E+ G NL      +L     + ++ V+ GD  P K  PG+ + ADL+
Sbjct: 97  DLPLD-DIDLLFIENVG-NLVCPADFDLGEHMRVVLLSVTEGDDKPLKY-PGMFKEADLI 153

Query: 125 VINKTDLASAIGADLAVMERDALRM 149
           VINK DLA A+G D+  M+ DA ++
Sbjct: 154 VINKADLAEAVGFDVEKMKADAKKI 178

A GTP hydrolase for assembly of nickel metallocenter of hydrogenase. A similar protein, ureG, is an accessory protein for urease, which also uses nickel. hits scoring 75 and above are safe as orthologs. [SS 1/05/04 I changed the role_ID and process GO from protein folding to to protein modification, since a protein folding role has not been established, but HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.] [Protein fate, Protein modification and repair]. Length = 208

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	178
COG0378	202	HypB Ni2+-binding GTPase involved in regulation of	100.0
COG0523	323	Putative GTPases (G3E family) [General function pr	100.0
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	99.97
TIGR00101	199	ureG urease accessory protein UreG. This model rep	99.97
PF02492	178	cobW: CobW/HypB/UreG, nucleotide-binding domain; I	99.96
PRK11537	318	putative GTP-binding protein YjiA; Provisional	99.95
TIGR02475	341	CobW cobalamin biosynthesis protein CobW. A broade	99.94
KOG2743	391	consensus Cobalamin synthesis protein [Coenzyme tr	99.94
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	99.94
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	99.87
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	99.86
PRK09435	332	membrane ATPase/protein kinase; Provisional	99.85
cd03112	158	CobW_like The function of this protein family is u	99.83
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	99.58
COG1160	444	Predicted GTPases [General function prediction onl	99.07
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	98.99
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	98.95
cd03114	148	ArgK-like The function of this protein family is u	98.93
PRK15467	158	ethanolamine utilization protein EutP; Provisional	98.91
cd00881	189	GTP_translation_factor GTP translation factor fami	98.91
cd01887	168	IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryo	98.89
COG1159	298	Era GTPase [General function prediction only]	98.88
PRK00089	292	era GTPase Era; Reviewed	98.87
TIGR02528	142	EutP ethanolamine utilization protein, EutP. This	98.86
PRK13768	253	GTPase; Provisional	98.86
cd01895	174	EngA2 EngA2 subfamily. This CD represents the seco	98.85
cd01889	192	SelB_euk SelB subfamily. SelB is an elongation fac	98.85
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	98.85
cd00880	163	Era_like Era (E. coli Ras-like protein)-like. This	98.84
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	98.83
KOG0092	200	consensus GTPase Rab5/YPT51 and related small G pr	98.82
TIGR03594	429	GTPase_EngA ribosome-associated GTPase EngA. EngA	98.82
PRK15494	339	era GTPase Era; Provisional	98.81
cd01890	179	LepA LepA subfamily. LepA belongs to the GTPase fa	98.79
cd04157	162	Arl6 Arl6 subfamily. Arl6 (Arf-like 6) forms a sub	98.78
PRK00093	435	GTP-binding protein Der; Reviewed	98.77
cd04171	164	SelB SelB subfamily. SelB is an elongation factor	98.77
cd04149	168	Arf6 Arf6 subfamily. Arf6 (ADP ribosylation factor	98.77
PTZ00099	176	rab6; Provisional	98.76
cd04154	173	Arl2 Arl2 subfamily. Arl2 (Arf-like 2) GTPases are	98.76
cd01897	168	NOG NOG1 is a nucleolar GTP-binding protein presen	98.74
cd01888	203	eIF2_gamma eIF2-gamma (gamma subunit of initiation	98.72
cd04165	224	GTPBP1_like GTPBP1-like. Mammalian GTP binding pro	98.71
cd04158	169	ARD1 ARD1 subfamily. ARD1 (ADP-ribosylation factor	98.71
cd04120	202	Rab12 Rab12 subfamily. Rab12 was first identified	98.71
cd04136	163	Rap_like Rap-like subfamily. The Rap subfamily con	98.7
KOG0462	650	consensus Elongation factor-type GTP-binding prote	98.7
cd04151	158	Arl1 Arl1 subfamily. Arl1 (Arf-like 1) localizes t	98.7
PF00009	188	GTP_EFTU: Elongation factor Tu GTP binding domain;	98.7
cd04150	159	Arf1_5_like Arf1-Arf5-like subfamily. This subfami	98.69
cd04152	183	Arl4_Arl7 Arl4/Arl7 subfamily. Arl4 (Arf-like 4) i	98.69
cd04107	201	Rab32_Rab38 Rab38/Rab32 subfamily. Rab32 and Rab38	98.68
cd04156	160	ARLTS1 ARLTS1 subfamily. ARLTS1 (Arf-like tumor su	98.68
cd04153	174	Arl5_Arl8 Arl5/Arl8 subfamily. Arl5 (Arf-like 5) a	98.68
cd00877	166	Ran Ran (Ras-related nuclear proteins) /TC4 subfam	98.66
smart00177	175	ARF ARF-like small GTPases; ARF, ADP-ribosylation	98.65
PRK03003	472	GTP-binding protein Der; Reviewed	98.65
cd01859	156	MJ1464 MJ1464. This family represents archaeal GTP	98.65
cd04175	164	Rap1 Rap1 subgroup. The Rap1 subgroup is part of t	98.64
cd04126	220	Rab20 Rab20 subfamily. Rab20 is one of several Rab	98.62
PLN00223	181	ADP-ribosylation factor; Provisional	98.62
cd01894	157	EngA1 EngA1 subfamily. This CD represents the firs	98.62
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	98.62
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	98.62
PRK09518	712	bifunctional cytidylate kinase/GTPase Der; Reviewe	98.62
cd00878	158	Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-lik	98.61
cd01849	155	YlqF_related_GTPase YlqF-related GTPases. These pr	98.61
cd04164	157	trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein	98.6
cd01879	158	FeoB Ferrous iron transport protein B (FeoB) subfa	98.6
smart00178	184	SAR Sar1p-like members of the Ras-family of small	98.6
cd04121	189	Rab40 Rab40 subfamily. This subfamily contains Rab	98.6
cd01858	157	NGP_1 NGP-1. Autoantigen NGP-1 (Nucleolar G-protei	98.6
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	98.59
cd04138	162	H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras,	98.59
cd00879	190	Sar1 Sar1 subfamily. Sar1 is an essential componen	98.59
cd01893	166	Miro1 Miro1 subfamily. Miro (mitochondrial Rho) pr	98.58
cd04141	172	Rit_Rin_Ric Rit/Rin/Ric subfamily. Rit (Ras-like p	98.58
cd04101	164	RabL4 RabL4 (Rab-like4) subfamily. RabL4s are nove	98.58
cd04145	164	M_R_Ras_like M-Ras/R-Ras-like subfamily. This subf	98.58
cd01863	161	Rab18 Rab18 subfamily. Mammalian Rab18 is implicat	98.58
TIGR02729	329	Obg_CgtA Obg family GTPase CgtA. This model descri	98.57
cd04122	166	Rab14 Rab14 subfamily. Rab14 GTPases are localized	98.57
PRK12299	335	obgE GTPase CgtA; Reviewed	98.57
cd04140	165	ARHI_like ARHI subfamily. ARHI (A Ras homolog memb	98.57
cd04110	199	Rab35 Rab35 subfamily. Rab35 is one of several Rab	98.57
cd04127	180	Rab27A Rab27a subfamily. The Rab27a subfamily cons	98.56
cd04128	182	Spg1 Spg1p. Spg1p (septum-promoting GTPase) was fi	98.56
cd01873	195	RhoBTB RhoBTB subfamily. Members of the RhoBTB sub	98.56
TIGR00157	245	ribosome small subunit-dependent GTPase A. The Aqu	98.56
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	98.56
cd04109	215	Rab28 Rab28 subfamily. First identified in maize,	98.55
cd01898	170	Obg Obg subfamily. The Obg nucleotide binding prot	98.55
cd01855	190	YqeH YqeH. YqeH is an essential GTP-binding protei	98.55
cd04113	161	Rab4 Rab4 subfamily. Rab4 has been implicated in n	98.55
cd04124	161	RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily	98.55
cd01865	165	Rab3 Rab3 subfamily. The Rab3 subfamily contains R	98.54
cd04176	163	Rap2 Rap2 subgroup. The Rap2 subgroup is part of t	98.53
cd01864	165	Rab19 Rab19 subfamily. Rab19 proteins are associat	98.53
cd04148	221	RGK RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Ki	98.52
cd04106	162	Rab23_lke Rab23-like subfamily. Rab23 is a member	98.52
cd01869	166	Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in ev	98.52
PRK09866	741	hypothetical protein; Provisional	98.51
cd04142	198	RRP22 RRP22 subfamily. RRP22 (Ras-related protein	98.51
PTZ00133	182	ADP-ribosylation factor; Provisional	98.51
KOG0088	218	consensus GTPase Rab21, small G protein superfamil	98.5
COG0532	509	InfB Translation initiation factor 2 (IF-2; GTPase	98.5
cd04123	162	Rab21 Rab21 subfamily. The localization and functi	98.5
cd04143	247	Rhes_like Rhes_like subfamily. This subfamily incl	98.5
smart00176	200	RAN Ran (Ras-related nuclear proteins) /TC4 subfam	98.49
KOG0094	221	consensus GTPase Rab6/YPT6/Ryh1, small G protein s	98.49
PTZ00327	460	eukaryotic translation initiation factor 2 gamma s	98.48
cd01867	167	Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Yp	98.48
cd01892	169	Miro2 Miro2 subfamily. Miro (mitochondrial Rho) pr	98.48
TIGR03156	351	GTP_HflX GTP-binding protein HflX. This protein fa	98.47
PTZ00369	189	Ras-like protein; Provisional	98.47
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	98.47
cd01860	163	Rab5_related Rab5-related subfamily. This subfamil	98.47
TIGR00475	581	selB selenocysteine-specific elongation factor Sel	98.47
cd04112	191	Rab26 Rab26 subfamily. First identified in rat pan	98.47
cd01856	171	YlqF YlqF. Proteins of the YlqF family contain all	98.47
cd01881	176	Obg_like The Obg-like subfamily consists of five w	98.47
cd00882	157	Ras_like_GTPase Ras-like GTPase superfamily. The R	98.46
cd04132	187	Rho4_like Rho4-like subfamily. Rho4 is a GTPase th	98.46
cd01871	174	Rac1_like Rac1-like subfamily. The Rac1-like subfa	98.46
PRK10512	614	selenocysteinyl-tRNA-specific translation factor;	98.45
cd04137	180	RheB Rheb (Ras Homolog Enriched in Brain) subfamil	98.45
cd04147	198	Ras_dva Ras-dva subfamily. Ras-dva (Ras - dorsal-v	98.45
cd04144	190	Ras2 Ras2 subfamily. The Ras2 subfamily, found exc	98.45
cd01874	175	Cdc42 Cdc42 subfamily. Cdc42 is an essential GTPas	98.45
PLN03118	211	Rab family protein; Provisional	98.44
cd04108	170	Rab36_Rab34 Rab34/Rab36 subfamily. Rab34, found pr	98.44
cd01866	168	Rab2 Rab2 subfamily. Rab2 is localized on cis-Golg	98.43
cd04134	189	Rho3 Rho3 subfamily. Rho3 is a member of the Rho f	98.43
cd04117	161	Rab15 Rab15 subfamily. Rab15 colocalizes with the	98.43
smart00174	174	RHO Rho (Ras homology) subfamily of Ras-like small	98.42
cd04161	167	Arl2l1_Arl13_like Arl2l1/Arl13 subfamily. Arl2l1 (	98.41
cd01861	161	Rab6 Rab6 subfamily. Rab6 is involved in microtubu	98.4
cd04172	182	Rnd3_RhoE_Rho8 Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE	98.4
CHL00189	742	infB translation initiation factor 2; Provisional	98.39
cd04174	232	Rnd1_Rho6 Rnd1/Rho6 subfamily. Rnd1/Rho6 is a memb	98.39
cd04114	169	Rab30 Rab30 subfamily. Rab30 appears to be associa	98.39
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	98.38
cd04111	211	Rab39 Rab39 subfamily. Found in eukaryotes, Rab39	98.38
cd01870	175	RhoA_like RhoA-like subfamily. The RhoA subfamily	98.38
cd04103	158	Centaurin_gamma Centaurin gamma. The centaurins (a	98.38
COG2403	449	Predicted GTPase [General function prediction only	98.38
COG0481	603	LepA Membrane GTPase LepA [Cell envelope biogenesi	98.37
PRK04213	201	GTP-binding protein; Provisional	98.36
cd04116	170	Rab9 Rab9 subfamily. Rab9 is found in late endosom	98.36
cd04130	173	Wrch_1 Wrch-1 subfamily. Wrch-1 (Wnt-1 responsive	98.36
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	98.36
cd01868	165	Rab11_like Rab11-like. Rab11a, Rab11b, and Rab25 a	98.35
PRK12298	390	obgE GTPase CgtA; Reviewed	98.35
PF00025	175	Arf: ADP-ribosylation factor family The prints ent	98.35
cd04133	176	Rop_like Rop subfamily. The Rop (Rho-related prote	98.35
cd01875	191	RhoG RhoG subfamily. RhoG is a GTPase with high se	98.35
PRK05291	449	trmE tRNA modification GTPase TrmE; Reviewed	98.34
COG0486	454	ThdF Predicted GTPase [General function prediction	98.34
cd04131	178	Rnd Rnd subfamily. The Rnd subfamily contains Rnd1	98.34
cd04177	168	RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the	98.34
cd04125	188	RabA_like RabA-like subfamily. RabA was first iden	98.33
cd04118	193	Rab24 Rab24 subfamily. Rab24 is distinct from othe	98.33
PLN03071	219	GTP-binding nuclear protein Ran; Provisional	98.32
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	98.32
TIGR00487	587	IF-2 translation initiation factor IF-2. This mode	98.32
cd01884	195	EF_Tu EF-Tu subfamily. This subfamily includes ort	98.32
cd00876	160	Ras Ras family. The Ras family of the Ras superfam	98.31
cd00157	171	Rho Rho (Ras homology) family. Members of the Rho	98.31
COG4917	148	EutP Ethanolamine utilization protein [Amino acid	98.3
cd01891	194	TypA_BipA TypA (tyrosine phosphorylated protein A)	98.3
TIGR03596	276	GTPase_YlqF ribosome biogenesis GTP-binding protei	98.29
PRK04000	411	translation initiation factor IF-2 subunit gamma;	98.28
PLN03110	216	Rab GTPase; Provisional	98.28
COG2262	411	HflX GTPases [General function prediction only]	98.27
PRK12289	352	GTPase RsgA; Reviewed	98.26
TIGR01393	595	lepA GTP-binding protein LepA. LepA (GUF1 in Sacca	98.26
PRK12297	424	obgE GTPase CgtA; Reviewed	98.26
PRK14845	1049	translation initiation factor IF-2; Provisional	98.24
cd04162	164	Arl9_Arfrp2_like Arl9/Arfrp2-like subfamily. Arl9	98.23
cd04115	170	Rab33B_Rab33A Rab33B/Rab33A subfamily. Rab33B is u	98.23
TIGR03680	406	eif2g_arch translation initiation factor 2 subunit	98.22
PRK05433	600	GTP-binding protein LepA; Provisional	98.22
PRK05306	787	infB translation initiation factor IF-2; Validated	98.21
cd00154	159	Rab Rab family. Rab GTPases form the largest famil	98.21
cd04135	174	Tc10 TC10 subfamily. TC10 is a Rho family protein	98.21
TIGR00437	591	feoB ferrous iron transporter FeoB. FeoB (773 amin	98.2
cd01883	219	EF1_alpha Eukaryotic elongation factor 1 (EF1) alp	98.2
cd04146	165	RERG_RasL11_like RERG/RasL11-like subfamily. RERG	98.2
TIGR03598	179	GTPase_YsxC ribosome biogenesis GTP-binding protei	98.19
PRK00454	196	engB GTP-binding protein YsxC; Reviewed	98.19
cd01876	170	YihA_EngB The YihA (EngB) subfamily. This subfamil	98.19
PLN03108	210	Rab family protein; Provisional	98.17
PRK09563	287	rbgA GTPase YlqF; Reviewed	98.16
KOG1423	379	consensus Ras-like GTPase ERA [Cell cycle control,	98.16
cd04173	222	Rnd2_Rho7 Rnd2/Rho7 subfamily. Rnd2/Rho7 is a memb	98.16
KOG0078	207	consensus GTP-binding protein SEC4, small G protei	98.15
PRK01889	356	GTPase RsgA; Reviewed	98.15
PRK12296	500	obgE GTPase CgtA; Reviewed	98.13
TIGR00491	590	aIF-2 translation initiation factor aIF-2/yIF-2. T	98.13
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	98.13
cd01857	141	HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to t	98.11
KOG0084	205	consensus GTPase Rab1/YPT1, small G protein superf	98.1
TIGR02034	406	CysN sulfate adenylyltransferase, large subunit. H	98.1
TIGR00483	426	EF-1_alpha translation elongation factor EF-1 alph	98.1
cd04166	208	CysN_ATPS CysN_ATPS subfamily. CysN, together with	98.1
cd01854	287	YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtil	98.09
PRK05124	474	cysN sulfate adenylyltransferase subunit 1; Provis	98.09
PRK11058	426	GTPase HflX; Provisional	98.08
PRK12317	425	elongation factor 1-alpha; Reviewed	98.07
TIGR03597	360	GTPase_YqeH ribosome biogenesis GTPase YqeH. This	98.06
COG3276	447	SelB Selenocysteine-specific translation elongatio	98.06
PRK03003	472	GTP-binding protein Der; Reviewed	98.05
PRK00098	298	GTPase RsgA; Reviewed	98.04
KOG0394	210	consensus Ras-related GTPase [General function pre	98.03
PRK12288	347	GTPase RsgA; Reviewed	98.03
cd04129	187	Rho2 Rho2 subfamily. Rho2 is a fungal GTPase that	98.03
PRK12736	394	elongation factor Tu; Reviewed	97.99
PF02421	156	FeoB_N: Ferrous iron transport protein B; InterPro	97.98
COG1160	444	Predicted GTPases [General function prediction onl	97.98
KOG1145	683	consensus Mitochondrial translation initiation fac	97.97
PRK05506	632	bifunctional sulfate adenylyltransferase subunit 1	97.94
TIGR03594	429	GTPase_EngA ribosome-associated GTPase EngA. EngA	97.93
KOG0098	216	consensus GTPase Rab2, small G protein superfamily	97.92
PRK00049	396	elongation factor Tu; Reviewed	97.91
PRK00093	435	GTP-binding protein Der; Reviewed	97.9
PRK09518	712	bifunctional cytidylate kinase/GTPase Der; Reviewe	97.87
KOG1489	366	consensus Predicted GTP-binding protein (ODN super	97.85
KOG0080	209	consensus GTPase Rab18, small G protein superfamil	97.83
PF00071	162	Ras: Ras family; InterPro: IPR001806 Small GTPases	97.83
PRK12735	396	elongation factor Tu; Reviewed	97.82
TIGR00231	161	small_GTP small GTP-binding protein domain. This m	97.81
PRK04004	586	translation initiation factor IF-2; Validated	97.81
PLN00043	447	elongation factor 1-alpha; Provisional	97.81
COG5257	415	GCD11 Translation initiation factor 2, gamma subun	97.81
PTZ00141	446	elongation factor 1- alpha; Provisional	97.8
KOG0079	198	consensus GTP-binding protein H-ray, small G prote	97.78
CHL00071	409	tufA elongation factor Tu	97.78
PRK10218	607	GTP-binding protein; Provisional	97.78
TIGR00485	394	EF-Tu translation elongation factor TU. This align	97.76
PRK14974	336	cell division protein FtsY; Provisional	97.76
PRK13796	365	GTPase YqeH; Provisional	97.76
cd04167	213	Snu114p Snu114p subfamily. Snu114p is one of sever	97.75
KOG0093	193	consensus GTPase Rab3, small G protein superfamily	97.73
COG0218	200	Predicted GTPase [General function prediction only	97.72
TIGR01394	594	TypA_BipA GTP-binding protein TypA/BipA. This bact	97.72
PRK09554	772	feoB ferrous iron transport protein B; Reviewed	97.69
PRK10416	318	signal recognition particle-docking protein FtsY;	97.66
KOG0081	219	consensus GTPase Rab27, small G protein superfamil	97.66
cd04178	172	Nucleostemin_like Nucleostemin-like. Nucleostemin	97.61
KOG0461	522	consensus Selenocysteine-specific elongation facto	97.61
TIGR00064	272	ftsY signal recognition particle-docking protein F	97.6
PLN03127	447	Elongation factor Tu; Provisional	97.6
cd01882	225	BMS1 Bms1. Bms1 is an essential, evolutionarily co	97.5
TIGR00450	442	mnmE_trmE_thdF tRNA modification GTPase TrmE. TrmE	97.47
cd01896	233	DRG The developmentally regulated GTP-binding prot	97.44
KOG0076	197	consensus GTP-binding ADP-ribosylation factor-like	97.42
KOG0072	182	consensus GTP-binding ADP-ribosylation factor-like	97.42
KOG0086	214	consensus GTPase Rab4, small G protein superfamily	97.4
KOG0083	192	consensus GTPase Rab26/Rab37, small G protein supe	97.4
COG1162	301	Predicted GTPases [General function prediction onl	97.36
PLN03126	478	Elongation factor Tu; Provisional	97.36
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	97.34
COG2895	431	CysN GTPases - Sulfate adenylate transferase subun	97.29
KOG0095	213	consensus GTPase Rab30, small G protein superfamil	97.27
cd04168	237	TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), T	97.23
COG1217	603	TypA Predicted membrane GTPase involved in stress	97.22
COG0536	369	Obg Predicted GTPase [General function prediction	97.22
PRK12740	668	elongation factor G; Reviewed	97.21
COG2229	187	Predicted GTPase [General function prediction only	97.2
KOG0087	222	consensus GTPase Rab11/YPT3, small G protein super	97.2
COG0370	653	FeoB Fe2+ transport system protein B [Inorganic io	97.11
cd01886	270	EF-G Elongation factor G (EF-G) subfamily. Translo	97.09
KOG1144	1064	consensus Translation initiation factor 5B (eIF-5B	97.05
PRK12739	691	elongation factor G; Reviewed	97.03
KOG0073	185	consensus GTP-binding ADP-ribosylation factor-like	97.02
cd01885	222	EF2 EF2 (for archaea and eukarya). Translocation r	96.98
COG5258	527	GTPBP1 GTPase [General function prediction only]	96.93
PRK13351	687	elongation factor G; Reviewed	96.9
KOG0097	215	consensus GTPase Rab14, small G protein superfamil	96.83
cd04170	268	EF-G_bact Elongation factor G (EF-G) subfamily. Tr	96.83
COG1084	346	Predicted GTPase [General function prediction only	96.83
KOG0395	196	consensus Ras-related GTPase [General function pre	96.8
COG5256	428	TEF1 Translation elongation factor EF-1alpha (GTPa	96.78
KOG0070	181	consensus GTP-binding ADP-ribosylation factor Arf1	96.76
PRK00741	526	prfC peptide chain release factor 3; Provisional	96.73
PTZ00132	215	GTP-binding nuclear protein Ran; Provisional	96.73
COG0050	394	TufB GTPases - translation elongation factors [Tra	96.67
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	96.64
COG1161	322	Predicted GTPases [General function prediction onl	96.58
cd04105	203	SR_beta Signal recognition particle receptor, beta	96.57
KOG0075	186	consensus GTP-binding ADP-ribosylation factor-like	96.57
PRK00007	693	elongation factor G; Reviewed	96.56
KOG0091	213	consensus GTPase Rab39, small G protein superfamil	96.54
cd01899	318	Ygr210 Ygr210 subfamily. Ygr210 is a member of Obg	96.51
KOG0460	449	consensus Mitochondrial translation elongation fac	96.49
TIGR00484	689	EF-G translation elongation factor EF-G. After pep	96.48
cd04104	197	p47_IIGP_like p47 (47-kDa) family. The p47 GTPase	96.48
KOG1191	531	consensus Mitochondrial GTPase [Translation, ribos	96.45
COG1163	365	DRG Predicted GTPase [General function prediction	96.44
KOG2484	435	consensus GTPase [General function prediction only	96.36
KOG1424	562	consensus Predicted GTP-binding protein MMR1 [Gene	96.22
KOG0458	603	consensus Elongation factor 1 alpha [Translation,	96.08
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.02
KOG0071	180	consensus GTP-binding ADP-ribosylation factor Arf6	95.97
KOG0466	466	consensus Translation initiation factor 2, gamma s	95.64
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	95.62
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.46
KOG4252	246	consensus GTP-binding protein [Signal transduction	95.41
KOG3883	198	consensus Ras family small GTPase [Signal transduc	95.27
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	95.19
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	94.85
COG1100	219	GTPase SAR1 and related small G proteins [General	94.81
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	94.78
TIGR00503	527	prfC peptide chain release factor 3. This translat	94.71
KOG0393	198	consensus Ras-related small GTPase, Rho type [Gene	94.67
PRK10867	433	signal recognition particle protein; Provisional	94.64
cd04169	267	RF3 RF3 subfamily. Peptide chain release factor 3	94.49
KOG0780	483	consensus Signal recognition particle, subunit Srp	94.48
PRK09602	396	translation-associated GTPase; Reviewed	94.2
PRK14489	366	putative bifunctional molybdopterin-guanine dinucl	93.72
TIGR00959	428	ffh signal recognition particle protein. This mode	93.44
KOG0090	238	consensus Signal recognition particle receptor, be	93.42
KOG4423	229	consensus GTP-binding protein-like, RAS superfamil	93.25
cd04102	202	RabL3 RabL3 (Rab-like3) subfamily. RabL3s are nove	93.2
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	92.98
PRK14494	229	putative molybdopterin-guanine dinucleotide biosyn	92.89
PRK07560	731	elongation factor EF-2; Reviewed	92.79
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	92.73
PLN00116	843	translation elongation factor EF-2 subunit; Provis	92.7
PRK00771	437	signal recognition particle protein Srp54; Provisi	92.5
KOG1490	620	consensus GTP-binding protein CRFG/NOG1 (ODN super	91.9
TIGR03172	232	probable selenium-dependent hydroxylase accessory	91.59
KOG0448	749	consensus Mitofusin 1 GTPase, involved in mitochon	91.51
PTZ00416	836	elongation factor 2; Provisional	91.42
PF08438	109	MMR_HSR1_C: GTPase of unknown function C-terminal;	91.39
KOG0410	410	consensus Predicted GTP binding protein [General f	91.18
cd03110	179	Fer4_NifH_child This protein family's function is	90.85
KOG2423	572	consensus Nucleolar GTPase [General function predi	90.77
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	90.08
KOG0467	887	consensus Translation elongation factor 2/ribosome	90.03
cd01852	196	AIG1 AIG1 (avrRpt2-induced gene 1). This represent	89.97
PF06858	58	NOG1: Nucleolar GTP-binding protein 1 (NOG1); Inte	89.18
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	88.9
KOG0468	971	consensus U5 snRNP-specific protein [Translation,	88.85
smart00053	240	DYNc Dynamin, GTPase. Large GTPases that mediate v	88.24
PRK14491	597	putative bifunctional molybdopterin-guanine dinucl	88.17
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	87.97
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	87.89
KOG0465	721	consensus Mitochondrial elongation factor [Transla	87.76
KOG3905	473	consensus Dynein light intermediate chain [Cell mo	87.73
PLN00023	334	GTP-binding protein; Provisional	87.67
KOG2485	335	consensus Conserved ATP/GTP binding protein [Gener	86.66
COG0480	697	FusA Translation elongation factors (GTPases) [Tra	86.31
KOG1143	591	consensus Predicted translation elongation factor	86.24
TIGR00490	720	aEF-2 translation elongation factor aEF-2. This mo	86.15
KOG0781	587	consensus Signal recognition particle receptor, al	86.06
KOG1954	532	consensus Endocytosis/signaling protein EHD1 [Sign	85.75
cd04170	268	EF-G_bact Elongation factor G (EF-G) subfamily. Tr	85.27
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	84.98
PF02606	326	LpxK: Tetraacyldisaccharide-1-P 4'-kinase; InterPr	84.46
KOG0074	185	consensus GTP-binding ADP-ribosylation factor-like	83.48
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	82.39
KOG1707	625	consensus Predicted Ras related/Rac-GTP binding pr	82.17
PF09439	181	SRPRB: Signal recognition particle receptor beta s	81.18
cd01850	276	CDC_Septin CDC/Septin. Septins are a conserved fam	80.41
KOG0077	193	consensus Vesicle coat complex COPII, GTPase subun	80.17

>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]

Probab=100.00  E-value=3.5e-32  Score=207.82  Aligned_cols=166  Identities=45%  Similarity=0.629  Sum_probs=145.9

Q ss_pred             CHHHHHHhhcCCcEEEEEecCCCchhHHHHHH-cCCCCccceeecccCC-CcccccccccccCHhHHHhhHhhCC-CCEE
Q 030407            1 MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMR-NGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNLFK-ADLL   77 (178)
Q Consensus         1 ~~~~~~~~~~~~~vaVI~nd~g~~iD~~li~~-~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~~-~d~i   77 (178)
                      ++++++.|++++++|||.||.-+.-|++++.+ .|.    +++...+|- | |+    |.+..+.++.+|...++ .|++
T Consensus        30 ie~~~~~L~~~~~~aVI~~Di~t~~Da~~l~~~~g~----~i~~v~TG~~C-H~----da~m~~~ai~~l~~~~~~~Dll  100 (202)
T COG0378          30 IEKTLRALKDEYKIAVITGDIYTKEDADRLRKLPGE----PIIGVETGKGC-HL----DASMNLEAIEELVLDFPDLDLL  100 (202)
T ss_pred             HHHHHHHHHhhCCeEEEeceeechhhHHHHHhCCCC----eeEEeccCCcc-CC----cHHHHHHHHHHHhhcCCcCCEE
Confidence            47889999888999999999999999999988 555    899999995 7 86    33333488888876654 7999


Q ss_pred             EEeCCcchhhhcccccccc-eEEEEEeCCCCCCCCcC-CCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCE
Q 030407           78 LCESGGDNLAANFSRELAD-YIIYIIDVSGGDKIPRK-GGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPF  155 (178)
Q Consensus        78 iiEttG~~~~~~~~~~~ad-~~I~VvD~~~~~~~~~~-~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i  155 (178)
                      |||+.| |+++++++++.+ ..|+|+|+++|++.+.+ +|..++ ||++||||+||++.+..+++.+.+..++.||.+|+
T Consensus       101 ~iEs~G-NL~~~~sp~L~d~~~v~VidvteGe~~P~K~gP~i~~-aDllVInK~DLa~~v~~dlevm~~da~~~np~~~i  178 (202)
T COG0378         101 FIESVG-NLVCPFSPDLGDHLRVVVIDVTEGEDIPRKGGPGIFK-ADLLVINKTDLAPYVGADLEVMARDAKEVNPEAPI  178 (202)
T ss_pred             EEecCc-ceecccCcchhhceEEEEEECCCCCCCcccCCCceeE-eeEEEEehHHhHHHhCccHHHHHHHHHHhCCCCCE
Confidence            999999 999999998876 99999999999999998 655555 99999999999999778889999999999999999


Q ss_pred             EEEecccCCCHHHHHHHHhhhh
Q 030407          156 IFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       156 ~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +++|++||+|+++|++++...+
T Consensus       179 i~~n~ktg~G~~~~~~~i~~~~  200 (202)
T COG0378         179 IFTNLKTGEGLDEWLRFIEPQA  200 (202)
T ss_pred             EEEeCCCCcCHHHHHHHHHhhc
Confidence            9999999999999999998653

>COG0523 Putative GTPases (G3E family) [General function prediction only]

Probab=100.00  E-value=1.3e-33  Score=233.81  Aligned_cols=158  Identities=22%  Similarity=0.242  Sum_probs=121.4

Q ss_pred             HHHHHHhhcCCcEEEEEecCC-CchhH-HHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhHhhCCCCEEE
Q 030407            2 LALCKFLRDKYSLAAVTNDIF-TKEDG-EFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNLFKADLLL   78 (178)
Q Consensus         2 ~~~~~~~~~~~~vaVI~nd~g-~~iD~-~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~~~d~ii   78 (178)
                      .+++++.. ++|+|||+|||| ++||+ .++...+.    ++.||+||| ||++  |+|+...+..|.+ . +..||+|+
T Consensus        19 ~~lL~~~~-g~kiAVIVNEfGEvgID~~~~l~~~~e----~~~El~nGCICCT~--r~dl~~~~~~L~~-~-~~~~D~iv   89 (323)
T COG0523          19 NHLLANRD-GKKIAVIVNEFGEVGIDGGALLSDTGE----EVVELTNGCICCTV--RDDLLPALERLLR-R-RDRPDRLV   89 (323)
T ss_pred             HHHHhccC-CCcEEEEEecCccccccCCCccccCCc----cEEEeCCceEEEec--cchhHHHHHHHHh-c-cCCCCEEE
Confidence            44555444 699999999999 99995 77776554    799999999 9984  8888655555544 2 44699999


Q ss_pred             EeCCcchh----hhcccc--cc-----cceEEEEEeCCCCCCCC----cCCCCCCCceeEEEEecCCCCCchhHhHHHHH
Q 030407           79 CESGGDNL----AANFSR--EL-----ADYIIYIIDVSGGDKIP----RKGGPGITQADLLVINKTDLASAIGADLAVME  143 (178)
Q Consensus        79 iEttG~~~----~~~~~~--~~-----ad~~I~VvD~~~~~~~~----~~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~  143 (178)
                      |||||++.    +.++..  ..     .|.+|+|||+.+.....    ..+..|+++||+|++||+|++++  ++++.++
T Consensus        90 IEtTGlA~P~pv~~t~~~~~~l~~~~~ld~vvtvVDa~~~~~~~~~~~~~~~~Qia~AD~ivlNK~Dlv~~--~~l~~l~  167 (323)
T COG0523          90 IETTGLADPAPVIQTFLTDPELADGVRLDGVVTVVDAAHFLEGLDAIAELAEDQLAFADVIVLNKTDLVDA--EELEALE  167 (323)
T ss_pred             EeCCCCCCCHHHHHHhccccccccceeeceEEEEEeHHHhhhhHHHHHHHHHHHHHhCcEEEEecccCCCH--HHHHHHH
Confidence            99999532    222221  11     38899999998865432    23557999999999999999999  7899999


Q ss_pred             HHHHhcCCCCCEEEEecccCCCHHHHHH
Q 030407          144 RDALRMRDGGPFIFAQVGWVIGIIFTLS  171 (178)
Q Consensus       144 ~~l~~~np~a~i~~~SA~~g~gi~el~~  171 (178)
                      ++++++||.|+++.+|. .+.+..+++.
T Consensus       168 ~~l~~lnp~A~i~~~~~-~~~~~~~ll~  194 (323)
T COG0523         168 ARLRKLNPRARIIETSY-GDVDLAELLD  194 (323)
T ss_pred             HHHHHhCCCCeEEEccc-cCCCHHHhhc
Confidence            99999999999999997 5566666654

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=99.97  E-value=8.3e-30  Score=207.47  Aligned_cols=166  Identities=22%  Similarity=0.186  Sum_probs=135.6

Q ss_pred             CHHHHHHhhcCCcEEEEEecCCCchhHHHHHHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCCCCEEEEe
Q 030407            1 MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLLLCE   80 (178)
Q Consensus         1 ~~~~~~~~~~~~~vaVI~nd~g~~iD~~li~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~~d~iiiE   80 (178)
                      |+++++.+..+.+++||.||+++..|+.+++..|+    +++++++||+||+. +.++.   .++..|. ..+.|++|||
T Consensus       121 l~~l~~~l~~~~~~~VI~gD~~t~~Da~rI~~~g~----pvvqi~tG~~Chl~-a~mv~---~Al~~L~-~~~~d~liIE  191 (290)
T PRK10463        121 LTETLMRLKDSVPCAVIEGDQQTVNDAARIRATGT----PAIQVNTGKGCHLD-AQMIA---DAAPRLP-LDDNGILFIE  191 (290)
T ss_pred             HHHHHHHhccCCCEEEECCCcCcHHHHHHHHhcCC----cEEEecCCCCCcCc-HHHHH---HHHHHHh-hcCCcEEEEE
Confidence            35667777766899999999995459999998887    79999999944441 33332   6666664 5678999999


Q ss_pred             CCcchhhhcccccc-cceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEe
Q 030407           81 SGGDNLAANFSREL-ADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQ  159 (178)
Q Consensus        81 ttG~~~~~~~~~~~-ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~S  159 (178)
                      ++| +++.|...++ .+..++++++.++++.+.+++.|++.||++|+||+||++....+++.+.+.++++||.++++++|
T Consensus       192 nvG-nLvcPa~fdlge~~~v~vlsV~eg~dkplKyp~~f~~ADIVVLNKiDLl~~~~~dle~~~~~lr~lnp~a~I~~vS  270 (290)
T PRK10463        192 NVG-NLVCPASFDLGEKHKVAVLSVTEGEDKPLKYPHMFAAASLMLLNKVDLLPYLNFDVEKCIACAREVNPEIEIILIS  270 (290)
T ss_pred             CCC-CccCCCccchhhceeEEEEECccccccchhccchhhcCcEEEEEhHHcCcccHHHHHHHHHHHHhhCCCCcEEEEE
Confidence            999 6666554332 45678999999998888889999999999999999999853367888999999999999999999


Q ss_pred             cccCCCHHHHHHHHhhh
Q 030407          160 VGWVIGIIFTLSITHYI  176 (178)
Q Consensus       160 A~~g~gi~el~~~l~~~  176 (178)
                      |++|+|+++|+++|.+.
T Consensus       271 A~tGeGld~L~~~L~~~  287 (290)
T PRK10463        271 ATSGEGMDQWLNWLETQ  287 (290)
T ss_pred             CCCCCCHHHHHHHHHHh
Confidence            99999999999999864

>TIGR00101 ureG urease accessory protein UreG

Probab=99.97  E-value=5.8e-30  Score=199.66  Aligned_cols=173  Identities=54%  Similarity=0.811  Sum_probs=139.1

Q ss_pred             HHHHHHhhcCCcEEEEEecCCCchhHHHHHHcCCCCccceeec-ccCC-CcccccccccccCHhHHHhhHhh-CCCCEEE
Q 030407            2 LALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAV-ETGG-CPHAAIREDISINLGPLEELSNL-FKADLLL   78 (178)
Q Consensus         2 ~~~~~~~~~~~~vaVI~nd~g~~iD~~li~~~~~~~~~~~~~l-~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~-~~~d~ii   78 (178)
                      .++++.+....+++++.||++...|+.++.+.+..+.++++.+ .+|| ||.  +|+|+...+.+|.++..+ .++|+|+
T Consensus        19 ~~l~~~l~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~--~~~~~~~~~~~L~~l~~~~~~~D~ii   96 (199)
T TIGR00101        19 EALTRALRQKYQLAVITNDIYTQEDAEFLVKNSALPPERILGVETGGCPHTA--IREDASMNLEAVAEMEARFPPLEMVF   96 (199)
T ss_pred             HHHHHhhCcCCcEEEEeCCcCChhHHHHHHHcCCCCcCceehhhcCCCccce--eccCHHHHHHHHHHHHhcCCCCCEEE
Confidence            3455665555789999999997789998877775444456665 6788 665  588876656777766533 3699999


Q ss_pred             EeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEE
Q 030407           79 CESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFA  158 (178)
Q Consensus        79 iEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~  158 (178)
                      |||+|.++.+++.+..++.+|+|+|+.+++..+..+..|+..||++++||+|+.+...++++.+.+.++++||.++++++
T Consensus        97 IEt~G~~l~~~~~~~l~~~~i~vvD~~~~~~~~~~~~~qi~~ad~~~~~k~d~~~~~~~~~~~~~~~~~~~~~~~~i~~~  176 (199)
T TIGR00101        97 IESGGDNLSATFSPELADLTIFVIDVAAGDKIPRKGGPGITRSDLLVINKIDLAPMVGADLGVMERDAKKMRGEKPFIFT  176 (199)
T ss_pred             EECCCCCcccccchhhhCcEEEEEEcchhhhhhhhhHhHhhhccEEEEEhhhccccccccHHHHHHHHHHhCCCCCEEEE
Confidence            99999777777766668999999999998876555567999999999999999874336788889999999999999999


Q ss_pred             ecccCCCHHHHHHHHhhh
Q 030407          159 QVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       159 SA~~g~gi~el~~~l~~~  176 (178)
                      ||++|+|+++|++++.+.
T Consensus       177 Sa~~g~gi~el~~~i~~~  194 (199)
T TIGR00101       177 NLKTKEGLDTVIDWIEHY  194 (199)
T ss_pred             ECCCCCCHHHHHHHHHhh
Confidence            999999999999998764

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.

>PF02492 cobW: CobW/HypB/UreG, nucleotide-binding domain; InterPro: IPR003495 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt

Probab=99.96  E-value=4.1e-30  Score=197.12  Aligned_cols=146  Identities=25%  Similarity=0.343  Sum_probs=105.5

Q ss_pred             CHHHHHHhhcCCcEEEEEecCC-CchhHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhHhhC--CCCE
Q 030407            1 MLALCKFLRDKYSLAAVTNDIF-TKEDGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNLF--KADL   76 (178)
Q Consensus         1 ~~~~~~~~~~~~~vaVI~nd~g-~~iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~--~~d~   76 (178)
                      |.++++...+++|+|||+|||| +++|+.++++.|.    .++++++|| ||++  ++|+.   .++.++.+.+  +||+
T Consensus        17 i~~ll~~~~~~~~~~vI~ne~g~~~iD~~~l~~~~~----~v~~l~~gcicc~~--~~~~~---~~l~~l~~~~~~~~d~   87 (178)
T PF02492_consen   17 INHLLKRNRQGERVAVIVNEFGEVNIDAELLQEDGV----PVVELNNGCICCTL--RDDLV---EALRRLLREYEERPDR   87 (178)
T ss_dssp             HHHHHHHHTTTS-EEEEECSTTSTHHHHHHHHTTT-----EEEEECTTTESS-T--TS-HH---HHHHHHCCCCHGC-SE
T ss_pred             HHHHHHHhcCCceeEEEEccccccccchhhhcccce----EEEEecCCCccccc--HHHHH---HHHHHHHHhcCCCcCE
Confidence            3566663445699999999999 9999999998776    799999999 9985  55553   6677777677  8999


Q ss_pred             EEEeCCcchhhhcc---cc-----cccceEEEEEeCCCCCC---CCcCCCCCCCceeEEEEecCCCCCchhH-hHHHHHH
Q 030407           77 LLCESGGDNLAANF---SR-----ELADYIIYIIDVSGGDK---IPRKGGPGITQADLLVINKTDLASAIGA-DLAVMER  144 (178)
Q Consensus        77 iiiEttG~~~~~~~---~~-----~~ad~~I~VvD~~~~~~---~~~~~~~qi~~adiiviNK~Dl~~~~~~-~~~~~~~  144 (178)
                      ||||++|++-..++   .+     -..+.+|+|+|+.+...   ....+.+|++.||+|++||+|++++  + .++++++
T Consensus        88 IiIE~sG~a~p~~l~~~~~~~~~~~~~~~iI~vVDa~~~~~~~~~~~~~~~Qi~~ADvIvlnK~D~~~~--~~~i~~~~~  165 (178)
T PF02492_consen   88 IIIETSGLADPAPLILQDPPLKEDFRLDSIITVVDATNFDELENIPELLREQIAFADVIVLNKIDLVSD--EQKIERVRE  165 (178)
T ss_dssp             EEEEEECSSGGGGHHHHSHHHHHHESESEEEEEEEGTTHGGHTTHCHHHHHHHCT-SEEEEE-GGGHHH--H--HHHHHH
T ss_pred             EEECCccccccchhhhccccccccccccceeEEeccccccccccchhhhhhcchhcCEEEEeccccCCh--hhHHHHHHH
Confidence            99999994322222   10     11378999999976522   2223456899999999999999988  6 4589999


Q ss_pred             HHHhcCCCCCEEE
Q 030407          145 DALRMRDGGPFIF  157 (178)
Q Consensus       145 ~l~~~np~a~i~~  157 (178)
                      .++++||.++|+.
T Consensus       166 ~ir~lnp~a~Iv~  178 (178)
T PF02492_consen  166 MIRELNPKAPIVQ  178 (178)
T ss_dssp             HHHHH-TTSEEE-
T ss_pred             HHHHHCCCCEEeC
Confidence            9999999999873

Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [].; PDB: 2WSM_B 1NIJ_A 2HF9_A 2HF8_B.

>PRK11537 putative GTP-binding protein YjiA; Provisional

Probab=99.95  E-value=3.4e-28  Score=201.72  Aligned_cols=144  Identities=19%  Similarity=0.302  Sum_probs=107.7

Q ss_pred             HHHHHHhhcCCcEEEEEecCC-CchhHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhHhh-----CCC
Q 030407            2 LALCKFLRDKYSLAAVTNDIF-TKEDGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNL-----FKA   74 (178)
Q Consensus         2 ~~~~~~~~~~~~vaVI~nd~g-~~iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~-----~~~   74 (178)
                      ++++++ ..++|+|||+|||| +++|+.++.+.+.    .+.+|+||| ||++  ++||...+   .++...     .+|
T Consensus        22 ~~ll~~-~~~~riaVi~NEfG~v~iD~~ll~~~~~----~v~eL~~GCiCCs~--~~~l~~~l---~~l~~~~~~~~~~~   91 (318)
T PRK11537         22 RHILNE-QHGYKIAVIENEFGEVSVDDQLIGDRAT----QIKTLTNGCICCSR--SNELEDAL---LDLLDNLDKGNIQF   91 (318)
T ss_pred             HHHHhc-ccCCcccccccCcCCccccHHHHhCcCc----eEEEECCCEEEEcc--CchHHHHH---HHHHHHHhccCCCC
Confidence            344443 23589999999999 9999999975443    789999999 9985  67776444   444322     269


Q ss_pred             CEEEEeCCcch----hhhccc--cc-----ccceEEEEEeCCCCCCCCcC---CCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           75 DLLLCESGGDN----LAANFS--RE-----LADYIIYIIDVSGGDKIPRK---GGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        75 d~iiiEttG~~----~~~~~~--~~-----~ad~~I~VvD~~~~~~~~~~---~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      |+|+|||||++    +...+.  +.     ..+.+|+|||+.++......   ...|++.||+||+||+|++++  .  +
T Consensus        92 d~IvIEttG~a~p~~i~~~~~~~~~l~~~~~l~~vvtvvDa~~~~~~~~~~~~~~~Qi~~AD~IvlnK~Dl~~~--~--~  167 (318)
T PRK11537         92 DRLVIECTGMADPGPIIQTFFSHEVLCQRYLLDGVIALVDAVHADEQMNQFTIAQSQVGYADRILLTKTDVAGE--A--E  167 (318)
T ss_pred             CEEEEECCCccCHHHHHHHHhcChhhcccEEeccEEEEEEhhhhhhhccccHHHHHHHHhCCEEEEeccccCCH--H--H
Confidence            99999999963    222221  11     13789999999876543322   235899999999999999976  4  6


Q ss_pred             HHHHHHHhcCCCCCEEEEe
Q 030407          141 VMERDALRMRDGGPFIFAQ  159 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~S  159 (178)
                      ++.+.++++||.|+++.++
T Consensus       168 ~~~~~l~~lnp~a~i~~~~  186 (318)
T PRK11537        168 KLRERLARINARAPVYTVV  186 (318)
T ss_pred             HHHHHHHHhCCCCEEEEec
Confidence            8899999999999999876

>TIGR02475 CobW cobalamin biosynthesis protein CobW

Probab=99.94  E-value=8.2e-27  Score=195.14  Aligned_cols=153  Identities=24%  Similarity=0.249  Sum_probs=113.5

Q ss_pred             CCcEEEEEecCC-CchhHHHHHHcCCC--CccceeecccCC-CcccccccccccCHhHHHhhHh-hCCCCEEEEeCCcch
Q 030407           11 KYSLAAVTNDIF-TKEDGEFLMRNGAL--PEERIRAVETGG-CPHAAIREDISINLGPLEELSN-LFKADLLLCESGGDN   85 (178)
Q Consensus        11 ~~~vaVI~nd~g-~~iD~~li~~~~~~--~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~-~~~~d~iiiEttG~~   85 (178)
                      ++|+|||+|||| ++||+.+++..+..  ..+.+++|+||| ||++  ++||.   .++.++.. ..+||+|+|||||++
T Consensus        30 ~~~iavi~Ne~G~~~ID~~ll~~~~~~~~~~~~v~el~nGCiCCs~--~~dl~---~~l~~l~~~~~~~d~IvIEtsG~a  104 (341)
T TIGR02475        30 GRRIAVIVNEFGDLGIDGEILKACGIEGCSEENIVELANGCICCTV--ADDFI---PTMTKLLARRQRPDHILIETSGLA  104 (341)
T ss_pred             CCcEEEEECCCccccchHHHHhccccccCCcceEEEeCCCCccccC--cHHHH---HHHHHHHhccCCCCEEEEeCCCCC
Confidence            589999999999 99999999765431  123689999999 9985  66664   56666654 467999999999963


Q ss_pred             ----hhhccc-cc-----ccceEEEEEeCCCCCCC---------------------C----cCCCCCCCceeEEEEecCC
Q 030407           86 ----LAANFS-RE-----LADYIIYIIDVSGGDKI---------------------P----RKGGPGITQADLLVINKTD  130 (178)
Q Consensus        86 ----~~~~~~-~~-----~ad~~I~VvD~~~~~~~---------------------~----~~~~~qi~~adiiviNK~D  130 (178)
                          ++..+. +.     ..+.+|+|||+.+....                     .    ..+..|+++||+|++||+|
T Consensus       105 ~P~~i~~~~~~~~l~~~~~l~~vvtvVDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Qi~~AD~IvlnK~D  184 (341)
T TIGR02475       105 LPKPLVQAFQWPEIRSRVTVDGVVTVVDGPAVAAGRFAADPDALDAQRAADDNLDHETPLEELFEDQLACADLVILNKAD  184 (341)
T ss_pred             CHHHHHHHhcCccccceEEeeeEEEEEECchhhhhccccchhhhhhhccccccccccchHHHHHHHHHHhCCEEEEeccc
Confidence                233332 11     13889999999754210                     0    0113589999999999999


Q ss_pred             CCCchhHhHHHHHHHHHhcCCC-CCEEEEecccCCCHHHHHH
Q 030407          131 LASAIGADLAVMERDALRMRDG-GPFIFAQVGWVIGIIFTLS  171 (178)
Q Consensus       131 l~~~~~~~~~~~~~~l~~~np~-a~i~~~SA~~g~gi~el~~  171 (178)
                      ++++  ++++.+++.++++||. ++++.++ ........+++
T Consensus       185 l~~~--~~l~~~~~~l~~~~~~~a~i~~~~-~~~v~~~~ll~  223 (341)
T TIGR02475       185 LLDA--AGLARVRAEIAAELPRAVKIVEAS-HGEVDARVLLG  223 (341)
T ss_pred             cCCH--HHHHHHHHHHHHhCCCCCEEEEcc-cCCCCHHHHhC
Confidence            9999  8999999999998875 5888876 33455666554

A broader CobW family is delineated by two PFAM models which identify the N- and C-terminal domains (pfam02492 and pfam07683).

>KOG2743 consensus Cobalamin synthesis protein [Coenzyme transport and metabolism]

Probab=99.94  E-value=1.1e-27  Score=193.09  Aligned_cols=152  Identities=19%  Similarity=0.189  Sum_probs=115.0

Q ss_pred             CCcEEEEEecCC--CchhHHHHHHcCC-CCccceeecccCC-CcccccccccccCHhHHHhhHhh-CCCCEEEEeCCcch
Q 030407           11 KYSLAAVTNDIF--TKEDGEFLMRNGA-LPEERIRAVETGG-CPHAAIREDISINLGPLEELSNL-FKADLLLCESGGDN   85 (178)
Q Consensus        11 ~~~vaVI~nd~g--~~iD~~li~~~~~-~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~-~~~d~iiiEttG~~   85 (178)
                      ++|+|||.||||  +.++..++.+.+. ..-+...+|+||| ||++  |+++.   +++.++.++ .+||+|++||||++
T Consensus        83 gKRIAVIlNEfGes~die~sl~~~~~gg~lyEewv~L~NGClCCtV--k~~gv---raie~lvqkkGkfD~IllETTGlA  157 (391)
T KOG2743|consen   83 GKRIAVILNEFGESSDIEKSLAVSQEGGELYEEWVELRNGCLCCTV--KDNGV---RAIENLVQKKGKFDHILLETTGLA  157 (391)
T ss_pred             CceEEEEhhhcccchhhhHHHHhccccchHHHHHHHhcCCeEEEEe--cchHH---HHHHHHHhcCCCcceEEEeccCCC
Confidence            399999999999  5899999876522 1125678999999 9986  55553   777777654 46999999999953


Q ss_pred             ----hhhcccccc-------cceEEEEEeCCCCCCCCc-----C----CCCCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           86 ----LAANFSREL-------ADYIIYIIDVSGGDKIPR-----K----GGPGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        86 ----~~~~~~~~~-------ad~~I~VvD~~~~~~~~~-----~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                          ++.+|+.+.       .|++|+|+|+.+......     .    .-.|+++||.|++||+||+++  +++..+++.
T Consensus       158 nPaPia~~Fw~dd~l~sdVkLDGIVTvvD~K~~~~~Lde~k~~g~i~EA~~QiA~AD~II~NKtDli~~--e~~~~l~q~  235 (391)
T KOG2743|consen  158 NPAPIASMFWLDDELGSDVKLDGIVTVVDAKHILKHLDEEKPDGLINEATRQIALADRIIMNKTDLVSE--EEVKKLRQR  235 (391)
T ss_pred             CcHHHHHHHhhhhhhcCceeeeeEEEEEehhhHHhhhcccCcccchHHHHHHHhhhheeeeccccccCH--HHHHHHHHH
Confidence                445565421       389999999987543221     1    224899999999999999999  999999999


Q ss_pred             HHhcCCCCCEEEEecccCCCHHHHH
Q 030407          146 ALRMRDGGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus       146 l~~~np~a~i~~~SA~~g~gi~el~  170 (178)
                      ++.+|.-|++++|-- ....+++++
T Consensus       236 I~~INslA~m~~Tky-~~vdlsnvL  259 (391)
T KOG2743|consen  236 IRSINSLAQMIETKY-SRVDLSNVL  259 (391)
T ss_pred             HHHhhhHHHhhhhhh-ccccHHHhc
Confidence            999999999988752 234455554

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=99.94  E-value=7.5e-26  Score=177.19  Aligned_cols=165  Identities=31%  Similarity=0.364  Sum_probs=124.6

Q ss_pred             HHHHHHhhcCCcEEEEEecCCCchhHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhHhhCCCCEEEEe
Q 030407            2 LALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNLFKADLLLCE   80 (178)
Q Consensus         2 ~~~~~~~~~~~~vaVI~nd~g~~iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~~~d~iiiE   80 (178)
                      +++++++..+.++||+.||++.++|..++++.|.    .++++.+|| ||..  ..++.   .++..+. ..++|+||||
T Consensus        40 ~~l~~~~~~~~~v~v~~~~~~~~~D~~~~~~~~~----~~~~l~~gcic~~~--~~~~~---~~l~~~~-~~~~d~IiIE  109 (207)
T TIGR00073        40 EKLIDNLKDEVKIAVIEGDVITKFDAERLRKYGA----PAIQINTGKECHLD--AHMVA---HALEDLP-LDDIDLLFIE  109 (207)
T ss_pred             HHHHHHHhcCCeEEEEECCCCCcccHHHHHHcCC----cEEEEcCCCcccCC--hHHHH---HHHHHhc-cCCCCEEEEe
Confidence            5666766555899999999998899999988776    789999999 7732  12221   4444333 3478999999


Q ss_pred             CCcchhhhcccc-cccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEe
Q 030407           81 SGGDNLAANFSR-ELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQ  159 (178)
Q Consensus        81 ttG~~~~~~~~~-~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~S  159 (178)
                      |+| .+..+... ...+..++|+|+.+++.....++.++..|+++++||+|+.++...+.+.+.+.+++.+|.++++++|
T Consensus       110 t~G-~l~~~~~~~~~~~~~i~Vvd~~~~d~~~~~~~~~~~~a~iiv~NK~Dl~~~~~~~~~~~~~~l~~~~~~~~i~~~S  188 (207)
T TIGR00073       110 NVG-NLVCPADFDLGEHMRVVLLSVTEGDDKPLKYPGMFKEADLIVINKADLAEAVGFDVEKMKADAKKINPEAEIILMS  188 (207)
T ss_pred             cCC-CcCCCcccccccCeEEEEEecCcccchhhhhHhHHhhCCEEEEEHHHccccchhhHHHHHHHHHHhCCCCCEEEEE
Confidence            999 33323222 1246678899998877655555667788999999999998642234667778888889999999999


Q ss_pred             cccCCCHHHHHHHHhhhh
Q 030407          160 VGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       160 A~~g~gi~el~~~l~~~~  177 (178)
                      |++|+|++++++++.+.+
T Consensus       189 a~~g~gv~~l~~~i~~~~  206 (207)
T TIGR00073       189 LKTGEGLDEWLEFLEGQV  206 (207)
T ss_pred             CCCCCCHHHHHHHHHHhh
Confidence            999999999999998754

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=99.87  E-value=2.6e-21  Score=156.58  Aligned_cols=168  Identities=19%  Similarity=0.093  Sum_probs=125.6

Q ss_pred             HHHHHHhhcC-CcEEEEEecCCCch-------hHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhHhhC
Q 030407            2 LALCKFLRDK-YSLAAVTNDIFTKE-------DGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNLF   72 (178)
Q Consensus         2 ~~~~~~~~~~-~~vaVI~nd~g~~i-------D~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~   72 (178)
                      .++++.|.++ +|||||.-|++++.       |..+|+.....++.+++++++++ --.+      +........+.+..
T Consensus        69 ~~L~~~l~~~G~rVaVlAVDPSSp~TGGsiLGDRiRM~~~~~~~~vFiRs~~srG~lGGl------S~at~~~i~~ldAa  142 (323)
T COG1703          69 EALGRELRERGHRVAVLAVDPSSPFTGGSILGDRIRMQRLAVDPGVFIRSSPSRGTLGGL------SRATREAIKLLDAA  142 (323)
T ss_pred             HHHHHHHHHCCcEEEEEEECCCCCCCCccccccHhhHHhhccCCCeEEeecCCCccchhh------hHHHHHHHHHHHhc
Confidence            5678888664 99999999999654       88899887655677999999988 3333      43443333455688


Q ss_pred             CCCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhc---
Q 030407           73 KADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRM---  149 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~---  149 (178)
                      +||+|||||+|+..........+|.+++|.-+..|++.+......++.||++|+||.|+.... .....+...++..   
T Consensus       143 G~DvIIVETVGvGQsev~I~~~aDt~~~v~~pg~GD~~Q~iK~GimEiaDi~vINKaD~~~A~-~a~r~l~~al~~~~~~  221 (323)
T COG1703         143 GYDVIIVETVGVGQSEVDIANMADTFLVVMIPGAGDDLQGIKAGIMEIADIIVINKADRKGAE-KAARELRSALDLLREV  221 (323)
T ss_pred             CCCEEEEEecCCCcchhHHhhhcceEEEEecCCCCcHHHHHHhhhhhhhheeeEeccChhhHH-HHHHHHHHHHHhhccc
Confidence            999999999997766555445679999999999999888877888999999999999975441 1111222222222   


Q ss_pred             ---C-CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          150 ---R-DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       150 ---n-p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                         + ...|++.|||.+|+|+++|++.+...
T Consensus       222 ~~~~~W~ppv~~t~A~~g~Gi~~L~~ai~~h  252 (323)
T COG1703         222 WRENGWRPPVVTTSALEGEGIDELWDAIEDH  252 (323)
T ss_pred             ccccCCCCceeEeeeccCCCHHHHHHHHHHH
Confidence               1 23599999999999999999988753

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=99.86  E-value=9.9e-22  Score=156.85  Aligned_cols=168  Identities=20%  Similarity=0.108  Sum_probs=113.4

Q ss_pred             HHHHHHhhc-CCcEEEEEecCCCch-------hHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhHhhC
Q 030407            2 LALCKFLRD-KYSLAAVTNDIFTKE-------DGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNLF   72 (178)
Q Consensus         2 ~~~~~~~~~-~~~vaVI~nd~g~~i-------D~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~   72 (178)
                      .++++++.+ ++|||||.-|+++++       |..+|+.....++.+++++.+++ .-.+      +........+++..
T Consensus        47 ~~l~~~~~~~g~~VaVlAVDPSSp~tGGAlLGDRiRM~~~~~d~~vfIRS~atRG~lGGl------s~~t~~~v~ll~aa  120 (266)
T PF03308_consen   47 DALIRELRERGKRVAVLAVDPSSPFTGGALLGDRIRMQELSRDPGVFIRSMATRGSLGGL------SRATRDAVRLLDAA  120 (266)
T ss_dssp             HHHHHHHHHTT--EEEEEE-GGGGCC---SS--GGGCHHHHTSTTEEEEEE---SSHHHH------HHHHHHHHHHHHHT
T ss_pred             HHHHHHHhhcCCceEEEEECCCCCCCCCcccccHHHhcCcCCCCCEEEeecCcCCCCCCc------cHhHHHHHHHHHHc
Confidence            567777765 499999999999654       88888765433456899999888 3333      33333334566688


Q ss_pred             CCCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCC-
Q 030407           73 KADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRD-  151 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np-  151 (178)
                      +||+|||||+|+..........+|.+++|+-+..|++.+......++.||++|+||.|+.... .....++..++-..+ 
T Consensus       121 G~D~IiiETVGvGQsE~~I~~~aD~~v~v~~Pg~GD~iQ~~KaGimEiaDi~vVNKaD~~gA~-~~~~~l~~~l~l~~~~  199 (266)
T PF03308_consen  121 GFDVIIIETVGVGQSEVDIADMADTVVLVLVPGLGDEIQAIKAGIMEIADIFVVNKADRPGAD-RTVRDLRSMLHLLRER  199 (266)
T ss_dssp             T-SEEEEEEESSSTHHHHHHTTSSEEEEEEESSTCCCCCTB-TTHHHH-SEEEEE--SHHHHH-HHHHHHHHHHHHCSTS
T ss_pred             CCCEEEEeCCCCCccHHHHHHhcCeEEEEecCCCccHHHHHhhhhhhhccEEEEeCCChHHHH-HHHHHHHHHHhhcccc
Confidence            999999999997776555555689999999999999998888888999999999999965441 112334444432221 


Q ss_pred             ----CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          152 ----GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       152 ----~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                          ..||+.|||.+|+||++|++.+.+.
T Consensus       200 ~~~W~ppV~~tsA~~~~Gi~eL~~~i~~~  228 (266)
T PF03308_consen  200 EDGWRPPVLKTSALEGEGIDELWEAIDEH  228 (266)
T ss_dssp             CTSB--EEEEEBTTTTBSHHHHHHHHHHH
T ss_pred             ccCCCCCEEEEEeCCCCCHHHHHHHHHHH
Confidence                3599999999999999999998764

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=99.85  E-value=1.3e-20  Score=156.90  Aligned_cols=170  Identities=17%  Similarity=0.092  Sum_probs=115.7

Q ss_pred             HHHHHHhhc-CCcEEEEEecCCCch-------hHHHHHHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCC
Q 030407            2 LALCKFLRD-KYSLAAVTNDIFTKE-------DGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFK   73 (178)
Q Consensus         2 ~~~~~~~~~-~~~vaVI~nd~g~~i-------D~~li~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~   73 (178)
                      .++++.+.+ +++++||.+|+++.+       |..+++..+..+  .+..-+.++||++.   ++...+.....+....+
T Consensus        74 ~~l~~~l~~~g~~v~vi~~Dp~s~~~~gallgd~~r~~~~~~~~--~~~~r~~~~~~~l~---~~a~~~~~~~~~~~~~g  148 (332)
T PRK09435         74 EALGMHLIEQGHKVAVLAVDPSSTRTGGSILGDKTRMERLSRHP--NAFIRPSPSSGTLG---GVARKTRETMLLCEAAG  148 (332)
T ss_pred             HHHHHHHHHCCCeEEEEEeCCCccccchhhhchHhHHHhhcCCC--CeEEEecCCccccc---chHHHHHHHHHHHhccC
Confidence            356667765 489999999998543       777776554322  32333335578762   33334433334445779


Q ss_pred             CCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchh--HhHHHHHHHHHhcCC
Q 030407           74 ADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIG--ADLAVMERDALRMRD  151 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~--~~~~~~~~~l~~~np  151 (178)
                      ||+|||||+|...........+|.+++++++..+++.+.....+++.||++|+||+|+.+...  .....+.+.++-.+|
T Consensus       149 ~d~viieT~Gv~qs~~~i~~~aD~vlvv~~p~~gd~iq~~k~gi~E~aDIiVVNKaDl~~~~~a~~~~~el~~~L~l~~~  228 (332)
T PRK09435        149 YDVILVETVGVGQSETAVAGMVDFFLLLQLPGAGDELQGIKKGIMELADLIVINKADGDNKTAARRAAAEYRSALRLLRP  228 (332)
T ss_pred             CCEEEEECCCCccchhHHHHhCCEEEEEecCCchHHHHHHHhhhhhhhheEEeehhcccchhHHHHHHHHHHHHHhcccc
Confidence            999999999965444444456899999998777776655455689999999999999987511  122234444433232


Q ss_pred             -----CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          152 -----GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       152 -----~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                           ..|++++||++|+|+++|++.+.+.
T Consensus       229 ~~~~w~~pVi~vSA~~g~GIdeL~~~I~~~  258 (332)
T PRK09435        229 KDPGWQPPVLTCSALEGEGIDEIWQAIEDH  258 (332)
T ss_pred             cccCCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence                 2699999999999999999988764

>cd03112 CobW_like The function of this protein family is unkown

Probab=99.83  E-value=5.8e-21  Score=143.86  Aligned_cols=115  Identities=25%  Similarity=0.353  Sum_probs=83.7

Q ss_pred             CCcEEEEEecCC-CchhHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHH-HhhH-hhCCCCEEEEeCCcch-
Q 030407           11 KYSLAAVTNDIF-TKEDGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPL-EELS-NLFKADLLLCESGGDN-   85 (178)
Q Consensus        11 ~~~vaVI~nd~g-~~iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l-~~l~-~~~~~d~iiiEttG~~-   85 (178)
                      +.++++|+||+| .++|+..+.+.+.    .+.++.+|| ||++  ++|+...+..+ .++. +.++||+|||||+|+. 
T Consensus        26 ~~~~~~i~~~~G~~~~d~~~~~~~~~----~v~~l~~GCiCC~~--~~~l~~~l~~l~~~~~~~~~~~d~I~IEt~G~~~   99 (158)
T cd03112          26 GRKIAVIENEFGEVGIDNQLVVDTDE----EIIEMNNGCICCTV--RGDLIRALLDLLERLDAGKIAFDRIVIETTGLAD   99 (158)
T ss_pred             CCcEEEEecCCCccchhHHHHhCCCc----eEEEeCCCEeEeeC--chhHHHHHHHHHHHHHhccCCCCEEEEECCCcCC
Confidence            589999999999 9999999986544    789999999 9986  66665444322 2332 2458999999999963 


Q ss_pred             ---hhhcc--cc-----cccceEEEEEeCCCCCCCC---cCCCCCCCceeEEEEecCCC
Q 030407           86 ---LAANF--SR-----ELADYIIYIIDVSGGDKIP---RKGGPGITQADLLVINKTDL  131 (178)
Q Consensus        86 ---~~~~~--~~-----~~ad~~I~VvD~~~~~~~~---~~~~~qi~~adiiviNK~Dl  131 (178)
                         +...+  .+     ...+.+++++|+.++....   ....+|++.||+||+||+|+
T Consensus       100 p~~~~~~~~~~~~~~~~~~~d~vv~vvDa~~~~~~~~~~~~~~~Qi~~ad~ivlnk~dl  158 (158)
T cd03112         100 PGPVAQTFFMDEELAERYLLDGVITLVDAKHANQHLDQQTEAQSQIAFADRILLNKTDL  158 (158)
T ss_pred             HHHHHHHHhhchhhhcceeeccEEEEEEhhHhHHHhhccHHHHHHHHHCCEEEEecccC
Confidence               11111  11     1248899999997754432   22446899999999999996

The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.

>TIGR00750 lao LAO/AO transport system ATPase

Probab=99.58  E-value=2e-14  Score=118.57  Aligned_cols=168  Identities=20%  Similarity=0.131  Sum_probs=98.6

Q ss_pred             HHHHHHhhc-CCcEEEEEecCCCch-------hHHHHHHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCC
Q 030407            2 LALCKFLRD-KYSLAAVTNDIFTKE-------DGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFK   73 (178)
Q Consensus         2 ~~~~~~~~~-~~~vaVI~nd~g~~i-------D~~li~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~   73 (178)
                      .+++..+.+ ++++++|.+|+..++       |...+......+...++++.++|  ++   +.+......+..+.+..+
T Consensus        52 ~~l~~~~~~~~~~v~~i~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~---~~~~~~~~~~~~~l~~~g  126 (300)
T TIGR00750        52 EALGMELRRRGLKVAVIAVDPSSPFTGGSILGDRTRMQRLATDPGAFIRSMPTRG--HL---GGLSQATRELILLLDAAG  126 (300)
T ss_pred             HHHHHHHHHCCCeEEEEecCCCCCcchhhhcccchhhhhcccCCCceeeecCccc--cc---cchhHHHHHHHHHHHhCC
Confidence            345565655 499999999988543       33334332221223556665533  11   011111223333445679


Q ss_pred             CCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHhHHHHH----HHHHhc
Q 030407           74 ADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVME----RDALRM  149 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~----~~l~~~  149 (178)
                      +|+|||||+|.+.........+|.++++.++..+++.........+.++++++||+|+.+.  .......    ..+..+
T Consensus       127 ~D~viidT~G~~~~e~~i~~~aD~i~vv~~~~~~~el~~~~~~l~~~~~ivv~NK~Dl~~~--~~~~~~~~~~~~~l~~l  204 (300)
T TIGR00750       127 YDVIIVETVGVGQSEVDIANMADTFVVVTIPGTGDDLQGIKAGLMEIADIYVVNKADGEGA--TNVTIARLMLALALEEI  204 (300)
T ss_pred             CCEEEEeCCCCchhhhHHHHhhceEEEEecCCccHHHHHHHHHHhhhccEEEEEcccccch--hHHHHHHHHHHHHHhhc
Confidence            9999999999543222222345777777666555443322233467789999999999876  3222111    111111


Q ss_pred             -----CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          150 -----RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       150 -----np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                           +...+++++||++|+|+++|++++.+.
T Consensus       205 ~~~~~~~~~~v~~iSA~~g~Gi~~L~~~i~~~  236 (300)
T TIGR00750       205 RRREDGWRPPVLTTSAVEGRGIDELWDAIEEH  236 (300)
T ss_pred             cccccCCCCCEEEEEccCCCCHHHHHHHHHHH
Confidence                 122479999999999999999988763

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>COG1160 Predicted GTPases [General function prediction only]

Probab=99.07  E-value=2.6e-10  Score=97.44  Aligned_cols=105  Identities=19%  Similarity=0.176  Sum_probs=74.9

Q ss_pred             CCCCEEEEeCCcch----hh---hccc-------ccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCC
Q 030407           72 FKADLLLCESGGDN----LA---ANFS-------RELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLAS  133 (178)
Q Consensus        72 ~~~d~iiiEttG~~----~~---~~~~-------~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~  133 (178)
                      .+-.|.+|+|.|+-    +.   ..|+       ...++.+++|+|++.+...++.    +..--..|.+||+||||+.+
T Consensus       224 ~~~~~~liDTAGiRrk~ki~e~~E~~Sv~rt~~aI~~a~vvllviDa~~~~~~qD~~ia~~i~~~g~~~vIvvNKWDl~~  303 (444)
T COG1160         224 DGRKYVLIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDLRIAGLIEEAGRGIVIVVNKWDLVE  303 (444)
T ss_pred             CCeEEEEEECCCCCcccccccceEEEeehhhHhHHhhcCEEEEEEECCCCchHHHHHHHHHHHHcCCCeEEEEEccccCC
Confidence            35678999999951    11   1111       1236999999999988655432    11123568999999999987


Q ss_pred             chhHhHHHHHHHHHhcCC---CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          134 AIGADLAVMERDALRMRD---GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       134 ~~~~~~~~~~~~l~~~np---~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.....+..++.+++..|   +||++++||++|.|+.++++.+...
T Consensus       304 ~~~~~~~~~k~~i~~~l~~l~~a~i~~iSA~~~~~i~~l~~~i~~~  349 (444)
T COG1160         304 EDEATMEEFKKKLRRKLPFLDFAPIVFISALTGQGLDKLFEAIKEI  349 (444)
T ss_pred             chhhHHHHHHHHHHHHhccccCCeEEEEEecCCCChHHHHHHHHHH
Confidence            532455666667766554   6899999999999999999987654

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=98.99  E-value=3.4e-09  Score=78.34  Aligned_cols=96  Identities=15%  Similarity=0.070  Sum_probs=71.6

Q ss_pred             EEEeCCcchhhhc-cc------ccccceEEEEEeCCCCCC-CCcCCCCCCCceeEEEEecCCCC-CchhHhHHHHHHHHH
Q 030407           77 LLCESGGDNLAAN-FS------RELADYIIYIIDVSGGDK-IPRKGGPGITQADLLVINKTDLA-SAIGADLAVMERDAL  147 (178)
Q Consensus        77 iiiEttG~~~~~~-~~------~~~ad~~I~VvD~~~~~~-~~~~~~~qi~~adiiviNK~Dl~-~~~~~~~~~~~~~l~  147 (178)
                      -+|+|.|--+..+ +.      ...+|.++++.|++.... .+..+...+..+.|-|+||+|+. ++  +++++.+++++
T Consensus        39 ~~IDTPGEyiE~~~~y~aLi~ta~dad~V~ll~dat~~~~~~pP~fa~~f~~pvIGVITK~Dl~~~~--~~i~~a~~~L~  116 (143)
T PF10662_consen   39 NTIDTPGEYIENPRFYHALIVTAQDADVVLLLQDATEPRSVFPPGFASMFNKPVIGVITKIDLPSDD--ANIERAKKWLK  116 (143)
T ss_pred             cEEECChhheeCHHHHHHHHHHHhhCCEEEEEecCCCCCccCCchhhcccCCCEEEEEECccCccch--hhHHHHHHHHH
Confidence            3489999422211 11      113699999999987643 33345556778899999999998 45  78888888998


Q ss_pred             hcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          148 RMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       148 ~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .... .++|.+|+.+|+||++|.++|++
T Consensus       117 ~aG~-~~if~vS~~~~eGi~eL~~~L~~  143 (143)
T PF10662_consen  117 NAGV-KEIFEVSAVTGEGIEELKDYLEE  143 (143)
T ss_pred             HcCC-CCeEEEECCCCcCHHHHHHHHhC
Confidence            6543 47899999999999999999864

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>cd04163 Era Era subfamily

Probab=98.95  E-value=2.3e-09  Score=78.72  Aligned_cols=102  Identities=14%  Similarity=0.035  Sum_probs=72.9

Q ss_pred             CCCEEEEeCCcchhhh---------c--ccccccceEEEEEeCCCCCCCCc-CCCC---CCCceeEEEEecCCCC-Cchh
Q 030407           73 KADLLLCESGGDNLAA---------N--FSRELADYIIYIIDVSGGDKIPR-KGGP---GITQADLLVINKTDLA-SAIG  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~---------~--~~~~~ad~~I~VvD~~~~~~~~~-~~~~---qi~~adiiviNK~Dl~-~~~~  136 (178)
                      +.++++++|.|..-..         .  .....+|.+++++|+++...... ....   ..+.+.++|+||+|+. .+  
T Consensus        50 ~~~~~liDtpG~~~~~~~~~~~~~~~~~~~~~~~d~i~~v~d~~~~~~~~~~~~~~~~~~~~~~~iiv~nK~Dl~~~~--  127 (168)
T cd04163          50 DAQIIFVDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEPIGEGDEFILELLKKSKTPVILVLNKIDLVKDK--  127 (168)
T ss_pred             CeEEEEEECCCCCcchHHHHHHHHHHHHHHHHhCCEEEEEEECCCccCchHHHHHHHHHHhCCCEEEEEEchhccccH--
Confidence            5789999999942110         0  01124689999999987632211 1111   1246789999999998 34  


Q ss_pred             HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 ~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+....+.++..++..+++.+|++++.|++++++.|.+.
T Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~l~~~l~~~  167 (168)
T cd04163         128 EDLLPLLEKLKELGPFAEIFPISALKGENVDELLEEIVKY  167 (168)
T ss_pred             HHHHHHHHHHHhccCCCceEEEEeccCCChHHHHHHHHhh
Confidence            5666677777777777899999999999999999998764

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.

>cd03114 ArgK-like The function of this protein family is unkown

Probab=98.93  E-value=3.8e-09  Score=78.73  Aligned_cols=122  Identities=24%  Similarity=0.236  Sum_probs=73.8

Q ss_pred             HHHHHhhc-CCcEEEEEecCC-CchhHHHHH------HcCCCCccceeecccCC-CcccccccccccCHhHHHhhHhhCC
Q 030407            3 ALCKFLRD-KYSLAAVTNDIF-TKEDGEFLM------RNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNLFK   73 (178)
Q Consensus         3 ~~~~~~~~-~~~vaVI~nd~g-~~iD~~li~------~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~~   73 (178)
                      ++...+.+ +.|+.++-.|++ ..-.+.++.      +....+.-.+..+..|+ |-..      ........+..+..+
T Consensus        18 ~l~~~~~~~g~~v~ii~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~   91 (148)
T cd03114          18 ALITALRARGKRVAVLAIDPSSPFSGGAILGDRIRMERHASDPGVFIRSLATRGFLGGL------SRATPEVIRVLDAAG   91 (148)
T ss_pred             HHHHHHHHCCCEEEEEEeCCCCCCcccchhcCceEhhheecCCCceEEEcCCcCccccc------chhHHHHHHHHHhcC
Confidence            45555654 499999999987 322222221      11000111344455444 2211      122222334444568


Q ss_pred             CCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCC
Q 030407           74 ADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTD  130 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~D  130 (178)
                      +|+|||||+|.+.........+|.++++..++..+.+...+.++++.||++++||+|
T Consensus        92 ~D~iiIDtaG~~~~~~~~~~~Ad~~ivv~tpe~~D~y~~~k~~~~~~~~~~~~~k~~  148 (148)
T cd03114          92 FDVIIVETVGVGQSEVDIASMADTTVVVMAPGAGDDIQAIKAGIMEIADIVVVNKAD  148 (148)
T ss_pred             CCEEEEECCccChhhhhHHHhCCEEEEEECCCchhHHHHhhhhHhhhcCEEEEeCCC
Confidence            999999999953222112234788999999887777777777889999999999998

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>PRK15467 ethanolamine utilization protein EutP; Provisional

Probab=98.91  E-value=6.1e-09  Score=78.11  Aligned_cols=81  Identities=17%  Similarity=0.156  Sum_probs=59.1

Q ss_pred             ccceEEEEEeCCCCCCCCcC-CCC-CCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHH
Q 030407           94 LADYIIYIIDVSGGDKIPRK-GGP-GITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLS  171 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~-~~~-qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~  171 (178)
                      .+|.+++|+|++.+...... ... ....+.++++||+|+.+.   +.+.+.+++++.....|++++||++|+|++++++
T Consensus        64 ~ad~il~v~d~~~~~s~~~~~~~~~~~~~~ii~v~nK~Dl~~~---~~~~~~~~~~~~~~~~p~~~~Sa~~g~gi~~l~~  140 (158)
T PRK15467         64 DVDMLIYVHGANDPESRLPAGLLDIGVSKRQIAVISKTDMPDA---DVAATRKLLLETGFEEPIFELNSHDPQSVQQLVD  140 (158)
T ss_pred             cCCEEEEEEeCCCcccccCHHHHhccCCCCeEEEEEccccCcc---cHHHHHHHHHHcCCCCCEEEEECCCccCHHHHHH
Confidence            47999999999876532211 001 123457999999999654   4456677777665557999999999999999999


Q ss_pred             HHhhhh
Q 030407          172 ITHYIV  177 (178)
Q Consensus       172 ~l~~~~  177 (178)
                      ++.+..
T Consensus       141 ~l~~~~  146 (158)
T PRK15467        141 YLASLT  146 (158)
T ss_pred             HHHHhc
Confidence            987653

>cd00881 GTP_translation_factor GTP translation factor family

Probab=98.91  E-value=5e-09  Score=79.21  Aligned_cols=102  Identities=15%  Similarity=0.045  Sum_probs=68.5

Q ss_pred             CCCEEEEeCCcchh-h---hcccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhH----H
Q 030407           73 KADLLLCESGGDNL-A---ANFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADL----A  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~-~---~~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~----~  140 (178)
                      ++++.|++|+|..- .   ..+. ..+|.+++|+|+.++......    +..+...+.++++||+|+..+  +..    +
T Consensus        61 ~~~~~liDtpG~~~~~~~~~~~~-~~~d~~i~v~d~~~~~~~~~~~~~~~~~~~~~~i~iv~nK~D~~~~--~~~~~~~~  137 (189)
T cd00881          61 DRRVNFIDTPGHEDFSSEVIRGL-SVSDGAILVVDANEGVQPQTREHLRIAREGGLPIIVAINKIDRVGE--EDLEEVLR  137 (189)
T ss_pred             CEEEEEEeCCCcHHHHHHHHHHH-HhcCEEEEEEECCCCCcHHHHHHHHHHHHCCCCeEEEEECCCCcch--hcHHHHHH
Confidence            57899999999421 1   1111 246999999999876432210    111235678999999999864  333    3


Q ss_pred             HHHHHHHhcC------------CCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          141 VMERDALRMR------------DGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       141 ~~~~~l~~~n------------p~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .+.+.++...            ...+++++||++|.|++++++++.+..
T Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~Sa~~g~gi~~l~~~l~~~l  186 (189)
T cd00881         138 EIKELLGLIGFISTKEEGTRNGLLVPIVPGSALTGIGVEELLEAIVEHL  186 (189)
T ss_pred             HHHHHHccccccchhhhhcccCCcceEEEEecccCcCHHHHHHHHHhhC
Confidence            3444444322            257999999999999999999987653

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.

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

Probab=98.89  E-value=8.3e-09  Score=76.76  Aligned_cols=102  Identities=14%  Similarity=0.081  Sum_probs=66.5

Q ss_pred             CCCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc----CCCCCCCceeEEEEecCCCCCchhHhHHHHH
Q 030407           72 FKADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR----KGGPGITQADLLVINKTDLASAIGADLAVME  143 (178)
Q Consensus        72 ~~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~----~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~  143 (178)
                      .+.++.+++|.|..    +...+ ...+|.+++|+|++++.....    ........+.++|+||+|+.+..   .+.+.
T Consensus        48 ~~~~~~iiDtpG~~~~~~~~~~~-~~~~d~il~v~d~~~~~~~~~~~~~~~~~~~~~p~ivv~NK~Dl~~~~---~~~~~  123 (168)
T cd01887          48 KIPGITFIDTPGHEAFTNMRARG-ASLTDIAILVVAADDGVMPQTIEAIKLAKAANVPFIVALNKIDKPNAN---PERVK  123 (168)
T ss_pred             CcceEEEEeCCCcHHHHHHHHHH-HhhcCEEEEEEECCCCccHHHHHHHHHHHHcCCCEEEEEEceeccccc---HHHHH
Confidence            36789999999941    11111 235799999999987542211    01112345679999999997541   12222


Q ss_pred             HHHHh--------cCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          144 RDALR--------MRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       144 ~~l~~--------~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ..++.        .....+++++||++|+|+++++++|.+.+
T Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~  165 (168)
T cd01887         124 NELSELGLQGEDEWGGDVQIVPTSAKTGEGIDDLLEAILLLA  165 (168)
T ss_pred             HHHHHhhccccccccCcCcEEEeecccCCCHHHHHHHHHHhh
Confidence            22211        12346899999999999999999998764

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.

>COG1159 Era GTPase [General function prediction only]

Probab=98.88  E-value=7.7e-09  Score=84.28  Aligned_cols=104  Identities=14%  Similarity=0.062  Sum_probs=77.2

Q ss_pred             hCCCCEEEEeCCcch---------hh--hcccccccceEEEEEeCCCCCCCCcC-CCCC---CCceeEEEEecCCCCCch
Q 030407           71 LFKADLLLCESGGDN---------LA--ANFSRELADYIIYIIDVSGGDKIPRK-GGPG---ITQADLLVINKTDLASAI  135 (178)
Q Consensus        71 ~~~~d~iiiEttG~~---------~~--~~~~~~~ad~~I~VvD~~~~~~~~~~-~~~q---i~~adiiviNK~Dl~~~~  135 (178)
                      ..+...|||.|.|..         +.  +......+|.+++|+|+.++....+. ...+   ...+.++++||+|...+ 
T Consensus        51 ~~~~QiIfvDTPGih~pk~~l~~~m~~~a~~sl~dvDlilfvvd~~~~~~~~d~~il~~lk~~~~pvil~iNKID~~~~-  129 (298)
T COG1159          51 TDNAQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKKTKTPVILVVNKIDKVKP-  129 (298)
T ss_pred             cCCceEEEEeCCCCCCcchHHHHHHHHHHHHHhccCcEEEEEEeccccCCccHHHHHHHHhhcCCCeEEEEEccccCCc-
Confidence            447889999999952         11  11112347999999999875433221 1122   24588999999999988 


Q ss_pred             hHh-HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          136 GAD-LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       136 ~~~-~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                       .. +..+.+..+...|...++++||++|.|++.|.+.+..-
T Consensus       130 -~~~l~~~~~~~~~~~~f~~ivpiSA~~g~n~~~L~~~i~~~  170 (298)
T COG1159         130 -KTVLLKLIAFLKKLLPFKEIVPISALKGDNVDTLLEIIKEY  170 (298)
T ss_pred             -HHHHHHHHHHHHhhCCcceEEEeeccccCCHHHHHHHHHHh
Confidence             55 56778888888899999999999999999999988653

>PRK00089 era GTPase Era; Reviewed

Probab=98.87  E-value=1.5e-08  Score=82.96  Aligned_cols=104  Identities=13%  Similarity=0.083  Sum_probs=71.7

Q ss_pred             CCCCEEEEeCCcchhh-----h----c--ccccccceEEEEEeCCCCCCCCc-CC---CCCCCceeEEEEecCCCC-Cch
Q 030407           72 FKADLLLCESGGDNLA-----A----N--FSRELADYIIYIIDVSGGDKIPR-KG---GPGITQADLLVINKTDLA-SAI  135 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~-----~----~--~~~~~ad~~I~VvD~~~~~~~~~-~~---~~qi~~adiiviNK~Dl~-~~~  135 (178)
                      .+..++|++|.|..-.     .    .  .....+|.+++|+|+++...... ..   ......+.++|+||+|+. +. 
T Consensus        51 ~~~qi~~iDTPG~~~~~~~l~~~~~~~~~~~~~~~D~il~vvd~~~~~~~~~~~i~~~l~~~~~pvilVlNKiDl~~~~-  129 (292)
T PRK00089         51 DDAQIIFVDTPGIHKPKRALNRAMNKAAWSSLKDVDLVLFVVDADEKIGPGDEFILEKLKKVKTPVILVLNKIDLVKDK-  129 (292)
T ss_pred             CCceEEEEECCCCCCchhHHHHHHHHHHHHHHhcCCEEEEEEeCCCCCChhHHHHHHHHhhcCCCEEEEEECCcCCCCH-
Confidence            3478999999994210     0    0  01124699999999987322111 11   112345789999999998 44 


Q ss_pred             hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          136 GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       136 ~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                       .++....+.+.+..+..+++++||++|.|++++++++.+.+
T Consensus       130 -~~l~~~~~~l~~~~~~~~i~~iSA~~~~gv~~L~~~L~~~l  170 (292)
T PRK00089        130 -EELLPLLEELSELMDFAEIVPISALKGDNVDELLDVIAKYL  170 (292)
T ss_pred             -HHHHHHHHHHHhhCCCCeEEEecCCCCCCHHHHHHHHHHhC
Confidence             45555566666666778999999999999999999987653

>TIGR02528 EutP ethanolamine utilization protein, EutP

Probab=98.86  E-value=1e-08  Score=74.62  Aligned_cols=79  Identities=14%  Similarity=0.010  Sum_probs=55.5

Q ss_pred             ccceEEEEEeCCCCCCCCc-CCCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHH
Q 030407           94 LADYIIYIIDVSGGDKIPR-KGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSI  172 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~-~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~  172 (178)
                      .+|.+++|+|++++..... .+......+.++|+||+|+.+.. ...+...+..+..+ ..+++++||++|+|+++++++
T Consensus        62 ~ad~vilv~d~~~~~s~~~~~~~~~~~~p~ilv~NK~Dl~~~~-~~~~~~~~~~~~~~-~~~~~~~Sa~~~~gi~~l~~~  139 (142)
T TIGR02528        62 DADVIALVQSATDPESRFPPGFASIFVKPVIGLVTKIDLAEAD-VDIERAKELLETAG-AEPIFEISSVDEQGLEALVDY  139 (142)
T ss_pred             cCCEEEEEecCCCCCcCCChhHHHhccCCeEEEEEeeccCCcc-cCHHHHHHHHHHcC-CCcEEEEecCCCCCHHHHHHH
Confidence            5799999999987765422 12222334789999999997531 23344455555432 348999999999999999998


Q ss_pred             Hh
Q 030407          173 TH  174 (178)
Q Consensus       173 l~  174 (178)
                      +.
T Consensus       140 l~  141 (142)
T TIGR02528       140 LN  141 (142)
T ss_pred             Hh
Confidence            74

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.

>PRK13768 GTPase; Provisional

Probab=98.86  E-value=1.2e-08  Score=82.39  Aligned_cols=109  Identities=17%  Similarity=0.102  Sum_probs=72.7

Q ss_pred             HHHhhHhhCCCCEEEEeCCcchhhhcc-------------cccccceEEEEEeCCCCCCCCc----CCC-----CCCCce
Q 030407           64 PLEELSNLFKADLLLCESGGDNLAANF-------------SRELADYIIYIIDVSGGDKIPR----KGG-----PGITQA  121 (178)
Q Consensus        64 ~l~~l~~~~~~d~iiiEttG~~~~~~~-------------~~~~ad~~I~VvD~~~~~~~~~----~~~-----~qi~~a  121 (178)
                      .+.......+.|++++++.|.  ...+             .....+.+++|+|++.+.....    .+.     .....+
T Consensus        87 ~l~~~l~~~~~~~~~~d~~g~--~~~~~~~~~~~~~~~~l~~~~~~~ii~liD~~~~~~~~d~~~~~~l~~~~~~~~~~~  164 (253)
T PRK13768         87 EIKEEIESLDADYVLVDTPGQ--MELFAFRESGRKLVERLSGSSKSVVVFLIDAVLAKTPSDFVSLLLLALSVQLRLGLP  164 (253)
T ss_pred             HHHHHHHhcCCCEEEEeCCcH--HHHHhhhHHHHHHHHHHHhcCCeEEEEEechHHhCCHHHHHHHHHHHHHHHHHcCCC
Confidence            333333455779999999993  1111             1101578999999976543211    000     124557


Q ss_pred             eEEEEecCCCCCchhHhHHHHHHH----------------------------HHhcCCCCCEEEEecccCCCHHHHHHHH
Q 030407          122 DLLVINKTDLASAIGADLAVMERD----------------------------ALRMRDGGPFIFAQVGWVIGIIFTLSIT  173 (178)
Q Consensus       122 diiviNK~Dl~~~~~~~~~~~~~~----------------------------l~~~np~a~i~~~SA~~g~gi~el~~~l  173 (178)
                      -++|+||+|+.+.  .+.+...+.                            +++.++..+++++|+++++|+++|+++|
T Consensus       165 ~i~v~nK~D~~~~--~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~~~vi~iSa~~~~gl~~L~~~I  242 (253)
T PRK13768        165 QIPVLNKADLLSE--EELERILKWLEDPEYLLEELKLEKGLQGLLSLELLRALEETGLPVRVIPVSAKTGEGFDELYAAI  242 (253)
T ss_pred             EEEEEEhHhhcCc--hhHHHHHHHHhCHHHHHHHHhcccchHHHHHHHHHHHHHHHCCCCcEEEEECCCCcCHHHHHHHH
Confidence            8999999999977  555444433                            3344667799999999999999999998


Q ss_pred             hhh
Q 030407          174 HYI  176 (178)
Q Consensus       174 ~~~  176 (178)
                      .+.
T Consensus       243 ~~~  245 (253)
T PRK13768        243 QEV  245 (253)
T ss_pred             HHH
Confidence            764

>cd01895 EngA2 EngA2 subfamily

Probab=98.85  E-value=1.6e-08  Score=74.91  Aligned_cols=105  Identities=17%  Similarity=0.141  Sum_probs=69.4

Q ss_pred             CCCCEEEEeCCcchhh-------hcc-------cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCC
Q 030407           72 FKADLLLCESGGDNLA-------ANF-------SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLAS  133 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~-------~~~-------~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~  133 (178)
                      .+.++.+++|.|..-.       ..+       ....+|.+++|+|+.++......    .......+.++++||+|+.+
T Consensus        48 ~~~~~~iiDtpG~~~~~~~~~~~e~~~~~~~~~~~~~~d~vi~v~d~~~~~~~~~~~~~~~~~~~~~~~iiv~nK~Dl~~  127 (174)
T cd01895          48 DGKKYTLIDTAGIRRKGKVEEGIEKYSVLRTLKAIERADVVLLVIDATEGITEQDLRIAGLILEEGKALVIVVNKWDLVE  127 (174)
T ss_pred             CCeeEEEEECCCCccccchhccHHHHHHHHHHHHHhhcCeEEEEEeCCCCcchhHHHHHHHHHhcCCCEEEEEeccccCC
Confidence            3567899999994100       000       11246899999999876432210    11112457799999999986


Q ss_pred             chhHhHHHHHHHHHhcCC---CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          134 AIGADLAVMERDALRMRD---GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       134 ~~~~~~~~~~~~l~~~np---~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ......+.+.+.+++..+   ..+++++||++|+|++++++.+.+.
T Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~~i~~~~~~l~~~  173 (174)
T cd01895         128 KDSKTMKEFKKEIRRKLPFLDYAPIVFISALTGQGVDKLFDAIDEV  173 (174)
T ss_pred             ccHHHHHHHHHHHHhhcccccCCceEEEeccCCCCHHHHHHHHHHh
Confidence            521234455555654433   5789999999999999999998764

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.

>cd01889 SelB_euk SelB subfamily

Probab=98.85  E-value=1.4e-08  Score=78.10  Aligned_cols=102  Identities=16%  Similarity=0.204  Sum_probs=67.0

Q ss_pred             CCCEEEEeCCcch-hhhccc--ccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHh----HHH
Q 030407           73 KADLLLCESGGDN-LAANFS--RELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGAD----LAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~~~--~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~----~~~  141 (178)
                      ++.+.+++|.|.. +...+.  ...+|.+++|+|++.+......    .......+-++++||+|+...  ..    .+.
T Consensus        67 ~~~~~i~DtpG~~~~~~~~~~~~~~~d~vi~VvD~~~~~~~~~~~~~~~~~~~~~~~iiv~NK~Dl~~~--~~~~~~~~~  144 (192)
T cd01889          67 NLQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDATKGIQTQTAECLVIGEILCKKLIVVLNKIDLIPE--EERERKIEK  144 (192)
T ss_pred             CceEEEEECCCcHHHHHHHHHHHhhCCEEEEEEECCCCccHHHHHHHHHHHHcCCCEEEEEECcccCCH--HHHHHHHHH
Confidence            6789999999942 112221  1246899999999876432210    111123466899999999865  33    233


Q ss_pred             HHHHHHhc-----CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRM-----RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~-----np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.+.++..     ....+++++||++|+|+++|+++|..+
T Consensus       145 ~~~~l~~~~~~~~~~~~~vi~iSa~~g~gi~~L~~~l~~~  184 (192)
T cd01889         145 MKKKLQKTLEKTRFKNSPIIPVSAKPGGGEAELGKDLNNL  184 (192)
T ss_pred             HHHHHHHHHHhcCcCCCCEEEEeccCCCCHHHHHHHHHhc
Confidence            33333321     345799999999999999999998764

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

>TIGR00436 era GTP-binding protein Era

Probab=98.85  E-value=1.2e-08  Score=82.94  Aligned_cols=103  Identities=11%  Similarity=0.007  Sum_probs=68.2

Q ss_pred             CCCEEEEeCCcchhh-----h-----c-ccccccceEEEEEeCCCCCCCCcCCC---CCCCceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDNLA-----A-----N-FSRELADYIIYIIDVSGGDKIPRKGG---PGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~~~-----~-----~-~~~~~ad~~I~VvD~~~~~~~~~~~~---~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      +..++|++|.|..-.     .     . .....+|.+++|+|++..........   .....+-++|+||+|+.+.  ..
T Consensus        47 ~~qii~vDTPG~~~~~~~l~~~~~~~~~~~l~~aDvvl~VvD~~~~~~~~~~i~~~l~~~~~p~ilV~NK~Dl~~~--~~  124 (270)
T TIGR00436        47 ASQIIFIDTPGFHEKKHSLNRLMMKEARSAIGGVDLILFVVDSDQWNGDGEFVLTKLQNLKRPVVLTRNKLDNKFK--DK  124 (270)
T ss_pred             CcEEEEEECcCCCCCcchHHHHHHHHHHHHHhhCCEEEEEEECCCCCchHHHHHHHHHhcCCCEEEEEECeeCCCH--HH
Confidence            456899999994210     0     0 01134799999999987543321111   1134567999999999865  44


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .......+....+..+++++||++|+|+++|++++.+.+
T Consensus       125 ~~~~~~~~~~~~~~~~v~~iSA~~g~gi~~L~~~l~~~l  163 (270)
T TIGR00436       125 LLPLIDKYAILEDFKDIVPISALTGDNTSFLAAFIEVHL  163 (270)
T ss_pred             HHHHHHHHHhhcCCCceEEEecCCCCCHHHHHHHHHHhC
Confidence            433333444444556899999999999999999987643

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

>cd00880 Era_like Era (E

Probab=98.84  E-value=2.1e-08  Score=72.50  Aligned_cols=102  Identities=21%  Similarity=0.083  Sum_probs=70.9

Q ss_pred             CCCEEEEeCCcchhhhc--------c--cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDNLAAN--------F--SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~--------~--~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+++.+++|.|..-...        .  ....+|.+++++|+.........    .......+.++|+||+|+..+  ..
T Consensus        44 ~~~~~~~Dt~g~~~~~~~~~~~~~~~~~~~~~~d~il~v~~~~~~~~~~~~~~~~~~~~~~~~~ivv~nK~D~~~~--~~  121 (163)
T cd00880          44 LGPVVLIDTPGIDEAGGLGREREELARRVLERADLILFVVDADLRADEEEEKLLELLRERGKPVLLVLNKIDLLPE--EE  121 (163)
T ss_pred             CCcEEEEECCCCCccccchhhHHHHHHHHHHhCCEEEEEEeCCCCCCHHHHHHHHHHHhcCCeEEEEEEccccCCh--hh
Confidence            67999999999421100        0  11246899999999876543222    122346678999999999877  44


Q ss_pred             HHHHH---HHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 LAVME---RDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~---~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .....   .......+..+++++||++++|++++++++.++
T Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~sa~~~~~v~~l~~~l~~~  162 (163)
T cd00880         122 EEELLELRLLILLLLLGLPVIAVSALTGEGIDELREALIEA  162 (163)
T ss_pred             HHHHHHHHHhhcccccCCceEEEeeeccCCHHHHHHHHHhh
Confidence            44332   233344567899999999999999999998765

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

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=98.83  E-value=1.1e-08  Score=76.32  Aligned_cols=100  Identities=18%  Similarity=0.162  Sum_probs=66.2

Q ss_pred             CCCEEEEeCCcch-hh---hcccccccceEEEEEeCCCCCCCCc------C---CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN-LA---ANFSRELADYIIYIIDVSGGDKIPR------K---GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~---~~~~~~~ad~~I~VvD~~~~~~~~~------~---~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ++.+.+++|.|.. ..   ..+ ...+|.+++|+|++.......      .   ....-..+-++++||+|+.+.  ...
T Consensus        49 ~~~~~l~Dt~G~~~~~~~~~~~-~~~~~~~v~vvd~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~NK~D~~~~--~~~  125 (167)
T cd04160          49 NARLKFWDLGGQESLRSLWDKY-YAECHAIIYVIDSTDRERFEESKSALEKVLRNEALEGVPLLILANKQDLPDA--LSV  125 (167)
T ss_pred             CEEEEEEECCCChhhHHHHHHH-hCCCCEEEEEEECchHHHHHHHHHHHHHHHhChhhcCCCEEEEEEccccccC--CCH
Confidence            5788999999942 11   111 235799999999976532110      0   001123567999999999766  444


Q ss_pred             HHHHHHHHhc----C-CCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRM----R-DGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~----n-p~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +.+.+.++..    + ...+++++||++|+|+++++++|.+
T Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~e~~~~l~~  166 (167)
T cd04160         126 EEIKEVFQDKAEEIGRRDCLVLPVSALEGTGVREGIEWLVE  166 (167)
T ss_pred             HHHHHHhccccccccCCceEEEEeeCCCCcCHHHHHHHHhc
Confidence            4455544432    1 2358999999999999999999864

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.

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

Probab=98.82  E-value=1.2e-08  Score=78.18  Aligned_cols=101  Identities=16%  Similarity=0.108  Sum_probs=72.1

Q ss_pred             CCCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCCc------CCCCCCC--ceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIPR------KGGPGIT--QADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~~------~~~~qi~--~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .....|..|.|.    +++++|++ .++..|+|+|.++.+....      ...++..  .--.+|.||+||.+....+.+
T Consensus        53 ~ikfeIWDTAGQERy~slapMYyR-gA~AAivvYDit~~~SF~~aK~WvkeL~~~~~~~~vialvGNK~DL~~~R~V~~~  131 (200)
T KOG0092|consen   53 TIKFEIWDTAGQERYHSLAPMYYR-GANAAIVVYDITDEESFEKAKNWVKELQRQASPNIVIALVGNKADLLERREVEFE  131 (200)
T ss_pred             EEEEEEEEcCCcccccccccceec-CCcEEEEEEecccHHHHHHHHHHHHHHHhhCCCCeEEEEecchhhhhhcccccHH
Confidence            467889999994    45667776 7899999999988654321      0111222  112568999999984325566


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ........  .+..+++||||||.|++++|..|.+-
T Consensus       132 ea~~yAe~--~gll~~ETSAKTg~Nv~~if~~Ia~~  165 (200)
T KOG0092|consen  132 EAQAYAES--QGLLFFETSAKTGENVNEIFQAIAEK  165 (200)
T ss_pred             HHHHHHHh--cCCEEEEEecccccCHHHHHHHHHHh
Confidence            66666654  46799999999999999999987653

>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA

Probab=98.82  E-value=1.2e-08  Score=87.64  Aligned_cols=102  Identities=20%  Similarity=0.198  Sum_probs=70.2

Q ss_pred             CCCEEEEeCCcchh-------hhcc-------cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCC-C
Q 030407           73 KADLLLCESGGDNL-------AANF-------SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLA-S  133 (178)
Q Consensus        73 ~~d~iiiEttG~~~-------~~~~-------~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~-~  133 (178)
                      +..+.+++|.|..-       ...+       ....+|.+++|+|++++......    ....-..+.++|+||+|+. +
T Consensus       219 ~~~~~liDT~G~~~~~~~~~~~e~~~~~~~~~~~~~ad~~ilV~D~~~~~~~~~~~~~~~~~~~~~~iiiv~NK~Dl~~~  298 (429)
T TIGR03594       219 GKKYLLIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEGITEQDLRIAGLILEAGKALVIVVNKWDLVKD  298 (429)
T ss_pred             CcEEEEEECCCccccccchhhHHHHHHHHHHHHHHhCCEEEEEEECCCCccHHHHHHHHHHHHcCCcEEEEEECcccCCC
Confidence            34789999999410       0111       11247999999999876543221    1111235789999999998 4


Q ss_pred             chhHhHHHHHHHHHhcC---CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          134 AIGADLAVMERDALRMR---DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       134 ~~~~~~~~~~~~l~~~n---p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .  +..+.+.+.++...   +.++++++||++|.|++++++++.+.
T Consensus       299 ~--~~~~~~~~~~~~~~~~~~~~~vi~~SA~~g~~v~~l~~~i~~~  342 (429)
T TIGR03594       299 E--KTREEFKKELRRKLPFLDFAPIVFISALTGQGVDKLLDAIDEV  342 (429)
T ss_pred             H--HHHHHHHHHHHHhcccCCCCceEEEeCCCCCCHHHHHHHHHHH
Confidence            4  55666666666543   45799999999999999999987654

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.

>PRK15494 era GTPase Era; Provisional

Probab=98.81  E-value=1.7e-08  Score=84.71  Aligned_cols=102  Identities=16%  Similarity=0.045  Sum_probs=70.1

Q ss_pred             CCCEEEEeCCcch-----hhhcc------cccccceEEEEEeCCCCCCCCc-CC---CCCCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDN-----LAANF------SRELADYIIYIIDVSGGDKIPR-KG---GPGITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~-----~~~~~------~~~~ad~~I~VvD~~~~~~~~~-~~---~~qi~~adiiviNK~Dl~~~~~~  137 (178)
                      +..++|++|.|..     +...+      ....+|++++|+|+........ ..   ......+.++|+||+|+.+.   
T Consensus        99 ~~qi~~~DTpG~~~~~~~l~~~~~r~~~~~l~~aDvil~VvD~~~s~~~~~~~il~~l~~~~~p~IlViNKiDl~~~---  175 (339)
T PRK15494         99 DTQVILYDTPGIFEPKGSLEKAMVRCAWSSLHSADLVLLIIDSLKSFDDITHNILDKLRSLNIVPIFLLNKIDIESK---  175 (339)
T ss_pred             CeEEEEEECCCcCCCcccHHHHHHHHHHHHhhhCCEEEEEEECCCCCCHHHHHHHHHHHhcCCCEEEEEEhhcCccc---
Confidence            4568999999941     11100      1135799999999876432211 11   11233466899999999754   


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ....+.+.++..++..+++++||++|.|+++++++|.+.+
T Consensus       176 ~~~~~~~~l~~~~~~~~i~~iSAktg~gv~eL~~~L~~~l  215 (339)
T PRK15494        176 YLNDIKAFLTENHPDSLLFPISALSGKNIDGLLEYITSKA  215 (339)
T ss_pred             cHHHHHHHHHhcCCCcEEEEEeccCccCHHHHHHHHHHhC
Confidence            3556667777677778999999999999999999987643

>cd01890 LepA LepA subfamily

Probab=98.79  E-value=3e-08  Score=74.76  Aligned_cols=102  Identities=18%  Similarity=0.039  Sum_probs=63.1

Q ss_pred             CCCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcC--CC--CCCCceeEEEEecCCCCCchhHh-HHHH
Q 030407           72 FKADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRK--GG--PGITQADLLVINKTDLASAIGAD-LAVM  142 (178)
Q Consensus        72 ~~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~--~~--~qi~~adiiviNK~Dl~~~~~~~-~~~~  142 (178)
                      .++.+.|+.|.|..    ....+. ..+|.+++|+|++.+......  +.  .....+-++|+||+|+.+..... .+++
T Consensus        65 ~~~~~~l~Dt~G~~~~~~~~~~~~-~~ad~~i~v~D~~~~~~~~~~~~~~~~~~~~~~iiiv~NK~Dl~~~~~~~~~~~~  143 (179)
T cd01890          65 QEYLLNLIDTPGHVDFSYEVSRSL-AACEGALLLVDATQGVEAQTLANFYLALENNLEIIPVINKIDLPSADPERVKQQI  143 (179)
T ss_pred             CcEEEEEEECCCChhhHHHHHHHH-HhcCeEEEEEECCCCccHhhHHHHHHHHHcCCCEEEEEECCCCCcCCHHHHHHHH
Confidence            35678899999931    111122 247999999999875432110  00  01234579999999996541111 1222


Q ss_pred             HHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          143 ERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       143 ~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+ .. +..+++++||++|+|++++++++.+.
T Consensus       144 ~~~~-~~-~~~~~~~~Sa~~g~gi~~l~~~l~~~  175 (179)
T cd01890         144 EDVL-GL-DPSEAILVSAKTGLGVEDLLEAIVER  175 (179)
T ss_pred             HHHh-CC-CcccEEEeeccCCCCHHHHHHHHHhh
Confidence            2221 11 33469999999999999999998764

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.

>cd04157 Arl6 Arl6 subfamily

Probab=98.78  E-value=3e-08  Score=73.32  Aligned_cols=101  Identities=14%  Similarity=0.045  Sum_probs=64.2

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCC--CCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGP--GITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~--qi~~adiiviNK~Dl~~~~~~  137 (178)
                      +..+-+++|.|..    +...+. ..+|.+++|+|+++......         ....  .-..+-++|+||+|+.+.  .
T Consensus        44 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~ii~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~iiv~NK~Dl~~~--~  120 (162)
T cd04157          44 NLSFTAFDMSGQGKYRGLWEHYY-KNIQGIIFVIDSSDRLRLVVVKDELELLLNHPDIKHRRVPILFFANKMDLPDA--L  120 (162)
T ss_pred             CEEEEEEECCCCHhhHHHHHHHH-ccCCEEEEEEeCCcHHHHHHHHHHHHHHHcCcccccCCCCEEEEEeCccccCC--C
Confidence            5677899999942    112222 35799999999987542110         0110  123567999999999765  3


Q ss_pred             hHHHHHHHHH--hc-CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDAL--RM-RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~--~~-np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+.+...++  .. +...+++++||++|+|+++++++|..+
T Consensus       121 ~~~~~~~~l~~~~~~~~~~~~~~~Sa~~g~gv~~~~~~l~~~  162 (162)
T cd04157         121 TAVKITQLLGLENIKDKPWHIFASNALTGEGLDEGVQWLQAQ  162 (162)
T ss_pred             CHHHHHHHhCCccccCceEEEEEeeCCCCCchHHHHHHHhcC
Confidence            3333333332  11 112368999999999999999998753

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

>PRK00093 GTP-binding protein Der; Reviewed

Probab=98.77  E-value=2.3e-08  Score=86.20  Aligned_cols=102  Identities=20%  Similarity=0.196  Sum_probs=69.8

Q ss_pred             CCCEEEEeCCcchh-------hh------cc-cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDNL-------AA------NF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~~-------~~------~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      +.++.+++|.|..-       ..      +. ....+|.+++|+|++.+...+..    .......+.++++||+|+.++
T Consensus       220 ~~~~~lvDT~G~~~~~~~~~~~e~~~~~~~~~~~~~ad~~ilViD~~~~~~~~~~~i~~~~~~~~~~~ivv~NK~Dl~~~  299 (435)
T PRK00093        220 GQKYTLIDTAGIRRKGKVTEGVEKYSVIRTLKAIERADVVLLVIDATEGITEQDLRIAGLALEAGRALVIVVNKWDLVDE  299 (435)
T ss_pred             CeeEEEEECCCCCCCcchhhHHHHHHHHHHHHHHHHCCEEEEEEeCCCCCCHHHHHHHHHHHHcCCcEEEEEECccCCCH
Confidence            45789999999410       00      11 11246999999999887543221    111123578999999999866


Q ss_pred             hhHhHHHHHHHHHhcC---CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          135 IGADLAVMERDALRMR---DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       135 ~~~~~~~~~~~l~~~n---p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                        ...+.+.+.++...   +.++++++||++|.|++++++.+.+.
T Consensus       300 --~~~~~~~~~~~~~l~~~~~~~i~~~SA~~~~gv~~l~~~i~~~  342 (435)
T PRK00093        300 --KTMEEFKKELRRRLPFLDYAPIVFISALTGQGVDKLLEAIDEA  342 (435)
T ss_pred             --HHHHHHHHHHHHhcccccCCCEEEEeCCCCCCHHHHHHHHHHH
Confidence              55556665555432   46899999999999999999987653

>cd04171 SelB SelB subfamily

Probab=98.77  E-value=4e-08  Score=72.55  Aligned_cols=101  Identities=12%  Similarity=0.003  Sum_probs=64.2

Q ss_pred             CCCEEEEeCCcch-hhh-cc-cccccceEEEEEeCCCCCCCCc-C---CCCCCCc-eeEEEEecCCCCCchhHh----HH
Q 030407           73 KADLLLCESGGDN-LAA-NF-SRELADYIIYIIDVSGGDKIPR-K---GGPGITQ-ADLLVINKTDLASAIGAD----LA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~-~~-~~~~ad~~I~VvD~~~~~~~~~-~---~~~qi~~-adiiviNK~Dl~~~~~~~----~~  140 (178)
                      +..+.+++|.|.. ... .. ....+|.+++|+|+.++..... .   ....... +-++++||+|+.++  ..    .+
T Consensus        50 ~~~~~~~DtpG~~~~~~~~~~~~~~ad~ii~V~d~~~~~~~~~~~~~~~~~~~~~~~~ilv~NK~Dl~~~--~~~~~~~~  127 (164)
T cd04171          50 GKRLGFIDVPGHEKFIKNMLAGAGGIDLVLLVVAADEGIMPQTREHLEILELLGIKRGLVVLTKADLVDE--DWLELVEE  127 (164)
T ss_pred             CcEEEEEECCChHHHHHHHHhhhhcCCEEEEEEECCCCccHhHHHHHHHHHHhCCCcEEEEEECccccCH--HHHHHHHH
Confidence            4568899999931 111 11 1225799999999976321111 0   0011222 56899999999865  32    23


Q ss_pred             HHHHHHHhcC-CCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMR-DGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~n-p~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+.+.++... ...+++++||++|+|++++++.+.+
T Consensus       128 ~~~~~~~~~~~~~~~~~~~Sa~~~~~v~~l~~~l~~  163 (164)
T cd04171         128 EIRELLAGTFLADAPIFPVSAVTGEGIEELKEYLDE  163 (164)
T ss_pred             HHHHHHHhcCcCCCcEEEEeCCCCcCHHHHHHHHhh
Confidence            4444444321 3469999999999999999998865

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

>cd04149 Arf6 Arf6 subfamily

Probab=98.77  E-value=2.3e-08  Score=75.41  Aligned_cols=101  Identities=16%  Similarity=0.128  Sum_probs=64.5

Q ss_pred             CCCEEEEeCCcch-hhh--cccccccceEEEEEeCCCCCCCCc---C---C-C-C-CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN-LAA--NFSRELADYIIYIIDVSGGDKIPR---K---G-G-P-GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~--~~~~~~ad~~I~VvD~~~~~~~~~---~---~-~-~-qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      +..+.+++|.|.. ...  ......+|++++|+|+++......   .   . . . .-..+-++|.||+|+...  ...+
T Consensus        52 ~~~~~l~Dt~G~~~~~~~~~~~~~~a~~ii~v~D~t~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~--~~~~  129 (168)
T cd04149          52 NVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDA--MKPH  129 (168)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHhccCCEEEEEEeCCchhhHHHHHHHHHHHhcCHhhcCCcEEEEEECcCCccC--CCHH
Confidence            5778999999942 111  111235799999999987532211   0   0 0 0 112467999999999754  3334


Q ss_pred             HHHHHHH--hcC-CCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDAL--RMR-DGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~--~~n-p~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ++.+.++  ..+ ...+++++||++|+|++++|++|.+
T Consensus       130 ~i~~~~~~~~~~~~~~~~~~~SAk~g~gv~~~~~~l~~  167 (168)
T cd04149         130 EIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLSS  167 (168)
T ss_pred             HHHHHcCCCccCCCcEEEEEeeCCCCCChHHHHHHHhc
Confidence            4554442  112 2236899999999999999999864

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

>PTZ00099 rab6; Provisional

Probab=98.76  E-value=3.1e-08  Score=75.71  Aligned_cols=102  Identities=17%  Similarity=0.050  Sum_probs=65.7

Q ss_pred             CCCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCC-----CCCCceeEEEEecCCCCCchhHhH
Q 030407           72 FKADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGG-----PGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        72 ~~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~-----~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ....+.|++|.|..    +...+. ..+|++++|+|.++......   .+.     ..-..+-++|.||+||.+......
T Consensus        27 ~~v~l~iwDt~G~e~~~~~~~~~~-~~ad~~ilv~D~t~~~sf~~~~~w~~~i~~~~~~~~piilVgNK~DL~~~~~v~~  105 (176)
T PTZ00099         27 GPVRLQLWDTAGQERFRSLIPSYI-RDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTY  105 (176)
T ss_pred             EEEEEEEEECCChHHhhhccHHHh-CCCcEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCeEEEEEECcccccccCCCH
Confidence            35789999999942    112232 35899999999987532211   000     011234589999999964311233


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +......+..  ...++++||++|+|++++|++|.+.
T Consensus       106 ~e~~~~~~~~--~~~~~e~SAk~g~nV~~lf~~l~~~  140 (176)
T PTZ00099        106 EEGMQKAQEY--NTMFHETSAKAGHNIKVLFKKIAAK  140 (176)
T ss_pred             HHHHHHHHHc--CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            3344444443  3478999999999999999998754

>cd04154 Arl2 Arl2 subfamily

Probab=98.76  E-value=2.4e-08  Score=75.31  Aligned_cols=99  Identities=16%  Similarity=0.121  Sum_probs=65.1

Q ss_pred             CCCEEEEeCCcchh-h---hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL-A---ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~-~---~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ++.+.++++.|..- .   ..+. ..+|.+++|+|++.......         .....-..+-++|+||+|+...  ...
T Consensus        57 ~~~l~l~D~~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~--~~~  133 (173)
T cd04154          57 GYKLNIWDVGGQKTLRPYWRNYF-ESTDALIWVVDSSDRLRLDDCKRELKELLQEERLAGATLLILANKQDLPGA--LSE  133 (173)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHh-CCCCEEEEEEECCCHHHHHHHHHHHHHHHhChhhcCCCEEEEEECcccccC--CCH
Confidence            56788999999421 1   1122 25799999999987532110         0101123467999999999765  344


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      +.+.+.++..   ....+++++||++|+|++++++++.
T Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~  171 (173)
T cd04154         134 EEIREALELDKISSHHWRIQPCSAVTGEGLLQGIDWLV  171 (173)
T ss_pred             HHHHHHhCccccCCCceEEEeccCCCCcCHHHHHHHHh
Confidence            4455444321   2346899999999999999999875

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.

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

Probab=98.74  E-value=4.4e-08  Score=73.02  Aligned_cols=100  Identities=15%  Similarity=0.112  Sum_probs=64.2

Q ss_pred             CCCEEEEeCCcchhh---hc-------c--cccccceEEEEEeCCCCCCCC-c---C----CCCCC-CceeEEEEecCCC
Q 030407           73 KADLLLCESGGDNLA---AN-------F--SRELADYIIYIIDVSGGDKIP-R---K----GGPGI-TQADLLVINKTDL  131 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~-------~--~~~~ad~~I~VvD~~~~~~~~-~---~----~~~qi-~~adiiviNK~Dl  131 (178)
                      +..+.|++|.|..-.   ..       .  .....|.+++|+|+++..... .   .    ..... ..+-++|+||+|+
T Consensus        46 ~~~~~i~Dt~G~~~~~~~~~~~~~~~~~~~~~~~~d~~l~v~d~~~~~~~~~~~~~~~~~~l~~~~~~~pvilv~NK~Dl  125 (168)
T cd01897          46 YLRWQVIDTPGLLDRPLEERNTIEMQAITALAHLRAAVLFLFDPSETCGYSLEEQLSLFEEIKPLFKNKPVIVVLNKIDL  125 (168)
T ss_pred             ceEEEEEECCCcCCccccCCchHHHHHHHHHHhccCcEEEEEeCCcccccchHHHHHHHHHHHhhcCcCCeEEEEEcccc
Confidence            467899999994100   00       0  011257899999998653311 0   0    11111 4567999999999


Q ss_pred             CCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          132 ASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       132 ~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.  .......+..+  .+..+++++||++|+|++++++++.+.
T Consensus       126 ~~~--~~~~~~~~~~~--~~~~~~~~~Sa~~~~gi~~l~~~l~~~  166 (168)
T cd01897         126 LTF--EDLSEIEEEEE--LEGEEVLKISTLTEEGVDEVKNKACEL  166 (168)
T ss_pred             Cch--hhHHHHHHhhh--hccCceEEEEecccCCHHHHHHHHHHH
Confidence            876  44443333322  245689999999999999999998764

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.

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

Probab=98.72  E-value=4.3e-08  Score=76.38  Aligned_cols=101  Identities=14%  Similarity=0.087  Sum_probs=63.1

Q ss_pred             CCEEEEeCCcch-hhhccc--ccccceEEEEEeCCCCC-CCC-cCC---CCCCCc-eeEEEEecCCCCCchhHhHHHHHH
Q 030407           74 ADLLLCESGGDN-LAANFS--RELADYIIYIIDVSGGD-KIP-RKG---GPGITQ-ADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        74 ~d~iiiEttG~~-~~~~~~--~~~ad~~I~VvD~~~~~-~~~-~~~---~~qi~~-adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      .-+.|+.|.|.. +...+.  ...+|.+++|+|+..+. ... ...   ...... +-++|+||+|+.++  .+.....+
T Consensus        83 ~~i~~iDtPG~~~~~~~~~~~~~~~D~~llVvd~~~~~~~~~t~~~l~~~~~~~~~~iiivvNK~Dl~~~--~~~~~~~~  160 (203)
T cd01888          83 RHVSFVDCPGHEILMATMLSGAAVMDGALLLIAANEPCPQPQTSEHLAALEIMGLKHIIIVQNKIDLVKE--EQALENYE  160 (203)
T ss_pred             cEEEEEECCChHHHHHHHHHhhhcCCEEEEEEECCCCCCCcchHHHHHHHHHcCCCcEEEEEEchhccCH--HHHHHHHH
Confidence            457899999931 111111  12359999999998742 111 100   001121 35789999999875  44333333


Q ss_pred             HHHhc-----CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          145 DALRM-----RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       145 ~l~~~-----np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+++.     ....+++++||++|+|++++++++.+.
T Consensus       161 ~i~~~~~~~~~~~~~i~~vSA~~g~gi~~L~~~l~~~  197 (203)
T cd01888         161 QIKKFVKGTIAENAPIIPISAQLKYNIDVLLEYIVKK  197 (203)
T ss_pred             HHHHHHhccccCCCcEEEEeCCCCCCHHHHHHHHHHh
Confidence            33322     135689999999999999999998764

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

>cd04165 GTPBP1_like GTPBP1-like

Probab=98.71  E-value=7.4e-08  Score=76.48  Aligned_cols=103  Identities=16%  Similarity=0.118  Sum_probs=66.4

Q ss_pred             CCCCEEEEeCCcch-h-hhccc-c--cccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHH
Q 030407           72 FKADLLLCESGGDN-L-AANFS-R--ELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVM  142 (178)
Q Consensus        72 ~~~d~iiiEttG~~-~-~~~~~-~--~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~  142 (178)
                      .+.-+-||.|.|.. . ..+.. .  ..+|.+++|+|+..+......    +......+-++++||+|+.++  ......
T Consensus        82 ~~~~i~liDtpG~~~~~~~~~~~~~~~~~D~~llVvda~~g~~~~d~~~l~~l~~~~ip~ivvvNK~D~~~~--~~~~~~  159 (224)
T cd04165          82 SSKLVTFIDLAGHERYLKTTLFGLTGYAPDYAMLVVAANAGIIGMTKEHLGLALALNIPVFVVVTKIDLAPA--NILQET  159 (224)
T ss_pred             CCcEEEEEECCCcHHHHHHHHHhhcccCCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCEEEEEECccccCH--HHHHHH
Confidence            35678899999931 1 11111 1  136899999999876533221    111234456999999999876  444443


Q ss_pred             HHHHHhc----------------------------CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          143 ERDALRM----------------------------RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       143 ~~~l~~~----------------------------np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+++.                            ....|+|.+||.+|+|+++|+++|..+
T Consensus       160 ~~~l~~~L~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~pi~~vSavtg~Gi~~L~~~L~~l  221 (224)
T cd04165         160 LKDLKRILKVPGVRKLPVPVKSDDDVVLAASNFSSERIVPIFQVSNVTGEGLDLLHAFLNLL  221 (224)
T ss_pred             HHHHHHHhcCCCccccceeeecccceeehhhcCCccccCcEEEeeCCCccCHHHHHHHHHhc
Confidence            3333221                            113599999999999999999998754

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

>cd04158 ARD1 ARD1 subfamily

Probab=98.71  E-value=4.7e-08  Score=73.58  Aligned_cols=99  Identities=15%  Similarity=0.158  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc------CCCC--CC-CceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR------KGGP--GI-TQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~------~~~~--qi-~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|..-    ...+. ..+|++++|+|+++......      ....  .. ..+-++|.||+|+...  ...
T Consensus        42 ~~~i~l~Dt~G~~~~~~~~~~~~-~~ad~ii~V~D~s~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~--~~~  118 (169)
T cd04158          42 NLKFTIWDVGGKHKLRPLWKHYY-LNTQAVVFVVDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAGA--LSV  118 (169)
T ss_pred             CEEEEEEECCCChhcchHHHHHh-ccCCEEEEEEeCCcHHHHHHHHHHHHHHhcChhhCCCCEEEEEeCcCcccC--CCH
Confidence            57788999999421    11122 34799999999987532211      0101  11 2457899999999755  344


Q ss_pred             HHHHHHHHhcCC-----CCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRMRD-----GGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~np-----~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +.+.+.++ .+.     ..+++++||++|.|++++|++|.+
T Consensus       119 ~~~~~~~~-~~~~~~~~~~~~~~~Sa~~g~gv~~~f~~l~~  158 (169)
T cd04158         119 EEMTELLS-LHKLCCGRSWYIQGCDARSGMGLYEGLDWLSR  158 (169)
T ss_pred             HHHHHHhC-CccccCCCcEEEEeCcCCCCCCHHHHHHHHHH
Confidence            44554443 211     136888999999999999999875

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

>cd04120 Rab12 Rab12 subfamily

Probab=98.71  E-value=5e-08  Score=76.20  Aligned_cols=101  Identities=19%  Similarity=0.110  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+-+.+|.|..    +...+. ..+|++|+|+|.++......  .+.      ..-..+-++|.||+||.+......+
T Consensus        48 ~v~l~iwDtaGqe~~~~l~~~y~-~~ad~iIlVfDvtd~~Sf~~l~~w~~~i~~~~~~~~piilVgNK~DL~~~~~v~~~  126 (202)
T cd04120          48 KIRLQIWDTAGQERFNSITSAYY-RSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETDREISRQ  126 (202)
T ss_pred             EEEEEEEeCCCchhhHHHHHHHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCcEEEEEECcccccccccCHH
Confidence            4778899999941    222233 36799999999987643211  000      0112456999999999654112223


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ...++.++. ...++++|||++|+||+++|+++.+
T Consensus       127 ~~~~~a~~~-~~~~~~etSAktg~gV~e~F~~l~~  160 (202)
T cd04120         127 QGEKFAQQI-TGMRFCEASAKDNFNVDEIFLKLVD  160 (202)
T ss_pred             HHHHHHHhc-CCCEEEEecCCCCCCHHHHHHHHHH
Confidence            333444332 2468999999999999999998764

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

>cd04136 Rap_like Rap-like subfamily

Probab=98.70  E-value=7.5e-08  Score=71.20  Aligned_cols=101  Identities=12%  Similarity=0.043  Sum_probs=63.5

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+-|++|.|..    +...+. ..+|.+++|+|.++......         .....-..+-++|+||+|+.+......
T Consensus        48 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~  126 (163)
T cd04136          48 QCMLEILDTAGTEQFTAMRDLYI-KNGQGFVLVYSITSQSSFNDLQDLREQILRVKDTENVPMVLVGNKCDLEDERVVSR  126 (163)
T ss_pred             EEEEEEEECCCccccchHHHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccceecH
Confidence            3556688999931    112222 25799999999976432110         011112346689999999975411222


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..++.+  .+++++||++|+|++++++++.+.
T Consensus       127 ~~~~~~~~~~~--~~~~~~Sa~~~~~v~~l~~~l~~~  161 (163)
T cd04136         127 EEGQALARQWG--CPFYETSAKSKINVDEVFADLVRQ  161 (163)
T ss_pred             HHHHHHHHHcC--CeEEEecCCCCCCHHHHHHHHHHh
Confidence            23333334333  689999999999999999998764

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.

>KOG0462 consensus Elongation factor-type GTP-binding protein [Translation, ribosomal structure and biogenesis]

Probab=98.70  E-value=2.9e-08  Score=86.56  Aligned_cols=98  Identities=22%  Similarity=0.214  Sum_probs=68.9

Q ss_pred             CCEEEEeCCcchhh--hcccccc--cceEEEEEeCCCCCCCCcCC----CCCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           74 ADLLLCESGGDNLA--ANFSREL--ADYIIYIIDVSGGDKIPRKG----GPGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        74 ~d~iiiEttG~~~~--~~~~~~~--ad~~I~VvD~~~~~~~~~~~----~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      +-.=+|.|.| ...  ....+.+  -+++++|||+.+|...+...    .-....+-|.|+||+|+.++   +.+++...
T Consensus       125 ylLNLIDTPG-HvDFs~EVsRslaac~G~lLvVDA~qGvqAQT~anf~lAfe~~L~iIpVlNKIDlp~a---dpe~V~~q  200 (650)
T KOG0462|consen  125 YLLNLIDTPG-HVDFSGEVSRSLAACDGALLVVDASQGVQAQTVANFYLAFEAGLAIIPVLNKIDLPSA---DPERVENQ  200 (650)
T ss_pred             eEEEeecCCC-cccccceehehhhhcCceEEEEEcCcCchHHHHHHHHHHHHcCCeEEEeeeccCCCCC---CHHHHHHH
Confidence            5566788888 111  1112222  38999999999987654321    11233467999999999877   55666777


Q ss_pred             HHhcC--CCCCEEEEecccCCCHHHHHHHHhh
Q 030407          146 ALRMR--DGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       146 l~~~n--p~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +.+++  |.++++.+|||+|.|++++++.+-+
T Consensus       201 ~~~lF~~~~~~~i~vSAK~G~~v~~lL~AII~  232 (650)
T KOG0462|consen  201 LFELFDIPPAEVIYVSAKTGLNVEELLEAIIR  232 (650)
T ss_pred             HHHHhcCCccceEEEEeccCccHHHHHHHHHh
Confidence            77663  7789999999999999999997643

>cd04151 Arl1 Arl1 subfamily

Probab=98.70  E-value=5.2e-08  Score=72.23  Aligned_cols=100  Identities=15%  Similarity=0.107  Sum_probs=63.5

Q ss_pred             CCCEEEEeCCcch-hh---hcccccccceEEEEEeCCCCCCCC---cCC------CCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN-LA---ANFSRELADYIIYIIDVSGGDKIP---RKG------GPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~---~~~~~~~ad~~I~VvD~~~~~~~~---~~~------~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|.. ..   ..+ ...++.+++|+|++......   ..+      ...-..+-++|+||+|+.++  ...
T Consensus        42 ~~~~~i~Dt~G~~~~~~~~~~~-~~~~~~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~piiiv~nK~Dl~~~--~~~  118 (158)
T cd04151          42 NLKFQVWDLGGQTSIRPYWRCY-YSNTDAIIYVVDSTDRDRLGTAKEELHAMLEEEELKGAVLLVFANKQDMPGA--LSE  118 (158)
T ss_pred             CEEEEEEECCCCHHHHHHHHHH-hcCCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhcCCcEEEEEeCCCCCCC--CCH
Confidence            5678899999942 11   112 23579999999997643211   000      01123567999999999755  223


Q ss_pred             HHHHHHHHhcC---CCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRMR---DGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~n---p~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .++.+.+....   ...+++++||++|.|+++++++|.+
T Consensus       119 ~~i~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~  157 (158)
T cd04151         119 AEISEKLGLSELKDRTWSIFKTSAIKGEGLDEGMDWLVN  157 (158)
T ss_pred             HHHHHHhCccccCCCcEEEEEeeccCCCCHHHHHHHHhc
Confidence            33333332111   1247999999999999999999864

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.

>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=98.70  E-value=2.4e-08  Score=76.67  Aligned_cols=102  Identities=18%  Similarity=0.124  Sum_probs=65.7

Q ss_pred             CCCCEEEEeCCcch--hhhcc-cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHH
Q 030407           72 FKADLLLCESGGDN--LAANF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        72 ~~~d~iiiEttG~~--~~~~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      ....+-||.|.|-.  ..... ....+|.+|+|+|+..+...+..    .......+-++++||+|+...   +.++..+
T Consensus        68 ~~~~i~~iDtPG~~~f~~~~~~~~~~~D~ailvVda~~g~~~~~~~~l~~~~~~~~p~ivvlNK~D~~~~---~~~~~~~  144 (188)
T PF00009_consen   68 NNRKITLIDTPGHEDFIKEMIRGLRQADIAILVVDANDGIQPQTEEHLKILRELGIPIIVVLNKMDLIEK---ELEEIIE  144 (188)
T ss_dssp             SSEEEEEEEESSSHHHHHHHHHHHTTSSEEEEEEETTTBSTHHHHHHHHHHHHTT-SEEEEEETCTSSHH---HHHHHHH
T ss_pred             cccceeecccccccceeecccceecccccceeeeecccccccccccccccccccccceEEeeeeccchhh---hHHHHHH
Confidence            35678899999931  01111 11246999999999877543221    111234457999999999833   3333333


Q ss_pred             HHH-----hc--CC--CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          145 DAL-----RM--RD--GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       145 ~l~-----~~--np--~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .++     ..  ++  ..|++++||++|.|+++|++.+.+.
T Consensus       145 ~~~~~l~~~~~~~~~~~~~vi~~Sa~~g~gi~~Ll~~l~~~  185 (188)
T PF00009_consen  145 EIKEKLLKEYGENGEEIVPVIPISALTGDGIDELLEALVEL  185 (188)
T ss_dssp             HHHHHHHHHTTSTTTSTEEEEEEBTTTTBTHHHHHHHHHHH
T ss_pred             HHHHHhccccccCccccceEEEEecCCCCCHHHHHHHHHHh
Confidence            332     22  11  3589999999999999999998765

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 ....

>cd04150 Arf1_5_like Arf1-Arf5-like subfamily

Probab=98.69  E-value=5.7e-08  Score=72.51  Aligned_cols=100  Identities=15%  Similarity=0.140  Sum_probs=62.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CC----CC-C-CCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KG----GP-G-ITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~----~~-q-i~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.++++.|..    +...+. ..+|++++|+|+++......   .+    .. . -..+-++++||+|+...  ...
T Consensus        43 ~~~~~l~D~~G~~~~~~~~~~~~-~~ad~~i~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~--~~~  119 (159)
T cd04150          43 NISFTVWDVGGQDKIRPLWRHYF-QNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNA--MSA  119 (159)
T ss_pred             CEEEEEEECCCCHhHHHHHHHHh-cCCCEEEEEEeCCCHHHHHHHHHHHHHHHhcHHhcCCCEEEEEECCCCCCC--CCH
Confidence            5668899999942    112222 35799999999986432110   00    00 0 12456999999999654  222


Q ss_pred             HHHHHHHH--hc-CCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDAL--RM-RDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~--~~-np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +++.+.+.  .. +....++++||++|+|++++|++|.+
T Consensus       120 ~~i~~~~~~~~~~~~~~~~~~~Sak~g~gv~~~~~~l~~  158 (159)
T cd04150         120 AEVTDKLGLHSLRNRNWYIQATCATSGDGLYEGLDWLSN  158 (159)
T ss_pred             HHHHHHhCccccCCCCEEEEEeeCCCCCCHHHHHHHHhc
Confidence            33333332  11 12346789999999999999999864

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

>cd04152 Arl4_Arl7 Arl4/Arl7 subfamily

Probab=98.69  E-value=6e-08  Score=74.10  Aligned_cols=102  Identities=16%  Similarity=0.150  Sum_probs=64.5

Q ss_pred             CCCCEEEEeCCcch-hh---hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHh
Q 030407           72 FKADLLLCESGGDN-LA---ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        72 ~~~d~iiiEttG~~-~~---~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+..+-+++|.|.. ..   ..+ ...+|++++|+|+++......         .+......+-++|+||+|+...  ..
T Consensus        50 ~~~~l~l~Dt~G~~~~~~~~~~~-~~~~d~ii~v~D~~~~~~~~~~~~~~~~i~~~~~~~~~p~iiv~NK~D~~~~--~~  126 (183)
T cd04152          50 KGITFHFWDVGGQEKLRPLWKSY-TRCTDGIVFVVDSVDVERMEEAKTELHKITRFSENQGVPVLVLANKQDLPNA--LS  126 (183)
T ss_pred             CceEEEEEECCCcHhHHHHHHHH-hccCCEEEEEEECCCHHHHHHHHHHHHHHHhhhhcCCCcEEEEEECcCcccc--CC
Confidence            35678899999942 11   122 225799999999987532110         1111234577999999999754  22


Q ss_pred             HHHHHHHHH--hcC--CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 LAVMERDAL--RMR--DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~--~~n--p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+.+.+.  +..  ...+++++||++|+|+++++++|.+.
T Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~SA~~~~gi~~l~~~l~~~  168 (183)
T cd04152         127 VSEVEKLLALHELSASTPWHVQPACAIIGEGLQEGLEKLYEM  168 (183)
T ss_pred             HHHHHHHhCccccCCCCceEEEEeecccCCCHHHHHHHHHHH
Confidence            233333332  121  12468999999999999999988754

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.

>cd04107 Rab32_Rab38 Rab38/Rab32 subfamily

Probab=98.68  E-value=1.1e-07  Score=73.69  Aligned_cols=102  Identities=18%  Similarity=0.065  Sum_probs=67.3

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc------------CCCCCCCceeEEEEecCCCCCchh
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR------------KGGPGITQADLLVINKTDLASAIG  136 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~------------~~~~qi~~adiiviNK~Dl~~~~~  136 (178)
                      .+.+.+++|+|..    +...+. ..++++++|+|.+.......            .....-..+-++|+||+|+.+...
T Consensus        49 ~~~l~l~Dt~G~~~~~~~~~~~~-~~a~~~ilv~D~t~~~s~~~~~~~~~~i~~~~~~~~~~~~piilv~NK~Dl~~~~~  127 (201)
T cd04107          49 VVRLQLWDIAGQERFGGMTRVYY-RGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPCLLLANKCDLKKRLA  127 (201)
T ss_pred             EEEEEEEECCCchhhhhhHHHHh-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhcccCCCCCcEEEEEECCCcccccc
Confidence            4678899999941    112222 35799999999987532211            011112346799999999973211


Q ss_pred             HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 ~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+.+.+..+..+ ..+++++||++|+|++++|++|.+.
T Consensus       128 ~~~~~~~~~~~~~~-~~~~~e~Sak~~~~v~e~f~~l~~~  166 (201)
T cd04107         128 KDGEQMDQFCKENG-FIGWFETSAKEGINIEEAMRFLVKN  166 (201)
T ss_pred             cCHHHHHHHHHHcC-CceEEEEeCCCCCCHHHHHHHHHHH
Confidence            34455666665442 3589999999999999999988654

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.

>cd04156 ARLTS1 ARLTS1 subfamily

Probab=98.68  E-value=6e-08  Score=71.71  Aligned_cols=102  Identities=17%  Similarity=0.129  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcch-hhhc--ccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN-LAAN--FSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~--~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      +..+.++++.|.. ....  .....+|.+++|+|+++......         .....-..+-++|+||+|+...  ...+
T Consensus        43 ~~~l~i~D~~G~~~~~~~~~~~~~~~~~iv~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~~  120 (160)
T cd04156          43 HLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGA--LTAE  120 (160)
T ss_pred             ceEEEEEECCCCHhHHHHHHHHhccCCEEEEEEECCcHHHHHHHHHHHHHHHhchhhcCCCEEEEEECcccccC--cCHH
Confidence            4678899999932 1111  11224799999999987542111         0011124567999999999654  2333


Q ss_pred             HHHHHHH--hcC--CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDAL--RMR--DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~--~~n--p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+...++  ...  +..+++++||++|+|+++++++|.++
T Consensus       121 ~i~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~~~~~i~~~  160 (160)
T cd04156         121 EITRRFKLKKYCSDRDWYVQPCSAVTGEGLAEAFRKLASF  160 (160)
T ss_pred             HHHHHcCCcccCCCCcEEEEecccccCCChHHHHHHHhcC
Confidence            4433332  111  23469999999999999999998753

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

>cd04153 Arl5_Arl8 Arl5/Arl8 subfamily

Probab=98.68  E-value=6.6e-08  Score=73.17  Aligned_cols=100  Identities=18%  Similarity=0.129  Sum_probs=64.3

Q ss_pred             CCCEEEEeCCcch-hh---hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN-LA---ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~---~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.++++.|.. ..   ..+. ..+|++++|+|+++......         .....-..+-++++||+|+...  ...
T Consensus        58 ~~~~~l~D~~G~~~~~~~~~~~~-~~~d~vi~V~D~s~~~~~~~~~~~l~~~~~~~~~~~~p~viv~NK~Dl~~~--~~~  134 (174)
T cd04153          58 NIRFLMWDIGGQESLRSSWNTYY-TNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGA--MTP  134 (174)
T ss_pred             CeEEEEEECCCCHHHHHHHHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhcCCCEEEEEECCCCCCC--CCH
Confidence            5779999999942 11   1122 35799999999987543211         0111123467999999999754  233


Q ss_pred             HHHHHHHHh---cCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALR---MRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~---~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +++.+.+..   .+...+++++||++|+|+++++++|.+
T Consensus       135 ~~i~~~l~~~~~~~~~~~~~~~SA~~g~gi~e~~~~l~~  173 (174)
T cd04153         135 AEISESLGLTSIRDHTWHIQGCCALTGEGLPEGLDWIAS  173 (174)
T ss_pred             HHHHHHhCcccccCCceEEEecccCCCCCHHHHHHHHhc
Confidence            334333321   122347999999999999999999864

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.

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

Probab=98.66  E-value=8.4e-08  Score=72.12  Aligned_cols=100  Identities=11%  Similarity=-0.012  Sum_probs=64.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCCC----C-CceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGPG----I-TQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~q----i-~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+...+++|.|..    +...+. ..+|++|+|+|.++......  .+...    . ..+-++|+||+|+...  .....
T Consensus        48 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~piiiv~nK~Dl~~~--~~~~~  124 (166)
T cd00877          48 KIRFNVWDTAGQEKFGGLRDGYY-IGGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCGNIPIVLCGNKVDIKDR--KVKAK  124 (166)
T ss_pred             EEEEEEEECCCChhhccccHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCcEEEEEEchhcccc--cCCHH
Confidence            5778899999942    112222 24799999999987543211  00000    1 4667999999999744  22222


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ..+..+.  ...+++++||++|+|++++|++|.+.+
T Consensus       125 ~~~~~~~--~~~~~~e~Sa~~~~~v~~~f~~l~~~~  158 (166)
T cd00877         125 QITFHRK--KNLQYYEISAKSNYNFEKPFLWLARKL  158 (166)
T ss_pred             HHHHHHH--cCCEEEEEeCCCCCChHHHHHHHHHHH
Confidence            2233222  245899999999999999999987643

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

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

Probab=98.65  E-value=9e-08  Score=72.61  Aligned_cols=102  Identities=16%  Similarity=0.137  Sum_probs=63.8

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---C---C-CC-C-CCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---K---G-GP-G-ITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~---~-~~-q-i~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.++++.|..    +...+. ..+|++|+|+|+++......   .   . .. . -..+-+||+||+|+...  ...
T Consensus        56 ~~~l~l~D~~G~~~~~~~~~~~~-~~ad~ii~v~D~t~~~s~~~~~~~l~~~~~~~~~~~~piilv~NK~Dl~~~--~~~  132 (175)
T smart00177       56 NISFTVWDVGGQDKIRPLWRHYY-TNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDA--MKA  132 (175)
T ss_pred             CEEEEEEECCCChhhHHHHHHHh-CCCCEEEEEEECCCHHHHHHHHHHHHHHhhCHhhcCCcEEEEEeCcCcccC--CCH
Confidence            5788999999931    112222 35799999999987532211   0   0 01 0 12457999999999754  222


Q ss_pred             HHHHHHHHh--c-CCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDALR--M-RDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l~~--~-np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +++.+.+..  . .....++++||++|+|+++++++|.+.+
T Consensus       133 ~~i~~~~~~~~~~~~~~~~~~~Sa~~g~gv~e~~~~l~~~~  173 (175)
T smart00177      133 AEITEKLGLHSIRDRNWYIQPTCATSGDGLYEGLTWLSNNL  173 (175)
T ss_pred             HHHHHHhCccccCCCcEEEEEeeCCCCCCHHHHHHHHHHHh
Confidence            333333221  1 1223577899999999999999987653

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).

>PRK03003 GTP-binding protein Der; Reviewed

Probab=98.65  E-value=9.4e-08  Score=83.58  Aligned_cols=102  Identities=16%  Similarity=0.050  Sum_probs=65.7

Q ss_pred             CCCEEEEeCCcch----h---hhcc-------cccccceEEEEEeCCCCCCCCcC-CCC---CCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN----L---AANF-------SRELADYIIYIIDVSGGDKIPRK-GGP---GITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~----~---~~~~-------~~~~ad~~I~VvD~~~~~~~~~~-~~~---qi~~adiiviNK~Dl~~~  134 (178)
                      +..+.|+.|.|..    .   ...+       ....+|.+++|+|++++...... ...   .-..+-++|+||+|+.++
T Consensus       258 ~~~~~l~DTaG~~~~~~~~~~~e~~~~~~~~~~i~~ad~vilV~Da~~~~s~~~~~~~~~~~~~~~piIiV~NK~Dl~~~  337 (472)
T PRK03003        258 GKTWRFVDTAGLRRRVKQASGHEYYASLRTHAAIEAAEVAVVLIDASEPISEQDQRVLSMVIEAGRALVLAFNKWDLVDE  337 (472)
T ss_pred             CEEEEEEECCCccccccccchHHHHHHHHHHHHHhcCCEEEEEEeCCCCCCHHHHHHHHHHHHcCCCEEEEEECcccCCh
Confidence            3456899999941    0   0111       11247999999999876543221 000   123467999999999865


Q ss_pred             hhHhHHHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          135 IGADLAVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       135 ~~~~~~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                        .....+.+.+++.   .+.++++++||++|.|++++|+.+.+.
T Consensus       338 --~~~~~~~~~i~~~l~~~~~~~~~~~SAk~g~gv~~lf~~i~~~  380 (472)
T PRK03003        338 --DRRYYLEREIDRELAQVPWAPRVNISAKTGRAVDKLVPALETA  380 (472)
T ss_pred             --hHHHHHHHHHHHhcccCCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence              3333333333321   245799999999999999999988764

>cd01859 MJ1464 MJ1464

Probab=98.65  E-value=1.2e-07  Score=70.45  Aligned_cols=78  Identities=15%  Similarity=0.216  Sum_probs=53.1

Q ss_pred             cceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHH
Q 030407           95 ADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~  170 (178)
                      +|.+++|+|++++......    +......+-++|+||+|+.++  ...+.... +.+ ....+++++||++|+|+++|+
T Consensus        13 aD~vl~V~D~~~~~~~~~~~l~~~~~~~~~p~iiv~NK~Dl~~~--~~~~~~~~-~~~-~~~~~~~~iSa~~~~gi~~L~   88 (156)
T cd01859          13 SDVVLEVLDARDPELTRSRKLERYVLELGKKLLIVLNKADLVPK--EVLEKWKS-IKE-SEGIPVVYVSAKERLGTKILR   88 (156)
T ss_pred             CCEEEEEeeCCCCcccCCHHHHHHHHhCCCcEEEEEEhHHhCCH--HHHHHHHH-HHH-hCCCcEEEEEccccccHHHHH
Confidence            6899999999765432211    111124567999999999765  44333322 222 244689999999999999999


Q ss_pred             HHHhhh
Q 030407          171 SITHYI  176 (178)
Q Consensus       171 ~~l~~~  176 (178)
                      +.+.+.
T Consensus        89 ~~l~~~   94 (156)
T cd01859          89 RTIKEL   94 (156)
T ss_pred             HHHHHH
Confidence            988764

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.

>cd04175 Rap1 Rap1 subgroup

Probab=98.64  E-value=1.1e-07  Score=70.69  Aligned_cols=102  Identities=11%  Similarity=0.037  Sum_probs=63.8

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+-+++|+|..    +...+ ...+|++++|+|.+.......         .....-..+-++++||+|+.+......
T Consensus        48 ~~~l~i~Dt~G~~~~~~~~~~~-~~~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~  126 (164)
T cd04175          48 QCMLEILDTAGTEQFTAMRDLY-MKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGK  126 (164)
T ss_pred             EEEEEEEECCCcccchhHHHHH-HhhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCcchhccEEcH
Confidence            4566689999931    11112 224799999999876432110         011112346799999999975411122


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +...+..++.+  .+++++||++|.|++++|+++.+..
T Consensus       127 ~~~~~~~~~~~--~~~~~~Sa~~~~~v~~~~~~l~~~l  162 (164)
T cd04175         127 EQGQNLARQWG--CAFLETSAKAKINVNEIFYDLVRQI  162 (164)
T ss_pred             HHHHHHHHHhC--CEEEEeeCCCCCCHHHHHHHHHHHh
Confidence            33333334333  5899999999999999999987643

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

>cd04126 Rab20 Rab20 subfamily

Probab=98.62  E-value=1.4e-07  Score=74.68  Aligned_cols=103  Identities=14%  Similarity=0.034  Sum_probs=65.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCC-----CCCCceeEEEEecCCCCC-------
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGG-----PGITQADLLVINKTDLAS-------  133 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~-----~qi~~adiiviNK~Dl~~-------  133 (178)
                      .+.+-|++|.|..    +...+. ..+|++|+|+|+++......   .+.     .--..+-++|.||+||.+       
T Consensus        43 ~~~l~iwDt~G~e~~~~l~~~~~-~~ad~~IlV~Dvt~~~Sf~~l~~~~~~l~~~~~~~~piIlVgNK~DL~~~~~~~~~  121 (220)
T cd04126          43 PYNISIWDTAGREQFHGLGSMYC-RGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTEEGALAGQ  121 (220)
T ss_pred             EEEEEEEeCCCcccchhhHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECcccccccccccc
Confidence            4678899999931    112222 35799999999987532211   000     001245699999999975       


Q ss_pred             ------------chhHhHHHHHHHHHhcCC------------CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          134 ------------AIGADLAVMERDALRMRD------------GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       134 ------------~~~~~~~~~~~~l~~~np------------~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                                  ......++..++.++.+.            ..+++++||++|+||+++|+.+.+.
T Consensus       122 ~~~~~~~~~~~~~r~v~~~e~~~~a~~~~~~~~~~~~~~~~~~~~~~E~SA~tg~~V~elf~~i~~~  188 (220)
T cd04126         122 EKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMCFETSAKTGYNVDELFEYLFNL  188 (220)
T ss_pred             cccccccccccccccCCHHHHHHHHHHhCccccccccccccccceEEEeeCCCCCCHHHHHHHHHHH
Confidence                        111223445555555431            2579999999999999999987653

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

>PLN00223 ADP-ribosylation factor; Provisional

Probab=98.62  E-value=1.3e-07  Score=72.41  Aligned_cols=102  Identities=15%  Similarity=0.112  Sum_probs=65.3

Q ss_pred             CCCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc------CC--CCC-CCceeEEEEecCCCCCchhHh
Q 030407           72 FKADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR------KG--GPG-ITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        72 ~~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~------~~--~~q-i~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+..+.++++.|..    +...+. ..+|++|+|+|+++......      ..  ... -..+-++++||.|+...  ..
T Consensus        59 ~~~~~~i~D~~Gq~~~~~~~~~~~-~~a~~iI~V~D~s~~~s~~~~~~~l~~~l~~~~~~~~piilv~NK~Dl~~~--~~  135 (181)
T PLN00223         59 KNISFTVWDVGGQDKIRPLWRHYF-QNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNA--MN  135 (181)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHh-ccCCEEEEEEeCCcHHHHHHHHHHHHHHhcCHhhCCCCEEEEEECCCCCCC--CC
Confidence            35778999999931    112222 35799999999987543211      00  011 13467999999999766  44


Q ss_pred             HHHHHHHHHhcC--CC-CCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 LAVMERDALRMR--DG-GPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~~~n--p~-a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+.+.+.-.+  +. ..++++||++|+|++++|++|.+.
T Consensus       136 ~~~~~~~l~l~~~~~~~~~~~~~Sa~~g~gv~e~~~~l~~~  176 (181)
T PLN00223        136 AAEITDKLGLHSLRQRHWYIQSTCATSGEGLYEGLDWLSNN  176 (181)
T ss_pred             HHHHHHHhCccccCCCceEEEeccCCCCCCHHHHHHHHHHH
Confidence            455555543111  11 245679999999999999998654

>cd01894 EngA1 EngA1 subfamily

Probab=98.62  E-value=1.9e-07  Score=68.30  Aligned_cols=98  Identities=20%  Similarity=0.165  Sum_probs=64.3

Q ss_pred             CCCEEEEeCCcchhhhc---------c--cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDNLAAN---------F--SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~---------~--~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~  137 (178)
                      +..+.+++|.|..-...         .  ....+|.+++|+|+.++......    +......+-++|+||+|+.+.  .
T Consensus        44 ~~~~~i~DtpG~~~~~~~~~~~~~~~~~~~~~~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~piiiv~nK~D~~~~--~  121 (157)
T cd01894          44 GREFILIDTGGIEPDDEGISKEIREQAELAIEEADVILFVVDGREGLTPADEEIAKYLRKSKKPVILVVNKVDNIKE--E  121 (157)
T ss_pred             CeEEEEEECCCCCCchhHHHHHHHHHHHHHHHhCCEEEEEEeccccCCccHHHHHHHHHhcCCCEEEEEECcccCCh--H
Confidence            46789999999421110         0  11246999999999765432211    111234567999999999876  3


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..   ...+.+. ...+++++||++|.|++++++++.+.
T Consensus       122 ~~---~~~~~~~-~~~~~~~~Sa~~~~gv~~l~~~l~~~  156 (157)
T cd01894         122 DE---AAEFYSL-GFGEPIPISAEHGRGIGDLLDAILEL  156 (157)
T ss_pred             HH---HHHHHhc-CCCCeEEEecccCCCHHHHHHHHHhh
Confidence            32   2223333 23478999999999999999998653

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.

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=98.62  E-value=1.5e-07  Score=69.79  Aligned_cols=102  Identities=14%  Similarity=0.086  Sum_probs=64.6

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+-+++|.|..    +...+. ..++++++|+|+++......  .       .......+-++|+||+|+.+......
T Consensus        47 ~~~l~i~Dt~g~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~pii~v~nK~Dl~~~~~~~~  125 (164)
T smart00173       47 VCLLDILDTAGQEEFSAMRDQYM-RTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLESERVVST  125 (164)
T ss_pred             EEEEEEEECCCcccchHHHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccceEcH
Confidence            3566789999931    112222 24699999999986432111  0       00111346689999999975411222


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +...+..+..  ..+++++||++|.|++++++.+.+..
T Consensus       126 ~~~~~~~~~~--~~~~~~~Sa~~~~~i~~l~~~l~~~~  161 (164)
T smart00173      126 EEGKELARQW--GCPFLETSAKERVNVDEAFYDLVREI  161 (164)
T ss_pred             HHHHHHHHHc--CCEEEEeecCCCCCHHHHHHHHHHHH
Confidence            3444444443  36899999999999999999887643

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=98.62  E-value=1.7e-07  Score=69.27  Aligned_cols=100  Identities=11%  Similarity=0.027  Sum_probs=65.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCC----CCCceeEEEEecCCCCCch
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGP----GITQADLLVINKTDLASAI  135 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~----qi~~adiiviNK~Dl~~~~  135 (178)
                      .+.+-+++|.|..    +...+. ..+|++++|+|+++......         .+..    .-..+-++|+||+|+.++.
T Consensus        48 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~d~~ilv~D~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~  126 (168)
T cd04119          48 EVRVNFFDLSGHPEYLEVRNEFY-KDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLTKHR  126 (168)
T ss_pred             EEEEEEEECCccHHHHHHHHHHh-ccCCEEEEEEECCCHHHHHhHHHHHHHHHHhccccccCCCceEEEEEEchhccccc
Confidence            4678899999942    112222 35799999999986532110         0110    1235679999999997431


Q ss_pred             hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          136 GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       136 ~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ....+...++.++.+  .+++++||++|+|+++++++|.+
T Consensus       127 ~~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~~~l~~  164 (168)
T cd04119         127 AVSEDEGRLWAESKG--FKYFETSACTGEGVNEMFQTLFS  164 (168)
T ss_pred             ccCHHHHHHHHHHcC--CeEEEEECCCCCCHHHHHHHHHH
Confidence            123344444555432  68999999999999999998764

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.

>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed

Probab=98.62  E-value=1.4e-07  Score=86.34  Aligned_cols=102  Identities=17%  Similarity=0.023  Sum_probs=68.8

Q ss_pred             CCCEEEEeCCcch-----h--hhcc-------cccccceEEEEEeCCCCCCCCcC-CC---CCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-----L--AANF-------SRELADYIIYIIDVSGGDKIPRK-GG---PGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-----~--~~~~-------~~~~ad~~I~VvD~~~~~~~~~~-~~---~qi~~adiiviNK~Dl~~~  134 (178)
                      +.++.|+.|.|..     .  ...+       ....+|.+++|+|++.+...+.. ..   .....+-++|+||+|+.++
T Consensus       497 ~~~~~liDTaG~~~~~~~~~~~e~~~~~r~~~~i~~advvilViDat~~~s~~~~~i~~~~~~~~~piIiV~NK~DL~~~  576 (712)
T PRK09518        497 GEDWLFIDTAGIKRRQHKLTGAEYYSSLRTQAAIERSELALFLFDASQPISEQDLKVMSMAVDAGRALVLVFNKWDLMDE  576 (712)
T ss_pred             CCEEEEEECCCcccCcccchhHHHHHHHHHHHHhhcCCEEEEEEECCCCCCHHHHHHHHHHHHcCCCEEEEEEchhcCCh
Confidence            4567899999941     0  0111       11246999999999887543221 00   1124578999999999876


Q ss_pred             hhHhHHHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          135 IGADLAVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       135 ~~~~~~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                        ...+.+.+.++..   .+.++++++||++|.|++++++.+.+.
T Consensus       577 --~~~~~~~~~~~~~l~~~~~~~ii~iSAktg~gv~~L~~~i~~~  619 (712)
T PRK09518        577 --FRRQRLERLWKTEFDRVTWARRVNLSAKTGWHTNRLAPAMQEA  619 (712)
T ss_pred             --hHHHHHHHHHHHhccCCCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence              4445555555432   256899999999999999999987654

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

Probab=98.61  E-value=1.6e-07  Score=69.30  Aligned_cols=100  Identities=16%  Similarity=0.095  Sum_probs=66.8

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.++++.|..-    ...+. ..+|.+++|+|++.......         .....-..+-++++||+|+...  ...
T Consensus        42 ~~~~~i~D~~G~~~~~~~~~~~~-~~~~~~i~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~piiiv~nK~D~~~~--~~~  118 (158)
T cd00878          42 NVSFTVWDVGGQDKIRPLWKHYY-ENTNGIIFVVDSSDRERIEEAKEELHKLLNEEELKGVPLLIFANKQDLPGA--LSV  118 (158)
T ss_pred             CEEEEEEECCCChhhHHHHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHhCcccCCCcEEEEeeccCCccc--cCH
Confidence            57899999999311    11111 24699999999987532110         0001123466999999999876  444


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +++.+.++..   ....+++++||++|.|+++++++|..
T Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~~~~~l~~  157 (158)
T cd00878         119 SELIEKLGLEKILGRRWHIQPCSAVTGDGLDEGLDWLLQ  157 (158)
T ss_pred             HHHHHhhChhhccCCcEEEEEeeCCCCCCHHHHHHHHhh
Confidence            5555555432   12458999999999999999999865

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

>cd01849 YlqF_related_GTPase YlqF-related GTPases

Probab=98.61  E-value=1.7e-07  Score=69.86  Aligned_cols=77  Identities=17%  Similarity=-0.063  Sum_probs=52.4

Q ss_pred             ceEEEEEeCCCCCCCCcC-C----CCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHH
Q 030407           96 DYIIYIIDVSGGDKIPRK-G----GPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus        96 d~~I~VvD~~~~~~~~~~-~----~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~  170 (178)
                      |.+++|+|+..+...... .    ......+-++|+||+|+.++  ++.......+++.. ..+++.+||++|.|+++|.
T Consensus         1 Dvvl~VvD~~~p~~~~~~~i~~~~~~~~~~p~IiVlNK~Dl~~~--~~~~~~~~~~~~~~-~~~ii~vSa~~~~gi~~L~   77 (155)
T cd01849           1 DVILEVLDARDPLGTRSPDIERVLIKEKGKKLILVLNKADLVPK--EVLRKWLAYLRHSY-PTIPFKISATNGQGIEKKE   77 (155)
T ss_pred             CEEEEEEeccCCccccCHHHHHHHHhcCCCCEEEEEechhcCCH--HHHHHHHHHHHhhC-CceEEEEeccCCcChhhHH
Confidence            678999999775433211 1    11234567999999999876  54443333344332 4679999999999999999


Q ss_pred             HHHhh
Q 030407          171 SITHY  175 (178)
Q Consensus       171 ~~l~~  175 (178)
                      +.+.+
T Consensus        78 ~~i~~   82 (155)
T cd01849          78 SAFTK   82 (155)
T ss_pred             HHHHH
Confidence            98754

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.

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

Probab=98.60  E-value=1.1e-07  Score=69.47  Aligned_cols=96  Identities=21%  Similarity=0.196  Sum_probs=65.9

Q ss_pred             CCCEEEEeCCcchhhh----------c-ccccccceEEEEEeCCCCCCCCc--CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNLAA----------N-FSRELADYIIYIIDVSGGDKIPR--KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~----------~-~~~~~ad~~I~VvD~~~~~~~~~--~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|..-..          . .....+|.+++|+|++.......  ........+.++|+||+|+.+.  ...
T Consensus        48 ~~~~~i~DtpG~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~d~~~~~~~~~~~~~~~~~~~~vi~v~nK~D~~~~--~~~  125 (157)
T cd04164          48 GIPVRLIDTAGIRETEDEIEKIGIERAREAIEEADLVLFVIDASRGLDEEDLEILELPADKPIIVVLNKSDLLPD--SEL  125 (157)
T ss_pred             CEEEEEEECCCcCCCcchHHHHHHHHHHHHHhhCCEEEEEEECCCCCCHHHHHHHHhhcCCCEEEEEEchhcCCc--ccc
Confidence            4678999999941100          0 01124699999999986443221  1111345678999999999877  333


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                             .......+++++||++|.|+++|+++|...+
T Consensus       126 -------~~~~~~~~~~~~Sa~~~~~v~~l~~~l~~~~  156 (157)
T cd04164         126 -------LSLLAGKPIIAISAKTGEGLDELKEALLELA  156 (157)
T ss_pred             -------ccccCCCceEEEECCCCCCHHHHHHHHHHhh
Confidence                   1223456999999999999999999988765

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.

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

Probab=98.60  E-value=1.3e-07  Score=69.52  Aligned_cols=101  Identities=14%  Similarity=0.108  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCcchh----------hhcccc-cccceEEEEEeCCCCCCCCcCC--CCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----------AANFSR-ELADYIIYIIDVSGGDKIPRKG--GPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----------~~~~~~-~~ad~~I~VvD~~~~~~~~~~~--~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +.++.+++|.|..-          ...+.. ..+|.+++|+|+..........  ......+-++|+||+|+.+.  ...
T Consensus        42 ~~~~~liDtpG~~~~~~~~~~~~~~~~~~~~~~~d~vi~v~d~~~~~~~~~~~~~~~~~~~~~iiv~NK~Dl~~~--~~~  119 (158)
T cd01879          42 GKEIEIVDLPGTYSLSPYSEDEKVARDFLLGEKPDLIVNVVDATNLERNLYLTLQLLELGLPVVVALNMIDEAEK--RGI  119 (158)
T ss_pred             CeEEEEEECCCccccCCCChhHHHHHHHhcCCCCcEEEEEeeCCcchhHHHHHHHHHHcCCCEEEEEehhhhccc--ccc
Confidence            45789999999421          111111 2579999999998653221110  01134567999999999765  322


Q ss_pred             H-HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 A-VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~-~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      . ......+..  +.+++++||++|+|++++++++.+.+
T Consensus       120 ~~~~~~~~~~~--~~~~~~iSa~~~~~~~~l~~~l~~~~  156 (158)
T cd01879         120 KIDLDKLSELL--GVPVVPTSARKGEGIDELKDAIAELA  156 (158)
T ss_pred             hhhHHHHHHhh--CCCeEEEEccCCCCHHHHHHHHHHHh
Confidence            2 222222322  35899999999999999999987653

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.

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

Probab=98.60  E-value=1.3e-07  Score=72.35  Aligned_cols=100  Identities=14%  Similarity=0.070  Sum_probs=65.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc------C---CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR------K---GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~------~---~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ++.+.++++.|..-    ...+. ..+|++++|+|+++......      .   ....-..+-++|+||+|+...  ...
T Consensus        60 ~~~~~~~D~~G~~~~~~~~~~~~-~~ad~ii~vvD~~~~~~~~~~~~~l~~l~~~~~~~~~piliv~NK~Dl~~~--~~~  136 (184)
T smart00178       60 NIKFTTFDLGGHQQARRLWKDYF-PEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYA--ASE  136 (184)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHh-CCCCEEEEEEECCcHHHHHHHHHHHHHHHcChhhcCCCEEEEEeCccccCC--CCH
Confidence            57789999999421    11222 35799999999987532111      0   001123467999999999654  334


Q ss_pred             HHHHHHHHhc----------CCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRM----------RDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~----------np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +++.+.+.-.          .+...++++||++|+|+++++++|.+
T Consensus       137 ~~i~~~l~l~~~~~~~~~~~~~~~~i~~~Sa~~~~g~~~~~~wl~~  182 (184)
T smart00178      137 DELRYALGLTNTTGSKGKVGVRPLEVFMCSVVRRMGYGEGFKWLSQ  182 (184)
T ss_pred             HHHHHHcCCCcccccccccCCceeEEEEeecccCCChHHHHHHHHh
Confidence            4555554211          12346999999999999999999865

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

>cd04121 Rab40 Rab40 subfamily

Probab=98.60  E-value=1.7e-07  Score=72.43  Aligned_cols=101  Identities=19%  Similarity=0.124  Sum_probs=67.2

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC-----CCCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP-----GITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~-----qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+.+-+++|+|..    +...+. ..+|++++|+|.++......  .+..     .-..+-++|.||.||........++
T Consensus        54 ~~~l~iwDt~G~~~~~~l~~~~~-~~ad~illVfD~t~~~Sf~~~~~w~~~i~~~~~~~piilVGNK~DL~~~~~v~~~~  132 (189)
T cd04121          54 RVKLQLWDTSGQGRFCTIFRSYS-RGAQGIILVYDITNRWSFDGIDRWIKEIDEHAPGVPKILVGNRLHLAFKRQVATEQ  132 (189)
T ss_pred             EEEEEEEeCCCcHHHHHHHHHHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCEEEEEECccchhccCCCHHH
Confidence            4677789999942    112222 36799999999987543211  0000     0134679999999996531123445


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+++.++.  ..+++++||++|.|++++|+++.+.
T Consensus       133 ~~~~a~~~--~~~~~e~SAk~g~~V~~~F~~l~~~  165 (189)
T cd04121         133 AQAYAERN--GMTFFEVSPLCNFNITESFTELARI  165 (189)
T ss_pred             HHHHHHHc--CCEEEEecCCCCCCHHHHHHHHHHH
Confidence            56666654  3589999999999999999988753

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

>cd01858 NGP_1 NGP-1

Probab=98.60  E-value=8.6e-08  Score=71.58  Aligned_cols=80  Identities=14%  Similarity=0.017  Sum_probs=54.8

Q ss_pred             ccceEEEEEeCCCCCCCCc-CCCC---CC--CceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHH
Q 030407           94 LADYIIYIIDVSGGDKIPR-KGGP---GI--TQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGII  167 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~-~~~~---qi--~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~  167 (178)
                      .+|.+++|+|+..+..... ....   ..  ..+-++|+||+|+.++  ++.....+.+++..+.. ++++||++|.|++
T Consensus         8 ~aD~il~VvD~~~p~~~~~~~i~~~l~~~~~~~p~ilVlNKiDl~~~--~~~~~~~~~~~~~~~~~-~~~iSa~~~~~~~   84 (157)
T cd01858           8 SSDVVIQVLDARDPMGTRCKHVEEYLKKEKPHKHLIFVLNKCDLVPT--WVTARWVKILSKEYPTI-AFHASINNPFGKG   84 (157)
T ss_pred             hCCEEEEEEECCCCccccCHHHHHHHHhccCCCCEEEEEEchhcCCH--HHHHHHHHHHhcCCcEE-EEEeeccccccHH
Confidence            4699999999987532211 1101   11  1457999999999877  55555555555444432 6889999999999


Q ss_pred             HHHHHHhhh
Q 030407          168 FTLSITHYI  176 (178)
Q Consensus       168 el~~~l~~~  176 (178)
                      +|++.+.+.
T Consensus        85 ~L~~~l~~~   93 (157)
T cd01858          85 SLIQLLRQF   93 (157)
T ss_pred             HHHHHHHHH
Confidence            999988754

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.

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=98.59  E-value=1.9e-07  Score=68.85  Aligned_cols=101  Identities=13%  Similarity=0.114  Sum_probs=64.6

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCC---c------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIP---R------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~---~------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ++.+.+++|.|..    ....+. ..++.+++++|........   .      ........+-++|+||+|+.+......
T Consensus        47 ~~~~~i~D~~g~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piiiv~NK~D~~~~~~~~~  125 (164)
T cd04139          47 DVQLNILDTAGQEDYAAIRDNYH-RSGEGFLLVFSITDMESFTATAEFREQILRVKDDDNVPLLLVGNKCDLEDKRQVSS  125 (164)
T ss_pred             EEEEEEEECCChhhhhHHHHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEccccccccccCH
Confidence            4678899999931    111222 2458899999987643210   0      011123567799999999976211233


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +......++.  ..+++++||++|+|++++++.+.+.
T Consensus       126 ~~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  160 (164)
T cd04139         126 EEAANLARQW--GVPYVETSAKTRQNVEKAFYDLVRE  160 (164)
T ss_pred             HHHHHHHHHh--CCeEEEeeCCCCCCHHHHHHHHHHH
Confidence            4444444443  3589999999999999999987653

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

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

Probab=98.59  E-value=2.2e-07  Score=68.27  Aligned_cols=99  Identities=14%  Similarity=0.118  Sum_probs=62.6

Q ss_pred             CEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHHH
Q 030407           75 DLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        75 d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+-+++|.|..    +...+. ..++.+++|+|.++......         .....-..+-++|+||+|+.+.. ...+.
T Consensus        50 ~~~i~Dt~G~~~~~~l~~~~~-~~~~~~i~v~~~~~~~s~~~~~~~~~~i~~~~~~~~~piivv~nK~Dl~~~~-~~~~~  127 (162)
T cd04138          50 LLDILDTAGQEEYSAMRDQYM-RTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAART-VSSRQ  127 (162)
T ss_pred             EEEEEECCCCcchHHHHHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccce-ecHHH
Confidence            34568999931    122222 24689999999876432111         01111234669999999997641 22334


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ..+..+..  ..+++++||++|+|++++|+++.+..
T Consensus       128 ~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~~  161 (162)
T cd04138         128 GQDLAKSY--GIPYIETSAKTRQGVEEAFYTLVREI  161 (162)
T ss_pred             HHHHHHHh--CCeEEEecCCCCCCHHHHHHHHHHHh
Confidence            44444433  35899999999999999999987653

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.

>cd00879 Sar1 Sar1 subfamily

Probab=98.59  E-value=2e-07  Score=71.15  Aligned_cols=101  Identities=14%  Similarity=0.103  Sum_probs=65.9

Q ss_pred             CCCEEEEeCCcchhh----hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNLA----ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~~----~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.++++.|....    ..+. ..++.+++|+|+++......         ........+-++++||+|+...  ...
T Consensus        62 ~~~~~l~D~~G~~~~~~~~~~~~-~~ad~iilV~D~~~~~s~~~~~~~~~~i~~~~~~~~~pvivv~NK~Dl~~~--~~~  138 (190)
T cd00879          62 NIKFKTFDLGGHEQARRLWKDYF-PEVDGIVFLVDAADPERFQESKEELDSLLSDEELANVPFLILGNKIDLPGA--VSE  138 (190)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHh-ccCCEEEEEEECCcHHHHHHHHHHHHHHHcCccccCCCEEEEEeCCCCCCC--cCH
Confidence            456788999993211    1122 24699999999976432110         0111123567999999999755  445


Q ss_pred             HHHHHHHHhcC--------------CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMR--------------DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~n--------------p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +++.+.++...              -..+++++||++|+|++++|++|.+.
T Consensus       139 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~e~~~~l~~~  189 (190)
T cd00879         139 EELRQALGLYGTTTGKGVSLKVSGIRPIEVFMCSVVKRQGYGEAFRWLSQY  189 (190)
T ss_pred             HHHHHHhCcccccccccccccccCceeEEEEEeEecCCCChHHHHHHHHhh
Confidence            56666654211              12468999999999999999998753

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.

>cd01893 Miro1 Miro1 subfamily

Probab=98.58  E-value=6.9e-08  Score=72.31  Aligned_cols=103  Identities=17%  Similarity=0.126  Sum_probs=65.5

Q ss_pred             CCCCEEEEeCCcchhh----hcccccccceEEEEEeCCCCCCCCc---CCCC-----CCCceeEEEEecCCCCCchhHhH
Q 030407           72 FKADLLLCESGGDNLA----ANFSRELADYIIYIIDVSGGDKIPR---KGGP-----GITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~----~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~-----qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ...++.++.|.|....    ..+ ...+|.+++|+|+++......   .+.+     ....+-++|+||+|+.+.  ...
T Consensus        45 ~~~~~~i~Dt~G~~~~~~~~~~~-~~~ad~~ilv~d~~~~~s~~~~~~~~~~~i~~~~~~~pviiv~nK~Dl~~~--~~~  121 (166)
T cd01893          45 ERVPTTIVDTSSRPQDRANLAAE-IRKANVICLVYSVDRPSTLERIRTKWLPLIRRLGVKVPIILVGNKSDLRDG--SSQ  121 (166)
T ss_pred             CeEEEEEEeCCCchhhhHHHhhh-cccCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEchhcccc--cch
Confidence            3577889999994211    111 135799999999987543221   1110     014567999999999765  221


Q ss_pred             ---HH-HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 ---AV-MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ---~~-~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                         +. +....+..+...+++++||++|.|++++|+.+.+.+
T Consensus       122 ~~~~~~~~~~~~~~~~~~~~~e~Sa~~~~~v~~lf~~~~~~~  163 (166)
T cd01893         122 AGLEEEMLPIMNEFREIETCVECSAKTLINVSEVFYYAQKAV  163 (166)
T ss_pred             hHHHHHHHHHHHHHhcccEEEEeccccccCHHHHHHHHHHHh
Confidence               12 222222222224899999999999999999988765

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.

>cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily

Probab=98.58  E-value=2.2e-07  Score=70.28  Aligned_cols=101  Identities=16%  Similarity=0.037  Sum_probs=65.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ...+-+++|.|..    +...+. ..+|++++|+|+++......         .....-..+-++|+||+|+.+......
T Consensus        49 ~~~l~i~Dt~G~~~~~~l~~~~~-~~~d~~ilv~d~~~~~Sf~~~~~~~~~i~~~~~~~~~piilvgNK~Dl~~~~~v~~  127 (172)
T cd04141          49 PALLDILDTAGQAEFTAMRDQYM-RCGEGFIICYSVTDRHSFQEASEFKKLITRVRLTEDIPLVLVGNKVDLESQRQVTT  127 (172)
T ss_pred             EEEEEEEeCCCchhhHHHhHHHh-hcCCEEEEEEECCchhHHHHHHHHHHHHHHhcCCCCCCEEEEEEChhhhhcCccCH
Confidence            4667789999931    112222 24799999999987643221         001112346799999999865311222


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..++.  +.+++++||++|.||+++|+++.+.
T Consensus       128 ~~~~~~a~~~--~~~~~e~Sa~~~~~v~~~f~~l~~~  162 (172)
T cd04141         128 EEGRNLAREF--NCPFFETSAALRHYIDDAFHGLVRE  162 (172)
T ss_pred             HHHHHHHHHh--CCEEEEEecCCCCCHHHHHHHHHHH
Confidence            3344444443  4689999999999999999988653

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

>cd04101 RabL4 RabL4 (Rab-like4) subfamily

Probab=98.58  E-value=1.1e-07  Score=70.63  Aligned_cols=102  Identities=21%  Similarity=0.142  Sum_probs=64.3

Q ss_pred             CCCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCC--cCCCC-----CCCceeEEEEecCCCCCchhHhHH
Q 030407           72 FKADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIP--RKGGP-----GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        72 ~~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~--~~~~~-----qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ....+.+++|+|...    ...+. ..+|.+++|+|.++.....  ..+..     ....+-++|+||+|+.+......+
T Consensus        50 ~~~~l~i~Dt~G~~~~~~~~~~~~-~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~~  128 (164)
T cd04101          50 NTVELFIFDSAGQELYSDMVSNYW-ESPSVFILVYDVSNKASFENCSRWVNKVRTASKHMPGVLVGNKMDLADKAEVTDA  128 (164)
T ss_pred             CEEEEEEEECCCHHHHHHHHHHHh-CCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCEEEEEECcccccccCCCHH
Confidence            357899999999321    11222 2479999999998753221  00100     123567999999999765111112


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ......+..  ..+++++||++|.|++++++.+.+.
T Consensus       129 ~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  162 (164)
T cd04101         129 QAQAFAQAN--QLKFFKTSALRGVGYEEPFESLARA  162 (164)
T ss_pred             HHHHHHHHc--CCeEEEEeCCCCCChHHHHHHHHHH
Confidence            222222222  3579999999999999999988764

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.

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

Probab=98.58  E-value=3e-07  Score=68.03  Aligned_cols=101  Identities=14%  Similarity=0.104  Sum_probs=64.4

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC-------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG-------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~-------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      +.+-+++|.|..    +...+. ..+|.+++|+|+++......  .+.       .--..+-++++||+|+........+
T Consensus        50 ~~~~i~Dt~G~~~~~~~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~piiiv~NK~Dl~~~~~~~~~  128 (164)
T cd04145          50 AILDILDTAGQEEFSAMREQYM-RTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEHQRKVSRE  128 (164)
T ss_pred             EEEEEEECCCCcchhHHHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCCEEEEeeCccccccceecHH
Confidence            567789999931    111222 24799999999987532111  000       0013467999999999754111233


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ...+..+..  ..+++++||++|+|++++|+.+.+.+
T Consensus       129 ~~~~~~~~~--~~~~~~~Sa~~~~~i~~l~~~l~~~~  163 (164)
T cd04145         129 EGQELARKL--KIPYIETSAKDRLNVDKAFHDLVRVI  163 (164)
T ss_pred             HHHHHHHHc--CCcEEEeeCCCCCCHHHHHHHHHHhh
Confidence            444444443  35899999999999999999987643

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

>cd01863 Rab18 Rab18 subfamily

Probab=98.58  E-value=3.5e-07  Score=67.65  Aligned_cols=99  Identities=18%  Similarity=0.124  Sum_probs=65.4

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ...+.+++|.|..    +...+ ...+|.+++|+|.++......         .+...-..+.++|+||+|+.... ...
T Consensus        48 ~~~~~l~D~~g~~~~~~~~~~~-~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~iv~nK~D~~~~~-~~~  125 (161)
T cd01863          48 KVKLAIWDTAGQERFRTLTSSY-YRGAQGVILVYDVTRRDTFTNLETWLNELETYSTNNDIVKMLVGNKIDKENRE-VTR  125 (161)
T ss_pred             EEEEEEEECCCchhhhhhhHHH-hCCCCEEEEEEECCCHHHHHhHHHHHHHHHHhCCCCCCcEEEEEECCcccccc-cCH
Confidence            4678999999931    11111 124799999999876532211         11122345679999999997331 233


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +...+..+..  ..+++++||++|+|++++++.+.+
T Consensus       126 ~~~~~~~~~~--~~~~~~~Sa~~~~gi~~~~~~~~~  159 (161)
T cd01863         126 EEGLKFARKH--NMLFIETSAKTRDGVQQAFEELVE  159 (161)
T ss_pred             HHHHHHHHHc--CCEEEEEecCCCCCHHHHHHHHHH
Confidence            4455555543  468999999999999999998754

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

>TIGR02729 Obg_CgtA Obg family GTPase CgtA

Probab=98.57  E-value=2.2e-07  Score=77.74  Aligned_cols=101  Identities=21%  Similarity=0.227  Sum_probs=67.3

Q ss_pred             CCEEEEeCCcch--------hhhcccc--cccceEEEEEeCCCCC--CCCc----------CCCC-CCCceeEEEEecCC
Q 030407           74 ADLLLCESGGDN--------LAANFSR--ELADYIIYIIDVSGGD--KIPR----------KGGP-GITQADLLVINKTD  130 (178)
Q Consensus        74 ~d~iiiEttG~~--------~~~~~~~--~~ad~~I~VvD~~~~~--~~~~----------~~~~-qi~~adiiviNK~D  130 (178)
                      ..+.|+.+.|..        +...|..  ..++.+++|+|++...  +...          .+.. ....+-++|+||+|
T Consensus       205 ~~~~i~D~PGli~~a~~~~gLg~~flrhierad~ll~VvD~s~~~~~~~~e~l~~l~~EL~~~~~~l~~kp~IIV~NK~D  284 (329)
T TIGR02729       205 RSFVIADIPGLIEGASEGAGLGHRFLKHIERTRVLLHLIDISPLDGRDPIEDYEIIRNELKKYSPELAEKPRIVVLNKID  284 (329)
T ss_pred             eEEEEEeCCCcccCCcccccHHHHHHHHHHhhCEEEEEEcCccccccCHHHHHHHHHHHHHHhhhhhccCCEEEEEeCcc
Confidence            568899999941        1112222  2368999999998642  1100          1111 13457799999999


Q ss_pred             CCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          131 LASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       131 l~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +.++  ...+.+.+.+.+.. ..+++++||++|+|++++++++.+..
T Consensus       285 L~~~--~~~~~~~~~l~~~~-~~~vi~iSAktg~GI~eL~~~I~~~l  328 (329)
T TIGR02729       285 LLDE--EELAELLKELKKAL-GKPVFPISALTGEGLDELLYALAELL  328 (329)
T ss_pred             CCCh--HHHHHHHHHHHHHc-CCcEEEEEccCCcCHHHHHHHHHHHh
Confidence            9876  55555555554332 25899999999999999999987764

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.

>cd04122 Rab14 Rab14 subfamily

Probab=98.57  E-value=2.4e-07  Score=69.15  Aligned_cols=100  Identities=14%  Similarity=0.066  Sum_probs=64.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+-+++|+|..    +...+. ..++++++|+|.++......  .+.      ..-..+-++|.||+|+.++.....+
T Consensus        50 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~iiiv~nK~Dl~~~~~~~~~  128 (166)
T cd04122          50 KIKLQIWDTAGQERFRAVTRSYY-RGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLEAQRDVTYE  128 (166)
T ss_pred             EEEEEEEECCCcHHHHHHHHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccCcCHH
Confidence            4677899999942    111222 35799999999987542211  000      0112457999999999765212234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ...+..+..  ..+++++||++|+|++++|+.+..
T Consensus       129 ~~~~~~~~~--~~~~~e~Sa~~~~~i~e~f~~l~~  161 (166)
T cd04122         129 EAKQFADEN--GLLFLECSAKTGENVEDAFLETAK  161 (166)
T ss_pred             HHHHHHHHc--CCEEEEEECCCCCCHHHHHHHHHH
Confidence            455555543  468999999999999999987754

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

>PRK12299 obgE GTPase CgtA; Reviewed

Probab=98.57  E-value=3.8e-07  Score=76.56  Aligned_cols=100  Identities=19%  Similarity=0.275  Sum_probs=64.6

Q ss_pred             CCEEEEeCCcch--------hhhcccc--cccceEEEEEeCCCCCCCCc---------CCCC-CCCceeEEEEecCCCCC
Q 030407           74 ADLLLCESGGDN--------LAANFSR--ELADYIIYIIDVSGGDKIPR---------KGGP-GITQADLLVINKTDLAS  133 (178)
Q Consensus        74 ~d~iiiEttG~~--------~~~~~~~--~~ad~~I~VvD~~~~~~~~~---------~~~~-qi~~adiiviNK~Dl~~  133 (178)
                      ..++++++.|..        +...|..  ..++.+++|+|+++.+....         .+.. ....+-++|+||+|+.+
T Consensus       206 ~~~~i~D~PGli~ga~~~~gLg~~flrhie~a~vlI~ViD~s~~~s~e~~~~~~~EL~~~~~~L~~kp~IIV~NKiDL~~  285 (335)
T PRK12299        206 KSFVIADIPGLIEGASEGAGLGHRFLKHIERTRLLLHLVDIEAVDPVEDYKTIRNELEKYSPELADKPRILVLNKIDLLD  285 (335)
T ss_pred             cEEEEEeCCCccCCCCccccHHHHHHHHhhhcCEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhcccCCeEEEEECcccCC
Confidence            458999999941        1122222  23689999999986532110         1111 13467899999999986


Q ss_pred             chhHhHH--HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          134 AIGADLA--VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       134 ~~~~~~~--~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +  .+..  ......+..  ..+++++||++|+|+++++++|.+.+
T Consensus       286 ~--~~~~~~~~~~~~~~~--~~~i~~iSAktg~GI~eL~~~L~~~l  327 (335)
T PRK12299        286 E--EEEREKRAALELAAL--GGPVFLISAVTGEGLDELLRALWELL  327 (335)
T ss_pred             c--hhHHHHHHHHHHHhc--CCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            6  3222  233333322  36899999999999999999987653

>cd04140 ARHI_like ARHI subfamily

Probab=98.57  E-value=2.3e-07  Score=69.32  Aligned_cols=102  Identities=11%  Similarity=-0.044  Sum_probs=64.2

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C-------CCC--CCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K-------GGP--GITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~--qi~~adiiviNK~Dl~~~~~~  137 (178)
                      ...+-+++|+|..    +...+ ...++.+++|+|.++......  .       ...  .-..+-++|.||+|+.+....
T Consensus        48 ~~~l~i~Dt~G~~~~~~~~~~~-~~~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~v  126 (165)
T cd04140          48 ICTLQITDTTGSHQFPAMQRLS-ISKGHAFILVYSVTSKQSLEELKPIYELICEIKGNNIEKIPIMLVGNKCDESHKREV  126 (165)
T ss_pred             EEEEEEEECCCCCcchHHHHHH-hhcCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCCEEEEEECccccccCee
Confidence            4667789999931    11111 124689999999987543211  0       000  023467999999999753101


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ..+......+.  ...+++++||++|+|++++|++|..+.
T Consensus       127 ~~~~~~~~~~~--~~~~~~e~SA~~g~~v~~~f~~l~~~~  164 (165)
T cd04140         127 SSNEGAACATE--WNCAFMETSAKTNHNVQELFQELLNLE  164 (165)
T ss_pred             cHHHHHHHHHH--hCCcEEEeecCCCCCHHHHHHHHHhcc
Confidence            12222333332  346899999999999999999987754

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

>cd04110 Rab35 Rab35 subfamily

Probab=98.57  E-value=2.5e-07  Score=71.63  Aligned_cols=100  Identities=14%  Similarity=0.113  Sum_probs=64.4

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CC-C---CC-CCceeEEEEecCCCCCchhHhHHHH
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KG-G---PG-ITQADLLVINKTDLASAIGADLAVM  142 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~-~---~q-i~~adiiviNK~Dl~~~~~~~~~~~  142 (178)
                      ..+.|+++.|..    +...+. ..++++++|+|+++......  .+ .   .. -..+-++|+||+|+.+......+..
T Consensus        55 ~~l~l~D~~G~~~~~~~~~~~~-~~a~~iilv~D~~~~~s~~~~~~~~~~i~~~~~~~piivVgNK~Dl~~~~~~~~~~~  133 (199)
T cd04110          55 VKLQIWDTAGQERFRTITSTYY-RGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCDDVCKVLVGNKNDDPERKVVETEDA  133 (199)
T ss_pred             EEEEEEeCCCchhHHHHHHHHh-CCCcEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCEEEEEECcccccccccCHHHH
Confidence            567789999932    112222 24689999999987543211  00 0   00 1245699999999976411222344


Q ss_pred             HHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          143 ERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       143 ~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+..+..+  .+++++||++|.||+++|+++.+.
T Consensus       134 ~~~~~~~~--~~~~e~Sa~~~~gi~~lf~~l~~~  165 (199)
T cd04110         134 YKFAGQMG--ISLFETSAKENINVEEMFNCITEL  165 (199)
T ss_pred             HHHHHHcC--CEEEEEECCCCcCHHHHHHHHHHH
Confidence            44444443  689999999999999999987654

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

>cd04127 Rab27A Rab27a subfamily

Probab=98.56  E-value=3.4e-07  Score=69.10  Aligned_cols=101  Identities=16%  Similarity=0.107  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CC-------CCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KG-------GPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~-------~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+-|++|+|..    +...+. ..+|++++|+|+++......  .+       ...-..+-++|.||+|+.++.....
T Consensus        62 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piiiv~nK~Dl~~~~~v~~  140 (180)
T cd04127          62 RIHLQLWDTAGQERFRSLTTAFF-RDAMGFLLIFDLTNEQSFLNVRNWMSQLQTHAYCENPDIVLCGNKADLEDQRQVSE  140 (180)
T ss_pred             EEEEEEEeCCChHHHHHHHHHHh-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEeCccchhcCccCH
Confidence            4678899999932    111222 35799999999986532211  00       0001235699999999975411223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..++.  ..+++++||++|.|++++|+.|.+.
T Consensus       141 ~~~~~~~~~~--~~~~~e~Sak~~~~v~~l~~~l~~~  175 (180)
T cd04127         141 EQAKALADKY--GIPYFETSAATGTNVEKAVERLLDL  175 (180)
T ss_pred             HHHHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            3445555544  3589999999999999999988653

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

>cd04128 Spg1 Spg1p

Probab=98.56  E-value=2.8e-07  Score=70.61  Aligned_cols=100  Identities=17%  Similarity=0.226  Sum_probs=61.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchh-Hh-
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIG-AD-  138 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~-~~-  138 (178)
                      .+++-+.+|.|..    +...+. ..+|++++|+|.++......  .+..      .-..+ ++|+||+||..... .+ 
T Consensus        48 ~~~l~iwDt~G~~~~~~~~~~~~-~~a~~iilv~D~t~~~s~~~i~~~~~~~~~~~~~~~p-ilVgnK~Dl~~~~~~~~~  125 (182)
T cd04128          48 EITFSIWDLGGQREFINMLPLVC-NDAVAILFMFDLTRKSTLNSIKEWYRQARGFNKTAIP-ILVGTKYDLFADLPPEEQ  125 (182)
T ss_pred             EEEEEEEeCCCchhHHHhhHHHC-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCE-EEEEEchhccccccchhh
Confidence            4678889999942    112222 35799999999987543211  0000      01223 78999999963200 11 


Q ss_pred             ---HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 ---LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ---~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                         .+...+..+..+  ++++++||++|+|++++|+++.+.
T Consensus       126 ~~~~~~~~~~a~~~~--~~~~e~SAk~g~~v~~lf~~l~~~  164 (182)
T cd04128         126 EEITKQARKYAKAMK--APLIFCSTSHSINVQKIFKIVLAK  164 (182)
T ss_pred             hhhHHHHHHHHHHcC--CEEEEEeCCCCCCHHHHHHHHHHH
Confidence               122233333332  689999999999999999987653

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

>cd01873 RhoBTB RhoBTB subfamily

Probab=98.56  E-value=1.4e-07  Score=73.18  Aligned_cols=103  Identities=17%  Similarity=0.052  Sum_probs=67.7

Q ss_pred             CCCCEEEEeCCcch--hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCc-------
Q 030407           72 FKADLLLCESGGDN--LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASA-------  134 (178)
Q Consensus        72 ~~~d~iiiEttG~~--~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~-------  134 (178)
                      ..+.+.+++|.|..  +...+ ...+|++++|+|.++......   .+...     -..+-++|.||+||.+.       
T Consensus        64 ~~v~l~iwDTaG~~~~~~~~~-~~~ad~iilv~d~t~~~Sf~~~~~~w~~~i~~~~~~~piilvgNK~DL~~~~~~~~~~  142 (195)
T cd01873          64 VSVSLRLWDTFGDHDKDRRFA-YGRSDVVLLCFSIASPNSLRNVKTMWYPEIRHFCPRVPVILVGCKLDLRYADLDEVNR  142 (195)
T ss_pred             EEEEEEEEeCCCChhhhhccc-CCCCCEEEEEEECCChhHHHHHHHHHHHHHHHhCCCCCEEEEEEchhccccccchhhh
Confidence            35788899999942  12222 236899999999987643211   11111     13456999999999631       


Q ss_pred             ------------hhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          135 ------------IGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       135 ------------~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                                  .....++.+++.++.  ++++++|||++|+|++++|+.+.+++
T Consensus       143 ~~~~~~~~~~~~~~V~~~e~~~~a~~~--~~~~~E~SAkt~~~V~e~F~~~~~~~  195 (195)
T cd01873         143 ARRPLARPIKNADILPPETGRAVAKEL--GIPYYETSVVTQFGVKDVFDNAIRAA  195 (195)
T ss_pred             cccccccccccCCccCHHHHHHHHHHh--CCEEEEcCCCCCCCHHHHHHHHHHhC
Confidence                        002234455555554  35899999999999999999887653

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.

>TIGR00157 ribosome small subunit-dependent GTPase A

Probab=98.56  E-value=1.8e-07  Score=75.18  Aligned_cols=78  Identities=13%  Similarity=0.004  Sum_probs=51.8

Q ss_pred             ccceEEEEEeCCCCCCCCc---CCCC---CCCceeEEEEecCCCCCchhHhHH-HHHHHHHhcCCCCCEEEEecccCCCH
Q 030407           94 LADYIIYIIDVSGGDKIPR---KGGP---GITQADLLVINKTDLASAIGADLA-VMERDALRMRDGGPFIFAQVGWVIGI  166 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~---~~~~---qi~~adiiviNK~Dl~~~~~~~~~-~~~~~l~~~np~a~i~~~SA~~g~gi  166 (178)
                      .+|.++.|+|+.++.....   ++..   .-...-++|+||+||.+.  .+.. +..+..++  .+.+++.+||++|+|+
T Consensus        36 n~D~viiV~d~~~p~~s~~~l~r~l~~~~~~~i~~vIV~NK~DL~~~--~~~~~~~~~~~~~--~g~~v~~~SAktg~gi  111 (245)
T TIGR00157        36 NIDQIVIVSSAVLPELSLNQLDRFLVVAEAQNIEPIIVLNKIDLLDD--EDMEKEQLDIYRN--IGYQVLMTSSKNQDGL  111 (245)
T ss_pred             cCCEEEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEEECcccCCC--HHHHHHHHHHHHH--CCCeEEEEecCCchhH
Confidence            4699999999986552211   1110   112345999999999865  3222 22333443  3468999999999999


Q ss_pred             HHHHHHHhh
Q 030407          167 IFTLSITHY  175 (178)
Q Consensus       167 ~el~~~l~~  175 (178)
                      +++++.+..
T Consensus       112 ~eLf~~l~~  120 (245)
T TIGR00157       112 KELIEALQN  120 (245)
T ss_pred             HHHHhhhcC
Confidence            999998753

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

>cd01878 HflX HflX subfamily

Probab=98.56  E-value=2.3e-07  Score=71.82  Aligned_cols=95  Identities=21%  Similarity=0.178  Sum_probs=62.6

Q ss_pred             CCEEEEeCCcchh------hhccc-----ccccceEEEEEeCCCCCCCCc-----CCCCCC---CceeEEEEecCCCCCc
Q 030407           74 ADLLLCESGGDNL------AANFS-----RELADYIIYIIDVSGGDKIPR-----KGGPGI---TQADLLVINKTDLASA  134 (178)
Q Consensus        74 ~d~iiiEttG~~~------~~~~~-----~~~ad~~I~VvD~~~~~~~~~-----~~~~qi---~~adiiviNK~Dl~~~  134 (178)
                      ..+.|++|.|..-      ...+.     ...+|.+++|+|++++.....     ....++   ..+.++|+||+|+.++
T Consensus        89 ~~~~i~Dt~G~~~~~~~~~~~~~~~~~~~~~~~d~ii~v~D~~~~~~~~~~~~~~~~l~~~~~~~~~viiV~NK~Dl~~~  168 (204)
T cd01878          89 REVLLTDTVGFIRDLPHQLVEAFRSTLEEVAEADLLLHVVDASDPDYEEQIETVEKVLKELGAEDIPMILVLNKIDLLDD  168 (204)
T ss_pred             ceEEEeCCCccccCCCHHHHHHHHHHHHHHhcCCeEEEEEECCCCChhhHHHHHHHHHHHcCcCCCCEEEEEEccccCCh
Confidence            4799999999410      01110     124689999999987543221     010112   2356999999999876


Q ss_pred             hhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          135 IGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       135 ~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                        ....   ...+  ....+++++||++|.|+++++++|.+
T Consensus       169 --~~~~---~~~~--~~~~~~~~~Sa~~~~gi~~l~~~L~~  202 (204)
T cd01878         169 --EELE---ERLE--AGRPDAVFISAKTGEGLDELLEAIEE  202 (204)
T ss_pred             --HHHH---HHhh--cCCCceEEEEcCCCCCHHHHHHHHHh
Confidence              3332   2233  34568999999999999999999865

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.

>cd04109 Rab28 Rab28 subfamily

Probab=98.55  E-value=3.3e-07  Score=71.82  Aligned_cols=101  Identities=16%  Similarity=0.062  Sum_probs=64.1

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--C-------CC-C-CCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--K-------GG-P-GITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~-~-qi~~adiiviNK~Dl~~~~~~  137 (178)
                      .+.+.|++|.|...    ...+. ..+|++++|+|+++......  .       .. . .-..+-++|.||+|+......
T Consensus        49 ~~~~~i~Dt~G~~~~~~l~~~~~-~~ad~iilV~D~t~~~s~~~~~~w~~~l~~~~~~~~~~~piilVgNK~DL~~~~~v  127 (215)
T cd04109          49 NVTLQVWDIGGQSIGGKMLDKYI-YGAHAVFLVYDVTNSQSFENLEDWYSMVRKVLKSSETQPLVVLVGNKTDLEHNRTV  127 (215)
T ss_pred             EEEEEEEECCCcHHHHHHHHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhccccCCCceEEEEEECccccccccc
Confidence            46788999999421    12232 35799999999987532211  0       00 0 011245789999999743112


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+...+..+..  ..+++++||++|+|++++|+++.+.
T Consensus       128 ~~~~~~~~~~~~--~~~~~~iSAktg~gv~~lf~~l~~~  164 (215)
T cd04109         128 KDDKHARFAQAN--GMESCLVSAKTGDRVNLLFQQLAAE  164 (215)
T ss_pred             CHHHHHHHHHHc--CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            233444444433  3589999999999999999987653

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

>cd01898 Obg Obg subfamily

Probab=98.55  E-value=3.9e-07  Score=67.87  Aligned_cols=100  Identities=20%  Similarity=0.234  Sum_probs=64.0

Q ss_pred             CCEEEEeCCcch--------hhhccc--ccccceEEEEEeCCCC-CCCCc---------CCCCC-CCceeEEEEecCCCC
Q 030407           74 ADLLLCESGGDN--------LAANFS--RELADYIIYIIDVSGG-DKIPR---------KGGPG-ITQADLLVINKTDLA  132 (178)
Q Consensus        74 ~d~iiiEttG~~--------~~~~~~--~~~ad~~I~VvD~~~~-~~~~~---------~~~~q-i~~adiiviNK~Dl~  132 (178)
                      ..+.|++|.|..        +...+.  ...+|.+++|+|+++. .....         ..... ...+-++|+||+|+.
T Consensus        48 ~~~~l~DtpG~~~~~~~~~~~~~~~~~~~~~~d~vi~v~D~~~~~~~~~~~~~~~~~l~~~~~~~~~~p~ivv~NK~Dl~  127 (170)
T cd01898          48 RSFVVADIPGLIEGASEGKGLGHRFLRHIERTRLLLHVIDLSGDDDPVEDYKTIRNELELYNPELLEKPRIVVLNKIDLL  127 (170)
T ss_pred             CeEEEEecCcccCcccccCCchHHHHHHHHhCCEEEEEEecCCCCCHHHHHHHHHHHHHHhCccccccccEEEEEchhcC
Confidence            378899999941        011111  1236899999999876 22110         01111 245679999999998


Q ss_pred             CchhHhHHH-HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          133 SAIGADLAV-MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       133 ~~~~~~~~~-~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.  ..... .....+.. ...+++++||++|.|++++++++.+.
T Consensus       128 ~~--~~~~~~~~~~~~~~-~~~~~~~~Sa~~~~gi~~l~~~i~~~  169 (170)
T cd01898         128 DE--EELFELLKELLKEL-WGKPVFPISALTGEGLDELLRKLAEL  169 (170)
T ss_pred             Cc--hhhHHHHHHHHhhC-CCCCEEEEecCCCCCHHHHHHHHHhh
Confidence            76  33332 33333332 24589999999999999999998754

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.

>cd01855 YqeH YqeH

Probab=98.55  E-value=3.8e-07  Score=70.11  Aligned_cols=82  Identities=13%  Similarity=0.023  Sum_probs=53.1

Q ss_pred             ccceEEEEEeCCCCCCCCc-CC-CCCCCceeEEEEecCCCCCchhHhHHHHHHHH-----HhcC-CCCCEEEEecccCCC
Q 030407           94 LADYIIYIIDVSGGDKIPR-KG-GPGITQADLLVINKTDLASAIGADLAVMERDA-----LRMR-DGGPFIFAQVGWVIG  165 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~-~~-~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l-----~~~n-p~a~i~~~SA~~g~g  165 (178)
                      .+|.+++|+|+++...... .. ......+-++|+||+|+.++. ...+.+..+.     +..+ +..+++++||++|+|
T Consensus        34 ~ad~il~VvD~~~~~~~~~~~l~~~~~~~~~ilV~NK~Dl~~~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~vSA~~~~g  112 (190)
T cd01855          34 KKALVVHVVDIFDFPGSLIPRLRLFGGNNPVILVGNKIDLLPKD-KNLVRIKNWLRAKAAAGLGLKPKDVILISAKKGWG  112 (190)
T ss_pred             CCcEEEEEEECccCCCccchhHHHhcCCCcEEEEEEchhcCCCC-CCHHHHHHHHHHHHHhhcCCCcccEEEEECCCCCC
Confidence            4789999999987542211 11 111234679999999997541 2222233332     2222 234799999999999


Q ss_pred             HHHHHHHHhhh
Q 030407          166 IIFTLSITHYI  176 (178)
Q Consensus       166 i~el~~~l~~~  176 (178)
                      +++|++.+.+.
T Consensus       113 i~eL~~~l~~~  123 (190)
T cd01855         113 VEELINAIKKL  123 (190)
T ss_pred             HHHHHHHHHHH
Confidence            99999998764

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.

>cd04113 Rab4 Rab4 subfamily

Probab=98.55  E-value=2.7e-07  Score=68.29  Aligned_cols=101  Identities=14%  Similarity=0.052  Sum_probs=66.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CC------CCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KG------GPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~------~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+-++++.|..    +...+. ..+|++++|+|+++......  .+      ...-..+-++++||+|+.+......+
T Consensus        48 ~~~l~l~D~~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iivv~nK~D~~~~~~~~~~  126 (161)
T cd04113          48 RVKLQIWDTAGQERFRSVTRSYY-RGAAGALLVYDITNRTSFEALPTWLSDARALASPNIVVILVGNKSDLADQREVTFL  126 (161)
T ss_pred             EEEEEEEECcchHHHHHhHHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEEchhcchhccCCHH
Confidence            3677899999942    112222 24699999999987543211  00      00123467999999999754212234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ......+..+  .+++++||++|+|++++|+.+.+.
T Consensus       127 ~~~~~~~~~~--~~~~~~Sa~~~~~i~~~~~~~~~~  160 (161)
T cd04113         127 EASRFAQENG--LLFLETSALTGENVEEAFLKCARS  160 (161)
T ss_pred             HHHHHHHHcC--CEEEEEECCCCCCHHHHHHHHHHh
Confidence            4455555443  689999999999999999988653

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

>cd04124 RabL2 RabL2 subfamily

Probab=98.55  E-value=1.6e-07  Score=70.00  Aligned_cols=98  Identities=14%  Similarity=0.084  Sum_probs=63.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC---C--CCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP---G--ITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~---q--i~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+.+-+++|+|..    +...+. ..+|.+++|+|+++......  .+..   +  -..+-++|+||+|+.+.  . .+.
T Consensus        48 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~p~ivv~nK~Dl~~~--~-~~~  123 (161)
T cd04124          48 TILVDFWDTAGQERFQTMHASYY-HKAHACILVFDVTRKITYKNLSKWYEELREYRPEIPCIVVANKIDLDPS--V-TQK  123 (161)
T ss_pred             EEEEEEEeCCCchhhhhhhHHHh-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCcEEEEEECccCchh--H-HHH
Confidence            4677899999932    112222 25799999999977543211  0100   0  13467999999999543  2 222


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+..+..  ..+++++||++|.|++++++.+.+.
T Consensus       124 ~~~~~~~~--~~~~~~~Sa~~~~gv~~l~~~l~~~  156 (161)
T cd04124         124 KFNFAEKH--NLPLYYVSAADGTNVVKLFQDAIKL  156 (161)
T ss_pred             HHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            23333322  3589999999999999999987654

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

>cd01865 Rab3 Rab3 subfamily

Probab=98.54  E-value=4.3e-07  Score=67.80  Aligned_cols=102  Identities=16%  Similarity=0.127  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC---C---CCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP---G---ITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~---q---i~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+.+++|.|..    +...+ ...+|++++|+|.++......  .+..   +   -..+-++|+||+|+.+......+
T Consensus        49 ~~~~~l~Dt~g~~~~~~~~~~~-~~~~~~~l~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piivv~nK~Dl~~~~~~~~~  127 (165)
T cd01865          49 RVKLQIWDTAGQERYRTITTAY-YRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDMEDERVVSSE  127 (165)
T ss_pred             EEEEEEEECCChHHHHHHHHHH-ccCCcEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCCEEEEEECcccCcccccCHH
Confidence            3678899999931    11112 235799999999976432211  0000   0   12346999999999754111223


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ...+..+..  ..+++++||++|.|++++++.+.+.+
T Consensus       128 ~~~~~~~~~--~~~~~~~Sa~~~~gv~~l~~~l~~~~  162 (165)
T cd01865         128 RGRQLADQL--GFEFFEASAKENINVKQVFERLVDII  162 (165)
T ss_pred             HHHHHHHHc--CCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            333334433  24799999999999999999987643

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

>cd04176 Rap2 Rap2 subgroup

Probab=98.53  E-value=1.8e-07  Score=69.47  Aligned_cols=100  Identities=15%  Similarity=0.034  Sum_probs=62.3

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ..+-|++|+|..    +...+. ..+|.+++|+|.++......  .       ....-..+.++|+||+|+.+......+
T Consensus        49 ~~l~i~Dt~G~~~~~~~~~~~~-~~ad~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piviv~nK~Dl~~~~~~~~~  127 (163)
T cd04176          49 SVLEILDTAGTEQFASMRDLYI-KNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESEREVSSA  127 (163)
T ss_pred             EEEEEEECCCcccccchHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccchhcCccCHH
Confidence            445678999931    112222 24799999999987542211  0       111124567999999999654111222


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ......+..  ..+++++||++|.|++++|+++.+.
T Consensus       128 ~~~~~~~~~--~~~~~~~Sa~~~~~v~~l~~~l~~~  161 (163)
T cd04176         128 EGRALAEEW--GCPFMETSAKSKTMVNELFAEIVRQ  161 (163)
T ss_pred             HHHHHHHHh--CCEEEEecCCCCCCHHHHHHHHHHh
Confidence            233333332  3589999999999999999988654

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

>cd01864 Rab19 Rab19 subfamily

Probab=98.53  E-value=4.2e-07  Score=67.71  Aligned_cols=101  Identities=12%  Similarity=0.023  Sum_probs=64.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CC------CCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KG------GPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~------~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.+++|.|...    ...+. ..+|.+++++|+++......  .+      ......+-++|+||+|+........+
T Consensus        51 ~~~l~i~D~~G~~~~~~~~~~~~-~~~d~~llv~d~~~~~s~~~~~~~~~~i~~~~~~~~p~ivv~nK~Dl~~~~~~~~~  129 (165)
T cd01864          51 RVKLQIWDTAGQERFRTITQSYY-RSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDLEEQREVLFE  129 (165)
T ss_pred             EEEEEEEECCChHHHHHHHHHHh-ccCCEEEEEEECcCHHHHHhHHHHHHHHHHhCCCCCcEEEEEECcccccccccCHH
Confidence            36789999999321    11222 24699999999987542211  01      00123456999999999754212233


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ...+..+. ....+++++||++|+|++++++.+.+
T Consensus       130 ~~~~~~~~-~~~~~~~e~Sa~~~~~v~~~~~~l~~  163 (165)
T cd01864         130 EACTLAEK-NGMLAVLETSAKESQNVEEAFLLMAT  163 (165)
T ss_pred             HHHHHHHH-cCCcEEEEEECCCCCCHHHHHHHHHH
Confidence            44444443 33347899999999999999998865

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.

>cd04148 RGK RGK subfamily

Probab=98.52  E-value=2.3e-07  Score=73.28  Aligned_cols=103  Identities=16%  Similarity=0.120  Sum_probs=65.7

Q ss_pred             CCCEEEEeCCcch-hhhccccc-ccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDN-LAANFSRE-LADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~~~~~-~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      ...+.+++|.|.. ........ .+|++++|+|+++......         ........+-++|.||+|+.+......+.
T Consensus        49 ~~~l~i~Dt~G~~~~~~~~~~~~~ad~iilV~d~td~~S~~~~~~~~~~l~~~~~~~~~piilV~NK~Dl~~~~~v~~~~  128 (221)
T cd04148          49 ESTLVVIDHWEQEMWTEDSCMQYQGDAFVVVYSVTDRSSFERASELRIQLRRNRQLEDRPIILVGNKSDLARSREVSVQE  128 (221)
T ss_pred             EEEEEEEeCCCcchHHHhHHhhcCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEChhccccceecHHH
Confidence            4678899999943 11122222 5799999999987532210         01111245679999999997651111222


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ..+.....  ..+++++||++|.|++++|+++.+.+
T Consensus       129 ~~~~a~~~--~~~~~e~SA~~~~gv~~l~~~l~~~~  162 (221)
T cd04148         129 GRACAVVF--DCKFIETSAGLQHNVDELLEGIVRQI  162 (221)
T ss_pred             HHHHHHHc--CCeEEEecCCCCCCHHHHHHHHHHHH
Confidence            23333322  36899999999999999999887653

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

>cd04106 Rab23_lke Rab23-like subfamily

Probab=98.52  E-value=1.5e-07  Score=69.61  Aligned_cols=100  Identities=15%  Similarity=0.093  Sum_probs=65.4

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC-----CCCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP-----GITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~-----qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      ..++.+++|.|..    +...+. ..+|.+++|+|+++......  .+..     .-..+-++|+||+|+.++.....++
T Consensus        50 ~~~~~i~D~~G~~~~~~~~~~~~-~~~~~~v~v~d~~~~~s~~~l~~~~~~~~~~~~~~p~iiv~nK~Dl~~~~~v~~~~  128 (162)
T cd04106          50 DVRLMLWDTAGQEEFDAITKAYY-RGAQACILVFSTTDRESFEAIESWKEKVEAECGDIPMVLVQTKIDLLDQAVITNEE  128 (162)
T ss_pred             EEEEEEeeCCchHHHHHhHHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCEEEEEEChhcccccCCCHHH
Confidence            5788999999931    112222 35799999999976542211  0100     1134679999999997641122344


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ..+..+..  ..+++++||++|.|+++++++|..
T Consensus       129 ~~~~~~~~--~~~~~~~Sa~~~~~v~~l~~~l~~  160 (162)
T cd04106         129 AEALAKRL--QLPLFRTSVKDDFNVTELFEYLAE  160 (162)
T ss_pred             HHHHHHHc--CCeEEEEECCCCCCHHHHHHHHHH
Confidence            44444443  348999999999999999999865

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

>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily

Probab=98.52  E-value=4.9e-07  Score=67.34  Aligned_cols=101  Identities=19%  Similarity=0.183  Sum_probs=64.3

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC----C--CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG----P--GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~----~--qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+-++++.|..    +...+. ..+|++++|+|+++......  .+.    .  .-..+-+++.||+|+..+.....+
T Consensus        50 ~~~~~i~D~~G~~~~~~~~~~~~-~~~~~ii~v~d~~~~~s~~~l~~~~~~~~~~~~~~~~~iiv~nK~Dl~~~~~~~~~  128 (166)
T cd01869          50 TIKLQIWDTAGQERFRTITSSYY-RGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTDKRVVDYS  128 (166)
T ss_pred             EEEEEEEECCCcHhHHHHHHHHh-CcCCEEEEEEECcCHHHHHhHHHHHHHHHHhCCCCCcEEEEEEChhcccccCCCHH
Confidence            3567788999932    111222 24799999999987542211  000    0  012467999999999654212223


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  ..+++++||++|+|++++|+.+.+.
T Consensus       129 ~~~~~~~~~--~~~~~~~Sa~~~~~v~~~~~~i~~~  162 (166)
T cd01869         129 EAQEFADEL--GIPFLETSAKNATNVEQAFMTMARE  162 (166)
T ss_pred             HHHHHHHHc--CCeEEEEECCCCcCHHHHHHHHHHH
Confidence            444444433  4689999999999999999988653

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

>PRK09866 hypothetical protein; Provisional

Probab=98.51  E-value=4.5e-07  Score=81.15  Aligned_cols=103  Identities=13%  Similarity=0.022  Sum_probs=66.6

Q ss_pred             CCCEEEEeCCcchhh--hcc------cccccceEEEEEeCCCCCCCCc-CC---CCCCC--ceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDNLA--ANF------SRELADYIIYIIDVSGGDKIPR-KG---GPGIT--QADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~~~--~~~------~~~~ad~~I~VvD~~~~~~~~~-~~---~~qi~--~adiiviNK~Dl~~~~~~~  138 (178)
                      ...+|||.|.|..-.  ..+      ....+|.+++|+|+..+....+ ..   ..+..  .+.++|+||+|+.+.....
T Consensus       229 ~~QIIFVDTPGIhk~~~~~L~k~M~eqL~eADvVLFVVDat~~~s~~DeeIlk~Lkk~~K~~PVILVVNKIDl~dreedd  308 (741)
T PRK09866        229 PGQLTLLDTPGPNEAGQPHLQKMLNQQLARASAVLAVLDYTQLKSISDEEVREAILAVGQSVPLYVLVNKFDQQDRNSDD  308 (741)
T ss_pred             cCCEEEEECCCCCCccchHHHHHHHHHHhhCCEEEEEEeCCCCCChhHHHHHHHHHhcCCCCCEEEEEEcccCCCcccch
Confidence            468899999995211  001      1124799999999977532211 11   11122  3678999999997631112


Q ss_pred             HHHHHHHHH-----hcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          139 LAVMERDAL-----RMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       139 ~~~~~~~l~-----~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+.+.+.++     ...+..+||++||++|.|++++++.|.+
T Consensus       309 kE~Lle~V~~~L~q~~i~f~eIfPVSAlkG~nid~LLdeI~~  350 (741)
T PRK09866        309 ADQVRALISGTLMKGCITPQQIFPVSSMWGYLANRARHELAN  350 (741)
T ss_pred             HHHHHHHHHHHHHhcCCCCceEEEEeCCCCCCHHHHHHHHHh
Confidence            344444443     2235779999999999999999998865

>cd04142 RRP22 RRP22 subfamily

Probab=98.51  E-value=5.6e-07  Score=69.94  Aligned_cols=102  Identities=13%  Similarity=-0.018  Sum_probs=62.8

Q ss_pred             CCCEEEEeCCcchh----h--h----c-ccccccceEEEEEeCCCCCCCCc--CC-------C--CCCCceeEEEEecCC
Q 030407           73 KADLLLCESGGDNL----A--A----N-FSRELADYIIYIIDVSGGDKIPR--KG-------G--PGITQADLLVINKTD  130 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~--~----~-~~~~~ad~~I~VvD~~~~~~~~~--~~-------~--~qi~~adiiviNK~D  130 (178)
                      .+.+.|++|.|..-    .  .    . .....+|.+++|+|+++......  .+       .  .--..+-++|.||+|
T Consensus        48 ~~~l~i~Dt~G~~~~~~~~~~e~~~~~~~~~~~ad~iilv~D~~~~~S~~~~~~~~~~i~~~~~~~~~~~piiivgNK~D  127 (198)
T cd04142          48 VYDLHILDVPNMQRYPGTAGQEWMDPRFRGLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRD  127 (198)
T ss_pred             EEEEEEEeCCCcccCCccchhHHHHHHHhhhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcccCCCCCCEEEEEECcc
Confidence            36778999988310    0  0    0 01124799999999987643211  00       0  011246799999999


Q ss_pred             CCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          131 LASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       131 l~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +........+...+..++. -..+++++||++|.|++++|+.+.+
T Consensus       128 l~~~~~~~~~~~~~~~~~~-~~~~~~e~Sak~g~~v~~lf~~i~~  171 (198)
T cd04142         128 QQRHRFAPRHVLSVLVRKS-WKCGYLECSAKYNWHILLLFKELLI  171 (198)
T ss_pred             ccccccccHHHHHHHHHHh-cCCcEEEecCCCCCCHHHHHHHHHH
Confidence            9653111222333333322 2468999999999999999997764

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.

>PTZ00133 ADP-ribosylation factor; Provisional

Probab=98.51  E-value=3.8e-07  Score=69.73  Aligned_cols=101  Identities=15%  Similarity=0.130  Sum_probs=62.1

Q ss_pred             CCCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---C----CCC-C-CCceeEEEEecCCCCCchhHh
Q 030407           72 FKADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---K----GGP-G-ITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        72 ~~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~----~~~-q-i~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+..+.+++|.|..    +...+. ..+|++|+|+|+++......   .    ... . -..+-++|+||.|+...  ..
T Consensus        59 ~~~~~~l~D~~G~~~~~~~~~~~~-~~ad~iI~v~D~t~~~s~~~~~~~l~~~~~~~~~~~~piilv~NK~Dl~~~--~~  135 (182)
T PTZ00133         59 KNLKFTMWDVGGQDKLRPLWRHYY-QNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNA--MS  135 (182)
T ss_pred             CCEEEEEEECCCCHhHHHHHHHHh-cCCCEEEEEEeCCCHHHHHHHHHHHHHHHhCHhhcCCCEEEEEeCCCCCCC--CC
Confidence            35778999999942    111222 35799999999976432110   0    001 0 12356899999999754  23


Q ss_pred             HHHHHHHHHhc--C-CCCCEEEEecccCCCHHHHHHHHhh
Q 030407          139 LAVMERDALRM--R-DGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       139 ~~~~~~~l~~~--n-p~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+.+.+.+...  . ...+++++||++|+|+++++++|.+
T Consensus       136 ~~~i~~~l~~~~~~~~~~~~~~~Sa~tg~gv~e~~~~l~~  175 (182)
T PTZ00133        136 TTEVTEKLGLHSVRQRNWYIQGCCATTAQGLYEGLDWLSA  175 (182)
T ss_pred             HHHHHHHhCCCcccCCcEEEEeeeCCCCCCHHHHHHHHHH
Confidence            33343333211  0 0124678999999999999999875

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

Probab=98.50  E-value=1.4e-07  Score=70.57  Aligned_cols=100  Identities=17%  Similarity=0.131  Sum_probs=69.5

Q ss_pred             CCCEEEEeCCcch---hhhcccccccceEEEEEeCCCCCCCCcC------CCCC--CCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDN---LAANFSRELADYIIYIIDVSGGDKIPRK------GGPG--ITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~---~~~~~~~~~ad~~I~VvD~~~~~~~~~~------~~~q--i~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      ..|.=|..|.|--   -..|.++...++.++|+|.++.+..+.-      ...+  -+.+-+||.||+||-.+.....+.
T Consensus        61 ra~L~IWDTAGQErfHALGPIYYRgSnGalLVyDITDrdSFqKVKnWV~Elr~mlGnei~l~IVGNKiDLEeeR~Vt~qe  140 (218)
T KOG0088|consen   61 RADLHIWDTAGQERFHALGPIYYRGSNGALLVYDITDRDSFQKVKNWVLELRTMLGNEIELLIVGNKIDLEEERQVTRQE  140 (218)
T ss_pred             eeeeeeeeccchHhhhccCceEEeCCCceEEEEeccchHHHHHHHHHHHHHHHHhCCeeEEEEecCcccHHHhhhhhHHH
Confidence            5789999999931   0133333468999999999987654321      1111  256779999999996542233444


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      .+++.+..  +|.++.|||+.++||.|+|+.|-
T Consensus       141 Ae~YAesv--GA~y~eTSAk~N~Gi~elFe~Lt  171 (218)
T KOG0088|consen  141 AEAYAESV--GALYMETSAKDNVGISELFESLT  171 (218)
T ss_pred             HHHHHHhh--chhheecccccccCHHHHHHHHH
Confidence            55555543  68999999999999999998653

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

Probab=98.50  E-value=4.4e-07  Score=79.07  Aligned_cols=101  Identities=15%  Similarity=0.115  Sum_probs=70.0

Q ss_pred             CCCEEEEeCCcchhhhcccc----cccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHH
Q 030407           73 KADLLLCESGGDNLAANFSR----ELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~~~----~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      .+-+.||.|.| .-+-+..+    ..+|.+|+|||+.++...+..    +......+-+|.+||+|+.+.   ...++..
T Consensus        54 ~~~itFiDTPG-HeAFt~mRaRGa~vtDIaILVVa~dDGv~pQTiEAI~hak~a~vP~iVAiNKiDk~~~---np~~v~~  129 (509)
T COG0532          54 IPGITFIDTPG-HEAFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGVPIVVAINKIDKPEA---NPDKVKQ  129 (509)
T ss_pred             CceEEEEcCCc-HHHHHHHHhcCCccccEEEEEEEccCCcchhHHHHHHHHHHCCCCEEEEEecccCCCC---CHHHHHH
Confidence            47899999999 22211111    246999999999988655431    222345567999999999855   4445555


Q ss_pred             HHHhc--CC-----CCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          145 DALRM--RD-----GGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       145 ~l~~~--np-----~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .+.+.  +|     ...++++||++|+|+++|++.+.-++
T Consensus       130 el~~~gl~~E~~gg~v~~VpvSA~tg~Gi~eLL~~ill~a  169 (509)
T COG0532         130 ELQEYGLVPEEWGGDVIFVPVSAKTGEGIDELLELILLLA  169 (509)
T ss_pred             HHHHcCCCHhhcCCceEEEEeeccCCCCHHHHHHHHHHHH
Confidence            54432  22     36899999999999999999876543

>cd04123 Rab21 Rab21 subfamily

Probab=98.50  E-value=5.8e-07  Score=66.05  Aligned_cols=101  Identities=21%  Similarity=0.161  Sum_probs=65.3

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CC------CCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KG------GPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~------~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+.++++.|..    +...+. ..+|.+++|+|.++......  .+      ...-..+-++++||+|+.++.....+
T Consensus        48 ~~~~~~~D~~g~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piiiv~nK~D~~~~~~~~~~  126 (162)
T cd04123          48 RIDLAIWDTAGQERYHALGPIYY-RDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLERQRVVSKS  126 (162)
T ss_pred             EEEEEEEECCchHHHHHhhHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccCCCHH
Confidence            3568899999931    112222 24799999999987643211  00      00114578999999999754212234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+..+..  ..+++++||++|+|++++++++.+.
T Consensus       127 ~~~~~~~~~--~~~~~~~s~~~~~gi~~~~~~l~~~  160 (162)
T cd04123         127 EAEEYAKSV--GAKHFETSAKTGKGIEELFLSLAKR  160 (162)
T ss_pred             HHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            444444444  3579999999999999999998654

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

>cd04143 Rhes_like Rhes_like subfamily

Probab=98.50  E-value=7.1e-07  Score=71.83  Aligned_cols=103  Identities=8%  Similarity=0.023  Sum_probs=66.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C-------C--------CCCCCceeEEEEecCCC
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K-------G--------GPGITQADLLVINKTDL  131 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~--------~~qi~~adiiviNK~Dl  131 (178)
                      .+.+-|++|+|..    +...+ ...+|.+|+|+|.++......  .       .        ......+-++|+||+|+
T Consensus        47 ~~~l~I~Dt~G~~~~~~~~~~~-~~~ad~iIlVfdv~~~~Sf~~i~~~~~~I~~~k~~~~~~~~~~~~~piIivgNK~Dl  125 (247)
T cd04143          47 VYQLDILDTSGNHPFPAMRRLS-ILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKADR  125 (247)
T ss_pred             EEEEEEEECCCChhhhHHHHHH-hccCCEEEEEEeCCCHHHHHHHHHHHHHHHHhhcccccccccCCCCcEEEEEECccc
Confidence            3667789999931    11111 224699999999987532110  0       0        01124567999999999


Q ss_pred             CCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          132 ASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       132 ~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ..+.....+++.+.+... ...+++++||++|.|++++|++|.+.+
T Consensus       126 ~~~~~v~~~ei~~~~~~~-~~~~~~evSAktg~gI~elf~~L~~~~  170 (247)
T cd04143         126 DFPREVQRDEVEQLVGGD-ENCAYFEVSAKKNSNLDEMFRALFSLA  170 (247)
T ss_pred             hhccccCHHHHHHHHHhc-CCCEEEEEeCCCCCCHHHHHHHHHHHh
Confidence            752113444555555432 245799999999999999999987654

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

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

Probab=98.49  E-value=1.4e-07  Score=73.60  Aligned_cols=99  Identities=9%  Similarity=-0.038  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC----C-CCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP----G-ITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~----q-i~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+.+-|++|+|..    +...+. ..++++|+|+|.+.......  .+..    . -..+-++|.||+|+.... ...+.
T Consensus        43 ~~~l~iwDt~G~e~~~~l~~~~~-~~ad~~ilV~D~t~~~S~~~i~~w~~~i~~~~~~~piilvgNK~Dl~~~~-v~~~~  120 (200)
T smart00176       43 PIRFNVWDTAGQEKFGGLRDGYY-IQGQCAIIMFDVTARVTYKNVPNWHRDLVRVCENIPIVLCGNKVDVKDRK-VKAKS  120 (200)
T ss_pred             EEEEEEEECCCchhhhhhhHHHh-cCCCEEEEEEECCChHHHHHHHHHHHHHHHhCCCCCEEEEEECccccccc-CCHHH
Confidence            5778899999941    222333 35799999999987643211  0100    0 134679999999986431 11122


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                       .+..+.  ...++++|||++|+||+++|++|.+.
T Consensus       121 -~~~~~~--~~~~~~e~SAk~~~~v~~~F~~l~~~  152 (200)
T smart00176      121 -ITFHRK--KNLQYYDISAKSNYNFEKPFLWLARK  152 (200)
T ss_pred             -HHHHHH--cCCEEEEEeCCCCCCHHHHHHHHHHH
Confidence             223232  24689999999999999999998753

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

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

Probab=98.49  E-value=7.8e-07  Score=68.63  Aligned_cols=101  Identities=19%  Similarity=0.163  Sum_probs=68.1

Q ss_pred             CCCCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCCc--CC-------CCCCCceeEEEEecCCCCCchhHh
Q 030407           72 FKADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIPR--KG-------GPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        72 ~~~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~-------~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      ..+-.=+..|.|-    ++++.|.+ .+..+|+|+|.++......  ++       ...=..--++|.||.||+++..-.
T Consensus        69 ~~vrLQlWDTAGQERFrslipsY~R-ds~vaviVyDit~~~Sfe~t~kWi~dv~~e~gs~~viI~LVGnKtDL~dkrqvs  147 (221)
T KOG0094|consen   69 RTVRLQLWDTAGQERFRSLIPSYIR-DSSVAVIVYDITDRNSFENTSKWIEDVRRERGSDDVIIFLVGNKTDLSDKRQVS  147 (221)
T ss_pred             cEEEEEEEecccHHHHhhhhhhhcc-CCeEEEEEEeccccchHHHHHHHHHHHHhccCCCceEEEEEcccccccchhhhh
Confidence            3567778899994    45566665 6788999999987543321  11       110011237889999999883222


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .++-....+++  ++.++.|||++|++|.++|..|..
T Consensus       148 ~eEg~~kAkel--~a~f~etsak~g~NVk~lFrrIaa  182 (221)
T KOG0094|consen  148 IEEGERKAKEL--NAEFIETSAKAGENVKQLFRRIAA  182 (221)
T ss_pred             HHHHHHHHHHh--CcEEEEecccCCCCHHHHHHHHHH
Confidence            33344445555  459999999999999999998764

>PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional

Probab=98.48  E-value=5.2e-07  Score=78.68  Aligned_cols=99  Identities=15%  Similarity=0.156  Sum_probs=63.9

Q ss_pred             CEEEEeCCcch-h-hhccc-ccccceEEEEEeCCCC-CCCCc-CC---CCCCCc-eeEEEEecCCCCCchhHhHHHHHHH
Q 030407           75 DLLLCESGGDN-L-AANFS-RELADYIIYIIDVSGG-DKIPR-KG---GPGITQ-ADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        75 d~iiiEttG~~-~-~~~~~-~~~ad~~I~VvD~~~~-~~~~~-~~---~~qi~~-adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      .+.||++.|-. . ..+.. ...+|.+++|+|+..+ ...+. .+   ...+.. .-++++||+|+++.  ++.+...+.
T Consensus       118 ~i~~IDtPGH~~fi~~m~~g~~~~D~alLVVda~~g~~~~qT~ehl~i~~~lgi~~iIVvlNKiDlv~~--~~~~~~~~e  195 (460)
T PTZ00327        118 HVSFVDCPGHDILMATMLNGAAVMDAALLLIAANESCPQPQTSEHLAAVEIMKLKHIIILQNKIDLVKE--AQAQDQYEE  195 (460)
T ss_pred             eEeeeeCCCHHHHHHHHHHHHhhCCEEEEEEECCCCccchhhHHHHHHHHHcCCCcEEEEEecccccCH--HHHHHHHHH
Confidence            57899999921 1 11111 1246999999999874 22211 11   111222 24789999999876  454444444


Q ss_pred             HHhc-----CCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          146 ALRM-----RDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       146 l~~~-----np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +++.     ...++++++||++|+|+++|++.|..
T Consensus       196 i~~~l~~~~~~~~~iipVSA~~G~nI~~Ll~~L~~  230 (460)
T PTZ00327        196 IRNFVKGTIADNAPIIPISAQLKYNIDVVLEYICT  230 (460)
T ss_pred             HHHHHHhhccCCCeEEEeeCCCCCCHHHHHHHHHh
Confidence            4332     24679999999999999999999874

>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2

Probab=98.48  E-value=7.2e-07  Score=66.71  Aligned_cols=101  Identities=17%  Similarity=0.087  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC----C--CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG----P--GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~----~--qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.++++.|..    +...+ ...+|++++++|+++......  .+.    .  .-..+-++|.||+|+.+......+
T Consensus        51 ~~~l~l~D~~g~~~~~~~~~~~-~~~ad~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~p~iiv~nK~Dl~~~~~~~~~  129 (167)
T cd01867          51 KIKLQIWDTAGQERFRTITTAY-YRGAMGIILVYDITDEKSFENIRNWMRNIEEHASEDVERMLVGNKCDMEEKRVVSKE  129 (167)
T ss_pred             EEEEEEEeCCchHHHHHHHHHH-hCCCCEEEEEEECcCHHHHHhHHHHHHHHHHhCCCCCcEEEEEECcccccccCCCHH
Confidence            3567889999932    11111 235799999999976543211  000    0  013456999999999754112334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  ..+++++||++|.|++++|+.+.+.
T Consensus       130 ~~~~~~~~~--~~~~~~~Sa~~~~~v~~~~~~i~~~  163 (167)
T cd01867         130 EGEALADEY--GIKFLETSAKANINVEEAFFTLAKD  163 (167)
T ss_pred             HHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            445555543  3489999999999999999988754

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

>cd01892 Miro2 Miro2 subfamily

Probab=98.48  E-value=2.5e-07  Score=69.77  Aligned_cols=102  Identities=16%  Similarity=-0.040  Sum_probs=62.0

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc------CCCCCCCceeEEEEecCCCCCchhHhHHHHH
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR------KGGPGITQADLLVINKTDLASAIGADLAVME  143 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~------~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~  143 (178)
                      ..+.+.++.|..    +...+ ...+|++++|+|+++......      .....-..+-++|+||+|+.+..........
T Consensus        54 ~~l~~~d~~g~~~~~~~~~~~-~~~~d~~llv~d~~~~~s~~~~~~~~~~~~~~~~~p~iiv~NK~Dl~~~~~~~~~~~~  132 (169)
T cd01892          54 KYLILREVGEDEVAILLNDAE-LAACDVACLVYDSSDPKSFSYCAEVYKKYFMLGEIPCLFVAAKADLDEQQQRYEVQPD  132 (169)
T ss_pred             EEEEEEecCCcccccccchhh-hhcCCEEEEEEeCCCHHHHHHHHHHHHHhccCCCCeEEEEEEcccccccccccccCHH
Confidence            566777888831    11122 235799999999977533211      1111124578999999999654101111222


Q ss_pred             HHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          144 RDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       144 ~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +..+..+ ..+++++||++|+|++++|+.+.+.+
T Consensus       133 ~~~~~~~-~~~~~~~Sa~~~~~v~~lf~~l~~~~  165 (169)
T cd01892         133 EFCRKLG-LPPPLHFSSKLGDSSNELFTKLATAA  165 (169)
T ss_pred             HHHHHcC-CCCCEEEEeccCccHHHHHHHHHHHh
Confidence            2333332 23568999999999999999887653

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.

>TIGR03156 GTP_HflX GTP-binding protein HflX

Probab=98.47  E-value=4e-07  Score=76.89  Aligned_cols=96  Identities=23%  Similarity=0.226  Sum_probs=62.5

Q ss_pred             CCCEEEEeCCcc-h-----hhhccc-----ccccceEEEEEeCCCCCCCCc-----CCCCCC---CceeEEEEecCCCCC
Q 030407           73 KADLLLCESGGD-N-----LAANFS-----RELADYIIYIIDVSGGDKIPR-----KGGPGI---TQADLLVINKTDLAS  133 (178)
Q Consensus        73 ~~d~iiiEttG~-~-----~~~~~~-----~~~ad~~I~VvD~~~~~~~~~-----~~~~qi---~~adiiviNK~Dl~~  133 (178)
                      +..+.|++|+|. .     +...|.     ...+|.+++|+|++++.....     .....+   ..+-++|+||+|+.+
T Consensus       236 ~~~i~l~DT~G~~~~l~~~lie~f~~tle~~~~ADlil~VvD~s~~~~~~~~~~~~~~L~~l~~~~~piIlV~NK~Dl~~  315 (351)
T TIGR03156       236 GGEVLLTDTVGFIRDLPHELVAAFRATLEEVREADLLLHVVDASDPDREEQIEAVEKVLEELGAEDIPQLLVYNKIDLLD  315 (351)
T ss_pred             CceEEEEecCcccccCCHHHHHHHHHHHHHHHhCCEEEEEEECCCCchHHHHHHHHHHHHHhccCCCCEEEEEEeecCCC
Confidence            467899999994 1     011121     124799999999987643211     010111   345699999999976


Q ss_pred             chhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          134 AIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       134 ~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .  .....    ...  ...+++++||++|+|+++|++.|.+.
T Consensus       316 ~--~~v~~----~~~--~~~~~i~iSAktg~GI~eL~~~I~~~  350 (351)
T TIGR03156       316 E--PRIER----LEE--GYPEAVFVSAKTGEGLDLLLEAIAER  350 (351)
T ss_pred             h--HhHHH----HHh--CCCCEEEEEccCCCCHHHHHHHHHhh
Confidence            5  33322    111  12468999999999999999998764

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).

>PTZ00369 Ras-like protein; Provisional

Probab=98.47  E-value=6e-07  Score=68.82  Aligned_cols=100  Identities=13%  Similarity=0.084  Sum_probs=62.2

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ..+-+++|.|..    +...+. ..++++++|+|+++......  .       ....-..+-++|+||+|+.+......+
T Consensus        53 ~~l~i~Dt~G~~~~~~l~~~~~-~~~d~iilv~D~s~~~s~~~~~~~~~~i~~~~~~~~~piiiv~nK~Dl~~~~~i~~~  131 (189)
T PTZ00369         53 CLLDILDTAGQEEYSAMRDQYM-RTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDSERQVSTG  131 (189)
T ss_pred             EEEEEEeCCCCccchhhHHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccCHH
Confidence            445578999932    112222 25799999999987542110  0       011113456999999998654111222


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  ..+++++||++|.|++++|+++.+.
T Consensus       132 ~~~~~~~~~--~~~~~e~Sak~~~gi~~~~~~l~~~  165 (189)
T PTZ00369        132 EGQELAKSF--GIPFLETSAKQRVNVDEAFYELVRE  165 (189)
T ss_pred             HHHHHHHHh--CCEEEEeeCCCCCCHHHHHHHHHHH
Confidence            333344433  3589999999999999999988653

>cd04155 Arl3 Arl3 subfamily

Probab=98.47  E-value=5.4e-07  Score=67.47  Aligned_cols=102  Identities=18%  Similarity=0.092  Sum_probs=64.0

Q ss_pred             CCCEEEEeCCcchh-hhc--ccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL-AAN--FSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~-~~~--~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      +.++.++++.|..- ...  .....+|.+++|+|+++......         +.......+.++++||+|+.+.  ...+
T Consensus        57 ~~~~~~~D~~G~~~~~~~~~~~~~~~~~ii~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~~--~~~~  134 (173)
T cd04155          57 GFKLNVWDIGGQRAIRPYWRNYFENTDCLIYVIDSADKKRLEEAGAELVELLEEEKLAGVPVLVFANKQDLATA--APAE  134 (173)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHhcCCCEEEEEEeCCCHHHHHHHHHHHHHHHhChhhcCCCEEEEEECCCCccC--CCHH
Confidence            56788999999421 111  11124688999999976321110         0111123567899999999776  4444


Q ss_pred             HHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+.++-.   +...+++++||++|+|+++++++|.++
T Consensus       135 ~i~~~l~~~~~~~~~~~~~~~Sa~~~~gi~~~~~~l~~~  173 (173)
T cd04155         135 EIAEALNLHDLRDRTWHIQACSAKTGEGLQEGMNWVCKN  173 (173)
T ss_pred             HHHHHcCCcccCCCeEEEEEeECCCCCCHHHHHHHHhcC
Confidence            554444311   111257899999999999999998753

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.

>cd01860 Rab5_related Rab5-related subfamily

Probab=98.47  E-value=8e-07  Score=65.73  Aligned_cols=101  Identities=15%  Similarity=0.045  Sum_probs=65.5

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CC------CCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KG------GPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~------~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+.++++.|..    ....+. ..+|++++|+|+++......  .+      ...-..+-++++||+|+.+......+
T Consensus        49 ~~~~~i~D~~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iivv~nK~D~~~~~~~~~~  127 (163)
T cd01860          49 TVKFEIWDTAGQERYRSLAPMYY-RGAAAAIVVYDITSEESFEKAKSWVKELQRNASPNIIIALVGNKADLESKRQVSTE  127 (163)
T ss_pred             EEEEEEEeCCchHHHHHHHHHHh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECccccccCcCCHH
Confidence            4567789999931    111122 24699999999986542211  00      00123456889999999743212344


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..+  .+++++||++|.|++++++.|.+.
T Consensus       128 ~~~~~~~~~~--~~~~~~Sa~~~~~v~~l~~~l~~~  161 (163)
T cd01860         128 EAQEYADENG--LLFFETSAKTGENVNELFTEIAKK  161 (163)
T ss_pred             HHHHHHHHcC--CEEEEEECCCCCCHHHHHHHHHHH
Confidence            5555555543  689999999999999999998764

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

>TIGR00475 selB selenocysteine-specific elongation factor SelB

Probab=98.47  E-value=5.4e-07  Score=80.75  Aligned_cols=102  Identities=12%  Similarity=0.047  Sum_probs=66.2

Q ss_pred             CCEEEEeCCcch-hhh-cc-cccccceEEEEEeCCCCCCCCcC----CCCCCCce-eEEEEecCCCCCchhHhHHH----
Q 030407           74 ADLLLCESGGDN-LAA-NF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQA-DLLVINKTDLASAIGADLAV----  141 (178)
Q Consensus        74 ~d~iiiEttG~~-~~~-~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~a-diiviNK~Dl~~~~~~~~~~----  141 (178)
                      ..+-|+++.|-. ... +. ....+|.+++|+|+.++...+..    .......+ -++++||+|++++  +..+.    
T Consensus        50 ~~v~~iDtPGhe~f~~~~~~g~~~aD~aILVVDa~~G~~~qT~ehl~il~~lgi~~iIVVlNK~Dlv~~--~~~~~~~~e  127 (581)
T TIGR00475        50 YRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPHTIVVITKADRVNE--EEIKRTEMF  127 (581)
T ss_pred             EEEEEEECCCHHHHHHHHHhhhccCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCeEEEEEECCCCCCH--HHHHHHHHH
Confidence            567899999931 111 11 11246999999999876432210    11113334 6999999999876  44433    


Q ss_pred             HHHHHHhc--CCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          142 MERDALRM--RDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       142 ~~~~l~~~--np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +.+.++..  .+..+++++||++|+|++++++.+..+.
T Consensus       128 i~~~l~~~~~~~~~~ii~vSA~tG~GI~eL~~~L~~l~  165 (581)
T TIGR00475       128 MKQILNSYIFLKNAKIFKTSAKTGQGIGELKKELKNLL  165 (581)
T ss_pred             HHHHHHHhCCCCCCcEEEEeCCCCCCchhHHHHHHHHH
Confidence            33334332  1357999999999999999999886643

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.

>cd04112 Rab26 Rab26 subfamily

Probab=98.47  E-value=7.4e-07  Score=68.43  Aligned_cols=101  Identities=15%  Similarity=0.167  Sum_probs=63.5

Q ss_pred             CCCEEEEeCCcch-h---hhcccccccceEEEEEeCCCCCCCCc--CC----C--CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN-L---AANFSRELADYIIYIIDVSGGDKIPR--KG----G--PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~-~---~~~~~~~~ad~~I~VvD~~~~~~~~~--~~----~--~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+-|++|.|.. .   ...+. ..+|++++|+|++.......  .+    .  ..-..+-++|+||+|+..+.....+
T Consensus        49 ~~~~~i~Dt~G~~~~~~~~~~~~-~~ad~~i~v~D~~~~~s~~~~~~~~~~i~~~~~~~~piiiv~NK~Dl~~~~~~~~~  127 (191)
T cd04112          49 KVKLQIWDTAGQERFRSVTHAYY-RDAHALLLLYDITNKASFDNIRAWLTEIKEYAQEDVVIMLLGNKADMSGERVVKRE  127 (191)
T ss_pred             EEEEEEEeCCCcHHHHHhhHHHc-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEEcccchhccccCHH
Confidence            3567789999931 1   11122 24799999999987532210  00    0  0113467899999999643111223


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ......+..  ..+++++||++|+|++++|+++.+.
T Consensus       128 ~~~~l~~~~--~~~~~e~Sa~~~~~v~~l~~~l~~~  161 (191)
T cd04112         128 DGERLAKEY--GVPFMETSAKTGLNVELAFTAVAKE  161 (191)
T ss_pred             HHHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            333333333  3589999999999999999998764

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.

>cd01856 YlqF YlqF

Probab=98.47  E-value=8.9e-07  Score=67.07  Aligned_cols=78  Identities=18%  Similarity=0.126  Sum_probs=52.9

Q ss_pred             ccceEEEEEeCCCCCCCCcC-CCCCC-CceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHH
Q 030407           94 LADYIIYIIDVSGGDKIPRK-GGPGI-TQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLS  171 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~-~~~qi-~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~  171 (178)
                      .+|.+++|+|+..+...... ....+ ....++|+||+|+.++  +......+.++..  ..+++.+||++|+|++++.+
T Consensus        19 ~aD~il~v~D~~~~~~~~~~~i~~~~~~k~~ilVlNK~Dl~~~--~~~~~~~~~~~~~--~~~vi~iSa~~~~gi~~L~~   94 (171)
T cd01856          19 LVDLVIEVRDARIPLSSRNPLLEKILGNKPRIIVLNKADLADP--KKTKKWLKYFESK--GEKVLFVNAKSGKGVKKLLK   94 (171)
T ss_pred             hCCEEEEEeeccCccCcCChhhHhHhcCCCEEEEEehhhcCCh--HHHHHHHHHHHhc--CCeEEEEECCCcccHHHHHH
Confidence            46999999999765432211 11111 3467999999999765  4443333333432  34789999999999999999


Q ss_pred             HHhh
Q 030407          172 ITHY  175 (178)
Q Consensus       172 ~l~~  175 (178)
                      .+..
T Consensus        95 ~l~~   98 (171)
T cd01856          95 AAKK   98 (171)
T ss_pred             HHHH
Confidence            8765

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.

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

Probab=98.47  E-value=1.3e-06  Score=65.26  Aligned_cols=102  Identities=20%  Similarity=0.150  Sum_probs=66.0

Q ss_pred             CCCEEEEeCCcchhhh--------cc--cccccceEEEEEeCCCCC-----CCCc----------CCCC------CCCce
Q 030407           73 KADLLLCESGGDNLAA--------NF--SRELADYIIYIIDVSGGD-----KIPR----------KGGP------GITQA  121 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~--------~~--~~~~ad~~I~VvD~~~~~-----~~~~----------~~~~------qi~~a  121 (178)
                      +..+.|++|.|..-..        .+  ....+|.++.|+|+....     ....          ....      ....+
T Consensus        43 ~~~~~i~DtpG~~~~~~~~~~~~~~~~~~~~~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p  122 (176)
T cd01881          43 GARIQVADIPGLIEGASEGRGLGNQFLAHIRRADAILHVVDASEDDDIGGVDPLEDYEILNAELKLYDLETILGLLTAKP  122 (176)
T ss_pred             CCeEEEEeccccchhhhcCCCccHHHHHHHhccCEEEEEEeccCCccccccCHHHHHHHHHHHHHHhhhhhHHHHHhhCC
Confidence            5678999999941110        11  112468999999998763     1100          0111      13567


Q ss_pred             eEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          122 DLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       122 diiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .++|+||+|+.+.  .................+++.+||++|+|++++++.+...
T Consensus       123 ~ivv~NK~Dl~~~--~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gl~~l~~~l~~~  175 (176)
T cd01881         123 VIYVLNKIDLDDA--EELEEELVRELALEEGAEVVPISAKTEEGLDELIRAIYEL  175 (176)
T ss_pred             eEEEEEchhcCch--hHHHHHHHHHHhcCCCCCEEEEehhhhcCHHHHHHHHHhh
Confidence            8999999999876  4443332222233345689999999999999999987653

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

>cd00882 Ras_like_GTPase Ras-like GTPase superfamily

Probab=98.46  E-value=7e-07  Score=63.52  Aligned_cols=100  Identities=20%  Similarity=0.168  Sum_probs=66.6

Q ss_pred             CCCEEEEeCCcchhhhcc---cccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNLAANF---SRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~---~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      +.++.++++.|.......   ....+|.+++|+|++.+.....         ........+-++++||+|+.+.  ....
T Consensus        44 ~~~~~l~D~~g~~~~~~~~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivv~nk~D~~~~--~~~~  121 (157)
T cd00882          44 KVKLQIWDTAGQERFRSLRRLYYRGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGNKIDLPEE--RVVS  121 (157)
T ss_pred             EEEEEEEecCChHHHHhHHHHHhcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhhccCCCcEEEEEeccccccc--cchH
Confidence            578999999994322111   1234699999999987542211         1122345567999999999876  3333


Q ss_pred             HHH-HHHHhcCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          141 VME-RDALRMRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       141 ~~~-~~l~~~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      ... .......+..+++.+|+++|.|++++++++.
T Consensus       122 ~~~~~~~~~~~~~~~~~~~s~~~~~~i~~~~~~l~  156 (157)
T cd00882         122 EEELAEQLAKELGVPYFETSAKTGENVEELFEELA  156 (157)
T ss_pred             HHHHHHHHHhhcCCcEEEEecCCCCChHHHHHHHh
Confidence            221 2222234568999999999999999999875

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

>cd04132 Rho4_like Rho4-like subfamily

Probab=98.46  E-value=2.8e-07  Score=70.13  Aligned_cols=103  Identities=17%  Similarity=0.060  Sum_probs=64.5

Q ss_pred             CCCEEEEeCCcchh-h--hcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchh----H
Q 030407           73 KADLLLCESGGDNL-A--ANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIG----A  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~-~--~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~----~  137 (178)
                      ...+.+++|.|..- .  .+.....+|++++|+|.++......   .+...     -..+-++|+||+|+.+...    .
T Consensus        48 ~~~l~i~Dt~G~~~~~~~~~~~~~~ad~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~v  127 (187)
T cd04132          48 IIELALWDTAGQEEYDRLRPLSYPDVDVLLICYAVDNPTSLDNVEDKWFPEVNHFCPGTPIMLVGLKTDLRKDKNLDRKV  127 (187)
T ss_pred             EEEEEEEECCCchhHHHHHHHhCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEeChhhhhCccccCCc
Confidence            46788999999321 0  1112235799999999987543211   01000     1346799999999965310    1


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+...+..+..+ ..+++++||++|+|++++|+.+.+.
T Consensus       128 ~~~~~~~~~~~~~-~~~~~e~Sa~~~~~v~~~f~~l~~~  165 (187)
T cd04132         128 TPAQAESVAKKQG-AFAYLECSAKTMENVEEVFDTAIEE  165 (187)
T ss_pred             CHHHHHHHHHHcC-CcEEEEccCCCCCCHHHHHHHHHHH
Confidence            1234444444332 2378999999999999999987654

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.

>cd01871 Rac1_like Rac1-like subfamily

Probab=98.46  E-value=2.4e-07  Score=70.31  Aligned_cols=101  Identities=14%  Similarity=0.039  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCC----C-CCceeEEEEecCCCCCchh----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGP----G-ITQADLLVINKTDLASAIG----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~----q-i~~adiiviNK~Dl~~~~~----  136 (178)
                      ...+.+++|.|..    +...+ ...+|.+|+|+|.++......   .+..    . -..+-++|.||+||.+...    
T Consensus        48 ~~~l~i~Dt~G~~~~~~~~~~~-~~~~d~~ilv~d~~~~~sf~~~~~~~~~~~~~~~~~~piilvgnK~Dl~~~~~~~~~  126 (174)
T cd01871          48 PVNLGLWDTAGQEDYDRLRPLS-YPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEK  126 (174)
T ss_pred             EEEEEEEECCCchhhhhhhhhh-cCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEeeChhhccChhhHHH
Confidence            4678899999942    11222 235799999999987543211   0100    0 1356799999999964310    


Q ss_pred             --------HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          137 --------ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       137 --------~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                              ...+...+..++.+ ..+++++||++|+|++++|+.+.+
T Consensus       127 ~~~~~~~~v~~~~~~~~~~~~~-~~~~~e~Sa~~~~~i~~~f~~l~~  172 (174)
T cd01871         127 LKEKKLTPITYPQGLAMAKEIG-AVKYLECSALTQKGLKTVFDEAIR  172 (174)
T ss_pred             HhhccCCCCCHHHHHHHHHHcC-CcEEEEecccccCCHHHHHHHHHH
Confidence                    11122333344433 358999999999999999998865

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

>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional

Probab=98.45  E-value=6.5e-07  Score=80.67  Aligned_cols=101  Identities=11%  Similarity=0.028  Sum_probs=64.5

Q ss_pred             CEEEEeCCcch-h-hhcc-cccccceEEEEEeCCCCCCCCcC-C---CCCCCce-eEEEEecCCCCCchhHhHHHHHHHH
Q 030407           75 DLLLCESGGDN-L-AANF-SRELADYIIYIIDVSGGDKIPRK-G---GPGITQA-DLLVINKTDLASAIGADLAVMERDA  146 (178)
Q Consensus        75 d~iiiEttG~~-~-~~~~-~~~~ad~~I~VvD~~~~~~~~~~-~---~~qi~~a-diiviNK~Dl~~~~~~~~~~~~~~l  146 (178)
                      -+-||.|.|-. . ..+. ....+|.+++|+|+.++...+.. +   ...+... -+||+||+|++++  +..+...+.+
T Consensus        52 ~i~~IDtPGhe~fi~~m~~g~~~~D~~lLVVda~eg~~~qT~ehl~il~~lgi~~iIVVlNKiDlv~~--~~~~~v~~ei  129 (614)
T PRK10512         52 VLGFIDVPGHEKFLSNMLAGVGGIDHALLVVACDDGVMAQTREHLAILQLTGNPMLTVALTKADRVDE--ARIAEVRRQV  129 (614)
T ss_pred             EEEEEECCCHHHHHHHHHHHhhcCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCeEEEEEECCccCCH--HHHHHHHHHH
Confidence            36799999931 1 1111 11246999999999876432211 1   1112233 3699999999876  4444434333


Q ss_pred             ----HhcC-CCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          147 ----LRMR-DGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       147 ----~~~n-p~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                          +..+ ...+++++||++|+|+++|++.|..+.
T Consensus       130 ~~~l~~~~~~~~~ii~VSA~tG~gI~~L~~~L~~~~  165 (614)
T PRK10512        130 KAVLREYGFAEAKLFVTAATEGRGIDALREHLLQLP  165 (614)
T ss_pred             HHHHHhcCCCCCcEEEEeCCCCCCCHHHHHHHHHhh
Confidence                3322 347899999999999999999987653

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

Probab=98.45  E-value=6.1e-07  Score=67.77  Aligned_cols=101  Identities=14%  Similarity=0.040  Sum_probs=63.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.++++.|..-    ...+. ..++..++++|.++......         ........+.++++||+|+........
T Consensus        48 ~~~~~l~D~~g~~~~~~~~~~~~-~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~NK~Dl~~~~~~~~  126 (180)
T cd04137          48 DYHLEIVDTAGQDEYSILPQKYS-IGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHTQRQVST  126 (180)
T ss_pred             EEEEEEEECCChHhhHHHHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEchhhhhcCccCH
Confidence            46778999999321    11122 24688999999987542211         011112347899999999974310122


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +......+..  ..+++++||++|+|+.++++++.+.
T Consensus       127 ~~~~~~~~~~--~~~~~~~Sa~~~~gv~~l~~~l~~~  161 (180)
T cd04137         127 EEGKELAESW--GAAFLESSARENENVEEAFELLIEE  161 (180)
T ss_pred             HHHHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            2233333333  3689999999999999999988754

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

>cd04147 Ras_dva Ras-dva subfamily

Probab=98.45  E-value=8.3e-07  Score=68.59  Aligned_cols=102  Identities=10%  Similarity=-0.019  Sum_probs=62.7

Q ss_pred             CCEEEEeCCcchh-h--hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCc-hhHhHH
Q 030407           74 ADLLLCESGGDNL-A--ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASA-IGADLA  140 (178)
Q Consensus        74 ~d~iiiEttG~~~-~--~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~-~~~~~~  140 (178)
                      ..+.|+++.|..- .  .......+|.+++|+|+++......         .....-..+-++|+||+|+.+. .....+
T Consensus        47 ~~l~i~D~~G~~~~~~~~~~~~~~ad~vilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~NK~Dl~~~~~~v~~~  126 (198)
T cd04147          47 LTLDILDTSGSYSFPAMRKLSIQNSDAFALVYAVDDPESFEEVERLREEILEVKEDKFVPIVVVGNKADSLEEERQVPAK  126 (198)
T ss_pred             EEEEEEECCCchhhhHHHHHHhhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEEccccccccccccHH
Confidence            5677899999311 1  1112235799999999987533211         0111123567999999999763 101122


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+.. ......+++++||++|.|++++++++.+.
T Consensus       127 ~~~~~~-~~~~~~~~~~~Sa~~g~gv~~l~~~l~~~  161 (198)
T cd04147         127 DALSTV-ELDWNCGFVETSAKDNENVLEVFKELLRQ  161 (198)
T ss_pred             HHHHHH-HhhcCCcEEEecCCCCCCHHHHHHHHHHH
Confidence            222222 12334689999999999999999988654

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.

>cd04144 Ras2 Ras2 subfamily

Probab=98.45  E-value=9e-07  Score=67.89  Aligned_cols=99  Identities=14%  Similarity=0.087  Sum_probs=62.4

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C-------CCC--CCCceeEEEEecCCCCCchhHh
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K-------GGP--GITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~--qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      +.+-|++|.|..    +...+. ..+|++++|+|.++......  .       ...  -...+-++|+||+|+.......
T Consensus        47 ~~l~i~Dt~G~~~~~~~~~~~~-~~ad~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilvgNK~Dl~~~~~v~  125 (190)
T cd04144          47 CMLEVLDTAGQEEYTALRDQWI-REGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVYEREVS  125 (190)
T ss_pred             EEEEEEECCCchhhHHHHHHHH-HhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcccCCCCCEEEEEEChhccccCccC
Confidence            557789999931    112222 25799999999977532211  0       000  0234568999999996431112


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+...+..+..+  .+++++||++|.|++++|+++.+
T Consensus       126 ~~~~~~~~~~~~--~~~~e~SAk~~~~v~~l~~~l~~  160 (190)
T cd04144         126 TEEGAALARRLG--CEFIEASAKTNVNVERAFYTLVR  160 (190)
T ss_pred             HHHHHHHHHHhC--CEEEEecCCCCCCHHHHHHHHHH
Confidence            223334444432  58999999999999999998765

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.

>cd01874 Cdc42 Cdc42 subfamily

Probab=98.45  E-value=2.7e-07  Score=70.12  Aligned_cols=101  Identities=16%  Similarity=0.075  Sum_probs=64.5

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchhHh--
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIGAD--  138 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~~~--  138 (178)
                      ++.+-+++|+|..    +...+. ..+|++|+|+|.++......   .+...     -..+-++|.||+|+.+.  .+  
T Consensus        48 ~~~l~i~Dt~G~~~~~~~~~~~~-~~a~~~ilv~d~~~~~s~~~~~~~w~~~i~~~~~~~piilvgnK~Dl~~~--~~~~  124 (175)
T cd01874          48 PYTLGLFDTAGQEDYDRLRPLSY-PQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDD--PSTI  124 (175)
T ss_pred             EEEEEEEECCCccchhhhhhhhc-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEECHhhhhC--hhhH
Confidence            4678899999942    112222 25799999999987543211   11100     13467999999999654  21  


Q ss_pred             ------------HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          139 ------------LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       139 ------------~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                                  .++..+..++. +..+++++||++|+|++++|+.+.+.|
T Consensus       125 ~~l~~~~~~~v~~~~~~~~a~~~-~~~~~~e~SA~tg~~v~~~f~~~~~~~  174 (175)
T cd01874         125 EKLAKNKQKPITPETGEKLARDL-KAVKYVECSALTQKGLKNVFDEAILAA  174 (175)
T ss_pred             HHhhhccCCCcCHHHHHHHHHHh-CCcEEEEecCCCCCCHHHHHHHHHHHh
Confidence                        12222233332 346899999999999999999887643

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

>PLN03118 Rab family protein; Provisional

Probab=98.44  E-value=6.9e-07  Score=69.70  Aligned_cols=101  Identities=17%  Similarity=0.111  Sum_probs=64.2

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc----------CCCCCCCceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR----------KGGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~----------~~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+.+.|++|.|..    +...+. ..+|.+++|+|.++......          .+...-...-++|+||+|+.......
T Consensus        61 ~~~l~l~Dt~G~~~~~~~~~~~~-~~~d~~vlv~D~~~~~sf~~~~~~~~~~~~~~~~~~~~~~ilv~NK~Dl~~~~~i~  139 (211)
T PLN03118         61 RLKLTIWDTAGQERFRTLTSSYY-RNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVDRESERDVS  139 (211)
T ss_pred             EEEEEEEECCCchhhHHHHHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccCccC
Confidence            4678899999931    112222 24799999999987532211          01111223568999999997541122


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+......++.  ..+++++||++|+|++++|+.|...
T Consensus       140 ~~~~~~~~~~~--~~~~~e~SAk~~~~v~~l~~~l~~~  175 (211)
T PLN03118        140 REEGMALAKEH--GCLFLECSAKTRENVEQCFEELALK  175 (211)
T ss_pred             HHHHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            23333444433  3579999999999999999988653

>cd04108 Rab36_Rab34 Rab34/Rab36 subfamily

Probab=98.44  E-value=1.3e-06  Score=66.00  Aligned_cols=102  Identities=16%  Similarity=0.045  Sum_probs=62.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC-----CCC--CceeEEEEecCCCCCchhH--
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG-----PGI--TQADLLVINKTDLASAIGA--  137 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~-----~qi--~~adiiviNK~Dl~~~~~~--  137 (178)
                      ...+-|++|+|..    +...+. ..+|.+++|+|+++......  .+.     ...  ..+-++|.||+|+.+....  
T Consensus        48 ~~~l~i~Dt~G~~~~~~~~~~~~-~~ad~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~iilVgnK~Dl~~~~~~~~  126 (170)
T cd04108          48 PFSLQLWDTAGQERFKCIASTYY-RGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDLSSPAQYAL  126 (170)
T ss_pred             EEEEEEEeCCChHHHHhhHHHHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEChhcCccccccc
Confidence            4567899999931    112222 25799999999976432110  000     000  1245899999999654110  


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ..+...+..++.  ..+++++||++|+|++++|+.+.+.+
T Consensus       127 ~~~~~~~~~~~~--~~~~~e~Sa~~g~~v~~lf~~l~~~~  164 (170)
T cd04108         127 MEQDAIKLAAEM--QAEYWSVSALSGENVREFFFRVAALT  164 (170)
T ss_pred             cHHHHHHHHHHc--CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            112233333333  35899999999999999999887654

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

>cd01866 Rab2 Rab2 subfamily

Probab=98.43  E-value=1.1e-06  Score=65.87  Aligned_cols=101  Identities=15%  Similarity=0.083  Sum_probs=65.3

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+.+++|+|..    +...+. ..+|.+++|+|+++......  .+..      .-..+-++|.||+|+.++.....+
T Consensus        52 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~il~v~d~~~~~s~~~~~~~~~~~~~~~~~~~pvivv~nK~Dl~~~~~~~~~  130 (168)
T cd01866          52 QIKLQIWDTAGQESFRSITRSYY-RGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCDLESRREVSYE  130 (168)
T ss_pred             EEEEEEEECCCcHHHHHHHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEECcccccccCCCHH
Confidence            4578899999931    122222 24699999999986432211  0100      013457999999999754212334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ......++.  ..+++++||++|+|++++|+.+.+.
T Consensus       131 ~~~~~~~~~--~~~~~e~Sa~~~~~i~~~~~~~~~~  164 (168)
T cd01866         131 EGEAFAKEH--GLIFMETSAKTASNVEEAFINTAKE  164 (168)
T ss_pred             HHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            445555543  4689999999999999999887654

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

>cd04134 Rho3 Rho3 subfamily

Probab=98.43  E-value=5.9e-07  Score=68.92  Aligned_cols=101  Identities=18%  Similarity=0.108  Sum_probs=64.5

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchhHhH-
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIGADL-  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~~~~-  139 (178)
                      +.++.|++|.|..    +...+ ...++.+|+|+|.++......   .+...     -..+-++|.||+||...  ... 
T Consensus        47 ~~~l~i~Dt~G~~~~~~l~~~~-~~~a~~~ilv~dv~~~~sf~~~~~~~~~~i~~~~~~~piilvgNK~Dl~~~--~~~~  123 (189)
T cd04134          47 HIELSLWDTAGQEEFDRLRSLS-YADTDVIMLCFSVDSPDSLENVESKWLGEIREHCPGVKLVLVALKCDLREA--RNER  123 (189)
T ss_pred             EEEEEEEECCCChhcccccccc-ccCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEChhhccC--hhhH
Confidence            4678899999941    11122 235789999999887543211   11111     13467999999999765  221 


Q ss_pred             -------------HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 -------------AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 -------------~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                                   ++..+..++. ...+++++||++|+|++++|+++.+.+
T Consensus       124 ~~~~~~~~~~v~~~~~~~~~~~~-~~~~~~e~SAk~~~~v~e~f~~l~~~~  173 (189)
T cd04134         124 DDLQRYGKHTISYEEGLAVAKRI-NALRYLECSAKLNRGVNEAFTEAARVA  173 (189)
T ss_pred             HHHhhccCCCCCHHHHHHHHHHc-CCCEEEEccCCcCCCHHHHHHHHHHHH
Confidence                         1223333332 236899999999999999999887643

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.

>cd04117 Rab15 Rab15 subfamily

Probab=98.43  E-value=1e-06  Score=65.69  Aligned_cols=101  Identities=14%  Similarity=0.075  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+-+++++|..    +...+. ..+|++++|+|.++......  .+.      ..-..+-++|.||.|+..+.....+
T Consensus        48 ~~~l~i~D~~g~~~~~~~~~~~~-~~~~~~i~v~d~~~~~sf~~~~~~~~~~~~~~~~~~~iilvgnK~Dl~~~~~v~~~  126 (161)
T cd04117          48 KVRIQIWDTAGQERYQTITKQYY-RRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQKRQVGDE  126 (161)
T ss_pred             EEEEEEEeCCCcHhHHhhHHHHh-cCCcEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccCCCHH
Confidence            3567788999932    111222 24699999999977532211  000      0113467999999999754211223


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.....+..+  .+++++||++|.|++++|++|.+.
T Consensus       127 ~~~~~~~~~~--~~~~e~Sa~~~~~v~~~f~~l~~~  160 (161)
T cd04117         127 QGNKLAKEYG--MDFFETSACTNSNIKESFTRLTEL  160 (161)
T ss_pred             HHHHHHHHcC--CEEEEEeCCCCCCHHHHHHHHHhh
Confidence            3344444443  579999999999999999998753

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

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

Probab=98.42  E-value=7.1e-07  Score=66.89  Aligned_cols=103  Identities=17%  Similarity=0.058  Sum_probs=64.4

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc---CCCC-----CCCceeEEEEecCCCCCchh-----
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR---KGGP-----GITQADLLVINKTDLASAIG-----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~-----qi~~adiiviNK~Dl~~~~~-----  136 (178)
                      .+.+.+++|.|..--   .......+|.+++++|.++......   .+..     --..+-++|+||+|+.+...     
T Consensus        45 ~~~~~i~Dt~G~~~~~~~~~~~~~~~d~~ilv~d~~~~~s~~~~~~~~~~~i~~~~~~~piilv~nK~Dl~~~~~~~~~~  124 (174)
T smart00174       45 PVELGLWDTAGQEDYDRLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFCPNTPIILVGTKLDLREDKSTLREL  124 (174)
T ss_pred             EEEEEEEECCCCcccchhchhhcCCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEecChhhhhChhhhhhh
Confidence            467889999994211   1112235799999999987533211   0100     01356799999999976310     


Q ss_pred             -------HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 -------ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 -------~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                             ...+...+..+..+ ..+++++||++|+|++++|+.+.+.
T Consensus       125 ~~~~~~~v~~~~~~~~~~~~~-~~~~~e~Sa~~~~~v~~lf~~l~~~  170 (174)
T smart00174      125 SKQKQEPVTYEQGEALAKRIG-AVKYLECSALTQEGVREVFEEAIRA  170 (174)
T ss_pred             hcccCCCccHHHHHHHHHHcC-CcEEEEecCCCCCCHHHHHHHHHHH
Confidence                   11122333444432 3479999999999999999987654

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

>cd04161 Arl2l1_Arl13_like Arl2l1/Arl13 subfamily

Probab=98.41  E-value=1.1e-06  Score=66.13  Aligned_cols=101  Identities=16%  Similarity=0.087  Sum_probs=64.3

Q ss_pred             CCCCEEEEeCCcch-hh---hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHh
Q 030407           72 FKADLLLCESGGDN-LA---ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        72 ~~~d~iiiEttG~~-~~---~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .++.+.++++.|.. ..   ..+. ..+|.+++|+|+++......         .....-..+-++|+||+|+...  ..
T Consensus        41 ~~~~~~i~D~~G~~~~~~~~~~~~-~~a~~ii~V~D~s~~~s~~~~~~~l~~l~~~~~~~~~piliv~NK~Dl~~~--~~  117 (167)
T cd04161          41 DKYEVCIFDLGGGANFRGIWVNYY-AEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNA--LL  117 (167)
T ss_pred             CCEEEEEEECCCcHHHHHHHHHHH-cCCCEEEEEEECCchhHHHHHHHHHHHHHcCccccCCcEEEEEeCCCCcCC--CC
Confidence            35788999999942 11   1222 35799999999987542211         0111124567999999999765  32


Q ss_pred             HHHHHHHH--Hhc----CCCCCEEEEecccC------CCHHHHHHHHhh
Q 030407          139 LAVMERDA--LRM----RDGGPFIFAQVGWV------IGIIFTLSITHY  175 (178)
Q Consensus       139 ~~~~~~~l--~~~----np~a~i~~~SA~~g------~gi~el~~~l~~  175 (178)
                      ...+.+.+  .++    +...+++.+||++|      .|+++-|+||.+
T Consensus       118 ~~~i~~~~~l~~~~~~~~~~~~~~~~Sa~~g~~~~~~~g~~~~~~wl~~  166 (167)
T cd04161         118 GADVIEYLSLEKLVNENKSLCHIEPCSAIEGLGKKIDPSIVEGLRWLLA  166 (167)
T ss_pred             HHHHHHhcCcccccCCCCceEEEEEeEceeCCCCccccCHHHHHHHHhc
Confidence            33333322  121    12247888999998      899999999864

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.

>cd01861 Rab6 Rab6 subfamily

Probab=98.40  E-value=1.4e-06  Score=64.20  Aligned_cols=100  Identities=17%  Similarity=0.126  Sum_probs=63.7

Q ss_pred             CCEEEEeCCcchhh----hcccccccceEEEEEeCCCCCCCCc--CC------CCCCCceeEEEEecCCCCCchhHhHHH
Q 030407           74 ADLLLCESGGDNLA----ANFSRELADYIIYIIDVSGGDKIPR--KG------GPGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        74 ~d~iiiEttG~~~~----~~~~~~~ad~~I~VvD~~~~~~~~~--~~------~~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      ..+.+++|.|..--    ..+. ..+|.+++|+|.+++.....  .+      ...-..+-++++||+|+.+......+.
T Consensus        49 ~~l~~~D~~G~~~~~~~~~~~~-~~~~~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilv~nK~D~~~~~~~~~~~  127 (161)
T cd01861          49 VRLQLWDTAGQERFRSLIPSYI-RDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDKRQVSTEE  127 (161)
T ss_pred             EEEEEEECCCcHHHHHHHHHHh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCEEEEEEEChhccccCccCHHH
Confidence            45789999994211    1111 24689999999976532211  00      011136789999999995431122233


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .....+..  ..+++++||++|.|++++++++.+.
T Consensus       128 ~~~~~~~~--~~~~~~~Sa~~~~~v~~l~~~i~~~  160 (161)
T cd01861         128 GEKKAKEL--NAMFIETSAKAGHNVKELFRKIASA  160 (161)
T ss_pred             HHHHHHHh--CCEEEEEeCCCCCCHHHHHHHHHHh
Confidence            34444433  4789999999999999999998653

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

>cd04172 Rnd3_RhoE_Rho8 Rnd3/RhoE/Rho8 subfamily

Probab=98.40  E-value=4.3e-07  Score=69.72  Aligned_cols=102  Identities=15%  Similarity=0.101  Sum_probs=65.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCc------
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASA------  134 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~------  134 (178)
                      .+.+-+++|.|..    +...+. ..+|++++|+|.++......   .+.+.     -..+-++|.||+||.+.      
T Consensus        52 ~~~l~iwDtaG~e~~~~~~~~~~-~~ad~~ilvyDit~~~Sf~~~~~~w~~~i~~~~~~~piilVgNK~DL~~~~~~~~~  130 (182)
T cd04172          52 RIELSLWDTSGSPYYDNVRPLSY-PDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDLRTDLTTLVE  130 (182)
T ss_pred             EEEEEEEECCCchhhHhhhhhhc-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCEEEEeEChhhhcChhhHHH
Confidence            4778899999941    222222 35799999999987643221   11111     13457999999998541      


Q ss_pred             ------hhHhHHHHHHHHHhcCCCCCEEEEecccCCC-HHHHHHHHhhh
Q 030407          135 ------IGADLAVMERDALRMRDGGPFIFAQVGWVIG-IIFTLSITHYI  176 (178)
Q Consensus       135 ------~~~~~~~~~~~l~~~np~a~i~~~SA~~g~g-i~el~~~l~~~  176 (178)
                            .....++..+..++.+ ..++++|||++|+| |+++|+.+.+.
T Consensus       131 ~~~~~~~~v~~~~~~~~a~~~~-~~~~~E~SAk~~~n~v~~~F~~~~~~  178 (182)
T cd04172         131 LSNHRQTPVSYDQGANMAKQIG-AATYIECSALQSENSVRDIFHVATLA  178 (182)
T ss_pred             HHhcCCCCCCHHHHHHHHHHcC-CCEEEECCcCCCCCCHHHHHHHHHHH
Confidence                  0022334555555442 24899999999998 99999987653

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

>CHL00189 infB translation initiation factor 2; Provisional

Probab=98.39  E-value=1.3e-06  Score=79.86  Aligned_cols=101  Identities=17%  Similarity=0.170  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCcch-hhhcc--cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           73 KADLLLCESGGDN-LAANF--SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~~--~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      +..+.|+.|.|-. .....  ....+|.+++|+|+..+...+..    .......+-++++||+|+.+.   ..+.+.+.
T Consensus       294 ~~kItfiDTPGhe~F~~mr~rg~~~aDiaILVVDA~dGv~~QT~E~I~~~k~~~iPiIVViNKiDl~~~---~~e~v~~e  370 (742)
T CHL00189        294 NQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVPIIVAINKIDKANA---NTERIKQQ  370 (742)
T ss_pred             ceEEEEEECCcHHHHHHHHHHHHHHCCEEEEEEECcCCCChhhHHHHHHHHhcCceEEEEEECCCcccc---CHHHHHHH
Confidence            4678999999931 11110  11247999999999876432210    111234567999999999754   22333333


Q ss_pred             HHh-------cCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          146 ALR-------MRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       146 l~~-------~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ++.       +....+++++||++|+|+++|++++..+
T Consensus       371 L~~~~ll~e~~g~~vpvv~VSAktG~GIdeLle~I~~l  408 (742)
T CHL00189        371 LAKYNLIPEKWGGDTPMIPISASQGTNIDKLLETILLL  408 (742)
T ss_pred             HHHhccchHhhCCCceEEEEECCCCCCHHHHHHhhhhh
Confidence            332       2223689999999999999999987654

>cd04174 Rnd1_Rho6 Rnd1/Rho6 subfamily

Probab=98.39  E-value=9.4e-07  Score=70.57  Aligned_cols=102  Identities=15%  Similarity=0.075  Sum_probs=66.0

Q ss_pred             CCCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCc-----
Q 030407           72 FKADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASA-----  134 (178)
Q Consensus        72 ~~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~-----  134 (178)
                      ..+.+-|++|.|..    +...+. ..+|++++|+|.++......   .+...     -..+-++|.||+||.+.     
T Consensus        59 ~~v~l~iwDTaG~e~~~~~~~~~~-~~ad~vIlVyDit~~~Sf~~~~~~w~~~i~~~~~~~piilVgNK~DL~~~~~~~~  137 (232)
T cd04174          59 QRVELSLWDTSGSPYYDNVRPLCY-SDSDAVLLCFDISRPETVDSALKKWKAEIMDYCPSTRILLIGCKTDLRTDLSTLM  137 (232)
T ss_pred             EEEEEEEEeCCCchhhHHHHHHHc-CCCcEEEEEEECCChHHHHHHHHHHHHHHHHhCCCCCEEEEEECcccccccchhh
Confidence            35788999999941    223333 36899999999987653321   11010     12356899999999531     


Q ss_pred             -------hhHhHHHHHHHHHhcCCCCCEEEEecccCC-CHHHHHHHHhh
Q 030407          135 -------IGADLAVMERDALRMRDGGPFIFAQVGWVI-GIIFTLSITHY  175 (178)
Q Consensus       135 -------~~~~~~~~~~~l~~~np~a~i~~~SA~~g~-gi~el~~~l~~  175 (178)
                             .....++.+++.++.+ ..++++|||++|+ |++++|+.+.+
T Consensus       138 ~l~~~~~~~Vs~~e~~~~a~~~~-~~~~~EtSAktg~~~V~e~F~~~~~  185 (232)
T cd04174         138 ELSNQKQAPISYEQGCALAKQLG-AEVYLECSAFTSEKSIHSIFRSASL  185 (232)
T ss_pred             hhccccCCcCCHHHHHHHHHHcC-CCEEEEccCCcCCcCHHHHHHHHHH
Confidence                   0022345555565543 2268999999998 89999998754

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.

>cd04114 Rab30 Rab30 subfamily

Probab=98.39  E-value=1.4e-06  Score=64.88  Aligned_cols=101  Identities=14%  Similarity=0.059  Sum_probs=63.4

Q ss_pred             CCCEEEEeCCcchh-hh--cccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhH-H
Q 030407           73 KADLLLCESGGDNL-AA--NFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADL-A  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~-~~--~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~-~  140 (178)
                      .+.+.++++.|..- ..  ......+|.+++++|++.......  .+.      ..-..+-++++||+|+.++  .+. .
T Consensus        55 ~~~~~~~D~~g~~~~~~~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~l~~~~~~~~~~i~v~NK~D~~~~--~~i~~  132 (169)
T cd04114          55 KIKLQIWDTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNKIDLAER--REVSQ  132 (169)
T ss_pred             EEEEEEEECCCcHHHHHHHHHHhcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccc--cccCH
Confidence            35677889999421 11  111224699999999976532210  010      1113456999999999754  221 2


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+.+.+..+ .+++++||++|+|++++|+.+.+.
T Consensus       133 ~~~~~~~~~~~-~~~~~~Sa~~~~gv~~l~~~i~~~  167 (169)
T cd04114         133 QRAEEFSDAQD-MYYLETSAKESDNVEKLFLDLACR  167 (169)
T ss_pred             HHHHHHHHHcC-CeEEEeeCCCCCCHHHHHHHHHHH
Confidence            23333444443 689999999999999999998753

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.

>cd01862 Rab7 Rab7 subfamily

Probab=98.38  E-value=9.5e-07  Score=65.79  Aligned_cols=101  Identities=14%  Similarity=0.084  Sum_probs=63.4

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C----CCCC------CCceeEEEEecCCCCCchhH
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K----GGPG------ITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~----~~~q------i~~adiiviNK~Dl~~~~~~  137 (178)
                      +-+-++++.|..    +...+. ..+|.+++++|+.+......  .    +...      -..+-++|+||+|+..+...
T Consensus        49 ~~~~~~D~~g~~~~~~~~~~~~-~~~d~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~  127 (172)
T cd01862          49 VTLQIWDTAGQERFQSLGVAFY-RGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPSDPENFPFVVLGNKIDLEEKRQV  127 (172)
T ss_pred             EEEEEEeCCChHHHHhHHHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCccCCCCceEEEEEECccccccccc
Confidence            445588999932    111122 24699999999976542110  0    0000      13567899999999843112


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+...+..+.. ...+++++||++|.|++++++.+.+.
T Consensus       128 ~~~~~~~~~~~~-~~~~~~~~Sa~~~~gv~~l~~~i~~~  165 (172)
T cd01862         128 STKKAQQWCQSN-GNIPYFETSAKEAINVEQAFETIARK  165 (172)
T ss_pred             CHHHHHHHHHHc-CCceEEEEECCCCCCHHHHHHHHHHH
Confidence            334445555443 33689999999999999999987754

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-

>cd04111 Rab39 Rab39 subfamily

Probab=98.38  E-value=1.4e-06  Score=68.22  Aligned_cols=100  Identities=13%  Similarity=0.098  Sum_probs=62.9

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.+++|+|...    ...+. ..+|.+++|+|.++......  .       ....-..+-++|.||+|+.+......
T Consensus        51 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~d~iilv~D~~~~~Sf~~l~~~~~~i~~~~~~~~~~iilvgNK~Dl~~~~~v~~  129 (211)
T cd04111          51 RIKLQLWDTAGQERFRSITRSYY-RNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCDLESQRQVTR  129 (211)
T ss_pred             EEEEEEEeCCcchhHHHHHHHHh-cCCcEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEccccccccccCH
Confidence            45788999999421    11222 34799999999987532211  0       00001123478899999975311222


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +...+..+..+  .+++++||++|+|++++|+.|.+
T Consensus       130 ~~~~~~~~~~~--~~~~e~Sak~g~~v~e~f~~l~~  163 (211)
T cd04111         130 EEAEKLAKDLG--MKYIETSARTGDNVEEAFELLTQ  163 (211)
T ss_pred             HHHHHHHHHhC--CEEEEEeCCCCCCHHHHHHHHHH
Confidence            33444444432  68999999999999999998865

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.

>cd01870 RhoA_like RhoA-like subfamily

Probab=98.38  E-value=7.8e-07  Score=66.71  Aligned_cols=102  Identities=17%  Similarity=0.142  Sum_probs=62.9

Q ss_pred             CCCEEEEeCCcchhhh---cccccccceEEEEEeCCCCCCCCc---CCCC---C--CCceeEEEEecCCCCCchhHhH--
Q 030407           73 KADLLLCESGGDNLAA---NFSRELADYIIYIIDVSGGDKIPR---KGGP---G--ITQADLLVINKTDLASAIGADL--  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~---~~~~~~ad~~I~VvD~~~~~~~~~---~~~~---q--i~~adiiviNK~Dl~~~~~~~~--  139 (178)
                      .+.+.+++|.|..--.   ......+|.+++++|..+......   .+..   +  -..+-++|+||+|+.+.  ...  
T Consensus        48 ~~~l~i~Dt~G~~~~~~~~~~~~~~~d~~i~v~~~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~~~  125 (175)
T cd01870          48 QVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRND--EHTRR  125 (175)
T ss_pred             EEEEEEEeCCCchhhhhccccccCCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeeChhcccC--hhhhh
Confidence            4678999999932111   111234688999999876432111   0100   0  13467899999998754  211  


Q ss_pred             ------------HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 ------------AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ------------~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                                  ...++..+..+ ..+++++||++|.|++++|+++.+.+
T Consensus       126 ~i~~~~~~~v~~~~~~~~~~~~~-~~~~~~~Sa~~~~~v~~lf~~l~~~~  174 (175)
T cd01870         126 ELAKMKQEPVKPEEGRDMANKIG-AFGYMECSAKTKEGVREVFEMATRAA  174 (175)
T ss_pred             hhhhccCCCccHHHHHHHHHHcC-CcEEEEeccccCcCHHHHHHHHHHHh
Confidence                        12222233322 34799999999999999999988654

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

>cd04103 Centaurin_gamma Centaurin gamma

Probab=98.38  E-value=1.2e-06  Score=65.59  Aligned_cols=99  Identities=13%  Similarity=0.119  Sum_probs=61.3

Q ss_pred             CCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCC--chhHhHHHH
Q 030407           74 ADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLAS--AIGADLAVM  142 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~--~~~~~~~~~  142 (178)
                      ..+-+.+|.|.. ...+. ..+|.+++|+|.++......  .       ....-..+-++|.||.|+..  +.....+..
T Consensus        47 ~~l~i~D~~g~~-~~~~~-~~~~~~ilv~d~~~~~sf~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~~~~~v~~~~~  124 (158)
T cd04103          47 HLLLIRDEGGAP-DAQFA-SWVDAVIFVFSLENEASFQTVYNLYHQLSSYRNISEIPLILVGTQDAISESNPRVIDDARA  124 (158)
T ss_pred             EEEEEEECCCCC-chhHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEeeHHHhhhcCCcccCHHHH
Confidence            456678888831 12222 35799999999987653321  0       11111235689999999842  210122223


Q ss_pred             HHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          143 ERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       143 ~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+..++. ...++++|||++|+||+++|+.+.+
T Consensus       125 ~~~~~~~-~~~~~~e~SAk~~~~i~~~f~~~~~  156 (158)
T cd04103         125 RQLCADM-KRCSYYETCATYGLNVERVFQEAAQ  156 (158)
T ss_pred             HHHHHHh-CCCcEEEEecCCCCCHHHHHHHHHh
Confidence            3333332 2368999999999999999998765

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.

>COG2403 Predicted GTPase [General function prediction only]

Probab=98.38  E-value=1.3e-06  Score=73.38  Aligned_cols=79  Identities=23%  Similarity=0.246  Sum_probs=62.8

Q ss_pred             CCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCC--CCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCC
Q 030407           74 ADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGP--GITQADLLVINKTDLASAIGADLAVMERDALRMRD  151 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~--qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np  151 (178)
                      -|+|++|-+|. --+++.+   |..|+|+|+.++-.....++.  .++.||++++||+|-++.  +..+++.+.++++||
T Consensus       225 aD~IlwdGgnn-dfPfvkp---d~~Ivvvda~rpg~ei~~~pGe~~irlAD~VIItkveea~~--~kvrkI~~~I~~iNP  298 (449)
T COG2403         225 ADFILWDGGNN-DFPFVKP---DLHIVVVDALRPGEEIGSFPGELRIRLADLVIITKVEEAMA--EKVRKIVRNIEEINP  298 (449)
T ss_pred             ccEEEEeCCCC-CCCcccC---CeeEEEecCCCCchhhccCCCceeeeeccEEEEecccccch--HHHHHHHHHHHhhCC
Confidence            49999999992 2233333   999999999885443333433  478899999999999988  899999999999999


Q ss_pred             CCCEEEE
Q 030407          152 GGPFIFA  158 (178)
Q Consensus       152 ~a~i~~~  158 (178)
                      .|.++.+
T Consensus       299 ~A~Vi~~  305 (449)
T COG2403         299 KAEVILA  305 (449)
T ss_pred             CcEEEec
Confidence            9988876

>COG0481 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]

Probab=98.37  E-value=7.2e-07  Score=76.99  Aligned_cols=96  Identities=23%  Similarity=0.248  Sum_probs=64.7

Q ss_pred             CCEEEEeCCcchhhhcc--ccccc--ceEEEEEeCCCCCCCCcC---C---CCCCCceeEEEEecCCCCCchhHhHHHHH
Q 030407           74 ADLLLCESGGDNLAANF--SRELA--DYIIYIIDVSGGDKIPRK---G---GPGITQADLLVINKTDLASAIGADLAVME  143 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~~--~~~~a--d~~I~VvD~~~~~~~~~~---~---~~qi~~adiiviNK~Dl~~~~~~~~~~~~  143 (178)
                      +-.=+|.|.| .+.-+|  ++.++  .+.++|||++.|-+.+..   |   ...++  -+-|+||+||..+   +.+++.
T Consensus        76 Y~lnlIDTPG-HVDFsYEVSRSLAACEGalLvVDAsQGveAQTlAN~YlAle~~Le--IiPViNKIDLP~A---dpervk  149 (603)
T COG0481          76 YVLNLIDTPG-HVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLALENNLE--IIPVLNKIDLPAA---DPERVK  149 (603)
T ss_pred             EEEEEcCCCC-ccceEEEehhhHhhCCCcEEEEECccchHHHHHHHHHHHHHcCcE--EEEeeecccCCCC---CHHHHH
Confidence            4455789999 222222  22232  678999999998654321   1   11122  3789999999766   556666


Q ss_pred             HHHHhcC--CCCCEEEEecccCCCHHHHHHHHhh
Q 030407          144 RDALRMR--DGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       144 ~~l~~~n--p~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +.++..-  +....+.+|||+|.||+++++.+-.
T Consensus       150 ~eIe~~iGid~~dav~~SAKtG~gI~~iLe~Iv~  183 (603)
T COG0481         150 QEIEDIIGIDASDAVLVSAKTGIGIEDVLEAIVE  183 (603)
T ss_pred             HHHHHHhCCCcchheeEecccCCCHHHHHHHHHh
Confidence            6666543  4568899999999999999997643

>PRK04213 GTP-binding protein; Provisional

Probab=98.36  E-value=3.9e-06  Score=64.66  Aligned_cols=80  Identities=10%  Similarity=-0.069  Sum_probs=49.4

Q ss_pred             cceEEEEEeCCCCCCCCcCCC---------------CCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcC-C----CCC
Q 030407           95 ADYIIYIIDVSGGDKIPRKGG---------------PGITQADLLVINKTDLASAIGADLAVMERDALRMR-D----GGP  154 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~~~~---------------~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~n-p----~a~  154 (178)
                      ++.++.|+|+.........+.               .....+-++|+||+|+.+......+++.+.+. .. +    ..+
T Consensus        91 ~~~vi~v~d~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~p~iiv~NK~Dl~~~~~~~~~~~~~~~~-~~~~~~~~~~~  169 (201)
T PRK04213         91 ILAAVLVVDGKSFIEIIERWEGRGEIPIDVEMFDFLRELGIPPIVAVNKMDKIKNRDEVLDEIAERLG-LYPPWRQWQDI  169 (201)
T ss_pred             heEEEEEEeCccccccccccccCCCcHHHHHHHHHHHHcCCCeEEEEECccccCcHHHHHHHHHHHhc-CCccccccCCc
Confidence            478899999865432111110               01234669999999997651112333333322 11 1    136


Q ss_pred             EEEEecccCCCHHHHHHHHhhh
Q 030407          155 FIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       155 i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ++++||++| |+++++++|...
T Consensus       170 ~~~~SA~~g-gi~~l~~~l~~~  190 (201)
T PRK04213        170 IAPISAKKG-GIEELKEAIRKR  190 (201)
T ss_pred             EEEEecccC-CHHHHHHHHHHh
Confidence            899999999 999999998764

>cd04116 Rab9 Rab9 subfamily

Probab=98.36  E-value=2.7e-06  Score=63.55  Aligned_cols=100  Identities=10%  Similarity=0.053  Sum_probs=65.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCC---CCCceeEEEEecCCCCCchh
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGP---GITQADLLVINKTDLASAIG  136 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~---qi~~adiiviNK~Dl~~~~~  136 (178)
                      .+.+.|+++.|..    +...+. ..+|.+++++|..+......         .+..   .-..+-++|+||+|+.... 
T Consensus        53 ~~~l~i~D~~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~-  130 (170)
T cd04116          53 FVTLQIWDTAGQERFRSLRTPFY-RGSDCCLLTFAVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVVLGNKNDIPERQ-  130 (170)
T ss_pred             EEEEEEEeCCChHHHHHhHHHHh-cCCCEEEEEEECCCHHHHHhHHHHHHHHHHhcccccCCCCcEEEEEECccccccc-
Confidence            5678889999931    112222 24689999999876532211         0000   1134679999999996431 


Q ss_pred             HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          137 ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       137 ~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ...+.+.+..++.+ ..+++++||++|+|++++|+.+.+
T Consensus       131 ~~~~~~~~~~~~~~-~~~~~e~Sa~~~~~v~~~~~~~~~  168 (170)
T cd04116         131 VSTEEAQAWCRENG-DYPYFETSAKDATNVAAAFEEAVR  168 (170)
T ss_pred             cCHHHHHHHHHHCC-CCeEEEEECCCCCCHHHHHHHHHh
Confidence            23345555655543 358999999999999999998765

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

>cd04130 Wrch_1 Wrch-1 subfamily

Probab=98.36  E-value=8.9e-07  Score=66.66  Aligned_cols=101  Identities=14%  Similarity=0.125  Sum_probs=62.3

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchh-----
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIG-----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~-----  136 (178)
                      ...+.+++|.|..--   .+.....+|.+++++|.++......   .+..+     -..+-++++||+|+.+...     
T Consensus        47 ~~~~~i~Dt~G~~~~~~~~~~~~~~a~~~i~v~d~~~~~sf~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~~  126 (173)
T cd04130          47 PVRLQLCDTAGQDEFDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHNPKAPIILVGTQADLRTDVNVLIQL  126 (173)
T ss_pred             EEEEEEEECCCChhhccccccccCCCcEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeeChhhccChhHHHHH
Confidence            356778999994111   1112235799999999987543211   01110     1245699999999975410     


Q ss_pred             -------HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          137 -------ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       137 -------~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                             ...+...++.++. ...+++++||++|.|++++|+.+.
T Consensus       127 ~~~~~~~v~~~~~~~~a~~~-~~~~~~e~Sa~~~~~v~~lf~~~~  170 (173)
T cd04130         127 ARYGEKPVSQSRAKALAEKI-GACEYIECSALTQKNLKEVFDTAI  170 (173)
T ss_pred             hhcCCCCcCHHHHHHHHHHh-CCCeEEEEeCCCCCCHHHHHHHHH
Confidence                   1122334444433 234899999999999999999764

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,

>smart00175 RAB Rab subfamily of small GTPases

Probab=98.36  E-value=2.3e-06  Score=63.12  Aligned_cols=100  Identities=15%  Similarity=0.088  Sum_probs=65.6

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC----C--CCceeEEEEecCCCCCchhHhHHH
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP----G--ITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~----q--i~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      ..+.++++.|..    +...+. ..+|.+++|+|+++......  .+..    .  -..+-++++||+|+........+.
T Consensus        49 ~~~~l~D~~G~~~~~~~~~~~~-~~~d~~ilv~d~~~~~s~~~~~~~l~~~~~~~~~~~pivvv~nK~D~~~~~~~~~~~  127 (164)
T smart00175       49 VKLQIWDTAGQERFRSITSSYY-RGAVGALLVYDITNRESFENLKNWLKELREYADPNVVIMLVGNKSDLEDQRQVSREE  127 (164)
T ss_pred             EEEEEEECCChHHHHHHHHHHh-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEEchhcccccCCCHHH
Confidence            567799999942    111222 24799999999987543211  0000    0  145789999999997631123344


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+..+..  +.+++++||++|+|++++++.+.+.
T Consensus       128 ~~~~~~~~--~~~~~e~Sa~~~~~i~~l~~~i~~~  160 (164)
T smart00175      128 AEAFAEEH--GLPFFETSAKTNTNVEEAFEELARE  160 (164)
T ss_pred             HHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            55555543  3579999999999999999988654

Rab GTPases are implicated in vesicle trafficking.

>cd01868 Rab11_like Rab11-like

Probab=98.35  E-value=1.7e-06  Score=64.19  Aligned_cols=101  Identities=13%  Similarity=0.029  Sum_probs=63.6

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CC-C-----CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KG-G-----PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~-~-----~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+-++++.|..-    ...+. ..++.+++|+|+++......  .+ .     ..-..+-++|+||+|+........+
T Consensus        51 ~~~~~l~D~~g~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~pi~vv~nK~Dl~~~~~~~~~  129 (165)
T cd01868          51 TIKAQIWDTAGQERYRAITSAYY-RGAVGALLVYDITKKQTFENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTE  129 (165)
T ss_pred             EEEEEEEeCCChHHHHHHHHHHH-CCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECccccccccCCHH
Confidence            35788999999421    12222 24688999999976432211  00 0     0012467899999999754112223


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  ..+++++||++|+|++++++.+..-
T Consensus       130 ~~~~~~~~~--~~~~~~~Sa~~~~~v~~l~~~l~~~  163 (165)
T cd01868         130 EAKAFAEKN--GLSFIETSALDGTNVEEAFKQLLTE  163 (165)
T ss_pred             HHHHHHHHc--CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            444444432  4689999999999999999987653

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

>PRK12298 obgE GTPase CgtA; Reviewed

Probab=98.35  E-value=2.1e-06  Score=73.43  Aligned_cols=101  Identities=17%  Similarity=0.153  Sum_probs=64.0

Q ss_pred             CEEEEeCCcchh--------hhccc--ccccceEEEEEeCCCCC--CCCc----------CCCC-CCCceeEEEEecCCC
Q 030407           75 DLLLCESGGDNL--------AANFS--RELADYIIYIIDVSGGD--KIPR----------KGGP-GITQADLLVINKTDL  131 (178)
Q Consensus        75 d~iiiEttG~~~--------~~~~~--~~~ad~~I~VvD~~~~~--~~~~----------~~~~-qi~~adiiviNK~Dl  131 (178)
                      .++|+.|.|..-        ...+.  ...++.+++|+|++..+  +...          .+.. ....+.++|+||+|+
T Consensus       208 ~i~~vDtPGi~~~a~~~~~Lg~~~l~~i~radvlL~VVD~s~~~~~d~~e~~~~l~~eL~~~~~~L~~kP~IlVlNKiDl  287 (390)
T PRK12298        208 SFVVADIPGLIEGASEGAGLGIRFLKHLERCRVLLHLIDIAPIDGSDPVENARIIINELEKYSPKLAEKPRWLVFNKIDL  287 (390)
T ss_pred             EEEEEeCCCccccccchhhHHHHHHHHHHhCCEEEEEeccCcccccChHHHHHHHHHHHHhhhhhhcCCCEEEEEeCCcc
Confidence            489999999421        11111  12368999999987321  1100          0111 124678999999999


Q ss_pred             CCchhHhHHHHHHHHHhcCCC-CCEEEEecccCCCHHHHHHHHhhhh
Q 030407          132 ASAIGADLAVMERDALRMRDG-GPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       132 ~~~~~~~~~~~~~~l~~~np~-a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .+.  .++....+.+++..+. .+++++||++++|+++|++.|.+..
T Consensus       288 ~~~--~el~~~l~~l~~~~~~~~~Vi~ISA~tg~GIdeLl~~I~~~L  332 (390)
T PRK12298        288 LDE--EEAEERAKAIVEALGWEGPVYLISAASGLGVKELCWDLMTFI  332 (390)
T ss_pred             CCh--HHHHHHHHHHHHHhCCCCCEEEEECCCCcCHHHHHHHHHHHh
Confidence            866  4444433444333333 4899999999999999999887643

>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=98.35  E-value=2.4e-06  Score=65.03  Aligned_cols=103  Identities=17%  Similarity=0.094  Sum_probs=67.9

Q ss_pred             CCCCEEEEeCCcchhhhccc---ccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           72 FKADLLLCESGGDNLAANFS---RELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~~~~~---~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+..+-+.|-.|..-..++.   ...++++|+|+|+++......         .....-..+-+|++||.|+.+.  ...
T Consensus        56 ~~~~~~~~d~gG~~~~~~~w~~y~~~~~~iIfVvDssd~~~l~e~~~~L~~ll~~~~~~~~piLIl~NK~D~~~~--~~~  133 (175)
T PF00025_consen   56 KGYSLTIWDLGGQESFRPLWKSYFQNADGIIFVVDSSDPERLQEAKEELKELLNDPELKDIPILILANKQDLPDA--MSE  133 (175)
T ss_dssp             TTEEEEEEEESSSGGGGGGGGGGHTTESEEEEEEETTGGGGHHHHHHHHHHHHTSGGGTTSEEEEEEESTTSTTS--STH
T ss_pred             CcEEEEEEeccccccccccceeeccccceeEEEEecccceeecccccchhhhcchhhcccceEEEEeccccccCc--chh
Confidence            45678899998942111111   235799999999986542211         0111124577999999999876  444


Q ss_pred             HHHHHHHH--hcC--CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDAL--RMR--DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~--~~n--p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.+...+.  .+.  ...+++.+||++|+|+.|.++||.+.
T Consensus       134 ~~i~~~l~l~~l~~~~~~~v~~~sa~~g~Gv~e~l~WL~~~  174 (175)
T PF00025_consen  134 EEIKEYLGLEKLKNKRPWSVFSCSAKTGEGVDEGLEWLIEQ  174 (175)
T ss_dssp             HHHHHHTTGGGTTSSSCEEEEEEBTTTTBTHHHHHHHHHHH
T ss_pred             hHHHhhhhhhhcccCCceEEEeeeccCCcCHHHHHHHHHhc
Confidence            55555442  332  23578999999999999999999764

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 ....

>cd04133 Rop_like Rop subfamily

Probab=98.35  E-value=6.3e-07  Score=68.46  Aligned_cols=103  Identities=17%  Similarity=0.080  Sum_probs=66.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCch-----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAI-----  135 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~-----  135 (178)
                      .+.+-|++|.|..    +...+. ..++++++|+|.++......   .+...     -..+-++|.||+||.+..     
T Consensus        48 ~v~l~i~Dt~G~~~~~~~~~~~~-~~a~~~ilvyd~~~~~Sf~~~~~~w~~~i~~~~~~~piilvgnK~Dl~~~~~~~~~  126 (176)
T cd04133          48 TVNLGLWDTAGQEDYNRLRPLSY-RGADVFVLAFSLISRASYENVLKKWVPELRHYAPNVPIVLVGTKLDLRDDKQYLAD  126 (176)
T ss_pred             EEEEEEEECCCCccccccchhhc-CCCcEEEEEEEcCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEeChhhccChhhhhh
Confidence            4778899999931    122222 35799999999987543321   11111     134569999999996431     


Q ss_pred             -----hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          136 -----GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       136 -----~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                           ....++..++.++.+ ..++++|||++|+||+++|+.+.+.+
T Consensus       127 ~~~~~~v~~~~~~~~a~~~~-~~~~~E~SAk~~~nV~~~F~~~~~~~  172 (176)
T cd04133         127 HPGASPITTAQGEELRKQIG-AAAYIECSSKTQQNVKAVFDAAIKVV  172 (176)
T ss_pred             ccCCCCCCHHHHHHHHHHcC-CCEEEECCCCcccCHHHHHHHHHHHH
Confidence                 012334444544432 23699999999999999999887643

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,

>cd01875 RhoG RhoG subfamily

Probab=98.35  E-value=5.8e-07  Score=69.20  Aligned_cols=102  Identities=15%  Similarity=0.053  Sum_probs=64.2

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCC-----CCCceeEEEEecCCCCCchh----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGP-----GITQADLLVINKTDLASAIG----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~-----qi~~adiiviNK~Dl~~~~~----  136 (178)
                      .+.+-+++|+|..    +...+. ..+|++|+|+|.++......   .+..     .-..+-++|.||.||.+...    
T Consensus        50 ~~~l~i~Dt~G~e~~~~l~~~~~-~~a~~~ilvydit~~~Sf~~~~~~w~~~i~~~~~~~piilvgNK~DL~~~~~~~~~  128 (191)
T cd01875          50 TVSLNLWDTAGQEEYDRLRTLSY-PQTNVFIICFSIASPSSYENVRHKWHPEVCHHCPNVPILLVGTKKDLRNDADTLKK  128 (191)
T ss_pred             EEEEEEEECCCchhhhhhhhhhc-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEeChhhhcChhhHHH
Confidence            5778899999941    222233 35799999999987543211   0100     01346799999999965410    


Q ss_pred             --------HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 --------ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 --------~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                              ...++..++.++.+ ..+++++||++|+|++++|+.+.+.
T Consensus       129 ~~~~~~~~v~~~~~~~~a~~~~-~~~~~e~SAk~g~~v~e~f~~l~~~  175 (191)
T cd01875         129 LKEQGQAPITPQQGGALAKQIH-AVKYLECSALNQDGVKEVFAEAVRA  175 (191)
T ss_pred             HhhccCCCCCHHHHHHHHHHcC-CcEEEEeCCCCCCCHHHHHHHHHHH
Confidence                    01112233333332 2479999999999999999988754

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

>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed

Probab=98.34  E-value=1.1e-06  Score=76.41  Aligned_cols=95  Identities=21%  Similarity=0.159  Sum_probs=63.0

Q ss_pred             CCCEEEEeCCcchh----------hhcc-cccccceEEEEEeCCCCCCCCcC--CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----------AANF-SRELADYIIYIIDVSGGDKIPRK--GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----------~~~~-~~~~ad~~I~VvD~~~~~~~~~~--~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.++.|.|..-          ..+. ....+|.+++|+|++++......  +...-..+-++|+||+|+.++  ...
T Consensus       262 g~~i~l~DT~G~~~~~~~ie~~gi~~~~~~~~~aD~il~VvD~s~~~s~~~~~~l~~~~~~piiiV~NK~DL~~~--~~~  339 (449)
T PRK05291        262 GIPLRLIDTAGIRETDDEVEKIGIERSREAIEEADLVLLVLDASEPLTEEDDEILEELKDKPVIVVLNKADLTGE--IDL  339 (449)
T ss_pred             CeEEEEEeCCCCCCCccHHHHHHHHHHHHHHHhCCEEEEEecCCCCCChhHHHHHHhcCCCCcEEEEEhhhcccc--chh
Confidence            45689999999410          0011 12247999999999876432210  111123467999999999866  332


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .      .  .+..+++++||++|+|+++|++++.+.+
T Consensus       340 ~------~--~~~~~~i~iSAktg~GI~~L~~~L~~~l  369 (449)
T PRK05291        340 E------E--ENGKPVIRISAKTGEGIDELREAIKELA  369 (449)
T ss_pred             h------h--ccCCceEEEEeeCCCCHHHHHHHHHHHH
Confidence            2      1  2345899999999999999999987653

>COG0486 ThdF Predicted GTPase [General function prediction only]

Probab=98.34  E-value=1.3e-06  Score=75.16  Aligned_cols=98  Identities=18%  Similarity=0.157  Sum_probs=67.5

Q ss_pred             hCCCCEEEEeCCcchhhhcc-------------cccccceEEEEEeCCCCCCCCc-CCCC-C-CCceeEEEEecCCCCCc
Q 030407           71 LFKADLLLCESGGDNLAANF-------------SRELADYIIYIIDVSGGDKIPR-KGGP-G-ITQADLLVINKTDLASA  134 (178)
Q Consensus        71 ~~~~d~iiiEttG~~~~~~~-------------~~~~ad~~I~VvD~~~~~~~~~-~~~~-q-i~~adiiviNK~Dl~~~  134 (178)
                      -.++-+.++.|.|+  +.+-             ....+|.+++|+|++.+.+..+ .... . -....++|+||+||.++
T Consensus       262 i~G~pv~l~DTAGi--Ret~d~VE~iGIeRs~~~i~~ADlvL~v~D~~~~~~~~d~~~~~~~~~~~~~i~v~NK~DL~~~  339 (454)
T COG0486         262 LNGIPVRLVDTAGI--RETDDVVERIGIERAKKAIEEADLVLFVLDASQPLDKEDLALIELLPKKKPIIVVLNKADLVSK  339 (454)
T ss_pred             ECCEEEEEEecCCc--ccCccHHHHHHHHHHHHHHHhCCEEEEEEeCCCCCchhhHHHHHhcccCCCEEEEEechhcccc
Confidence            45778899999994  3221             1123799999999998633221 1111 1 12356999999999987


Q ss_pred             hhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          135 IGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       135 ~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                        .....+     +..+..+++.+||++|+|++.|.+.|.+..
T Consensus       340 --~~~~~~-----~~~~~~~~i~iSa~t~~Gl~~L~~~i~~~~  375 (454)
T COG0486         340 --IELESE-----KLANGDAIISISAKTGEGLDALREAIKQLF  375 (454)
T ss_pred             --cccchh-----hccCCCceEEEEecCccCHHHHHHHHHHHH
Confidence              443333     233455899999999999999999987754

>cd04131 Rnd Rnd subfamily

Probab=98.34  E-value=7.7e-07  Score=67.94  Aligned_cols=102  Identities=15%  Similarity=0.081  Sum_probs=64.5

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCch-----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAI-----  135 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~-----  135 (178)
                      .+.+-+++|.|..    +...+. ..+|++++|+|.++......   .+...     -..+-++|.||+||.+..     
T Consensus        48 ~~~l~iwDt~G~~~~~~~~~~~~-~~a~~~ilvfdit~~~Sf~~~~~~w~~~i~~~~~~~~iilVgnK~DL~~~~~~~~~  126 (178)
T cd04131          48 RIELSLWDTSGSPYYDNVRPLCY-PDSDAVLICFDISRPETLDSVLKKWRGEIQEFCPNTKVLLVGCKTDLRTDLSTLME  126 (178)
T ss_pred             EEEEEEEECCCchhhhhcchhhc-CCCCEEEEEEECCChhhHHHHHHHHHHHHHHHCCCCCEEEEEEChhhhcChhHHHH
Confidence            4778899999942    112222 35799999999987654321   11100     134579999999995410     


Q ss_pred             -------hHhHHHHHHHHHhcCCCCCEEEEecccCCC-HHHHHHHHhhh
Q 030407          136 -------GADLAVMERDALRMRDGGPFIFAQVGWVIG-IIFTLSITHYI  176 (178)
Q Consensus       136 -------~~~~~~~~~~l~~~np~a~i~~~SA~~g~g-i~el~~~l~~~  176 (178)
                             ....++..+..++.+ ..+++++||++|+| |+++|+.+.+.
T Consensus       127 ~~~~~~~~v~~~e~~~~a~~~~-~~~~~E~SA~~~~~~v~~~F~~~~~~  174 (178)
T cd04131         127 LSHQRQAPVSYEQGCAIAKQLG-AEIYLECSAFTSEKSVRDIFHVATMA  174 (178)
T ss_pred             HHhcCCCCCCHHHHHHHHHHhC-CCEEEECccCcCCcCHHHHHHHHHHH
Confidence                   012234444444432 23789999999995 99999987653

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.

>cd04177 RSR1 RSR1 subgroup

Probab=98.34  E-value=2.3e-06  Score=64.02  Aligned_cols=101  Identities=12%  Similarity=0.035  Sum_probs=62.8

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CC-------CCCCCceeEEEEecCCCCCchhHhHH
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KG-------GPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~-------~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ..+-+++|.|..    +...+. ..++..++|+|.++......  .+       ...-..+-++++||.|+.+......+
T Consensus        49 ~~~~i~Dt~G~~~~~~~~~~~~-~~~~~~vlv~~~~~~~s~~~~~~~~~~i~~~~~~~~~piiiv~nK~D~~~~~~~~~~  127 (168)
T cd04177          49 CDLEILDTAGTEQFTAMRELYI-KSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLEDDRQVSRE  127 (168)
T ss_pred             EEEEEEeCCCcccchhhhHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCCEEEEEEChhccccCccCHH
Confidence            567789999931    111121 24688999999876532110  00       01113456899999999754212223


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..++. ...+++++||++|+|++++|+++.+.
T Consensus       128 ~~~~~~~~~-~~~~~~~~SA~~~~~i~~~f~~i~~~  162 (168)
T cd04177         128 DGVSLSQQW-GNVPFYETSARKRTNVDEVFIDLVRQ  162 (168)
T ss_pred             HHHHHHHHc-CCceEEEeeCCCCCCHHHHHHHHHHH
Confidence            333443433 23689999999999999999988653

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

>cd04125 RabA_like RabA-like subfamily

Probab=98.33  E-value=1.6e-06  Score=66.15  Aligned_cols=100  Identities=14%  Similarity=0.161  Sum_probs=62.9

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+-+++|.|..-    ...+. ..+|++++|+|.++......         .+.. -..+-++++||+|+.+......
T Consensus        48 ~~~~~i~Dt~g~~~~~~~~~~~~-~~~d~iilv~d~~~~~s~~~i~~~~~~i~~~~~-~~~~~ivv~nK~Dl~~~~~v~~  125 (188)
T cd04125          48 IIKLQIWDTNGQERFRSLNNSYY-RGAHGYLLVYDVTDQESFENLKFWINEINRYAR-ENVIKVIVANKSDLVNNKVVDS  125 (188)
T ss_pred             EEEEEEEECCCcHHHHhhHHHHc-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCC-CCCeEEEEEECCCCcccccCCH
Confidence            46678899999321    11122 35799999999987543211         0100 1135699999999975411122


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +......+..  ..+++++||++|.|++++|+.|.+.
T Consensus       126 ~~~~~~~~~~--~~~~~evSa~~~~~i~~~f~~l~~~  160 (188)
T cd04125         126 NIAKSFCDSL--NIPFFETSAKQSINVEEAFILLVKL  160 (188)
T ss_pred             HHHHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            2333333332  3489999999999999999987654

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.

>cd04118 Rab24 Rab24 subfamily

Probab=98.33  E-value=1.4e-06  Score=66.59  Aligned_cols=100  Identities=12%  Similarity=-0.037  Sum_probs=61.7

Q ss_pred             CCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCCC---C--CCceeEEEEecCCCCCchh----Hh
Q 030407           74 ADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGGP---G--ITQADLLVINKTDLASAIG----AD  138 (178)
Q Consensus        74 ~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~---q--i~~adiiviNK~Dl~~~~~----~~  138 (178)
                      ..+-++++.|..-    ...+. ..+|.+++|+|.++......  .+..   +  -..+-++|+||+|+.+...    ..
T Consensus        50 ~~l~i~D~~G~~~~~~~~~~~~-~~~d~iilv~d~~~~~s~~~~~~~~~~i~~~~~~~piilv~nK~Dl~~~~~~~~~v~  128 (193)
T cd04118          50 VTLGIWDTAGSERYEAMSRIYY-RGAKAAIVCYDLTDSSSFERAKFWVKELQNLEEHCKIYLCGTKSDLIEQDRSLRQVD  128 (193)
T ss_pred             EEEEEEECCCchhhhhhhHhhc-CCCCEEEEEEECCCHHHHHHHHHHHHHHHhcCCCCCEEEEEEcccccccccccCccC
Confidence            4456789999311    11122 25799999999976532211  0000   1  1346799999999975310    01


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+.+..+..  ..+++++||++|+|++++++.+.+.
T Consensus       129 ~~~~~~~~~~~--~~~~~~~Sa~~~~gv~~l~~~i~~~  164 (193)
T cd04118         129 FHDVQDFADEI--KAQHFETSSKTGQNVDELFQKVAED  164 (193)
T ss_pred             HHHHHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            12233333333  4689999999999999999988754

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

>PLN03071 GTP-binding nuclear protein Ran; Provisional

Probab=98.32  E-value=9.6e-07  Score=69.62  Aligned_cols=99  Identities=10%  Similarity=-0.012  Sum_probs=63.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC-----CCCCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG-----PGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~-----~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      ...+-+++|.|..    +...+. ..++++|+|+|.++......  .+.     ..-..+-++|.||+|+.... ...+.
T Consensus        61 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~~~~ilvfD~~~~~s~~~i~~w~~~i~~~~~~~piilvgNK~Dl~~~~-v~~~~  138 (219)
T PLN03071         61 KIRFYCWDTAGQEKFGGLRDGYY-IHGQCAIIMFDVTARLTYKNVPTWHRDLCRVCENIPIVLCGNKVDVKNRQ-VKAKQ  138 (219)
T ss_pred             EEEEEEEECCCchhhhhhhHHHc-ccccEEEEEEeCCCHHHHHHHHHHHHHHHHhCCCCcEEEEEEchhhhhcc-CCHHH
Confidence            4678899999941    122222 25789999999987643211  000     01135679999999996431 11122


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      + +..+.  ...+++++||++|.|++++|++|.+.
T Consensus       139 ~-~~~~~--~~~~~~e~SAk~~~~i~~~f~~l~~~  170 (219)
T PLN03071        139 V-TFHRK--KNLQYYEISAKSNYNFEKPFLYLARK  170 (219)
T ss_pred             H-HHHHh--cCCEEEEcCCCCCCCHHHHHHHHHHH
Confidence            2 23332  24589999999999999999987653

>cd04159 Arl10_like Arl10-like subfamily

Probab=98.32  E-value=2.7e-06  Score=61.83  Aligned_cols=100  Identities=14%  Similarity=0.091  Sum_probs=62.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+-++++.|..-    ...+ ...+|.+++|+|++.......         ........+-++|+||+|+.+.  ...
T Consensus        43 ~~~~~~~D~~g~~~~~~~~~~~-~~~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~p~iiv~nK~D~~~~--~~~  119 (159)
T cd04159          43 NVTLKVWDLGGQPRFRSMWERY-CRGVNAIVYVVDAADRTALEAAKNELHDLLEKPSLEGIPLLVLGNKNDLPGA--LSV  119 (159)
T ss_pred             CEEEEEEECCCCHhHHHHHHHH-HhcCCEEEEEEECCCHHHHHHHHHHHHHHHcChhhcCCCEEEEEeCccccCC--cCH
Confidence            35677888999311    1111 124689999999976432110         0001123456899999999766  443


Q ss_pred             HHHHHHHH--hc-CCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDAL--RM-RDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~--~~-np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +.+...+.  .. ....+++++||++|.|++++++++.+
T Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~  158 (159)
T cd04159         120 DELIEQMNLKSITDREVSCYSISCKEKTNIDIVLDWLIK  158 (159)
T ss_pred             HHHHHHhCcccccCCceEEEEEEeccCCChHHHHHHHhh
Confidence            33333332  11 12357899999999999999999865

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.

>TIGR00487 IF-2 translation initiation factor IF-2

Probab=98.32  E-value=2.6e-06  Score=76.37  Aligned_cols=98  Identities=12%  Similarity=0.119  Sum_probs=61.9

Q ss_pred             CEEEEeCCcch-hhhcc--cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHHHH
Q 030407           75 DLLLCESGGDN-LAANF--SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERDAL  147 (178)
Q Consensus        75 d~iiiEttG~~-~~~~~--~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~  147 (178)
                      .+.|+.|.|-. .....  ....+|.+++|+|+.++...+..    +......+-++++||+|+.+.   ..+++.+.++
T Consensus       136 ~i~~iDTPGhe~F~~~r~rga~~aDiaILVVda~dgv~~qT~e~i~~~~~~~vPiIVviNKiDl~~~---~~e~v~~~L~  212 (587)
T TIGR00487       136 MITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVPIIVAINKIDKPEA---NPDRVKQELS  212 (587)
T ss_pred             EEEEEECCCCcchhhHHHhhhccCCEEEEEEECCCCCCHhHHHHHHHHHHcCCCEEEEEECcccccC---CHHHHHHHHH
Confidence            67899999921 11110  11246999999999876432211    111234567999999999654   2233334433


Q ss_pred             hc-------CCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          148 RM-------RDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       148 ~~-------np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ..       ....+++++||++|+|++++++++..
T Consensus       213 ~~g~~~~~~~~~~~~v~iSAktGeGI~eLl~~I~~  247 (587)
T TIGR00487       213 EYGLVPEDWGGDTIFVPVSALTGDGIDELLDMILL  247 (587)
T ss_pred             HhhhhHHhcCCCceEEEEECCCCCChHHHHHhhhh
Confidence            22       12357999999999999999998753

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.

>cd01884 EF_Tu EF-Tu subfamily

Probab=98.32  E-value=3.4e-06  Score=65.55  Aligned_cols=102  Identities=11%  Similarity=0.092  Sum_probs=61.6

Q ss_pred             CCCEEEEeCCcch--hhhcc-cccccceEEEEEeCCCCCCCCcC----CCCCCCce-eEEEEecCCCCCchhHhHH----
Q 030407           73 KADLLLCESGGDN--LAANF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQA-DLLVINKTDLASAIGADLA----  140 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~a-diiviNK~Dl~~~~~~~~~----  140 (178)
                      +..+.||.|.|..  +.... ....+|.+++|+|+..+...+..    .......+ -++++||+|+.+.. +..+    
T Consensus        64 ~~~i~~iDtPG~~~~~~~~~~~~~~~D~~ilVvda~~g~~~~~~~~~~~~~~~~~~~iIvviNK~D~~~~~-~~~~~~~~  142 (195)
T cd01884          64 NRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPYIVVFLNKADMVDDE-ELLELVEM  142 (195)
T ss_pred             CeEEEEEECcCHHHHHHHHHHHhhhCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCcEEEEEeCCCCCCcH-HHHHHHHH
Confidence            5678999999931  11111 11246999999999876433211    11112333 46889999997541 2222    


Q ss_pred             HHHHHHHhc--C-CCCCEEEEecccCCCH----------HHHHHHHhh
Q 030407          141 VMERDALRM--R-DGGPFIFAQVGWVIGI----------IFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~--n-p~a~i~~~SA~~g~gi----------~el~~~l~~  175 (178)
                      ++.+.++..  + ..++++++||++|.++          ..|++.|..
T Consensus       143 ~i~~~l~~~g~~~~~v~iipiSa~~g~n~~~~~~w~~~~~~l~~~l~~  190 (195)
T cd01884         143 EVRELLSKYGFDGDNTPIVRGSALKALEGDDPNKWVKKILELLDALDS  190 (195)
T ss_pred             HHHHHHHHhcccccCCeEEEeeCccccCCCCCCcchhcHhHHHHHHHh
Confidence            344444433  2 2479999999999974          566666654

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.

>cd00876 Ras Ras family

Probab=98.31  E-value=2.7e-06  Score=62.31  Aligned_cols=101  Identities=16%  Similarity=0.062  Sum_probs=65.2

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.++++.|...    ...+ ...+|.+++|+|..+......  .       .......+-++++||+|+........
T Consensus        46 ~~~~~l~D~~g~~~~~~~~~~~-~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~~~~~~~  124 (160)
T cd00876          46 TYTLDILDTAGQEEFSAMRDLY-IRQGDGFILVYSITDRESFEEIKGYREQILRVKDDEDIPIVLVGNKCDLENERQVSK  124 (160)
T ss_pred             EEEEEEEECCChHHHHHHHHHH-HhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECCcccccceecH
Confidence            35677899999321    1111 224689999999876532111  0       00112456799999999986311233


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+..+  .+++++||++|.|+++++++|.+.
T Consensus       125 ~~~~~~~~~~~--~~~~~~S~~~~~~i~~l~~~l~~~  159 (160)
T cd00876         125 EEGKALAKEWG--CPFIETSAKDNINIDEVFKLLVRE  159 (160)
T ss_pred             HHHHHHHHHcC--CcEEEeccCCCCCHHHHHHHHHhh
Confidence            44555555443  689999999999999999988653

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

>cd00157 Rho Rho (Ras homology) family

Probab=98.31  E-value=7.2e-07  Score=66.41  Aligned_cols=102  Identities=14%  Similarity=0.006  Sum_probs=63.7

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCcC---CC-----CCCCceeEEEEecCCCCCchhH----
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPRK---GG-----PGITQADLLVINKTDLASAIGA----  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~~---~~-----~qi~~adiiviNK~Dl~~~~~~----  137 (178)
                      .+.+.++++.|..--   .......+|++++++|+++.......   +.     .....+-++|+||+|+.++...    
T Consensus        47 ~~~l~~~D~~g~~~~~~~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~p~ivv~nK~Dl~~~~~~~~~~  126 (171)
T cd00157          47 QVNLGLWDTAGQEEYDRLRPLSYPNTDVFLICFSVDSPSSFENVKTKWIPEIRHYCPNVPIILVGTKIDLRDDENTLKKL  126 (171)
T ss_pred             EEEEEEEeCCCcccccccchhhcCCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEccHHhhhchhhhhhc
Confidence            456889999993211   11111247999999999764322110   00     0113567999999999866211    


Q ss_pred             -------hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          138 -------DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       138 -------~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                             ..+...+..... ...+++++||++|+|++++++.+.+
T Consensus       127 ~~~~~~v~~~~~~~~~~~~-~~~~~~~~Sa~~~~gi~~l~~~i~~  170 (171)
T cd00157         127 EKGKEPITPEEGEKLAKEI-GAIGYMECSALTQEGVKEVFEEAIR  170 (171)
T ss_pred             ccCCCccCHHHHHHHHHHh-CCeEEEEeecCCCCCHHHHHHHHhh
Confidence                   122333333333 2348999999999999999998764

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

>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]

Probab=98.30  E-value=6.1e-06  Score=59.58  Aligned_cols=99  Identities=18%  Similarity=0.134  Sum_probs=71.5

Q ss_pred             CEEEEeCCcchhhhc--ccc-----cccceEEEEEeCCCCCCC-CcCCCCCCCceeEEEEecCCCCCchhHhHHHHHHHH
Q 030407           75 DLLLCESGGDNLAAN--FSR-----ELADYIIYIIDVSGGDKI-PRKGGPGITQADLLVINKTDLASAIGADLAVMERDA  146 (178)
Q Consensus        75 d~iiiEttG~~~~~~--~~~-----~~ad~~I~VvD~~~~~~~-~~~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l  146 (178)
                      |.-.|.|.|--+..+  |..     ..+|.++.|-.+.++... +..+........|-|++|+||++.  ++++..++++
T Consensus        38 d~~~IDTPGEy~~~~~~Y~aL~tt~~dadvi~~v~~and~~s~f~p~f~~~~~k~vIgvVTK~DLaed--~dI~~~~~~L  115 (148)
T COG4917          38 DKGDIDTPGEYFEHPRWYHALITTLQDADVIIYVHAANDPESRFPPGFLDIGVKKVIGVVTKADLAED--ADISLVKRWL  115 (148)
T ss_pred             CccccCCchhhhhhhHHHHHHHHHhhccceeeeeecccCccccCCcccccccccceEEEEecccccch--HhHHHHHHHH
Confidence            667788999422211  111     135778888877665432 222333344558999999999987  8999999999


Q ss_pred             HhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          147 LRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       147 ~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ++.. .-+||.+|+.+..|+++|+++|...
T Consensus       116 ~eaG-a~~IF~~s~~d~~gv~~l~~~L~~~  144 (148)
T COG4917         116 REAG-AEPIFETSAVDNQGVEELVDYLASL  144 (148)
T ss_pred             HHcC-CcceEEEeccCcccHHHHHHHHHhh
Confidence            9875 5699999999999999999998753

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

Probab=98.30  E-value=3e-06  Score=65.22  Aligned_cols=96  Identities=14%  Similarity=0.128  Sum_probs=58.3

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc-C---CCCCCCceeEEEEecCCCCCchh-HhHHHHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR-K---GGPGITQADLLVINKTDLASAIG-ADLAVME  143 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~-~---~~~qi~~adiiviNK~Dl~~~~~-~~~~~~~  143 (178)
                      +..+.+++|.|..    ....+. ..+|.+++|+|++++..... .   ...+...+-++++||+|+.+... ...+.+.
T Consensus        64 ~~~~~l~DtpG~~~~~~~~~~~~-~~~d~~ilV~d~~~~~~~~~~~~~~~~~~~~~p~iiv~NK~Dl~~~~~~~~~~~~~  142 (194)
T cd01891          64 DTKINIVDTPGHADFGGEVERVL-SMVDGVLLLVDASEGPMPQTRFVLKKALELGLKPIVVINKIDRPDARPEEVVDEVF  142 (194)
T ss_pred             CEEEEEEECCCcHHHHHHHHHHH-HhcCEEEEEEECCCCccHHHHHHHHHHHHcCCCEEEEEECCCCCCCCHHHHHHHHH
Confidence            5678899999941    111122 25799999999987532111 0   00113456799999999975421 1234444


Q ss_pred             HHHHhc-----CCCCCEEEEecccCCCHHHH
Q 030407          144 RDALRM-----RDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       144 ~~l~~~-----np~a~i~~~SA~~g~gi~el  169 (178)
                      +.++..     ....+++++||++|.|+.++
T Consensus       143 ~~~~~~~~~~~~~~~~iv~~Sa~~g~~~~~~  173 (194)
T cd01891         143 DLFIELGATEEQLDFPVLYASAKNGWASLNL  173 (194)
T ss_pred             HHHHHhCCccccCccCEEEeehhcccccccc
Confidence            444322     12468999999999777544

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

>TIGR03596 GTPase_YlqF ribosome biogenesis GTP-binding protein YlqF

Probab=98.29  E-value=2.9e-06  Score=69.33  Aligned_cols=79  Identities=18%  Similarity=0.078  Sum_probs=53.8

Q ss_pred             ccceEEEEEeCCCCCCCCcC-CCCCC-CceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHH
Q 030407           94 LADYIIYIIDVSGGDKIPRK-GGPGI-TQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLS  171 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~-~~~qi-~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~  171 (178)
                      .+|.++.|+|+..+...... ....+ ..+-++|+||+|++++  ...+...+.+++  ...+++.+||++|.|+++|.+
T Consensus        21 ~aDvVl~V~Dar~p~~~~~~~i~~~l~~kp~IiVlNK~DL~~~--~~~~~~~~~~~~--~~~~vi~iSa~~~~gi~~L~~   96 (276)
T TIGR03596        21 LVDVVIEVLDARIPLSSRNPMIDEIRGNKPRLIVLNKADLADP--AVTKQWLKYFEE--KGIKALAINAKKGKGVKKIIK   96 (276)
T ss_pred             hCCEEEEEEeCCCCCCCCChhHHHHHCCCCEEEEEEccccCCH--HHHHHHHHHHHH--cCCeEEEEECCCcccHHHHHH
Confidence            46999999999765432211 11111 3457999999999866  444444444443  235789999999999999998


Q ss_pred             HHhhh
Q 030407          172 ITHYI  176 (178)
Q Consensus       172 ~l~~~  176 (178)
                      .+.+.
T Consensus        97 ~i~~~  101 (276)
T TIGR03596        97 AAKKL  101 (276)
T ss_pred             HHHHH
Confidence            87654

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.

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

Probab=98.28  E-value=3.1e-06  Score=72.87  Aligned_cols=101  Identities=17%  Similarity=0.106  Sum_probs=63.5

Q ss_pred             CCEEEEeCCcch-hhhcccc--cccceEEEEEeCCCCC-CCCc-C---CCCCCCc-eeEEEEecCCCCCchhHhH----H
Q 030407           74 ADLLLCESGGDN-LAANFSR--ELADYIIYIIDVSGGD-KIPR-K---GGPGITQ-ADLLVINKTDLASAIGADL----A  140 (178)
Q Consensus        74 ~d~iiiEttG~~-~~~~~~~--~~ad~~I~VvD~~~~~-~~~~-~---~~~qi~~-adiiviNK~Dl~~~~~~~~----~  140 (178)
                      ..+.|+.|.|-. +...+..  ..+|.+++|+|++++. .... .   ....... .-++|+||+|+.++  .+.    +
T Consensus        85 ~~i~liDtPG~~~f~~~~~~~~~~~D~~llVVDa~~~~~~~~t~~~l~~l~~~~i~~iiVVlNK~Dl~~~--~~~~~~~~  162 (411)
T PRK04000         85 RRVSFVDAPGHETLMATMLSGAALMDGAILVIAANEPCPQPQTKEHLMALDIIGIKNIVIVQNKIDLVSK--ERALENYE  162 (411)
T ss_pred             cEEEEEECCCHHHHHHHHHHHHhhCCEEEEEEECCCCCCChhHHHHHHHHHHcCCCcEEEEEEeeccccc--hhHHHHHH
Confidence            567899999931 1122211  2359999999998764 2211 0   0011222 34888999999875  333    2


Q ss_pred             HHHHHHHhc-CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRM-RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~-np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+.++.. ....+++++||++|+|+++|++.|...
T Consensus       163 ~i~~~l~~~~~~~~~ii~vSA~~g~gI~~L~~~L~~~  199 (411)
T PRK04000        163 QIKEFVKGTVAENAPIIPVSALHKVNIDALIEAIEEE  199 (411)
T ss_pred             HHHHHhccccCCCCeEEEEECCCCcCHHHHHHHHHHh
Confidence            333333321 234689999999999999999998763

>PLN03110 Rab GTPase; Provisional

Probab=98.28  E-value=2e-06  Score=67.52  Aligned_cols=101  Identities=10%  Similarity=0.038  Sum_probs=62.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+-|++|+|..    +...+. ..++++++|+|.++......  .+.      ..-..+-++|.||+|+........+
T Consensus        60 ~~~l~l~Dt~G~~~~~~~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~piiiv~nK~Dl~~~~~~~~~  138 (216)
T PLN03110         60 TVKAQIWDTAGQERYRAITSAYY-RGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIMMAGNKSDLNHLRSVAEE  138 (216)
T ss_pred             EEEEEEEECCCcHHHHHHHHHHh-CCCCEEEEEEECCChHHHHHHHHHHHHHHHhCCCCCeEEEEEEChhcccccCCCHH
Confidence            4578888999931    112222 35799999999976532211  000      0113467999999999654111112


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ....... . ...+++++||++|+|++++|+.+...
T Consensus       139 ~~~~l~~-~-~~~~~~e~SA~~g~~v~~lf~~l~~~  172 (216)
T PLN03110        139 DGQALAE-K-EGLSFLETSALEATNVEKAFQTILLE  172 (216)
T ss_pred             HHHHHHH-H-cCCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            2222222 2 35789999999999999999987543

>COG2262 HflX GTPases [General function prediction only]

Probab=98.27  E-value=2.5e-06  Score=72.40  Aligned_cols=98  Identities=18%  Similarity=0.176  Sum_probs=64.3

Q ss_pred             CCCEEEEeCCcc------hhhhcccc-----cccceEEEEEeCCCCCCCCc-----C-C--CCCCCceeEEEEecCCCCC
Q 030407           73 KADLLLCESGGD------NLAANFSR-----ELADYIIYIIDVSGGDKIPR-----K-G--GPGITQADLLVINKTDLAS  133 (178)
Q Consensus        73 ~~d~iiiEttG~------~~~~~~~~-----~~ad~~I~VvD~~~~~~~~~-----~-~--~~qi~~adiiviNK~Dl~~  133 (178)
                      +..+++-+|+|-      -+.+.|..     ..+|.++.|||++++.....     . .  ...-..+-++|.||+|+++
T Consensus       239 g~~vlLtDTVGFI~~LP~~LV~AFksTLEE~~~aDlllhVVDaSdp~~~~~~~~v~~vL~el~~~~~p~i~v~NKiD~~~  318 (411)
T COG2262         239 GRKVLLTDTVGFIRDLPHPLVEAFKSTLEEVKEADLLLHVVDASDPEILEKLEAVEDVLAEIGADEIPIILVLNKIDLLE  318 (411)
T ss_pred             CceEEEecCccCcccCChHHHHHHHHHHHHhhcCCEEEEEeecCChhHHHHHHHHHHHHHHcCCCCCCEEEEEecccccC
Confidence            467999999993      12222221     13699999999998732110     0 0  0112346799999999987


Q ss_pred             chhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          134 AIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       134 ~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +  ..   ....+....|  ..+.+||++|+|++.|.+.|....
T Consensus       319 ~--~~---~~~~~~~~~~--~~v~iSA~~~~gl~~L~~~i~~~l  355 (411)
T COG2262         319 D--EE---ILAELERGSP--NPVFISAKTGEGLDLLRERIIELL  355 (411)
T ss_pred             c--hh---hhhhhhhcCC--CeEEEEeccCcCHHHHHHHHHHHh
Confidence            7  43   2223333333  689999999999999999876543

>PRK12289 GTPase RsgA; Reviewed

Probab=98.26  E-value=1.8e-06  Score=72.91  Aligned_cols=77  Identities=21%  Similarity=0.173  Sum_probs=53.6

Q ss_pred             cceEEEEEeCCCCCCCC---cCCC---CCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHH
Q 030407           95 ADYIIYIIDVSGGDKIP---RKGG---PGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~---~~~~---~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                      +|.+++|+|+.++....   ..+.   ......-++|+||+||+++  .+.+...+.++.+  +.+++++||++|+|+++
T Consensus        90 vD~vLlV~d~~~p~~~~~~LdR~L~~a~~~~ip~ILVlNK~DLv~~--~~~~~~~~~~~~~--g~~v~~iSA~tg~GI~e  165 (352)
T PRK12289         90 ADQILLVFALAEPPLDPWQLSRFLVKAESTGLEIVLCLNKADLVSP--TEQQQWQDRLQQW--GYQPLFISVETGIGLEA  165 (352)
T ss_pred             CCEEEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEEEchhcCCh--HHHHHHHHHHHhc--CCeEEEEEcCCCCCHHH
Confidence            58999999997643211   1111   1123456999999999876  5555555555543  45899999999999999


Q ss_pred             HHHHHhh
Q 030407          169 TLSITHY  175 (178)
Q Consensus       169 l~~~l~~  175 (178)
                      |++.+..
T Consensus       166 L~~~L~~  172 (352)
T PRK12289        166 LLEQLRN  172 (352)
T ss_pred             Hhhhhcc
Confidence            9998753

>TIGR01393 lepA GTP-binding protein LepA

Probab=98.26  E-value=3.2e-06  Score=75.96  Aligned_cols=100  Identities=20%  Similarity=0.095  Sum_probs=62.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcC--CC--CCCCceeEEEEecCCCCCchhHhHHHHHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRK--GG--PGITQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~--~~--~qi~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      .+.+.|+.|.|..    ....+ ...+|++++|+|++++...+..  +.  .....+-++|+||+|+.+.  . .+...+
T Consensus        69 ~~~l~liDTPG~~dF~~~v~~~-l~~aD~aILVvDat~g~~~qt~~~~~~~~~~~ipiIiViNKiDl~~~--~-~~~~~~  144 (595)
T TIGR01393        69 TYVLNLIDTPGHVDFSYEVSRS-LAACEGALLLVDAAQGIEAQTLANVYLALENDLEIIPVINKIDLPSA--D-PERVKK  144 (595)
T ss_pred             EEEEEEEECCCcHHHHHHHHHH-HHhCCEEEEEecCCCCCCHhHHHHHHHHHHcCCCEEEEEECcCCCcc--C-HHHHHH
Confidence            3668899999931    11111 1246999999999886543221  00  0123356999999999754  1 122222


Q ss_pred             HHHhcC--CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          145 DALRMR--DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       145 ~l~~~n--p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+++..  +..+++++||++|.|++++++.|.+.
T Consensus       145 el~~~lg~~~~~vi~vSAktG~GI~~Lle~I~~~  178 (595)
T TIGR01393       145 EIEEVIGLDASEAILASAKTGIGIEEILEAIVKR  178 (595)
T ss_pred             HHHHHhCCCcceEEEeeccCCCCHHHHHHHHHHh
Confidence            333222  22368999999999999999988654

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.

>PRK12297 obgE GTPase CgtA; Reviewed

Probab=98.26  E-value=5.7e-06  Score=71.52  Aligned_cols=99  Identities=20%  Similarity=0.209  Sum_probs=62.4

Q ss_pred             CCCEEEEeCCcch--------hhhcccc--cccceEEEEEeCCCCC--CCC----------cCCCC-CCCceeEEEEecC
Q 030407           73 KADLLLCESGGDN--------LAANFSR--ELADYIIYIIDVSGGD--KIP----------RKGGP-GITQADLLVINKT  129 (178)
Q Consensus        73 ~~d~iiiEttG~~--------~~~~~~~--~~ad~~I~VvD~~~~~--~~~----------~~~~~-qi~~adiiviNK~  129 (178)
                      +..++|+.+.|..        +...|..  ..++.+++|+|++..+  +..          ..+.+ ....+-+||+||+
T Consensus       205 ~~~~~laD~PGliega~~~~gLg~~fLrhier~~llI~VID~s~~~~~dp~e~~~~i~~EL~~y~~~L~~kP~IVV~NK~  284 (424)
T PRK12297        205 GRSFVMADIPGLIEGASEGVGLGHQFLRHIERTRVIVHVIDMSGSEGRDPIEDYEKINKELKLYNPRLLERPQIVVANKM  284 (424)
T ss_pred             CceEEEEECCCCcccccccchHHHHHHHHHhhCCEEEEEEeCCccccCChHHHHHHHHHHHhhhchhccCCcEEEEEeCC
Confidence            3568899999941        1112221  2368999999997531  110          01212 2356789999999


Q ss_pred             CCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          130 DLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       130 Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      |+...  .  +.+.+..+.+.  .+++++||++|+|+++|++++.+.+
T Consensus       285 DL~~~--~--e~l~~l~~~l~--~~i~~iSA~tgeGI~eL~~~L~~~l  326 (424)
T PRK12297        285 DLPEA--E--ENLEEFKEKLG--PKVFPISALTGQGLDELLYAVAELL  326 (424)
T ss_pred             CCcCC--H--HHHHHHHHHhC--CcEEEEeCCCCCCHHHHHHHHHHHH
Confidence            98543  2  22222223322  5899999999999999999887543

>PRK14845 translation initiation factor IF-2; Provisional

Probab=98.24  E-value=4.9e-06  Score=78.62  Aligned_cols=101  Identities=19%  Similarity=0.155  Sum_probs=61.6

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchh---------
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIG---------  136 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~---------  136 (178)
                      |.+.|+.|.|..    +... ....+|.+++|+|++++...+..    .......+-++++||+|+.+...         
T Consensus       526 p~i~fiDTPGhe~F~~lr~~-g~~~aDivlLVVDa~~Gi~~qT~e~I~~lk~~~iPiIVViNKiDL~~~~~~~~~~~~~~  604 (1049)
T PRK14845        526 PGLLFIDTPGHEAFTSLRKR-GGSLADLAVLVVDINEGFKPQTIEAINILRQYKTPFVVAANKIDLIPGWNISEDEPFLL  604 (1049)
T ss_pred             CcEEEEECCCcHHHHHHHHh-hcccCCEEEEEEECcccCCHhHHHHHHHHHHcCCCEEEEEECCCCccccccccchhhhh
Confidence            558999999931    1111 11247999999999876432211    00112346799999999974200         


Q ss_pred             -------HhHHHHHHH-------HH-------------hcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          137 -------ADLAVMERD-------AL-------------RMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       137 -------~~~~~~~~~-------l~-------------~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                             ...+++...       +.             +.....+++++||+||+||++|+++|..
T Consensus       605 ~~~~q~~~~~~el~~~l~~v~~~L~~~G~~~e~~~~~~d~~~~v~iVpVSA~tGeGId~Ll~~l~~  670 (1049)
T PRK14845        605 NFNEQDQHALTELEIKLYELIGKLYELGFDADRFDRVQDFTRTVAIVPVSAKTGEGIPELLMMVAG  670 (1049)
T ss_pred             hhhhhHHHHHHHHHHHHHHHhhHHHhcCcchhhhhhhhhcCCCceEEEEEcCCCCCHHHHHHHHHH
Confidence                   001112111       11             1123569999999999999999988754

>cd04162 Arl9_Arfrp2_like Arl9/Arfrp2-like subfamily

Probab=98.23  E-value=2.4e-06  Score=64.02  Aligned_cols=101  Identities=15%  Similarity=0.127  Sum_probs=63.1

Q ss_pred             CCCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc------CC-CCCCCceeEEEEecCCCCCchhHhHH
Q 030407           72 FKADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR------KG-GPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        72 ~~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~------~~-~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+..+-++++.|..    +...+. ..+|++++|+|+++......      .. ...-..+-++|+||+|+..+  ...+
T Consensus        42 ~~~~l~i~Dt~G~~~~~~~~~~~~-~~ad~ii~V~D~t~~~s~~~~~~~l~~~~~~~~~~piilv~NK~Dl~~~--~~~~  118 (164)
T cd04162          42 QDAIMELLEIGGSQNLRKYWKRYL-SGSQGLIFVVDSADSERLPLARQELHQLLQHPPDLPLVVLANKQDLPAA--RSVQ  118 (164)
T ss_pred             CCeEEEEEECCCCcchhHHHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHhCCCCCcEEEEEeCcCCcCC--CCHH
Confidence            35778899999942    112222 35799999999987532110      01 00123457999999999765  3333


Q ss_pred             HHHHHH--Hhc--CCCCCEEEEeccc------CCCHHHHHHHHhh
Q 030407          141 VMERDA--LRM--RDGGPFIFAQVGW------VIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l--~~~--np~a~i~~~SA~~------g~gi~el~~~l~~  175 (178)
                      .+.+.+  .++  ....+++++||++      ++|++++|+.+-.
T Consensus       119 ~i~~~~~~~~~~~~~~~~~~~~Sa~~~~s~~~~~~v~~~~~~~~~  163 (164)
T cd04162         119 EIHKELELEPIARGRRWILQGTSLDDDGSPSRMEAVKDLLSQLIN  163 (164)
T ss_pred             HHHHHhCChhhcCCCceEEEEeeecCCCChhHHHHHHHHHHHHhc
Confidence            333222  112  1235789999999      9999999998753

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.

>cd04115 Rab33B_Rab33A Rab33B/Rab33A subfamily

Probab=98.23  E-value=6.2e-06  Score=61.88  Aligned_cols=102  Identities=14%  Similarity=0.086  Sum_probs=63.1

Q ss_pred             CCCEEEEeCCcch-hhhc---ccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN-LAAN---FSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~---~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ...+-+++|.|.. ....   .....+|++++|+|+++......  .       ....-..+-++|+||+|+........
T Consensus        50 ~~~~~i~Dt~G~~~~~~~~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~~~~~~  129 (170)
T cd04115          50 RIKVQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQIQVPT  129 (170)
T ss_pred             EEEEEEEeCCChHHHHHhhHHHhhcCCCEEEEEEECCCHHHHHhHHHHHHHHHHhcCCCCCCEEEEEECccchhhcCCCH
Confidence            4678899999932 1111   11224699999999987543211  0       11112356799999999865411112


Q ss_pred             HHHHHHHHhcCCCCCEEEEeccc---CCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGW---VIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~---g~gi~el~~~l~~~  176 (178)
                      +...+..+..  ..+++++||++   +.+++++|..+.+.
T Consensus       130 ~~~~~~~~~~--~~~~~e~Sa~~~~~~~~i~~~f~~l~~~  167 (170)
T cd04115         130 DLAQRFADAH--SMPLFETSAKDPSENDHVEAIFMTLAHK  167 (170)
T ss_pred             HHHHHHHHHc--CCcEEEEeccCCcCCCCHHHHHHHHHHH
Confidence            2233333332  36899999999   99999999877653

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

>TIGR03680 eif2g_arch translation initiation factor 2 subunit gamma

Probab=98.22  E-value=4.2e-06  Score=71.96  Aligned_cols=102  Identities=17%  Similarity=0.093  Sum_probs=63.7

Q ss_pred             CCCEEEEeCCcch-hh-hccc-ccccceEEEEEeCCCCC-CCCc-CCC---CCCCc-eeEEEEecCCCCCchhHhH----
Q 030407           73 KADLLLCESGGDN-LA-ANFS-RELADYIIYIIDVSGGD-KIPR-KGG---PGITQ-ADLLVINKTDLASAIGADL----  139 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~~~-~~~ad~~I~VvD~~~~~-~~~~-~~~---~qi~~-adiiviNK~Dl~~~~~~~~----  139 (178)
                      ...+.|+.|.|-. .. .++. ...+|.+++|+|++++. ..+. .+.   ..+.. .-++++||+|+.++  +..    
T Consensus        79 ~~~i~liDtPGh~~f~~~~~~g~~~aD~aIlVVDa~~g~~~~qt~e~l~~l~~~gi~~iIVvvNK~Dl~~~--~~~~~~~  156 (406)
T TIGR03680        79 LRRVSFVDAPGHETLMATMLSGAALMDGALLVIAANEPCPQPQTKEHLMALEIIGIKNIVIVQNKIDLVSK--EKALENY  156 (406)
T ss_pred             ccEEEEEECCCHHHHHHHHHHHHHHCCEEEEEEECCCCccccchHHHHHHHHHcCCCeEEEEEEccccCCH--HHHHHHH
Confidence            3568899999931 11 1111 12369999999998764 2111 100   11222 24888999999876  333    


Q ss_pred             HHHHHHHHhc-CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRM-RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~-np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +++.+.++.. ....+++++||++|+|+++|+++|...
T Consensus       157 ~~i~~~l~~~~~~~~~ii~vSA~~g~gi~~L~e~L~~~  194 (406)
T TIGR03680       157 EEIKEFVKGTVAENAPIIPVSALHNANIDALLEAIEKF  194 (406)
T ss_pred             HHHHhhhhhcccCCCeEEEEECCCCCChHHHHHHHHHh
Confidence            3333333322 124689999999999999999998763

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

>PRK05433 GTP-binding protein LepA; Provisional

Probab=98.22  E-value=4.6e-06  Score=75.04  Aligned_cols=100  Identities=18%  Similarity=0.122  Sum_probs=63.1

Q ss_pred             CCCEEEEeCCcch-h---hhcccccccceEEEEEeCCCCCCCCcC--C--CCCCCceeEEEEecCCCCCchhHhHHHHHH
Q 030407           73 KADLLLCESGGDN-L---AANFSRELADYIIYIIDVSGGDKIPRK--G--GPGITQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        73 ~~d~iiiEttG~~-~---~~~~~~~~ad~~I~VvD~~~~~~~~~~--~--~~qi~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      ++.+-|+.|.|.. .   ...+ ...+|++++|+|++++...+..  +  ......+-++|+||+|+.+.   ..+...+
T Consensus        73 ~~~lnLiDTPGh~dF~~~v~~s-l~~aD~aILVVDas~gv~~qt~~~~~~~~~~~lpiIvViNKiDl~~a---~~~~v~~  148 (600)
T PRK05433         73 TYILNLIDTPGHVDFSYEVSRS-LAACEGALLVVDASQGVEAQTLANVYLALENDLEIIPVLNKIDLPAA---DPERVKQ  148 (600)
T ss_pred             cEEEEEEECCCcHHHHHHHHHH-HHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCcc---cHHHHHH
Confidence            4668899999931 0   0111 1246999999999887543211  0  00123356999999999754   1222223


Q ss_pred             HHHhcC--CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          145 DALRMR--DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       145 ~l~~~n--p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+++..  +..+++++||++|.|+++++++|...
T Consensus       149 ei~~~lg~~~~~vi~iSAktG~GI~~Ll~~I~~~  182 (600)
T PRK05433        149 EIEDVIGIDASDAVLVSAKTGIGIEEVLEAIVER  182 (600)
T ss_pred             HHHHHhCCCcceEEEEecCCCCCHHHHHHHHHHh
Confidence            333221  22369999999999999999998653

>PRK05306 infB translation initiation factor IF-2; Validated

Probab=98.21  E-value=5.5e-06  Score=76.44  Aligned_cols=99  Identities=13%  Similarity=0.145  Sum_probs=62.0

Q ss_pred             CCEEEEeCCcch-hhhccc--ccccceEEEEEeCCCCCCCCc----CCCCCCCceeEEEEecCCCCCchhHhHHHHHHHH
Q 030407           74 ADLLLCESGGDN-LAANFS--RELADYIIYIIDVSGGDKIPR----KGGPGITQADLLVINKTDLASAIGADLAVMERDA  146 (178)
Q Consensus        74 ~d~iiiEttG~~-~~~~~~--~~~ad~~I~VvD~~~~~~~~~----~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l  146 (178)
                      ..+.|+.|.|-. ......  ...+|.+++|+|+.++...+.    .+......+-++++||+|+...   ..+.+.+.+
T Consensus       337 ~~ItfiDTPGhe~F~~m~~rga~~aDiaILVVdAddGv~~qT~e~i~~a~~~~vPiIVviNKiDl~~a---~~e~V~~eL  413 (787)
T PRK05306        337 GKITFLDTPGHEAFTAMRARGAQVTDIVVLVVAADDGVMPQTIEAINHAKAAGVPIIVAINKIDKPGA---NPDRVKQEL  413 (787)
T ss_pred             EEEEEEECCCCccchhHHHhhhhhCCEEEEEEECCCCCCHhHHHHHHHHHhcCCcEEEEEECcccccc---CHHHHHHHH
Confidence            456789999931 011111  123689999999987643221    1111234567999999999654   222333322


Q ss_pred             Hh-------cCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          147 LR-------MRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       147 ~~-------~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ..       +....+++++||++|+|+++|++++..
T Consensus       414 ~~~~~~~e~~g~~vp~vpvSAktG~GI~eLle~I~~  449 (787)
T PRK05306        414 SEYGLVPEEWGGDTIFVPVSAKTGEGIDELLEAILL  449 (787)
T ss_pred             HHhcccHHHhCCCceEEEEeCCCCCCchHHHHhhhh
Confidence            22       223468999999999999999998753

>cd00154 Rab Rab family

Probab=98.21  E-value=7.1e-06  Score=59.51  Aligned_cols=99  Identities=15%  Similarity=0.082  Sum_probs=63.3

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ..++.++++.|...    ...+. ..+|.+++++|+.+......  .+.      ..-..+-++++||+|+..+.....+
T Consensus        48 ~~~~~l~D~~g~~~~~~~~~~~~-~~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~~~~~~~~  126 (159)
T cd00154          48 TVKLQIWDTAGQERFRSITPSYY-RGAHGAILVYDITNRESFENLDKWLKELKEYAPENIPIILVGNKIDLEDQRQVSTE  126 (159)
T ss_pred             EEEEEEEecCChHHHHHHHHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEEcccccccccccHH
Confidence            46788999999421    11111 24699999999977432110  000      0012456999999999622112334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      .+.+..+.  ...+++.+||++|.|++++++++.
T Consensus       127 ~~~~~~~~--~~~~~~~~sa~~~~~i~~~~~~i~  158 (159)
T cd00154         127 EAQQFAKE--NGLLFFETSAKTGENVEELFQSLA  158 (159)
T ss_pred             HHHHHHHH--cCCeEEEEecCCCCCHHHHHHHHh
Confidence            45555544  356899999999999999999875

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

>cd04135 Tc10 TC10 subfamily

Probab=98.21  E-value=4.4e-06  Score=62.56  Aligned_cols=103  Identities=13%  Similarity=0.036  Sum_probs=62.5

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc---CC-----CCCCCceeEEEEecCCCCCchh-----
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR---KG-----GPGITQADLLVINKTDLASAIG-----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~---~~-----~~qi~~adiiviNK~Dl~~~~~-----  136 (178)
                      .+.+-+++|.|...-   .......+|.+++++|..+......   .+     ...-..+-++++||+|+.+...     
T Consensus        47 ~~~~~i~Dt~G~~~~~~~~~~~~~~~~~~ilv~~~~~~~s~~~~~~~~~~~l~~~~~~~piivv~nK~Dl~~~~~~~~~~  126 (174)
T cd04135          47 QYLLGLYDTAGQEDYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPYLLVGTQIDLRDDPKTLARL  126 (174)
T ss_pred             EEEEEEEeCCCcccccccccccCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeEchhhhcChhhHHHH
Confidence            356678999993211   1111234689999999977543211   00     0112345699999999965410     


Q ss_pred             -------HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 -------ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 -------~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                             ...+......++.+ ..+++++||++|.|++++|+.+...
T Consensus       127 ~~~~~~~v~~~~~~~~~~~~~-~~~~~e~Sa~~~~gi~~~f~~~~~~  172 (174)
T cd04135         127 NDMKEKPVTVEQGQKLAKEIG-AHCYVECSALTQKGLKTVFDEAILA  172 (174)
T ss_pred             hhccCCCCCHHHHHHHHHHcC-CCEEEEecCCcCCCHHHHHHHHHHH
Confidence                   01122333444432 3479999999999999999977553

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

>TIGR00437 feoB ferrous iron transporter FeoB

Probab=98.20  E-value=2.4e-06  Score=76.73  Aligned_cols=101  Identities=16%  Similarity=0.116  Sum_probs=62.8

Q ss_pred             CCCEEEEeCCcch-hh---------hcc-cccccceEEEEEeCCCCCCCCcCCC--CCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN-LA---------ANF-SRELADYIIYIIDVSGGDKIPRKGG--PGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~---------~~~-~~~~ad~~I~VvD~~~~~~~~~~~~--~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|.. ..         ..+ ....+|.++.|+|+++.+.......  .....+-++++||+|+.++  ...
T Consensus        40 ~~~i~lvDtPG~~~~~~~s~~e~v~~~~l~~~~aDvvI~VvDat~ler~l~l~~ql~~~~~PiIIVlNK~Dl~~~--~~i  117 (591)
T TIGR00437        40 GEDIEIVDLPGIYSLTTFSLEEEVARDYLLNEKPDLVVNVVDASNLERNLYLTLQLLELGIPMILALNLVDEAEK--KGI  117 (591)
T ss_pred             CeEEEEEECCCccccCccchHHHHHHHHHhhcCCCEEEEEecCCcchhhHHHHHHHHhcCCCEEEEEehhHHHHh--CCC
Confidence            3457889999941 11         111 1124699999999987543211000  1134567999999999754  221


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..-.+.+.+.. +.+++++||++|+|++++++.+.+.
T Consensus       118 ~~d~~~L~~~l-g~pvv~tSA~tg~Gi~eL~~~i~~~  153 (591)
T TIGR00437       118 RIDEEKLEERL-GVPVVPTSATEGRGIERLKDAIRKA  153 (591)
T ss_pred             hhhHHHHHHHc-CCCEEEEECCCCCCHHHHHHHHHHH
Confidence            11122333222 3689999999999999999998764

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.

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

Probab=98.20  E-value=2.1e-06  Score=67.60  Aligned_cols=96  Identities=14%  Similarity=0.139  Sum_probs=56.1

Q ss_pred             CCCCEEEEeCCcch-hhh-ccc-ccccceEEEEEeCCCCCCC-------CcC----CCCCCC-ceeEEEEecCCCCCc--
Q 030407           72 FKADLLLCESGGDN-LAA-NFS-RELADYIIYIIDVSGGDKI-------PRK----GGPGIT-QADLLVINKTDLASA--  134 (178)
Q Consensus        72 ~~~d~iiiEttG~~-~~~-~~~-~~~ad~~I~VvD~~~~~~~-------~~~----~~~qi~-~adiiviNK~Dl~~~--  134 (178)
                      .++.+.|++|.|.. ... .+. ...+|.+++|+|++.+...       ...    ...... .+-++++||+|+.++  
T Consensus        75 ~~~~i~liDtpG~~~~~~~~~~~~~~~d~~i~VvDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiivvNK~Dl~~~~~  154 (219)
T cd01883          75 EKYRFTILDAPGHRDFVPNMITGASQADVAVLVVDARKGEFEAGFEKGGQTREHALLARTLGVKQLIVAVNKMDDVTVNW  154 (219)
T ss_pred             CCeEEEEEECCChHHHHHHHHHHhhhCCEEEEEEECCCCccccccccccchHHHHHHHHHcCCCeEEEEEEccccccccc
Confidence            36788999999931 111 111 1246999999999875210       000    001122 245779999999832  


Q ss_pred             hhHhHHHHHH----HHHhcC---CCCCEEEEecccCCCHH
Q 030407          135 IGADLAVMER----DALRMR---DGGPFIFAQVGWVIGII  167 (178)
Q Consensus       135 ~~~~~~~~~~----~l~~~n---p~a~i~~~SA~~g~gi~  167 (178)
                      ..+..+.+.+    .++...   ...+++++||++|+|++
T Consensus       155 ~~~~~~~i~~~l~~~l~~~~~~~~~~~ii~iSA~tg~gi~  194 (219)
T cd01883         155 SEERYDEIKKELSPFLKKVGYNPKDVPFIPISGLTGDNLI  194 (219)
T ss_pred             cHHHHHHHHHHHHHHHHHcCCCcCCceEEEeecCcCCCCC
Confidence            1122333333    334332   13689999999999986

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

>cd04146 RERG_RasL11_like RERG/RasL11-like subfamily

Probab=98.20  E-value=2.5e-06  Score=63.48  Aligned_cols=101  Identities=15%  Similarity=0.054  Sum_probs=62.8

Q ss_pred             CCEEEEeCCcchh--hh--cccccccceEEEEEeCCCCCCCCc---------CCCC-CCCceeEEEEecCCCCCchhHhH
Q 030407           74 ADLLLCESGGDNL--AA--NFSRELADYIIYIIDVSGGDKIPR---------KGGP-GITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        74 ~d~iiiEttG~~~--~~--~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~-qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ..+-++++.|..-  ..  ......+|.+++++|+++......         .... ....+-++|+||+|+........
T Consensus        47 ~~~~i~D~~g~~~~~~~~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~v~~  126 (165)
T cd04146          47 VSLEILDTAGQQQADTEQLERSIRWADGFVLVYSITDRSSFDEISQLKQLIREIKKRDREIPVILVGNKADLLHYRQVST  126 (165)
T ss_pred             EEEEEEECCCCcccccchHHHHHHhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCchHHhCccCH
Confidence            4567899999321  00  001124799999999987643210         0111 12456799999999864311122


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccC-CCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWV-IGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g-~gi~el~~~l~~~  176 (178)
                      +...+..+..+  .+++++||++| .|++++|+.+.+.
T Consensus       127 ~~~~~~~~~~~--~~~~e~Sa~~~~~~v~~~f~~l~~~  162 (165)
T cd04146         127 EEGEKLASELG--CLFFEVSAAEDYDGVHSVFHELCRE  162 (165)
T ss_pred             HHHHHHHHHcC--CEEEEeCCCCCchhHHHHHHHHHHH
Confidence            33444444443  58999999999 5999999988654

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

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

Probab=98.19  E-value=2.1e-06  Score=65.21  Aligned_cols=91  Identities=15%  Similarity=0.086  Sum_probs=57.6

Q ss_pred             CEEEEeCCcchhh--------------hcccc--cccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           75 DLLLCESGGDNLA--------------ANFSR--ELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        75 d~iiiEttG~~~~--------------~~~~~--~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      .+.++.|.|....              ..+..  ...+.+++|+|++++......    .......+-++++||+|+.++
T Consensus        65 ~~~liDtpG~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~ii~vvd~~~~~~~~~~~~~~~~~~~~~pviiv~nK~D~~~~  144 (179)
T TIGR03598        65 GFRLVDLPGYGYAKVSKEEKEKWQKLIEEYLEKRENLKGVVLLMDIRHPLKELDLEMLEWLRERGIPVLIVLTKADKLKK  144 (179)
T ss_pred             cEEEEeCCCCccccCChhHHHHHHHHHHHHHHhChhhcEEEEEecCCCCCCHHHHHHHHHHHHcCCCEEEEEECcccCCH
Confidence            6899999994210              01111  124789999999765332211    111234567999999999865


Q ss_pred             hhHh----HHHHHHHHHhcCCCCCEEEEecccCCCHH
Q 030407          135 IGAD----LAVMERDALRMRDGGPFIFAQVGWVIGII  167 (178)
Q Consensus       135 ~~~~----~~~~~~~l~~~np~a~i~~~SA~~g~gi~  167 (178)
                        .+    .+.+++.++...+..+++++||++|+|++
T Consensus       145 --~~~~~~~~~i~~~l~~~~~~~~v~~~Sa~~g~gi~  179 (179)
T TIGR03598       145 --SELNKQLKKIKKALKKDADDPSVQLFSSLKKTGID  179 (179)
T ss_pred             --HHHHHHHHHHHHHHhhccCCCceEEEECCCCCCCC
Confidence              33    34455555544344689999999999974

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.

>PRK00454 engB GTP-binding protein YsxC; Reviewed

Probab=98.19  E-value=4.6e-06  Score=63.70  Aligned_cols=102  Identities=15%  Similarity=0.013  Sum_probs=64.1

Q ss_pred             CCEEEEeCCcchh-------h-------hcccc--cccceEEEEEeCCCCCCCCc----CCCCCCCceeEEEEecCCCCC
Q 030407           74 ADLLLCESGGDNL-------A-------ANFSR--ELADYIIYIIDVSGGDKIPR----KGGPGITQADLLVINKTDLAS  133 (178)
Q Consensus        74 ~d~iiiEttG~~~-------~-------~~~~~--~~ad~~I~VvD~~~~~~~~~----~~~~qi~~adiiviNK~Dl~~  133 (178)
                      .++.|+.|.|...       .       ..+..  ...+.+++++|+..+.....    .+........++++||+|+.+
T Consensus        70 ~~l~l~DtpG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~d~~~~~~~~~~~i~~~l~~~~~~~iiv~nK~Dl~~  149 (196)
T PRK00454         70 DKLRLVDLPGYGYAKVSKEEKEKWQKLIEEYLRTRENLKGVVLLIDSRHPLKELDLQMIEWLKEYGIPVLIVLTKADKLK  149 (196)
T ss_pred             CeEEEeCCCCCCCcCCCchHHHHHHHHHHHHHHhCccceEEEEEEecCCCCCHHHHHHHHHHHHcCCcEEEEEECcccCC
Confidence            6789999999421       0       11111  12356788889876432211    011112345689999999987


Q ss_pred             chhHhHHHHHHHHHhcC-C-CCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          134 AIGADLAVMERDALRMR-D-GGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       134 ~~~~~~~~~~~~l~~~n-p-~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .  .+.+...+.+++.. + ..+++++||++|+|++++++.+.+.+
T Consensus       150 ~--~~~~~~~~~i~~~l~~~~~~~~~~Sa~~~~gi~~l~~~i~~~~  193 (196)
T PRK00454        150 K--GERKKQLKKVRKALKFGDDEVILFSSLKKQGIDELRAAIAKWL  193 (196)
T ss_pred             H--HHHHHHHHHHHHHHHhcCCceEEEEcCCCCCHHHHHHHHHHHh
Confidence            6  45444333333221 1 46999999999999999999988765

>cd01876 YihA_EngB The YihA (EngB) subfamily

Probab=98.19  E-value=6e-06  Score=60.58  Aligned_cols=81  Identities=16%  Similarity=0.067  Sum_probs=54.1

Q ss_pred             cceEEEEEeCCCCCCCCc----CCCCCCCceeEEEEecCCCCCchhHhHHHHH----HHHHhcCCCCCEEEEecccCCCH
Q 030407           95 ADYIIYIIDVSGGDKIPR----KGGPGITQADLLVINKTDLASAIGADLAVME----RDALRMRDGGPFIFAQVGWVIGI  166 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~----~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~----~~l~~~np~a~i~~~SA~~g~gi  166 (178)
                      .+.++.++|.........    .+......+.++++||+|+.++  .+.....    ..++...+..+++++||+++.|+
T Consensus        82 ~~~~~~v~d~~~~~~~~~~~~~~~l~~~~~~vi~v~nK~D~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~Sa~~~~~~  159 (170)
T cd01876          82 LKGVVLLIDSRHGPTEIDLEMLDWLEELGIPFLVVLTKADKLKK--SELAKALKEIKKELKLFEIDPPIILFSSLKGQGI  159 (170)
T ss_pred             hhEEEEEEEcCcCCCHhHHHHHHHHHHcCCCEEEEEEchhcCCh--HHHHHHHHHHHHHHHhccCCCceEEEecCCCCCH
Confidence            367888999876532211    1111234567999999999866  4433333    33332345679999999999999


Q ss_pred             HHHHHHHhhhh
Q 030407          167 IFTLSITHYIV  177 (178)
Q Consensus       167 ~el~~~l~~~~  177 (178)
                      ++++++|.+.+
T Consensus       160 ~~l~~~l~~~~  170 (170)
T cd01876         160 DELRALIEKWL  170 (170)
T ss_pred             HHHHHHHHHhC
Confidence            99999998753

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.

>PLN03108 Rab family protein; Provisional

Probab=98.17  E-value=7.3e-06  Score=64.07  Aligned_cols=99  Identities=16%  Similarity=0.122  Sum_probs=62.5

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CC-C-----CCCCceeEEEEecCCCCCchhHhHHH
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KG-G-----PGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~-~-----~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      ..+-+++|.|..    +...+. ..+|.+++|+|++.......  .+ .     ..-..+-+++.||+|+........+.
T Consensus        55 i~l~l~Dt~G~~~~~~~~~~~~-~~ad~~vlv~D~~~~~s~~~l~~~~~~~~~~~~~~~piiiv~nK~Dl~~~~~~~~~~  133 (210)
T PLN03108         55 IKLQIWDTAGQESFRSITRSYY-RGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCDLAHRRAVSTEE  133 (210)
T ss_pred             EEEEEEeCCCcHHHHHHHHHHh-ccCCEEEEEEECCcHHHHHHHHHHHHHHHHhcCCCCcEEEEEECccCccccCCCHHH
Confidence            446688999931    111122 24689999999987542211  00 0     00134569999999997531123344


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ..+..++.  ..+++++||++|.|++++|+++.+
T Consensus       134 ~~~~~~~~--~~~~~e~Sa~~~~~v~e~f~~l~~  165 (210)
T PLN03108        134 GEQFAKEH--GLIFMEASAKTAQNVEEAFIKTAA  165 (210)
T ss_pred             HHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHH
Confidence            55555544  358999999999999999987654

>PRK09563 rbgA GTPase YlqF; Reviewed

Probab=98.16  E-value=6.4e-06  Score=67.66  Aligned_cols=79  Identities=19%  Similarity=0.093  Sum_probs=53.9

Q ss_pred             ccceEEEEEeCCCCCCCCcC-CCCCC-CceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHH
Q 030407           94 LADYIIYIIDVSGGDKIPRK-GGPGI-TQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLS  171 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~-~~~qi-~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~  171 (178)
                      .+|.++.|+|+..+...... ....+ ..+-++|+||+|+.+.  ...+...+.+++.  ..+++.+||+++.|++++.+
T Consensus        24 ~aDvIL~VvDar~p~~~~~~~l~~~~~~kp~iiVlNK~DL~~~--~~~~~~~~~~~~~--~~~vi~vSa~~~~gi~~L~~   99 (287)
T PRK09563         24 LVDVVIEVLDARIPLSSENPMIDKIIGNKPRLLILNKSDLADP--EVTKKWIEYFEEQ--GIKALAINAKKGQGVKKILK   99 (287)
T ss_pred             hCCEEEEEEECCCCCCCCChhHHHHhCCCCEEEEEEchhcCCH--HHHHHHHHHHHHc--CCeEEEEECCCcccHHHHHH
Confidence            36999999999765432211 11111 3567999999999766  4444444444432  35789999999999999998


Q ss_pred             HHhhh
Q 030407          172 ITHYI  176 (178)
Q Consensus       172 ~l~~~  176 (178)
                      .+.++
T Consensus       100 ~l~~~  104 (287)
T PRK09563        100 AAKKL  104 (287)
T ss_pred             HHHHH
Confidence            87654

>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]

Probab=98.16  E-value=5.6e-06  Score=68.17  Aligned_cols=107  Identities=16%  Similarity=0.105  Sum_probs=65.7

Q ss_pred             hCCCCEEEEeCCcchh----h-----hc----c--cccccceEEEEEeCCCCCCC--Cc---CCCCCCCceeEEEEecCC
Q 030407           71 LFKADLLLCESGGDNL----A-----AN----F--SRELADYIIYIIDVSGGDKI--PR---KGGPGITQADLLVINKTD  130 (178)
Q Consensus        71 ~~~~d~iiiEttG~~~----~-----~~----~--~~~~ad~~I~VvD~~~~~~~--~~---~~~~qi~~adiiviNK~D  130 (178)
                      ..+..+||..|.|+..    .     ..    .  ....+|.+++|+|++.....  +.   .....-..+-++|+||+|
T Consensus       117 s~eTQlvf~DTPGlvs~~~~r~~~l~~s~lq~~~~a~q~AD~vvVv~Das~tr~~l~p~vl~~l~~ys~ips~lvmnkid  196 (379)
T KOG1423|consen  117 SGETQLVFYDTPGLVSKKMHRRHHLMMSVLQNPRDAAQNADCVVVVVDASATRTPLHPRVLHMLEEYSKIPSILVMNKID  196 (379)
T ss_pred             cCceEEEEecCCcccccchhhhHHHHHHhhhCHHHHHhhCCEEEEEEeccCCcCccChHHHHHHHHHhcCCceeeccchh
Confidence            5578899999999511    0     00    0  11247999999999852211  10   001112346799999999


Q ss_pred             CCCch-----------hHhHHHHHHHHHhcCCC----------------CCEEEEecccCCCHHHHHHHHhhhh
Q 030407          131 LASAI-----------GADLAVMERDALRMRDG----------------GPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       131 l~~~~-----------~~~~~~~~~~l~~~np~----------------a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .....           +.++....-.+++....                -++|++||++|+||+++.++|..++
T Consensus       197 ~~k~k~~Ll~l~~~Lt~g~l~~~kl~v~~~f~~~p~~~~~~~~~gwshfe~vF~vSaL~G~GikdlkqyLmsqa  270 (379)
T KOG1423|consen  197 KLKQKRLLLNLKDLLTNGELAKLKLEVQEKFTDVPSDEKWRTICGWSHFERVFMVSALYGEGIKDLKQYLMSQA  270 (379)
T ss_pred             cchhhhHHhhhHHhccccccchhhhhHHHHhccCCcccccccccCcccceeEEEEecccccCHHHHHHHHHhcC
Confidence            86441           01222222233333322                3599999999999999999998775

>cd04173 Rnd2_Rho7 Rnd2/Rho7 subfamily

Probab=98.16  E-value=2.7e-06  Score=67.50  Aligned_cols=102  Identities=11%  Similarity=0.048  Sum_probs=63.8

Q ss_pred             CCCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCC-----CCCceeEEEEecCCCCCch----
Q 030407           72 FKADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGP-----GITQADLLVINKTDLASAI----  135 (178)
Q Consensus        72 ~~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~-----qi~~adiiviNK~Dl~~~~----  135 (178)
                      ..+.+-|++|+|..    +.+.+. ..+|++++|+|.++......   .+..     .-..+-++|.||+||.+..    
T Consensus        47 ~~v~L~iwDt~G~e~~~~l~~~~~-~~~d~illvfdis~~~Sf~~i~~~w~~~~~~~~~~~piiLVgnK~DL~~~~~~~~  125 (222)
T cd04173          47 RRIELNMWDTSGSSYYDNVRPLAY-PDSDAVLICFDISRPETLDSVLKKWQGETQEFCPNAKVVLVGCKLDMRTDLATLR  125 (222)
T ss_pred             EEEEEEEEeCCCcHHHHHHhHHhc-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEECcccccchhhhh
Confidence            35778899999942    222222 36799999999987643211   1111     0134579999999996421    


Q ss_pred             --------hHhHHHHHHHHHhcCCCCCEEEEecccCCC-HHHHHHHHhh
Q 030407          136 --------GADLAVMERDALRMRDGGPFIFAQVGWVIG-IIFTLSITHY  175 (178)
Q Consensus       136 --------~~~~~~~~~~l~~~np~a~i~~~SA~~g~g-i~el~~~l~~  175 (178)
                              +...++..++.++. ...+++++||+++++ |+++|+....
T Consensus       126 ~~~~~~~~pIs~e~g~~~ak~~-~~~~y~E~SAk~~~~~V~~~F~~~~~  173 (222)
T cd04173         126 ELSKQRLIPVTHEQGTVLAKQV-GAVSYVECSSRSSERSVRDVFHVATV  173 (222)
T ss_pred             hhhhccCCccCHHHHHHHHHHc-CCCEEEEcCCCcCCcCHHHHHHHHHH
Confidence                    01122333344433 234899999999995 9999987654

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

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

Probab=98.15  E-value=7.9e-06  Score=63.62  Aligned_cols=98  Identities=16%  Similarity=0.130  Sum_probs=64.5

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .-.=++.|.|-.    +...|+ ..|+++++|+|.++......         ++.+- ...-++|.||+|+..+.....+
T Consensus        61 i~lQiWDtaGQerf~ti~~sYy-rgA~gi~LvyDitne~Sfeni~~W~~~I~e~a~~-~v~~~LvGNK~D~~~~R~V~~e  138 (207)
T KOG0078|consen   61 IKLQIWDTAGQERFRTITTAYY-RGAMGILLVYDITNEKSFENIRNWIKNIDEHASD-DVVKILVGNKCDLEEKRQVSKE  138 (207)
T ss_pred             EEEEEEEcccchhHHHHHHHHH-hhcCeeEEEEEccchHHHHHHHHHHHHHHhhCCC-CCcEEEeeccccccccccccHH
Confidence            445567788831    122233 36899999999987533211         11110 2234999999999874223445


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +-++..++.  +.++++||||+|.+|+|.|-.|.+
T Consensus       139 ~ge~lA~e~--G~~F~EtSAk~~~NI~eaF~~La~  171 (207)
T KOG0078|consen  139 RGEALAREY--GIKFFETSAKTNFNIEEAFLSLAR  171 (207)
T ss_pred             HHHHHHHHh--CCeEEEccccCCCCHHHHHHHHHH
Confidence            556666655  789999999999999999977654

>PRK01889 GTPase RsgA; Reviewed

Probab=98.15  E-value=8.8e-06  Score=68.88  Aligned_cols=76  Identities=12%  Similarity=0.066  Sum_probs=50.7

Q ss_pred             cceEEEEEeCCCCCCCC--cCCC---CCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHH
Q 030407           95 ADYIIYIIDVSGGDKIP--RKGG---PGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~--~~~~---~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el  169 (178)
                      .|.+++|+++.......  +++.   ......-+||+||+||+++  .+  ...++++..+++.+++.+|+++|.|+++|
T Consensus       113 vD~vliV~s~~p~~~~~~ldr~L~~a~~~~i~piIVLNK~DL~~~--~~--~~~~~~~~~~~g~~Vi~vSa~~g~gl~~L  188 (356)
T PRK01889        113 VDTVFIVCSLNHDFNLRRIERYLALAWESGAEPVIVLTKADLCED--AE--EKIAEVEALAPGVPVLAVSALDGEGLDVL  188 (356)
T ss_pred             CCEEEEEEecCCCCChhHHHHHHHHHHHcCCCEEEEEEChhcCCC--HH--HHHHHHHHhCCCCcEEEEECCCCccHHHH
Confidence            47788888885322210  1111   1122345999999999876  22  22344455567789999999999999999


Q ss_pred             HHHHh
Q 030407          170 LSITH  174 (178)
Q Consensus       170 ~~~l~  174 (178)
                      .+++.
T Consensus       189 ~~~L~  193 (356)
T PRK01889        189 AAWLS  193 (356)
T ss_pred             HHHhh
Confidence            99885

>PRK12296 obgE GTPase CgtA; Reviewed

Probab=98.13  E-value=6.7e-06  Score=72.27  Aligned_cols=100  Identities=18%  Similarity=0.189  Sum_probs=64.0

Q ss_pred             CCEEEEeCCcch--------hhhcccc--cccceEEEEEeCCCCC---CCC----------cCCCC----------CCCc
Q 030407           74 ADLLLCESGGDN--------LAANFSR--ELADYIIYIIDVSGGD---KIP----------RKGGP----------GITQ  120 (178)
Q Consensus        74 ~d~iiiEttG~~--------~~~~~~~--~~ad~~I~VvD~~~~~---~~~----------~~~~~----------qi~~  120 (178)
                      ..+.|+.+.|+.        +...|..  ..++.+++|+|++...   +..          ..+..          ....
T Consensus       206 ~~f~laDtPGliegas~g~gLg~~fLrhieradvLv~VVD~s~~e~~rdp~~d~~~i~~EL~~y~~~l~~~~~~~~l~~k  285 (500)
T PRK12296        206 TRFTVADVPGLIPGASEGKGLGLDFLRHIERCAVLVHVVDCATLEPGRDPLSDIDALEAELAAYAPALDGDLGLGDLAER  285 (500)
T ss_pred             eEEEEEECCCCccccchhhHHHHHHHHHHHhcCEEEEEECCcccccccCchhhHHHHHHHHHHhhhcccccchhhhhcCC
Confidence            467889999941        1111221  2368999999997532   100          01111          1245


Q ss_pred             eeEEEEecCCCCCchhHhH-HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          121 ADLLVINKTDLASAIGADL-AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       121 adiiviNK~Dl~~~~~~~~-~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +-+||+||+|+.+.  .++ +.+...++..  ..+++++||++++|+++|+++|.+.+
T Consensus       286 P~IVVlNKiDL~da--~el~e~l~~~l~~~--g~~Vf~ISA~tgeGLdEL~~~L~ell  339 (500)
T PRK12296        286 PRLVVLNKIDVPDA--RELAEFVRPELEAR--GWPVFEVSAASREGLRELSFALAELV  339 (500)
T ss_pred             CEEEEEECccchhh--HHHHHHHHHHHHHc--CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            78999999999765  333 3334444433  35899999999999999999887654

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

Probab=98.13  E-value=1.3e-05  Score=71.98  Aligned_cols=101  Identities=19%  Similarity=0.085  Sum_probs=61.8

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchh---------
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIG---------  136 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~---------  136 (178)
                      +.+.|+.|.|..    +...+. ..+|.+++|+|++++...+..    .......+-++++||+|+.+...         
T Consensus        69 ~~l~~iDTpG~e~f~~l~~~~~-~~aD~~IlVvD~~~g~~~qt~e~i~~l~~~~vpiIVv~NK~Dl~~~~~~~~~~~f~e  147 (590)
T TIGR00491        69 PGLLFIDTPGHEAFTNLRKRGG-ALADLAILIVDINEGFKPQTQEALNILRMYKTPFVVAANKIDRIPGWRSHEGRPFME  147 (590)
T ss_pred             CcEEEEECCCcHhHHHHHHHHH-hhCCEEEEEEECCcCCCHhHHHHHHHHHHcCCCEEEEEECCCccchhhhccCchHHH
Confidence            348999999931    111121 357999999999876432211    01112345799999999974200         


Q ss_pred             ---HhHHHHH-----------HHHH-------------hcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          137 ---ADLAVME-----------RDAL-------------RMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       137 ---~~~~~~~-----------~~l~-------------~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                         .+.+.+.           ..+.             +.....+++++||++|+|+++|++++..
T Consensus       148 ~sak~~~~v~~~~~~~~~~lv~~l~~~G~~~e~~~~i~~~~~~v~iVpVSA~tGeGideLl~~l~~  213 (590)
T TIGR00491       148 SFSKQEIQVQQNLDTKVYNLVIKLHEEGFEAERFDRVTDFTKTVAIIPISAITGEGIPELLTMLAG  213 (590)
T ss_pred             HHHhhhHHHHHHHHHHHHHHHHHHHhcCccHHhhhhhhhcCCCceEEEeecCCCCChhHHHHHHHH
Confidence               0000010           1111             2334579999999999999999998753

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.

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=98.13  E-value=1.5e-05  Score=64.83  Aligned_cols=112  Identities=13%  Similarity=0.059  Sum_probs=66.7

Q ss_pred             hHHHhhHhhC--CCCEEEEeCCcchhhhcccc-------------cccceEEEEEeCCCCCCCCcCCCCC---------C
Q 030407           63 GPLEELSNLF--KADLLLCESGGDNLAANFSR-------------ELADYIIYIIDVSGGDKIPRKGGPG---------I  118 (178)
Q Consensus        63 ~~l~~l~~~~--~~d~iiiEttG~~~~~~~~~-------------~~ad~~I~VvD~~~~~~~~~~~~~q---------i  118 (178)
                      ..+.++.++.  .+||++|.|.|  ....|.+             ...-.+++|+|..+..........+         -
T Consensus       103 dqv~~~iek~~~~~~~~liDTPG--QIE~FtWSAsGsIIte~lass~ptvv~YvvDt~rs~~p~tFMSNMlYAcSilykt  180 (366)
T KOG1532|consen  103 DQVIELIEKRAEEFDYVLIDTPG--QIEAFTWSASGSIITETLASSFPTVVVYVVDTPRSTSPTTFMSNMLYACSILYKT  180 (366)
T ss_pred             HHHHHHHHHhhcccCEEEEcCCC--ceEEEEecCCccchHhhHhhcCCeEEEEEecCCcCCCchhHHHHHHHHHHHHHhc
Confidence            4444444433  58999999999  3222221             1124578999986643221111111         2


Q ss_pred             CceeEEEEecCCCCCch--hHhH---HHHHHHHHh-------------------cCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          119 TQADLLVINKTDLASAI--GADL---AVMERDALR-------------------MRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       119 ~~adiiviNK~Dl~~~~--~~~~---~~~~~~l~~-------------------~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      +.+-+++.||+|+.+..  .+..   +.+++.+.+                   -....+.+-+|+.+|+|.+++|..+.
T Consensus       181 klp~ivvfNK~Dv~d~~fa~eWm~DfE~FqeAl~~~~~~y~s~l~~SmSL~leeFY~~lrtv~VSs~tG~G~ddf~~av~  260 (366)
T KOG1532|consen  181 KLPFIVVFNKTDVSDSEFALEWMTDFEAFQEALNEAESSYMSNLTRSMSLMLEEFYRSLRTVGVSSVTGEGFDDFFTAVD  260 (366)
T ss_pred             cCCeEEEEecccccccHHHHHHHHHHHHHHHHHHhhccchhHHhhhhHHHHHHHHHhhCceEEEecccCCcHHHHHHHHH
Confidence            34569999999998762  1111   223333332                   11235889999999999999999876


Q ss_pred             hh
Q 030407          175 YI  176 (178)
Q Consensus       175 ~~  176 (178)
                      +-
T Consensus       261 ~~  262 (366)
T KOG1532|consen  261 ES  262 (366)
T ss_pred             HH
Confidence            53

>cd01857 HSR1_MMR1 HSR1/MMR1

Probab=98.11  E-value=6e-06  Score=60.56  Aligned_cols=68  Identities=13%  Similarity=0.086  Sum_probs=46.6

Q ss_pred             ccceEEEEEeCCCCCCCCc-C---CCCCC--CceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCC
Q 030407           94 LADYIIYIIDVSGGDKIPR-K---GGPGI--TQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIG  165 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~-~---~~~qi--~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~g  165 (178)
                      .+|.+++|+|+..+..... .   +....  ..+-++|+||+|+.++  .+.....+.+++..  .+++++||++|.+
T Consensus        11 ~aD~vl~ViD~~~p~~~~~~~l~~~l~~~~~~k~~iivlNK~DL~~~--~~~~~~~~~~~~~~--~~ii~iSa~~~~~   84 (141)
T cd01857          11 RSDIVVQIVDARNPLLFRPPDLERYVKEVDPRKKNILLLNKADLLTE--EQRKAWAEYFKKEG--IVVVFFSALKENA   84 (141)
T ss_pred             hCCEEEEEEEccCCcccCCHHHHHHHHhccCCCcEEEEEechhcCCH--HHHHHHHHHHHhcC--CeEEEEEecCCCc
Confidence            4699999999987654322 1   11111  4467999999999876  55555556665443  5899999998875

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.

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

Probab=98.10  E-value=1.3e-05  Score=61.92  Aligned_cols=99  Identities=16%  Similarity=0.126  Sum_probs=63.6

Q ss_pred             CCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           74 ADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        74 ~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ..+=+.+|.|-    ++...+++ .++++|+|+|.+.......         ++.. -...-++|.||+|+.+......+
T Consensus        58 iKlQIWDTAGQERFrtit~syYR-~ahGii~vyDiT~~~SF~~v~~Wi~Ei~~~~~-~~v~~lLVGNK~Dl~~~~~v~~~  135 (205)
T KOG0084|consen   58 IKLQIWDTAGQERFRTITSSYYR-GAHGIIFVYDITKQESFNNVKRWIQEIDRYAS-ENVPKLLVGNKCDLTEKRVVSTE  135 (205)
T ss_pred             EEEEeeeccccHHHhhhhHhhcc-CCCeEEEEEEcccHHHhhhHHHHHHHhhhhcc-CCCCeEEEeeccccHhheecCHH
Confidence            45567789994    23344554 6899999999987443211         1110 11246999999999765212223


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ..++...+ ++-.++++||||++.++++.|..+..
T Consensus       136 ~a~~fa~~-~~~~~f~ETSAK~~~NVe~~F~~la~  169 (205)
T KOG0084|consen  136 EAQEFADE-LGIPIFLETSAKDSTNVEDAFLTLAK  169 (205)
T ss_pred             HHHHHHHh-cCCcceeecccCCccCHHHHHHHHHH
Confidence            33444433 33334999999999999999987654

>TIGR02034 CysN sulfate adenylyltransferase, large subunit

Probab=98.10  E-value=9e-06  Score=69.92  Aligned_cols=96  Identities=15%  Similarity=0.134  Sum_probs=57.7

Q ss_pred             CCCEEEEeCCcch-h-hhc-ccccccceEEEEEeCCCCCCCCcC----CCCCCCc-eeEEEEecCCCCCchhHhHHHHHH
Q 030407           73 KADLLLCESGGDN-L-AAN-FSRELADYIIYIIDVSGGDKIPRK----GGPGITQ-ADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        73 ~~d~iiiEttG~~-~-~~~-~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~-adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      +..+.||.|.|-. . ..+ .....+|.+++|+|+..+...+..    ....+.. .-++++||+|+.+...+..+.+.+
T Consensus        79 ~~~~~liDtPGh~~f~~~~~~~~~~aD~allVVda~~G~~~qt~~~~~~~~~~~~~~iivviNK~D~~~~~~~~~~~i~~  158 (406)
T TIGR02034        79 KRKFIVADTPGHEQYTRNMATGASTADLAVLLVDARKGVLEQTRRHSYIASLLGIRHVVLAVNKMDLVDYDEEVFENIKK  158 (406)
T ss_pred             CeEEEEEeCCCHHHHHHHHHHHHhhCCEEEEEEECCCCCccccHHHHHHHHHcCCCcEEEEEEecccccchHHHHHHHHH
Confidence            4578999999931 1 111 112246999999999877543221    0111222 246799999998642122333333


Q ss_pred             HH----HhcC-CCCCEEEEecccCCCHHH
Q 030407          145 DA----LRMR-DGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       145 ~l----~~~n-p~a~i~~~SA~~g~gi~e  168 (178)
                      .+    +... ...+++++||++|+|+++
T Consensus       159 ~~~~~~~~~~~~~~~iipiSA~~g~ni~~  187 (406)
T TIGR02034       159 DYLAFAEQLGFRDVTFIPLSALKGDNVVS  187 (406)
T ss_pred             HHHHHHHHcCCCCccEEEeecccCCCCcc
Confidence            33    3222 246899999999999986

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).

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

Probab=98.10  E-value=1.1e-05  Score=69.68  Aligned_cols=96  Identities=16%  Similarity=0.146  Sum_probs=57.8

Q ss_pred             CCCEEEEeCCcch-hh-hcc-cccccceEEEEEeCCCCCCC---Cc-C---CCCCCCc-eeEEEEecCCCCCchhHhH--
Q 030407           73 KADLLLCESGGDN-LA-ANF-SRELADYIIYIIDVSGGDKI---PR-K---GGPGITQ-ADLLVINKTDLASAIGADL--  139 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~~-~~~~ad~~I~VvD~~~~~~~---~~-~---~~~qi~~-adiiviNK~Dl~~~~~~~~--  139 (178)
                      ++.+.|++|.|.. .. ... ....+|.+++|+|++++...   +. .   ....+.. .-++++||+|+.+...+..  
T Consensus        84 ~~~i~iiDtpGh~~f~~~~~~~~~~aD~~ilVvDa~~~~~~~~~~t~~~~~~~~~~~~~~iIVviNK~Dl~~~~~~~~~~  163 (426)
T TIGR00483        84 KYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEFEVQPQTREHAFLARTLGINQLIVAINKMDSVNYDEEEFEA  163 (426)
T ss_pred             CeEEEEEECCCHHHHHHHHHhhhhhCCEEEEEEECCCCCcccCCchHHHHHHHHHcCCCeEEEEEEChhccCccHHHHHH
Confidence            5678999999931 11 111 11347999999999887321   11 0   0111222 3577999999975311222  


Q ss_pred             --HHHHHHHHhcC---CCCCEEEEecccCCCHHH
Q 030407          140 --AVMERDALRMR---DGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       140 --~~~~~~l~~~n---p~a~i~~~SA~~g~gi~e  168 (178)
                        +++.+.++...   ...+++++||++|+|+++
T Consensus       164 ~~~ei~~~~~~~g~~~~~~~~i~iSA~~g~ni~~  197 (426)
T TIGR00483       164 IKKEVSNLIKKVGYNPDTVPFIPISAWNGDNVIK  197 (426)
T ss_pred             HHHHHHHHHHHcCCCcccceEEEeeccccccccc
Confidence              33444444332   236899999999999986

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.

>cd04166 CysN_ATPS CysN_ATPS subfamily

Probab=98.10  E-value=8.6e-06  Score=63.60  Aligned_cols=96  Identities=16%  Similarity=0.103  Sum_probs=56.7

Q ss_pred             CCCEEEEeCCcch-hh-hcc-cccccceEEEEEeCCCCCCCCcC----CCCCCCce-eEEEEecCCCCCchhHhH----H
Q 030407           73 KADLLLCESGGDN-LA-ANF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQA-DLLVINKTDLASAIGADL----A  140 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~a-diiviNK~Dl~~~~~~~~----~  140 (178)
                      +..+.|+.|.|.. .. ... ....+|.+++|+|++.+......    ........ -++|+||+|+.+...+..    .
T Consensus        76 ~~~~~liDTpG~~~~~~~~~~~~~~ad~~llVvD~~~~~~~~~~~~~~~~~~~~~~~iIvviNK~D~~~~~~~~~~~i~~  155 (208)
T cd04166          76 KRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARKGVLEQTRRHSYILSLLGIRHVVVAVNKMDLVDYSEEVFEEIVA  155 (208)
T ss_pred             CceEEEEECCcHHHHHHHHHHhhhhCCEEEEEEECCCCccHhHHHHHHHHHHcCCCcEEEEEEchhcccCCHHHHHHHHH
Confidence            5678999999931 11 111 11246999999999876422110    11112222 356899999975311222    2


Q ss_pred             HHHHHHHhcC-CCCCEEEEecccCCCHHH
Q 030407          141 VMERDALRMR-DGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       141 ~~~~~l~~~n-p~a~i~~~SA~~g~gi~e  168 (178)
                      .+.+.++.++ +..+++++||++|.|+++
T Consensus       156 ~~~~~~~~~~~~~~~ii~iSA~~g~ni~~  184 (208)
T cd04166         156 DYLAFAAKLGIEDITFIPISALDGDNVVS  184 (208)
T ss_pred             HHHHHHHHcCCCCceEEEEeCCCCCCCcc
Confidence            3333334443 346799999999999975

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.

>cd01854 YjeQ_engC YjeQ/EngC

Probab=98.09  E-value=3.4e-06  Score=69.30  Aligned_cols=77  Identities=13%  Similarity=0.060  Sum_probs=50.9

Q ss_pred             cceEEEEEeCCCCC-CCC--cCCC---CCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHH
Q 030407           95 ADYIIYIIDVSGGD-KIP--RKGG---PGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus        95 ad~~I~VvD~~~~~-~~~--~~~~---~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                      +|.+++|+|+..+. ...  +++.   ......-++|+||+||.++  .+.........  ..+.+++.+||++|.|+++
T Consensus        79 vD~vllV~d~~~p~~s~~~ldr~L~~~~~~~ip~iIVlNK~DL~~~--~~~~~~~~~~~--~~g~~v~~vSA~~g~gi~~  154 (287)
T cd01854          79 VDQLVIVVSLNEPFFNPRLLDRYLVAAEAAGIEPVIVLTKADLLDD--EEEELELVEAL--ALGYPVLAVSAKTGEGLDE  154 (287)
T ss_pred             CCEEEEEEEcCCCCCCHHHHHHHHHHHHHcCCCEEEEEEHHHCCCh--HHHHHHHHHHH--hCCCeEEEEECCCCccHHH
Confidence            58899999997764 211  1111   1123346999999999866  33222222222  2457999999999999999


Q ss_pred             HHHHHhh
Q 030407          169 TLSITHY  175 (178)
Q Consensus       169 l~~~l~~  175 (178)
                      |++.+..
T Consensus       155 L~~~L~~  161 (287)
T cd01854         155 LREYLKG  161 (287)
T ss_pred             HHhhhcc
Confidence            9988753

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.

>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional

Probab=98.09  E-value=8.9e-06  Score=71.33  Aligned_cols=97  Identities=14%  Similarity=0.145  Sum_probs=59.3

Q ss_pred             CCCEEEEeCCcch-hh-hcc-cccccceEEEEEeCCCCCCCCcC-C---CCCCC-ceeEEEEecCCCCCchhHhHHHHHH
Q 030407           73 KADLLLCESGGDN-LA-ANF-SRELADYIIYIIDVSGGDKIPRK-G---GPGIT-QADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~~-~~~~ad~~I~VvD~~~~~~~~~~-~---~~qi~-~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      +..++||.|.|-. .. ... ....+|.+++|+|+..+...+.. +   ...+. ..-++++||+|+.+...+..+.+.+
T Consensus       106 ~~~i~~iDTPGh~~f~~~~~~~l~~aD~allVVDa~~G~~~qt~~~~~l~~~lg~~~iIvvvNKiD~~~~~~~~~~~i~~  185 (474)
T PRK05124        106 KRKFIIADTPGHEQYTRNMATGASTCDLAILLIDARKGVLDQTRRHSFIATLLGIKHLVVAVNKMDLVDYSEEVFERIRE  185 (474)
T ss_pred             CcEEEEEECCCcHHHHHHHHHHHhhCCEEEEEEECCCCccccchHHHHHHHHhCCCceEEEEEeeccccchhHHHHHHHH
Confidence            5678999999921 10 111 11346999999999876533211 0   01111 2357899999998542133444444


Q ss_pred             HHH----hc--CCCCCEEEEecccCCCHHHH
Q 030407          145 DAL----RM--RDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       145 ~l~----~~--np~a~i~~~SA~~g~gi~el  169 (178)
                      .++    ..  .+..+++++||++|+|++++
T Consensus       186 ~l~~~~~~~~~~~~~~iipvSA~~g~ni~~~  216 (474)
T PRK05124        186 DYLTFAEQLPGNLDIRFVPLSALEGDNVVSQ  216 (474)
T ss_pred             HHHHHHHhcCCCCCceEEEEEeecCCCcccc
Confidence            443    22  24689999999999999763

>PRK11058 GTPase HflX; Provisional

Probab=98.08  E-value=1.8e-05  Score=68.56  Aligned_cols=96  Identities=17%  Similarity=0.155  Sum_probs=59.1

Q ss_pred             CEEEEeCCcc-h-----hhhccc-----ccccceEEEEEeCCCCCCCCc-----CCC---CCCCceeEEEEecCCCCCch
Q 030407           75 DLLLCESGGD-N-----LAANFS-----RELADYIIYIIDVSGGDKIPR-----KGG---PGITQADLLVINKTDLASAI  135 (178)
Q Consensus        75 d~iiiEttG~-~-----~~~~~~-----~~~ad~~I~VvD~~~~~~~~~-----~~~---~qi~~adiiviNK~Dl~~~~  135 (178)
                      .++++.|+|. .     +...|.     ...+|.+++|+|++++.....     ...   ..-..+.++|+||+|+.+. 
T Consensus       246 ~~~l~DTaG~~r~lp~~lve~f~~tl~~~~~ADlIL~VvDaS~~~~~e~l~~v~~iL~el~~~~~pvIiV~NKiDL~~~-  324 (426)
T PRK11058        246 ETVLADTVGFIRHLPHDLVAAFKATLQETRQATLLLHVVDAADVRVQENIEAVNTVLEEIDAHEIPTLLVMNKIDMLDD-  324 (426)
T ss_pred             eEEEEecCcccccCCHHHHHHHHHHHHHhhcCCEEEEEEeCCCccHHHHHHHHHHHHHHhccCCCCEEEEEEcccCCCc-
Confidence            6789999994 1     011121     124799999999987642111     000   1113467999999999754 


Q ss_pred             hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          136 GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       136 ~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                       .. .....  ...+ ...++.+||++|+|+++|++++...
T Consensus       325 -~~-~~~~~--~~~~-~~~~v~ISAktG~GIdeL~e~I~~~  360 (426)
T PRK11058        325 -FE-PRIDR--DEEN-KPIRVWLSAQTGAGIPLLFQALTER  360 (426)
T ss_pred             -hh-HHHHH--HhcC-CCceEEEeCCCCCCHHHHHHHHHHH
Confidence             22 11111  1111 1235889999999999999988654

>PRK12317 elongation factor 1-alpha; Reviewed

Probab=98.07  E-value=1.1e-05  Score=69.61  Aligned_cols=96  Identities=13%  Similarity=0.073  Sum_probs=56.8

Q ss_pred             CCCEEEEeCCcch-hhh-ccc-ccccceEEEEEeCCC--CCCCCc-CC---CCCCCc-eeEEEEecCCCCCchhHhH---
Q 030407           73 KADLLLCESGGDN-LAA-NFS-RELADYIIYIIDVSG--GDKIPR-KG---GPGITQ-ADLLVINKTDLASAIGADL---  139 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~-~~~-~~~ad~~I~VvD~~~--~~~~~~-~~---~~qi~~-adiiviNK~Dl~~~~~~~~---  139 (178)
                      ++.+.|+.|.|.. ... ... ...+|.+++|+|+.+  +..... .+   ...+.. .-++++||+|+.+...+..   
T Consensus        83 ~~~i~liDtpG~~~~~~~~~~~~~~aD~~ilVvDa~~~~~~~~~~~~~~~~~~~~~~~~iivviNK~Dl~~~~~~~~~~~  162 (425)
T PRK12317         83 KYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAADDAGGVMPQTREHVFLARTLGINQLIVAINKMDAVNYDEKRYEEV  162 (425)
T ss_pred             CeEEEEEECCCcccchhhHhhchhcCCEEEEEEEcccCCCCCcchHHHHHHHHHcCCCeEEEEEEccccccccHHHHHHH
Confidence            5788999999931 111 111 124699999999986  322111 00   011222 3578999999986311222   


Q ss_pred             -HHHHHHHHhcC--C-CCCEEEEecccCCCHHH
Q 030407          140 -AVMERDALRMR--D-GGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       140 -~~~~~~l~~~n--p-~a~i~~~SA~~g~gi~e  168 (178)
                       +++.+.++...  + ..+++++||++|+|+++
T Consensus       163 ~~~i~~~l~~~g~~~~~~~ii~iSA~~g~gi~~  195 (425)
T PRK12317        163 KEEVSKLLKMVGYKPDDIPFIPVSAFEGDNVVK  195 (425)
T ss_pred             HHHHHHHHHhhCCCcCcceEEEeecccCCCccc
Confidence             33444443332  1 36899999999999987

>TIGR03597 GTPase_YqeH ribosome biogenesis GTPase YqeH

Probab=98.06  E-value=6.7e-06  Score=69.67  Aligned_cols=81  Identities=19%  Similarity=0.076  Sum_probs=51.6

Q ss_pred             ccceEEEEEeCCCCCCCCcC-CCCCC-CceeEEEEecCCCCCchhHhHHHHHHHH----HhcC-CCCCEEEEecccCCCH
Q 030407           94 LADYIIYIIDVSGGDKIPRK-GGPGI-TQADLLVINKTDLASAIGADLAVMERDA----LRMR-DGGPFIFAQVGWVIGI  166 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~-~~~qi-~~adiiviNK~Dl~~~~~~~~~~~~~~l----~~~n-p~a~i~~~SA~~g~gi  166 (178)
                      .++.++.|+|+.+....... ....+ ...-++|+||+||.+.. ...+.+.+++    ++.+ +...++.+||++|.|+
T Consensus        63 ~~~~Il~VvD~~d~~~s~~~~l~~~~~~~piilV~NK~DLl~k~-~~~~~~~~~l~~~~k~~g~~~~~i~~vSAk~g~gv  141 (360)
T TIGR03597        63 SNALIVYVVDIFDFEGSLIPELKRFVGGNPVLLVGNKIDLLPKS-VNLSKIKEWMKKRAKELGLKPVDIILVSAKKGNGI  141 (360)
T ss_pred             CCcEEEEEEECcCCCCCccHHHHHHhCCCCEEEEEEchhhCCCC-CCHHHHHHHHHHHHHHcCCCcCcEEEecCCCCCCH
Confidence            46899999998665422110 00001 33568999999998651 2233444443    3322 1136999999999999


Q ss_pred             HHHHHHHhh
Q 030407          167 IFTLSITHY  175 (178)
Q Consensus       167 ~el~~~l~~  175 (178)
                      +++++.+.+
T Consensus       142 ~eL~~~l~~  150 (360)
T TIGR03597       142 DELLDKIKK  150 (360)
T ss_pred             HHHHHHHHH
Confidence            999999865

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.

>COG3276 SelB Selenocysteine-specific translation elongation factor [Translation, ribosomal structure and biogenesis]

Probab=98.06  E-value=1.2e-05  Score=68.76  Aligned_cols=103  Identities=11%  Similarity=0.034  Sum_probs=69.9

Q ss_pred             CCCEEEEeCCcch--hhhc-ccccccceEEEEEeCCCCCCCCcC-C---CCCCCcee-EEEEecCCCCCchhHhHHHHHH
Q 030407           73 KADLLLCESGGDN--LAAN-FSRELADYIIYIIDVSGGDKIPRK-G---GPGITQAD-LLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~-~~~~~ad~~I~VvD~~~~~~~~~~-~---~~qi~~ad-iiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      +.-.-|||++|-.  +... ......|..++|||+.+|...+.. +   ...+.... +||+||+|++++  +.+++..+
T Consensus        49 d~~~~fIDvpgh~~~i~~miag~~~~d~alLvV~~deGl~~qtgEhL~iLdllgi~~giivltk~D~~d~--~r~e~~i~  126 (447)
T COG3276          49 DGVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKNGIIVLTKADRVDE--ARIEQKIK  126 (447)
T ss_pred             CCceEEeeCCCcHHHHHHHHhhhcCCceEEEEEeCccCcchhhHHHHHHHHhcCCCceEEEEeccccccH--HHHHHHHH
Confidence            3467789999921  1111 111245899999999877654321 1   11233333 999999999988  66666555


Q ss_pred             HHHhc--CCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          145 DALRM--RDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       145 ~l~~~--np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .+.+-  .+.++++.+|+++|+||++|.+.|..+.
T Consensus       127 ~Il~~l~l~~~~i~~~s~~~g~GI~~Lk~~l~~L~  161 (447)
T COG3276         127 QILADLSLANAKIFKTSAKTGRGIEELKNELIDLL  161 (447)
T ss_pred             HHHhhcccccccccccccccCCCHHHHHHHHHHhh
Confidence            55432  3578999999999999999999887653

>PRK03003 GTP-binding protein Der; Reviewed

Probab=98.05  E-value=7.6e-06  Score=71.64  Aligned_cols=98  Identities=15%  Similarity=0.104  Sum_probs=60.7

Q ss_pred             CCCEEEEeCCcch-----hhh------cccccccceEEEEEeCCCCCCCCcC-CC---CCCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDN-----LAA------NFSRELADYIIYIIDVSGGDKIPRK-GG---PGITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~-----~~~------~~~~~~ad~~I~VvD~~~~~~~~~~-~~---~qi~~adiiviNK~Dl~~~~~~  137 (178)
                      +..+.+++|.|..     +..      ......+|++++|+|++.+...... ..   .....+-++|+||+|+...  .
T Consensus        85 ~~~~~l~DT~G~~~~~~~~~~~~~~~~~~~~~~aD~il~VvD~~~~~s~~~~~i~~~l~~~~~piilV~NK~Dl~~~--~  162 (472)
T PRK03003         85 GRRFTVVDTGGWEPDAKGLQASVAEQAEVAMRTADAVLFVVDATVGATATDEAVARVLRRSGKPVILAANKVDDERG--E  162 (472)
T ss_pred             CcEEEEEeCCCcCCcchhHHHHHHHHHHHHHHhCCEEEEEEECCCCCCHHHHHHHHHHHHcCCCEEEEEECccCCcc--c
Confidence            4568899999942     100      0112247999999999876432211 11   1124578999999999654  2


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      . +. .+.. .. .....+++||++|.|++++++++.+.
T Consensus       163 ~-~~-~~~~-~~-g~~~~~~iSA~~g~gi~eL~~~i~~~  197 (472)
T PRK03003        163 A-DA-AALW-SL-GLGEPHPVSALHGRGVGDLLDAVLAA  197 (472)
T ss_pred             h-hh-HHHH-hc-CCCCeEEEEcCCCCCcHHHHHHHHhh
Confidence            1 11 1111 12 12245799999999999999987653

>PRK00098 GTPase RsgA; Reviewed

Probab=98.04  E-value=8.2e-06  Score=67.40  Aligned_cols=77  Identities=12%  Similarity=0.008  Sum_probs=51.0

Q ss_pred             cceEEEEEeCCCCCCCCc---CCC---CCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHH
Q 030407           95 ADYIIYIIDVSGGDKIPR---KGG---PGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~---~~~---~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                      +|.+++|+|+.++.....   ++.   ......-++|+||+||.+.. ...+...+..+..  +.+++++||++|+|+++
T Consensus        81 iD~vllV~d~~~p~~~~~~idr~L~~~~~~~ip~iIVlNK~DL~~~~-~~~~~~~~~~~~~--g~~v~~vSA~~g~gi~~  157 (298)
T PRK00098         81 VDQAVLVFAAKEPDFSTDLLDRFLVLAEANGIKPIIVLNKIDLLDDL-EEARELLALYRAI--GYDVLELSAKEGEGLDE  157 (298)
T ss_pred             CCEEEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEEEhHHcCCCH-HHHHHHHHHHHHC--CCeEEEEeCCCCccHHH
Confidence            588999999976532211   111   11234569999999997441 3333344444433  35899999999999999


Q ss_pred             HHHHHh
Q 030407          169 TLSITH  174 (178)
Q Consensus       169 l~~~l~  174 (178)
                      |++.+.
T Consensus       158 L~~~l~  163 (298)
T PRK00098        158 LKPLLA  163 (298)
T ss_pred             HHhhcc
Confidence            998875

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

Probab=98.03  E-value=2.5e-05  Score=59.85  Aligned_cols=102  Identities=14%  Similarity=0.100  Sum_probs=69.6

Q ss_pred             CCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCCc------CC-----CCC-CCceeEEEEecCCCCCc--h
Q 030407           74 ADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIPR------KG-----GPG-ITQADLLVINKTDLASA--I  135 (178)
Q Consensus        74 ~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~~------~~-----~~q-i~~adiiviNK~Dl~~~--~  135 (178)
                      +-.-+..|.|.    ++..+|++ ++|.++.++|+........      ++     +.. -.++=+|+.||+|+...  .
T Consensus        58 vtlQiWDTAGQERFqsLg~aFYR-gaDcCvlvydv~~~~Sfe~L~~Wr~EFl~qa~~~~Pe~FPFVilGNKiD~~~~~~r  136 (210)
T KOG0394|consen   58 VTLQIWDTAGQERFQSLGVAFYR-GADCCVLVYDVNNPKSFENLENWRKEFLIQASPQDPETFPFVILGNKIDVDGGKSR  136 (210)
T ss_pred             EEEEEEecccHHHhhhcccceec-CCceEEEEeecCChhhhccHHHHHHHHHHhcCCCCCCcccEEEEcccccCCCCccc
Confidence            45667888883    23334444 7899999999976543211      11     111 24566999999999652  1


Q ss_pred             hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          136 GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       136 ~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      -...++.++|.++ +...|+|+||||.+.++++-|+.+.+.|
T Consensus       137 ~VS~~~Aq~WC~s-~gnipyfEtSAK~~~NV~~AFe~ia~~a  177 (210)
T KOG0394|consen  137 QVSEKKAQTWCKS-KGNIPYFETSAKEATNVDEAFEEIARRA  177 (210)
T ss_pred             eeeHHHHHHHHHh-cCCceeEEecccccccHHHHHHHHHHHH
Confidence            1334567777776 4578999999999999999999876654

>PRK12288 GTPase RsgA; Reviewed

Probab=98.03  E-value=1.8e-05  Score=66.85  Aligned_cols=79  Identities=15%  Similarity=0.038  Sum_probs=49.1

Q ss_pred             cceEEEEEeCCCCCCCC--cCC---CCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhc-CCCCCEEEEecccCCCHHH
Q 030407           95 ADYIIYIIDVSGGDKIP--RKG---GPGITQADLLVINKTDLASAIGADLAVMERDALRM-RDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~--~~~---~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~-np~a~i~~~SA~~g~gi~e  168 (178)
                      .|.+++|.+........  ..+   .......-++|+||+||.++  .+.+.+.++.+.. ..+.+++.+||++|+|+++
T Consensus       121 vD~vlIV~s~~p~~s~~~Ldr~L~~a~~~~i~~VIVlNK~DL~~~--~~~~~~~~~~~~y~~~g~~v~~vSA~tg~Gide  198 (347)
T PRK12288        121 IDQIVIVSAVLPELSLNIIDRYLVACETLGIEPLIVLNKIDLLDD--EGRAFVNEQLDIYRNIGYRVLMVSSHTGEGLEE  198 (347)
T ss_pred             ccEEEEEEeCCCCCCHHHHHHHHHHHHhcCCCEEEEEECccCCCc--HHHHHHHHHHHHHHhCCCeEEEEeCCCCcCHHH
Confidence            47777777764322111  111   11223456999999999876  4333333332221 2346999999999999999


Q ss_pred             HHHHHhh
Q 030407          169 TLSITHY  175 (178)
Q Consensus       169 l~~~l~~  175 (178)
                      |++.+..
T Consensus       199 L~~~L~~  205 (347)
T PRK12288        199 LEAALTG  205 (347)
T ss_pred             HHHHHhh
Confidence            9998864

>cd04129 Rho2 Rho2 subfamily

Probab=98.03  E-value=1.3e-05  Score=61.29  Aligned_cols=103  Identities=17%  Similarity=0.051  Sum_probs=62.0

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc---CCCC-----CCCceeEEEEecCCCCCchh-----
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR---KGGP-----GITQADLLVINKTDLASAIG-----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~-----qi~~adiiviNK~Dl~~~~~-----  136 (178)
                      ..++.++++.|..-.   .+.....++.++.++|.+.......   .+..     .-..+-++|.||+|+.+...     
T Consensus        48 ~~~l~i~Dt~g~~~~~~~~~~~~~~a~~~llv~~i~~~~s~~~~~~~~~~~i~~~~~~~piilvgnK~Dl~~~~~~~~~~  127 (187)
T cd04129          48 PVQLALWDTAGQEEYERLRPLSYSKAHVILIGFAVDTPDSLENVRTKWIEEVRRYCPNVPVILVGLKKDLRQDAVAKEEY  127 (187)
T ss_pred             EEEEEEEECCCChhccccchhhcCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEeeChhhhhCccccccc
Confidence            356778899993211   1112234688999999876432211   0100     01356799999999854200     


Q ss_pred             -----HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 -----ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 -----~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                           ...+......++. ...+++++||++|+|++++|+.+.+.
T Consensus       128 ~~~~~~~~~~~~~~~~~~-~~~~~~e~Sa~~~~~v~~~f~~l~~~  171 (187)
T cd04129         128 RTQRFVPIQQGKRVAKEI-GAKKYMECSALTGEGVDDVFEAATRA  171 (187)
T ss_pred             ccCCcCCHHHHHHHHHHh-CCcEEEEccCCCCCCHHHHHHHHHHH
Confidence                 1112333333333 22479999999999999999998754

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).

>PRK12736 elongation factor Tu; Reviewed

Probab=97.99  E-value=3.2e-05  Score=66.23  Aligned_cols=102  Identities=14%  Similarity=0.123  Sum_probs=63.0

Q ss_pred             CCCEEEEeCCcch--hhhccc-ccccceEEEEEeCCCCCCCCc-CCC---CCCCce-eEEEEecCCCCCchhHhH-----
Q 030407           73 KADLLLCESGGDN--LAANFS-RELADYIIYIIDVSGGDKIPR-KGG---PGITQA-DLLVINKTDLASAIGADL-----  139 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~~-~~~ad~~I~VvD~~~~~~~~~-~~~---~qi~~a-diiviNK~Dl~~~~~~~~-----  139 (178)
                      +..+.||.|.|-.  +..+.. ...+|.+++|+|+..+...+. .+.   .....+ -++++||+|++++  ++.     
T Consensus        74 ~~~i~~iDtPGh~~f~~~~~~~~~~~d~~llVvd~~~g~~~~t~~~~~~~~~~g~~~~IvviNK~D~~~~--~~~~~~i~  151 (394)
T PRK12736         74 KRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVGVPYLVVFLNKVDLVDD--EELLELVE  151 (394)
T ss_pred             CcEEEEEECCCHHHHHHHHHHHHhhCCEEEEEEECCCCCchhHHHHHHHHHHcCCCEEEEEEEecCCcch--HHHHHHHH
Confidence            4578999999921  111111 124699999999987643221 111   112344 3678999999854  222     


Q ss_pred             HHHHHHHHhcC---CCCCEEEEecccCC--------CHHHHHHHHhhh
Q 030407          140 AVMERDALRMR---DGGPFIFAQVGWVI--------GIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~n---p~a~i~~~SA~~g~--------gi~el~~~l~~~  176 (178)
                      +++.+.++...   ...+++++||++|.        ++++|++.+.+.
T Consensus       152 ~~i~~~l~~~~~~~~~~~ii~vSa~~g~~~~~~~~~~i~~Ll~~l~~~  199 (394)
T PRK12736        152 MEVRELLSEYDFPGDDIPVIRGSALKALEGDPKWEDAIMELMDAVDEY  199 (394)
T ss_pred             HHHHHHHHHhCCCcCCccEEEeeccccccCCCcchhhHHHHHHHHHHh
Confidence            23444444443   24699999999983        688888887654

>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=97.98  E-value=2.6e-07  Score=69.41  Aligned_cols=95  Identities=21%  Similarity=0.185  Sum_probs=57.6

Q ss_pred             CCCEEEEeCCcc-hhh---------hccc-ccccceEEEEEeCCCCCCCCcCCCC---CCCceeEEEEecCCCCCchhH-
Q 030407           73 KADLLLCESGGD-NLA---------ANFS-RELADYIIYIIDVSGGDKIPRKGGP---GITQADLLVINKTDLASAIGA-  137 (178)
Q Consensus        73 ~~d~iiiEttG~-~~~---------~~~~-~~~ad~~I~VvD~~~~~~~~~~~~~---qi~~adiiviNK~Dl~~~~~~-  137 (178)
                      +..+.||.+.|. ++.         ..+. ....|.++.|+|+++..... ....   .+..+-++++||+|++..... 
T Consensus        46 ~~~~~lvDlPG~ysl~~~s~ee~v~~~~l~~~~~D~ii~VvDa~~l~r~l-~l~~ql~e~g~P~vvvlN~~D~a~~~g~~  124 (156)
T PF02421_consen   46 DQQVELVDLPGIYSLSSKSEEERVARDYLLSEKPDLIIVVVDATNLERNL-YLTLQLLELGIPVVVVLNKMDEAERKGIE  124 (156)
T ss_dssp             TEEEEEEE----SSSSSSSHHHHHHHHHHHHTSSSEEEEEEEGGGHHHHH-HHHHHHHHTTSSEEEEEETHHHHHHTTEE
T ss_pred             CceEEEEECCCcccCCCCCcHHHHHHHHHhhcCCCEEEEECCCCCHHHHH-HHHHHHHHcCCCEEEEEeCHHHHHHcCCE
Confidence            467888888884 111         1111 12359999999998743211 1111   245678999999999865211 


Q ss_pred             -hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHH
Q 030407          138 -DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSIT  173 (178)
Q Consensus       138 -~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l  173 (178)
                       ..+.+.+.+     +.|++++||++|+|+++|++.|
T Consensus       125 id~~~Ls~~L-----g~pvi~~sa~~~~g~~~L~~~I  156 (156)
T PF02421_consen  125 IDAEKLSERL-----GVPVIPVSARTGEGIDELKDAI  156 (156)
T ss_dssp             E-HHHHHHHH-----TS-EEEEBTTTTBTHHHHHHHH
T ss_pred             ECHHHHHHHh-----CCCEEEEEeCCCcCHHHHHhhC
Confidence             223444433     4689999999999999999875

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 ....

>COG1160 Predicted GTPases [General function prediction only]

Probab=97.98  E-value=2e-05  Score=67.79  Aligned_cols=98  Identities=19%  Similarity=0.144  Sum_probs=65.3

Q ss_pred             CCCEEEEeCCcchhhh--cc----------cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchh
Q 030407           73 KADLLLCESGGDNLAA--NF----------SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIG  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~--~~----------~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~  136 (178)
                      +..+.+|.|-|.-...  .+          ....||.+++|||+..|....+.    +......+.++|+||+|-...  
T Consensus        50 ~~~f~lIDTgGl~~~~~~~l~~~i~~Qa~~Ai~eADvilfvVD~~~Git~~D~~ia~~Lr~~~kpviLvvNK~D~~~~--  127 (444)
T COG1160          50 GREFILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIAKILRRSKKPVILVVNKIDNLKA--  127 (444)
T ss_pred             CceEEEEECCCCCcCCchHHHHHHHHHHHHHHHhCCEEEEEEeCCCCCCHHHHHHHHHHHhcCCCEEEEEEcccCchh--
Confidence            4568888888842111  11          12347999999999887654331    112344678999999997643  


Q ss_pred             HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 ~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +  +...++.. + ...+++++||.+|.|+.+|++.+.+.
T Consensus       128 e--~~~~efys-l-G~g~~~~ISA~Hg~Gi~dLld~v~~~  163 (444)
T COG1160         128 E--ELAYEFYS-L-GFGEPVPISAEHGRGIGDLLDAVLEL  163 (444)
T ss_pred             h--hhHHHHHh-c-CCCCceEeehhhccCHHHHHHHHHhh
Confidence            2  22222332 2 35689999999999999999987664

>KOG1145 consensus Mitochondrial translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]

Probab=97.97  E-value=3.4e-05  Score=67.85  Aligned_cols=99  Identities=15%  Similarity=0.145  Sum_probs=65.9

Q ss_pred             CCEEEEeCCcchhhhcc---cc--cccceEEEEEeCCCCCCCCc----CCCCCCCceeEEEEecCCCCCchhHhHHHHHH
Q 030407           74 ADLLLCESGGDNLAANF---SR--ELADYIIYIIDVSGGDKIPR----KGGPGITQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~~---~~--~~ad~~I~VvD~~~~~~~~~----~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      --+-|..|.|  .++..   .+  ..+|.+|+||-+.+|...+.    ++...-..+-+|.+||+|....   ..+++.+
T Consensus       201 ~~iTFLDTPG--HaAF~aMRaRGA~vtDIvVLVVAadDGVmpQT~EaIkhAk~A~VpiVvAinKiDkp~a---~pekv~~  275 (683)
T KOG1145|consen  201 KSITFLDTPG--HAAFSAMRARGANVTDIVVLVVAADDGVMPQTLEAIKHAKSANVPIVVAINKIDKPGA---NPEKVKR  275 (683)
T ss_pred             CEEEEecCCc--HHHHHHHHhccCccccEEEEEEEccCCccHhHHHHHHHHHhcCCCEEEEEeccCCCCC---CHHHHHH
Confidence            4567777888  22111   11  23589999999887765432    1222223356999999998755   4455554


Q ss_pred             HHH-------hcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          145 DAL-------RMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       145 ~l~-------~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .+-       .+....+++++||++|+|++.|.+.+.-+|
T Consensus       276 eL~~~gi~~E~~GGdVQvipiSAl~g~nl~~L~eaill~A  315 (683)
T KOG1145|consen  276 ELLSQGIVVEDLGGDVQVIPISALTGENLDLLEEAILLLA  315 (683)
T ss_pred             HHHHcCccHHHcCCceeEEEeecccCCChHHHHHHHHHHH
Confidence            443       334567999999999999999999877654

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

Probab=97.94  E-value=3.5e-05  Score=69.84  Aligned_cols=96  Identities=16%  Similarity=0.151  Sum_probs=57.8

Q ss_pred             CCCEEEEeCCcch-hh-hcc-cccccceEEEEEeCCCCCCCCcC----CCCCCC-ceeEEEEecCCCCCchhHhHHHHHH
Q 030407           73 KADLLLCESGGDN-LA-ANF-SRELADYIIYIIDVSGGDKIPRK----GGPGIT-QADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~-~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      +..++||.|.|.. .. .+. ....+|.+++|+|+..+...+..    ....+. ..-++++||+|+++...+..+.+..
T Consensus       103 ~~~~~liDtPG~~~f~~~~~~~~~~aD~~llVvda~~g~~~~t~e~~~~~~~~~~~~iivvvNK~D~~~~~~~~~~~i~~  182 (632)
T PRK05506        103 KRKFIVADTPGHEQYTRNMVTGASTADLAIILVDARKGVLTQTRRHSFIASLLGIRHVVLAVNKMDLVDYDQEVFDEIVA  182 (632)
T ss_pred             CceEEEEECCChHHHHHHHHHHHHhCCEEEEEEECCCCccccCHHHHHHHHHhCCCeEEEEEEecccccchhHHHHHHHH
Confidence            4578999999931 11 111 12346999999999876433211    111122 2347799999998531133344433


Q ss_pred             HHH----hc-CCCCCEEEEecccCCCHHH
Q 030407          145 DAL----RM-RDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       145 ~l~----~~-np~a~i~~~SA~~g~gi~e  168 (178)
                      .++    .. .+..+++++||++|+|+++
T Consensus       183 ~i~~~~~~~~~~~~~iipiSA~~g~ni~~  211 (632)
T PRK05506        183 DYRAFAAKLGLHDVTFIPISALKGDNVVT  211 (632)
T ss_pred             HHHHHHHHcCCCCccEEEEecccCCCccc
Confidence            332    22 2346899999999999874

>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA

Probab=97.93  E-value=2.5e-05  Score=67.20  Aligned_cols=98  Identities=19%  Similarity=0.125  Sum_probs=63.0

Q ss_pred             CCCEEEEeCCcchh-----hh-----cc-cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDNL-----AA-----NF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~-----~~-----~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~  137 (178)
                      +..+.+++|.|...     ..     .. ....+|.+++|+|+..+......    +......+-++|+||+|+.+.  .
T Consensus        46 ~~~~~liDTpG~~~~~~~~~~~~~~~~~~~~~~ad~vl~vvD~~~~~~~~d~~i~~~l~~~~~piilVvNK~D~~~~--~  123 (429)
T TIGR03594        46 GREFILIDTGGIEEDDDGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEEIAKWLRKSGKPVILVANKIDGKKE--D  123 (429)
T ss_pred             CeEEEEEECCCCCCcchhHHHHHHHHHHHHHhhCCEEEEEEeCCCCCCHHHHHHHHHHHHhCCCEEEEEECccCCcc--c
Confidence            45689999999411     00     00 11246999999999876433211    111234567999999999765  2


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..  .. ...++ ...+++++||++|.|++++++.+.+.
T Consensus       124 ~~--~~-~~~~l-g~~~~~~vSa~~g~gv~~ll~~i~~~  158 (429)
T TIGR03594       124 AV--AA-EFYSL-GFGEPIPISAEHGRGIGDLLDAILEL  158 (429)
T ss_pred             cc--HH-HHHhc-CCCCeEEEeCCcCCChHHHHHHHHHh
Confidence            21  11 12222 34489999999999999999987654

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.

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

Probab=97.92  E-value=2.1e-05  Score=60.47  Aligned_cols=101  Identities=15%  Similarity=0.074  Sum_probs=67.5

Q ss_pred             hCCCCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCCc--CCC---CCC---CceeEEEEecCCCCCchhHh
Q 030407           71 LFKADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIPR--KGG---PGI---TQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        71 ~~~~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~---~qi---~~adiiviNK~Dl~~~~~~~  138 (178)
                      ..+..+=+..|.|.    ++...|+. .+.+.++|+|.++.+....  .+.   .|-   ..--+++.||+||.......
T Consensus        52 ~k~IKlqiwDtaGqe~frsv~~syYr-~a~GalLVydit~r~sF~hL~~wL~D~rq~~~~NmvImLiGNKsDL~~rR~Vs  130 (216)
T KOG0098|consen   52 GKQIKLQIWDTAGQESFRSVTRSYYR-GAAGALLVYDITRRESFNHLTSWLEDARQHSNENMVIMLIGNKSDLEARREVS  130 (216)
T ss_pred             CceEEEEEEecCCcHHHHHHHHHHhc-cCcceEEEEEccchhhHHHHHHHHHHHHHhcCCCcEEEEEcchhhhhcccccc
Confidence            34677788899994    23344444 6789999999987654311  000   111   12247889999998653344


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      .++-+++.++  .+-..++|||++++|++|.|.-..
T Consensus       131 ~EEGeaFA~e--hgLifmETSakt~~~VEEaF~nta  164 (216)
T KOG0098|consen  131 KEEGEAFARE--HGLIFMETSAKTAENVEEAFINTA  164 (216)
T ss_pred             HHHHHHHHHH--cCceeehhhhhhhhhHHHHHHHHH
Confidence            5666777776  355778999999999999987543

>PRK00049 elongation factor Tu; Reviewed

Probab=97.91  E-value=5.6e-05  Score=64.83  Aligned_cols=103  Identities=13%  Similarity=0.129  Sum_probs=63.0

Q ss_pred             CCCEEEEeCCcch--hhhcc-cccccceEEEEEeCCCCCCCCc-CC---CCCCCceeE-EEEecCCCCCchhHhHH----
Q 030407           73 KADLLLCESGGDN--LAANF-SRELADYIIYIIDVSGGDKIPR-KG---GPGITQADL-LVINKTDLASAIGADLA----  140 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~-~~~~ad~~I~VvD~~~~~~~~~-~~---~~qi~~adi-iviNK~Dl~~~~~~~~~----  140 (178)
                      +..+.||.|.|..  +.... ....+|.+++|+|+..+...+. .+   ......+-+ +++||+|+++.. +..+    
T Consensus        74 ~~~i~~iDtPG~~~f~~~~~~~~~~aD~~llVVDa~~g~~~qt~~~~~~~~~~g~p~iiVvvNK~D~~~~~-~~~~~~~~  152 (396)
T PRK00049         74 KRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFLNKCDMVDDE-ELLELVEM  152 (396)
T ss_pred             CeEEEEEECCCHHHHHHHHHhhhccCCEEEEEEECCCCCchHHHHHHHHHHHcCCCEEEEEEeecCCcchH-HHHHHHHH
Confidence            4578999999931  11111 1134799999999987643321 11   111234555 579999998541 2222    


Q ss_pred             HHHHHHHhcC---CCCCEEEEecccCC----------CHHHHHHHHhhh
Q 030407          141 VMERDALRMR---DGGPFIFAQVGWVI----------GIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~n---p~a~i~~~SA~~g~----------gi~el~~~l~~~  176 (178)
                      ++.+.++...   ...+++++||++|.          |+..|++.|..+
T Consensus       153 ~i~~~l~~~~~~~~~~~iv~iSa~~g~~~~~~~~w~~~~~~ll~~l~~~  201 (396)
T PRK00049        153 EVRELLSKYDFPGDDTPIIRGSALKALEGDDDEEWEKKILELMDAVDSY  201 (396)
T ss_pred             HHHHHHHhcCCCccCCcEEEeecccccCCCCcccccccHHHHHHHHHhc
Confidence            3444444321   24799999999975          678888888754

>PRK00093 GTP-binding protein Der; Reviewed

Probab=97.90  E-value=3.8e-05  Score=66.29  Aligned_cols=97  Identities=19%  Similarity=0.107  Sum_probs=61.7

Q ss_pred             CCCEEEEeCCcchh-----h----hcc--cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDNL-----A----ANF--SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~-----~----~~~--~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~  137 (178)
                      +..+.+++|.|..-     .    ...  ....+|.+++|+|+..+......    +......+-++|+||+|+.+.  +
T Consensus        48 ~~~~~liDT~G~~~~~~~~~~~~~~~~~~~~~~ad~il~vvd~~~~~~~~~~~~~~~l~~~~~piilv~NK~D~~~~--~  125 (435)
T PRK00093         48 GREFILIDTGGIEPDDDGFEKQIREQAELAIEEADVILFVVDGRAGLTPADEEIAKILRKSNKPVILVVNKVDGPDE--E  125 (435)
T ss_pred             CcEEEEEECCCCCCcchhHHHHHHHHHHHHHHhCCEEEEEEECCCCCCHHHHHHHHHHHHcCCcEEEEEECccCccc--h
Confidence            47889999999421     0    000  11247999999999875432211    111124567999999997653  2


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .  ...+. ..+ ...+++++||++|.|++++++.+.+
T Consensus       126 ~--~~~~~-~~l-g~~~~~~iSa~~g~gv~~l~~~I~~  159 (435)
T PRK00093        126 A--DAYEF-YSL-GLGEPYPISAEHGRGIGDLLDAILE  159 (435)
T ss_pred             h--hHHHH-Hhc-CCCCCEEEEeeCCCCHHHHHHHHHh
Confidence            1  11222 222 2335799999999999999998764

>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed

Probab=97.87  E-value=3.6e-05  Score=70.67  Aligned_cols=98  Identities=16%  Similarity=0.055  Sum_probs=61.2

Q ss_pred             CCCEEEEeCCcchh-----hhcc------cccccceEEEEEeCCCCCCCCcC-C---CCCCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDNL-----AANF------SRELADYIIYIIDVSGGDKIPRK-G---GPGITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~-----~~~~------~~~~ad~~I~VvD~~~~~~~~~~-~---~~qi~~adiiviNK~Dl~~~~~~  137 (178)
                      +..+.+++|.|...     ...+      ....+|.+++|+|++.+...... .   ......+-++|+||+|+...  .
T Consensus       322 ~~~~~liDT~G~~~~~~~~~~~~~~~~~~~~~~aD~iL~VvDa~~~~~~~d~~i~~~Lr~~~~pvIlV~NK~D~~~~--~  399 (712)
T PRK09518        322 GTDFKLVDTGGWEADVEGIDSAIASQAQIAVSLADAVVFVVDGQVGLTSTDERIVRMLRRAGKPVVLAVNKIDDQAS--E  399 (712)
T ss_pred             CEEEEEEeCCCcCCCCccHHHHHHHHHHHHHHhCCEEEEEEECCCCCCHHHHHHHHHHHhcCCCEEEEEECcccccc--h
Confidence            34678999999421     0001      11347999999999875432211 1   11234577999999998654  2


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..  .....+ + .....+++||++|.|++++++.+...
T Consensus       400 ~~--~~~~~~-l-g~~~~~~iSA~~g~GI~eLl~~i~~~  434 (712)
T PRK09518        400 YD--AAEFWK-L-GLGEPYPISAMHGRGVGDLLDEALDS  434 (712)
T ss_pred             hh--HHHHHH-c-CCCCeEEEECCCCCCchHHHHHHHHh
Confidence            21  122222 1 22356899999999999999987654

>KOG1489 consensus Predicted GTP-binding protein (ODN superfamily) [General function prediction only]

Probab=97.85  E-value=2.5e-05  Score=64.56  Aligned_cols=78  Identities=18%  Similarity=0.173  Sum_probs=50.9

Q ss_pred             cceEEEEEeCCCCCCC---Cc---------CCCC-CCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecc
Q 030407           95 ADYIIYIIDVSGGDKI---PR---------KGGP-GITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVG  161 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~---~~---------~~~~-qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~  161 (178)
                      ...+++|+|.+.+...   ..         .|.+ ....+-+||.||+|+.+.   +...+.+..+.+ +...|+++||+
T Consensus       275 ~~~l~fVvD~s~~~~~~p~~~~~lL~~ELe~yek~L~~rp~liVaNKiD~~ea---e~~~l~~L~~~l-q~~~V~pvsA~  350 (366)
T KOG1489|consen  275 CKGLLFVVDLSGKQLRNPWQQLQLLIEELELYEKGLADRPALIVANKIDLPEA---EKNLLSSLAKRL-QNPHVVPVSAK  350 (366)
T ss_pred             hceEEEEEECCCcccCCHHHHHHHHHHHHHHHhhhhccCceEEEEeccCchhH---HHHHHHHHHHHc-CCCcEEEeeec
Confidence            3678999999877321   00         1111 234568999999999644   222223333332 33379999999


Q ss_pred             cCCCHHHHHHHHhhh
Q 030407          162 WVIGIIFTLSITHYI  176 (178)
Q Consensus       162 ~g~gi~el~~~l~~~  176 (178)
                      +|+|+++|++.+.+.
T Consensus       351 ~~egl~~ll~~lr~~  365 (366)
T KOG1489|consen  351 SGEGLEELLNGLREL  365 (366)
T ss_pred             cccchHHHHHHHhhc
Confidence            999999999987653

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

Probab=97.83  E-value=2.6e-05  Score=58.69  Aligned_cols=100  Identities=20%  Similarity=0.114  Sum_probs=68.2

Q ss_pred             hCCCCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhH
Q 030407           71 LFKADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        71 ~~~~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~  137 (178)
                      ...+.+-+..|.|.    .+.+.|++ .+.++|+|+|++..+....         .|...-....++|.||+|.-++...
T Consensus        57 g~~~KlaiWDTAGqErFRtLTpSyyR-gaqGiIlVYDVT~Rdtf~kLd~W~~Eld~Ystn~diikmlVgNKiDkes~R~V  135 (209)
T KOG0080|consen   57 GKRLKLAIWDTAGQERFRTLTPSYYR-GAQGIILVYDVTSRDTFVKLDIWLKELDLYSTNPDIIKMLVGNKIDKESERVV  135 (209)
T ss_pred             CceEEEEEEeccchHhhhccCHhHhc-cCceeEEEEEccchhhHHhHHHHHHHHHhhcCCccHhHhhhcccccchhcccc
Confidence            34678889999993    13344544 7899999999988654321         1111123345899999998654324


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHH
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSIT  173 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l  173 (178)
                      ..++-.++.++.  ..-++++|||+.+|++..|+.+
T Consensus       136 ~reEG~kfAr~h--~~LFiE~SAkt~~~V~~~Feel  169 (209)
T KOG0080|consen  136 DREEGLKFARKH--RCLFIECSAKTRENVQCCFEEL  169 (209)
T ss_pred             cHHHHHHHHHhh--CcEEEEcchhhhccHHHHHHHH
Confidence            455555566654  4688999999999999988754

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

Probab=97.83  E-value=4e-05  Score=56.52  Aligned_cols=100  Identities=17%  Similarity=0.144  Sum_probs=67.4

Q ss_pred             CCCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHh
Q 030407           72 FKADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        72 ~~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      ..+.+-++++.|...    ...+ ...+|++|+++|.++......  .       +.. -..+-+++.||.|+.+.....
T Consensus        46 ~~~~l~i~D~~g~~~~~~~~~~~-~~~~~~~ii~fd~~~~~S~~~~~~~~~~i~~~~~-~~~~iivvg~K~D~~~~~~v~  123 (162)
T PF00071_consen   46 KPVNLEIWDTSGQERFDSLRDIF-YRNSDAIIIVFDVTDEESFENLKKWLEEIQKYKP-EDIPIIVVGNKSDLSDEREVS  123 (162)
T ss_dssp             EEEEEEEEEETTSGGGHHHHHHH-HTTESEEEEEEETTBHHHHHTHHHHHHHHHHHST-TTSEEEEEEETTTGGGGSSSC
T ss_pred             ccccccccccccccccccccccc-cccccccccccccccccccccccccccccccccc-ccccceeeeccccccccccch
Confidence            357788999999421    1112 224699999999876432211  0       111 124678999999998632134


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+..++..++.+  .+++++||+++.|+.++|..+.+
T Consensus       124 ~~~~~~~~~~~~--~~~~e~Sa~~~~~v~~~f~~~i~  158 (162)
T PF00071_consen  124 VEEAQEFAKELG--VPYFEVSAKNGENVKEIFQELIR  158 (162)
T ss_dssp             HHHHHHHHHHTT--SEEEEEBTTTTTTHHHHHHHHHH
T ss_pred             hhHHHHHHHHhC--CEEEEEECCCCCCHHHHHHHHHH
Confidence            456666776654  79999999999999999987654

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 ....

>PRK12735 elongation factor Tu; Reviewed

Probab=97.82  E-value=8.6e-05  Score=63.68  Aligned_cols=102  Identities=11%  Similarity=0.103  Sum_probs=62.6

Q ss_pred             CCCEEEEeCCcch--hhhcc-cccccceEEEEEeCCCCCCCCc-CCCC---CCCceeE-EEEecCCCCCchhHh-HH---
Q 030407           73 KADLLLCESGGDN--LAANF-SRELADYIIYIIDVSGGDKIPR-KGGP---GITQADL-LVINKTDLASAIGAD-LA---  140 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~-~~~~ad~~I~VvD~~~~~~~~~-~~~~---qi~~adi-iviNK~Dl~~~~~~~-~~---  140 (178)
                      +..+.|+.|.|..  +..+. ....+|.+++|+|+..+...+. .+..   ....+.+ +++||+|+.+.  ++ .+   
T Consensus        74 ~~~i~~iDtPGh~~f~~~~~~~~~~aD~~llVvda~~g~~~qt~e~l~~~~~~gi~~iivvvNK~Dl~~~--~~~~~~~~  151 (396)
T PRK12735         74 NRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFLNKCDMVDD--EELLELVE  151 (396)
T ss_pred             CcEEEEEECCCHHHHHHHHHhhhccCCEEEEEEECCCCCchhHHHHHHHHHHcCCCeEEEEEEecCCcch--HHHHHHHH
Confidence            4568999999931  11111 1124699999999987643221 1111   1233445 47999999854  22 22   


Q ss_pred             -HHHHHHHhcC-C--CCCEEEEecccC----------CCHHHHHHHHhhh
Q 030407          141 -VMERDALRMR-D--GGPFIFAQVGWV----------IGIIFTLSITHYI  176 (178)
Q Consensus       141 -~~~~~l~~~n-p--~a~i~~~SA~~g----------~gi~el~~~l~~~  176 (178)
                       ++.+.++... +  ..+++++||++|          .|+..|++.|..+
T Consensus       152 ~ei~~~l~~~~~~~~~~~ii~~Sa~~g~n~~~~~~w~~~~~~Ll~~l~~~  201 (396)
T PRK12735        152 MEVRELLSKYDFPGDDTPIIRGSALKALEGDDDEEWEAKILELMDAVDSY  201 (396)
T ss_pred             HHHHHHHHHcCCCcCceeEEecchhccccCCCCCcccccHHHHHHHHHhc
Confidence             3444444332 2  378999999998          4789999888754

>TIGR00231 small_GTP small GTP-binding protein domain

Probab=97.81  E-value=6.5e-05  Score=53.98  Aligned_cols=53  Identities=23%  Similarity=0.117  Sum_probs=40.6

Q ss_pred             CceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          119 TQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       119 ~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      ..+.++++||+|+...  ...+...+.+... +..+++++||++|.|+.+++++|.
T Consensus       108 ~~p~ivv~nK~D~~~~--~~~~~~~~~~~~~-~~~~~~~~sa~~~~gv~~~~~~l~  160 (161)
T TIGR00231       108 NVPIILVGNKIDLRDA--KLKTHVAFLFAKL-NGEPIIPLSAETGKNIDSAFKIVE  160 (161)
T ss_pred             CCcEEEEEEcccCCcc--hhhHHHHHHHhhc-cCCceEEeecCCCCCHHHHHHHhh
Confidence            5578999999999876  3344444444443 345799999999999999999875

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.

>PRK04004 translation initiation factor IF-2; Validated

Probab=97.81  E-value=9.2e-05  Score=66.58  Aligned_cols=99  Identities=16%  Similarity=0.074  Sum_probs=59.0

Q ss_pred             CEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchh----------
Q 030407           75 DLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIG----------  136 (178)
Q Consensus        75 d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~----------  136 (178)
                      .+.|+.|.|..    +.... ...+|.+++|+|++++...+..    .......+-++++||+|+.+...          
T Consensus        72 ~i~~iDTPG~e~f~~~~~~~-~~~aD~~IlVvDa~~g~~~qt~e~i~~~~~~~vpiIvviNK~D~~~~~~~~~~~~~~e~  150 (586)
T PRK04004         72 GLLFIDTPGHEAFTNLRKRG-GALADIAILVVDINEGFQPQTIEAINILKRRKTPFVVAANKIDRIPGWKSTEDAPFLES  150 (586)
T ss_pred             CEEEEECCChHHHHHHHHHh-HhhCCEEEEEEECCCCCCHhHHHHHHHHHHcCCCEEEEEECcCCchhhhhhcCchHHHH
Confidence            47899999931    11111 1246999999999876322210    11112345699999999863200          


Q ss_pred             -----Hh-HH-------HHHHHHHh-------------cCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          137 -----AD-LA-------VMERDALR-------------MRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       137 -----~~-~~-------~~~~~l~~-------------~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                           .. .+       ++...+.+             +....+++++||++|+|+++|++.+.
T Consensus       151 ~~~~~~~v~~~f~~~l~ev~~~L~~~g~~~e~~~~~~~~~~~v~ivpiSA~tGeGi~dLl~~i~  214 (586)
T PRK04004        151 IEKQSQRVQQELEEKLYELIGQLSELGFSADRFDRVKDFTKTVAIVPVSAKTGEGIPDLLMVLA  214 (586)
T ss_pred             HhhhhHHHHHHHHHHHHHHHHHHHhcCCChhhhhhhhccCCCceEeeccCCCCCChHHHHHHHH
Confidence                 00 00       11122221             12346899999999999999998764

>PLN00043 elongation factor 1-alpha; Provisional

Probab=97.81  E-value=0.00014  Score=63.33  Aligned_cols=96  Identities=16%  Similarity=0.046  Sum_probs=55.8

Q ss_pred             CCCEEEEeCCcch--hhhcc-cccccceEEEEEeCCCCCCC-CcCCCCC----------CCce-eEEEEecCCCCCch--
Q 030407           73 KADLLLCESGGDN--LAANF-SRELADYIIYIIDVSGGDKI-PRKGGPG----------ITQA-DLLVINKTDLASAI--  135 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~-~~~~ad~~I~VvD~~~~~~~-~~~~~~q----------i~~a-diiviNK~Dl~~~~--  135 (178)
                      +.-+-||+|.|-.  +..+. ....+|..|+|+|+..+.-. ...+..|          +..+ -++++||+|+.+..  
T Consensus        84 ~~~i~liDtPGh~df~~~~~~g~~~aD~aIlVVda~~G~~e~g~~~~~qT~eh~~~~~~~gi~~iIV~vNKmD~~~~~~~  163 (447)
T PLN00043         84 KYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGGFEAGISKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYS  163 (447)
T ss_pred             CEEEEEEECCCHHHHHHHHHhhhhhccEEEEEEEcccCceecccCCCchHHHHHHHHHHcCCCcEEEEEEcccCCchhhh
Confidence            4567889999921  11111 11247999999999875211 0011111          2333 37789999987320  


Q ss_pred             hH----hHHHHHHHHHhcC--C-CCCEEEEecccCCCHHH
Q 030407          136 GA----DLAVMERDALRMR--D-GGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       136 ~~----~~~~~~~~l~~~n--p-~a~i~~~SA~~g~gi~e  168 (178)
                      .+    -.+++...+++..  + ..+++++||++|+|+.+
T Consensus       164 ~~~~~~i~~ei~~~l~~~g~~~~~~~~ipiSa~~G~ni~~  203 (447)
T PLN00043        164 KARYDEIVKEVSSYLKKVGYNPDKIPFVPISGFEGDNMIE  203 (447)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCcccceEEEEeccccccccc
Confidence            01    1344555555432  1 36899999999999853

>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]

Probab=97.81  E-value=5e-05  Score=63.07  Aligned_cols=101  Identities=18%  Similarity=0.140  Sum_probs=64.6

Q ss_pred             EEEEeCCcch-h-hhccc-ccccceEEEEEeCCCCCCCCcCCC-----CCCCc-eeEEEEecCCCCCch--hHhHHHHHH
Q 030407           76 LLLCESGGDN-L-AANFS-RELADYIIYIIDVSGGDKIPRKGG-----PGITQ-ADLLVINKTDLASAI--GADLAVMER  144 (178)
Q Consensus        76 ~iiiEttG~~-~-~~~~~-~~~ad~~I~VvD~~~~~~~~~~~~-----~qi~~-adiiviNK~Dl~~~~--~~~~~~~~~  144 (178)
                      +=|+.+.|-- + +.+.+ ..+-|+.++|+.+.+.-.++....     +.+.. --+|+-||+||++..  .+..+++.+
T Consensus        88 VSfVDaPGHe~LMATMLsGAAlMDgAlLvIaANEpcPQPQT~EHl~AleIigik~iiIvQNKIDlV~~E~AlE~y~qIk~  167 (415)
T COG5257          88 VSFVDAPGHETLMATMLSGAALMDGALLVIAANEPCPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRERALENYEQIKE  167 (415)
T ss_pred             EEEeeCCchHHHHHHHhcchhhhcceEEEEecCCCCCCCchHHHHHHHhhhccceEEEEecccceecHHHHHHHHHHHHH
Confidence            4478888821 1 22222 112389999999987543332111     11222 347889999999872  122344555


Q ss_pred             HHHhc-CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          145 DALRM-RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       145 ~l~~~-np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +++.- ..++||+++||..+.+|+.|+++|.+.
T Consensus       168 FvkGt~Ae~aPIIPiSA~~~~NIDal~e~i~~~  200 (415)
T COG5257         168 FVKGTVAENAPIIPISAQHKANIDALIEAIEKY  200 (415)
T ss_pred             HhcccccCCCceeeehhhhccCHHHHHHHHHHh
Confidence            56533 356899999999999999999998865

>PTZ00141 elongation factor 1- alpha; Provisional

Probab=97.80  E-value=5e-05  Score=66.15  Aligned_cols=104  Identities=14%  Similarity=0.136  Sum_probs=61.3

Q ss_pred             CCCEEEEeCCcch--hhhccc-ccccceEEEEEeCCCCCC-------CCc-CC---CCCCCcee-EEEEecCCCC--Cch
Q 030407           73 KADLLLCESGGDN--LAANFS-RELADYIIYIIDVSGGDK-------IPR-KG---GPGITQAD-LLVINKTDLA--SAI  135 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~~-~~~ad~~I~VvD~~~~~~-------~~~-~~---~~qi~~ad-iiviNK~Dl~--~~~  135 (178)
                      +..+.||.|.|-.  +..+.. ...+|.+++|+|+..+..       .+. .+   ...+.... ++++||+|..  +..
T Consensus        84 ~~~i~lIDtPGh~~f~~~~~~g~~~aD~ailVVda~~G~~e~~~~~~~qT~eh~~~~~~~gi~~iiv~vNKmD~~~~~~~  163 (446)
T PTZ00141         84 KYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFEAGISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYS  163 (446)
T ss_pred             CeEEEEEECCChHHHHHHHHHhhhhcCEEEEEEEcCCCceecccCCCccHHHHHHHHHHcCCCeEEEEEEccccccchhh
Confidence            5678899999921  111111 124699999999988641       110 11   11133344 5899999943  221


Q ss_pred             hHhHHHHHHHHH----hc--CC-CCCEEEEecccCCCHHH------------HHHHHhhh
Q 030407          136 GADLAVMERDAL----RM--RD-GGPFIFAQVGWVIGIIF------------TLSITHYI  176 (178)
Q Consensus       136 ~~~~~~~~~~l~----~~--np-~a~i~~~SA~~g~gi~e------------l~~~l~~~  176 (178)
                      .+..+.+.+.++    ..  ++ ..+++++||.+|+|+.+            |++.|..+
T Consensus       164 ~~~~~~i~~~i~~~l~~~g~~~~~~~~ipiSa~~g~ni~~~~~~~~Wy~G~tL~~~l~~~  223 (446)
T PTZ00141        164 QERYDEIKKEVSAYLKKVGYNPEKVPFIPISGWQGDNMIEKSDNMPWYKGPTLLEALDTL  223 (446)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCcccceEEEeecccCCCcccCCCCCcccchHHHHHHHhCC
Confidence            133333333333    22  22 47899999999999964            77777653

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

Probab=97.78  E-value=2.2e-05  Score=58.32  Aligned_cols=103  Identities=17%  Similarity=0.154  Sum_probs=71.0

Q ss_pred             CCCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CC----CCC-CCceeEEEEecCCCCCchhHhHH
Q 030407           72 FKADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KG----GPG-ITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        72 ~~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~----~~q-i~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .....-|..|.|--    +..+++. ..+++++|+|+++++....  ++    ..+ -..+-++|.||.|+++......+
T Consensus        55 ~~VkLqIwDtAGqErFrtitstyyr-gthgv~vVYDVTn~ESF~Nv~rWLeei~~ncdsv~~vLVGNK~d~~~RrvV~t~  133 (198)
T KOG0079|consen   55 DRVKLQIWDTAGQERFRTITSTYYR-GTHGVIVVYDVTNGESFNNVKRWLEEIRNNCDSVPKVLVGNKNDDPERRVVDTE  133 (198)
T ss_pred             cEEEEEEeecccHHHHHHHHHHHcc-CCceEEEEEECcchhhhHhHHHHHHHHHhcCccccceecccCCCCccceeeehH
Confidence            35777788999932    2344554 5799999999999875432  11    111 12346999999999875323445


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ..+++..+.  +.+.|+||||..+++++.|.-|.+++
T Consensus       134 dAr~~A~~m--gie~FETSaKe~~NvE~mF~cit~qv  168 (198)
T KOG0079|consen  134 DARAFALQM--GIELFETSAKENENVEAMFHCITKQV  168 (198)
T ss_pred             HHHHHHHhc--CchheehhhhhcccchHHHHHHHHHH
Confidence            556666554  56999999999999999998766543

>CHL00071 tufA elongation factor Tu

Probab=97.78  E-value=6.9e-05  Score=64.54  Aligned_cols=90  Identities=11%  Similarity=0.117  Sum_probs=55.0

Q ss_pred             CCCEEEEeCCcch--hhhcc-cccccceEEEEEeCCCCCCCCcC----CCCCCCce-eEEEEecCCCCCchhHh-H----
Q 030407           73 KADLLLCESGGDN--LAANF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQA-DLLVINKTDLASAIGAD-L----  139 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~a-diiviNK~Dl~~~~~~~-~----  139 (178)
                      +..+.||.|.|-.  +.... ....+|.+++|+|+..+...+..    .......+ -++++||+|+++.  .+ .    
T Consensus        74 ~~~~~~iDtPGh~~~~~~~~~~~~~~D~~ilVvda~~g~~~qt~~~~~~~~~~g~~~iIvvvNK~D~~~~--~~~~~~~~  151 (409)
T CHL00071         74 NRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVGVPNIVVFLNKEDQVDD--EELLELVE  151 (409)
T ss_pred             CeEEEEEECCChHHHHHHHHHHHHhCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCEEEEEEEccCCCCH--HHHHHHHH
Confidence            4568999999931  11111 11246999999999876432211    11112344 4678999999875  32 2    


Q ss_pred             HHHHHHHHhcC-C--CCCEEEEecccCC
Q 030407          140 AVMERDALRMR-D--GGPFIFAQVGWVI  164 (178)
Q Consensus       140 ~~~~~~l~~~n-p--~a~i~~~SA~~g~  164 (178)
                      +++.+.++... +  ..+++++||++|.
T Consensus       152 ~~l~~~l~~~~~~~~~~~ii~~Sa~~g~  179 (409)
T CHL00071        152 LEVRELLSKYDFPGDDIPIVSGSALLAL  179 (409)
T ss_pred             HHHHHHHHHhCCCCCcceEEEcchhhcc
Confidence            24455555432 2  3799999999986

>PRK10218 GTP-binding protein; Provisional

Probab=97.78  E-value=6.2e-05  Score=67.85  Aligned_cols=103  Identities=13%  Similarity=0.083  Sum_probs=64.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCch-hHhHHHHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAI-GADLAVME  143 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~-~~~~~~~~  143 (178)
                      +..+-+++|.|..    ....+ ...+|++++|+|+..+...+..    .......+-++++||+|+.... ...++.+.
T Consensus        67 ~~~inliDTPG~~df~~~v~~~-l~~aDg~ILVVDa~~G~~~qt~~~l~~a~~~gip~IVviNKiD~~~a~~~~vl~ei~  145 (607)
T PRK10218         67 DYRINIVDTPGHADFGGEVERV-MSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIVVINKVDRPGARPDWVVDQVF  145 (607)
T ss_pred             CEEEEEEECCCcchhHHHHHHH-HHhCCEEEEEEecccCccHHHHHHHHHHHHcCCCEEEEEECcCCCCCchhHHHHHHH
Confidence            5778999999931    11111 1247999999999876433211    1112344569999999997542 12234444


Q ss_pred             HHHHhcC-----CCCCEEEEecccCC----------CHHHHHHHHhhh
Q 030407          144 RDALRMR-----DGGPFIFAQVGWVI----------GIIFTLSITHYI  176 (178)
Q Consensus       144 ~~l~~~n-----p~a~i~~~SA~~g~----------gi~el~~~l~~~  176 (178)
                      ..+..+.     -..|++++||++|.          |+..|++.+...
T Consensus       146 ~l~~~l~~~~~~~~~PVi~~SA~~G~~~~~~~~~~~~i~~Lld~Ii~~  193 (607)
T PRK10218        146 DLFVNLDATDEQLDFPIVYASALNGIAGLDHEDMAEDMTPLYQAIVDH  193 (607)
T ss_pred             HHHhccCccccccCCCEEEeEhhcCcccCCccccccchHHHHHHHHHh
Confidence            4443221     13689999999998          688998876543

>TIGR00485 EF-Tu translation elongation factor TU

Probab=97.76  E-value=8.9e-05  Score=63.51  Aligned_cols=101  Identities=11%  Similarity=0.132  Sum_probs=59.7

Q ss_pred             CCCEEEEeCCcch--hhhccc-ccccceEEEEEeCCCCCCCCc-CC---CCCCCceeE-EEEecCCCCCchhHh-H----
Q 030407           73 KADLLLCESGGDN--LAANFS-RELADYIIYIIDVSGGDKIPR-KG---GPGITQADL-LVINKTDLASAIGAD-L----  139 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~~-~~~ad~~I~VvD~~~~~~~~~-~~---~~qi~~adi-iviNK~Dl~~~~~~~-~----  139 (178)
                      +..+.||.|.|-.  +..++. ...+|.+++|+|+..+...+. .+   ......+-+ +++||+|+.++  ++ .    
T Consensus        74 ~~~~~liDtpGh~~f~~~~~~~~~~~D~~ilVvda~~g~~~qt~e~l~~~~~~gi~~iIvvvNK~Dl~~~--~~~~~~~~  151 (394)
T TIGR00485        74 NRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMPQTREHILLARQVGVPYIVVFLNKCDMVDD--EELLELVE  151 (394)
T ss_pred             CEEEEEEECCchHHHHHHHHHHHhhCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCEEEEEEEecccCCH--HHHHHHHH
Confidence            4568899999931  111111 123699999999987643221 11   111233445 57999999865  22 2    


Q ss_pred             HHHHHHHHhcC-C--CCCEEEEecccCC--------CHHHHHHHHhh
Q 030407          140 AVMERDALRMR-D--GGPFIFAQVGWVI--------GIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~n-p--~a~i~~~SA~~g~--------gi~el~~~l~~  175 (178)
                      +++.+.++... +  ..+++++||++|.        ++..+++.|..
T Consensus       152 ~~i~~~l~~~~~~~~~~~ii~vSa~~g~~g~~~~~~~~~~ll~~l~~  198 (394)
T TIGR00485       152 MEVRELLSEYDFPGDDTPIIRGSALKALEGDAEWEAKILELMDAVDE  198 (394)
T ss_pred             HHHHHHHHhcCCCccCccEEECccccccccCCchhHhHHHHHHHHHh
Confidence            23555555442 2  2799999999885        45566666553

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=97.76  E-value=0.00021  Score=60.09  Aligned_cols=150  Identities=19%  Similarity=0.286  Sum_probs=83.8

Q ss_pred             HHHHHHhhcC-CcEEEEEecCC-C-chhHH--HHHHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCCCCE
Q 030407            2 LALCKFLRDK-YSLAAVTNDIF-T-KEDGE--FLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADL   76 (178)
Q Consensus         2 ~~~~~~~~~~-~~vaVI~nd~g-~-~iD~~--li~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~~d~   76 (178)
                      .++..++.+. ++++++..|.. . .++..  +....|+    ++.....|..+.       .....++... ...++|+
T Consensus       158 akLA~~l~~~g~~V~li~~Dt~R~~a~eqL~~~a~~lgv----~v~~~~~g~dp~-------~v~~~ai~~~-~~~~~Dv  225 (336)
T PRK14974        158 AKLAYYLKKNGFSVVIAAGDTFRAGAIEQLEEHAERLGV----KVIKHKYGADPA-------AVAYDAIEHA-KARGIDV  225 (336)
T ss_pred             HHHHHHHHHcCCeEEEecCCcCcHHHHHHHHHHHHHcCC----ceecccCCCCHH-------HHHHHHHHHH-HhCCCCE
Confidence            3566666654 88999888854 3 23221  1222343    444443444331       0011333332 3557999


Q ss_pred             EEEeCCcchhh-----hc---cc-ccccceEEEEEeCCCCCCCCcC--CCCCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           77 LLCESGGDNLA-----AN---FS-RELADYIIYIIDVSGGDKIPRK--GGPGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        77 iiiEttG~~~~-----~~---~~-~~~ad~~I~VvD~~~~~~~~~~--~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      |+|+|.|....     ..   +. ....|.+++|+|+..+.+....  .....-..+-+++||.|.....+..+..    
T Consensus       226 VLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~~~a~~f~~~~~~~giIlTKlD~~~~~G~~ls~----  301 (336)
T PRK14974        226 VLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQAREFNEAVGIDGVILTKVDADAKGGAALSI----  301 (336)
T ss_pred             EEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccchhHHHHHHHHHhcCCCCEEEEeeecCCCCccHHHHH----
Confidence            99999995311     01   10 0123778999999876543221  1111123589999999997653333333    


Q ss_pred             HHhcCCCCCEEEEecccCCCHHHHHH
Q 030407          146 ALRMRDGGPFIFAQVGWVIGIIFTLS  171 (178)
Q Consensus       146 l~~~np~a~i~~~SA~~g~gi~el~~  171 (178)
                      ....  +.|+.+++  +|+++++|..
T Consensus       302 ~~~~--~~Pi~~i~--~Gq~v~Dl~~  323 (336)
T PRK14974        302 AYVI--GKPILFLG--VGQGYDDLIP  323 (336)
T ss_pred             HHHH--CcCEEEEe--CCCChhhccc
Confidence            3322  46899988  8999988753

>PRK13796 GTPase YqeH; Provisional

Probab=97.76  E-value=4.2e-05  Score=64.98  Aligned_cols=79  Identities=14%  Similarity=-0.012  Sum_probs=49.4

Q ss_pred             ceEEEEEeCCCCCCCCcC-CCCCC-CceeEEEEecCCCCCchhHhHHHHHHHHH----hcC-CCCCEEEEecccCCCHHH
Q 030407           96 DYIIYIIDVSGGDKIPRK-GGPGI-TQADLLVINKTDLASAIGADLAVMERDAL----RMR-DGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus        96 d~~I~VvD~~~~~~~~~~-~~~qi-~~adiiviNK~Dl~~~~~~~~~~~~~~l~----~~n-p~a~i~~~SA~~g~gi~e  168 (178)
                      +.+++|+|+.+....... ..... ...-++|+||+||.+.. ...+++.++++    ..+ +...++.+||++|.|+++
T Consensus        71 ~lIv~VVD~~D~~~s~~~~L~~~~~~kpviLViNK~DLl~~~-~~~~~i~~~l~~~~k~~g~~~~~v~~vSAk~g~gI~e  149 (365)
T PRK13796         71 ALVVNVVDIFDFNGSWIPGLHRFVGNNPVLLVGNKADLLPKS-VKKNKVKNWLRQEAKELGLRPVDVVLISAQKGHGIDE  149 (365)
T ss_pred             cEEEEEEECccCCCchhHHHHHHhCCCCEEEEEEchhhCCCc-cCHHHHHHHHHHHHHhcCCCcCcEEEEECCCCCCHHH
Confidence            478999998765422110 00001 23568999999998641 22233333333    222 123799999999999999


Q ss_pred             HHHHHhh
Q 030407          169 TLSITHY  175 (178)
Q Consensus       169 l~~~l~~  175 (178)
                      +++.+.+
T Consensus       150 L~~~I~~  156 (365)
T PRK13796        150 LLEAIEK  156 (365)
T ss_pred             HHHHHHH
Confidence            9998864

>cd04167 Snu114p Snu114p subfamily

Probab=97.75  E-value=1.9e-05  Score=61.77  Aligned_cols=95  Identities=16%  Similarity=0.085  Sum_probs=58.4

Q ss_pred             CCCEEEEeCCcch-hh-hc-ccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc-----hhHhHH
Q 030407           73 KADLLLCESGGDN-LA-AN-FSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA-----IGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~-~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~-----~~~~~~  140 (178)
                      ++.+.++.|.|.. .. .. .....+|.+++|+|+.++......    .......+.++|+||+|++..     ..+..+
T Consensus        70 ~~~i~iiDtpG~~~f~~~~~~~~~~aD~~llVvD~~~~~~~~~~~~~~~~~~~~~p~iiviNK~D~~~~~~~l~~~~~~~  149 (213)
T cd04167          70 SYLFNIIDTPGHVNFMDEVAAALRLSDGVVLVVDVVEGVTSNTERLIRHAILEGLPIVLVINKIDRLILELKLPPNDAYF  149 (213)
T ss_pred             EEEEEEEECCCCcchHHHHHHHHHhCCEEEEEEECCCCCCHHHHHHHHHHHHcCCCEEEEEECcccCcccccCCHHHHHH
Confidence            4678899999931 11 11 111246999999999876533211    011123678999999998621     114445


Q ss_pred             HHHHHHHhcCCCC------------C----EEEEecccCCCHH
Q 030407          141 VMERDALRMRDGG------------P----FIFAQVGWVIGII  167 (178)
Q Consensus       141 ~~~~~l~~~np~a------------~----i~~~SA~~g~gi~  167 (178)
                      ++.+.++++||.+            |    +++.||+.|-++.
T Consensus       150 ~l~~~i~~~n~~~~~~~~~~~~~~~p~~~nv~~~s~~~~w~~~  192 (213)
T cd04167         150 KLRHIIDEVNNIIASFSTTLSFLFSPENGNVCFASSKFGFCFT  192 (213)
T ss_pred             HHHHHHHHHHHHHHHhcCCCceEeccCCCeEEEEecCCCeEEe
Confidence            6666666665432            2    7788999887765

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.

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

Probab=97.73  E-value=6.5e-05  Score=55.79  Aligned_cols=101  Identities=15%  Similarity=0.026  Sum_probs=70.1

Q ss_pred             CCCEEEEeCCcchh---hhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDNL---AANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~---~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      ..++=+..|.|.-.   ..+.....+++.|+++|.++......  .+.      .......|+|.||+|+-++.....++
T Consensus        69 RiklQiwDTagqEryrtiTTayyRgamgfiLmyDitNeeSf~svqdw~tqIktysw~naqvilvgnKCDmd~eRvis~e~  148 (193)
T KOG0093|consen   69 RIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNSVQDWITQIKTYSWDNAQVILVGNKCDMDSERVISHER  148 (193)
T ss_pred             EEEEEEEecccchhhhHHHHHHhhccceEEEEEecCCHHHHHHHHHHHHHheeeeccCceEEEEecccCCccceeeeHHH
Confidence            47788888888421   12333346899999999987543211  111      22345679999999997764344566


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+....++  +-.+|++|||.+.+++.+|+.+..
T Consensus       149 g~~l~~~L--GfefFEtSaK~NinVk~~Fe~lv~  180 (193)
T KOG0093|consen  149 GRQLADQL--GFEFFETSAKENINVKQVFERLVD  180 (193)
T ss_pred             HHHHHHHh--ChHHhhhcccccccHHHHHHHHHH
Confidence            66666666  348999999999999999997653

>COG0218 Predicted GTPase [General function prediction only]

Probab=97.72  E-value=0.00012  Score=56.88  Aligned_cols=79  Identities=10%  Similarity=-0.050  Sum_probs=55.5

Q ss_pred             ceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHHHH-hc--CCCCC--EEEEecccCCCH
Q 030407           96 DYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERDAL-RM--RDGGP--FIFAQVGWVIGI  166 (178)
Q Consensus        96 d~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~-~~--np~a~--i~~~SA~~g~gi  166 (178)
                      ..++.++|+.++....+.    +..+...+-+|++||+|.++.  .+..+....++ .+  .|...  ++..|+.+++|+
T Consensus       108 ~~vvlliD~r~~~~~~D~em~~~l~~~~i~~~vv~tK~DKi~~--~~~~k~l~~v~~~l~~~~~~~~~~~~~ss~~k~Gi  185 (200)
T COG0218         108 KGVVLLIDARHPPKDLDREMIEFLLELGIPVIVVLTKADKLKK--SERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKGI  185 (200)
T ss_pred             eEEEEEEECCCCCcHHHHHHHHHHHHcCCCeEEEEEccccCCh--hHHHHHHHHHHHHhcCCCCccceEEEEecccccCH
Confidence            568999999987654331    223355677999999999987  55544444444 22  23333  889999999999


Q ss_pred             HHHHHHHhhh
Q 030407          167 IFTLSITHYI  176 (178)
Q Consensus       167 ~el~~~l~~~  176 (178)
                      +++.+.|...
T Consensus       186 ~~l~~~i~~~  195 (200)
T COG0218         186 DELKAKILEW  195 (200)
T ss_pred             HHHHHHHHHH
Confidence            9999987653

>TIGR01394 TypA_BipA GTP-binding protein TypA/BipA

Probab=97.72  E-value=7.7e-05  Score=67.15  Aligned_cols=103  Identities=14%  Similarity=0.121  Sum_probs=64.0

Q ss_pred             CCCEEEEeCCcch-hh---hcccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchh-HhHHHHH
Q 030407           73 KADLLLCESGGDN-LA---ANFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIG-ADLAVME  143 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~---~~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~-~~~~~~~  143 (178)
                      +..+-||.|.|-. ..   ..+ ...+|.+++|+|+..+...+..    .......+-++++||+|+..... +..+++.
T Consensus        63 ~~kinlIDTPGh~DF~~ev~~~-l~~aD~alLVVDa~~G~~~qT~~~l~~a~~~~ip~IVviNKiD~~~a~~~~v~~ei~  141 (594)
T TIGR01394        63 GTKINIVDTPGHADFGGEVERV-LGMVDGVLLLVDASEGPMPQTRFVLKKALELGLKPIVVINKIDRPSARPDEVVDEVF  141 (594)
T ss_pred             CEEEEEEECCCHHHHHHHHHHH-HHhCCEEEEEEeCCCCCcHHHHHHHHHHHHCCCCEEEEEECCCCCCcCHHHHHHHHH
Confidence            5678899999921 00   111 1246999999999876432211    11123345699999999965411 1233444


Q ss_pred             HHHHhcCC-----CCCEEEEecccCC----------CHHHHHHHHhhh
Q 030407          144 RDALRMRD-----GGPFIFAQVGWVI----------GIIFTLSITHYI  176 (178)
Q Consensus       144 ~~l~~~np-----~a~i~~~SA~~g~----------gi~el~~~l~~~  176 (178)
                      ..+..+..     ..|++++||++|.          |++.|++.+...
T Consensus       142 ~l~~~~g~~~e~l~~pvl~~SA~~g~~~~~~~~~~~gi~~Lld~Iv~~  189 (594)
T TIGR01394       142 DLFAELGADDEQLDFPIVYASGRAGWASLDLDDPSDNMAPLFDAIVRH  189 (594)
T ss_pred             HHHHhhccccccccCcEEechhhcCcccccCcccccCHHHHHHHHHHh
Confidence            44433211     3589999999995          899999987654

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.

>PRK09554 feoB ferrous iron transport protein B; Reviewed

Probab=97.69  E-value=5.3e-05  Score=70.08  Aligned_cols=101  Identities=16%  Similarity=0.095  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcch-hh---h----------ccc-ccccceEEEEEeCCCCCCCCcC--CCCCCCceeEEEEecCCCCCch
Q 030407           73 KADLLLCESGGDN-LA---A----------NFS-RELADYIIYIIDVSGGDKIPRK--GGPGITQADLLVINKTDLASAI  135 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~---~----------~~~-~~~ad~~I~VvD~~~~~~~~~~--~~~qi~~adiiviNK~Dl~~~~  135 (178)
                      +.++.++.|.|.. +.   .          .+. ...+|.++.|+|+++.......  .......+-++++||+|+.++ 
T Consensus        49 ~~~i~lvDtPG~ysl~~~~~~~s~~E~i~~~~l~~~~aD~vI~VvDat~ler~l~l~~ql~e~giPvIvVlNK~Dl~~~-  127 (772)
T PRK09554         49 DHQVTLVDLPGTYSLTTISSQTSLDEQIACHYILSGDADLLINVVDASNLERNLYLTLQLLELGIPCIVALNMLDIAEK-  127 (772)
T ss_pred             ceEEEEEECCCccccccccccccHHHHHHHHHHhccCCCEEEEEecCCcchhhHHHHHHHHHcCCCEEEEEEchhhhhc-
Confidence            5678899999941 11   0          010 1236999999999875432110  001235678999999999754 


Q ss_pred             hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          136 GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       136 ~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                       .....-.+.+++.. +.|++++||++|+|++++.+.+...
T Consensus       128 -~~i~id~~~L~~~L-G~pVvpiSA~~g~GIdeL~~~I~~~  166 (772)
T PRK09554        128 -QNIRIDIDALSARL-GCPVIPLVSTRGRGIEALKLAIDRH  166 (772)
T ss_pred             -cCcHHHHHHHHHHh-CCCEEEEEeecCCCHHHHHHHHHHh
Confidence             22221122233222 3589999999999999999988654

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=97.66  E-value=0.00054  Score=57.21  Aligned_cols=148  Identities=15%  Similarity=0.146  Sum_probs=82.3

Q ss_pred             HHHHHhhcC-CcEEEEEecCC-C-chhHHH--HHHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCCCCEE
Q 030407            3 ALCKFLRDK-YSLAAVTNDIF-T-KEDGEF--LMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLL   77 (178)
Q Consensus         3 ~~~~~~~~~-~~vaVI~nd~g-~-~iD~~l--i~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~~d~i   77 (178)
                      ++..++.+. ++|+++.-|.. . .++...  -...++    ++.....+.-+..       ...+++... ...++|+|
T Consensus       133 kLA~~l~~~g~~V~Li~~D~~r~~a~eql~~~a~~~~i----~~~~~~~~~dpa~-------~v~~~l~~~-~~~~~D~V  200 (318)
T PRK10416        133 KLAHKYKAQGKKVLLAAGDTFRAAAIEQLQVWGERVGV----PVIAQKEGADPAS-------VAFDAIQAA-KARGIDVL  200 (318)
T ss_pred             HHHHHHHhcCCeEEEEecCccchhhHHHHHHHHHHcCc----eEEEeCCCCCHHH-------HHHHHHHHH-HhCCCCEE
Confidence            455566554 89999999975 4 333321  122333    3333333332211       112333322 25689999


Q ss_pred             EEeCCcchh---------hh------cccccccceEEEEEeCCCCCCCCcCCCCCC--CceeEEEEecCCCCCchhHhHH
Q 030407           78 LCESGGDNL---------AA------NFSRELADYIIYIIDVSGGDKIPRKGGPGI--TQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        78 iiEttG~~~---------~~------~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi--~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ||+|.|...         ..      ...+...+..++|+|++.+...........  -..+-+|+||.|....    ..
T Consensus       201 iIDTaGr~~~~~~l~~eL~~~~~v~~~~~~~~p~~~~LVl~a~~g~~~~~~a~~f~~~~~~~giIlTKlD~t~~----~G  276 (318)
T PRK10416        201 IIDTAGRLHNKTNLMEELKKIKRVIKKADPDAPHEVLLVLDATTGQNALSQAKAFHEAVGLTGIILTKLDGTAK----GG  276 (318)
T ss_pred             EEeCCCCCcCCHHHHHHHHHHHHHHhhhcCCCCceEEEEEECCCChHHHHHHHHHHhhCCCCEEEEECCCCCCC----cc
Confidence            999999421         00      111222367899999987653322111111  1357899999996544    23


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHH
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~  170 (178)
                      .+.+.....  ..|+.+++  +|+++++|.
T Consensus       277 ~~l~~~~~~--~~Pi~~v~--~Gq~~~Dl~  302 (318)
T PRK10416        277 VVFAIADEL--GIPIKFIG--VGEGIDDLQ  302 (318)
T ss_pred             HHHHHHHHH--CCCEEEEe--CCCChhhCc
Confidence            334444433  56899998  899998774

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

Probab=97.66  E-value=5.5e-05  Score=56.87  Aligned_cols=80  Identities=14%  Similarity=0.060  Sum_probs=50.6

Q ss_pred             cceEEEEEeCCCCCCCCc--CCCCC------CCceeEE-EEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCC
Q 030407           95 ADYIIYIIDVSGGDKIPR--KGGPG------ITQADLL-VINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIG  165 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~--~~~~q------i~~adii-viNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~g  165 (178)
                      +=+.+.++|.++......  .+..|      -+.+||| +.||+||.+......++..+...+.  +.|+|+|||-+|.+
T Consensus        91 AMGFlLiFDlT~eqSFLnvrnWlSQL~~hAYcE~PDivlcGNK~DL~~~R~Vs~~qa~~La~ky--glPYfETSA~tg~N  168 (219)
T KOG0081|consen   91 AMGFLLIFDLTSEQSFLNVRNWLSQLQTHAYCENPDIVLCGNKADLEDQRVVSEDQAAALADKY--GLPYFETSACTGTN  168 (219)
T ss_pred             hccceEEEeccchHHHHHHHHHHHHHHHhhccCCCCEEEEcCccchhhhhhhhHHHHHHHHHHh--CCCeeeeccccCcC
Confidence            456789999876543221  12222      3456755 5899999765222223333333333  56999999999999


Q ss_pred             HHHHHHHHhhh
Q 030407          166 IIFTLSITHYI  176 (178)
Q Consensus       166 i~el~~~l~~~  176 (178)
                      +++-.+.|...
T Consensus       169 v~kave~Lldl  179 (219)
T KOG0081|consen  169 VEKAVELLLDL  179 (219)
T ss_pred             HHHHHHHHHHH
Confidence            99988866543

>cd04178 Nucleostemin_like Nucleostemin-like

Probab=97.61  E-value=7.9e-05  Score=56.81  Aligned_cols=52  Identities=21%  Similarity=0.213  Sum_probs=33.6

Q ss_pred             ceEEEEEeCCCCCCCCc----CC--CCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhc
Q 030407           96 DYIIYIIDVSGGDKIPR----KG--GPGITQADLLVINKTDLASAIGADLAVMERDALRM  149 (178)
Q Consensus        96 d~~I~VvD~~~~~~~~~----~~--~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~  149 (178)
                      |.++.|+|+..+.....    ..  ......+-++|+||+|++++  +.+....+.+++.
T Consensus         1 DvVl~VvDar~p~~~~~~~i~~~~~l~~~~kp~IlVlNK~DL~~~--~~l~~~~~~~~~~   58 (172)
T cd04178           1 DVILEVLDARDPLGCRCPQVEEAVLQAGGNKKLVLVLNKIDLVPK--ENVEKWLKYLRRE   58 (172)
T ss_pred             CEEEEEEECCCCCCCCCHHHHHHHHhccCCCCEEEEEehhhcCCH--HHHHHHHHHHHhh
Confidence            67899999977543221    11  11123567999999999887  6666555555544

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

>KOG0461 consensus Selenocysteine-specific elongation factor [Translation, ribosomal structure and biogenesis]

Probab=97.61  E-value=0.00029  Score=59.22  Aligned_cols=110  Identities=16%  Similarity=0.171  Sum_probs=69.9

Q ss_pred             hhHhhCCCCEEEEeCCcc-hhhhccc--ccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCch--hH
Q 030407           67 ELSNLFKADLLLCESGGD-NLAANFS--RELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAI--GA  137 (178)
Q Consensus        67 ~l~~~~~~d~iiiEttG~-~~~~~~~--~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~--~~  137 (178)
                      +|.+..+..+-+|.+.|- ++..+..  ....|.+++|+|+..|...+..    ..+.+-.--+||+||+|+.++-  ..
T Consensus        63 rLpq~e~lq~tlvDCPGHasLIRtiiggaqiiDlm~lviDv~kG~QtQtAEcLiig~~~c~klvvvinkid~lpE~qr~s  142 (522)
T KOG0461|consen   63 RLPQGEQLQFTLVDCPGHASLIRTIIGGAQIIDLMILVIDVQKGKQTQTAECLIIGELLCKKLVVVINKIDVLPENQRAS  142 (522)
T ss_pred             ccCccccceeEEEeCCCcHHHHHHHHhhhheeeeeeEEEehhcccccccchhhhhhhhhccceEEEEeccccccchhhhh
Confidence            344445788999999992 2222221  1124899999999887654321    1111223358999999998651  13


Q ss_pred             hHHHHHHHHHh----c--CCCCCEEEEecccC----CCHHHHHHHHhhh
Q 030407          138 DLAVMERDALR----M--RDGGPFIFAQVGWV----IGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~----~--np~a~i~~~SA~~g----~gi~el~~~l~~~  176 (178)
                      .+++....++.    .  ...+||+++||+.|    ++|.||.+.|...
T Consensus       143 ki~k~~kk~~KtLe~t~f~g~~PI~~vsa~~G~~~~~~i~eL~e~l~s~  191 (522)
T KOG0461|consen  143 KIEKSAKKVRKTLESTGFDGNSPIVEVSAADGYFKEEMIQELKEALESR  191 (522)
T ss_pred             HHHHHHHHHHHHHHhcCcCCCCceeEEecCCCccchhHHHHHHHHHHHh
Confidence            33444443332    1  23489999999999    9999999988654

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=97.60  E-value=0.00081  Score=54.94  Aligned_cols=147  Identities=16%  Similarity=0.197  Sum_probs=82.1

Q ss_pred             HHHHHhhcC-CcEEEEEecCC-C-chhHH--HHHHcCCCCccceeecccCCCcccccccccccC-HhHHHhhHhhCCCCE
Q 030407            3 ALCKFLRDK-YSLAAVTNDIF-T-KEDGE--FLMRNGALPEERIRAVETGGCPHAAIREDISIN-LGPLEELSNLFKADL   76 (178)
Q Consensus         3 ~~~~~~~~~-~~vaVI~nd~g-~-~iD~~--li~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~-l~~l~~l~~~~~~d~   76 (178)
                      ++..++.+. +||++|.-|.. . ..+..  +.+..|+    ++.....+..+        ... ...+.... ..++|+
T Consensus        91 kLA~~l~~~g~~V~li~~D~~r~~a~~ql~~~~~~~~i----~~~~~~~~~dp--------~~~~~~~l~~~~-~~~~D~  157 (272)
T TIGR00064        91 KLANKLKKQGKSVLLAAGDTFRAAAIEQLEEWAKRLGV----DVIKQKEGADP--------AAVAFDAIQKAK-ARNIDV  157 (272)
T ss_pred             HHHHHHHhcCCEEEEEeCCCCCHHHHHHHHHHHHhCCe----EEEeCCCCCCH--------HHHHHHHHHHHH-HCCCCE
Confidence            566666554 89999999965 4 33321  2233343    33333332211        111 13343332 568999


Q ss_pred             EEEeCCcchhh---------------hcccccccceEEEEEeCCCCCCCCcC---CCCCCCceeEEEEecCCCCCchhHh
Q 030407           77 LLCESGGDNLA---------------ANFSRELADYIIYIIDVSGGDKIPRK---GGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        77 iiiEttG~~~~---------------~~~~~~~ad~~I~VvD~~~~~~~~~~---~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      |||+|.|....               ..+.....|.+++|+|++.+.+....   +.+.+ ..+-+|+||.|.....+..
T Consensus       158 ViIDT~G~~~~d~~~~~el~~~~~~~~~~~~~~~~~~~LVl~a~~~~~~~~~~~~f~~~~-~~~g~IlTKlDe~~~~G~~  236 (272)
T TIGR00064       158 VLIDTAGRLQNKVNLMDELKKIKRVIKKVDKDAPDEVLLVLDATTGQNALEQAKVFNEAV-GLTGIILTKLDGTAKGGII  236 (272)
T ss_pred             EEEeCCCCCcchHHHHHHHHHHHHHHhcccCCCCceEEEEEECCCCHHHHHHHHHHHhhC-CCCEEEEEccCCCCCccHH
Confidence            99999994211               01111225889999999765432111   11112 2579999999987653233


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHH
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLS  171 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~  171 (178)
                      +    ......  ..|+.+++  +|+++++|..
T Consensus       237 l----~~~~~~--~~Pi~~~~--~Gq~~~dl~~  261 (272)
T TIGR00064       237 L----SIAYEL--KLPIKFIG--VGEKIDDLAP  261 (272)
T ss_pred             H----HHHHHH--CcCEEEEe--CCCChHhCcc
Confidence            3    233322  36888888  8999877743

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PLN03127 Elongation factor Tu; Provisional

Probab=97.60  E-value=0.00015  Score=63.20  Aligned_cols=102  Identities=14%  Similarity=0.172  Sum_probs=59.4

Q ss_pred             CCCEEEEeCCcch--hhhcc-cccccceEEEEEeCCCCCCCCc-CC---CCCCCcee-EEEEecCCCCCchhHh-HHHHH
Q 030407           73 KADLLLCESGGDN--LAANF-SRELADYIIYIIDVSGGDKIPR-KG---GPGITQAD-LLVINKTDLASAIGAD-LAVME  143 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~-~~~~ad~~I~VvD~~~~~~~~~-~~---~~qi~~ad-iiviNK~Dl~~~~~~~-~~~~~  143 (178)
                      +..++||.|.|..  +..+. ....+|.+++|+|+..+...+. .+   ......+. ++++||+|+++.  .+ .+.+.
T Consensus       123 ~~~i~~iDtPGh~~f~~~~~~g~~~aD~allVVda~~g~~~qt~e~l~~~~~~gip~iIvviNKiDlv~~--~~~~~~i~  200 (447)
T PLN03127        123 KRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVVFLNKVDVVDD--EELLELVE  200 (447)
T ss_pred             CeEEEEEECCCccchHHHHHHHHhhCCEEEEEEECCCCCchhHHHHHHHHHHcCCCeEEEEEEeeccCCH--HHHHHHHH
Confidence            4568999999931  01111 1123699999999987643221 11   11233454 678999999864  32 22333


Q ss_pred             HHHHhc----C---CCCCEEEEecc---cCCC-------HHHHHHHHhhh
Q 030407          144 RDALRM----R---DGGPFIFAQVG---WVIG-------IIFTLSITHYI  176 (178)
Q Consensus       144 ~~l~~~----n---p~a~i~~~SA~---~g~g-------i~el~~~l~~~  176 (178)
                      +.+++.    .   ...|++++||.   +|.|       +.+|++.+..+
T Consensus       201 ~~i~~~l~~~~~~~~~vpiip~Sa~sa~~g~n~~~~~~~i~~Ll~~l~~~  250 (447)
T PLN03127        201 MELRELLSFYKFPGDEIPIIRGSALSALQGTNDEIGKNAILKLMDAVDEY  250 (447)
T ss_pred             HHHHHHHHHhCCCCCcceEEEeccceeecCCCcccccchHHHHHHHHHHh
Confidence            233322    1   13688888875   5555       78888887654

>cd01882 BMS1 Bms1

Probab=97.50  E-value=0.00026  Score=56.11  Aligned_cols=89  Identities=18%  Similarity=0.130  Sum_probs=53.2

Q ss_pred             CCCEEEEeCCcchhhhccc-ccccceEEEEEeCCCCCCCCcC-CC---CCCCceeE-EEEecCCCCCchhHhHHHHHHHH
Q 030407           73 KADLLLCESGGDNLAANFS-RELADYIIYIIDVSGGDKIPRK-GG---PGITQADL-LVINKTDLASAIGADLAVMERDA  146 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~~-~~~ad~~I~VvD~~~~~~~~~~-~~---~qi~~adi-iviNK~Dl~~~~~~~~~~~~~~l  146 (178)
                      +..+.+++|.|. +..... ...+|.+++|+|+..+...... ..   .....+.+ +|+||+|+.++. ...+.+.+.+
T Consensus        82 ~~~i~~vDtPg~-~~~~l~~ak~aDvVllviDa~~~~~~~~~~i~~~l~~~g~p~vi~VvnK~D~~~~~-~~~~~~~~~l  159 (225)
T cd01882          82 KRRLTFIECPND-INAMIDIAKVADLVLLLIDASFGFEMETFEFLNILQVHGFPRVMGVLTHLDLFKKN-KTLRKTKKRL  159 (225)
T ss_pred             CceEEEEeCCch-HHHHHHHHHhcCEEEEEEecCcCCCHHHHHHHHHHHHcCCCeEEEEEeccccCCcH-HHHHHHHHHH
Confidence            455788899883 221111 1346999999999876433211 00   01123444 499999998541 2334444333


Q ss_pred             H-----hcCCCCCEEEEecccC
Q 030407          147 L-----RMRDGGPFIFAQVGWV  163 (178)
Q Consensus       147 ~-----~~np~a~i~~~SA~~g  163 (178)
                      +     +..++.+++++||++.
T Consensus       160 ~~~~~~~~~~~~ki~~iSa~~~  181 (225)
T cd01882         160 KHRFWTEVYQGAKLFYLSGIVH  181 (225)
T ss_pred             HHHHHHhhCCCCcEEEEeeccC
Confidence            2     3468899999999986

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.

>TIGR00450 mnmE_trmE_thdF tRNA modification GTPase TrmE

Probab=97.47  E-value=0.00034  Score=60.93  Aligned_cols=94  Identities=17%  Similarity=0.049  Sum_probs=56.6

Q ss_pred             CCCEEEEeCCcch----hhh-------cccccccceEEEEEeCCCCCCCCcCCCC---CCCceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDN----LAA-------NFSRELADYIIYIIDVSGGDKIPRKGGP---GITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~-------~~~~~~ad~~I~VvD~~~~~~~~~~~~~---qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      +..+.++.|.|..    ...       ......+|.+++|+|++++......+..   ....+-++|+||+|+.++   +
T Consensus       250 g~~v~l~DTaG~~~~~~~ie~~gi~~~~~~~~~aD~il~V~D~s~~~s~~~~~l~~~~~~~~piIlV~NK~Dl~~~---~  326 (442)
T TIGR00450       250 GILIKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIYVLDASQPLTKDDFLIIDLNKSKKPFILVLNKIDLKIN---S  326 (442)
T ss_pred             CEEEEEeeCCCcccchhHHHHHHHHHHHHHHhhCCEEEEEEECCCCCChhHHHHHHHhhCCCCEEEEEECccCCCc---c
Confidence            3456889999941    000       0111247999999999876432211111   123456999999999654   2


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+.+   .+..  ..+++.+||++ .||+++++.+.+
T Consensus       327 ~~~~---~~~~--~~~~~~vSak~-~gI~~~~~~L~~  357 (442)
T TIGR00450       327 LEFF---VSSK--VLNSSNLSAKQ-LKIKALVDLLTQ  357 (442)
T ss_pred             hhhh---hhhc--CCceEEEEEec-CCHHHHHHHHHH
Confidence            2221   2222  34789999998 588888776654

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.

>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins

Probab=97.44  E-value=0.0003  Score=56.10  Aligned_cols=47  Identities=19%  Similarity=0.015  Sum_probs=36.1

Q ss_pred             ceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          120 QADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       120 ~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+-++|+||+|+.+.  ++.+.   +.+  .  .+++++||++|.|++++++.+.+
T Consensus       177 ~p~iiV~NK~Dl~~~--~~~~~---~~~--~--~~~~~~SA~~g~gi~~l~~~i~~  223 (233)
T cd01896         177 IPCLYVYNKIDLISI--EELDL---LAR--Q--PNSVVISAEKGLNLDELKERIWD  223 (233)
T ss_pred             eeEEEEEECccCCCH--HHHHH---Hhc--C--CCEEEEcCCCCCCHHHHHHHHHH
Confidence            356899999999877  55442   211  2  36899999999999999998765

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.

>KOG0076 consensus GTP-binding ADP-ribosylation factor-like protein yARL3 [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.42  E-value=8.4e-05  Score=56.54  Aligned_cols=80  Identities=21%  Similarity=0.177  Sum_probs=56.2

Q ss_pred             ccceEEEEEeCCCCCCCCcC---------CCCCCCceeEEEEecCCCCCchhHhHHHHHHHHH--hcC--CCCCEEEEec
Q 030407           94 LADYIIYIIDVSGGDKIPRK---------GGPGITQADLLVINKTDLASAIGADLAVMERDAL--RMR--DGGPFIFAQV  160 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~---------~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~--~~n--p~a~i~~~SA  160 (178)
                      .+|++|+++|+++.+..+..         ...+-..+-++..||-|+.+.  .+.+.+.....  +.+  |..++.++||
T Consensus        92 ~~H~ii~viDa~~~eR~~~~~t~~~~v~~~E~leg~p~L~lankqd~q~~--~~~~El~~~~~~~e~~~~rd~~~~pvSa  169 (197)
T KOG0076|consen   92 LAHGIIYVIDATDRERFEESKTAFEKVVENEKLEGAPVLVLANKQDLQNA--MEAAELDGVFGLAELIPRRDNPFQPVSA  169 (197)
T ss_pred             HhceeEEeecCCCHHHHHHHHHHHHHHHHHHHhcCCchhhhcchhhhhhh--hhHHHHHHHhhhhhhcCCccCccccchh
Confidence            57999999999885433221         112234567899999999877  45555554443  444  4568999999


Q ss_pred             ccCCCHHHHHHHHhh
Q 030407          161 GWVIGIIFTLSITHY  175 (178)
Q Consensus       161 ~~g~gi~el~~~l~~  175 (178)
                      .+|+||+|-.+++..
T Consensus       170 l~gegv~egi~w~v~  184 (197)
T KOG0076|consen  170 LTGEGVKEGIEWLVK  184 (197)
T ss_pred             hhcccHHHHHHHHHH
Confidence            999999998887643

>KOG0072 consensus GTP-binding ADP-ribosylation factor-like protein ARL1 [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.42  E-value=0.00035  Score=51.79  Aligned_cols=100  Identities=15%  Similarity=0.093  Sum_probs=59.5

Q ss_pred             CCCEEEEeCCcchhhh---cccccccceEEEEEeCCCCCCCCcC--------CCCCCCce-eEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNLAA---NFSRELADYIIYIIDVSGGDKIPRK--------GGPGITQA-DLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~---~~~~~~ad~~I~VvD~~~~~~~~~~--------~~~qi~~a-diiviNK~Dl~~~~~~~~~  140 (178)
                      ++.+=..|--| ++++   +|. ...+.+|+|||.++.+.....        ..+.++.| -+++.||-|....  -...
T Consensus        63 k~~vwdLggqt-SirPyWRcYy-~dt~avIyVVDssd~dris~a~~el~~mL~E~eLq~a~llv~anKqD~~~~--~t~~  138 (182)
T KOG0072|consen   63 KFQVWDLGGQT-SIRPYWRCYY-ADTDAVIYVVDSSDRDRISIAGVELYSMLQEEELQHAKLLVFANKQDYSGA--LTRS  138 (182)
T ss_pred             cceeeEccCcc-cccHHHHHHh-cccceEEEEEeccchhhhhhhHHHHHHHhccHhhcCceEEEEeccccchhh--hhHH
Confidence            45544545444 3331   222 356899999999876543210        11123333 5778999998644  2222


Q ss_pred             HHHHHHH--hc-CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDAL--RM-RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~--~~-np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ++...+.  ++ +....|+.+||.+|+|+++..+||.+.
T Consensus       139 E~~~~L~l~~Lk~r~~~Iv~tSA~kg~Gld~~~DWL~~~  177 (182)
T KOG0072|consen  139 EVLKMLGLQKLKDRIWQIVKTSAVKGEGLDPAMDWLQRP  177 (182)
T ss_pred             HHHHHhChHHHhhheeEEEeeccccccCCcHHHHHHHHH
Confidence            2221111  11 233689999999999999999999864

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

Probab=97.40  E-value=0.00038  Score=52.10  Aligned_cols=94  Identities=15%  Similarity=0.130  Sum_probs=57.2

Q ss_pred             CCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCCc--CC---CCCC---CceeEEEEecCCCCCchhHhHH-
Q 030407           74 ADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIPR--KG---GPGI---TQADLLVINKTDLASAIGADLA-  140 (178)
Q Consensus        74 ~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~---~~qi---~~adiiviNK~Dl~~~~~~~~~-  140 (178)
                      ...=|..|.|-    ++...|++ .+.+.++|+|++..+....  .+   .+.+   ....+++.||.||-++  -+.. 
T Consensus        58 vKLQIWDTAGQErFRSVtRsYYR-GAAGAlLVYD~TsrdsfnaLtnWL~DaR~lAs~nIvviL~GnKkDL~~~--R~Vtf  134 (214)
T KOG0086|consen   58 VKLQIWDTAGQERFRSVTRSYYR-GAAGALLVYDITSRDSFNALTNWLTDARTLASPNIVVILCGNKKDLDPE--REVTF  134 (214)
T ss_pred             EEEEEeecccHHHHHHHHHHHhc-cccceEEEEeccchhhHHHHHHHHHHHHhhCCCcEEEEEeCChhhcChh--hhhhH
Confidence            34456677773    12334444 6788999999988764422  01   1122   2345777899999766  3322 


Q ss_pred             -HHHHHHHhcCCCCCEEEEecccCCCHHHHHHH
Q 030407          141 -VMERDALRMRDGGPFIFAQVGWVIGIIFTLSI  172 (178)
Q Consensus       141 -~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~  172 (178)
                       +..++.++ | ..-.++|||+||++++|-|-.
T Consensus       135 lEAs~FaqE-n-el~flETSa~TGeNVEEaFl~  165 (214)
T KOG0086|consen  135 LEASRFAQE-N-ELMFLETSALTGENVEEAFLK  165 (214)
T ss_pred             HHHHhhhcc-c-ceeeeeecccccccHHHHHHH
Confidence             22223332 2 346789999999999998743

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

Probab=97.40  E-value=0.0001  Score=53.96  Aligned_cols=99  Identities=18%  Similarity=0.171  Sum_probs=61.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      +...=+..|.|..    +...|+ ..+|..+.+.|..+......  .+..      +-..+-.++.||+|++.+.....+
T Consensus        46 kvklqiwdtagqerfrsvt~ayy-rda~allllydiankasfdn~~~wlsei~ey~k~~v~l~llgnk~d~a~er~v~~d  124 (192)
T KOG0083|consen   46 KVKLQIWDTAGQERFRSVTHAYY-RDADALLLLYDIANKASFDNCQAWLSEIHEYAKEAVALMLLGNKCDLAHERAVKRD  124 (192)
T ss_pred             EEEEEEeeccchHHHhhhhHhhh-cccceeeeeeecccchhHHHHHHHHHHHHHHHHhhHhHhhhccccccchhhccccc
Confidence            4667788888831    112233 36899999999987543321  0111      223456899999999764212222


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      .-++..++.  +.|+.+||||||.+++--|-.|.
T Consensus       125 dg~kla~~y--~ipfmetsaktg~nvd~af~~ia  156 (192)
T KOG0083|consen  125 DGEKLAEAY--GIPFMETSAKTGFNVDLAFLAIA  156 (192)
T ss_pred             hHHHHHHHH--CCCceeccccccccHhHHHHHHH
Confidence            222222322  46999999999999998776554

>COG1162 Predicted GTPases [General function prediction only]

Probab=97.36  E-value=0.00042  Score=57.15  Aligned_cols=96  Identities=19%  Similarity=0.167  Sum_probs=59.4

Q ss_pred             CEEEEeCC---cchhhh------cccc-c--ccceEEEEEeCCCCCCCCc---CCC---CCCCceeEEEEecCCCCCchh
Q 030407           75 DLLLCESG---GDNLAA------NFSR-E--LADYIIYIIDVSGGDKIPR---KGG---PGITQADLLVINKTDLASAIG  136 (178)
Q Consensus        75 d~iiiEtt---G~~~~~------~~~~-~--~ad~~I~VvD~~~~~~~~~---~~~---~qi~~adiiviNK~Dl~~~~~  136 (178)
                      |++.+|..   |+ +..      .+.+ .  ..|-.++|+.+..++-...   ++.   +--...-+|++||+||+++  
T Consensus        49 D~V~~~~~~~~g~-I~~i~~Rkn~L~Rp~v~n~d~~iiIvs~~~P~~~~~~ldR~Lv~ae~~gi~pvIvlnK~DL~~~--  125 (301)
T COG1162          49 DRVVFEDENNNGV-IEKILPRKNVLIRPPVANNDQAIIVVSLVDPDFNTNLLDRYLVLAEAGGIEPVIVLNKIDLLDD--  125 (301)
T ss_pred             CeEEEecCCCcce-EEEEecccCceeCCcccccceEEEEEeccCCCCCHHHHHHHHHHHHHcCCcEEEEEEccccCcc--
Confidence            88888887   42 211      1111 1  1355677777766543211   110   1112235999999999988  


Q ss_pred             HhHH--HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          137 ADLA--VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       137 ~~~~--~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ++.+  +.....+.+  +.+++.+|+++++|+++|.+.+..
T Consensus       126 ~~~~~~~~~~~y~~~--gy~v~~~s~~~~~~~~~l~~~l~~  164 (301)
T COG1162         126 EEAAVKELLREYEDI--GYPVLFVSAKNGDGLEELAELLAG  164 (301)
T ss_pred             hHHHHHHHHHHHHhC--CeeEEEecCcCcccHHHHHHHhcC
Confidence            5544  333444433  579999999999999999998764

>PLN03126 Elongation factor Tu; Provisional

Probab=97.36  E-value=0.00055  Score=60.22  Aligned_cols=90  Identities=12%  Similarity=0.112  Sum_probs=54.3

Q ss_pred             CCCEEEEeCCcch--hhhccc-ccccceEEEEEeCCCCCCCCc-CCC---CCCCce-eEEEEecCCCCCchhHh-HH---
Q 030407           73 KADLLLCESGGDN--LAANFS-RELADYIIYIIDVSGGDKIPR-KGG---PGITQA-DLLVINKTDLASAIGAD-LA---  140 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~~-~~~ad~~I~VvD~~~~~~~~~-~~~---~qi~~a-diiviNK~Dl~~~~~~~-~~---  140 (178)
                      +..+.||.|.|-.  +..+.. ...+|..++|+|+..+...+. .+.   .....+ -++++||+|+++.  ++ .+   
T Consensus       143 ~~~i~liDtPGh~~f~~~~~~g~~~aD~ailVVda~~G~~~qt~e~~~~~~~~gi~~iIvvvNK~Dl~~~--~~~~~~i~  220 (478)
T PLN03126        143 NRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQVDD--EELLELVE  220 (478)
T ss_pred             CcEEEEEECCCHHHHHHHHHHHHhhCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCeEEEEEecccccCH--HHHHHHHH
Confidence            5578999999931  111111 124699999999987753321 111   112334 3678999999874  32 22   


Q ss_pred             -HHHHHHHhc--C-CCCCEEEEecccCC
Q 030407          141 -VMERDALRM--R-DGGPFIFAQVGWVI  164 (178)
Q Consensus       141 -~~~~~l~~~--n-p~a~i~~~SA~~g~  164 (178)
                       ++.+.++..  + ...+++++||.+|.
T Consensus       221 ~~i~~~l~~~g~~~~~~~~vp~Sa~~g~  248 (478)
T PLN03126        221 LEVRELLSSYEFPGDDIPIISGSALLAL  248 (478)
T ss_pred             HHHHHHHHhcCCCcCcceEEEEEccccc
Confidence             344445443  1 25799999999884

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=97.34  E-value=0.00018  Score=57.70  Aligned_cols=102  Identities=17%  Similarity=0.099  Sum_probs=52.3

Q ss_pred             CCCEEEEeCCcchhhhcc-------------cccccceEEEEEeCCCCCCCCcCCC---------CCCCceeEEEEecCC
Q 030407           73 KADLLLCESGGDNLAANF-------------SRELADYIIYIIDVSGGDKIPRKGG---------PGITQADLLVINKTD  130 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~-------------~~~~ad~~I~VvD~~~~~~~~~~~~---------~qi~~adiiviNK~D  130 (178)
                      +.+|+++.|.|-  ...|             .....-.+++++|+....+......         -.++.+-+.|+||+|
T Consensus        90 ~~~y~l~DtPGQ--iElf~~~~~~~~i~~~L~~~~~~~~v~LvD~~~~~~~~~f~s~~L~s~s~~~~~~lP~vnvlsK~D  167 (238)
T PF03029_consen   90 EDDYLLFDTPGQ--IELFTHSDSGRKIVERLQKNGRLVVVFLVDSSFCSDPSKFVSSLLLSLSIMLRLELPHVNVLSKID  167 (238)
T ss_dssp             H-SEEEEE--SS--HHHHHHSHHHHHHHHTSSS----EEEEEE-GGG-SSHHHHHHHHHHHHHHHHHHTSEEEEEE--GG
T ss_pred             CCcEEEEeCCCC--EEEEEechhHHHHHHHHhhhcceEEEEEEecccccChhhHHHHHHHHHHHHhhCCCCEEEeeeccC
Confidence            459999999993  2111             1112346889999876543211100         024678899999999


Q ss_pred             CCCchh-HhH-----------------HHHHHHHHhc---CCCC-CEEEEecccCCCHHHHHHHHhhh
Q 030407          131 LASAIG-ADL-----------------AVMERDALRM---RDGG-PFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       131 l~~~~~-~~~-----------------~~~~~~l~~~---np~a-~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.++.. ..+                 ..+.+.+.+.   .... ++++.|+++++|+++|+..+++.
T Consensus       168 l~~~~~~~~l~~~~d~~~l~~~~~~~~~~l~~~i~~~l~~~~~~~~f~pls~~~~~~~~~L~~~id~a  235 (238)
T PF03029_consen  168 LLSKYLEFILEWFEDPDSLEDLLESDYKKLNEEIAELLDDFGLVIRFIPLSSKDGEGMEELLAAIDKA  235 (238)
T ss_dssp             GS-HHHHHHHHHHHSHHHHHHHHHT-HHHHHHHHHHHCCCCSSS---EE-BTTTTTTHHHHHHHHHHH
T ss_pred             cccchhHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHhhcCCCceEEEEECCChHHHHHHHHHHHHH
Confidence            998310 000                 1111222222   1334 89999999999999999998865

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>COG2895 CysN GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]

Probab=97.29  E-value=0.00041  Score=58.35  Aligned_cols=92  Identities=16%  Similarity=0.199  Sum_probs=56.3

Q ss_pred             CCCEEEEeCCcchhhhcccc------cccceEEEEEeCCCCCCCCc-CCC---CCCCc-eeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDNLAANFSR------ELADYIIYIIDVSGGDKIPR-KGG---PGITQ-ADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~~~------~~ad~~I~VvD~~~~~~~~~-~~~---~qi~~-adiiviNK~Dl~~~~~~~~~~  141 (178)
                      +=++|+..|.|-   ..|.+      .-+|..|++||+..|...+. .+.   ..+.. --++.+||+||++...+.-++
T Consensus        85 KRkFIiADTPGH---eQYTRNMaTGASTadlAIlLVDAR~Gvl~QTrRHs~I~sLLGIrhvvvAVNKmDLvdy~e~~F~~  161 (431)
T COG2895          85 KRKFIIADTPGH---EQYTRNMATGASTADLAILLVDARKGVLEQTRRHSFIASLLGIRHVVVAVNKMDLVDYSEEVFEA  161 (431)
T ss_pred             cceEEEecCCcH---HHHhhhhhcccccccEEEEEEecchhhHHHhHHHHHHHHHhCCcEEEEEEeeecccccCHHHHHH
Confidence            447899999992   12221      12589999999987753322 111   11222 247889999999873222222


Q ss_pred             ----HHHHHHhcC-CCCCEEEEecccCCCHH
Q 030407          142 ----MERDALRMR-DGGPFIFAQVGWVIGII  167 (178)
Q Consensus       142 ----~~~~l~~~n-p~a~i~~~SA~~g~gi~  167 (178)
                          +..+.+++. ....++++||+.|.++-
T Consensus       162 I~~dy~~fa~~L~~~~~~~IPiSAl~GDNV~  192 (431)
T COG2895         162 IVADYLAFAAQLGLKDVRFIPISALLGDNVV  192 (431)
T ss_pred             HHHHHHHHHHHcCCCcceEEechhccCCccc
Confidence                333334443 23589999999999874

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

Probab=97.27  E-value=0.00014  Score=54.14  Aligned_cols=99  Identities=17%  Similarity=0.124  Sum_probs=61.8

Q ss_pred             CCCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCC---CcCCCC--C---CCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKI---PRKGGP--G---ITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~---~~~~~~--q---i~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      +...=+..|.|-    ++...|++ .++.+|.|.|.+-.+..   ++...+  +   -+.--|+|.||+|+.+.. +-.+
T Consensus        55 kiklqiwdtagqerfrsitqsyyr-sahalilvydiscqpsfdclpewlreie~yan~kvlkilvgnk~d~~drr-evp~  132 (213)
T KOG0095|consen   55 KIKLQIWDTAGQERFRSITQSYYR-SAHALILVYDISCQPSFDCLPEWLREIEQYANNKVLKILVGNKIDLADRR-EVPQ  132 (213)
T ss_pred             EEEEEEeeccchHHHHHHHHHHhh-hcceEEEEEecccCcchhhhHHHHHHHHHHhhcceEEEeeccccchhhhh-hhhH
Confidence            566778889993    23344444 57999999998754432   111111  1   112259999999998652 2222


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      ++-+...+. ....+++|||+..++++.||..+.
T Consensus       133 qigeefs~~-qdmyfletsakea~nve~lf~~~a  165 (213)
T KOG0095|consen  133 QIGEEFSEA-QDMYFLETSAKEADNVEKLFLDLA  165 (213)
T ss_pred             HHHHHHHHh-hhhhhhhhcccchhhHHHHHHHHH
Confidence            333333222 345788999999999999997653

>cd04168 TetM_like Tet(M)-like subfamily

Probab=97.23  E-value=0.00096  Score=53.35  Aligned_cols=60  Identities=17%  Similarity=0.201  Sum_probs=37.9

Q ss_pred             CCCEEEEeCCcch-hh---hcccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCC
Q 030407           73 KADLLLCESGGDN-LA---ANFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLAS  133 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~---~~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~  133 (178)
                      +..+.+++|.|.. ..   ..+ ...+|.+++|+|+..+......    .......+-++++||+|+..
T Consensus        63 ~~~i~liDTPG~~~f~~~~~~~-l~~aD~~IlVvd~~~g~~~~~~~~~~~~~~~~~P~iivvNK~D~~~  130 (237)
T cd04168          63 DTKVNLIDTPGHMDFIAEVERS-LSVLDGAILVISAVEGVQAQTRILWRLLRKLNIPTIIFVNKIDRAG  130 (237)
T ss_pred             CEEEEEEeCCCccchHHHHHHH-HHHhCeEEEEEeCCCCCCHHHHHHHHHHHHcCCCEEEEEECccccC
Confidence            5788999999931 01   111 1246999999999886432110    01112345699999999975

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.

>COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]

Probab=97.22  E-value=0.0028  Score=55.24  Aligned_cols=101  Identities=15%  Similarity=0.146  Sum_probs=63.4

Q ss_pred             CCCEEEEeCCcchhhhc---ccc--cccceEEEEEeCCCCCCCCcCCCC----CCCceeEEEEecCCCCCchhHh-HHHH
Q 030407           73 KADLLLCESGGDNLAAN---FSR--ELADYIIYIIDVSGGDKIPRKGGP----GITQADLLVINKTDLASAIGAD-LAVM  142 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~---~~~--~~ad~~I~VvD~~~~~~~~~~~~~----qi~~adiiviNK~Dl~~~~~~~-~~~~  142 (178)
                      +.-+=+|.|.|  .+..   ..+  ...|+++++||+.+|...+.++--    -....-|+|+||+|..++.+++ ..++
T Consensus        67 ~~~INIvDTPG--HADFGGEVERvl~MVDgvlLlVDA~EGpMPQTrFVlkKAl~~gL~PIVVvNKiDrp~Arp~~Vvd~v  144 (603)
T COG1217          67 GTRINIVDTPG--HADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALALGLKPIVVINKIDRPDARPDEVVDEV  144 (603)
T ss_pred             CeEEEEecCCC--cCCccchhhhhhhhcceEEEEEEcccCCCCchhhhHHHHHHcCCCcEEEEeCCCCCCCCHHHHHHHH
Confidence            45666888999  3211   111  236999999999998866544321    1223459999999998764333 2333


Q ss_pred             HHHHHhcCC-----CCCEEEEecccCC----------CHHHHHHHHhh
Q 030407          143 ERDALRMRD-----GGPFIFAQVGWVI----------GIIFTLSITHY  175 (178)
Q Consensus       143 ~~~l~~~np-----~a~i~~~SA~~g~----------gi~el~~~l~~  175 (178)
                      ....-++..     .-|+++.||+.|.          .+..||+.|.+
T Consensus       145 fDLf~~L~A~deQLdFPivYAS~~~G~a~~~~~~~~~~m~pLfe~I~~  192 (603)
T COG1217         145 FDLFVELGATDEQLDFPIVYASARNGTASLDPEDEADDMAPLFETILD  192 (603)
T ss_pred             HHHHHHhCCChhhCCCcEEEeeccCceeccCccccccchhHHHHHHHH
Confidence            333333332     2489999998763          56777877654

>COG0536 Obg Predicted GTPase [General function prediction only]

Probab=97.22  E-value=0.00095  Score=55.88  Aligned_cols=80  Identities=18%  Similarity=0.108  Sum_probs=53.0

Q ss_pred             ceEEEEEeCCCCCCCC------------cCCC-CCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEeccc
Q 030407           96 DYIIYIIDVSGGDKIP------------RKGG-PGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGW  162 (178)
Q Consensus        96 d~~I~VvD~~~~~~~~------------~~~~-~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~  162 (178)
                      ..++.|+|.+..+...            ..|. .....+-+||+||+|++.+. ++.+.+.+.+.+.......+++||.+
T Consensus       239 ~vL~hviD~s~~~~~dp~~~~~~i~~EL~~Y~~~L~~K~~ivv~NKiD~~~~~-e~~~~~~~~l~~~~~~~~~~~ISa~t  317 (369)
T COG0536         239 RVLLHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKPRIVVLNKIDLPLDE-EELEELKKALAEALGWEVFYLISALT  317 (369)
T ss_pred             heeEEEEecCcccCCCHHHHHHHHHHHHHHhhHHhccCceEEEEeccCCCcCH-HHHHHHHHHHHHhcCCCcceeeehhc
Confidence            3577889987544210            0121 22456779999999954331 67777777777554443333499999


Q ss_pred             CCCHHHHHHHHhhh
Q 030407          163 VIGIIFTLSITHYI  176 (178)
Q Consensus       163 g~gi~el~~~l~~~  176 (178)
                      ++|+++|...+.++
T Consensus       318 ~~g~~~L~~~~~~~  331 (369)
T COG0536         318 REGLDELLRALAEL  331 (369)
T ss_pred             ccCHHHHHHHHHHH
Confidence            99999999877654

>PRK12740 elongation factor G; Reviewed

Probab=97.21  E-value=0.001  Score=60.74  Aligned_cols=63  Identities=16%  Similarity=0.176  Sum_probs=39.7

Q ss_pred             CCCCEEEEeCCcch-h-hhcc-cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           72 FKADLLLCESGGDN-L-AANF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        72 ~~~d~iiiEttG~~-~-~~~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      .++++.+|.|.|.. . .... ....+|.+++|+|++.+......    .......+.++|+||+|+...
T Consensus        58 ~~~~i~liDtPG~~~~~~~~~~~l~~aD~vllvvd~~~~~~~~~~~~~~~~~~~~~p~iiv~NK~D~~~~  127 (668)
T PRK12740         58 KGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTETVWRQAEKYGVPRIIFVNKMDRAGA  127 (668)
T ss_pred             CCEEEEEEECCCcHHHHHHHHHHHHHhCeEEEEEeCCCCcCHHHHHHHHHHHHcCCCEEEEEECCCCCCC
Confidence            36889999999931 1 0111 11246999999999876532211    111134567999999998754

>COG2229 Predicted GTPase [General function prediction only]

Probab=97.20  E-value=0.0014  Score=50.29  Aligned_cols=99  Identities=17%  Similarity=-0.005  Sum_probs=66.9

Q ss_pred             CCEEEEeCCcchhhhcccc----cccceEEEEEeCCCCCCCCcC----CCCCCC-ceeEEEEecCCCCCchhHhHHHHHH
Q 030407           74 ADLLLCESGGDNLAANFSR----ELADYIIYIIDVSGGDKIPRK----GGPGIT-QADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~~~~----~~ad~~I~VvD~~~~~~~~~~----~~~qi~-~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      .-+=+.-|.| ..+..|.+    ..+.+.|++||.+.+....+.    +-.... .+-+|.+||.||.+.  -..+++++
T Consensus        68 ~~v~LfgtPG-q~RF~fm~~~l~~ga~gaivlVDss~~~~~~a~~ii~f~~~~~~ip~vVa~NK~DL~~a--~ppe~i~e  144 (187)
T COG2229          68 TGVHLFGTPG-QERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVVAINKQDLFDA--LPPEKIRE  144 (187)
T ss_pred             ceEEEecCCC-cHHHHHHHHHHhCCcceEEEEEecCCCcchHHHHHHHHHhhccCCCEEEEeeccccCCC--CCHHHHHH
Confidence            4455556777 22222222    247899999999887654111    001111 466899999999887  55567777


Q ss_pred             HHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          145 DALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       145 ~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+..-+-..+++.++|.+++|..+.++.++.
T Consensus       145 ~l~~~~~~~~vi~~~a~e~~~~~~~L~~ll~  175 (187)
T COG2229         145 ALKLELLSVPVIEIDATEGEGARDQLDVLLL  175 (187)
T ss_pred             HHHhccCCCceeeeecccchhHHHHHHHHHh
Confidence            7765545679999999999999999987764

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

Probab=97.20  E-value=0.00032  Score=54.86  Aligned_cols=101  Identities=13%  Similarity=0.028  Sum_probs=63.7

Q ss_pred             hCCCCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCC---cCCCC-----CCCceeEEEEecCCCCCchhHh
Q 030407           71 LFKADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIP---RKGGP-----GITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        71 ~~~~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~---~~~~~-----qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      ...+...|..|.|.    ++.+.|+ .++-+.+.|+|.+......   +++.+     .-...-++|.||+||..-....
T Consensus        60 ~k~vkaqIWDTAGQERyrAitSaYY-rgAvGAllVYDITr~~Tfenv~rWL~ELRdhad~nivimLvGNK~DL~~lraV~  138 (222)
T KOG0087|consen   60 GKTVKAQIWDTAGQERYRAITSAYY-RGAVGALLVYDITRRQTFENVERWLKELRDHADSNIVIMLVGNKSDLNHLRAVP  138 (222)
T ss_pred             CcEEEEeeecccchhhhccccchhh-cccceeEEEEechhHHHHHHHHHHHHHHHhcCCCCeEEEEeecchhhhhccccc
Confidence            34578899999994    1223344 3788999999998754322   11111     1234568999999997521011


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      .+..+...+.  ..-.+++|||+.+.++++.|+.+.
T Consensus       139 te~~k~~Ae~--~~l~f~EtSAl~~tNVe~aF~~~l  172 (222)
T KOG0087|consen  139 TEDGKAFAEK--EGLFFLETSALDATNVEKAFERVL  172 (222)
T ss_pred             hhhhHhHHHh--cCceEEEecccccccHHHHHHHHH
Confidence            2233333322  245899999999999999997654

>COG0370 FeoB Fe2+ transport system protein B [Inorganic ion transport and metabolism]

Probab=97.11  E-value=0.0002  Score=64.47  Aligned_cols=98  Identities=16%  Similarity=0.158  Sum_probs=64.3

Q ss_pred             CCCEEEEeCCcc-hh---------hhcccc-cccceEEEEEeCCCCCCCCcCCCC---CCCceeEEEEecCCCCCchh--
Q 030407           73 KADLLLCESGGD-NL---------AANFSR-ELADYIIYIIDVSGGDKIPRKGGP---GITQADLLVINKTDLASAIG--  136 (178)
Q Consensus        73 ~~d~iiiEttG~-~~---------~~~~~~-~~ad~~I~VvD~~~~~~~~~~~~~---qi~~adiiviNK~Dl~~~~~--  136 (178)
                      +-++=+|...|. ++         +..|.. ...|.+|.|+|+++-+.... ..-   .+..+-++++|++|.+...+  
T Consensus        49 ~~~i~ivDLPG~YSL~~~S~DE~Var~~ll~~~~D~ivnVvDAtnLeRnLy-ltlQLlE~g~p~ilaLNm~D~A~~~Gi~  127 (653)
T COG0370          49 GHEIEIVDLPGTYSLTAYSEDEKVARDFLLEGKPDLIVNVVDATNLERNLY-LTLQLLELGIPMILALNMIDEAKKRGIR  127 (653)
T ss_pred             CceEEEEeCCCcCCCCCCCchHHHHHHHHhcCCCCEEEEEcccchHHHHHH-HHHHHHHcCCCeEEEeccHhhHHhcCCc
Confidence            456788888884 11         111211 23599999999987543211 011   14556799999999875521  


Q ss_pred             HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 ~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      -+.+++.+.+     +.|+++|||++|+|++++.+.+.+.
T Consensus       128 ID~~~L~~~L-----GvPVv~tvA~~g~G~~~l~~~i~~~  162 (653)
T COG0370         128 IDIEKLSKLL-----GVPVVPTVAKRGEGLEELKRAIIEL  162 (653)
T ss_pred             ccHHHHHHHh-----CCCEEEEEeecCCCHHHHHHHHHHh
Confidence            2233444333     5799999999999999999987654

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

Probab=97.09  E-value=0.00084  Score=54.75  Aligned_cols=89  Identities=10%  Similarity=-0.013  Sum_probs=52.5

Q ss_pred             CCCEEEEeCCcch-hh-hcc-cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchh-HhHHHHHH
Q 030407           73 KADLLLCESGGDN-LA-ANF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIG-ADLAVMER  144 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~-~~~~~~~~  144 (178)
                      +..+.||.|.|.. .. ... ....+|.+++|+|+..+......    .......+-++++||+|+.+... ..++.+++
T Consensus        63 ~~~i~liDTPG~~df~~~~~~~l~~aD~ailVVDa~~g~~~~t~~~~~~~~~~~~p~ivviNK~D~~~a~~~~~~~~l~~  142 (270)
T cd01886          63 DHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQADRYNVPRIAFVNKMDRTGADFFRVVEQIRE  142 (270)
T ss_pred             CEEEEEEECCCcHHHHHHHHHHHHHcCEEEEEEECCCCCCHHHHHHHHHHHHcCCCEEEEEECCCCCCCCHHHHHHHHHH
Confidence            5788999999931 11 111 11246999999999886533211    11123456799999999975411 12334444


Q ss_pred             HHHhcCCCCCEEEEeccc
Q 030407          145 DALRMRDGGPFIFAQVGW  162 (178)
Q Consensus       145 ~l~~~np~a~i~~~SA~~  162 (178)
                      .++ ..+...++++|+..
T Consensus       143 ~l~-~~~~~~~~Pisa~~  159 (270)
T cd01886         143 KLG-ANPVPLQLPIGEED  159 (270)
T ss_pred             HhC-CCceEEEeccccCC
Confidence            433 23556778888763

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

>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]

Probab=97.05  E-value=0.0018  Score=59.06  Aligned_cols=103  Identities=17%  Similarity=0.070  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCC-----ch----
Q 030407           73 KADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLAS-----AI----  135 (178)
Q Consensus        73 ~~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~-----~~----  135 (178)
                      -|-.++|.|.|-    ++..... .+-|..|.|+|..+|.+.+..    ..+.-..+=||.+||+|..=     +.    
T Consensus       539 vPg~lvIdtpghEsFtnlRsrgs-slC~~aIlvvdImhGlepqtiESi~lLR~rktpFivALNKiDRLYgwk~~p~~~i~  617 (1064)
T KOG1144|consen  539 VPGLLVIDTPGHESFTNLRSRGS-SLCDLAILVVDIMHGLEPQTIESINLLRMRKTPFIVALNKIDRLYGWKSCPNAPIV  617 (1064)
T ss_pred             CCeeEEecCCCchhhhhhhhccc-cccceEEEEeehhccCCcchhHHHHHHHhcCCCeEEeehhhhhhcccccCCCchHH
Confidence            478999999992    1221111 245889999999999765431    11222345699999999851     10    


Q ss_pred             -------hHhHHHHHHHHHh---------cC-----------CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          136 -------GADLAVMERDALR---------MR-----------DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       136 -------~~~~~~~~~~l~~---------~n-----------p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                             +.....+..++..         +|           ....+++|||.+|+||..|+-+|..+
T Consensus       618 ~~lkkQ~k~v~~EF~~R~~~ii~efaEQgLN~~LyykNk~~~~~vsiVPTSA~sGeGipdLl~llv~l  685 (1064)
T KOG1144|consen  618 EALKKQKKDVQNEFKERLNNIIVEFAEQGLNAELYYKNKEMGETVSIVPTSAISGEGIPDLLLLLVQL  685 (1064)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHcccchhheeecccccceEEeeecccccCCCcHHHHHHHHHH
Confidence                   0111222222221         22           12478999999999999999887654

>PRK12739 elongation factor G; Reviewed

Probab=97.03  E-value=0.0014  Score=60.10  Aligned_cols=62  Identities=13%  Similarity=0.140  Sum_probs=39.0

Q ss_pred             CCCEEEEeCCcch-h-hhccc-ccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-L-AANFS-RELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-~-~~~~~-~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      +..+.||.|.|.. . ..... ...+|++++|+|+..+...+..    +......+-++++||+|+.++
T Consensus        72 ~~~i~liDTPG~~~f~~e~~~al~~~D~~ilVvDa~~g~~~qt~~i~~~~~~~~~p~iv~iNK~D~~~~  140 (691)
T PRK12739         72 GHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQSETVWRQADKYGVPRIVFVNKMDRIGA  140 (691)
T ss_pred             CEEEEEEcCCCHHHHHHHHHHHHHHhCeEEEEEeCCCCCCHHHHHHHHHHHHcCCCEEEEEECCCCCCC
Confidence            5778999999931 0 11111 1236999999999887543221    111123456999999999854

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

Probab=97.02  E-value=0.0015  Score=49.38  Aligned_cols=101  Identities=16%  Similarity=0.140  Sum_probs=64.0

Q ss_pred             CCCCEEEEeCCcchhhhccc---ccccceEEEEEeCCCCCCCCcC--------CCCCCC-ceeEEEEecCCCCCchhHhH
Q 030407           72 FKADLLLCESGGDNLAANFS---RELADYIIYIIDVSGGDKIPRK--------GGPGIT-QADLLVINKTDLASAIGADL  139 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~~~~~---~~~ad~~I~VvD~~~~~~~~~~--------~~~qi~-~adiiviNK~Dl~~~~~~~~  139 (178)
                      ..+...+.+--|..--..|.   +..+|+.|+|+|.++....+..        ..+++. .+-+|+.||.|+.+.  -..
T Consensus        58 ~~~~L~iwDvGGq~~lr~~W~nYfestdglIwvvDssD~~r~~e~~~~L~~lL~eerlaG~~~Lvlank~dl~~~--l~~  135 (185)
T KOG0073|consen   58 KGYTLNIWDVGGQKTLRSYWKNYFESTDGLIWVVDSSDRMRMQECKQELTELLVEERLAGAPLLVLANKQDLPGA--LSL  135 (185)
T ss_pred             cceEEEEEEcCCcchhHHHHHHhhhccCeEEEEEECchHHHHHHHHHHHHHHHhhhhhcCCceEEEEecCcCccc--cCH
Confidence            46778888877731112222   1346999999999764322210        123333 478999999999865  333


Q ss_pred             HHHH--HHHHhcC--CCCCEEEEecccCCCHHHHHHHHh
Q 030407          140 AVME--RDALRMR--DGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       140 ~~~~--~~l~~~n--p~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      +.+.  -.+.++.  .+.+++.+||.+|+++.+=+++|-
T Consensus       136 ~~i~~~~~L~~l~ks~~~~l~~cs~~tge~l~~gidWL~  174 (185)
T KOG0073|consen  136 EEISKALDLEELAKSHHWRLVKCSAVTGEDLLEGIDWLC  174 (185)
T ss_pred             HHHHHhhCHHHhccccCceEEEEeccccccHHHHHHHHH
Confidence            3333  2233442  356999999999998888888764

>cd01885 EF2 EF2 (for archaea and eukarya)

Probab=96.98  E-value=0.0013  Score=52.14  Aligned_cols=59  Identities=22%  Similarity=0.177  Sum_probs=37.3

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCC
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLA  132 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~  132 (178)
                      ++.+.|+.|.|..    ....+ ...+|++++|+|+..+...+..    .......+-++++||+|+.
T Consensus        72 ~~~i~iiDTPG~~~f~~~~~~~-l~~aD~~ilVvD~~~g~~~~t~~~l~~~~~~~~p~ilviNKiD~~  138 (222)
T cd01885          72 EYLINLIDSPGHVDFSSEVTAA-LRLCDGALVVVDAVEGVCVQTETVLRQALKERVKPVLVINKIDRL  138 (222)
T ss_pred             ceEEEEECCCCccccHHHHHHH-HHhcCeeEEEEECCCCCCHHHHHHHHHHHHcCCCEEEEEECCCcc
Confidence            5667889999931    11111 1357999999999887543211    0011223569999999986

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

>COG5258 GTPBP1 GTPase [General function prediction only]

Probab=96.93  E-value=0.0051  Score=52.54  Aligned_cols=98  Identities=11%  Similarity=0.132  Sum_probs=61.3

Q ss_pred             EEEEeCCcch--hhhccc---ccccceEEEEEeCCCCCCCCcC-CC---CCCCceeEEEEecCCCCCchhHhHHHHHHHH
Q 030407           76 LLLCESGGDN--LAANFS---RELADYIIYIIDVSGGDKIPRK-GG---PGITQADLLVINKTDLASAIGADLAVMERDA  146 (178)
Q Consensus        76 ~iiiEttG~~--~~~~~~---~~~ad~~I~VvD~~~~~~~~~~-~~---~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l  146 (178)
                      +-|+.|.|--  +..+..   -...|..+++|-+.++.....+ +.   .-++.+.+++++|+|+.+.  +..+.+.+.+
T Consensus       203 VsfVDtvGHEpwLrTtirGL~gqk~dYglLvVaAddG~~~~tkEHLgi~~a~~lPviVvvTK~D~~~d--dr~~~v~~ei  280 (527)
T COG5258         203 VSFVDTVGHEPWLRTTIRGLLGQKVDYGLLVVAADDGVTKMTKEHLGIALAMELPVIVVVTKIDMVPD--DRFQGVVEEI  280 (527)
T ss_pred             EEEEecCCccHHHHHHHHHHhccccceEEEEEEccCCcchhhhHhhhhhhhhcCCEEEEEEecccCcH--HHHHHHHHHH
Confidence            5577888810  111111   0124778888888777544321 11   2367889999999999987  5544433333


Q ss_pred             Hh----cC--C---------------------CCCEEEEecccCCCHHHHHHHHhh
Q 030407          147 LR----MR--D---------------------GGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       147 ~~----~n--p---------------------~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+    .+  |                     -+|||.||+-||+|++-|.+++..
T Consensus       281 ~~~Lk~v~Rip~~vk~~~d~v~aa~a~k~~~~vvPi~~tSsVTg~GldlL~e~f~~  336 (527)
T COG5258         281 SALLKRVGRIPLIVKDTDDVVLAAKAMKAGRGVVPIFYTSSVTGEGLDLLDEFFLL  336 (527)
T ss_pred             HHHHHHhcccceeeeccchhHHhhhhhhcCCceEEEEEEecccCccHHHHHHHHHh
Confidence            22    11  1                     249999999999999988877653

>PRK13351 elongation factor G; Reviewed

Probab=96.90  E-value=0.0027  Score=58.22  Aligned_cols=61  Identities=18%  Similarity=0.204  Sum_probs=39.0

Q ss_pred             CCCEEEEeCCcch-hh---hcccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-LA---ANFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~---~~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      +..+.|+.|.|.. ..   ..+ ...+|++++|+|++.+......    .......+-++++||+|+...
T Consensus        72 ~~~i~liDtPG~~df~~~~~~~-l~~aD~~ilVvd~~~~~~~~~~~~~~~~~~~~~p~iiviNK~D~~~~  140 (687)
T PRK13351         72 NHRINLIDTPGHIDFTGEVERS-LRVLDGAVVVFDAVTGVQPQTETVWRQADRYGIPRLIFINKMDRVGA  140 (687)
T ss_pred             CEEEEEEECCCcHHHHHHHHHH-HHhCCEEEEEEeCCCCCCHHHHHHHHHHHhcCCCEEEEEECCCCCCC
Confidence            5678999999931 11   111 1246999999999876543211    111123467999999999754

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

Probab=96.83  E-value=0.0041  Score=46.01  Aligned_cols=96  Identities=17%  Similarity=0.141  Sum_probs=57.5

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--------CCCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--------KGGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--------~~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      +...-+.+|.|-.    +...+.+ .+.+.+.|.|.++......        +.......+-+++.||.||-+......+
T Consensus        59 kiklqiwdtagqerfravtrsyyr-gaagalmvyditrrstynhlsswl~dar~ltnpnt~i~lignkadle~qrdv~ye  137 (215)
T KOG0097|consen   59 KIKLQIWDTAGQERFRAVTRSYYR-GAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLESQRDVTYE  137 (215)
T ss_pred             EEEEEEeecccHHHHHHHHHHHhc-cccceeEEEEehhhhhhhhHHHHHhhhhccCCCceEEEEecchhhhhhcccCcHH
Confidence            4555566666621    1123333 5778899999876432210        0011123456888999999765323334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHH
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLS  171 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~  171 (178)
                      +..++.++ | +.-+++.|||+|+++++-|-
T Consensus       138 eak~faee-n-gl~fle~saktg~nvedafl  166 (215)
T KOG0097|consen  138 EAKEFAEE-N-GLMFLEASAKTGQNVEDAFL  166 (215)
T ss_pred             HHHHHHhh-c-CeEEEEecccccCcHHHHHH
Confidence            44544443 2 45789999999999988663

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

Probab=96.83  E-value=0.00074  Score=54.69  Aligned_cols=97  Identities=13%  Similarity=0.109  Sum_probs=55.4

Q ss_pred             CCCEEEEeCCcch-hh-hcc-cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           73 KADLLLCESGGDN-LA-ANF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      +.++.+|.|.|.. .. ... ....+|.+++|+|++.+......    .......+-++++||+|+...   ..+...+.
T Consensus        63 ~~~i~liDtPG~~~f~~~~~~~l~~aD~~i~Vvd~~~g~~~~~~~~~~~~~~~~~p~iivvNK~D~~~~---~~~~~~~~  139 (268)
T cd04170          63 GHKINLIDTPGYADFVGETRAALRAADAALVVVSAQSGVEVGTEKLWEFADEAGIPRIIFINKMDRERA---DFDKTLAA  139 (268)
T ss_pred             CEEEEEEECcCHHHHHHHHHHHHHHCCEEEEEEeCCCCCCHHHHHHHHHHHHcCCCEEEEEECCccCCC---CHHHHHHH
Confidence            5788999999931 11 111 11246999999999876543211    112234567999999999865   23334444


Q ss_pred             HHhcCCCCCEEEE--ecccCCCHHHHHHHH
Q 030407          146 ALRMRDGGPFIFA--QVGWVIGIIFTLSIT  173 (178)
Q Consensus       146 l~~~np~a~i~~~--SA~~g~gi~el~~~l  173 (178)
                      +++... .+++++  +.++|.++..+.+.+
T Consensus       140 l~~~~~-~~~~~~~ip~~~~~~~~~~vd~~  168 (268)
T cd04170         140 LQEAFG-RPVVPLQLPIGEGDDFKGVVDLL  168 (268)
T ss_pred             HHHHhC-CCeEEEEecccCCCceeEEEEcc
Confidence            554322 234433  456666655444433

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

>COG1084 Predicted GTPase [General function prediction only]

Probab=96.83  E-value=0.0031  Score=52.55  Aligned_cols=99  Identities=19%  Similarity=0.125  Sum_probs=64.6

Q ss_pred             CCEEEEeCCcchhhhc-------------ccccccceEEEEEeCCCCCCCCc----C----CCCCCCceeEEEEecCCCC
Q 030407           74 ADLLLCESGGDNLAAN-------------FSRELADYIIYIIDVSGGDKIPR----K----GGPGITQADLLVINKTDLA  132 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~-------------~~~~~ad~~I~VvD~~~~~~~~~----~----~~~qi~~adiiviNK~Dl~  132 (178)
                      +-|=+|.|.|+ +-.|             ....+.+.+++++|++..-.+..    .    ..+.+..+-++|+||+|+.
T Consensus       215 ~R~QvIDTPGl-LDRPl~ErN~IE~qAi~AL~hl~~~IlF~~D~Se~cgy~lE~Q~~L~~eIk~~f~~p~v~V~nK~D~~  293 (346)
T COG1084         215 LRIQVIDTPGL-LDRPLEERNEIERQAILALRHLAGVILFLFDPSETCGYSLEEQISLLEEIKELFKAPIVVVINKIDIA  293 (346)
T ss_pred             ceEEEecCCcc-cCCChHHhcHHHHHHHHHHHHhcCeEEEEEcCccccCCCHHHHHHHHHHHHHhcCCCeEEEEeccccc
Confidence            35678999994 2111             11234688999999976322211    0    1122455679999999999


Q ss_pred             CchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          133 SAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       133 ~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.  +.++++...+.... .-.....++..+.|++.+.+.+.+.
T Consensus       294 ~~--e~~~~~~~~~~~~~-~~~~~~~~~~~~~~~d~~~~~v~~~  334 (346)
T COG1084         294 DE--EKLEEIEASVLEEG-GEEPLKISATKGCGLDKLREEVRKT  334 (346)
T ss_pred             ch--hHHHHHHHHHHhhc-cccccceeeeehhhHHHHHHHHHHH
Confidence            88  77777776665432 2235677888899999888766554

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

Probab=96.80  E-value=0.0033  Score=48.91  Aligned_cols=101  Identities=13%  Similarity=0.028  Sum_probs=62.9

Q ss_pred             CCCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCCc--CCCCC-------CCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIPR--KGGPG-------ITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~q-------i~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ....-|+.|.|.    .+...+. ...++.++|++.++......  .+..+       -..+-++|.||+|+........
T Consensus        50 ~~~l~ilDt~g~~~~~~~~~~~~-~~~~gF~lVysitd~~SF~~~~~l~~~I~r~~~~~~~PivlVGNK~Dl~~~R~V~~  128 (196)
T KOG0395|consen   50 VCMLEILDTAGQEEFSAMRDLYI-RNGDGFLLVYSITDRSSFEEAKQLREQILRVKGRDDVPIILVGNKCDLERERQVSE  128 (196)
T ss_pred             EEEEEEEcCCCcccChHHHHHhh-ccCcEEEEEEECCCHHHHHHHHHHHHHHHHhhCcCCCCEEEEEEcccchhccccCH
Confidence            355568889881    1111122 23589999999987543211  00011       1257799999999986311233


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+.+  ..+++++||+...+++++|..|.+.
T Consensus       129 eeg~~la~~~--~~~f~E~Sak~~~~v~~~F~~L~r~  163 (196)
T KOG0395|consen  129 EEGKALARSW--GCAFIETSAKLNYNVDEVFYELVRE  163 (196)
T ss_pred             HHHHHHHHhc--CCcEEEeeccCCcCHHHHHHHHHHH
Confidence            3334444443  3469999999999999999987664

>COG5256 TEF1 Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]

Probab=96.78  E-value=0.006  Score=52.29  Aligned_cols=94  Identities=16%  Similarity=0.138  Sum_probs=56.1

Q ss_pred             CCCEEEEeCCcchhhh----cc-cccccceEEEEEeCCCCCCCC-cCCCCC----------CC-ceeEEEEecCCCCCch
Q 030407           73 KADLLLCESGGDNLAA----NF-SRELADYIIYIIDVSGGDKIP-RKGGPG----------IT-QADLLVINKTDLASAI  135 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~----~~-~~~~ad~~I~VvD~~~~~~~~-~~~~~q----------i~-~adiiviNK~Dl~~~~  135 (178)
                      .+-+=++.+.|  ...    +. ...-+|..|+|+|+..+.... .....|          +. .--||++||.|+++..
T Consensus        84 k~~~tIiDaPG--HrdFvknmItGasqAD~aVLVV~a~~~efE~g~~~~gQtrEH~~La~tlGi~~lIVavNKMD~v~wd  161 (428)
T COG5256          84 KYNFTIIDAPG--HRDFVKNMITGASQADVAVLVVDARDGEFEAGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWD  161 (428)
T ss_pred             CceEEEeeCCc--hHHHHHHhhcchhhccEEEEEEECCCCccccccccCCchhHHHHHHHhcCCceEEEEEEcccccccC
Confidence            45677888888  221    11 112369999999998763110 011112          11 1248899999999753


Q ss_pred             hHhHHHHHHHHHh------cCC-CCCEEEEecccCCCHHH
Q 030407          136 GADLAVMERDALR------MRD-GGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       136 ~~~~~~~~~~l~~------~np-~a~i~~~SA~~g~gi~e  168 (178)
                      .+..+++.+.+..      .+| ..+++++||.+|+++.+
T Consensus       162 e~rf~ei~~~v~~l~k~~G~~~~~v~FIPiSg~~G~Nl~~  201 (428)
T COG5256         162 EERFEEIVSEVSKLLKMVGYNPKDVPFIPISGFKGDNLTK  201 (428)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCccCCeEEecccccCCcccc
Confidence            2333444433332      234 36899999999999865

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

Probab=96.76  E-value=0.0045  Score=47.42  Aligned_cols=102  Identities=17%  Similarity=0.152  Sum_probs=63.4

Q ss_pred             CCCEEEEeCCcch-hh---hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN-LA---ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~---~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +...-+.+-.|-. +.   .+|. ...+++|+|||.++.+....         ..+..-..+-++..||-|+..+  -..
T Consensus        60 n~~f~vWDvGGq~k~R~lW~~Y~-~~t~~lIfVvDS~Dr~Ri~eak~eL~~~l~~~~l~~~~llv~aNKqD~~~a--ls~  136 (181)
T KOG0070|consen   60 NISFTVWDVGGQEKLRPLWKHYF-QNTQGLIFVVDSSDRERIEEAKEELHRMLAEPELRNAPLLVFANKQDLPGA--LSA  136 (181)
T ss_pred             ceEEEEEecCCCcccccchhhhc-cCCcEEEEEEeCCcHHHHHHHHHHHHHHHcCcccCCceEEEEechhhcccc--CCH
Confidence            4566677777721 11   2222 24689999999987643321         1111112356888999999866  333


Q ss_pred             HHHHHHHH--hcC-CCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDAL--RMR-DGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l~--~~n-p~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .++.+.+.  ++. ..-.+-.++|.+|+|+.|-++++...+
T Consensus       137 ~ei~~~L~l~~l~~~~w~iq~~~a~~G~GL~egl~wl~~~~  177 (181)
T KOG0070|consen  137 AEITNKLGLHSLRSRNWHIQSTCAISGEGLYEGLDWLSNNL  177 (181)
T ss_pred             HHHHhHhhhhccCCCCcEEeeccccccccHHHHHHHHHHHH
Confidence            33333332  232 234778899999999999999987654

>PRK00741 prfC peptide chain release factor 3; Provisional

Probab=96.73  E-value=0.0056  Score=54.53  Aligned_cols=62  Identities=16%  Similarity=0.183  Sum_probs=38.7

Q ss_pred             CCCEEEEeCCcch-hhh-cc-cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-LAA-NF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~-~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      +..+-++.|.|.. ... +. ....+|++|+|+|++.+......    .......+-++++||+|+...
T Consensus        78 ~~~inliDTPG~~df~~~~~~~l~~aD~aIlVvDa~~gv~~~t~~l~~~~~~~~iPiiv~iNK~D~~~a  146 (526)
T PRK00741         78 DCLINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKGVEPQTRKLMEVCRLRDTPIFTFINKLDRDGR  146 (526)
T ss_pred             CEEEEEEECCCchhhHHHHHHHHHHCCEEEEEEecCCCCCHHHHHHHHHHHhcCCCEEEEEECCccccc
Confidence            5678899999931 111 11 11246999999999876432210    111234567999999998753

>PTZ00132 GTP-binding nuclear protein Ran; Provisional

Probab=96.73  E-value=0.0036  Score=48.72  Aligned_cols=97  Identities=11%  Similarity=-0.027  Sum_probs=58.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+-+++|.|..    +...+. ..++.+++++|.++......         ...+  ..+-++++||+|+.+.  ...
T Consensus        57 ~i~i~~~Dt~g~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~--~~~i~lv~nK~Dl~~~--~~~  131 (215)
T PTZ00132         57 PICFNVWDTAGQEKFGGLRDGYY-IKGQCAIIMFDVTSRITYKNVPNWHRDIVRVCE--NIPIVLVGNKVDVKDR--QVK  131 (215)
T ss_pred             EEEEEEEECCCchhhhhhhHHHh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhCC--CCCEEEEEECccCccc--cCC
Confidence            4566778888831    111122 24688999999976432210         0111  1245788999998654  221


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ....+..+..  ..+++++||++|.|+++.|.+|.+.
T Consensus       132 ~~~~~~~~~~--~~~~~e~Sa~~~~~v~~~f~~ia~~  166 (215)
T PTZ00132        132 ARQITFHRKK--NLQYYDISAKSNYNFEKPFLWLARR  166 (215)
T ss_pred             HHHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            2222333332  3589999999999999999877653

>COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]

Probab=96.67  E-value=0.0068  Score=50.12  Aligned_cols=73  Identities=15%  Similarity=0.111  Sum_probs=48.5

Q ss_pred             ceEEEEEeCCCCCCCCcC----CCCCCCc-eeEEEEecCCCCCchhHhHHHHHHHHHhc-----CC--CCCEEEEeccc-
Q 030407           96 DYIIYIIDVSGGDKIPRK----GGPGITQ-ADLLVINKTDLASAIGADLAVMERDALRM-----RD--GGPFIFAQVGW-  162 (178)
Q Consensus        96 d~~I~VvD~~~~~~~~~~----~~~qi~~-adiiviNK~Dl~~~~~~~~~~~~~~l~~~-----np--~a~i~~~SA~~-  162 (178)
                      |..|+|+.+.++...+.+    ..+|+.. .-++++||+|+++.. +-++.++..++++     +|  ..||+.-||+. 
T Consensus       100 DgAILVVsA~dGpmPqTrEHiLlarqvGvp~ivvflnK~Dmvdd~-ellelVemEvreLLs~y~f~gd~~Pii~gSal~a  178 (394)
T COG0050         100 DGAILVVAATDGPMPQTREHILLARQVGVPYIVVFLNKVDMVDDE-ELLELVEMEVRELLSEYGFPGDDTPIIRGSALKA  178 (394)
T ss_pred             CccEEEEEcCCCCCCcchhhhhhhhhcCCcEEEEEEecccccCcH-HHHHHHHHHHHHHHHHcCCCCCCcceeechhhhh
Confidence            889999999998765432    3456665 357789999999851 4445455455544     34  46999999865 


Q ss_pred             CCCHHHH
Q 030407          163 VIGIIFT  169 (178)
Q Consensus       163 g~gi~el  169 (178)
                      .+|-+.|
T Consensus       179 le~~~~~  185 (394)
T COG0050         179 LEGDAKW  185 (394)
T ss_pred             hcCCcch
Confidence            4444333

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=96.64  E-value=0.007  Score=45.31  Aligned_cols=74  Identities=22%  Similarity=0.222  Sum_probs=46.7

Q ss_pred             HHHHHHhhcC-CcEEEEEecCC-Cch-----hHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhHhhC-
Q 030407            2 LALCKFLRDK-YSLAAVTNDIF-TKE-----DGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNLF-   72 (178)
Q Consensus         2 ~~~~~~~~~~-~~vaVI~nd~g-~~i-----D~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~-   72 (178)
                      .+++++++++ +|+|+|.++.+ ..+     |..++...|.    ....+.++| ||... +......+   .++.... 
T Consensus        17 ~~l~~~l~~~G~~V~viK~~~~~~~~d~~~~D~~~~~~aga----~~v~~~~~~~~~~~~-~~~~~~~l---~~ll~~~~   88 (155)
T TIGR00176        17 ERLVKALKARGYRVATIKHDHHDFDIDKNGKDSYRHREAGA----DQVIVASSRRYAFMH-ETQEERDL---EALLDRLP   88 (155)
T ss_pred             HHHHHHHHhcCCeEEEEecccccccCCCccccHHHHHhCCC----CEEEEecCCeEEEEE-ecCCCcCH---HHHHhhCC
Confidence            5677777664 89999999877 544     4556665565    456777888 77431 11001233   3333222 


Q ss_pred             CCCEEEEeCCc
Q 030407           73 KADLLLCESGG   83 (178)
Q Consensus        73 ~~d~iiiEttG   83 (178)
                      .+|+||||.-+
T Consensus        89 ~~D~vlVEG~k   99 (155)
T TIGR00176        89 DLDIILVEGFK   99 (155)
T ss_pred             CCCEEEECCCC
Confidence            48999999988

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>COG1161 Predicted GTPases [General function prediction only]

Probab=96.58  E-value=0.0062  Score=50.95  Aligned_cols=73  Identities=19%  Similarity=0.097  Sum_probs=48.4

Q ss_pred             cceEEEEEeCCCCCCCCcCC-CCC-CCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHH
Q 030407           95 ADYIIYIIDVSGGDKIPRKG-GPG-ITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~~~-~~q-i~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~  170 (178)
                      .|.++-|+|+..+....... .+. -..+.++|+||+||++.  ...++..+...+.+ ....+.+|++.+.+...+.
T Consensus        35 ~d~vvevvDar~P~~s~~~~l~~~v~~k~~i~vlNK~DL~~~--~~~~~W~~~~~~~~-~~~~~~v~~~~~~~~~~i~  109 (322)
T COG1161          35 VDVVVEVVDARDPLGTRNPELERIVKEKPKLLVLNKADLAPK--EVTKKWKKYFKKEE-GIKPIFVSAKSRQGGKKIR  109 (322)
T ss_pred             CCEEEEEEeccccccccCccHHHHHccCCcEEEEehhhcCCH--HHHHHHHHHHHhcC-CCccEEEEeecccCccchH
Confidence            59999999998776543211 111 12344999999999988  66555555555443 3456777888777766666

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

Probab=96.57  E-value=0.0046  Score=48.10  Aligned_cols=61  Identities=18%  Similarity=0.195  Sum_probs=37.3

Q ss_pred             CCCEEEEeCCcch-hhh---ccccccc-ceEEEEEeCCCCC-CCCc--CC------CCC---CCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-LAA---NFSRELA-DYIIYIIDVSGGD-KIPR--KG------GPG---ITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~---~~~~~~a-d~~I~VvD~~~~~-~~~~--~~------~~q---i~~adiiviNK~Dl~~~  134 (178)
                      +..+-++++.|.. +..   .+.. .+ +++|+|+|+.... ....  .+      ..+   -..+-+++.||.|+..+
T Consensus        47 ~~~~~l~D~pG~~~~~~~~~~~~~-~~~~~vV~VvD~~~~~~~~~~~~~~l~~il~~~~~~~~~~pvliv~NK~Dl~~a  124 (203)
T cd04105          47 GKKFRLVDVPGHPKLRDKLLETLK-NSAKGIVFVVDSATFQKNLKDVAEFLYDILTDLEKVKNKIPVLIACNKQDLFTA  124 (203)
T ss_pred             CceEEEEECCCCHHHHHHHHHHHh-ccCCEEEEEEECccchhHHHHHHHHHHHHHHHHhhccCCCCEEEEecchhhccc
Confidence            5678899999932 111   1122 34 8999999998762 1111  00      001   14567999999999754

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

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

Probab=96.57  E-value=0.014  Score=43.60  Aligned_cols=81  Identities=19%  Similarity=0.087  Sum_probs=55.0

Q ss_pred             ccceEEEEEeCCCCCCCCc--------CCCC-CCCceeEEEEecCCCCCchhHhHHHHHHHHH--hcC-CCCCEEEEecc
Q 030407           94 LADYIIYIIDVSGGDKIPR--------KGGP-GITQADLLVINKTDLASAIGADLAVMERDAL--RMR-DGGPFIFAQVG  161 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~--------~~~~-qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~--~~n-p~a~i~~~SA~  161 (178)
                      ..+.++++||+.+++....        ...+ ....+-+++.||.|+.++  -....+..++.  .+. ...-.|.+|++
T Consensus        88 ~v~aivY~VDaad~~k~~~sr~EL~~LL~k~~l~gip~LVLGnK~d~~~A--L~~~~li~rmgL~sitdREvcC~siSck  165 (186)
T KOG0075|consen   88 GVSAIVYVVDAADPDKLEASRSELHDLLDKPSLTGIPLLVLGNKIDLPGA--LSKIALIERMGLSSITDREVCCFSISCK  165 (186)
T ss_pred             cCcEEEEEeecCCcccchhhHHHHHHHhcchhhcCCcEEEecccccCccc--ccHHHHHHHhCccccccceEEEEEEEEc
Confidence            4688999999988654321        1122 345678999999999877  33334433332  111 12456899999


Q ss_pred             cCCCHHHHHHHHhhh
Q 030407          162 WVIGIIFTLSITHYI  176 (178)
Q Consensus       162 ~g~gi~el~~~l~~~  176 (178)
                      +..+|+.+.++|-+.
T Consensus       166 e~~Nid~~~~Wli~h  180 (186)
T KOG0075|consen  166 EKVNIDITLDWLIEH  180 (186)
T ss_pred             CCccHHHHHHHHHHH
Confidence            999999999998654

>PRK00007 elongation factor G; Reviewed

Probab=96.56  E-value=0.0032  Score=57.81  Aligned_cols=88  Identities=10%  Similarity=-0.002  Sum_probs=53.5

Q ss_pred             CCCEEEEeCCcch--hhhccc-ccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           73 KADLLLCESGGDN--LAANFS-RELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~~-~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      +..+.||.|.|..  ...... ...+|++++|+|+..+...+..    +......+-++++||+|+.++  . ...+.+.
T Consensus        74 ~~~~~liDTPG~~~f~~ev~~al~~~D~~vlVvda~~g~~~qt~~~~~~~~~~~~p~iv~vNK~D~~~~--~-~~~~~~~  150 (693)
T PRK00007         74 DHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVGGVEPQSETVWRQADKYKVPRIAFVNKMDRTGA--D-FYRVVEQ  150 (693)
T ss_pred             CeEEEEEeCCCcHHHHHHHHHHHHHcCEEEEEEECCCCcchhhHHHHHHHHHcCCCEEEEEECCCCCCC--C-HHHHHHH
Confidence            5789999999931  011111 1236999999999887543321    111233466999999999876  2 3334444


Q ss_pred             HHhcC---CCCCEEEEecccC
Q 030407          146 ALRMR---DGGPFIFAQVGWV  163 (178)
Q Consensus       146 l~~~n---p~a~i~~~SA~~g  163 (178)
                      +++..   +.+.++++||.+|
T Consensus       151 i~~~l~~~~~~~~ipisa~~~  171 (693)
T PRK00007        151 IKDRLGANPVPIQLPIGAEDD  171 (693)
T ss_pred             HHHHhCCCeeeEEecCccCCc
Confidence            44332   3356778888776

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

Probab=96.54  E-value=0.015  Score=44.09  Aligned_cols=111  Identities=17%  Similarity=0.176  Sum_probs=69.4

Q ss_pred             HhHHHhhHhhCCCCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCCc---C-----CCCC--CCceeEEEEe
Q 030407           62 LGPLEELSNLFKADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIPR---K-----GGPG--ITQADLLVIN  127 (178)
Q Consensus        62 l~~l~~l~~~~~~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~~---~-----~~~q--i~~adiiviN  127 (178)
                      +..+.++...+....=+..|.|-    ++...|++ ..=+++.|+|.++......   .     ..-|  -+.-=.+|..
T Consensus        46 farlie~~pg~riklqlwdtagqerfrsitksyyr-nsvgvllvyditnr~sfehv~~w~~ea~m~~q~P~k~VFlLVGh  124 (213)
T KOG0091|consen   46 FARLIELRPGYRIKLQLWDTAGQERFRSITKSYYR-NSVGVLLVYDITNRESFEHVENWVKEAAMATQGPDKVVFLLVGH  124 (213)
T ss_pred             HHHHHhcCCCcEEEEEEeeccchHHHHHHHHHHhh-cccceEEEEeccchhhHHHHHHHHHHHHHhcCCCCeeEEEEecc
Confidence            35555665445678889999993    23344444 3456889999987643211   0     0011  1112378899


Q ss_pred             cCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          128 KTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       128 K~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      |+||.+..-...++.++..+.  -+..+++|||++|.+++|-|..|.+
T Consensus       125 KsDL~SqRqVt~EEaEklAa~--hgM~FVETSak~g~NVeEAF~mlaq  170 (213)
T KOG0091|consen  125 KSDLQSQRQVTAEEAEKLAAS--HGMAFVETSAKNGCNVEEAFDMLAQ  170 (213)
T ss_pred             ccchhhhccccHHHHHHHHHh--cCceEEEecccCCCcHHHHHHHHHH
Confidence            999987621223344444432  3568999999999999999886643

>cd01899 Ygr210 Ygr210 subfamily

Probab=96.51  E-value=0.0054  Score=51.27  Aligned_cols=51  Identities=8%  Similarity=-0.057  Sum_probs=37.5

Q ss_pred             ceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHH-HHhh
Q 030407          120 QADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLS-ITHY  175 (178)
Q Consensus       120 ~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~-~l~~  175 (178)
                      .+-++++||+|+.+.  .+..   +.++...+..+++++||+.+.|+++|.+ .+.+
T Consensus       215 KPvI~VlNK~Dl~~~--~~~~---~~l~~~~~~~~iI~iSA~~e~~L~~L~~~~i~~  266 (318)
T cd01899         215 KPMVIAANKADIPDA--ENNI---SKLRLKYPDEIVVPTSAEAELALRRAAKQGLIK  266 (318)
T ss_pred             CcEEEEEEHHHccCh--HHHH---HHHHhhCCCCeEEEEeCcccccHHHHHHhhHHH
Confidence            467999999998755  3322   2333344567899999999999999997 4544

Ygr210 is a member of Obg-like family and present in archaea and fungi. They are characterized by a distinct glycine-rich motif immediately following the Walker B motif. The Ygr210 and YyaF/YchF subfamilies appear to form one major branch of the Obg-like family. Among eukaryotes, the Ygr210 subfamily is represented only in fungi. These fungal proteins form a tight cluster with their archaeal orthologs, which suggests the possibility of horizontal transfer from archaea to fungi.

>KOG0460 consensus Mitochondrial translation elongation factor Tu [Translation, ribosomal structure and biogenesis]

Probab=96.49  E-value=0.0095  Score=50.15  Aligned_cols=79  Identities=22%  Similarity=0.224  Sum_probs=52.1

Q ss_pred             ceEEEEEeCCCCCCCCcC----CCCCCCcee-EEEEecCCCCCchhHhHHHHHHHHHhcC-------CCCCEEEEeccc-
Q 030407           96 DYIIYIIDVSGGDKIPRK----GGPGITQAD-LLVINKTDLASAIGADLAVMERDALRMR-------DGGPFIFAQVGW-  162 (178)
Q Consensus        96 d~~I~VvD~~~~~~~~~~----~~~qi~~ad-iiviNK~Dl~~~~~~~~~~~~~~l~~~n-------p~a~i~~~SA~~-  162 (178)
                      |+.|+||.+++|...+.+    ..+|+...+ ++.+||.|++++. +.++-++-.+|++-       ...||+.-||+- 
T Consensus       142 DGaILVVaatDG~MPQTrEHlLLArQVGV~~ivvfiNKvD~V~d~-e~leLVEmE~RElLse~gf~Gd~~PvI~GSAL~A  220 (449)
T KOG0460|consen  142 DGAILVVAATDGPMPQTREHLLLARQVGVKHIVVFINKVDLVDDP-EMLELVEMEIRELLSEFGFDGDNTPVIRGSALCA  220 (449)
T ss_pred             CceEEEEEcCCCCCcchHHHHHHHHHcCCceEEEEEecccccCCH-HHHHHHHHHHHHHHHHcCCCCCCCCeeecchhhh
Confidence            789999999998765532    345665554 5669999999441 56666665566541       246999988853 


Q ss_pred             --C----CC---HHHHHHHHhh
Q 030407          163 --V----IG---IIFTLSITHY  175 (178)
Q Consensus       163 --g----~g---i~el~~~l~~  175 (178)
                        |    .|   |.+|++.++.
T Consensus       221 Leg~~peig~~aI~kLldavDs  242 (449)
T KOG0460|consen  221 LEGRQPEIGLEAIEKLLDAVDS  242 (449)
T ss_pred             hcCCCccccHHHHHHHHHHHhc
Confidence              3    23   5666665554

>TIGR00484 EF-G translation elongation factor EF-G

Probab=96.48  E-value=0.0056  Score=56.19  Aligned_cols=88  Identities=11%  Similarity=0.028  Sum_probs=52.7

Q ss_pred             CCCEEEEeCCcchh--hhc-ccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           73 KADLLLCESGGDNL--AAN-FSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        73 ~~d~iiiEttG~~~--~~~-~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      +..+.|+.|.|..-  ... .....+|.+++|+|+..+...+..    .......+-++++||+|+..+  . .....+.
T Consensus        74 ~~~i~liDTPG~~~~~~~~~~~l~~~D~~ilVvda~~g~~~~~~~~~~~~~~~~~p~ivviNK~D~~~~--~-~~~~~~~  150 (689)
T TIGR00484        74 GHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSETVWRQANRYEVPRIAFVNKMDKTGA--N-FLRVVNQ  150 (689)
T ss_pred             CeEEEEEECCCCcchhHHHHHHHHHhCEEEEEEeCCCCCChhHHHHHHHHHHcCCCEEEEEECCCCCCC--C-HHHHHHH
Confidence            57789999999420  000 011246999999999876543211    111234467999999999865  2 3333444


Q ss_pred             HHhc---CCCCCEEEEecccC
Q 030407          146 ALRM---RDGGPFIFAQVGWV  163 (178)
Q Consensus       146 l~~~---np~a~i~~~SA~~g  163 (178)
                      +++.   ++...++++|+++|
T Consensus       151 i~~~l~~~~~~~~ipis~~~~  171 (689)
T TIGR00484       151 IKQRLGANAVPIQLPIGAEDN  171 (689)
T ss_pred             HHHHhCCCceeEEeccccCCC
Confidence            4333   33345778888766

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.

>cd04104 p47_IIGP_like p47 (47-kDa) family

Probab=96.48  E-value=0.0099  Score=45.86  Aligned_cols=102  Identities=12%  Similarity=-0.023  Sum_probs=57.3

Q ss_pred             CCCEEEEeCCcchh----hhcc----cccccceEEEEEeCCCCCCCCcCCC---CCCCceeEEEEecCCCCCchh-----
Q 030407           73 KADLLLCESGGDNL----AANF----SRELADYIIYIIDVSGGDKIPRKGG---PGITQADLLVINKTDLASAIG-----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~----~~~~ad~~I~VvD~~~~~~~~~~~~---~qi~~adiiviNK~Dl~~~~~-----  136 (178)
                      .+++.+++|.|..-    ...+    .....|.++++.|. ........+.   .......++|+||+|+..+..     
T Consensus        51 ~~~l~l~DtpG~~~~~~~~~~~l~~~~~~~~d~~l~v~~~-~~~~~d~~~~~~l~~~~~~~ilV~nK~D~~~~~~~~~~~  129 (197)
T cd04104          51 FPNVTLWDLPGIGSTAFPPDDYLEEMKFSEYDFFIIISST-RFSSNDVKLAKAIQCMGKKFYFVRTKVDRDLSNEQRSKP  129 (197)
T ss_pred             CCCceEEeCCCCCcccCCHHHHHHHhCccCcCEEEEEeCC-CCCHHHHHHHHHHHHhCCCEEEEEecccchhhhhhcccc
Confidence            35789999999421    0111    11224666666443 2211111111   112345699999999964311     


Q ss_pred             ------HhHHHHHHHHHhcC-----CCCCEEEEecc--cCCCHHHHHHHHhh
Q 030407          137 ------ADLAVMERDALRMR-----DGGPFIFAQVG--WVIGIIFTLSITHY  175 (178)
Q Consensus       137 ------~~~~~~~~~l~~~n-----p~a~i~~~SA~--~g~gi~el~~~l~~  175 (178)
                            .-++.+++.+.+..     +..+||.+|+.  .+.|+..|.+.+..
T Consensus       130 ~~~~~~~~l~~i~~~~~~~~~~~~~~~p~v~~vS~~~~~~~~~~~l~~~~~~  181 (197)
T cd04104         130 RSFNREQVLQEIRDNCLENLQEAGVSEPPVFLVSNFDPSDYDFPKLRETLLK  181 (197)
T ss_pred             ccccHHHHHHHHHHHHHHHHHHcCCCCCCEEEEeCCChhhcChHHHHHHHHH
Confidence                  11334444444322     34699999998  68999999987654

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

>KOG1191 consensus Mitochondrial GTPase [Translation, ribosomal structure and biogenesis]

Probab=96.45  E-value=0.0035  Score=54.78  Aligned_cols=104  Identities=21%  Similarity=0.108  Sum_probs=61.8

Q ss_pred             hCCCCEEEEeCCcchhhh-c-------------ccccccceEEEEEeCCCCCCCCc-C---------------CCCCCCc
Q 030407           71 LFKADLLLCESGGDNLAA-N-------------FSRELADYIIYIIDVSGGDKIPR-K---------------GGPGITQ  120 (178)
Q Consensus        71 ~~~~d~iiiEttG~~~~~-~-------------~~~~~ad~~I~VvD~~~~~~~~~-~---------------~~~qi~~  120 (178)
                      -.++-+.++.|.|.  .. .             -....+|.+++|+|+........ +               ...+.+.
T Consensus       313 ~~G~~v~L~DTAGi--Re~~~~~iE~~gI~rA~k~~~~advi~~vvda~~~~t~sd~~i~~~l~~~~~g~~~~~~~~~~~  390 (531)
T KOG1191|consen  313 VNGVPVRLSDTAGI--REESNDGIEALGIERARKRIERADVILLVVDAEESDTESDLKIARILETEGVGLVVIVNKMEKQ  390 (531)
T ss_pred             cCCeEEEEEecccc--ccccCChhHHHhHHHHHHHHhhcCEEEEEecccccccccchHHHHHHHHhccceEEEecccccc
Confidence            45788999999994  21 0             01123699999999954332111 0               0112345


Q ss_pred             eeEEEEecCCCCCchhHhHHHHHHHHH-hcCCCCCEEE-EecccCCCHHHHHHHHhhh
Q 030407          121 ADLLVINKTDLASAIGADLAVMERDAL-RMRDGGPFIF-AQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       121 adiiviNK~Dl~~~~~~~~~~~~~~l~-~~np~a~i~~-~SA~~g~gi~el~~~l~~~  176 (178)
                      .-+++.||+|+.++-+........+.. ...+.-++.. +|++||+|++.|.+.+.+.
T Consensus       391 ~~i~~~nk~D~~s~~~~~~~~~~~~~~~~~~~~~~i~~~vs~~tkeg~~~L~~all~~  448 (531)
T KOG1191|consen  391 RIILVANKSDLVSKIPEMTKIPVVYPSAEGRSVFPIVVEVSCTTKEGCERLSTALLNI  448 (531)
T ss_pred             ceEEEechhhccCccccccCCceeccccccCcccceEEEeeechhhhHHHHHHHHHHH
Confidence            679999999998761111110011111 1223334544 9999999999999987654

>COG1163 DRG Predicted GTPase [General function prediction only]

Probab=96.44  E-value=0.0063  Score=50.79  Aligned_cols=47  Identities=19%  Similarity=0.112  Sum_probs=37.8

Q ss_pred             ceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          120 QADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       120 ~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+-++|+||+|+++.  ++.+.+.+.     |  +.+++||++|.|+++|.+.+-+
T Consensus       240 ~p~l~v~NKiD~~~~--e~~~~l~~~-----~--~~v~isa~~~~nld~L~e~i~~  286 (365)
T COG1163         240 KPALYVVNKIDLPGL--EELERLARK-----P--NSVPISAKKGINLDELKERIWD  286 (365)
T ss_pred             eeeEEEEecccccCH--HHHHHHHhc-----c--ceEEEecccCCCHHHHHHHHHH
Confidence            457999999999987  666655432     2  7899999999999999987654

>KOG2484 consensus GTPase [General function prediction only]

Probab=96.36  E-value=0.0088  Score=51.07  Aligned_cols=63  Identities=16%  Similarity=0.128  Sum_probs=43.1

Q ss_pred             cceEEEEEeCCCCCCCCc-CCCCCC-----CceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecc
Q 030407           95 ADYIIYIIDVSGGDKIPR-KGGPGI-----TQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVG  161 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~-~~~~qi-----~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~  161 (178)
                      +|+++.|+||.++....- ...+++     ..--|+|+||+||++.  +.++....+++.-.|  .+.+.++.
T Consensus       147 sDVVleVlDARDPlgtR~~~vE~~V~~~~gnKkLILVLNK~DLVPr--Ev~e~Wl~YLr~~~p--tv~fkast  215 (435)
T KOG2484|consen  147 SDVVLEVLDARDPLGTRCPEVEEAVLQAHGNKKLILVLNKIDLVPR--EVVEKWLVYLRREGP--TVAFKAST  215 (435)
T ss_pred             hheEEEeeeccCCCCCCChhHHHHHHhccCCceEEEEeehhccCCH--HHHHHHHHHHHhhCC--cceeeccc
Confidence            599999999988764421 111122     1235999999999999  888888888887666  44444333

>KOG1424 consensus Predicted GTP-binding protein MMR1 [General function prediction only]

Probab=96.22  E-value=0.0072  Score=53.11  Aligned_cols=64  Identities=17%  Similarity=0.157  Sum_probs=45.6

Q ss_pred             cceEEEEEeCCCCCCCCc----CC-CCCC-CceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEeccc
Q 030407           95 ADYIIYIIDVSGGDKIPR----KG-GPGI-TQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGW  162 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~----~~-~~qi-~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~  162 (178)
                      .|.+|-+||+.++.-..-    .| .+.. ..+.++++||+||+++  ++...-.++.+..|  .++++-||.-
T Consensus       175 SDivvqIVDARnPllfr~~dLe~Yvke~d~~K~~~LLvNKaDLl~~--~qr~aWa~YF~~~n--i~~vf~SA~~  244 (562)
T KOG1424|consen  175 SDIVVQIVDARNPLLFRSPDLEDYVKEVDPSKANVLLVNKADLLPP--EQRVAWAEYFRQNN--IPVVFFSALA  244 (562)
T ss_pred             cceEEEEeecCCccccCChhHHHHHhccccccceEEEEehhhcCCH--HHHHHHHHHHHhcC--ceEEEEeccc
Confidence            599999999988643211    11 1222 3578999999999998  77777666666554  7888888865

>KOG0458 consensus Elongation factor 1 alpha [Translation, ribosomal structure and biogenesis]

Probab=96.08  E-value=0.014  Score=52.00  Aligned_cols=74  Identities=20%  Similarity=0.096  Sum_probs=44.7

Q ss_pred             cceEEEEEeCCCCCCC-CcCCCCCC----------C-ceeEEEEecCCCCCchhHhHHHHH----HHHHhc----CCCCC
Q 030407           95 ADYIIYIIDVSGGDKI-PRKGGPGI----------T-QADLLVINKTDLASAIGADLAVME----RDALRM----RDGGP  154 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~-~~~~~~qi----------~-~adiiviNK~Dl~~~~~~~~~~~~----~~l~~~----np~a~  154 (178)
                      +|..|+|+|++.+.-. .....+|.          . ..-+|++||.|+++-.....+.+.    .++++.    -+...
T Consensus       279 aD~avLvvd~s~~~FE~gfd~~gQtrEha~llr~Lgi~qlivaiNKmD~V~Wsq~RF~eIk~~l~~fL~~~~gf~es~v~  358 (603)
T KOG0458|consen  279 ADVAVLVVDASTGEFESGFDPGGQTREHALLLRSLGISQLIVAINKMDLVSWSQDRFEEIKNKLSSFLKESCGFKESSVK  358 (603)
T ss_pred             cceEEEEEECCcchhhhccCCCCchHHHHHHHHHcCcceEEEEeecccccCccHHHHHHHHHHHHHHHHHhcCcccCCcc
Confidence            5899999999875321 11112221          1 235889999999975212333333    333221    13458


Q ss_pred             EEEEecccCCCHHH
Q 030407          155 FIFAQVGWVIGIIF  168 (178)
Q Consensus       155 i~~~SA~~g~gi~e  168 (178)
                      ++++|+.+|+|+-.
T Consensus       359 FIPiSGl~GeNL~k  372 (603)
T KOG0458|consen  359 FIPISGLSGENLIK  372 (603)
T ss_pred             eEecccccCCcccc
Confidence            99999999999753

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.02  E-value=0.014  Score=50.68  Aligned_cols=145  Identities=17%  Similarity=0.118  Sum_probs=75.8

Q ss_pred             HHHHHhhc-CCcEEEEEecCC-C-chhHHHHH--HcCCCCccceeecccCCCcccccccccccC-HhHHHhhHhhCCCCE
Q 030407            3 ALCKFLRD-KYSLAAVTNDIF-T-KEDGEFLM--RNGALPEERIRAVETGGCPHAAIREDISIN-LGPLEELSNLFKADL   76 (178)
Q Consensus         3 ~~~~~~~~-~~~vaVI~nd~g-~-~iD~~li~--~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~-l~~l~~l~~~~~~d~   76 (178)
                      ++..++++ ++||+++.-|.. . .++.....  ..++    ++....++.        |.... .+++..+. ..++|+
T Consensus       119 KLA~~l~~~G~kV~lV~~D~~R~aA~eQLk~~a~~~~v----p~~~~~~~~--------dp~~i~~~~l~~~~-~~~~Dv  185 (429)
T TIGR01425       119 KLAYYYQRKGFKPCLVCADTFRAGAFDQLKQNATKARI----PFYGSYTES--------DPVKIASEGVEKFK-KENFDI  185 (429)
T ss_pred             HHHHHHHHCCCCEEEEcCcccchhHHHHHHHHhhccCC----eEEeecCCC--------CHHHHHHHHHHHHH-hCCCCE
Confidence            56666665 489999999987 3 44443221  1222    333332222        11110 13444433 458999


Q ss_pred             EEEeCCcchhh---------hcccccccceEEEEEeCCCCCCCCc---CCCCCCCceeEEEEecCCCCCchhHhHHHHHH
Q 030407           77 LLCESGGDNLA---------ANFSRELADYIIYIIDVSGGDKIPR---KGGPGITQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        77 iiiEttG~~~~---------~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      |||.|.|-...         ........+.+++|+|++.+.+...   .+.. .-..+-+|+||.|-....+..+.    
T Consensus       186 ViIDTaGr~~~d~~lm~El~~i~~~~~p~e~lLVlda~~Gq~a~~~a~~F~~-~~~~~g~IlTKlD~~argG~aLs----  260 (429)
T TIGR01425       186 IIVDTSGRHKQEDSLFEEMLQVAEAIQPDNIIFVMDGSIGQAAEAQAKAFKD-SVDVGSVIITKLDGHAKGGGALS----  260 (429)
T ss_pred             EEEECCCCCcchHHHHHHHHHHhhhcCCcEEEEEeccccChhHHHHHHHHHh-ccCCcEEEEECccCCCCccHHhh----
Confidence            99999993210         0011112377899999987643211   1111 11247899999998654222222    


Q ss_pred             HHHhcCCCCCEEEEecccCCCHHHH
Q 030407          145 DALRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       145 ~l~~~np~a~i~~~SA~~g~gi~el  169 (178)
                      ....  .+.|+.+++  +|++++++
T Consensus       261 ~~~~--t~~PI~fig--~Ge~v~Dl  281 (429)
T TIGR01425       261 AVAA--TKSPIIFIG--TGEHIDDF  281 (429)
T ss_pred             hHHH--HCCCeEEEc--CCCChhhc
Confidence            2221  134666665  46666655

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

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

Probab=95.97  E-value=0.014  Score=43.16  Aligned_cols=81  Identities=16%  Similarity=0.060  Sum_probs=53.3

Q ss_pred             ccceEEEEEeCCCCCCCCcC--------CCCCCCc-eeEEEEecCCCCCchhHhHHHHHHHHH---hcCCCCCEEEEecc
Q 030407           94 LADYIIYIIDVSGGDKIPRK--------GGPGITQ-ADLLVINKTDLASAIGADLAVMERDAL---RMRDGGPFIFAQVG  161 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~--------~~~qi~~-adiiviNK~Dl~~~~~~~~~~~~~~l~---~~np~a~i~~~SA~  161 (178)
                      ...++|+|+|+...+...+.        ..++++. .-+|..||-|+.++  -..+++...++   -.+..--+.+++|.
T Consensus        84 gtqglIFV~Dsa~~dr~eeAr~ELh~ii~~~em~~~~~LvlANkQDlp~A--~~pqei~d~leLe~~r~~~W~vqp~~a~  161 (180)
T KOG0071|consen   84 GTQGLIFVVDSADRDRIEEARNELHRIINDREMRDAIILILANKQDLPDA--MKPQEIQDKLELERIRDRNWYVQPSCAL  161 (180)
T ss_pred             CCceEEEEEeccchhhHHHHHHHHHHHhCCHhhhcceEEEEecCcccccc--cCHHHHHHHhccccccCCccEeeccccc
Confidence            45789999999776433210        1123433 35777999999877  44445444443   11233467889999


Q ss_pred             cCCCHHHHHHHHhhh
Q 030407          162 WVIGIIFTLSITHYI  176 (178)
Q Consensus       162 ~g~gi~el~~~l~~~  176 (178)
                      +|.|+.|=+.+|...
T Consensus       162 ~gdgL~eglswlsnn  176 (180)
T KOG0071|consen  162 SGDGLKEGLSWLSNN  176 (180)
T ss_pred             cchhHHHHHHHHHhh
Confidence            999999999888754

>KOG0466 consensus Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]

Probab=95.64  E-value=0.019  Score=47.79  Aligned_cols=54  Identities=15%  Similarity=0.075  Sum_probs=41.3

Q ss_pred             eEEEEecCCCCCch--hHhHHHHHHHHHhcC-CCCCEEEEecccCCCHHHHHHHHhh
Q 030407          122 DLLVINKTDLASAI--GADLAVMERDALRMR-DGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       122 diiviNK~Dl~~~~--~~~~~~~~~~l~~~n-p~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      -+|+-||+||+.+.  .++.+++.++++.-+ .++|++++||.-+.+|+-+.+++-+
T Consensus       182 iiilQNKiDli~e~~A~eq~e~I~kFi~~t~ae~aPiiPisAQlkyNId~v~eyivk  238 (466)
T KOG0466|consen  182 IIILQNKIDLIKESQALEQHEQIQKFIQGTVAEGAPIIPISAQLKYNIDVVCEYIVK  238 (466)
T ss_pred             EEEEechhhhhhHHHHHHHHHHHHHHHhccccCCCceeeehhhhccChHHHHHHHHh
Confidence            47889999999762  233455666666544 4679999999999999999998753

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=95.62  E-value=0.0084  Score=47.97  Aligned_cols=79  Identities=22%  Similarity=0.291  Sum_probs=47.1

Q ss_pred             ccCC-CcccccccccccCHhHHHhhHhhCCCCEEEEeCCcchhhhcccc---cccceEEEEEeCCCCCC-CC---cCCCC
Q 030407           45 ETGG-CPHAAIREDISINLGPLEELSNLFKADLLLCESGGDNLAANFSR---ELADYIIYIIDVSGGDK-IP---RKGGP  116 (178)
Q Consensus        45 ~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~~~d~iiiEttG~~~~~~~~~---~~ad~~I~VvD~~~~~~-~~---~~~~~  116 (178)
                      ..|| |+-       ...++.+.+-+.....|+|++.|--  -..+|.+   ...|.+|.|+|++...- ..   .+...
T Consensus       111 GeGC~Cp~-------~allR~~l~~l~~~~~e~VivDtEA--GiEHfgRg~~~~vD~vivVvDpS~~sl~taeri~~L~~  181 (255)
T COG3640         111 GEGCACPM-------NALLRRLLRHLILNRYEVVIVDTEA--GIEHFGRGTIEGVDLVIVVVDPSYKSLRTAERIKELAE  181 (255)
T ss_pred             CCcccchH-------HHHHHHHHHHHhcccCcEEEEeccc--chhhhccccccCCCEEEEEeCCcHHHHHHHHHHHHHHH
Confidence            5688 662       2223444333335679999999854  2345554   34699999999975311 11   11222


Q ss_pred             CCC-ceeEEEEecCCCC
Q 030407          117 GIT-QADLLVINKTDLA  132 (178)
Q Consensus       117 qi~-~adiiviNK~Dl~  132 (178)
                      .+. ..-.+|+||+|-.
T Consensus       182 elg~k~i~~V~NKv~e~  198 (255)
T COG3640         182 ELGIKRIFVVLNKVDEE  198 (255)
T ss_pred             HhCCceEEEEEeeccch
Confidence            344 4468999999954

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=95.46  E-value=0.12  Score=38.81  Aligned_cols=118  Identities=13%  Similarity=0.164  Sum_probs=62.6

Q ss_pred             HHHHHhhc-CCcEEEEEecCC-CchhHHHHH---HcCCCCccceeecccCCCcccccccccccCH-hHHHhhHhhCCCCE
Q 030407            3 ALCKFLRD-KYSLAAVTNDIF-TKEDGEFLM---RNGALPEERIRAVETGGCPHAAIREDISINL-GPLEELSNLFKADL   76 (178)
Q Consensus         3 ~~~~~~~~-~~~vaVI~nd~g-~~iD~~li~---~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l-~~l~~l~~~~~~d~   76 (178)
                      ++...+.+ ++|++++-.|+. .....++..   ..+.    ++.....  -.      |+...+ +.+... ...++|+
T Consensus        19 ~la~~~~~~g~~v~~i~~D~~~~~~~~~l~~~~~~~~~----~~~~~~~--~~------~~~~~~~~~~~~~-~~~~~d~   85 (173)
T cd03115          19 KLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGEQVGV----PVFEEGE--GK------DPVSIAKRAIEHA-REENFDV   85 (173)
T ss_pred             HHHHHHHHCCCcEEEEEcCCCChHHHHHHHHhcccCCe----EEEecCC--CC------CHHHHHHHHHHHH-HhCCCCE
Confidence            45555654 489999999987 444333321   1122    2222211  11      112112 233333 2568999


Q ss_pred             EEEeCCcchh-----hhc---ccc-cccceEEEEEeCCCCCCCCc---CCCCCCCceeEEEEecCCCCCc
Q 030407           77 LLCESGGDNL-----AAN---FSR-ELADYIIYIIDVSGGDKIPR---KGGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        77 iiiEttG~~~-----~~~---~~~-~~ad~~I~VvD~~~~~~~~~---~~~~qi~~adiiviNK~Dl~~~  134 (178)
                      |+|+|.|..-     ...   +.. ...+.+++|+|+....+...   .+..... .+-+|+||.|....
T Consensus        86 viiDt~g~~~~~~~~l~~l~~l~~~~~~~~~~lVv~~~~~~~~~~~~~~~~~~~~-~~~viltk~D~~~~  154 (173)
T cd03115          86 VIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDAMTGQDAVNQAKAFNEALG-ITGVILTKLDGDAR  154 (173)
T ss_pred             EEEECcccchhhHHHHHHHHHHHhhcCCCeEEEEEECCCChHHHHHHHHHHhhCC-CCEEEEECCcCCCC
Confidence            9999999521     111   111 12588999999865432211   1112233 47899999998765

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

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

Probab=95.41  E-value=0.01  Score=45.63  Aligned_cols=96  Identities=14%  Similarity=0.130  Sum_probs=61.0

Q ss_pred             EEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCCc---CCC----CCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           77 LLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIPR---KGG----PGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        77 iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~----~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      .+.||.|.    ++...|++ ++...++|+..++......   .+.    +-=+.+-++|-||+||++..--.-+.++..
T Consensus        72 mlWdtagqeEfDaItkAyyr-gaqa~vLVFSTTDr~SFea~~~w~~kv~~e~~~IPtV~vqNKIDlveds~~~~~evE~l  150 (246)
T KOG4252|consen   72 MLWDTAGQEEFDAITKAYYR-GAQASVLVFSTTDRYSFEATLEWYNKVQKETERIPTVFVQNKIDLVEDSQMDKGEVEGL  150 (246)
T ss_pred             HHHHhccchhHHHHHHHHhc-cccceEEEEecccHHHHHHHHHHHHHHHHHhccCCeEEeeccchhhHhhhcchHHHHHH
Confidence            34456662    22223333 6788999998876543221   111    112456799999999997621222345555


Q ss_pred             HHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          146 ALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       146 l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+.++  .+.+.+|++...++...|.+|.+
T Consensus       151 ak~l~--~RlyRtSvked~NV~~vF~YLae  178 (246)
T KOG4252|consen  151 AKKLH--KRLYRTSVKEDFNVMHVFAYLAE  178 (246)
T ss_pred             HHHhh--hhhhhhhhhhhhhhHHHHHHHHH
Confidence            55554  48899999999999999988753

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

Probab=95.27  E-value=0.095  Score=39.46  Aligned_cols=99  Identities=15%  Similarity=0.103  Sum_probs=65.7

Q ss_pred             CCCEEEEeCCcchhh-----hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDNLA-----ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~~~-----~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .--+.|-.|.|+.--     ..+. ..+|+.++|+++.+....+.         ++...=+.+.+++.||.|+.++....
T Consensus        59 rE~l~lyDTaGlq~~~~eLprhy~-q~aDafVLVYs~~d~eSf~rv~llKk~Idk~KdKKEvpiVVLaN~rdr~~p~~vd  137 (198)
T KOG3883|consen   59 REQLRLYDTAGLQGGQQELPRHYF-QFADAFVLVYSPMDPESFQRVELLKKEIDKHKDKKEVPIVVLANKRDRAEPREVD  137 (198)
T ss_pred             hheEEEeecccccCchhhhhHhHh-ccCceEEEEecCCCHHHHHHHHHHHHHHhhccccccccEEEEechhhcccchhcC
Confidence            345777889994211     1111 24699999999977654321         22233456779999999998763233


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      .+....|.++  ...+.++++|+....+-|.|.++.
T Consensus       138 ~d~A~~Wa~r--Ekvkl~eVta~dR~sL~epf~~l~  171 (198)
T KOG3883|consen  138 MDVAQIWAKR--EKVKLWEVTAMDRPSLYEPFTYLA  171 (198)
T ss_pred             HHHHHHHHhh--hheeEEEEEeccchhhhhHHHHHH
Confidence            4445555553  356899999999999988887764

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.19  E-value=0.24  Score=43.00  Aligned_cols=146  Identities=18%  Similarity=0.177  Sum_probs=82.3

Q ss_pred             HHHHHhhcC-CcEEEEEecCC--CchhHHHH--HHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCCCCEE
Q 030407            3 ALCKFLRDK-YSLAAVTNDIF--TKEDGEFL--MRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLL   77 (178)
Q Consensus         3 ~~~~~~~~~-~~vaVI~nd~g--~~iD~~li--~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~~d~i   77 (178)
                      +|.+||+++ +|++++.-|.-  .-+|....  +..++    ++....++--+-       .-.=.++... +...+|+|
T Consensus       119 KLA~~lkk~~~kvllVaaD~~RpAA~eQL~~La~q~~v----~~f~~~~~~~Pv-------~Iak~al~~a-k~~~~Dvv  186 (451)
T COG0541         119 KLAKYLKKKGKKVLLVAADTYRPAAIEQLKQLAEQVGV----PFFGSGTEKDPV-------EIAKAALEKA-KEEGYDVV  186 (451)
T ss_pred             HHHHHHHHcCCceEEEecccCChHHHHHHHHHHHHcCC----ceecCCCCCCHH-------HHHHHHHHHH-HHcCCCEE
Confidence            577888775 99999999988  47777543  33344    455553222221       0001445444 36689999


Q ss_pred             EEeCCcc-hhhhcc--------cccccceEEEEEeCCCCCCCCc---CCCCCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           78 LCESGGD-NLAANF--------SRELADYIIYIIDVSGGDKIPR---KGGPGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        78 iiEttG~-~~~~~~--------~~~~ad~~I~VvD~~~~~~~~~---~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      ||.|.|= .+-...        .....|-+++|+|+..|.+...   .+.+.+.. .=|+++|.|--..-+..+..    
T Consensus       187 IvDTAGRl~ide~Lm~El~~Ik~~~~P~E~llVvDam~GQdA~~~A~aF~e~l~i-tGvIlTKlDGdaRGGaALS~----  261 (451)
T COG0541         187 IVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAMIGQDAVNTAKAFNEALGI-TGVILTKLDGDARGGAALSA----  261 (451)
T ss_pred             EEeCCCcccccHHHHHHHHHHHhhcCCCeEEEEEecccchHHHHHHHHHhhhcCC-ceEEEEcccCCCcchHHHhh----
Confidence            9999992 111111        0011378999999988754321   12222222 36889999975442222221    


Q ss_pred             HHhcCCCCCEEEEecccCCCHHHH
Q 030407          146 ALRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       146 l~~~np~a~i~~~SA~~g~gi~el  169 (178)
                      .. . .+.||-++.  +||.+++|
T Consensus       262 ~~-~-tg~PIkFiG--tGEki~dL  281 (451)
T COG0541         262 RA-I-TGKPIKFIG--TGEKIDDL  281 (451)
T ss_pred             HH-H-HCCCeEEEe--cCCCcccC
Confidence            11 1 245777765  46666654

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=94.85  E-value=0.11  Score=43.61  Aligned_cols=148  Identities=18%  Similarity=0.217  Sum_probs=83.5

Q ss_pred             HHHHHHhhcC-CcEEEEEecCC--CchhHHHH--HHcCCCCccceeecccCCCcccccccccccC-HhHHHhhHhhCCCC
Q 030407            2 LALCKFLRDK-YSLAAVTNDIF--TKEDGEFL--MRNGALPEERIRAVETGGCPHAAIREDISIN-LGPLEELSNLFKAD   75 (178)
Q Consensus         2 ~~~~~~~~~~-~~vaVI~nd~g--~~iD~~li--~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~-l~~l~~l~~~~~~d   75 (178)
                      -++..+|++. +||-+-.-|=-  ..++..-+  ++.|+    +++.-..|.-+        .+. ..++..- +..++|
T Consensus       157 aKLA~~l~~~g~~VllaA~DTFRAaAiEQL~~w~er~gv----~vI~~~~G~Dp--------AaVafDAi~~A-kar~~D  223 (340)
T COG0552         157 AKLAKYLKQQGKSVLLAAGDTFRAAAIEQLEVWGERLGV----PVISGKEGADP--------AAVAFDAIQAA-KARGID  223 (340)
T ss_pred             HHHHHHHHHCCCeEEEEecchHHHHHHHHHHHHHHHhCC----eEEccCCCCCc--------HHHHHHHHHHH-HHcCCC
Confidence            4677777654 88888887733  24554333  33454    45554334422        222 2666544 367999


Q ss_pred             EEEEeCCcc-----hhh----------hcccccccceEEEEEeCCCCCCCCc---CCCCCCCceeEEEEecCCCCCchhH
Q 030407           76 LLLCESGGD-----NLA----------ANFSRELADYIIYIIDVSGGDKIPR---KGGPGITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        76 ~iiiEttG~-----~~~----------~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~qi~~adiiviNK~Dl~~~~~~  137 (178)
                      +++|.|.|=     ++.          .+..+.-.+-++.++|++.|.+...   .+.+.+. =|=++++|.|-...   
T Consensus       224 vvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~llvlDAttGqnal~QAk~F~eav~-l~GiIlTKlDgtAK---  299 (340)
T COG0552         224 VVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATTGQNALSQAKIFNEAVG-LDGIILTKLDGTAK---  299 (340)
T ss_pred             EEEEeCcccccCchhHHHHHHHHHHHhccccCCCCceEEEEEEcccChhHHHHHHHHHHhcC-CceEEEEecccCCC---
Confidence            999999992     111          1112211255778889998864321   1111111 27899999994322   


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHH
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLS  171 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~  171 (178)
                       -..+.+..+++  +.||.++-  -|+++++|..
T Consensus       300 -GG~il~I~~~l--~~PI~fiG--vGE~~~DL~~  328 (340)
T COG0552         300 -GGIILSIAYEL--GIPIKFIG--VGEGYDDLRP  328 (340)
T ss_pred             -cceeeeHHHHh--CCCEEEEe--CCCChhhccc
Confidence             22233333444  35888876  4888888854

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

Probab=94.81  E-value=0.12  Score=39.91  Aligned_cols=102  Identities=17%  Similarity=0.062  Sum_probs=58.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcC---CC------CCCCceeEEEEecCCCCCchhHh-
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRK---GG------PGITQADLLVINKTDLASAIGAD-  138 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~---~~------~qi~~adiiviNK~Dl~~~~~~~-  138 (178)
                      .++..++.|.|.-    +...+. ..+++++.++|..........   +.      ..-..+-+++.||+|+....... 
T Consensus        53 ~~~~~~~Dt~gq~~~~~~~~~y~-~~~~~~l~~~d~~~~~~~~~~~~~~~~~l~~~~~~~~~iilv~nK~Dl~~~~~~~~  131 (219)
T COG1100          53 NIKLQLWDTAGQEEYRSLRPEYY-RGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFDEQSSSE  131 (219)
T ss_pred             EEEEEeecCCCHHHHHHHHHHHh-cCCCEEEEEEecccchhhhHHHHHHHHHHHHhCCCCceEEEEecccccccchhHHH
Confidence            4567888888831    112222 357899999998763322110   00      00135679999999998762111 


Q ss_pred             -----------HHHHHHHHHhc-CCCCCEEEEecc--cCCCHHHHHHHHhh
Q 030407          139 -----------LAVMERDALRM-RDGGPFIFAQVG--WVIGIIFTLSITHY  175 (178)
Q Consensus       139 -----------~~~~~~~l~~~-np~a~i~~~SA~--~g~gi~el~~~l~~  175 (178)
                                 ........... ......+.+|++  ++.++.+++..+..
T Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~v~~~~~~~~~  182 (219)
T COG1100         132 EILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKELLR  182 (219)
T ss_pred             HHHhhhhcCcchhhhHhHHhhhhhcccceeEeecccCCCcCHHHHHHHHHH
Confidence                       11111111111 112348999999  99999999986554

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.78  E-value=0.2  Score=43.40  Aligned_cols=96  Identities=16%  Similarity=0.138  Sum_probs=53.7

Q ss_pred             hHHHhhHhhCCCCEEEEeCCcchhh---------hcccccccceEEEEEeCCCCCCC-C---cCCCCCCCceeEEEEecC
Q 030407           63 GPLEELSNLFKADLLLCESGGDNLA---------ANFSRELADYIIYIIDVSGGDKI-P---RKGGPGITQADLLVINKT  129 (178)
Q Consensus        63 ~~l~~l~~~~~~d~iiiEttG~~~~---------~~~~~~~ad~~I~VvD~~~~~~~-~---~~~~~qi~~adiiviNK~  129 (178)
                      .++..+.+..++|+|||.|.|-+..         ........+.+++|+|++..... .   ..+..  ..-+-++++|.
T Consensus       310 ~aL~~lk~~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~~~F~~--~~idglI~TKL  387 (436)
T PRK11889        310 RALTYFKEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIITNFKD--IHIDGIVFTKF  387 (436)
T ss_pred             HHHHHHHhccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHHHHhcC--CCCCEEEEEcc
Confidence            4444443234799999999995321         11111123667888998654321 1   11211  23479999999


Q ss_pred             CCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHH
Q 030407          130 DLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       130 Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                      |-....    ..+.......  +.|+.+++  +|+++.+
T Consensus       388 DET~k~----G~iLni~~~~--~lPIsyit--~GQ~VPe  418 (436)
T PRK11889        388 DETASS----GELLKIPAVS--SAPIVLMT--DGQDVKK  418 (436)
T ss_pred             cCCCCc----cHHHHHHHHH--CcCEEEEe--CCCCCCc
Confidence            987552    3344444433  34777766  4666654

>TIGR00503 prfC peptide chain release factor 3

Probab=94.71  E-value=0.028  Score=50.16  Aligned_cols=62  Identities=16%  Similarity=0.173  Sum_probs=38.6

Q ss_pred             CCCEEEEeCCcch-hhh-cc-cccccceEEEEEeCCCCCCCCc-C---CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-LAA-NF-SRELADYIIYIIDVSGGDKIPR-K---GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~-~~-~~~~ad~~I~VvD~~~~~~~~~-~---~~~qi~~adiiviNK~Dl~~~  134 (178)
                      +..+.|+.|.|.. ... .. ....+|++|+|+|+..+..... .   .......+-++++||+|+...
T Consensus        79 ~~~inliDTPG~~df~~~~~~~l~~aD~aIlVvDa~~gv~~~t~~l~~~~~~~~~PiivviNKiD~~~~  147 (527)
T TIGR00503        79 DCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTRLRDTPIFTFMNKLDRDIR  147 (527)
T ss_pred             CeEEEEEECCChhhHHHHHHHHHHhCCEEEEEEECCCCCCHHHHHHHHHHHhcCCCEEEEEECccccCC
Confidence            6788899999931 111 11 1124799999999987643221 0   111123467999999999654

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.

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

Probab=94.67  E-value=0.099  Score=40.78  Aligned_cols=99  Identities=15%  Similarity=0.055  Sum_probs=60.1

Q ss_pred             CCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCC---cCC-CCC----CCceeEEEEecCCCCCch------
Q 030407           74 ADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIP---RKG-GPG----ITQADLLVINKTDLASAI------  135 (178)
Q Consensus        74 ~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~---~~~-~~q----i~~adiiviNK~Dl~~~~------  135 (178)
                      ...=+.+|.|.    .+. ++.+..+|.+++.++..++....   .++ ++.    -..+-++|.+|.||-+..      
T Consensus        53 v~L~LwDTAGqedYDrlR-plsY~~tdvfl~cfsv~~p~S~~nv~~kW~pEi~~~cp~vpiiLVGtk~DLr~d~~~~~~l  131 (198)
T KOG0393|consen   53 VELGLWDTAGQEDYDRLR-PLSYPQTDVFLLCFSVVSPESFENVKSKWIPEIKHHCPNVPIILVGTKADLRDDPSTLEKL  131 (198)
T ss_pred             EEEeeeecCCCccccccc-ccCCCCCCEEEEEEEcCChhhHHHHHhhhhHHHHhhCCCCCEEEEeehHHhhhCHHHHHHH
Confidence            44556677773    122 45555678888888876654432   122 221    134679999999998531      


Q ss_pred             ------hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          136 ------GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       136 ------~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                            +...++..+..+++. ...++++||++.+|+.+.|+..-
T Consensus       132 ~~~~~~~Vt~~~g~~lA~~ig-a~~y~EcSa~tq~~v~~vF~~a~  175 (198)
T KOG0393|consen  132 QRQGLEPVTYEQGLELAKEIG-AVKYLECSALTQKGVKEVFDEAI  175 (198)
T ss_pred             HhccCCcccHHHHHHHHHHhC-cceeeeehhhhhCCcHHHHHHHH
Confidence                  011122223333332 26899999999999999998543

>PRK10867 signal recognition particle protein; Provisional

Probab=94.64  E-value=0.28  Score=42.79  Aligned_cols=147  Identities=15%  Similarity=0.106  Sum_probs=75.5

Q ss_pred             HHHHHhh-c-CCcEEEEEecCC-C-chhHH--HHHHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCCCCE
Q 030407            3 ALCKFLR-D-KYSLAAVTNDIF-T-KEDGE--FLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADL   76 (178)
Q Consensus         3 ~~~~~~~-~-~~~vaVI~nd~g-~-~iD~~--li~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~~d~   76 (178)
                      +++.++. + ++|+++|.-|.- . .++..  +-+..|+    ++.....+..+.        .......+..+..++|+
T Consensus       119 kLA~~l~~~~G~kV~lV~~D~~R~aa~eQL~~~a~~~gv----~v~~~~~~~dp~--------~i~~~a~~~a~~~~~Dv  186 (433)
T PRK10867        119 KLAKYLKKKKKKKVLLVAADVYRPAAIEQLKTLGEQIGV----PVFPSGDGQDPV--------DIAKAALEEAKENGYDV  186 (433)
T ss_pred             HHHHHHHHhcCCcEEEEEccccchHHHHHHHHHHhhcCC----eEEecCCCCCHH--------HHHHHHHHHHHhcCCCE
Confidence            4555564 3 589999999977 4 33332  1233344    444332222221        11122223334567999


Q ss_pred             EEEeCCcch-----hhhc---c-cccccceEEEEEeCCCCCCCCc---CCCCCCCceeEEEEecCCCCCchhHhHHHHHH
Q 030407           77 LLCESGGDN-----LAAN---F-SRELADYIIYIIDVSGGDKIPR---KGGPGITQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        77 iiiEttG~~-----~~~~---~-~~~~ad~~I~VvD~~~~~~~~~---~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      |||+|.|..     +...   + .....+.+++|+|+..+.+...   .+...+. -+-+|+||.|-....    ..+.+
T Consensus       187 VIIDTaGrl~~d~~lm~eL~~i~~~v~p~evllVlda~~gq~av~~a~~F~~~~~-i~giIlTKlD~~~rg----G~als  261 (433)
T PRK10867        187 VIVDTAGRLHIDEELMDELKAIKAAVNPDEILLVVDAMTGQDAVNTAKAFNEALG-LTGVILTKLDGDARG----GAALS  261 (433)
T ss_pred             EEEeCCCCcccCHHHHHHHHHHHHhhCCCeEEEEEecccHHHHHHHHHHHHhhCC-CCEEEEeCccCcccc----cHHHH
Confidence            999999931     1100   0 0011366799999876532211   1111222 257889999965432    12333


Q ss_pred             HHHhcCCCCCEEEEecccCCCHHHHH
Q 030407          145 DALRMRDGGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus       145 ~l~~~np~a~i~~~SA~~g~gi~el~  170 (178)
                      .....  +.|+.+++  +|+++++|.
T Consensus       262 i~~~~--~~PI~fig--~Ge~v~DLe  283 (433)
T PRK10867        262 IRAVT--GKPIKFIG--TGEKLDDLE  283 (433)
T ss_pred             HHHHH--CcCEEEEe--CCCccccCc
Confidence            33332  35777766  367776553

>cd04169 RF3 RF3 subfamily

Probab=94.49  E-value=0.033  Score=45.33  Aligned_cols=63  Identities=16%  Similarity=0.161  Sum_probs=39.3

Q ss_pred             CCCCEEEEeCCcch-hhh-cc-cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           72 FKADLLLCESGGDN-LAA-NF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        72 ~~~d~iiiEttG~~-~~~-~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      .+..+.++.|.|.. ... .. ....+|.+++|+|++.+......    .......+-++++||+|+...
T Consensus        69 ~~~~i~liDTPG~~df~~~~~~~l~~aD~~IlVvda~~g~~~~~~~i~~~~~~~~~P~iivvNK~D~~~a  138 (267)
T cd04169          69 RDCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGIPIITFINKLDREGR  138 (267)
T ss_pred             CCEEEEEEECCCchHHHHHHHHHHHHCCEEEEEEECCCCccHHHHHHHHHHHhcCCCEEEEEECCccCCC
Confidence            36788999999932 111 11 11246999999999876432110    111123467999999998765

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.

>KOG0780 consensus Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.48  E-value=0.14  Score=44.04  Aligned_cols=145  Identities=17%  Similarity=0.179  Sum_probs=76.4

Q ss_pred             HHHHHhhcC-CcEEEEEecCC-C-chhHHHHHH--cCCCCccceeecccCCCccccccccccc-CHhHHHhhHhhCCCCE
Q 030407            3 ALCKFLRDK-YSLAAVTNDIF-T-KEDGEFLMR--NGALPEERIRAVETGGCPHAAIREDISI-NLGPLEELSNLFKADL   76 (178)
Q Consensus         3 ~~~~~~~~~-~~vaVI~nd~g-~-~iD~~li~~--~~~~~~~~~~~l~~GcCc~l~i~~dl~~-~l~~l~~l~~~~~~d~   76 (178)
                      ++.-||+++ +|++.+.-|-- . -+|......  .++    ++.-  ++.      .-|... ..+.+.+. ++.+||+
T Consensus       120 KlA~y~kkkG~K~~LvcaDTFRagAfDQLkqnA~k~~i----P~yg--syt------e~dpv~ia~egv~~f-Kke~fdv  186 (483)
T KOG0780|consen  120 KLAYYYKKKGYKVALVCADTFRAGAFDQLKQNATKARV----PFYG--SYT------EADPVKIASEGVDRF-KKENFDV  186 (483)
T ss_pred             HHHHHHHhcCCceeEEeecccccchHHHHHHHhHhhCC----eeEe--ccc------ccchHHHHHHHHHHH-HhcCCcE
Confidence            566788765 99999999966 3 677654422  222    2221  111      001110 01444444 3668999


Q ss_pred             EEEeCCcchhh--hccc-------ccccceEEEEEeCCCCCCCCc---CCCCCCCceeEEEEecCCCCCchhHhHHHHHH
Q 030407           77 LLCESGGDNLA--ANFS-------RELADYIIYIIDVSGGDKIPR---KGGPGITQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        77 iiiEttG~~~~--~~~~-------~~~ad~~I~VvD~~~~~~~~~---~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      ||+.|||-...  ..|.       ....|.+|+|+|++-|.....   .+.+-+.. --++++|.|--..-+..+..+. 
T Consensus       187 IIvDTSGRh~qe~sLfeEM~~v~~ai~Pd~vi~VmDasiGQaae~Qa~aFk~~vdv-g~vIlTKlDGhakGGgAlSaVa-  264 (483)
T KOG0780|consen  187 IIVDTSGRHKQEASLFEEMKQVSKAIKPDEIIFVMDASIGQAAEAQARAFKETVDV-GAVILTKLDGHAKGGGALSAVA-  264 (483)
T ss_pred             EEEeCCCchhhhHHHHHHHHHHHhhcCCCeEEEEEeccccHhHHHHHHHHHHhhcc-ceEEEEecccCCCCCceeeehh-
Confidence            99999993110  1111       111388999999987653211   11111111 2578999996433112222221 


Q ss_pred             HHHhcCCCCCEEEEecccCCCHHHH
Q 030407          145 DALRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       145 ~l~~~np~a~i~~~SA~~g~gi~el  169 (178)
                           ....||+++-  |||++++|
T Consensus       265 -----aTksPIiFIG--tGEhmdDl  282 (483)
T KOG0780|consen  265 -----ATKSPIIFIG--TGEHMDDL  282 (483)
T ss_pred             -----hhCCCEEEEe--cCcccccc
Confidence                 1234676664  67777765

>PRK09602 translation-associated GTPase; Reviewed

Probab=94.20  E-value=0.077  Score=45.70  Aligned_cols=48  Identities=10%  Similarity=0.023  Sum_probs=33.8

Q ss_pred             ceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHH-HHHHH
Q 030407          120 QADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIF-TLSIT  173 (178)
Q Consensus       120 ~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~e-l~~~l  173 (178)
                      .+-++|+||+|+.+.. ..+..+.    +. +..+++++||+.+.++++ +.+.+
T Consensus       218 KPvI~VlNK~D~~~~~-~~l~~i~----~~-~~~~vvpISA~~e~~l~~~l~~~i  266 (396)
T PRK09602        218 KPMVIAANKADLPPAE-ENIERLK----EE-KYYIVVPTSAEAELALRRAAKAGL  266 (396)
T ss_pred             CCEEEEEEchhcccch-HHHHHHH----hc-CCCcEEEEcchhhhhHHHHHHHhH
Confidence            5679999999986431 2233322    23 567899999999999988 54444

>PRK14489 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional

Probab=93.72  E-value=0.25  Score=42.04  Aligned_cols=79  Identities=15%  Similarity=0.077  Sum_probs=48.2

Q ss_pred             CHHHHHHhhcC-CcEEEEEecCC-Cc-----hhHHHHHHcCCCCccceeecccCCCcccccccccc-cCHhHHHhhHhhC
Q 030407            1 MLALCKFLRDK-YSLAAVTNDIF-TK-----EDGEFLMRNGALPEERIRAVETGGCPHAAIREDIS-INLGPLEELSNLF   72 (178)
Q Consensus         1 ~~~~~~~~~~~-~~vaVI~nd~g-~~-----iD~~li~~~~~~~~~~~~~l~~GcCc~l~i~~dl~-~~l~~l~~l~~~~   72 (178)
                      ++++++.|+++ .|||+|..+-. ..     -|..+++..|.    ..+.+.++..|++.-+.+-. ..+..+.......
T Consensus       222 ~~~l~~~l~~~g~~v~~iKh~~h~~~~d~~g~Ds~r~~~aGa----~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  297 (366)
T PRK14489        222 LEKLIPELIARGYRIGLIKHSHHRVDIDKPGKDSHRLRAAGA----NPTMIVCPERWALMRETPEEAVPFKVLIATFDPE  297 (366)
T ss_pred             HHHHHHHHHHcCCEEEEEEECCcccCCCCCCChhHHHHhCCC----ceEEEEcCCeEEEEEeCCCCCcCHHHHHHhcCCc
Confidence            36788888875 99999998744 33     48999988887    55666566666542111101 1232222111123


Q ss_pred             CCCEEEEeCCc
Q 030407           73 KADLLLCESGG   83 (178)
Q Consensus        73 ~~d~iiiEttG   83 (178)
                      +.|+||+|.--
T Consensus       298 ~~D~vlvEG~k  308 (366)
T PRK14489        298 EVDLILVEGFK  308 (366)
T ss_pred             CCCEEEEcccc
Confidence            68999999744

>TIGR00959 ffh signal recognition particle protein

Probab=93.44  E-value=0.98  Score=39.40  Aligned_cols=145  Identities=17%  Similarity=0.139  Sum_probs=75.6

Q ss_pred             HHHHHhh--cCCcEEEEEecCC-Cc-hhHH--HHHHcCCCCccceeecccCCCcccccccccccCH-hHHHhhHhhCCCC
Q 030407            3 ALCKFLR--DKYSLAAVTNDIF-TK-EDGE--FLMRNGALPEERIRAVETGGCPHAAIREDISINL-GPLEELSNLFKAD   75 (178)
Q Consensus         3 ~~~~~~~--~~~~vaVI~nd~g-~~-iD~~--li~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l-~~l~~l~~~~~~d   75 (178)
                      +++.++.  .++|+++|--|.- .. .+..  +-+..|+    ++....++-++.        ... .++.. ....++|
T Consensus       118 kLA~~l~~~~g~kV~lV~~D~~R~~a~~QL~~~a~~~gv----p~~~~~~~~~P~--------~i~~~al~~-~~~~~~D  184 (428)
T TIGR00959       118 KLAYYLKKKQGKKVLLVACDLYRPAAIEQLKVLGQQVGV----PVFALGKGQSPV--------EIARRALEY-AKENGFD  184 (428)
T ss_pred             HHHHHHHHhCCCeEEEEeccccchHHHHHHHHHHHhcCC----ceEecCCCCCHH--------HHHHHHHHH-HHhcCCC
Confidence            5566654  3589999999976 43 3321  1122343    344433222331        111 23333 3356799


Q ss_pred             EEEEeCCcch-----hhh---ccc-ccccceEEEEEeCCCCCCCCc---CCCCCCCceeEEEEecCCCCCchhHhHHHHH
Q 030407           76 LLLCESGGDN-----LAA---NFS-RELADYIIYIIDVSGGDKIPR---KGGPGITQADLLVINKTDLASAIGADLAVME  143 (178)
Q Consensus        76 ~iiiEttG~~-----~~~---~~~-~~~ad~~I~VvD~~~~~~~~~---~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~  143 (178)
                      +|||+|.|..     +..   .+. ....+.+++|+|+..+.+...   .+...+. -+-+|+||.|-....    ..+.
T Consensus       185 vVIIDTaGr~~~d~~l~~eL~~i~~~~~p~e~lLVvda~tgq~~~~~a~~f~~~v~-i~giIlTKlD~~~~~----G~~l  259 (428)
T TIGR00959       185 VVIVDTAGRLQIDEELMEELAAIKEILNPDEILLVVDAMTGQDAVNTAKTFNERLG-LTGVVLTKLDGDARG----GAAL  259 (428)
T ss_pred             EEEEeCCCccccCHHHHHHHHHHHHhhCCceEEEEEeccchHHHHHHHHHHHhhCC-CCEEEEeCccCcccc----cHHH
Confidence            9999999931     111   011 111377899999976532211   1111222 257889999965432    1233


Q ss_pred             HHHHhcCCCCCEEEEecccCCCHHHH
Q 030407          144 RDALRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       144 ~~l~~~np~a~i~~~SA~~g~gi~el  169 (178)
                      +.....  +.|+.+++.  |+.++++
T Consensus       260 si~~~~--~~PI~fi~~--Ge~i~dl  281 (428)
T TIGR00959       260 SVRSVT--GKPIKFIGV--GEKIDDL  281 (428)
T ss_pred             HHHHHH--CcCEEEEeC--CCChhhC
Confidence            333333  357777663  6767655

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>KOG0090 consensus Signal recognition particle receptor, beta subunit (small G protein superfamily) [Intracellular trafficking, secretion, and vesicular transport]

Probab=93.42  E-value=0.13  Score=40.74  Aligned_cols=22  Identities=18%  Similarity=-0.230  Sum_probs=18.4

Q ss_pred             CEEEEecccCCCHHHHHHHHhhh
Q 030407          154 PFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       154 ~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+.|+++| ++++|.+|+.+.
T Consensus       216 ~F~e~S~~~~-~i~~~~~wi~~~  237 (238)
T KOG0090|consen  216 TFAEASAKTG-EIDQWESWIREA  237 (238)
T ss_pred             EEeecccCcC-ChHHHHHHHHHh
Confidence            5677899988 999999998764

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

Probab=93.25  E-value=0.42  Score=37.17  Aligned_cols=79  Identities=10%  Similarity=-0.074  Sum_probs=51.7

Q ss_pred             ccceEEEEEeCCCCCCCCc---C-----CCCCC----CceeEEEEecCCCCCchh-HhHHHHHHHHHhcCCCCCEEEEec
Q 030407           94 LADYIIYIIDVSGGDKIPR---K-----GGPGI----TQADLLVINKTDLASAIG-ADLAVMERDALRMRDGGPFIFAQV  160 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~---~-----~~~qi----~~adiiviNK~Dl~~~~~-~~~~~~~~~l~~~np~a~i~~~SA  160 (178)
                      .+++...|+|.++..+...   +     .+-|+    ..|.++..||+|.-.... +...++.++ ...|..+..+.||+
T Consensus        98 ea~~~~iVfdvt~s~tfe~~skwkqdldsk~qLpng~Pv~~vllankCd~e~~a~~~~~~~~d~f-~kengf~gwtets~  176 (229)
T KOG4423|consen   98 EAHGAFIVFDVTRSLTFEPVSKWKQDLDSKLQLPNGTPVPCVLLANKCDQEKSAKNEATRQFDNF-KKENGFEGWTETSA  176 (229)
T ss_pred             CCcceEEEEEccccccccHHHHHHHhccCcccCCCCCcchheeccchhccChHhhhhhHHHHHHH-HhccCccceeeecc
Confidence            4677889999987543211   1     11122    346799999999864411 112233333 34578899999999


Q ss_pred             ccCCCHHHHHHHH
Q 030407          161 GWVIGIIFTLSIT  173 (178)
Q Consensus       161 ~~g~gi~el~~~l  173 (178)
                      |.+.+|+|..+.+
T Consensus       177 Kenkni~Ea~r~l  189 (229)
T KOG4423|consen  177 KENKNIPEAQREL  189 (229)
T ss_pred             ccccChhHHHHHH
Confidence            9999999987754

>cd04102 RabL3 RabL3 (Rab-like3) subfamily

Probab=93.20  E-value=0.13  Score=40.18  Aligned_cols=61  Identities=18%  Similarity=0.149  Sum_probs=38.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CC---------------CCC---CCce
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KG---------------GPG---ITQA  121 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~---------------~~q---i~~a  121 (178)
                      .+.+-|.+|.|..    +...+.. .+|++|+|+|.++......         ..               .++   -..+
T Consensus        53 ~~~l~IwDtaG~e~~~~l~~~~yr-~ad~iIlVyDvtn~~Sf~~l~~W~~ei~~~~~~~~~~~~~~~~~~~~~~~~~~~P  131 (202)
T cd04102          53 TFFVELWDVGGSESVKSTRAVFYN-QVNGIILVHDLTNRKSSQNLQRWSLEALNKDTFPTGLLVTNGDYDSEQFGGNQIP  131 (202)
T ss_pred             EEEEEEEecCCchhHHHHHHHHhC-cCCEEEEEEECcChHHHHHHHHHHHHHHHhhccccccccccccccccccCCCCce
Confidence            4667788999941    2233333 5799999999987642210         00               001   1346


Q ss_pred             eEEEEecCCCCCc
Q 030407          122 DLLVINKTDLASA  134 (178)
Q Consensus       122 diiviNK~Dl~~~  134 (178)
                      -++|.||+|+.++
T Consensus       132 iilVGnK~Dl~~~  144 (202)
T cd04102         132 LLVIGTKLDQIPE  144 (202)
T ss_pred             EEEEEECccchhh
Confidence            7999999999754

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.98  E-value=0.91  Score=39.17  Aligned_cols=144  Identities=13%  Similarity=0.099  Sum_probs=70.9

Q ss_pred             HHHHHhhc-CCcEEEEEecCC-Cc-hhHHHHHHcCCCCccceeecccCCCcccccccccccCH-hHHHhhHhhCCCCEEE
Q 030407            3 ALCKFLRD-KYSLAAVTNDIF-TK-EDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINL-GPLEELSNLFKADLLL   78 (178)
Q Consensus         3 ~~~~~~~~-~~~vaVI~nd~g-~~-iD~~li~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l-~~l~~l~~~~~~d~ii   78 (178)
                      ++..++.+ ++++++|.-|.. ++ ++. +-..... .+-++...      +     + ...+ .++..+....++|+||
T Consensus       225 kLA~~l~~~g~~V~lItaDtyR~gAveQ-Lk~yae~-lgvpv~~~------~-----d-p~dL~~al~~l~~~~~~D~VL  290 (407)
T PRK12726        225 KLGWQLLKQNRTVGFITTDTFRSGAVEQ-FQGYADK-LDVELIVA------T-----S-PAELEEAVQYMTYVNCVDHIL  290 (407)
T ss_pred             HHHHHHHHcCCeEEEEeCCccCccHHHH-HHHHhhc-CCCCEEec------C-----C-HHHHHHHHHHHHhcCCCCEEE
Confidence            45555543 589999999987 53 332 2211110 00022211      1     1 1122 4444443235799999


Q ss_pred             EeCCcchhh--------hccc-ccccceEEEEEeCCCCCCCCcCCCC--CCCceeEEEEecCCCCCchhHhHHHHHHHHH
Q 030407           79 CESGGDNLA--------ANFS-RELADYIIYIIDVSGGDKIPRKGGP--GITQADLLVINKTDLASAIGADLAVMERDAL  147 (178)
Q Consensus        79 iEttG~~~~--------~~~~-~~~ad~~I~VvD~~~~~~~~~~~~~--qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~  147 (178)
                      |.|.|.+..        ..+. ....+..++|++++...........  ..-..+-++++|.|-...    ...+.+...
T Consensus       291 IDTAGr~~~d~~~l~EL~~l~~~~~p~~~~LVLsag~~~~d~~~i~~~f~~l~i~glI~TKLDET~~----~G~~Lsv~~  366 (407)
T PRK12726        291 IDTVGRNYLAEESVSEISAYTDVVHPDLTCFTFSSGMKSADVMTILPKLAEIPIDGFIITKMDETTR----IGDLYTVMQ  366 (407)
T ss_pred             EECCCCCccCHHHHHHHHHHhhccCCceEEEECCCcccHHHHHHHHHhcCcCCCCEEEEEcccCCCC----ccHHHHHHH
Confidence            999994211        0011 1112555667776432211111000  112247899999998654    233444443


Q ss_pred             hcCCCCCEEEEecccCCCHHH
Q 030407          148 RMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       148 ~~np~a~i~~~SA~~g~gi~e  168 (178)
                      ..  +.|+.++|  +|+++++
T Consensus       367 ~t--glPIsylt--~GQ~Vpd  383 (407)
T PRK12726        367 ET--NLPVLYMT--DGQNITE  383 (407)
T ss_pred             HH--CCCEEEEe--cCCCCCc
Confidence            33  45777776  5777765

>PRK14494 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein; Provisional

Probab=92.89  E-value=0.39  Score=38.33  Aligned_cols=72  Identities=22%  Similarity=0.312  Sum_probs=45.8

Q ss_pred             HHHHHHhhcC-CcEEEEEec---CC-CchhHHHHHHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCCCCE
Q 030407            2 LALCKFLRDK-YSLAAVTND---IF-TKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADL   76 (178)
Q Consensus         2 ~~~~~~~~~~-~~vaVI~nd---~g-~~iD~~li~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~~d~   76 (178)
                      .+++++|+++ +|||+|-..   +- .+-|..++...|.    .++.+.++..+.+ ++.  ...+..+..   ..++|+
T Consensus        19 ~~l~~~L~~~G~~V~viK~~~~~~d~~~~Dt~r~~~aGA----~~v~~~~~~~~~~-~~~--~~~l~~ll~---~l~~Dl   88 (229)
T PRK14494         19 EKILKNLKERGYRVATAKHTHHEFDKPDTDTYRFKKAGA----EVVVVSTDETAAF-LYD--RMDLNEILS---LLDADF   88 (229)
T ss_pred             HHHHHHHHhCCCeEEEEEecccCCCCCCchHHHHHHcCC----cEEEEecCCeEEE-Eec--CCCHHHHHh---hcCCCE
Confidence            5788888764 999999642   22 2568889888876    5566655555543 121  123443333   237899


Q ss_pred             EEEeCCc
Q 030407           77 LLCESGG   83 (178)
Q Consensus        77 iiiEttG   83 (178)
                      ||||.-.
T Consensus        89 vlVEGfk   95 (229)
T PRK14494         89 LLIEGFK   95 (229)
T ss_pred             EEEeCCC
Confidence            9999444

>PRK07560 elongation factor EF-2; Reviewed

Probab=92.79  E-value=0.29  Score=45.43  Aligned_cols=60  Identities=18%  Similarity=0.098  Sum_probs=36.3

Q ss_pred             CCCEEEEeCCcch-hh-hcc-cccccceEEEEEeCCCCCCCCcC-CCC---CCCceeEEEEecCCCC
Q 030407           73 KADLLLCESGGDN-LA-ANF-SRELADYIIYIIDVSGGDKIPRK-GGP---GITQADLLVINKTDLA  132 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~~-~~~~ad~~I~VvD~~~~~~~~~~-~~~---qi~~adiiviNK~Dl~  132 (178)
                      ++-+.||.|.|.. .. ... ....+|++++|+|+..+...+.. ...   ....+-++++||+|+.
T Consensus        86 ~~~i~liDtPG~~df~~~~~~~l~~~D~avlVvda~~g~~~~t~~~~~~~~~~~~~~iv~iNK~D~~  152 (731)
T PRK07560         86 EYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQTETVLRQALRERVKPVLFINKVDRL  152 (731)
T ss_pred             cEEEEEEcCCCccChHHHHHHHHHhcCEEEEEEECCCCCCccHHHHHHHHHHcCCCeEEEEECchhh
Confidence            4557899999931 11 111 11246999999999887543221 001   1123459999999986

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 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=92.73  E-value=0.24  Score=38.47  Aligned_cols=144  Identities=15%  Similarity=0.091  Sum_probs=74.4

Q ss_pred             HHHHHhhc-CCcEEEEEecCC-C-chhHHH--HHHcCCCCccceeecccCCCcccccccccccCH-hHHHhhHhhCCCCE
Q 030407            3 ALCKFLRD-KYSLAAVTNDIF-T-KEDGEF--LMRNGALPEERIRAVETGGCPHAAIREDISINL-GPLEELSNLFKADL   76 (178)
Q Consensus         3 ~~~~~~~~-~~~vaVI~nd~g-~-~iD~~l--i~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l-~~l~~l~~~~~~d~   76 (178)
                      ++..+++. ++||++|.-|.. . .+|...  -+..|+    ++......        +|....+ +++... +..++|+
T Consensus        20 KLAa~~~~~~~~v~lis~D~~R~ga~eQL~~~a~~l~v----p~~~~~~~--------~~~~~~~~~~l~~~-~~~~~D~   86 (196)
T PF00448_consen   20 KLAARLKLKGKKVALISADTYRIGAVEQLKTYAEILGV----PFYVARTE--------SDPAEIAREALEKF-RKKGYDL   86 (196)
T ss_dssp             HHHHHHHHTT--EEEEEESTSSTHHHHHHHHHHHHHTE----EEEESSTT--------SCHHHHHHHHHHHH-HHTTSSE
T ss_pred             HHHHHHhhccccceeecCCCCCccHHHHHHHHHHHhcc----ccchhhcc--------hhhHHHHHHHHHHH-hhcCCCE
Confidence            56666654 599999999988 6 444321  222343    33332211        1111112 334433 3568999


Q ss_pred             EEEeCCcchhhh---------cccccccceEEEEEeCCCCCCCCcC---CCCCCCceeEEEEecCCCCCchhHhHHHHHH
Q 030407           77 LLCESGGDNLAA---------NFSRELADYIIYIIDVSGGDKIPRK---GGPGITQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        77 iiiEttG~~~~~---------~~~~~~ad~~I~VvD~~~~~~~~~~---~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      |||.|.|.+...         .......+-+.+|++++.+.+....   +...+ ..+-++++|.|-....    ..+..
T Consensus        87 vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~~~~~~~-~~~~lIlTKlDet~~~----G~~l~  161 (196)
T PF00448_consen   87 VLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQALAFYEAF-GIDGLILTKLDETARL----GALLS  161 (196)
T ss_dssp             EEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHHHHHHHS-STCEEEEESTTSSSTT----HHHHH
T ss_pred             EEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHHHHhhcc-cCceEEEEeecCCCCc----cccee
Confidence            999999953211         0111123678999999775432111   00001 1367889999987553    33444


Q ss_pred             HHHhcCCCCCEEEEecccCCCHHH
Q 030407          145 DALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       145 ~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                      .+.+.  ..|+-.+|  +|+++++
T Consensus       162 ~~~~~--~~Pi~~it--~Gq~V~D  181 (196)
T PF00448_consen  162 LAYES--GLPISYIT--TGQRVDD  181 (196)
T ss_dssp             HHHHH--TSEEEEEE--SSSSTTG
T ss_pred             HHHHh--CCCeEEEE--CCCChhc
Confidence            44433  34677766  4666643

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 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PLN00116 translation elongation factor EF-2 subunit; Provisional

Probab=92.70  E-value=0.14  Score=48.18  Aligned_cols=57  Identities=19%  Similarity=0.253  Sum_probs=35.4

Q ss_pred             EEEEeCCcch-h-hhccc-ccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCC
Q 030407           76 LLLCESGGDN-L-AANFS-RELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLA  132 (178)
Q Consensus        76 ~iiiEttG~~-~-~~~~~-~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~  132 (178)
                      +=||.|.|-. . ..... ...+|+.|+|+|+..|...+..    .......+-++++||+|+.
T Consensus       100 inliDtPGh~dF~~e~~~al~~~D~ailVvda~~Gv~~~t~~~~~~~~~~~~p~i~~iNK~D~~  163 (843)
T PLN00116        100 INLIDSPGHVDFSSEVTAALRITDGALVVVDCIEGVCVQTETVLRQALGERIRPVLTVNKMDRC  163 (843)
T ss_pred             EEEECCCCHHHHHHHHHHHHhhcCEEEEEEECCCCCcccHHHHHHHHHHCCCCEEEEEECCccc
Confidence            3489999921 0 11111 1246999999999987654321    1111234669999999998

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=92.50  E-value=0.74  Score=40.26  Aligned_cols=143  Identities=17%  Similarity=0.175  Sum_probs=73.4

Q ss_pred             HHHHHhhcC-CcEEEEEecCC-Cc-hhHHH--HHHcCCCCccceeecccCCCcccccccccccCH-hHHHhhHhhCCCCE
Q 030407            3 ALCKFLRDK-YSLAAVTNDIF-TK-EDGEF--LMRNGALPEERIRAVETGGCPHAAIREDISINL-GPLEELSNLFKADL   76 (178)
Q Consensus         3 ~~~~~~~~~-~~vaVI~nd~g-~~-iD~~l--i~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l-~~l~~l~~~~~~d~   76 (178)
                      ++..++.++ +++++|..|.. .. .|...  -+..++    ++.....        +.|....+ .++..+   ...|+
T Consensus       114 kLA~~L~~~g~kV~lV~~D~~R~aa~eQL~~la~~~gv----p~~~~~~--------~~d~~~i~~~al~~~---~~~Dv  178 (437)
T PRK00771        114 KLARYFKKKGLKVGLVAADTYRPAAYDQLKQLAEKIGV----PFYGDPD--------NKDAVEIAKEGLEKF---KKADV  178 (437)
T ss_pred             HHHHHHHHcCCeEEEecCCCCCHHHHHHHHHHHHHcCC----cEEecCC--------ccCHHHHHHHHHHHh---hcCCE
Confidence            566667654 89999999977 32 33221  122233    2222111        01111112 222222   24699


Q ss_pred             EEEeCCcchhh-h-------cc-cccccceEEEEEeCCCCCCCCc---CCCCCCCceeEEEEecCCCCCchhHhHHHHHH
Q 030407           77 LLCESGGDNLA-A-------NF-SRELADYIIYIIDVSGGDKIPR---KGGPGITQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        77 iiiEttG~~~~-~-------~~-~~~~ad~~I~VvD~~~~~~~~~---~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      |||+|.|.... .       .+ .....|.+++|+|++.+.+...   .+...+. .+-+|+||.|-....    ..+..
T Consensus       179 VIIDTAGr~~~d~~lm~El~~l~~~~~pdevlLVvda~~gq~av~~a~~F~~~l~-i~gvIlTKlD~~a~~----G~~ls  253 (437)
T PRK00771        179 IIVDTAGRHALEEDLIEEMKEIKEAVKPDEVLLVIDATIGQQAKNQAKAFHEAVG-IGGIIITKLDGTAKG----GGALS  253 (437)
T ss_pred             EEEECCCcccchHHHHHHHHHHHHHhcccceeEEEeccccHHHHHHHHHHHhcCC-CCEEEEecccCCCcc----cHHHH
Confidence            99999993211 0       01 1112478999999977642211   1111122 367899999976442    23333


Q ss_pred             HHHhcCCCCCEEEEecccCCCHHHH
Q 030407          145 DALRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       145 ~l~~~np~a~i~~~SA~~g~gi~el  169 (178)
                      .....  +.|+.+++  +|+.+++|
T Consensus       254 ~~~~~--~~Pi~fig--~Ge~v~Dl  274 (437)
T PRK00771        254 AVAET--GAPIKFIG--TGEKIDDL  274 (437)
T ss_pred             HHHHH--CcCEEEEe--cCCCcccC
Confidence            33322  45787776  47777665

>KOG1490 consensus GTP-binding protein CRFG/NOG1 (ODN superfamily) [General function prediction only]

Probab=91.90  E-value=0.24  Score=43.91  Aligned_cols=94  Identities=15%  Similarity=0.125  Sum_probs=55.9

Q ss_pred             CEEEEeCCcchhhhc-------------ccccccceEEEEEeCCCC--CCCCc--C----CCCC-CCceeEEEEecCCCC
Q 030407           75 DLLLCESGGDNLAAN-------------FSRELADYIIYIIDVSGG--DKIPR--K----GGPG-ITQADLLVINKTDLA  132 (178)
Q Consensus        75 d~iiiEttG~~~~~~-------------~~~~~ad~~I~VvD~~~~--~~~~~--~----~~~q-i~~adiiviNK~Dl~  132 (178)
                      -|-+|.|.|+ +..|             ...++...+++++|.++.  .....  +    ..+. ....-|+|+||+|+.
T Consensus       216 rwQViDTPGI-LD~plEdrN~IEmqsITALAHLraaVLYfmDLSe~CGySva~QvkLfhsIKpLFaNK~~IlvlNK~D~m  294 (620)
T KOG1490|consen  216 RWQVIDTPGI-LDRPEEDRNIIEMQIITALAHLRSAVLYFMDLSEMCGYSVAAQVKLYHSIKPLFANKVTILVLNKIDAM  294 (620)
T ss_pred             eeeecCCccc-cCcchhhhhHHHHHHHHHHHHhhhhheeeeechhhhCCCHHHHHHHHHHhHHHhcCCceEEEeeccccc
Confidence            5678888894 1111             112233568899998752  21110  0    1111 234579999999998


Q ss_pred             Cch--hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHH
Q 030407          133 SAI--GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus       133 ~~~--~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~  170 (178)
                      .+.  .++-+++.+.+.+. +..+++.+|..+.+|+-++.
T Consensus       295 ~~edL~~~~~~ll~~~~~~-~~v~v~~tS~~~eegVm~Vr  333 (620)
T KOG1490|consen  295 RPEDLDQKNQELLQTIIDD-GNVKVVQTSCVQEEGVMDVR  333 (620)
T ss_pred             CccccCHHHHHHHHHHHhc-cCceEEEecccchhceeeHH
Confidence            761  12223344444433 45799999999999998764

>TIGR03172 probable selenium-dependent hydroxylase accessory protein YqeC

Probab=91.59  E-value=1.6  Score=34.85  Aligned_cols=42  Identities=19%  Similarity=0.366  Sum_probs=24.8

Q ss_pred             hHHHhhHhhCCCCEEEEeCCcch---hh-----hcccccccceEEEEEeC
Q 030407           63 GPLEELSNLFKADLLLCESGGDN---LA-----ANFSRELADYIIYIIDV  104 (178)
Q Consensus        63 ~~l~~l~~~~~~d~iiiEttG~~---~~-----~~~~~~~ad~~I~VvD~  104 (178)
                      +.+..+.+.+.+|+|+||+=|+.   +-     .|..+...+.+|-|+..
T Consensus        87 e~l~~l~~~~~~D~vLVEADGAk~~PlKaP~~~EPVIP~~t~~VI~V~gl  136 (232)
T TIGR03172        87 STVDDLSDFQHFDVILVEADGAKCRPLKAPSDHEPVIPKSSTTVIGVAGI  136 (232)
T ss_pred             HHHHHHHhccCCCEEEEECCCcCCCcccCCCCCCCccCCCCCEEEEEeCH
Confidence            34444443334799999999952   11     22333445777777754

This uncharacterized protein family includes YqeC from Escherichia coli. A phylogenetic profiling analysis shows correlation with SelD, the selenium donor protein, even in species where SelD contributes to neither selenocysteine nor selenouridine biosynthesis. Instead, this family, and families TIGR03309 and TIGR03310 appear to mark selenium-dependent molybdenum hydroxylase maturation systems.

>KOG0448 consensus Mitofusin 1 GTPase, involved in mitochondrila biogenesis [Posttranslational modification, protein turnover, chaperones]

Probab=91.51  E-value=0.29  Score=44.68  Aligned_cols=88  Identities=13%  Similarity=0.115  Sum_probs=54.4

Q ss_pred             CEEEEeCCcchhhhcccc------cccceEEEEEeCCCCCCCCcC---C-CCCCCceeEEEEecCCCCCchhHhHHHHHH
Q 030407           75 DLLLCESGGDNLAANFSR------ELADYIIYIIDVSGGDKIPRK---G-GPGITQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        75 d~iiiEttG~~~~~~~~~------~~ad~~I~VvD~~~~~~~~~~---~-~~qi~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      |+++|.+.|+.+.+....      ..+|..|+|+.+.+.....++   + ...-+---.|+.||+|.....++-.+.+.+
T Consensus       207 DivliDsPGld~~se~tswid~~cldaDVfVlV~NaEntlt~sek~Ff~~vs~~KpniFIlnnkwDasase~ec~e~V~~  286 (749)
T KOG0448|consen  207 DIVLIDSPGLDVDSELTSWIDSFCLDADVFVLVVNAENTLTLSEKQFFHKVSEEKPNIFILNNKWDASASEPECKEDVLK  286 (749)
T ss_pred             cceeccCCCCCCchhhhHHHHHHhhcCCeEEEEecCccHhHHHHHHHHHHhhccCCcEEEEechhhhhcccHHHHHHHHH
Confidence            889999999654332211      236999999998764322111   0 000022237888999987653355666777


Q ss_pred             HHHhcCCC------CCEEEEeccc
Q 030407          145 DALRMRDG------GPFIFAQVGW  162 (178)
Q Consensus       145 ~l~~~np~------a~i~~~SA~~  162 (178)
                      +++++.|.      -.+|++||+.
T Consensus       287 Qi~eL~v~~~~eA~DrvfFVS~~e  310 (749)
T KOG0448|consen  287 QIHELSVVTEKEAADRVFFVSAKE  310 (749)
T ss_pred             HHHhcCcccHhhhcCeeEEEeccc
Confidence            77777553      4899999653

>PTZ00416 elongation factor 2; Provisional

Probab=91.42  E-value=0.22  Score=46.97  Aligned_cols=60  Identities=20%  Similarity=0.123  Sum_probs=37.9

Q ss_pred             CCCEEEEeCCcch--hhhcc-cccccceEEEEEeCCCCCCCCcC-CCC---CCCceeEEEEecCCCC
Q 030407           73 KADLLLCESGGDN--LAANF-SRELADYIIYIIDVSGGDKIPRK-GGP---GITQADLLVINKTDLA  132 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~-~~~~ad~~I~VvD~~~~~~~~~~-~~~---qi~~adiiviNK~Dl~  132 (178)
                      ++-+.||.|.|..  ..... ....+|++|+|+|+..+...+.. ...   ....+-++++||+|+.
T Consensus        91 ~~~i~liDtPG~~~f~~~~~~al~~~D~ailVvda~~g~~~~t~~~~~~~~~~~~p~iv~iNK~D~~  157 (836)
T PTZ00416         91 PFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVEGVCVQTETVLRQALQERIRPVLFINKVDRA  157 (836)
T ss_pred             ceEEEEEcCCCHHhHHHHHHHHHhcCCeEEEEEECCCCcCccHHHHHHHHHHcCCCEEEEEEChhhh
Confidence            3457899999931  11111 11246999999999887554321 111   1234679999999997

>PF08438 MMR_HSR1_C: GTPase of unknown function C-terminal; InterPro: IPR013646 This domain is found at the C terminus of IPR002917 from INTERPRO in archaeal and eukaryotic GTP-binding proteins

Probab=91.39  E-value=0.15  Score=36.05  Aligned_cols=33  Identities=18%  Similarity=0.245  Sum_probs=18.4

Q ss_pred             EEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEeccc
Q 030407          125 VINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGW  162 (178)
Q Consensus       125 viNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~  162 (178)
                      +.||+|+..+ .+.++++    ++..|..+++++||..
T Consensus         1 AaNK~D~~~a-~~ni~kl----~~~~~~~~vVp~SA~a   33 (109)
T PF08438_consen    1 AANKADLPAA-DENIEKL----KEKYPDEPVVPTSAAA   33 (109)
T ss_dssp             EEE-GGG-S--HHHHHHH----HHHHTT-EEEEE-HHH
T ss_pred             CCcccccccc-HhHHHHH----HHhCCCCceeeccHHH
Confidence            5899997443 1444444    4445778999999864

; PDB: 1WXQ_A.

>KOG0410 consensus Predicted GTP binding protein [General function prediction only]

Probab=91.18  E-value=0.11  Score=43.78  Aligned_cols=92  Identities=18%  Similarity=0.062  Sum_probs=54.8

Q ss_pred             CCCEEEEeCCcc------hhhhccccc-----ccceEEEEEeCCCCCCCCcC-----CCCCCCce-------eEEEEecC
Q 030407           73 KADLLLCESGGD------NLAANFSRE-----LADYIIYIIDVSGGDKIPRK-----GGPGITQA-------DLLVINKT  129 (178)
Q Consensus        73 ~~d~iiiEttG~------~~~~~~~~~-----~ad~~I~VvD~~~~~~~~~~-----~~~qi~~a-------diiviNK~  129 (178)
                      +--+++..|+|-      .+.+.|...     -+|.++-|+|.+++.....+     ...++..+       =+=|=||+
T Consensus       225 g~~vlltDTvGFisdLP~~LvaAF~ATLeeVaeadlllHvvDiShP~ae~q~e~Vl~vL~~igv~~~pkl~~mieVdnki  304 (410)
T KOG0410|consen  225 GNFVLLTDTVGFISDLPIQLVAAFQATLEEVAEADLLLHVVDISHPNAEEQRETVLHVLNQIGVPSEPKLQNMIEVDNKI  304 (410)
T ss_pred             CcEEEEeechhhhhhCcHHHHHHHHHHHHHHhhcceEEEEeecCCccHHHHHHHHHHHHHhcCCCcHHHHhHHHhhcccc
Confidence            567899999993      122333321     25899999999987532110     00112111       13355777


Q ss_pred             CCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          130 DLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       130 Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      |..+.  +. +.        -|. -.+.+||++|.|++++++.+...
T Consensus       305 D~e~~--~~-e~--------E~n-~~v~isaltgdgl~el~~a~~~k  339 (410)
T KOG0410|consen  305 DYEED--EV-EE--------EKN-LDVGISALTGDGLEELLKAEETK  339 (410)
T ss_pred             ccccc--cC-cc--------ccC-CccccccccCccHHHHHHHHHHH
Confidence            76544  11 10        111 26889999999999999987654

>cd03110 Fer4_NifH_child This protein family's function is unkown

Probab=90.85  E-value=0.58  Score=35.11  Aligned_cols=75  Identities=15%  Similarity=0.027  Sum_probs=42.4

Q ss_pred             hCCCCEEEEeCCcchhhh-ccc-ccccceEEEEEeCCCCCCCCc----CCCCCCCceeEEEEecCCCCCchhHhHHHHHH
Q 030407           71 LFKADLLLCESGGDNLAA-NFS-RELADYIIYIIDVSGGDKIPR----KGGPGITQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        71 ~~~~d~iiiEttG~~~~~-~~~-~~~ad~~I~VvD~~~~~~~~~----~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      ..++|+|||.|.|. ... ... ...+|.+++++.+....-...    +........-.+|+||+|..+.   ..+.+.+
T Consensus        90 ~~~~d~viiDtpp~-~~~~~~~~l~~aD~vliv~~~~~~~~~~~~~~~~~l~~~~~~~~vV~N~~~~~~~---~~~~~~~  165 (179)
T cd03110          90 AEGAELIIIDGPPG-IGCPVIASLTGADAALLVTEPTPSGLHDLERAVELVRHFGIPVGVVINKYDLNDE---IAEEIED  165 (179)
T ss_pred             hcCCCEEEEECcCC-CcHHHHHHHHcCCEEEEEecCCcccHHHHHHHHHHHHHcCCCEEEEEeCCCCCcc---hHHHHHH
Confidence            36899999999972 221 111 134799999998865321100    0001112234799999997544   2344555


Q ss_pred             HHHhc
Q 030407          145 DALRM  149 (178)
Q Consensus       145 ~l~~~  149 (178)
                      .+++.
T Consensus       166 ~~~~~  170 (179)
T cd03110         166 YCEEE  170 (179)
T ss_pred             HHHHc
Confidence            66554

It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.

>KOG2423 consensus Nucleolar GTPase [General function prediction only]

Probab=90.77  E-value=1.1  Score=38.77  Aligned_cols=80  Identities=15%  Similarity=0.078  Sum_probs=45.0

Q ss_pred             cceEEEEEeCCCCCCCCcCC------CCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHH
Q 030407           95 ADYIIYIIDVSGGDKIPRKG------GPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~~~------~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                      .|++|-|+|+.++....-.+      .+--..--+.|+||+||++.  -........+....|... |-.|-.+..|=-.
T Consensus       214 SDVvvqVlDARDPmGTrc~~ve~ylkke~phKHli~vLNKvDLVPt--wvt~~Wv~~lSkeyPTiA-fHAsi~nsfGKga  290 (572)
T KOG2423|consen  214 SDVVVQVLDARDPMGTRCKHVEEYLKKEKPHKHLIYVLNKVDLVPT--WVTAKWVRHLSKEYPTIA-FHASINNSFGKGA  290 (572)
T ss_pred             cceeEEeeeccCCcccccHHHHHHHhhcCCcceeEEEeeccccccH--HHHHHHHHHHhhhCccee-eehhhcCccchhH
Confidence            58999999998764332110      00111224899999999876  222333333434444221 3334455667667


Q ss_pred             HHHHHhhhh
Q 030407          169 TLSITHYIV  177 (178)
Q Consensus       169 l~~~l~~~~  177 (178)
                      |++.|.+|+
T Consensus       291 lI~llRQf~  299 (572)
T KOG2423|consen  291 LIQLLRQFA  299 (572)
T ss_pred             HHHHHHHHH
Confidence            777776664

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=90.08  E-value=0.61  Score=38.12  Aligned_cols=96  Identities=15%  Similarity=0.150  Sum_probs=54.4

Q ss_pred             hHHHhhHhhCCCCEEEEeCCcchhh---------hcccccccceEEEEEeCCCCC-CCC---cCCCCCCCceeEEEEecC
Q 030407           63 GPLEELSNLFKADLLLCESGGDNLA---------ANFSRELADYIIYIIDVSGGD-KIP---RKGGPGITQADLLVINKT  129 (178)
Q Consensus        63 ~~l~~l~~~~~~d~iiiEttG~~~~---------~~~~~~~ad~~I~VvD~~~~~-~~~---~~~~~qi~~adiiviNK~  129 (178)
                      .++..+.+..++|+|||.|.|-+..         ........+.+++|+|++... +..   ..+..  -..+-++++|.
T Consensus       144 ~~l~~l~~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LVl~a~~~~~d~~~~~~~f~~--~~~~~~I~TKl  221 (270)
T PRK06731        144 RALTYFKEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEIITNFKD--IHIDGIVFTKF  221 (270)
T ss_pred             HHHHHHHhcCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEEEcCccCHHHHHHHHHHhCC--CCCCEEEEEee
Confidence            4444444335799999999994311         111111125688999987543 211   12222  23489999999


Q ss_pred             CCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHH
Q 030407          130 DLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       130 Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                      |-....    ..+.......  +.|+.+++  +|+++.+
T Consensus       222 Det~~~----G~~l~~~~~~--~~Pi~~it--~Gq~vp~  252 (270)
T PRK06731        222 DETASS----GELLKIPAVS--SAPIVLMT--DGQDVKK  252 (270)
T ss_pred             cCCCCc----cHHHHHHHHH--CcCEEEEe--CCCCCCc
Confidence            987653    2333333333  45777766  5777664

>KOG0467 consensus Translation elongation factor 2/ribosome biogenesis protein RIA1 and related proteins [Translation, ribosomal structure and biogenesis]

Probab=90.03  E-value=0.53  Score=43.60  Aligned_cols=57  Identities=30%  Similarity=0.263  Sum_probs=36.1

Q ss_pred             CCCCEEEEeCCcchh-----hhcccccccceEEEEEeCCCCCCCCcC-CCCC--C-CceeEEEEecCC
Q 030407           72 FKADLLLCESGGDNL-----AANFSRELADYIIYIIDVSGGDKIPRK-GGPG--I-TQADLLVINKTD  130 (178)
Q Consensus        72 ~~~d~iiiEttG~~~-----~~~~~~~~ad~~I~VvD~~~~~~~~~~-~~~q--i-~~adiiviNK~D  130 (178)
                      .++-+-+|.+.| .+     .....+ +.|+.++++|+.+|--.+.. ..+|  + ...-++|+||+|
T Consensus        70 ~~~~~nlidspg-hvdf~sevssas~-l~d~alvlvdvvegv~~qt~~vlrq~~~~~~~~~lvinkid  135 (887)
T KOG0467|consen   70 KDYLINLIDSPG-HVDFSSEVSSASR-LSDGALVLVDVVEGVCSQTYAVLRQAWIEGLKPILVINKID  135 (887)
T ss_pred             CceEEEEecCCC-ccchhhhhhhhhh-hcCCcEEEEeeccccchhHHHHHHHHHHccCceEEEEehhh
Confidence            367788899999 22     122222 56999999999887543321 0011  1 234699999999

>cd01852 AIG1 AIG1 (avrRpt2-induced gene 1)

Probab=89.97  E-value=0.9  Score=34.72  Aligned_cols=101  Identities=9%  Similarity=0.057  Sum_probs=57.8

Q ss_pred             CCCEEEEeCCcchhh------------hc--ccccccceEEEEEeCCCCCCCCcC--------CCCCCCceeEEEEecCC
Q 030407           73 KADLLLCESGGDNLA------------AN--FSRELADYIIYIIDVSGGDKIPRK--------GGPGITQADLLVINKTD  130 (178)
Q Consensus        73 ~~d~iiiEttG~~~~------------~~--~~~~~ad~~I~VvD~~~~~~~~~~--------~~~qi~~adiiviNK~D  130 (178)
                      +..+.+|+|.|..-.            ..  ......|.+++|+|+.+.......        +.+.+-..-++|+||+|
T Consensus        48 ~~~i~viDTPG~~d~~~~~~~~~~~i~~~~~~~~~g~~~illVi~~~~~t~~d~~~l~~l~~~fg~~~~~~~ivv~T~~d  127 (196)
T cd01852          48 GRRVNVIDTPGLFDTSVSPEQLSKEIVRCLSLSAPGPHAFLLVVPLGRFTEEEEQAVETLQELFGEKVLDHTIVLFTRGD  127 (196)
T ss_pred             CeEEEEEECcCCCCccCChHHHHHHHHHHHHhcCCCCEEEEEEEECCCcCHHHHHHHHHHHHHhChHhHhcEEEEEECcc
Confidence            567899999994210            00  112346899999998762211111        11111234589999999


Q ss_pred             CCCchhHhH--------HHHHHHHHhcCCCCCEEEEe-----cccCCCHHHHHHHHhhhh
Q 030407          131 LASAIGADL--------AVMERDALRMRDGGPFIFAQ-----VGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       131 l~~~~~~~~--------~~~~~~l~~~np~a~i~~~S-----A~~g~gi~el~~~l~~~~  177 (178)
                      ...+  ..+        ..+...++...  .+++..+     +..+.++++|++.+.+++
T Consensus       128 ~l~~--~~~~~~~~~~~~~l~~l~~~c~--~r~~~f~~~~~~~~~~~q~~~Ll~~i~~~~  183 (196)
T cd01852         128 DLEG--GTLEDYLENSCEALKRLLEKCG--GRYVAFNNKAKGEEQEQQVKELLAKVESMV  183 (196)
T ss_pred             ccCC--CcHHHHHHhccHHHHHHHHHhC--CeEEEEeCCCCcchhHHHHHHHHHHHHHHH
Confidence            8764  222        22333333322  2343433     567899999999988765

This represents Arabidoposis protein AIG1 that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This subfamily also includes IAN-4 protein, which has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family. The evolutionary conservation of the IAN family provides a unique example of a plant pathogen response gene conserved in animals. The IAN/IMAP subfamily has been proposed to regulate apoptosis in vertebrates and angiosperm plants, particularly in relation to cancer, diabetes, and infections. The human IAN genes were renamed GIMAP (GTPase of the immunity associated proteins).

>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=89.18  E-value=0.24  Score=30.90  Aligned_cols=38  Identities=34%  Similarity=0.410  Sum_probs=18.4

Q ss_pred             cccceEEEEEeCCCCCCCCc--------CCCCCC-CceeEEEEecCC
Q 030407           93 ELADYIIYIIDVSGGDKIPR--------KGGPGI-TQADLLVINKTD  130 (178)
Q Consensus        93 ~~ad~~I~VvD~~~~~~~~~--------~~~~qi-~~adiiviNK~D  130 (178)
                      .+.+.+++++|+++.-.+..        ...+.+ ..+-++|+||+|
T Consensus        12 hL~~~ilfi~D~Se~CGysie~Q~~L~~~ik~~F~~~P~i~V~nK~D   58 (58)
T PF06858_consen   12 HLADAILFIIDPSEQCGYSIEEQLSLFKEIKPLFPNKPVIVVLNKID   58 (58)
T ss_dssp             GT-SEEEEEE-TT-TTSS-HHHHHHHHHHHHHHTTTS-EEEEE--TT
T ss_pred             hhcceEEEEEcCCCCCCCCHHHHHHHHHHHHHHcCCCCEEEEEeccC
Confidence            35688999999986432211        011123 456788888887

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.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=88.90  E-value=2.9  Score=35.84  Aligned_cols=89  Identities=11%  Similarity=0.072  Sum_probs=49.4

Q ss_pred             CCCCEEEEeCCcchhh--------hcc-cccccceEEEEEeCCCCCCCCc----CCCCC-------CCceeEEEEecCCC
Q 030407           72 FKADLLLCESGGDNLA--------ANF-SRELADYIIYIIDVSGGDKIPR----KGGPG-------ITQADLLVINKTDL  131 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~--------~~~-~~~~ad~~I~VvD~~~~~~~~~----~~~~q-------i~~adiiviNK~Dl  131 (178)
                      .++|+|+|.|.|.+..        ..+ ......-.++|++++.+.+...    .|...       +..-+-+|++|.|-
T Consensus       214 ~~~DlVLIDTaG~~~~d~~l~e~La~L~~~~~~~~~lLVLsAts~~~~l~evi~~f~~~~~~p~~~~~~~~~~I~TKlDE  293 (374)
T PRK14722        214 RNKHMVLIDTIGMSQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGDTLNEVVQAYRSAAGQPKAALPDLAGCILTKLDE  293 (374)
T ss_pred             cCCCEEEEcCCCCCcccHHHHHHHHHHhccCCCCeEEEEecCccChHHHHHHHHHHHHhhcccccccCCCCEEEEecccc
Confidence            4689999999995311        111 1111245688999987643211    11110       11236788999997


Q ss_pred             CCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHH
Q 030407          132 ASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       132 ~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                      ...    ...+...+.+.  ..|+.+++  +|+++.+
T Consensus       294 t~~----~G~~l~~~~~~--~lPi~yvt--~Gq~VPe  322 (374)
T PRK14722        294 ASN----LGGVLDTVIRY--KLPVHYVS--TGQKVPE  322 (374)
T ss_pred             CCC----ccHHHHHHHHH--CcCeEEEe--cCCCCCc
Confidence            654    33344444432  34677766  4666654

>KOG0468 consensus U5 snRNP-specific protein [Translation, ribosomal structure and biogenesis]

Probab=88.85  E-value=0.23  Score=45.45  Aligned_cols=39  Identities=28%  Similarity=0.347  Sum_probs=29.1

Q ss_pred             ccceEEEEEeCCCCCCCCc----CCCCCCCceeEEEEecCCCC
Q 030407           94 LADYIIYIIDVSGGDKIPR----KGGPGITQADLLVINKTDLA  132 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~----~~~~qi~~adiiviNK~Dl~  132 (178)
                      .+|+++.++|+.+|.....    ++..|=..|-.+|+||+|+.
T Consensus       220 ~sDgvVlvvDv~EGVmlntEr~ikhaiq~~~~i~vviNKiDRL  262 (971)
T KOG0468|consen  220 LSDGVVLVVDVAEGVMLNTERIIKHAIQNRLPIVVVINKVDRL  262 (971)
T ss_pred             hcceEEEEEEcccCceeeHHHHHHHHHhccCcEEEEEehhHHH
Confidence            4699999999988865432    23344566889999999974

>smart00053 DYNc Dynamin, GTPase

Probab=88.24  E-value=1.1  Score=35.91  Aligned_cols=61  Identities=20%  Similarity=0.107  Sum_probs=36.8

Q ss_pred             CCEEEEeCCcchhhh-----------------cccccccceEEEEEeCCCCCCCCc--CCCC---CCCceeEEEEecCCC
Q 030407           74 ADLLLCESGGDNLAA-----------------NFSRELADYIIYIIDVSGGDKIPR--KGGP---GITQADLLVINKTDL  131 (178)
Q Consensus        74 ~d~iiiEttG~~~~~-----------------~~~~~~ad~~I~VvD~~~~~~~~~--~~~~---qi~~adiiviNK~Dl  131 (178)
                      ||+.||.+.|..-.+                 .|.....+.+++|+|+..+.....  ....   .....-++|+||+|.
T Consensus       125 ~~ltLIDlPGl~~~~~~~~~~~~~~~i~~lv~~yi~~~~~IIL~Vvda~~d~~~~d~l~ia~~ld~~~~rti~ViTK~D~  204 (240)
T smart00053      125 LNLTLIDLPGITKVAVGDQPPDIEEQIKDMIKQFISKEECLILAVTPANVDLANSDALKLAKEVDPQGERTIGVITKLDL  204 (240)
T ss_pred             CceEEEeCCCccccccCCccHHHHHHHHHHHHHHHhCccCeEEEEEECCCCCCchhHHHHHHHHHHcCCcEEEEEECCCC
Confidence            899999999952110                 011112357899999876433222  1111   123456899999999


Q ss_pred             CCc
Q 030407          132 ASA  134 (178)
Q Consensus       132 ~~~  134 (178)
                      .++
T Consensus       205 ~~~  207 (240)
T smart00053      205 MDE  207 (240)
T ss_pred             CCc
Confidence            876

Large GTPases that mediate vesicle trafficking. Dynamin participates in the endocytic uptake of receptors, associated ligands, and plasma membrane following an exocytic event.

>PRK14491 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional

Probab=88.17  E-value=1.6  Score=39.63  Aligned_cols=78  Identities=22%  Similarity=0.152  Sum_probs=46.7

Q ss_pred             CHHHHHHhhcC-CcEEEEEe-----cCC-CchhHHHHHHcCCCCccceeecccCC-Cccccccc--ccccCHhHHHhhHh
Q 030407            1 MLALCKFLRDK-YSLAAVTN-----DIF-TKEDGEFLMRNGALPEERIRAVETGG-CPHAAIRE--DISINLGPLEELSN   70 (178)
Q Consensus         1 ~~~~~~~~~~~-~~vaVI~n-----d~g-~~iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~--dl~~~l~~l~~l~~   70 (178)
                      +++++++|+++ .|||+|..     |+- .+-|..++...|.    ..+.+.+.. +-.. .+.  +-...+..+...+.
T Consensus        27 ie~li~~L~~~G~rVavIKh~~h~~d~d~~gkDs~r~~~aGA----~~v~i~s~~~~a~~-~~~~~~~~~~l~~~l~~l~  101 (597)
T PRK14491         27 LEQLIPELNQRGLRLAVIKHAHHNFDVDQPGKDSYRLRKAGA----SQMLVASRVRWALM-TETPRDGEPELPHLLKQID  101 (597)
T ss_pred             HHHHHHHHHhCCceEEEEEcCCcCCCCCCCCchHHHHHHcCC----cEEEEEcCCeEEEE-EEcCcCCCcCHHHHHHhcC
Confidence            47889999875 99999999     333 3568888887776    344555555 3221 110  00112322222111


Q ss_pred             hCCCCEEEEeCCc
Q 030407           71 LFKADLLLCESGG   83 (178)
Q Consensus        71 ~~~~d~iiiEttG   83 (178)
                      ..++|+||||.-+
T Consensus       102 ~~~~D~vlvEG~k  114 (597)
T PRK14491        102 ADKVDIVLVEGFK  114 (597)
T ss_pred             cCCCCEEEEcCCC
Confidence            2368999999888

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=87.97  E-value=3.7  Score=35.77  Aligned_cols=86  Identities=14%  Similarity=0.114  Sum_probs=47.7

Q ss_pred             CCCCEEEEeCCcchhh---------hccc-ccccceEEEEEeCCCCCCCCcCCC---CCCCceeEEEEecCCCCCchhHh
Q 030407           72 FKADLLLCESGGDNLA---------ANFS-RELADYIIYIIDVSGGDKIPRKGG---PGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~---------~~~~-~~~ad~~I~VvD~~~~~~~~~~~~---~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .++|+|||+|.|.+-.         .... .....-..+|++++..........   ..+. .+-++++|.|-...    
T Consensus       298 ~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~~~~~f~~~~-~~~vI~TKlDet~~----  372 (424)
T PRK05703        298 RDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLKDIYKHFSRLP-LDGLIFTKLDETSS----  372 (424)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHHHHHHHhCCCC-CCEEEEeccccccc----
Confidence            3699999999995211         1111 001135678888866532211111   1122 35799999998654    


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCH
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGI  166 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi  166 (178)
                      ...+...+...  +.|+.+++  +|+++
T Consensus       373 ~G~i~~~~~~~--~lPv~yit--~Gq~V  396 (424)
T PRK05703        373 LGSILSLLIES--GLPISYLT--NGQRV  396 (424)
T ss_pred             ccHHHHHHHHH--CCCEEEEe--CCCCC
Confidence            23455555443  44777766  46775

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=87.89  E-value=3  Score=36.08  Aligned_cols=88  Identities=10%  Similarity=0.041  Sum_probs=47.0

Q ss_pred             CCCEEEEeCCcchhh---------hcccccccceEEEEEeCCCCCCCCcCCCCCCCc--eeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDNLA---------ANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ--ADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---------~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~--adiiviNK~Dl~~~~~~~~~~  141 (178)
                      ..|+|||.|+|.+..         ..+......-+-+|++++.........-.+++.  -+-++++|.|-.+.    +..
T Consensus       281 ~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~~f~~~~i~~~I~TKlDET~s----~G~  356 (407)
T COG1419         281 DCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIKQFSLFPIDGLIFTKLDETTS----LGN  356 (407)
T ss_pred             cCCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHHHhccCCcceeEEEcccccCc----hhH
Confidence            679999999995421         111111123355677776532211111112221  25789999997654    445


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHH
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                      +...+.+-  ..|+-+++  +|+.|.+
T Consensus       357 ~~s~~~e~--~~PV~YvT--~GQ~VPe  379 (407)
T COG1419         357 LFSLMYET--RLPVSYVT--NGQRVPE  379 (407)
T ss_pred             HHHHHHHh--CCCeEEEe--CCCCCCc
Confidence            55555543  33666665  4666554

>KOG0465 consensus Mitochondrial elongation factor [Translation, ribosomal structure and biogenesis]

Probab=87.76  E-value=1.4  Score=40.09  Aligned_cols=82  Identities=13%  Similarity=0.207  Sum_probs=49.9

Q ss_pred             CCCEEEEeCCcchhhhccccc----ccceEEEEEeCCCCCCCCcC-CCCCC---CceeEEEEecCCCCCchhHhHHHHHH
Q 030407           73 KADLLLCESGGDNLAANFSRE----LADYIIYIIDVSGGDKIPRK-GGPGI---TQADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~~~~----~ad~~I~VvD~~~~~~~~~~-~~~qi---~~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      .+.+-+|.|.| .+.-++.-+    ..|+.|+|+|+..|...+.. .-.|+   ..+-+..+||.|.+.+  .-...+.+
T Consensus       103 ~~~iNiIDTPG-HvDFT~EVeRALrVlDGaVlvl~aV~GVqsQt~tV~rQ~~ry~vP~i~FiNKmDRmGa--~~~~~l~~  179 (721)
T KOG0465|consen  103 DYRINIIDTPG-HVDFTFEVERALRVLDGAVLVLDAVAGVESQTETVWRQMKRYNVPRICFINKMDRMGA--SPFRTLNQ  179 (721)
T ss_pred             cceeEEecCCC-ceeEEEEehhhhhhccCeEEEEEcccceehhhHHHHHHHHhcCCCeEEEEehhhhcCC--ChHHHHHH
Confidence            57889999999 333333221    24999999999888654431 12232   3567999999999877  33233333


Q ss_pred             HHHhcCCCCCEEE
Q 030407          145 DALRMRDGGPFIF  157 (178)
Q Consensus       145 ~l~~~np~a~i~~  157 (178)
                      ....+++.+-++.
T Consensus       180 i~~kl~~~~a~vq  192 (721)
T KOG0465|consen  180 IRTKLNHKPAVVQ  192 (721)
T ss_pred             HHhhcCCchheeE
Confidence            3334455543333

>KOG3905 consensus Dynein light intermediate chain [Cell motility]

Probab=87.73  E-value=1.6  Score=36.91  Aligned_cols=56  Identities=18%  Similarity=0.221  Sum_probs=41.4

Q ss_pred             CCceeEEEEecCCCCCc-------hhHhHHHHHHHHHhc--CCCCCEEEEecccCCCHHHHHHHH
Q 030407          118 ITQADLLVINKTDLASA-------IGADLAVMERDALRM--RDGGPFIFAQVGWVIGIIFTLSIT  173 (178)
Q Consensus       118 i~~adiiviNK~Dl~~~-------~~~~~~~~~~~l~~~--np~a~i~~~SA~~g~gi~el~~~l  173 (178)
                      +....+||++|+|.++-       ..+....+..++|..  .-++..++||+|...+|+-|..+|
T Consensus       221 lGi~vlVV~TK~D~~s~leke~eyrDehfdfiq~~lRkFCLr~GaaLiyTSvKE~KNidllyKYi  285 (473)
T KOG3905|consen  221 LGIPVLVVCTKCDAVSVLEKEHEYRDEHFDFIQSHLRKFCLRYGAALIYTSVKETKNIDLLYKYI  285 (473)
T ss_pred             CCCcEEEEEeccchhhHhhhcchhhHHHHHHHHHHHHHHHHHcCceeEEeecccccchHHHHHHH
Confidence            45667999999999642       123445566666643  357899999999999999998875

>PLN00023 GTP-binding protein; Provisional

Probab=87.67  E-value=0.4  Score=40.40  Aligned_cols=76  Identities=17%  Similarity=0.210  Sum_probs=44.4

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCC----------C-CCceeEEEEec
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGP----------G-ITQADLLVINK  128 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~----------q-i~~adiiviNK  128 (178)
                      .+.+-|.+|.|..    +...+.. .++++|+|+|.+.......         ....          . -...-+||.||
T Consensus        82 ~v~LqIWDTAGqErfrsL~~~yyr-~AdgiILVyDITdr~SFenL~kWl~eI~~~~~~s~p~~s~~~~~~~ipIILVGNK  160 (334)
T PLN00023         82 DFFVELWDVSGHERYKDCRSLFYS-QINGVIFVHDLSQRRTKTSLQKWASEVAATGTFSAPLGSGGPGGLPVPYIVIGNK  160 (334)
T ss_pred             eEEEEEEECCCChhhhhhhHHhcc-CCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcccccccccccccCCCCcEEEEEEC
Confidence            4667889999931    2233333 5899999999987432110         0100          0 12457999999


Q ss_pred             CCCCCchh------HhHHHHHHHHHhc
Q 030407          129 TDLASAIG------ADLAVMERDALRM  149 (178)
Q Consensus       129 ~Dl~~~~~------~~~~~~~~~l~~~  149 (178)
                      +||.+...      ...+..+++.++.
T Consensus       161 ~DL~~~~~~r~~s~~~~e~a~~~A~~~  187 (334)
T PLN00023        161 ADIAPKEGTRGSSGNLVDAARQWVEKQ  187 (334)
T ss_pred             ccccccccccccccccHHHHHHHHHHc
Confidence            99975410      1245556666543

>KOG2485 consensus Conserved ATP/GTP binding protein [General function prediction only]

Probab=86.66  E-value=1.5  Score=36.63  Aligned_cols=78  Identities=18%  Similarity=0.081  Sum_probs=44.0

Q ss_pred             ccceEEEEEeCCCCCCCCcC-CCCCC-CceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEec--ccCCCHHHH
Q 030407           94 LADYIIYIIDVSGGDKIPRK-GGPGI-TQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQV--GWVIGIIFT  169 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~-~~~qi-~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA--~~g~gi~el  169 (178)
                      ..|.+|-|=|+.-+...... +..++ ...-|||+||.||+++  .+.....+.++..+-. .++..+.  .+..++..+
T Consensus        46 ~~D~iiEvrDaRiPLssrn~~~~~~~~~k~riiVlNK~DLad~--~~~k~~iq~~~~~~~~-~~~~~~c~~~~~~~v~~l  122 (335)
T KOG2485|consen   46 LVDCIIEVRDARIPLSSRNELFQDFLPPKPRIIVLNKMDLADP--KEQKKIIQYLEWQNLE-SYIKLDCNKDCNKQVSPL  122 (335)
T ss_pred             cccEEEEeeccccCCccccHHHHHhcCCCceEEEEecccccCc--hhhhHHHHHHHhhccc-chhhhhhhhhhhhccccH
Confidence            45889999998655432110 11111 3456999999999997  5666666666544322 3333333  333345555


Q ss_pred             HHHHh
Q 030407          170 LSITH  174 (178)
Q Consensus       170 ~~~l~  174 (178)
                      +..+.
T Consensus       123 ~~il~  127 (335)
T KOG2485|consen  123 LKILT  127 (335)
T ss_pred             HHHHH
Confidence            54443

>COG0480 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]

Probab=86.31  E-value=0.85  Score=42.19  Aligned_cols=61  Identities=18%  Similarity=0.253  Sum_probs=39.6

Q ss_pred             CCCEEEEeCCcchhhhc--ccc--cccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDNLAAN--FSR--ELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~--~~~--~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      ++.+=+|.|.| .+--+  ..+  ...|+.|.|+|+..|...+..    .......+-++++||.|.+..
T Consensus        75 ~~~iNlIDTPG-HVDFt~EV~rslrvlDgavvVvdaveGV~~QTEtv~rqa~~~~vp~i~fiNKmDR~~a  143 (697)
T COG0480          75 DYRINLIDTPG-HVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETVWRQADKYGVPRILFVNKMDRLGA  143 (697)
T ss_pred             ceEEEEeCCCC-ccccHHHHHHHHHhhcceEEEEECCCCeeecHHHHHHHHhhcCCCeEEEEECcccccc
Confidence            36777999999 22111  111  135999999999988654421    111234467999999999866

>KOG1143 consensus Predicted translation elongation factor [Translation, ribosomal structure and biogenesis]

Probab=86.24  E-value=2.8  Score=36.22  Aligned_cols=76  Identities=11%  Similarity=0.108  Sum_probs=46.1

Q ss_pred             ceEEEEEeCCCCCCCCc-CCC---CCCCceeEEEEecCCCCCchhHhHHHHHHHHHhc----------------------
Q 030407           96 DYIIYIIDVSGGDKIPR-KGG---PGITQADLLVINKTDLASAIGADLAVMERDALRM----------------------  149 (178)
Q Consensus        96 d~~I~VvD~~~~~~~~~-~~~---~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~----------------------  149 (178)
                      |....||.+..+-..-. .+.   .-+..+=+++++|+|+.++  .-+++..+.+..+                      
T Consensus       276 h~A~LvVsA~~Gi~~tTrEHLgl~~AL~iPfFvlvtK~Dl~~~--~~~~~tv~~l~nll~~~Gc~kvp~~Vt~~ddAv~A  353 (591)
T KOG1143|consen  276 HFACLVVSADRGITWTTREHLGLIAALNIPFFVLVTKMDLVDR--QGLKKTVKDLSNLLAKAGCTKVPKRVTTKDDAVKA  353 (591)
T ss_pred             ceEEEEEEcCCCCccccHHHHHHHHHhCCCeEEEEEeeccccc--hhHHHHHHHHHHHHhhcCccccceEeechHHHHHH
Confidence            66677777766543211 111   1245567999999999987  3333322222211                      


Q ss_pred             -----CC-CCCEEEEecccCCCHHHHHHHH
Q 030407          150 -----RD-GGPFIFAQVGWVIGIIFTLSIT  173 (178)
Q Consensus       150 -----np-~a~i~~~SA~~g~gi~el~~~l  173 (178)
                           .| -.|||.+|..+|+|+.-+-.+|
T Consensus       354 aq~~~s~nivPif~vSsVsGegl~ll~~fL  383 (591)
T KOG1143|consen  354 AQELCSGNIVPIFAVSSVSGEGLRLLRTFL  383 (591)
T ss_pred             HHHhccCCceeEEEEeecCccchhHHHHHH
Confidence                 11 1499999999999998765544

>TIGR00490 aEF-2 translation elongation factor aEF-2

Probab=86.15  E-value=0.8  Score=42.47  Aligned_cols=62  Identities=16%  Similarity=0.060  Sum_probs=38.1

Q ss_pred             CCCCEEEEeCCcch-hh-hcc-cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCC
Q 030407           72 FKADLLLCESGGDN-LA-ANF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLAS  133 (178)
Q Consensus        72 ~~~d~iiiEttG~~-~~-~~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~  133 (178)
                      .++.+.|+.|.|.. .. ... ....+|++++|+|+..+......    .......+-++++||+|...
T Consensus        84 ~~~~i~liDTPG~~~f~~~~~~al~~aD~~llVvda~~g~~~~t~~~~~~~~~~~~p~ivviNKiD~~~  152 (720)
T TIGR00490        84 NEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCAVEGVMPQTETVLRQALKENVKPVLFINKVDRLI  152 (720)
T ss_pred             CceEEEEEeCCCccccHHHHHHHHHhcCEEEEEEecCCCCCccHHHHHHHHHHcCCCEEEEEEChhccc
Confidence            36889999999931 01 111 11246999999999876433211    10112234589999999964

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.

>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.06  E-value=3  Score=37.03  Aligned_cols=100  Identities=14%  Similarity=0.157  Sum_probs=57.1

Q ss_pred             HhhCCCCEEEEeCCcchhh-hccc--------ccccceEEEEEeCCCCCCCCc---C------CCCCCCceeEEEEecCC
Q 030407           69 SNLFKADLLLCESGGDNLA-ANFS--------RELADYIIYIIDVSGGDKIPR---K------GGPGITQADLLVINKTD  130 (178)
Q Consensus        69 ~~~~~~d~iiiEttG~~~~-~~~~--------~~~ad~~I~VvD~~~~~~~~~---~------~~~qi~~adiiviNK~D  130 (178)
                      .+..+||+|+|.|.|-..- ++..        ....|.+++|-.+--|.+..+   +      ...+-+.-|-++++|.|
T Consensus       462 a~~~gfDVvLiDTAGR~~~~~~lm~~l~k~~~~~~pd~i~~vgealvg~dsv~q~~~fn~al~~~~~~r~id~~~ltk~d  541 (587)
T KOG0781|consen  462 ARNQGFDVVLIDTAGRMHNNAPLMTSLAKLIKVNKPDLILFVGEALVGNDSVDQLKKFNRALADHSTPRLIDGILLTKFD  541 (587)
T ss_pred             HHhcCCCEEEEeccccccCChhHHHHHHHHHhcCCCceEEEehhhhhCcHHHHHHHHHHHHHhcCCCccccceEEEEecc
Confidence            4466899999999993110 1111        112388998877654433211   1      11244556899999999


Q ss_pred             CCCchhHhHHHHHHHHHhcCCCCCEEEEe------cccCCCHHHHHHHH
Q 030407          131 LASAIGADLAVMERDALRMRDGGPFIFAQ------VGWVIGIIFTLSIT  173 (178)
Q Consensus       131 l~~~~~~~~~~~~~~l~~~np~a~i~~~S------A~~g~gi~el~~~l  173 (178)
                      .++.   .+..+....-  -.+.||+++-      -+...+++.+...|
T Consensus       542 tv~d---~vg~~~~m~y--~~~~pi~fvg~gqtysdlr~l~v~~vv~~l  585 (587)
T KOG0781|consen  542 TVDD---KVGAAVSMVY--ITGKPILFVGVGQTYSDLRKLNVKAVVATL  585 (587)
T ss_pred             chhh---HHHHHhhhee--ecCCceEEEecCcchhhhhhccHHHHHHHh
Confidence            8866   3333333222  2467888763      33445555555444

>KOG1954 consensus Endocytosis/signaling protein EHD1 [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=85.75  E-value=1.1  Score=38.63  Aligned_cols=68  Identities=19%  Similarity=0.242  Sum_probs=39.7

Q ss_pred             CEEEEeCCcc-h-----hhhccc--------ccccceEEEEEeCCCCCCCCcCCCC---C---CCceeEEEEecCCCCCc
Q 030407           75 DLLLCESGGD-N-----LAANFS--------RELADYIIYIIDVSGGDKIPRKGGP---G---ITQADLLVINKTDLASA  134 (178)
Q Consensus        75 d~iiiEttG~-~-----~~~~~~--------~~~ad~~I~VvD~~~~~~~~~~~~~---q---i~~adiiviNK~Dl~~~  134 (178)
                      .+=||||.|+ +     +...|.        .+.+|.++.++|+-..+ ....+.+   +   -+.--.||+||+|.++.
T Consensus       148 ~vtiVdtPGILsgeKQrisR~ydF~~v~~WFaeR~D~IiLlfD~hKLD-IsdEf~~vi~aLkG~EdkiRVVLNKADqVdt  226 (532)
T KOG1954|consen  148 SVTIVDTPGILSGEKQRISRGYDFTGVLEWFAERVDRIILLFDAHKLD-ISDEFKRVIDALKGHEDKIRVVLNKADQVDT  226 (532)
T ss_pred             heeeeccCcccccchhcccccCChHHHHHHHHHhccEEEEEechhhcc-ccHHHHHHHHHhhCCcceeEEEeccccccCH
Confidence            3568999994 1     111111        13469999999985432 2111111   1   12334899999999988


Q ss_pred             hhHhHHHHHHH
Q 030407          135 IGADLAVMERD  145 (178)
Q Consensus       135 ~~~~~~~~~~~  145 (178)
                        .++-++...
T Consensus       227 --qqLmRVyGA  235 (532)
T KOG1954|consen  227 --QQLMRVYGA  235 (532)
T ss_pred             --HHHHHHHHH
Confidence              676665533

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

Probab=85.27  E-value=1.5  Score=35.33  Aligned_cols=27  Identities=15%  Similarity=-0.027  Sum_probs=23.4

Q ss_pred             CCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          151 DGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       151 p~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ...|++..||+++.|+++|++.+...+
T Consensus       239 ~~~pv~~gSa~~~~G~~~ll~~~~~~~  265 (268)
T cd04170         239 LLVPVLCGSALTNIGVRELLDALVHLL  265 (268)
T ss_pred             CEEEEEEeeCCCCcCHHHHHHHHHHhC
Confidence            446899999999999999999987653

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

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=84.98  E-value=2.9  Score=31.53  Aligned_cols=73  Identities=21%  Similarity=0.225  Sum_probs=42.9

Q ss_pred             CHHHHHHhhcC-CcEEEEEecCC------CchhHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhHhhC
Q 030407            1 MLALCKFLRDK-YSLAAVTNDIF------TKEDGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNLF   72 (178)
Q Consensus         1 ~~~~~~~~~~~-~~vaVI~nd~g------~~iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~   72 (178)
                      ++++++.|+.+ +|||+|--.-.      .+-|.-+..+.|.    ..+-+.++. ---++-..+  ..|+.+..+....
T Consensus        19 ie~lv~~L~~~G~rVa~iKH~hh~~~~D~~GkDs~r~~~aGa----~~~v~~s~~~~~~~~~~~~--~~L~~vl~~l~~~   92 (161)
T COG1763          19 IEKLVRKLKARGYRVATVKHAHHDFDLDKPGKDTYRHRKAGA----DQVVVASDHRTALMTRTPD--RDLDAVLSRLDPL   92 (161)
T ss_pred             HHHHHHHHHhCCcEEEEEEecCCCCCCCCCCCccchhhcccc----ceEEEecCCEEEEEEecCC--cCHHHHHHhcCcc
Confidence            46888999875 99999986533      2557777777665    333333444 111110111  3455555544344


Q ss_pred             CCCEEEEe
Q 030407           73 KADLLLCE   80 (178)
Q Consensus        73 ~~d~iiiE   80 (178)
                       +|+++||
T Consensus        93 -~D~vLVE   99 (161)
T COG1763          93 -LDLVLVE   99 (161)
T ss_pred             -cCEEEEe
Confidence             7999999

>PF02606 LpxK: Tetraacyldisaccharide-1-P 4'-kinase; InterPro: IPR003758 Tetraacyldisaccharide 4'-kinase phosphorylates the 4'-position of a tetraacyldisaccharide 1-phosphate precursor (DS-1-P) of lipid A, but the enzyme has not yet been purified because of instability []

Probab=84.46  E-value=9.3  Score=32.08  Aligned_cols=124  Identities=15%  Similarity=0.181  Sum_probs=64.1

Q ss_pred             HHHHHHhhcC-CcEEEEEecCCCchhH--HHHHHcCC--CCccceeecccCC-CcccccccccccCHhHHHhhHhhCCCC
Q 030407            2 LALCKFLRDK-YSLAAVTNDIFTKEDG--EFLMRNGA--LPEERIRAVETGG-CPHAAIREDISINLGPLEELSNLFKAD   75 (178)
Q Consensus         2 ~~~~~~~~~~-~~vaVI~nd~g~~iD~--~li~~~~~--~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~~~d   75 (178)
                      ..++++|+++ +|+|||.--.|-.-.+  .++...+.  ..+|+-..+..-+ |+-. +..|   -..+...+.+.+++|
T Consensus        55 ~~L~~~L~~~G~~~~IlSRGYg~~~~~~~~~v~~~~~~~~~GDEp~lla~~~~~~V~-V~~d---R~~~~~~~~~~~~~d  130 (326)
T PF02606_consen   55 IWLARLLQARGYRPAILSRGYGRKSKGEPILVSDGSDAEEVGDEPLLLARKLPVPVI-VGPD---RVAAARAALKEFPAD  130 (326)
T ss_pred             HHHHHHHHhcCCceEEEcCCCCCCCCCCeEEEeCCCChhhhcCHHHHHHHhcCCcEE-EeCc---HHHHHHHHHHHCCCC
Confidence            3567888765 9999998877721111  00100000  0011222332222 3322 2111   124555555555688


Q ss_pred             EEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCc--------CCCCCCCceeEEEEecCCCCCc
Q 030407           76 LLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPR--------KGGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        76 ~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~--------~~~~qi~~adiiviNK~Dl~~~  134 (178)
                      +|+.+= |  +....  -..|.-|+++|+.++.....        .-...++.||++++||.+....
T Consensus       131 viilDD-G--fQh~~--L~rDl~Ivl~D~~~~~gng~lLPaG~LREp~~~l~rAD~vi~~~~~~~~~  192 (326)
T PF02606_consen  131 VIILDD-G--FQHRR--LKRDLDIVLVDADRPFGNGFLLPAGPLREPLSALKRADAVIVTGCDASDP  192 (326)
T ss_pred             EEEEcC-C--ccccc--ccCCcEEEEEeCCCCCcCCccCCCCcccCChhHhCcccEEEEcCCCcchh
Confidence            888542 2  21111  11388999999876532211        1123578899999999998655

This enzyme is involved in the synthesis of lipid A portion of the bacterial lipopolysaccharide layer (LPS).; GO: 0005524 ATP binding, 0009029 tetraacyldisaccharide 4'-kinase activity, 0009245 lipid A biosynthetic process

>KOG0074 consensus GTP-binding ADP-ribosylation factor-like protein ARL3 [General function prediction only]

Probab=83.48  E-value=0.36  Score=35.98  Aligned_cols=80  Identities=18%  Similarity=0.099  Sum_probs=48.9

Q ss_pred             ccceEEEEEeCCCCCCCCc---CC------CCCCCceeEEEEecCCCCCchhHhHHHHHHH--HHhcC-CCCCEEEEecc
Q 030407           94 LADYIIYIIDVSGGDKIPR---KG------GPGITQADLLVINKTDLASAIGADLAVMERD--ALRMR-DGGPFIFAQVG  161 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~---~~------~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~--l~~~n-p~a~i~~~SA~  161 (178)
                      ..|.+|+|+|.++......   .+      ...-+.|..|..||-|++.+  +..+.....  +..+. ....|-.+||+
T Consensus        85 nvd~lIyVIDS~D~krfeE~~~el~ELleeeKl~~vpvlIfankQdllta--a~~eeia~klnl~~lrdRswhIq~csal  162 (185)
T KOG0074|consen   85 NVDGLIYVIDSTDEKRFEEISEELVELLEEEKLAEVPVLIFANKQDLLTA--AKVEEIALKLNLAGLRDRSWHIQECSAL  162 (185)
T ss_pred             ccceEEEEEeCCchHhHHHHHHHHHHHhhhhhhhccceeehhhhhHHHhh--cchHHHHHhcchhhhhhceEEeeeCccc
Confidence            4699999999754321111   01      11234578999999999877  333332211  11111 12477889999


Q ss_pred             cCCCHHHHHHHHhh
Q 030407          162 WVIGIIFTLSITHY  175 (178)
Q Consensus       162 ~g~gi~el~~~l~~  175 (178)
                      +++|+..-.+++..
T Consensus       163 s~eg~~dg~~wv~s  176 (185)
T KOG0074|consen  163 SLEGSTDGSDWVQS  176 (185)
T ss_pred             cccCccCcchhhhc
Confidence            99999887777653

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=82.39  E-value=3.3  Score=36.13  Aligned_cols=90  Identities=12%  Similarity=0.055  Sum_probs=50.1

Q ss_pred             hCCCCEEEEeCCcchhh---------hc---ccccccceEEEEEeCCCCCCCCcCCCC--CCCceeEEEEecCCCCCchh
Q 030407           71 LFKADLLLCESGGDNLA---------AN---FSRELADYIIYIIDVSGGDKIPRKGGP--GITQADLLVINKTDLASAIG  136 (178)
Q Consensus        71 ~~~~d~iiiEttG~~~~---------~~---~~~~~ad~~I~VvD~~~~~~~~~~~~~--qi~~adiiviNK~Dl~~~~~  136 (178)
                      ..++|+|||.|.|.+..         ..   .......-.++|+|++.+.........  ..-..+-+|++|.|-...  
T Consensus       297 ~~~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~~~~f~~~~~~glIlTKLDEt~~--  374 (432)
T PRK12724        297 RDGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTVLKAYESLNYRRILLTKLDEADF--  374 (432)
T ss_pred             hCCCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHHHHHhcCCCCCEEEEEcccCCCC--
Confidence            46899999999995311         00   101012357899999876522111100  111247999999998654  


Q ss_pred             HhHHHHHHHHHhcCCCCCEEEEecccCCCHHH
Q 030407          137 ADLAVMERDALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       137 ~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                        ...+.......  +.|+.+++  +|+++.+
T Consensus       375 --~G~il~i~~~~--~lPI~ylt--~GQ~VPe  400 (432)
T PRK12724        375 --LGSFLELADTY--SKSFTYLS--VGQEVPF  400 (432)
T ss_pred             --ccHHHHHHHHH--CCCEEEEe--cCCCCCC
Confidence              23344444433  34776665  3555543

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

Probab=82.17  E-value=1.2  Score=40.01  Aligned_cols=81  Identities=16%  Similarity=0.012  Sum_probs=49.4

Q ss_pred             ccceEEEEEeCCCCCCCC---cCC--------CCCCCceeEEEEecCCCCCchhHhHHH-HHHHHHhcCCC-CCEEEEec
Q 030407           94 LADYIIYIIDVSGGDKIP---RKG--------GPGITQADLLVINKTDLASAIGADLAV-MERDALRMRDG-GPFIFAQV  160 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~---~~~--------~~qi~~adiiviNK~Dl~~~~~~~~~~-~~~~l~~~np~-a~i~~~SA  160 (178)
                      .+|.+..+....+.....   .++        ....+.+.|+|.||+|+.+......+. +...+.+ ++. -.-+.+||
T Consensus        79 kA~vi~lvyavd~~~T~D~ist~WLPlir~~~~~~~~~PVILvGNK~d~~~~~~~s~e~~~~pim~~-f~EiEtciecSA  157 (625)
T KOG1707|consen   79 KADVICLVYAVDDESTVDRISTKWLPLIRQLFGDYHETPVILVGNKSDNGDNENNSDEVNTLPIMIA-FAEIETCIECSA  157 (625)
T ss_pred             hcCEEEEEEecCChHHhhhhhhhhhhhhhcccCCCccCCEEEEeeccCCccccccchhHHHHHHHHH-hHHHHHHHhhhh
Confidence            357777777766543221   111        123678899999999998652121122 2222221 221 25689999


Q ss_pred             ccCCCHHHHHHHHhh
Q 030407          161 GWVIGIIFTLSITHY  175 (178)
Q Consensus       161 ~~g~gi~el~~~l~~  175 (178)
                      ++-.++.|+|-+-++
T Consensus       158 ~~~~n~~e~fYyaqK  172 (625)
T KOG1707|consen  158 LTLANVSELFYYAQK  172 (625)
T ss_pred             hhhhhhHhhhhhhhh
Confidence            999999999977654

>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=81.18  E-value=0.54  Score=36.20  Aligned_cols=62  Identities=27%  Similarity=0.266  Sum_probs=33.3

Q ss_pred             CCCEEEEeCCcch-hhhccc-----ccccceEEEEEeCCCCCCCCcC------------CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-LAANFS-----RELADYIIYIIDVSGGDKIPRK------------GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~~~-----~~~ad~~I~VvD~~~~~~~~~~------------~~~qi~~adiiviNK~Dl~~~  134 (178)
                      +..+-+|+..|-. +...+.     ...+.++|+|+|++........            ....-..+-+|+.||.|+..+
T Consensus        48 ~~~~~lvD~PGH~rlr~~~~~~~~~~~~~k~IIfvvDSs~~~~~~~~~Ae~Ly~iL~~~~~~~~~~piLIacNK~Dl~~A  127 (181)
T PF09439_consen   48 GKKLRLVDIPGHPRLRSKLLDELKYLSNAKGIIFVVDSSTDQKELRDVAEYLYDILSDTEVQKNKPPILIACNKQDLFTA  127 (181)
T ss_dssp             GTCECEEEETT-HCCCHHHHHHHHHHGGEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHCCTT--EEEEEEE-TTSTT-
T ss_pred             CCEEEEEECCCcHHHHHHHHHhhhchhhCCEEEEEEeCccchhhHHHHHHHHHHHHHhhhhccCCCCEEEEEeCcccccc
Confidence            4567788999931 221111     1236789999999752110000            001124567999999999875

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.

>cd01850 CDC_Septin CDC/Septin

Probab=80.41  E-value=3  Score=34.05  Aligned_cols=64  Identities=16%  Similarity=0.103  Sum_probs=35.2

Q ss_pred             cceEEEEEeCCC-CCCCCc-CCCCCC--CceeEEEEecCCCCCchhHhHHHHHHHHHhcC--CCCCEEEEec
Q 030407           95 ADYIIYIIDVSG-GDKIPR-KGGPGI--TQADLLVINKTDLASAIGADLAVMERDALRMR--DGGPFIFAQV  160 (178)
Q Consensus        95 ad~~I~VvD~~~-~~~~~~-~~~~qi--~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~n--p~a~i~~~SA  160 (178)
                      +|.++++++++. +....+ ....++  ..+-++|+||+|+.++  .++..+.+.+++.-  -+.++|..+.
T Consensus       115 vh~~ly~i~~~~~~l~~~D~~~lk~l~~~v~vi~VinK~D~l~~--~e~~~~k~~i~~~l~~~~i~~~~~~~  184 (276)
T cd01850         115 VHACLYFIEPTGHGLKPLDIEFMKRLSKRVNIIPVIAKADTLTP--EELKEFKQRIMEDIEEHNIKIYKFPE  184 (276)
T ss_pred             eEEEEEEEeCCCCCCCHHHHHHHHHHhccCCEEEEEECCCcCCH--HHHHHHHHHHHHHHHHcCCceECCCC
Confidence            478889998864 221110 000001  3467999999999876  55544444333221  2356776554

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.

>KOG0077 consensus Vesicle coat complex COPII, GTPase subunit SAR1 [Intracellular trafficking, secretion, and vesicular transport]

Probab=80.17  E-value=0.65  Score=35.47  Aligned_cols=80  Identities=15%  Similarity=0.124  Sum_probs=47.1

Q ss_pred             ccceEEEEEeCCCCCCCCcCCC--------CC-CCceeEEEEecCCCCCchhHhHHHHHHHH--Hhc----C------C-
Q 030407           94 LADYIIYIIDVSGGDKIPRKGG--------PG-ITQADLLVINKTDLASAIGADLAVMERDA--LRM----R------D-  151 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~~~--------~q-i~~adiiviNK~Dl~~~~~~~~~~~~~~l--~~~----n------p-  151 (178)
                      .+|++|++||+-..+.......        +. -..+-+|..||+|...+  ...++++..+  ...    +      + 
T Consensus        87 ~v~~iv~lvda~d~er~~es~~eld~ll~~e~la~vp~lilgnKId~p~a--~se~~l~~~l~l~~~t~~~~~v~~~~~~  164 (193)
T KOG0077|consen   87 QVDAIVYLVDAYDQERFAESKKELDALLSDESLATVPFLILGNKIDIPYA--ASEDELRFHLGLSNFTTGKGKVNLTDSN  164 (193)
T ss_pred             hhceeEeeeehhhHHHhHHHHHHHHHHHhHHHHhcCcceeecccccCCCc--ccHHHHHHHHHHHHHhcccccccccCCC
Confidence            4689999999976543322110        11 23457899999999876  3333332211  111    0      1 


Q ss_pred             --CCCEEEEecccCCCHHHHHHHHhh
Q 030407          152 --GGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       152 --~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                        -.+++.+|...+.|--+-|.++..
T Consensus       165 ~rp~evfmcsi~~~~gy~e~fkwl~q  190 (193)
T KOG0077|consen  165 VRPLEVFMCSIVRKMGYGEGFKWLSQ  190 (193)
T ss_pred             CCeEEEEEEEEEccCccceeeeehhh
Confidence              136788888888886666666543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	178
2hf9_A	226	Crystal Structure Of Hypb From Methanocaldococcus J		2e-12
2hf8_A	226	Crystal Structure Of Hypb From Methanocaldococcus J		3e-11
2wsm_A	221	Crystal Structure Of Hydrogenase Maturation Factor		2e-06

>pdb|2HF9|A Chain A, Crystal Structure Of Hypb From Methanocaldococcus Jannaschii In The Triphosphate Form Length = 226

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 54/144 (37%), Positives = 78/144 (54%), Gaps = 13/144 (9%)
Query: 8   LRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEE 67
           L+DKY +A +  D+  K D E + ++GA    ++  + TG   H     D  +    LE+
Sbjct: 62  LKDKYKIACIAGDVIAKFDAERMEKHGA----KVVPLNTGKECHL----DAHLVGHALED 113
Query: 68  LSNLFKADLLLCESGGDNLA-ANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ-ADLLV 125
           L NL + DLL  E+ G+ +  A+F       I+ I    G D I +   PGI + ADL+V
Sbjct: 114 L-NLDEIDLLFIENVGNLICPADFDLGTHKRIVVISTTEGDDTIEKH--PGIMKTADLIV 170
Query: 126 INKTDLASAIGADLAVMERDALRM 149
           INK DLA A+GAD+  ME DA R+
Sbjct: 171 INKIDLADAVGADIKKMENDAKRI 194

>pdb|2HF8|A Chain A, Crystal Structure Of Hypb From Methanocaldococcus Jannaschii In The Triphosphate Form, In Complex With Zinc Length = 226

Iteration: 1
 Score = 64.3 bits (155), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 53/144 (36%), Positives = 76/144 (52%), Gaps = 13/144 (9%)
Query: 8   LRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEE 67
           L+DKY +A +  D+  K D E   ++GA    ++  + TG   H     D  +    LE+
Sbjct: 62  LKDKYKIACIAGDVIAKFDAERXEKHGA----KVVPLNTGKECHL----DAHLVGHALED 113
Query: 68  LSNLFKADLLLCESGGDNLA-ANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ-ADLLV 125
           L NL + DLL  E+ G+ +  A+F       I+ I    G D I +   PGI + ADL+V
Sbjct: 114 L-NLDEIDLLFIENVGNLICPADFDLGTHKRIVVISTTEGDDTIEKH--PGIXKTADLIV 170
Query: 126 INKTDLASAIGADLAVMERDALRM 149
           INK DLA A+GAD+   E DA R+
Sbjct: 171 INKIDLADAVGADIKKXENDAKRI 194

>pdb|2WSM|A Chain A, Crystal Structure Of Hydrogenase Maturation Factor Hypb From Archaeoglobus Fulgidus Length = 221

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 45/138 (32%), Positives = 69/138 (50%), Gaps = 13/138 (9%)
Query: 10  DKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELS 69
           ++  + A+  D+ +K D E + R G   E    A+ TG   H     D  +    L++ S
Sbjct: 56  NEVKIGAMLGDVVSKADYERVRRFGIKAE----AISTGKECHL----DAHMIYHRLKKFS 107
Query: 70  NLFKADLLLCESGGDNLAANFSRELAD-YIIYIIDVSGGDKIPRKGGPGITQADLLVINK 128
           +    DLLL E+ G NL      +L + Y + ++ V+ GD +  K       ADL+VINK
Sbjct: 108 D---CDLLLIENVG-NLICPVDFDLGENYRVVMVSVTEGDDVVEKHPEIFRVADLIVINK 163
Query: 129 TDLASAIGADLAVMERDA 146
             LA A+GAD+  M+ DA
Sbjct: 164 VALAEAVGADVEKMKADA 181

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	178
2hf9_A	226	Probable hydrogenase nickel incorporation protein	4e-71
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	3e-69

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A* Length = 226

 Score =  213 bits (545), Expect = 4e-71
 Identities = 50/160 (31%), Positives = 76/160 (47%), Gaps = 9/160 (5%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           +  L   L+DKY +A +  D+  K D E + ++GA    ++  + TG   H     D  +
Sbjct: 55  IEKLIDNLKDKYKIACIAGDVIAKFDAERMEKHGA----KVVPLNTGKECHL----DAHL 106

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
               LE+L NL + DLL  E+ G+ +            I +I  + GD    K    +  
Sbjct: 107 VGHALEDL-NLDEIDLLFIENVGNLICPADFDLGTHKRIVVISTTEGDDTIEKHPGIMKT 165

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQV 160
           ADL+VINK DLA A+GAD+  ME DA R+      +   +
Sbjct: 166 ADLIVINKIDLADAVGADIKKMENDAKRINPDAEVVLLSL 205

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus} Length = 221

 Score =  208 bits (532), Expect = 3e-69
 Identities = 42/160 (26%), Positives = 73/160 (45%), Gaps = 11/160 (6%)

Query: 1   MLALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDISI 60
           +    + + ++  + A+  D+ +K D E + R G     +  A+ TG   H     D  +
Sbjct: 47  IERTIERIGNEVKIGAMLGDVVSKADYERVRRFGI----KAEAISTGKECHL----DAHM 98

Query: 61  NLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQ 120
               L++ S+    DLLL E+ G+ +         +Y + ++ V+ GD +  K       
Sbjct: 99  IYHRLKKFSDC---DLLLIENVGNLICPVDFDLGENYRVVMVSVTEGDDVVEKHPEIFRV 155

Query: 121 ADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQV 160
           ADL+VINK  LA A+GAD+  M+ DA  +      I   +
Sbjct: 156 ADLIVINKVALAEAVGADVEKMKADAKLINPRAKIIEMDL 195

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	178
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	99.8
2hf9_A	226	Probable hydrogenase nickel incorporation protein	99.75
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	99.75
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	99.71
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	99.65
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	99.48
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	99.39
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	99.33
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	98.97
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	98.95
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	98.93
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	98.86
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	98.86
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	98.85
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	98.83
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	98.82
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	98.82
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	98.82
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	98.81
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	98.8
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	98.77
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	98.77
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	98.76
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	98.74
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	98.74
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	98.74
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	98.74
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	98.72
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	98.71
4dcu_A	456	GTP-binding protein ENGA; GTPase, GDP, protein bin	98.71
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	98.71
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	98.7
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	98.7
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	98.7
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	98.7
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	98.7
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	98.7
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	98.69
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	98.69
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	98.69
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	98.69
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	98.69
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	98.69
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	98.68
2fh5_B	214	SR-beta, signal recognition particle receptor beta	98.68
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	98.68
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	98.67
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	98.67
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	98.66
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	98.66
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	98.66
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	98.66
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	98.66
3o47_A	329	ADP-ribosylation factor GTPase-activating protein	98.65
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	98.65
3lvq_E	497	ARF-GAP with SH3 domain, ANK repeat and PH domain	98.64
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	98.64
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	98.64
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	98.64
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	98.63
3gee_A	476	MNME, tRNA modification GTPase MNME; G protein, cy	98.63
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	98.63
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	98.63
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	98.63
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	98.62
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	98.62
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	98.62
1wb1_A	482	Translation elongation factor SELB; selenocysteine	98.62
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	98.62
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	98.62
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	98.61
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	98.6
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	98.6
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	98.6
3sjy_A	403	Translation initiation factor 2 subunit gamma; zin	98.6
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	98.6
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	98.59
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	98.59
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	98.58
1xzp_A	482	Probable tRNA modification GTPase TRME; GTP-bindin	98.58
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	98.57
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	98.57
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	98.57
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	98.57
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	98.56
4djt_A	218	GTP-binding nuclear protein GSP1; structural genom	98.55
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	98.55
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	98.54
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	98.54
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	98.54
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	98.54
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	98.54
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	98.53
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	98.53
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	98.53
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	98.52
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	98.52
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	98.51
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	98.5
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	98.5
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	98.5
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	98.49
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	98.48
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	98.48
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	98.47
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	98.47
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	98.47
3geh_A	462	MNME, tRNA modification GTPase MNME; G protein, U3	98.47
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	98.46
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	98.46
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	98.45
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	98.44
3th5_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	97.82
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	98.44
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	98.43
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	98.43
1s0u_A	408	EIF-2-gamma, translation initiation factor 2 gamma	98.42
3l0i_B	199	RAS-related protein RAB-1A; GEF-GDF-RAB complex, G	98.41
2hjg_A	436	GTP-binding protein ENGA; GTPase ENGA KH-domain, h	98.41
1kk1_A	410	EIF2gamma; initiation of translation; HET: GNP; 1.	98.41
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	98.41
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	98.4
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	98.4
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	98.34
3c5h_A	255	Glucocorticoid receptor DNA-binding factor 1; RAS,	98.34
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	98.32
3j2k_7	439	ERF3, eukaryotic polypeptide chain release factor	98.31
3cnl_A	262	YLQF, putative uncharacterized protein; circular p	98.29
3cb4_D	599	GTP-binding protein LEPA; GTPase, OB-fold, membran	98.28
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	98.27
2ywe_A	600	GTP-binding protein LEPA; G domain, beta-barrel, f	98.27
3tr5_A	528	RF-3, peptide chain release factor 3; protein synt	98.26
3a1s_A	258	Iron(II) transport protein B; FEOB, iron transport	98.25
3p26_A	483	Elongation factor 1 alpha-like protein; GTP/GDP bi	98.25
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	98.25
3i8s_A	274	Ferrous iron transport protein B; GTPase, GPCR, ir	98.24
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	98.24
1g7s_A	594	Translation initiation factor IF2/EIF5B; translati	98.23
1puj_A	282	YLQF, conserved hypothetical protein YLQF; structu	98.23
2c78_A	405	Elongation factor TU-A; hydrolase, GTPase, transla	98.22
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	98.22
2elf_A	370	Protein translation elongation factor 1A; tRNA, py	98.21
1zun_B	434	Sulfate adenylate transferase, subunit 1/adenylyls	98.2
1d2e_A	397	Elongation factor TU (EF-TU); G-protein, beta-barr	98.19
1lnz_A	342	SPO0B-associated GTP-binding protein; GTPase, OBG,	98.18
3dpu_A	535	RAB family protein; roccor, G-domain, COR, GTP-bin	98.15
3llu_A	196	RAS-related GTP-binding protein C; structural geno	98.14
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	98.14
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	98.13
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	98.13
2wji_A	165	Ferrous iron transport protein B homolog; membrane	98.11
1zo1_I	501	IF2, translation initiation factor 2; E. coli, rib	98.08
3izy_P	537	Translation initiation factor IF-2, mitochondrial;	98.08
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	98.05
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	98.05
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	98.04
1jny_A	435	EF-1-alpha, elongation factor 1-alpha, EF-TU, TUF-	98.03
3izq_1	611	HBS1P, elongation factor 1 alpha-like protein; NO-	98.03
3h2y_A	368	GTPase family protein; GTP-binding protein YQEH, p	98.02
3avx_A	1289	Elongation factor TS, elongation factor TU, linke	98.01
3ec1_A	369	YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase	98.01
2j69_A	695	Bacterial dynamin-like protein; FZO, FZL, GTPase,	97.99
3mca_A	592	HBS1, elongation factor 1 alpha-like protein; prot	97.98
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	97.96
3qq5_A	423	Small GTP-binding protein; hydrogenase, H-cluster,	97.95
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	97.95
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	97.92
2hjg_A	436	GTP-binding protein ENGA; GTPase ENGA KH-domain, h	97.91
1r5b_A	467	Eukaryotic peptide chain release factor GTP-bindi	97.89
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	97.89
3l82_B	227	F-box only protein 4; TRFH domain, helix, GTPase d	97.84
1f60_A	458	Elongation factor EEF1A; protein-protein complex,	97.83
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	97.83
2qpt_A	550	EH domain-containing protein-2; protein-nucleotide	97.82
3t5d_A	274	Septin-7; GTP-binding protein, cytoskeleton, signa	97.81
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	97.81
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	97.76
2x2e_A	353	Dynamin-1; nitration, hydrolase, membrane fission,	97.73
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	97.72
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	97.72
1dar_A	691	EF-G, elongation factor G; ribosomal translocase,	97.7
3r7w_A	307	Gtpase1, GTP-binding protein GTR1; RAG gtpases, GT	97.67
3zvr_A	772	Dynamin-1; hydrolase, DRP1, DRP, endocytosis, mito	97.66
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	97.65
2h5e_A	529	Peptide chain release factor RF-3; beta barrel, tr	97.64
2rdo_7	704	EF-G, elongation factor G; elongation factor G, EF	97.62
1cip_A	353	Protein (guanine nucleotide-binding protein alpha-	97.62
4dcu_A	456	GTP-binding protein ENGA; GTPase, GDP, protein bin	97.61
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	97.54
2xtz_A	354	Guanine nucleotide-binding protein alpha-1 subuni;	97.52
2xex_A	693	Elongation factor G; GTPase, translation, biosynth	97.47
1zcb_A	362	G alpha I/13; GTP-binding, lipoprotein, membrane,	97.46
3vqt_A	548	RF-3, peptide chain release factor 3; translation,	97.43
1udx_A	416	The GTP-binding protein OBG; TGS domain, riken str	97.4
3l2o_B	312	F-box only protein 4; small G protein fold, UBL co	97.35
2dy1_A	665	Elongation factor G; translocation, GTP complex, s	97.33
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	97.21
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	97.2
1azs_C	402	GS-alpha; complex (lyase/hydrolase), hydrolase, si	97.19
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	97.18
3j25_A	638	Tetracycline resistance protein TETM; antibiotic r	97.12
3ohm_A	327	Guanine nucleotide-binding protein G(Q) subunit A;	97.02
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	97.02
3r7w_B	331	Gtpase2, GTP-binding protein GTR2; RAG gtpases, GT	96.92
4fid_A	340	G protein alpha subunit; RAS-like domain, all-heli	96.87
1nrj_B	218	SR-beta, signal recognition particle receptor beta	96.66
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	96.57
3t34_A	360	Dynamin-related protein 1A, linker, dynamin-relat	96.38
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	96.35
4fn5_A	709	EF-G 1, elongation factor G 1; translation, transl	96.27
2qag_A	361	Septin-2, protein NEDD5; cell cycle, cell division	96.13
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	96.09
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.88
1wxq_A	397	GTP-binding protein; structural genomics, riken st	94.98
2ged_A	193	SR-beta, signal recognition particle receptor beta	94.92
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	94.74
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	94.02
1n0u_A	842	EF-2, elongation factor 2; G-protein, CIS-proline,	94.0
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	91.85
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	90.5
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	87.4
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	87.23
2xxa_A	433	Signal recognition particle protein; protein trans	86.72
2dby_A	368	GTP-binding protein; GDP, structural genomics, NPP	85.38
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	81.94
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	81.83

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=99.80  E-value=6.5e-20  Score=141.88  Aligned_cols=162  Identities=26%  Similarity=0.301  Sum_probs=113.7

Q ss_pred             HHHHHHhhcCCcEEEEEecCCCchhHHHHHHcCCCCccceeecccCC-CcccccccccccCH-hHHHhhHhhCCCCEEEE
Q 030407            2 LALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINL-GPLEELSNLFKADLLLC   79 (178)
Q Consensus         2 ~~~~~~~~~~~~vaVI~nd~g~~iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l-~~l~~l~~~~~~d~iii   79 (178)
                      .+++..+....++++|.||++.++|...++..|.    .+..+.+|| ||..      ...+ ..+.   ...++|+++|
T Consensus        48 ~~l~~~~~~~~~~~~i~~d~~~~~d~~~~~~~~~----~~~~~~~~~~~~~~------~~~~~~~~~---~~~~~d~iii  114 (221)
T 2wsm_A           48 ERTIERIGNEVKIGAMLGDVVSKADYERVRRFGI----KAEAISTGKECHLD------AHMIYHRLK---KFSDCDLLLI  114 (221)
T ss_dssp             HHHHHHHTTTSCEEEEECSCCCHHHHHHHHTTTC----EEEECCCTTCSSCC------HHHHHTTGG---GGTTCSEEEE
T ss_pred             HHHHHHhccCCeEEEEecCCCCchhHHHHHhCCC----cEEEecCCceeecc------cHHHHHHHH---hcCCCCEEEE
Confidence            3555555445789999999998899998876565    678888898 6632      1112 1111   2457999999


Q ss_pred             eCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEe
Q 030407           80 ESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQ  159 (178)
Q Consensus        80 EttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~S  159 (178)
                      ||+|....+.+.....+..++|+|++.+......+..+...+.++|+||+|+.+......+.+.+.+++.+|.++++++|
T Consensus       115 dt~G~~~~~~~~~~~~~~~i~vvd~~~~~~~~~~~~~~~~~~~iiv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~i~~~S  194 (221)
T 2wsm_A          115 ENVGNLICPVDFDLGENYRVVMVSVTEGDDVVEKHPEIFRVADLIVINKVALAEAVGADVEKMKADAKLINPRAKIIEMD  194 (221)
T ss_dssp             EEEEBSSGGGGCCCSCSEEEEEEEGGGCTTHHHHCHHHHHTCSEEEEECGGGHHHHTCCHHHHHHHHHHHCTTSEEEECB
T ss_pred             eCCCCCCCCchhccccCcEEEEEeCCCcchhhhhhhhhhhcCCEEEEecccCCcchhhHHHHHHHHHHHhCCCCeEEEee
Confidence            99994122212111357899999998765332222233566899999999996431124667777888778889999999


Q ss_pred             cccCCCHHHHHHHHhhh
Q 030407          160 VGWVIGIIFTLSITHYI  176 (178)
Q Consensus       160 A~~g~gi~el~~~l~~~  176 (178)
                      |++|+|+++++++|.+.
T Consensus       195 a~~g~gi~~l~~~l~~~  211 (221)
T 2wsm_A          195 LKTGKGFEEWIDFLRGI  211 (221)
T ss_dssp             TTTTBTHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHH
Confidence            99999999999988754

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=99.75  E-value=4.5e-18  Score=131.92  Aligned_cols=164  Identities=32%  Similarity=0.433  Sum_probs=113.9

Q ss_pred             HHHHHHhhcCCcEEEEEecCCCchhHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhHhhCCCCEEEEe
Q 030407            2 LALCKFLRDKYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNLFKADLLLCE   80 (178)
Q Consensus         2 ~~~~~~~~~~~~vaVI~nd~g~~iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~~~d~iiiE   80 (178)
                      .+++..+....++++|.+||+.++|...++..|.    .+..+.+|| ||--  ..|+   -+.+..+. ..++|++++|
T Consensus        56 ~~l~~~~~~~~~~~~i~~d~~~~~d~~~~~~~~~----~~~~~~~~~~~~l~--~~~~---~~~~~~l~-~~~~d~~~id  125 (226)
T 2hf9_A           56 EKLIDNLKDKYKIACIAGDVIAKFDAERMEKHGA----KVVPLNTGKECHLD--AHLV---GHALEDLN-LDEIDLLFIE  125 (226)
T ss_dssp             HHHHHHHTTTCCEEEEEEETTTHHHHHHHHTTTC----EEEEEECTTCSSCC--HHHH---HHHHTTSC-GGGCSEEEEE
T ss_pred             HHHHHHhccCCeEEEEECCCCCCccHHHHHhcCC----cEEEecCCceEecc--HHHH---HHHHHHHh-cCCCCEEEEe
Confidence            3455555445799999999998899998887665    678888898 6521  1111   13333332 3478999999


Q ss_pred             CCcchhh-hcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEe
Q 030407           81 SGGDNLA-ANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQ  159 (178)
Q Consensus        81 ttG~~~~-~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~S  159 (178)
                      ++|.... ..|. ...+..+.++|+..+...+..+..++..++++|+||+|+.+......+.+.+.+++.++.++++++|
T Consensus       126 ~~g~i~~~~s~~-~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~iiv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~S  204 (226)
T 2hf9_A          126 NVGNLICPADFD-LGTHKRIVVISTTEGDDTIEKHPGIMKTADLIVINKIDLADAVGADIKKMENDAKRINPDAEVVLLS  204 (226)
T ss_dssp             CCSCSSGGGGCC-CSCSEEEEEEEGGGCTTTTTTCHHHHTTCSEEEEECGGGHHHHTCCHHHHHHHHHHHCTTSEEEECC
T ss_pred             CCCCccCcchhh-hccCcEEEEEecCcchhhHhhhhhHhhcCCEEEEeccccCchhHHHHHHHHHHHHHhCCCCeEEEEE
Confidence            9993222 2222 2345677889976554444334445678899999999996531124566777777778888999999


Q ss_pred             cccCCCHHHHHHHHhhh
Q 030407          160 VGWVIGIIFTLSITHYI  176 (178)
Q Consensus       160 A~~g~gi~el~~~l~~~  176 (178)
                      |++|+|++++++.+.+.
T Consensus       205 a~~g~gv~~l~~~l~~~  221 (226)
T 2hf9_A          205 LKTMEGFDKVLEFIEKS  221 (226)
T ss_dssp             TTTCTTHHHHHHHHHHH
T ss_pred             ecCCCCHHHHHHHHHHH
Confidence            99999999999988654

>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=99.75  E-value=1.2e-17  Score=139.13  Aligned_cols=166  Identities=17%  Similarity=0.124  Sum_probs=103.3

Q ss_pred             HHHHHHhhc-CCcEEEEEecCC-Cchh------HHHHHHcCCCCccceeecccCC-CcccccccccccCH-hHHHhhHhh
Q 030407            2 LALCKFLRD-KYSLAAVTNDIF-TKED------GEFLMRNGALPEERIRAVETGG-CPHAAIREDISINL-GPLEELSNL   71 (178)
Q Consensus         2 ~~~~~~~~~-~~~vaVI~nd~g-~~iD------~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l-~~l~~l~~~   71 (178)
                      .+++..+.. ++|++++.+|++ ...+      ...+...+..++..++++.++| ||.+      .... ..+ .....
T Consensus        97 ~~L~~~l~~~g~kV~vi~~Dp~~~~~~g~~l~d~~~~~~~~~~~~~~i~~~~~~~~~~~~------~~~t~d~i-~~~~~  169 (355)
T 3p32_A           97 EALGMHLIERGHRVAVLAVDPSSTRTGGSILGDKTRMARLAVHPNAYIRPSPTSGTLGGV------TRATRETV-VLLEA  169 (355)
T ss_dssp             HHHHHHHHTTTCCEEEEEEC----------------CHHHHTCTTEEEECCC--CCHHHH------HHHHHHHH-HHHHH
T ss_pred             HHHHHHHHhCCCceEEEecCCCCCcccchhccchhhHHhhccCCCeeEEECCCCccccch------hHHHHHHH-HHHhh
Confidence            355666654 599999999999 4433      3333322211234678888888 7754      2222 444 34445


Q ss_pred             CCCCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHhHHH----HHHHHH
Q 030407           72 FKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLAV----MERDAL  147 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~~~~----~~~~l~  147 (178)
                      .++|++||||+|+..........+|.+++|+|+..++.........++.++++|+||+|+.+.  ...+.    +.+.++
T Consensus       170 ~~~~~iiiDTpGi~~~~~~~~~~aD~vl~V~d~~~~~~~~~l~~~~~~~p~ivVlNK~Dl~~~--~~~~~~~~~l~~~l~  247 (355)
T 3p32_A          170 AGFDVILIETVGVGQSEVAVANMVDTFVLLTLARTGDQLQGIKKGVLELADIVVVNKADGEHH--KEARLAARELSAAIR  247 (355)
T ss_dssp             TTCCEEEEEECSCSSHHHHHHTTCSEEEEEEESSTTCTTTTCCTTSGGGCSEEEEECCCGGGH--HHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCcHHHHHHHhCCEEEEEECCCCCccHHHHHHhHhhcCCEEEEECCCCcCh--hHHHHHHHHHHHHHh
Confidence            689999999999533222222457999999999876654333333466799999999999765  33333    333333


Q ss_pred             hcCC-----CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          148 RMRD-----GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       148 ~~np-----~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+|     ..+++++||++|+|+++|+++|.+.
T Consensus       248 ~~~~~~~~~~~~vi~iSA~~g~Gi~~L~~~i~~~  281 (355)
T 3p32_A          248 LIYPREALWRPPVLTMSAVEGRGLAELWDTVERH  281 (355)
T ss_dssp             HHSTTCCSCCCCEEEEBGGGTBSHHHHHHHHHHH
T ss_pred             hccccccCCCCceEEEEcCCCCCHHHHHHHHHHH
Confidence            3332     4689999999999999999988764

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=99.71  E-value=5.7e-17  Score=135.03  Aligned_cols=167  Identities=16%  Similarity=0.076  Sum_probs=90.5

Q ss_pred             HHHHHHhhc-CCcEEEEEecCC-Cchh------HHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhHhhC
Q 030407            2 LALCKFLRD-KYSLAAVTNDIF-TKED------GEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNLF   72 (178)
Q Consensus         2 ~~~~~~~~~-~~~vaVI~nd~g-~~iD------~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~   72 (178)
                      ++++..+.+ +.+++|+.+|++ ...+      ..+|+..+..+...+....++| ||..+     ....+.+..+ ...
T Consensus        92 n~L~~~~~~~~~~v~V~~~dp~~~~~~g~~l~d~~rm~~~~~~~~~~v~~~~~~~~lgg~t-----r~~~~~~~~~-~~~  165 (349)
T 2www_A           92 EYFGKMLTERGHKLSVLAVDPSSCTSGGSLLGDKTRMTELSRDMNAYIRPSPTRGTLGGVT-----RTTNEAILLC-EGA  165 (349)
T ss_dssp             HHHHHHHHHTTCCEEEEECCC----------------CCSTTCTTEEEECC---------C-----TTHHHHHHHH-HHT
T ss_pred             HHHHHHhhhcCCeEEEEeecCCCCCcCcchhchHHHHHHhcCCCCEEEEecCCccccccch-----HHHHHHHHhh-ccC
Confidence            455555554 489999999999 5554      4444443321222455667778 66431     1112444333 356


Q ss_pred             CCCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHh----HHHHHHHHHh
Q 030407           73 KADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGAD----LAVMERDALR  148 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~----~~~~~~~l~~  148 (178)
                      ++|++|+||+|...........+|.+++|+|++.+..........++.++++|+||+|+.+.  ..    .+.+...++.
T Consensus       166 ~~~~iliDT~Gi~~~~~~l~~~~d~vl~V~d~~~~~~~~~i~~~il~~~~ivVlNK~Dl~~~--~~~~~~~~~l~~~l~~  243 (349)
T 2www_A          166 GYDIILIETVGVGQSEFAVADMVDMFVLLLPPAGGDELQGIKRGIIEMADLVAVTKSDGDLI--VPARRIQAEYVSALKL  243 (349)
T ss_dssp             TCSEEEEECCCC--CHHHHHTTCSEEEEEECCC------------CCSCSEEEECCCSGGGH--HHHHHHHHHHHHHHTT
T ss_pred             CCCEEEEECCCcchhhhhHHhhCCEEEEEEcCCcchhHHHhHHHHHhcCCEEEEeeecCCCc--hhHHHHHHHHHHHHHh
Confidence            89999999999431111112357999999999876533211123456789999999999754  32    2233333443


Q ss_pred             cCC-----CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          149 MRD-----GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       149 ~np-----~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+|     ..+++++||++|+|+++|+++|.+.
T Consensus       244 ~~~~a~~~~~~vi~iSA~~g~Gi~~L~~~I~~~  276 (349)
T 2www_A          244 LRKRSQVWKPKVIRISARSGEGISEMWDKMKDF  276 (349)
T ss_dssp             CC-----CCCEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             cCccccCCCceEEEEecCCCCCHHHHHHHHHHH
Confidence            343     4589999999999999999998764

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=99.65  E-value=1.5e-17  Score=136.69  Aligned_cols=139  Identities=21%  Similarity=0.318  Sum_probs=99.1

Q ss_pred             cCCcEEEEEecCC-CchhHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhH---hhCC--CCEEEEeCC
Q 030407           10 DKYSLAAVTNDIF-TKEDGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELS---NLFK--ADLLLCESG   82 (178)
Q Consensus        10 ~~~~vaVI~nd~g-~~iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~---~~~~--~d~iiiEtt   82 (178)
                      .++|+|||+||+| +.+|+..+...+    +.+.+++||| ||+.  |+|+.   ..+..+.   +...  +|++++|++
T Consensus        29 ~~~~~aVi~~d~G~i~idg~~l~~~~----~~~~el~~gCicc~~--~~~~~---~~l~~l~~~~q~~~~~~~~~v~E~~   99 (318)
T 1nij_A           29 HGYKIAVIENEFGEVSVDDQLIGDRA----TQIKTLTNGCICCSR--SNELE---DALLDLLDNLDKGNIQFDRLVIECT   99 (318)
T ss_dssp             CCCCEEEECSSCCSCCEEEEEECTTS----CEEEEETTSCEEECT--TSCHH---HHHHHHHHHHHHTSCCCSEEEEEEE
T ss_pred             CCCcEEEEEecCcccCccHHHHhCCC----CCEEEECCCceEEcc--cHHHH---HHHHHHHhHHhcCCCCCCEEEEeCC
Confidence            4689999999999 999998775433    3789999999 9985  56654   3444442   3333  599999999


Q ss_pred             cchh----hhcc--cc-----cccceEEEEEeCCCCCCCCcC---CCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHh
Q 030407           83 GDNL----AANF--SR-----ELADYIIYIIDVSGGDKIPRK---GGPGITQADLLVINKTDLASAIGADLAVMERDALR  148 (178)
Q Consensus        83 G~~~----~~~~--~~-----~~ad~~I~VvD~~~~~~~~~~---~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~  148 (178)
                      |.+.    ...+  ..     ...+.+++++|+.+.......   ...|...||++++||.|+.++  .  +.+.+.+++
T Consensus       100 ~l~~p~~~~~~~~~~~~~~~~~~l~~~l~~vd~~~~~~~~~~ls~g~~Q~~~ad~ill~k~dl~de--~--~~l~~~l~~  175 (318)
T 1nij_A          100 GMADPGPIIQTFFSHEVLCQRYLLDGVIALVDAVHADEQMNQFTIAQSQVGYADRILLTKTDVAGE--A--EKLHERLAR  175 (318)
T ss_dssp             TTCCHHHHHHHHHHSHHHHHHEEEEEEEEEEETTTHHHHHHHCHHHHHHHHTCSEEEEECTTTCSC--T--HHHHHHHHH
T ss_pred             CCCCHHHHHHHHhcCccccCeEEECCEEEEEEHHHHHHHHhhchHHHHHHHhCCEEEEECcccCCH--H--HHHHHHHHH
Confidence            9531    1122  11     123678999999764322111   124677899999999999976  3  778888888


Q ss_pred             cCCCCCEEEEecc
Q 030407          149 MRDGGPFIFAQVG  161 (178)
Q Consensus       149 ~np~a~i~~~SA~  161 (178)
                      +||.++++.+|..
T Consensus       176 l~~~~~ii~~sh~  188 (318)
T 1nij_A          176 INARAPVYTVTHG  188 (318)
T ss_dssp             HCSSSCEEECCSS
T ss_pred             hCCCCeEEEeccc
Confidence            9999999998853

>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=99.48  E-value=1.1e-13  Score=114.71  Aligned_cols=168  Identities=17%  Similarity=0.109  Sum_probs=89.3

Q ss_pred             HHHHHhhc-CCcEEEEEecCC-CchhHHHHHHcCCCCccceeecccCC-CcccccccccccCH----hHHHhhHhhCCCC
Q 030407            3 ALCKFLRD-KYSLAAVTNDIF-TKEDGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINL----GPLEELSNLFKAD   75 (178)
Q Consensus         3 ~~~~~~~~-~~~vaVI~nd~g-~~iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l----~~l~~l~~~~~~d   75 (178)
                      +++..+.+ +.+++++.+|++ +..++.++.....  .+......+++ ||..+ ++-+....    +.+..+ ...+++
T Consensus        75 ~l~~~~~~~~~~v~v~~~d~~~~~~~~~il~d~~~--~~~~~~~~~~~i~~~~~-~~~l~g~~~~~~~~~~~~-~~~~~~  150 (341)
T 2p67_A           75 AFGMLLIREGLKVAVIAVDPSSPVTGGSILGDKTR--MNDLARAEAAFIRPVPS-SGHLGGASQRARELMLLC-EAAGYD  150 (341)
T ss_dssp             HHHHHHHHTTCCEEEEEECCC-----------------CTTTTCTTEEEEEECC------CHHHHHHHHHHHH-HHTTCS
T ss_pred             HHHHHHHhcCCeEEEEeecCCcCCCCcceecccch--HHhhccCCCceeecCcc-ccccchhHHHHHHHHHHh-hccCCC
Confidence            44444443 589999999999 6666555432110  01112234666 66431 11011111    222221 245899


Q ss_pred             EEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHhHH----HHHHHHHhcCC
Q 030407           76 LLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLA----VMERDALRMRD  151 (178)
Q Consensus        76 ~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~~~----~~~~~l~~~np  151 (178)
                      ++||||.|..-........+|.+++|+|++.++........+...+.++|+||+|+.+.  ....    .+.+.++..++
T Consensus       151 i~liDTpG~~~~~~~~~~~aD~vl~Vvd~~~~~~~~~l~~~~~~~p~ivv~NK~Dl~~~--~~~~~~~~~l~~~l~~~~~  228 (341)
T 2p67_A          151 VVIVETVGVGQSETEVARMVDCFISLQIAGGGDDLQGIKKGLMEVADLIVINKDDGDNH--TNVAIARHMYESALHILRR  228 (341)
T ss_dssp             EEEEEEECCTTHHHHHHTTCSEEEEEECC------CCCCHHHHHHCSEEEECCCCTTCH--HHHHHHHHHHHHHHHHSCC
T ss_pred             EEEEeCCCccchHHHHHHhCCEEEEEEeCCccHHHHHHHHhhhcccCEEEEECCCCCCh--HHHHHHHHHHHHHHHhccc
Confidence            99999999422111112357999999999766432211111234578999999999865  3333    33333333343


Q ss_pred             -----CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          152 -----GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       152 -----~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                           ..+++++||++|+|+++++++|.+.
T Consensus       229 ~~~~~~~~vi~iSA~~g~gi~~L~~~l~~~  258 (341)
T 2p67_A          229 KYDEWQPRVLTCSALEKRGIDEIWHAIIDF  258 (341)
T ss_dssp             SBTTBCCEEEECBGGGTBSHHHHHHHHHHH
T ss_pred             cccCCCCcEEEeeCCCCCCHHHHHHHHHHH
Confidence                 4589999999999999999988764

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=99.39  E-value=2.4e-12  Score=106.64  Aligned_cols=169  Identities=15%  Similarity=0.105  Sum_probs=92.3

Q ss_pred             HHHHhhc-CCcEEEEEecCC-CchhHHHH---HHcCCCCcc-ceeecccCCCcccccccccccCHhHHHhhHhhCCCCEE
Q 030407            4 LCKFLRD-KYSLAAVTNDIF-TKEDGEFL---MRNGALPEE-RIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLL   77 (178)
Q Consensus         4 ~~~~~~~-~~~vaVI~nd~g-~~iD~~li---~~~~~~~~~-~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~~d~i   77 (178)
                      ++..+.. +.+++++.+|++ ...++.+.   .+.+....+ ....-....||++  ++......+++. +....++|++
T Consensus        75 l~g~~~~~~g~v~i~~~d~~~~~~~~~~~~~~~~i~~v~q~~~~~~~~~~~~~~l--~G~tr~~~e~~~-~~~~~~~~~i  151 (337)
T 2qm8_A           75 LGSLLTAAGHKVAVLAVDPSSTRTGGSILGDKTRMARLAIDRNAFIRPSPSSGTL--GGVAAKTRETML-LCEAAGFDVI  151 (337)
T ss_dssp             HHHHHHHTTCCEEEEEECGGGGSSCCCSSCCGGGSTTGGGCTTEEEECCCCCSSH--HHHHHHHHHHHH-HHHHTTCCEE
T ss_pred             HHHhhhhCCCEEEEEEEcCcccccccchHHHhhhheeeccCcccccccCcccccc--cchHHHHHHHHH-HHhcCCCCEE
Confidence            3444443 489999999987 33211100   011211100 1111122336765  222222223332 2335689999


Q ss_pred             EEeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHh----HHHHHHHHHhcCC--
Q 030407           78 LCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGAD----LAVMERDALRMRD--  151 (178)
Q Consensus        78 iiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~----~~~~~~~l~~~np--  151 (178)
                      ||||+|...........+|.+++++|+..++..........+.++++++||+|+.+.. ..    .+.+...+..++|  
T Consensus       152 liDT~Gi~~~~~~v~~~~d~vl~v~d~~~~~~~~~i~~~i~~~~~ivvlNK~Dl~~~~-~~s~~~~~~l~~a~~l~~~~~  230 (337)
T 2qm8_A          152 LVETVGVGQSETAVADLTDFFLVLMLPGAGDELQGIKKGIFELADMIAVNKADDGDGE-RRASAAASEYRAALHILTPPS  230 (337)
T ss_dssp             EEEECSSSSCHHHHHTTSSEEEEEECSCC------CCTTHHHHCSEEEEECCSTTCCH-HHHHHHHHHHHHHHTTBCCSB
T ss_pred             EEECCCCCcchhhHHhhCCEEEEEEcCCCcccHHHHHHHHhccccEEEEEchhccCch-hHHHHHHHHHHHHHHhccccc
Confidence            9999994321111123579999999987554322111122456899999999986541 11    2333333333343  


Q ss_pred             ---CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          152 ---GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       152 ---~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                         ..+++.+||++|+|+++|++.|.+.
T Consensus       231 ~~~~~~vl~~Sal~g~gi~~L~~~I~~~  258 (337)
T 2qm8_A          231 ATWTPPVVTISGLHGKGLDSLWSRIEDH  258 (337)
T ss_dssp             TTBCCCEEEEBTTTTBSHHHHHHHHHHH
T ss_pred             cCCCCCEEEEeCCCCCCHHHHHHHHHHH
Confidence               4689999999999999999988764

>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=99.33  E-value=6.9e-13  Score=104.77  Aligned_cols=161  Identities=16%  Similarity=0.077  Sum_probs=92.1

Q ss_pred             HHHHHHhhcCCcEEEEEecCC-Cch------------hHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHh
Q 030407            2 LALCKFLRDKYSLAAVTNDIF-TKE------------DGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEE   67 (178)
Q Consensus         2 ~~~~~~~~~~~~vaVI~nd~g-~~i------------D~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~   67 (178)
                      .+++.++..++|+++|-+|++ ...            +..-+...+        ...+|| ||+....   ......+.+
T Consensus        32 ~~La~~l~~g~~v~vvd~D~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~---~~~~~~l~~  100 (262)
T 1yrb_A           32 GEFGRYLEDNYKVAYVNLDTGVKELPYEPSIDVREFVTVEEIMREG--------YGPNGAIVESYDRL---MEKFNEYLN  100 (262)
T ss_dssp             HHHHHHHTTTSCEEEEECCSSCSCCSSCCSEEGGGTCCHHHHHTTT--------CCHHHHHHHHHHHH---HTTHHHHHH
T ss_pred             HHHHHHHHCCCeEEEEeCCCCccccCCCCCCChhhcccHHHHhhcc--------CCCCCcEEecHHHH---hhhHHHHHH
Confidence            345555664599999999998 443            111110001        124666 5532110   111122222


Q ss_pred             hHh--hCCCCEEEEeCCcchhhhcc---------cccccceEEEEEeCCCCCCCCcCC---------CCCCCceeEEEEe
Q 030407           68 LSN--LFKADLLLCESGGDNLAANF---------SRELADYIIYIIDVSGGDKIPRKG---------GPGITQADLLVIN  127 (178)
Q Consensus        68 l~~--~~~~d~iiiEttG~~~~~~~---------~~~~ad~~I~VvD~~~~~~~~~~~---------~~qi~~adiiviN  127 (178)
                      ..+  ..++|++||+|.|..-..+.         .... +.+++++|+..........         ..+...+.++|+|
T Consensus       101 ~l~~~~~~~d~iiiDtpG~~~~~~~~~l~~~~~~~~~~-~~iv~vvD~~~~~~~~~~~~~~~~~~~~~~~~~~p~~iv~N  179 (262)
T 1yrb_A          101 KILRLEKENDYVLIDTPGQMETFLFHEFGVRLMENLPY-PLVVYISDPEILKKPNDYCFVRFFALLIDLRLGATTIPALN  179 (262)
T ss_dssp             HHHHHHHHCSEEEEECCSSHHHHHHSHHHHHHHHTSSS-CEEEEEECGGGCCSHHHHHHHHHHHHHHHHHHTSCEEEEEC
T ss_pred             HHHHHhhcCCEEEEeCCCccchhhhhhhHHHHHHHHhh-ceEEeccchhhhcCHHHHHHHHHHHHHHhcccCCCeEEEEe
Confidence            221  12589999999994211100         1123 7888999986543321110         1123457899999


Q ss_pred             cCCCCCchhHhHHHHHHH----------------------------HHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          128 KTDLASAIGADLAVMERD----------------------------ALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       128 K~Dl~~~~~~~~~~~~~~----------------------------l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      |+|+.+.  .+.+.+.+.                            +++.++..+++++||++|+|+++|++++.+.
T Consensus       180 K~D~~~~--~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~SA~~~~gi~~l~~~i~~~  254 (262)
T 1yrb_A          180 KVDLLSE--EEKERHRKYFEDIDYLTARLKLDPSMQGLMAYKMCSMMTEVLPPVRVLYLSAKTREGFEDLETLAYEH  254 (262)
T ss_dssp             CGGGCCH--HHHHHHHHHHHCHHHHHHHHHHCCSHHHHHHHHHHHHHHHHSCCCCCEECCTTTCTTHHHHHHHHHHH
T ss_pred             ccccccc--ccHHHHHHHHhChHHHHHHHhccccccchhHhHHHHHHHHhcCcccceEEEecCcccHHHHHHHHHHH
Confidence            9999876  333222222                            2444566789999999999999999998764

>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=98.97  E-value=8.5e-10  Score=89.97  Aligned_cols=102  Identities=16%  Similarity=0.108  Sum_probs=70.5

Q ss_pred             CCCEEEEeCCcchhhh-------------cccccccceEEEEEeCCCCCCCCcC-----CCCCCCceeEEEEecCCCC-C
Q 030407           73 KADLLLCESGGDNLAA-------------NFSRELADYIIYIIDVSGGDKIPRK-----GGPGITQADLLVINKTDLA-S  133 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~-------------~~~~~~ad~~I~VvD~~~~~~~~~~-----~~~qi~~adiiviNK~Dl~-~  133 (178)
                      +..++|++|.|..-..             ......+|.+++|+|++++......     .......+.++|+||+|+. +
T Consensus        58 ~~~i~lvDTPG~~~~~~~~~l~~~~~~~~~~~l~~aD~il~VvD~~~~~~~~~~~~~~~~l~~~~~pvilV~NK~Dl~~~  137 (308)
T 3iev_A           58 EAQIIFLDTPGIYEPKKSDVLGHSMVEIAKQSLEEADVILFMIDATEGWRPRDEEIYQNFIKPLNKPVIVVINKIDKIGP  137 (308)
T ss_dssp             TEEEEEEECCCCCCCCTTCHHHHHHHHHHHHHHHHCSEEEEEEETTTBSCHHHHHHHHHHTGGGCCCEEEEEECGGGSSS
T ss_pred             CCeEEEEECcCCCccccchhHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCchhHHHHHHHHHhcCCCEEEEEECccCCCC
Confidence            6789999999941100             0011246999999999876432211     1112346789999999998 5


Q ss_pred             chhHhHHHHHHHHHhcC-CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          134 AIGADLAVMERDALRMR-DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       134 ~~~~~~~~~~~~l~~~n-p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .  .......+.+++.. +..+++++||++|+|++++++.+.+.
T Consensus       138 ~--~~~~~~~~~l~~~~~~~~~i~~vSA~~g~gv~~L~~~l~~~  179 (308)
T 3iev_A          138 A--KNVLPLIDEIHKKHPELTEIVPISALKGANLDELVKTILKY  179 (308)
T ss_dssp             G--GGGHHHHHHHHHHCTTCCCEEECBTTTTBSHHHHHHHHHHH
T ss_pred             H--HHHHHHHHHHHHhccCCCeEEEEeCCCCCCHHHHHHHHHHh
Confidence            5  44455555555554 67899999999999999999988764

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=98.95  E-value=1.3e-09  Score=83.45  Aligned_cols=104  Identities=7%  Similarity=-0.075  Sum_probs=69.0

Q ss_pred             CCCCEEEEeCCcchh--------------hhcccc--cccceEEEEEeCCCCCCCCc-C---CCCCCCceeEEEEecCCC
Q 030407           72 FKADLLLCESGGDNL--------------AANFSR--ELADYIIYIIDVSGGDKIPR-K---GGPGITQADLLVINKTDL  131 (178)
Q Consensus        72 ~~~d~iiiEttG~~~--------------~~~~~~--~~ad~~I~VvD~~~~~~~~~-~---~~~qi~~adiiviNK~Dl  131 (178)
                      .+..+.|++|.|..-              ...+..  ..+|.+++|+|++++..... .   .......+.++|+||+|+
T Consensus        77 ~~~~~~l~DtpG~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~vi~v~d~~~~~~~~~~~~~~~l~~~~~p~i~v~nK~Dl  156 (223)
T 4dhe_A           77 AEPVAHLVDLPGYGYAEVPGAAKAHWEQLLSSYLQTRPQLCGMILMMDARRPLTELDRRMIEWFAPTGKPIHSLLTKCDK  156 (223)
T ss_dssp             TSCSEEEEECCCCCSSCCCSTHHHHHHHHHHHHHHHCTTEEEEEEEEETTSCCCHHHHHHHHHHGGGCCCEEEEEECGGG
T ss_pred             CCCcEEEEcCCCCCcccCChhhHHHHHHHHHHHHhcCcCcCEEEEEEeCCCCCCHHHHHHHHHHHhcCCCEEEEEecccc
Confidence            357899999999311              111111  12578999999987533211 0   011134567999999999


Q ss_pred             CCchhHhH----HHHHHHHHhc-----CCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          132 ASAIGADL----AVMERDALRM-----RDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       132 ~~~~~~~~----~~~~~~l~~~-----np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .+.  .+.    +.+.+.++..     .+..+++++||++|+|+++++++|.+..
T Consensus       157 ~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~SA~~g~gv~~l~~~l~~~~  209 (223)
T 4dhe_A          157 LTR--QESINALRATQKSLDAYRDAGYAGKLTVQLFSALKRTGLDDAHALIESWL  209 (223)
T ss_dssp             SCH--HHHHHHHHHHHHHHHHHHHHTCCSCEEEEEEBTTTTBSHHHHHHHHHHHH
T ss_pred             CCh--hhHHHHHHHHHHHHHhhhhcccCCCCeEEEeecCCCcCHHHHHHHHHHhc
Confidence            876  443    3344445443     3567999999999999999999987653

>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=98.93  E-value=2.5e-09  Score=81.10  Aligned_cols=102  Identities=12%  Similarity=0.043  Sum_probs=68.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|..    +...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.+.  ...
T Consensus        68 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~--~~~  144 (198)
T 1f6b_A           68 GMTFTTFDLGGHIQARRVWKNYL-PAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEA--ISE  144 (198)
T ss_dssp             TEEEEEEEECC----CCGGGGGG-GGCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTSCEEEEEECTTSTTC--CCH
T ss_pred             CEEEEEEECCCcHhhHHHHHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHhCcccCCCcEEEEEECCCcccc--CCH
Confidence            4678899999932    112222 25799999999987542211         0101123467999999999865  445


Q ss_pred             HHHHHHHHhcC---------------CCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDALRMR---------------DGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l~~~n---------------p~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +++.+.++...               ...+++++||++|+|+++++++|.+..
T Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~g~gv~~l~~~l~~~l  197 (198)
T 1f6b_A          145 ERLREMFGLYGQTTGKGSVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYI  197 (198)
T ss_dssp             HHHHHHHTCTTTCCCSSCCCTTTCCSCCEEEEECBTTTTBSHHHHHHHHHTTC
T ss_pred             HHHHHHhCcccccccccccccccccCceEEEEEEECCCCCCHHHHHHHHHHhc
Confidence            55666655321               345899999999999999999987654

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=98.86  E-value=2.2e-09  Score=79.97  Aligned_cols=103  Identities=10%  Similarity=0.027  Sum_probs=67.1

Q ss_pred             CCCEEEEeCCcchh--------------hhcccc--cccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCC
Q 030407           73 KADLLLCESGGDNL--------------AANFSR--ELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLA  132 (178)
Q Consensus        73 ~~d~iiiEttG~~~--------------~~~~~~--~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~  132 (178)
                      +..+.+++|.|...              ...+..  ..++.+++|+|++........    +......+.++|+||+|+.
T Consensus        67 ~~~~~i~Dt~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~v~d~~~~~~~~~~~~~~~~~~~~~p~i~v~nK~Dl~  146 (195)
T 3pqc_A           67 NSKYYFVDLPGYGYAKVSKKERMLWKRLVEDYFKNRWSLQMVFLLVDGRIPPQDSDLMMVEWMKSLNIPFTIVLTKMDKV  146 (195)
T ss_dssp             TTTEEEEECCCBSSSCCCHHHHHHHHHHHHHHHHHCTTEEEEEEEEETTSCCCHHHHHHHHHHHHTTCCEEEEEECGGGS
T ss_pred             CCcEEEEECCCCccccCChhhHHHHHHHHHHHHhcCcCceEEEEEecCCCCCCHHHHHHHHHHHHcCCCEEEEEEChhcC
Confidence            45688999999311              111111  124889999998765332110    1112356789999999998


Q ss_pred             CchhHhHHHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          133 SAIGADLAVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       133 ~~~~~~~~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ++  .+.+...+.+++.   ....+++++||++|+|++++++++.+.+
T Consensus       147 ~~--~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~l~~~l~~~l  192 (195)
T 3pqc_A          147 KM--SERAKKLEEHRKVFSKYGEYTIIPTSSVTGEGISELLDLISTLL  192 (195)
T ss_dssp             CG--GGHHHHHHHHHHHHHSSCCSCEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             Ch--HHHHHHHHHHHHHHhhcCCCceEEEecCCCCCHHHHHHHHHHHh
Confidence            76  4444444433332   2346999999999999999999987654

>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=98.86  E-value=8.5e-09  Score=76.91  Aligned_cols=102  Identities=13%  Similarity=0.104  Sum_probs=67.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|..    +...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.+.  ...
T Consensus        59 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~--~~~  135 (187)
T 1zj6_A           59 NTRFLMWDIGGQESLRSSWNTYY-TNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKEC--MTV  135 (187)
T ss_dssp             TEEEEEEECCC----CGGGHHHH-TTCCEEEEEEETTCTTTHHHHHHHHHHHHTSGGGTTCEEEEEEECTTSTTC--CCH
T ss_pred             CEEEEEEECCCCHhHHHHHHHHh-cCCCEEEEEEeCCCHHHHHHHHHHHHHHHhchhhCCCeEEEEEECCCCcCC--CCH
Confidence            4788999999941    111122 24799999999987643211         0100124567999999999875  344


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +++.+.+...   ....+++++||++|+|+++++++|.+.+
T Consensus       136 ~~i~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~~  176 (187)
T 1zj6_A          136 AEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRL  176 (187)
T ss_dssp             HHHHHHHTGGGCCSSCEEEEECBTTTTBTHHHHHHHHHHHH
T ss_pred             HHHHHHhChhhhcCCCcEEEEccCCCCcCHHHHHHHHHHHH
Confidence            5555554421   2345899999999999999999987643

>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=98.85  E-value=5.6e-09  Score=78.58  Aligned_cols=101  Identities=11%  Similarity=0.077  Sum_probs=67.9

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|...    ...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.+.  ...
T Consensus        66 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~--~~~  142 (190)
T 1m2o_B           66 NIKFTTFDLGGHIQARRLWKDYF-PEVNGIVFLVDAADPERFDEARVELDALFNIAELKDVPFVILGNKIDAPNA--VSE  142 (190)
T ss_dssp             TEEEEEEECCCSGGGTTSGGGGC-TTCCEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCCEEEEEECTTSTTC--CCH
T ss_pred             CEEEEEEECCCCHHHHHHHHHHH-hcCCEEEEEEECCChHHHHHHHHHHHHHHcchhhcCCCEEEEEECCCCcCC--CCH
Confidence            46788999999421    11222 25799999999987643211         0101123467999999999875  444


Q ss_pred             HHHHHHHHhcC----------CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMR----------DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~n----------p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +++.+.++...          ...+++++||++|+|+++++++|.+.
T Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~  189 (190)
T 1m2o_B          143 AELRSALGLLNTTGSQRIEGQRPVEVFMCSVVMRNGYLEAFQWLSQY  189 (190)
T ss_dssp             HHHHHHTTCSSCCC---CCSSCCEEEEECBTTTTBSHHHHHHHHHTT
T ss_pred             HHHHHHhCCccccccccccccceEEEEEeECCcCCCHHHHHHHHHhh
Confidence            55555554321          34579999999999999999998754

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=98.83  E-value=3.2e-09  Score=79.56  Aligned_cols=102  Identities=15%  Similarity=-0.001  Sum_probs=67.8

Q ss_pred             CCCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---C---CCCC----------CCceeEEEEecCCC
Q 030407           72 FKADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---K---GGPG----------ITQADLLVINKTDL  131 (178)
Q Consensus        72 ~~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---~---~~~q----------i~~adiiviNK~Dl  131 (178)
                      ....+.|++|.|..-    ...+. ..+|.+++|+|+++......   .   ....          -..+-++|+||+|+
T Consensus        61 ~~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~ii~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl  139 (199)
T 4bas_A           61 GRVAFTVFDMGGAKKFRGLWETYY-DNIDAVIFVVDSSDHLRLCVVKSEIQAMLKHEDIRRELPGGGRVPFLFFANKMDA  139 (199)
T ss_dssp             TTEEEEEEEECCSGGGGGGGGGGC-TTCSEEEEEEETTCGGGHHHHHHHHHHHHTSHHHHSBCTTSCBCCEEEEEECTTS
T ss_pred             CCEEEEEEECCCCHhHHHHHHHHH-hcCCEEEEEEECCcHHHHHHHHHHHHHHHhChhhhhcccccCCCCEEEEEECcCC
Confidence            467889999999421    11222 25799999999987643211   0   0000          14567999999999


Q ss_pred             CCchhHhHHHHHHHHHh----cCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          132 ASAIGADLAVMERDALR----MRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       132 ~~~~~~~~~~~~~~l~~----~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.  ...+++.+.+..    .....+++++||++|+|++++|++|.+.
T Consensus       140 ~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~~l~~~l~~~  186 (199)
T 4bas_A          140 AGA--KTAAELVEILDLTTLMGDHPFVIFASNGLKGTGVHEGFSWLQET  186 (199)
T ss_dssp             TTC--CCHHHHHHHHTHHHHHTTSCEEEEECBTTTTBTHHHHHHHHHHH
T ss_pred             CCC--CCHHHHHHHhcchhhccCCeeEEEEeeCCCccCHHHHHHHHHHH
Confidence            876  444444443321    1245689999999999999999988764

>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=98.82  E-value=1.5e-08  Score=74.85  Aligned_cols=101  Identities=15%  Similarity=0.135  Sum_probs=65.3

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|..    +...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.++  ...
T Consensus        61 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~  137 (183)
T 1moz_A           61 NLKLNVWDLGGQTSIRPYWRCYY-ADTAAVIFVVDSTDKDRMSTASKELHLMLQEEELQDAALLVFANKQDQPGA--LSA  137 (183)
T ss_dssp             TEEEEEEEEC----CCTTGGGTT-TTEEEEEEEEETTCTTTHHHHHHHHHHHTTSSTTSSCEEEEEEECTTSTTC--CCH
T ss_pred             CEEEEEEECCCCHhHHHHHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHcChhhCCCeEEEEEECCCCCCC--CCH
Confidence            4678899999932    111111 24699999999987643211         0111234567999999999876  444


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.+.+.+...   ....+++++||++|+|+++++++|.+.
T Consensus       138 ~~i~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~  177 (183)
T 1moz_A          138 SEVSKELNLVELKDRSWSIVASSAIKGEGITEGLDWLIDV  177 (183)
T ss_dssp             HHHHHHTTTTTCCSSCEEEEEEBGGGTBTHHHHHHHHHHH
T ss_pred             HHHHHHhCcccccCCceEEEEccCCCCcCHHHHHHHHHHH
Confidence            4555444321   123479999999999999999988754

>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=98.82  E-value=1.8e-08  Score=73.48  Aligned_cols=101  Identities=14%  Similarity=0.066  Sum_probs=67.1

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---C------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---K------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---~------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|..-    ...+. ..+|.+++|+|+++......   .      ....-..+-++|+||+|+.+.  ...
T Consensus        50 ~~~~~~~Dt~G~~~~~~~~~~~~-~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~  126 (171)
T 1upt_A           50 NLKFQVWDLGGLTSIRPYWRCYY-SNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQA--MTS  126 (171)
T ss_dssp             TEEEEEEEECCCGGGGGGGGGGC-TTCSEEEEEEETTCCTTHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC--CCH
T ss_pred             CEEEEEEECCCChhhhHHHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhCCCEEEEEEECCCCcCC--CCH
Confidence            56788999999421    11122 25799999999987643211   0      000124567999999999876  444


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.+.+.+...   ....+++++||++|+|++++++++.+.
T Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~  166 (171)
T 1upt_A          127 SEMANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVET  166 (171)
T ss_dssp             HHHHHHHTGGGCTTSCEEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHhCchhccCCceEEEECcCCCCcCHHHHHHHHHHH
Confidence            4444444311   123489999999999999999988764

>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=98.82  E-value=9.5e-09  Score=76.37  Aligned_cols=101  Identities=14%  Similarity=0.060  Sum_probs=67.7

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|..-    ...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.++  ...
T Consensus        61 ~~~~~~~Dt~G~~~~~~~~~~~~-~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~  137 (186)
T 1ksh_A           61 GFKLNIWDVGGQKSLRSYWRNYF-ESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGA--LSC  137 (186)
T ss_dssp             TEEEEEEEECCSHHHHTTGGGGC-TTCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC--CCH
T ss_pred             CEEEEEEECCCCHhHHHHHHHHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHhChhcCCCcEEEEEeCccCCCC--CCH
Confidence            57789999999421    11222 35799999999987643211         0101124567999999999876  444


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.+.+.+...   ....+++++||++|+|++++++++.+.
T Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~  177 (186)
T 1ksh_A          138 NAIQEALELDSIRSHHWRIQGCSAVTGEDLLPGIDWLLDD  177 (186)
T ss_dssp             HHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHhChhhccCCceEEEEeeCCCCCCHHHHHHHHHHH
Confidence            4555444311   234589999999999999999988764

>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=98.81  E-value=1.2e-08  Score=76.30  Aligned_cols=102  Identities=14%  Similarity=0.075  Sum_probs=68.8

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCC--CCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPG--ITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~q--i~~adiiviNK~Dl~~~~~~  137 (178)
                      +..+.+++|.|..    +...+. ..+|.+++|+|+++......         .....  -..+-++|+||+|+.+.  .
T Consensus        66 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~  142 (190)
T 2h57_A           66 SLSFTVFDMSGQGRYRNLWEHYY-KEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKHRRIPILFFANKMDLRDA--V  142 (190)
T ss_dssp             SCEEEEEEECCSTTTGGGGGGGG-GGCSEEEEEEETTCHHHHHHHHHHHHHHHHSTTTTTSCCCEEEEEECTTSTTC--C
T ss_pred             CEEEEEEECCCCHHHHHHHHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHhChhhccCCCeEEEEEeCcCcccC--C
Confidence            5789999999942    111222 34799999999987532111         01111  24567999999999876  4


Q ss_pred             hHHHHHHHHH--hcC-CCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          138 DLAVMERDAL--RMR-DGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       138 ~~~~~~~~l~--~~n-p~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ..+.+.+.++  .+. ...+++++||++|+|+++++++|.+.+
T Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i  185 (190)
T 2h57_A          143 TSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI  185 (190)
T ss_dssp             CHHHHHHHHTGGGCCSSCEEEEECBTTTTBTHHHHHHHHHHHC
T ss_pred             CHHHHHHHhChhhccCCceEEEEccCCCCcCHHHHHHHHHHHH
Confidence            5555665553  221 346899999999999999999987653

>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=98.80  E-value=6.1e-09  Score=77.91  Aligned_cols=102  Identities=9%  Similarity=0.036  Sum_probs=67.1

Q ss_pred             CCEEEEeCCcchh--------------hhcccc--cccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCC
Q 030407           74 ADLLLCESGGDNL--------------AANFSR--ELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLAS  133 (178)
Q Consensus        74 ~d~iiiEttG~~~--------------~~~~~~--~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~  133 (178)
                      ..+.+++|.|...              ...+..  ...|.+++|+|++++......    +......+.++|+||+|+.+
T Consensus        69 ~~~~l~Dt~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~p~i~v~nK~Dl~~  148 (195)
T 1svi_A           69 DELHFVDVPGYGFAKVSKSEREAWGRMIETYITTREELKAVVQIVDLRHAPSNDDVQMYEFLKYYGIPVIVIATKADKIP  148 (195)
T ss_dssp             TTEEEEECCCBCCCSSCHHHHHHHHHHHHHHHHHCTTEEEEEEEEETTSCCCHHHHHHHHHHHHTTCCEEEEEECGGGSC
T ss_pred             CcEEEEECCCCCccccCHHHHHHHHHHHHHHHhhhhcCCEEEEEEECCCCCCHHHHHHHHHHHHcCCCEEEEEECcccCC
Confidence            3689999999310              111111  123899999999875432211    11113456899999999987


Q ss_pred             chhHhHHHHHHHHHh-c--CCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          134 AIGADLAVMERDALR-M--RDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       134 ~~~~~~~~~~~~l~~-~--np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +  .+.+...+.+++ +  .+..+++++||++|+|+++++++|.+.+
T Consensus       149 ~--~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~l~~~l~~~l  193 (195)
T 1svi_A          149 K--GKWDKHAKVVRQTLNIDPEDELILFSSETKKGKDEAWGAIKKMI  193 (195)
T ss_dssp             G--GGHHHHHHHHHHHHTCCTTSEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             h--HHHHHHHHHHHHHHcccCCCceEEEEccCCCCHHHHHHHHHHHh
Confidence            7  444443333332 2  3467999999999999999999987653

>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=98.77  E-value=1.7e-08  Score=73.15  Aligned_cols=101  Identities=13%  Similarity=0.101  Sum_probs=66.4

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---C------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---K------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---~------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|..-    ...+. ..+|.+++|+|+++......   .      ....-..+-++|+||+|+.++  ...
T Consensus        43 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~  119 (164)
T 1r8s_A           43 NISFTVWDVGGQDKIRPLWRHYF-QNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNA--MNA  119 (164)
T ss_dssp             SCEEEEEECCCCGGGHHHHHHHT-TTCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC--CCH
T ss_pred             CEEEEEEEcCCChhhHHHHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhcCCeEEEEEECcCCcCC--CCH
Confidence            57889999999421    11122 35799999999987542211   0      001124567999999999876  344


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.+.+.....   ....+++++||++|+|++++++++.+.
T Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~  159 (164)
T 1r8s_A          120 AEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQ  159 (164)
T ss_dssp             HHHHHHTTGGGCSSCCEEEEECBTTTTBTHHHHHHHHHHH
T ss_pred             HHHHHHhCcccccCccEEEEEcccCCCcCHHHHHHHHHHH
Confidence            4444433211   123479999999999999999998764

>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=98.77  E-value=2.2e-08  Score=74.37  Aligned_cols=101  Identities=14%  Similarity=0.096  Sum_probs=66.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc------CCCC---CCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR------KGGP---GITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~------~~~~---qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|..-    ...+. ..+|.+++|+|+++......      ....   .-..+-++|+||+|+.+.  ...
T Consensus        64 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~ii~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~--~~~  140 (181)
T 2h17_A           64 NTRFLMWDIGGQESLRSSWNTYY-TNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKEC--MTV  140 (181)
T ss_dssp             TEEEEEEEESSSGGGTCGGGGGG-TTCCEEEEEEETTCTTTHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC--CCH
T ss_pred             CEEEEEEECCCCHhHHHHHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHhChhhCCCeEEEEEECCCcccC--CCH
Confidence            47889999999421    11122 24799999999987643221      0001   123467999999999875  344


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +++.+.+...   ....+++++||++|+|+++++++|.+.
T Consensus       141 ~~i~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~  180 (181)
T 2h17_A          141 AEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSR  180 (181)
T ss_dssp             HHHHHHTTGGGCCSSCEEEEECBTTTTBTHHHHHHHHHTC
T ss_pred             HHHHHHhCcccccCCceEEEEccCCCCcCHHHHHHHHHhh
Confidence            4454444211   123489999999999999999998653

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=98.76  E-value=2.5e-08  Score=74.39  Aligned_cols=101  Identities=16%  Similarity=0.105  Sum_probs=66.7

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|..-    ...+ ...+|.+++|+|+++......         .....-..+-++|+||+|+.++  ...
T Consensus        65 ~~~~~~~Dt~G~~~~~~~~~~~-~~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~  141 (189)
T 2x77_A           65 NISFEVWDLGGQTGVRPYWRCY-FSDTDAVIYVVDSTDRDRMGVAKHELYALLDEDELRKSLLLIFANKQDLPDA--ASE  141 (189)
T ss_dssp             TEEEEEEEECCSSSSCCCCSSS-STTCCEEEEEEETTCCTTHHHHHHHHHHHHTCSTTTTCEEEEEEECTTSTTC--CCH
T ss_pred             CEEEEEEECCCCHhHHHHHHHH-hhcCCEEEEEEeCCCHHHHHHHHHHHHHHHhhhhcCCCeEEEEEECCCCcCC--CCH
Confidence            56789999999321    1111 124799999999987643211         0111124567999999999876  444


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +++.+.+...   ....+++++||++|+|++++++++.+.
T Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~  181 (189)
T 2x77_A          142 AEIAEQLGVSSIMNRTWTIVKSSSKTGDGLVEGMDWLVER  181 (189)
T ss_dssp             HHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHhChhhccCCceEEEEccCCCccCHHHHHHHHHHH
Confidence            4444443311   123479999999999999999988654

>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=98.74  E-value=1.5e-08  Score=75.73  Aligned_cols=103  Identities=17%  Similarity=0.030  Sum_probs=66.9

Q ss_pred             CCCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc------CCCC---CCCceeEEEEecCCCCCchhHh
Q 030407           72 FKADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR------KGGP---GITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        72 ~~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~------~~~~---qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+..+.+++|.|..-    ...+. ..+|.+++|+|+++......      ....   .-..+-++|+||+|+.+.  ..
T Consensus        65 ~~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~ii~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~--~~  141 (188)
T 1zd9_A           65 GNVTIKLWDIGGQPRFRSMWERYC-RGVSAIVYMVDAADQEKIEASKNELHNLLDKPQLQGIPVLVLGNKRDLPGA--LD  141 (188)
T ss_dssp             TTEEEEEEEECCSHHHHTTHHHHH-TTCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCCEEEEEECTTSTTC--CC
T ss_pred             CCEEEEEEECCCCHhHHHHHHHHH-ccCCEEEEEEECCCHHHHHHHHHHHHHHHhCcccCCCCEEEEEECCCCccC--CC
Confidence            357788999999421    11122 24799999999987543211      0001   123467999999999865  33


Q ss_pred             HHHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          139 LAVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       139 ~~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .+++.+.+...   ....+++++||++|+|+++++++|.+.+
T Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~SA~~g~gv~~l~~~l~~~~  183 (188)
T 1zd9_A          142 EKELIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHS  183 (188)
T ss_dssp             HHHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHTC
T ss_pred             HHHHHHHhChhhhccCCeeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34444433321   1345789999999999999999987653

>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=98.74  E-value=2e-08  Score=72.89  Aligned_cols=101  Identities=13%  Similarity=0.086  Sum_probs=61.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.+++|.|..-    ...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.++.....
T Consensus        48 ~~~~~i~D~~g~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~  126 (166)
T 3q72_A           48 EASLMVYDIWEQDGGRWLPGHCM-AMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVSV  126 (166)
T ss_dssp             EEEEEEEECC----------------CCEEEEEEETTCHHHHHHHHHHHHHHHHCC---CCCEEEEEECTTCCSSCCSCH
T ss_pred             EEEEEEEECCCCccchhhhhhhh-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeccccccccccCH
Confidence            46778999999321    11122 24799999999986532110         011112346799999999986421233


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+..  ..+++++||++|+|++++++++.+.
T Consensus       127 ~~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  161 (166)
T 3q72_A          127 DEGRACAVVF--DCKFIETSAALHHNVQALFEGVVRQ  161 (166)
T ss_dssp             HHHHHHHHHT--TCEEEECBGGGTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHHh--CCcEEEeccCCCCCHHHHHHHHHHH
Confidence            3444444443  4699999999999999999988664

>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=98.74  E-value=2.8e-08  Score=72.99  Aligned_cols=102  Identities=14%  Similarity=0.099  Sum_probs=63.2

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--C----------CCCCCCceeEEEEecCCCCCchh
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--K----------GGPGITQADLLVINKTDLASAIG  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~----------~~~qi~~adiiviNK~Dl~~~~~  136 (178)
                      .+.+.+++|.|..-    ...+. ..+|.+++|+|+++......  .          ....-..+-++|+||+|+.+...
T Consensus        57 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~  135 (182)
T 1ky3_A           57 VATMQVWDTAGQERFQSLGVAFY-RGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEESKK  135 (182)
T ss_dssp             CEEEEEECCC----------CCS-TTCCEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSCTTTCCEEEEEECTTSCGGGC
T ss_pred             EEEEEEEECCCChHhhhhhHHHh-hcCCEEEEEEECCChHHHHHHHHHHHHHHHHhcccCcCCCcEEEEEECCccccccc
Confidence            46789999999311    11122 24799999999987532110  0          00112346799999999964310


Q ss_pred             -HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 -ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 -~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                       ...+...+..+. .+..+++++||++|+|+++++++|.+.
T Consensus       136 ~v~~~~~~~~~~~-~~~~~~~~~Sa~~~~gi~~l~~~l~~~  175 (182)
T 1ky3_A          136 IVSEKSAQELAKS-LGDIPLFLTSAKNAINVDTAFEEIARS  175 (182)
T ss_dssp             CSCHHHHHHHHHH-TTSCCEEEEBTTTTBSHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHh-cCCCeEEEEecCCCCCHHHHHHHHHHH
Confidence             123334444332 346789999999999999999988654

>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=98.74  E-value=1.1e-08  Score=76.19  Aligned_cols=100  Identities=17%  Similarity=0.061  Sum_probs=68.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCC--------cC----C-CCCCCceeEEEEecCCCCCch
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIP--------RK----G-GPGITQADLLVINKTDLASAI  135 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~--------~~----~-~~qi~~adiiviNK~Dl~~~~  135 (178)
                      ...+.+++|.|..    +...+. ..+|.+++|+|++.+....        ..    . ...-..+-++|+||+|+.+. 
T Consensus        73 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~D~~~~~~~~~~~s~~~l~~~l~~~~~~~~~~piilv~NK~Dl~~~-  150 (198)
T 3t1o_A           73 KTRFHLYTVPGQVFYNASRKLIL-RGVDGIVFVADSAPNRLRANAESMRNMRENLAEYGLTLDDVPIVIQVNKRDLPDA-  150 (198)
T ss_dssp             EEEEEEEECCSCCSCSHHHHHHT-TTCCEEEEEEECCGGGHHHHHHHHHHHHHHHHHTTCCTTSSCEEEEEECTTSTTC-
T ss_pred             ceEEEEEeCCChHHHHHHHHHHH-hcCCEEEEEEECCcchhhHhHHHHHHHHHHHHhhccccCCCCEEEEEEchhcccc-
Confidence            4678899999931    112222 2579999999998431100        00    0 01124467999999999877 


Q ss_pred             hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          136 GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       136 ~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                       ...+.+.+..+.. ...+++++||++|+|+++++++|.+.
T Consensus       151 -~~~~~~~~~~~~~-~~~~~~~~Sa~~~~gv~~l~~~l~~~  189 (198)
T 3t1o_A          151 -LPVEMVRAVVDPE-GKFPVLEAVATEGKGVFETLKEVSRL  189 (198)
T ss_dssp             -CCHHHHHHHHCTT-CCSCEEECBGGGTBTHHHHHHHHHHH
T ss_pred             -cCHHHHHHHHHhc-CCceEEEEecCCCcCHHHHHHHHHHH
Confidence             5566667666643 22389999999999999999987654

>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=98.72  E-value=2.2e-08  Score=75.44  Aligned_cols=102  Identities=12%  Similarity=0.089  Sum_probs=65.1

Q ss_pred             CCCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHh
Q 030407           72 FKADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        72 ~~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+..+.+++|.|..    +...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.+.  ..
T Consensus        71 ~~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~iilv~D~~~~~s~~~~~~~l~~~~~~~~~~~~piilv~NK~Dl~~~--~~  147 (192)
T 2b6h_A           71 KNICFTVWDVGGQDKIRPLWRHYF-QNTQGLIFVVDSNDRERVQESADELQKMLQEDELRDAVLLVFANKQDMPNA--MP  147 (192)
T ss_dssp             TTEEEEEEECC-----CTTHHHHH-HTCCEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC--CC
T ss_pred             CCEEEEEEECCCCHhHHHHHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHhcccccCCCeEEEEEECCCCCCC--CC
Confidence            35788999999931    111111 24799999999987643211         0001124567999999999876  44


Q ss_pred             HHHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 LAVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+++.+.+...   ....+++++||++|+|+++++++|.+.
T Consensus       148 ~~~i~~~~~~~~~~~~~~~~~~~SA~~g~gi~~l~~~l~~~  188 (192)
T 2b6h_A          148 VSELTDKLGLQHLRSRTWYVQATCATQGTGLYDGLDWLSHE  188 (192)
T ss_dssp             HHHHHHHTTGGGCSSCCEEEEECBTTTTBTHHHHHHHHHHH
T ss_pred             HHHHHHHhCcccccCCceEEEECcCCCcCCHHHHHHHHHHH
Confidence            44444443321   123479999999999999999988754

>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=98.71  E-value=1e-08  Score=79.53  Aligned_cols=100  Identities=20%  Similarity=0.153  Sum_probs=67.2

Q ss_pred             CCCEEEEeCCcc----hhhhcccccccceEEEEEeCCCCCCCCc---CCCC-----CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGD----NLAANFSRELADYIIYIIDVSGGDKIPR---KGGP-----GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~----~~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~-----qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+-|++|.|.    ++...+.. .++++++|+|.+.......   .+..     .-..+-++|.||+|+.+......+
T Consensus        61 ~v~l~iwDtaGqe~~~~l~~~~~~-~a~~~ilv~di~~~~Sf~~i~~~~~~i~~~~~~~~piilVgNK~Dl~~~r~V~~~  139 (216)
T 4dkx_A           61 TIRLQLWDTAGLERFRSLIPSYIR-DSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQVSIE  139 (216)
T ss_dssp             EEEEEEECCSCTTTCGGGHHHHHT-TCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTTSSEEEEEEECTTCGGGCCSCHH
T ss_pred             EEEEEEEECCCchhhhhHHHHHhc-cccEEEEEeecchhHHHHHHHHHHHHHHHhcCCCCeEEEEeeccchHhcCcccHH
Confidence            467779999993    12233333 5799999999987532211   0000     012356899999999754213345


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +..++.++.+  +++++|||++|+||+++|+.|.+
T Consensus       140 e~~~~a~~~~--~~~~e~SAktg~nV~e~F~~i~~  172 (216)
T 4dkx_A          140 EGERKAKELN--VMFIETSAKAGYNVKQLFRRVAA  172 (216)
T ss_dssp             HHHHHHHHHT--CEEEEEBTTTTBSHHHHHHHHHH
T ss_pred             HHhhHHHHhC--CeeEEEeCCCCcCHHHHHHHHHH
Confidence            5566666654  68999999999999999998764

>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=98.71  E-value=4.1e-09  Score=90.18  Aligned_cols=103  Identities=16%  Similarity=0.124  Sum_probs=69.0

Q ss_pred             CCEEEEeCCcch--------------hhhcccccccceEEEEEeCCCCCCCCcC-CC---CCCCceeEEEEecCCCCCch
Q 030407           74 ADLLLCESGGDN--------------LAANFSRELADYIIYIIDVSGGDKIPRK-GG---PGITQADLLVINKTDLASAI  135 (178)
Q Consensus        74 ~d~iiiEttG~~--------------~~~~~~~~~ad~~I~VvD~~~~~~~~~~-~~---~qi~~adiiviNK~Dl~~~~  135 (178)
                      ..+.|+.|.|..              +........+|.+++|+|++++...... ..   .....+-++|+||+|+.+..
T Consensus       243 ~~~~l~DT~G~~~~~~~~~~~e~~~~~~~~~~~~~ad~~llviD~~~~~~~~~~~~~~~~~~~~~~~ilv~NK~Dl~~~~  322 (456)
T 4dcu_A          243 QEFVIVDTAGMRKKGKVYETTEKYSVLRALKAIDRSEVVAVVLDGEEGIIEQDKRIAGYAHEAGKAVVIVVNKWDAVDKD  322 (456)
T ss_dssp             EEEEETTGGGTTTBTTBCCCCSHHHHHHHHHHHHHCSEEEEEEETTTCCCHHHHHHHHHHHHTTCEEEEEEECGGGSCCC
T ss_pred             ceEEEEECCCCCcCcccchHHHHHHHHHHHHHHhhCCEEEEEEeCCCCcCHHHHHHHHHHHHcCCCEEEEEEChhcCCCc
Confidence            467889999931              0011112246999999999876432211 10   11245779999999998642


Q ss_pred             hHhHHHHHHHHHhcC---CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          136 GADLAVMERDALRMR---DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       136 ~~~~~~~~~~l~~~n---p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ....+++.+.+++..   +.++++++||++|+|++++++.+.+.
T Consensus       323 ~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~g~gv~~l~~~i~~~  366 (456)
T 4dcu_A          323 ESTMKEFEENIRDHFQFLDYAPILFMSALTKKRIHTLMPAIIKA  366 (456)
T ss_dssp             SSHHHHHHHHHHHHCGGGTTSCEEECCTTTCTTGGGHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcccCCCCCEEEEcCCCCcCHHHHHHHHHHH
Confidence            234556666666553   36899999999999999999988654

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=98.71  E-value=9.8e-09  Score=76.70  Aligned_cols=101  Identities=19%  Similarity=0.175  Sum_probs=65.7

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.|++|.|..-    ...+. ..+|.+++|+|+++......  .+..      .-..+-++|+||+|+.+......+
T Consensus        64 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~p~ilv~nK~Dl~~~~~~~~~  142 (196)
T 3tkl_A           64 TIKLQIWDTAGQERFRTITSSYY-RGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYT  142 (196)
T ss_dssp             EEEEEEEEECCSGGGCTTHHHHH-TTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCTTTCCSCHH
T ss_pred             EEEEEEEECCCcHhhhhhHHHHH-hhCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECcccccccccCHH
Confidence            36788999999321    11111 24799999999987432111  0000      013467999999999765212233


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  ..+++++||++|+|++++|++|.+.
T Consensus       143 ~~~~~~~~~--~~~~~~~Sa~~g~gv~~l~~~l~~~  176 (196)
T 3tkl_A          143 TAKEFADSL--GIPFLETSAKNATNVEQSFMTMAAE  176 (196)
T ss_dssp             HHHHHHHHT--TCCEEEECTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCcEEEEeCCCCCCHHHHHHHHHHH
Confidence            444444444  3689999999999999999987654

>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=98.70  E-value=6.3e-08  Score=70.96  Aligned_cols=101  Identities=8%  Similarity=0.042  Sum_probs=66.1

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--C----------CCCCCCceeEEEEecCCCCCchh
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--K----------GGPGITQADLLVINKTDLASAIG  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~----------~~~qi~~adiiviNK~Dl~~~~~  136 (178)
                      .+.+.+++|.|..-    ...+. ..+|.+++|+|+++......  .          .......+-++|+||+|+.+.. 
T Consensus        55 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~p~i~v~nK~Dl~~~~-  132 (177)
T 1wms_A           55 FVTMQIWDTAGQERFRSLRTPFY-RGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDISERQ-  132 (177)
T ss_dssp             EEEEEEEECCCCGGGHHHHGGGG-TTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTCSCTTTSCEEEEEECTTCSSCS-
T ss_pred             EEEEEEEeCCCchhhhhhHHHHH-hcCCEEEEEEECcCHHHHHHHHHHHHHHHHHccccccCCCcEEEEEECCcccccc-
Confidence            36789999999421    12222 24799999999987532110  0          0001234679999999997431 


Q ss_pred             HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 ~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+...+..+. ....+++++||++|+|++++++++.+.
T Consensus       133 ~~~~~~~~~~~~-~~~~~~~~~Sa~~~~gi~~l~~~l~~~  171 (177)
T 1wms_A          133 VSTEEAQAWCRD-NGDYPYFETSAKDATNVAAAFEEAVRR  171 (177)
T ss_dssp             SCHHHHHHHHHH-TTCCCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHh-cCCceEEEEeCCCCCCHHHHHHHHHHH
Confidence            233445555443 345799999999999999999987654

>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=98.70  E-value=2.5e-08  Score=75.16  Aligned_cols=102  Identities=11%  Similarity=0.063  Sum_probs=65.3

Q ss_pred             CCCEEEEeCCcchhhhc---ccccccceEEEEEeCCCCCCCCc--CCC-------C---CCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDNLAAN---FSRELADYIIYIIDVSGGDKIPR--KGG-------P---GITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~---~~~~~ad~~I~VvD~~~~~~~~~--~~~-------~---qi~~adiiviNK~Dl~~~~~~  137 (178)
                      .+.+.|++|.|..--..   .....+|.+++|+|+++......  .+.       .   .-..+-++|+||+|+.+.. .
T Consensus        56 ~~~~~l~Dt~G~~~~~~~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~-~  134 (207)
T 1vg8_A           56 LVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQ-V  134 (207)
T ss_dssp             EEEEEEEEECSSGGGSCSCCGGGTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSSGGGSCEEEEEECTTSSCCC-S
T ss_pred             EEEEEEEeCCCcHHHHHhHHHHHhCCcEEEEEEECCCHHHHHHHHHHHHHHHHhcccccCCCCcEEEEEECCCCcccc-c
Confidence            46789999999321111   11124799999999987532110  000       0   0134569999999997431 2


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+...++.+. ....+++++||++|+|+++++++|.+.
T Consensus       135 ~~~~~~~~~~~-~~~~~~~~~Sa~~g~gi~~l~~~l~~~  172 (207)
T 1vg8_A          135 ATKRAQAWCYS-KNNIPYFETSAKEAINVEQAFQTIARN  172 (207)
T ss_dssp             CHHHHHHHHHH-TTSCCEEECBTTTTBSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHh-cCCceEEEEeCCCCCCHHHHHHHHHHH
Confidence            23444444432 345799999999999999999988654

>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=98.70  E-value=1.4e-08  Score=74.36  Aligned_cols=101  Identities=14%  Similarity=0.052  Sum_probs=66.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.+++|.|..-    ...+. ..+|.+++|+|+++......  .+.      .....+-++|+||+|+.++.....+
T Consensus        63 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~  141 (179)
T 1z0f_A           63 KIKLQIWDTAGQERFRAVTRSYY-RGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIILIGNKADLEAQRDVTYE  141 (179)
T ss_dssp             EEEEEEEECTTGGGTCHHHHHHH-HTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHH
T ss_pred             EEEEEEEECCCChHhhhhHHHHh-ccCCEEEEEEeCcCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECcccccccccCHH
Confidence            46789999999321    11111 24699999999987532111  000      0123467999999999754212334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  +.+++++||++|+|++++++++.+.
T Consensus       142 ~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  175 (179)
T 1z0f_A          142 EAKQFAEEN--GLLFLEASAKTGENVEDAFLEAAKK  175 (179)
T ss_dssp             HHHHHHHHT--TCEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            555555554  4689999999999999999987654

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=98.70  E-value=6.2e-09  Score=76.49  Aligned_cols=100  Identities=13%  Similarity=0.079  Sum_probs=65.2

Q ss_pred             CCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCCCC-----CCceeEEEEecCCCCCchhHhHHHH
Q 030407           74 ADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGGPG-----ITQADLLVINKTDLASAIGADLAVM  142 (178)
Q Consensus        74 ~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~q-----i~~adiiviNK~Dl~~~~~~~~~~~  142 (178)
                      +.+.+++|.|..-    ...+. ..+|.+++|+|+++......  .+...     -..+-++|+||+|+.+......+..
T Consensus        58 ~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~~~~  136 (181)
T 3tw8_B           58 VKLQIWDTAGQERFRTITSTYY-RGTHGVIVVYDVTSAESFVNVKRWLHEINQNCDDVCRILVGNKNDDPERKVVETEDA  136 (181)
T ss_dssp             EEEEEEEETTGGGCSSCCGGGG-TTCSEEEEEEETTCHHHHHHHHHHHHHHHHHCTTSEEEEEEECTTCGGGCCSCHHHH
T ss_pred             EEEEEEcCCCchhhhhhHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCEEEEEECCCCchhcccCHHHH
Confidence            6788999999321    11122 24799999999987532211  00000     1245699999999976421223444


Q ss_pred             HHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          143 ERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       143 ~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+..+..  +.+++++||++|+|++++++++.+.
T Consensus       137 ~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  168 (181)
T 3tw8_B          137 YKFAGQM--GIQLFETSAKENVNVEEMFNCITEL  168 (181)
T ss_dssp             HHHHHHH--TCCEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHc--CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4444444  3589999999999999999988764

>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=98.70  E-value=1.5e-08  Score=76.30  Aligned_cols=101  Identities=10%  Similarity=0.079  Sum_probs=67.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.|++|.|..    +...+. ..+|++++|+|+++......         .+...-..+-++|+||+|+.++.....
T Consensus        61 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~  139 (206)
T 2bov_A           61 EVQIDILDTAGQEDYAAIRDNYF-RSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSV  139 (206)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHH-HHCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTCSCCCEEEEEECTTCGGGCCSCH
T ss_pred             EEEEEEEcCCChhhhHHHHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEeccCccccccccH
Confidence            3678899999931    111222 24699999999986432110         011112346799999999976421334


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.+.+..+..+  .+++++||++|+|+++++++|.+.
T Consensus       140 ~~~~~~~~~~~--~~~~~~Sa~~g~gi~~l~~~l~~~  174 (206)
T 2bov_A          140 EEAKNRAEQWN--VNYVETSAKTRANVDKVFFDLMRE  174 (206)
T ss_dssp             HHHHHHHHHHT--CEEEEECTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHhC--CeEEEEeCCCCCCHHHHHHHHHHH
Confidence            55666666543  589999999999999999987654

>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=98.70  E-value=2.8e-08  Score=74.02  Aligned_cols=102  Identities=18%  Similarity=0.086  Sum_probs=66.2

Q ss_pred             CCCEEEEeCCcchh-h---hcccccccceEEEEEeCCCCCCCCc------CCCC---CCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL-A---ANFSRELADYIIYIIDVSGGDKIPR------KGGP---GITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~-~---~~~~~~~ad~~I~VvD~~~~~~~~~------~~~~---qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|..- .   ..+ ...+|.+++|+|+++......      ....   .-..+-++|+||+|+.+.  ...
T Consensus        59 ~~~l~i~Dt~G~~~~~~~~~~~-~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~--~~~  135 (181)
T 1fzq_A           59 GFKLNVWDIGGQRKIRPYWRSY-FENTDILIYVIDSADRKRFEETGQELTELLEEEKLSCVPVLIFANKQDLLTA--APA  135 (181)
T ss_dssp             TEEEEEEECSSCGGGHHHHHHH-HTTCSEEEEEEETTCGGGHHHHHHHHHHHTTCGGGTTCCEEEEEECTTSTTC--CCH
T ss_pred             CEEEEEEECCCCHHHHHHHHHH-hCCCCEEEEEEECcCHHHHHHHHHHHHHHHhChhhcCCCEEEEEECcCcccC--CCH
Confidence            56788999999421 1   111 135799999999987542211      0001   123467999999999876  344


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +.+.+.+...   ....+++++||++|+|++++++++.+.+
T Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~~  176 (181)
T 1fzq_A          136 SEIAEGLNLHTIRDRVWQIQSCSALTGEGVQDGMNWVCKNV  176 (181)
T ss_dssp             HHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHTC
T ss_pred             HHHHHHhCchhccCCceEEEEccCCCCCCHHHHHHHHHHHH
Confidence            4444433211   1235799999999999999999987643

>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=98.69  E-value=8e-09  Score=74.74  Aligned_cols=101  Identities=10%  Similarity=0.075  Sum_probs=66.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.+++|.|..    +...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.++.....
T Consensus        51 ~~~~~l~D~~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~  129 (168)
T 1u8z_A           51 EVQIDILDTAGQEDYAAIRDNYF-RSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSV  129 (168)
T ss_dssp             EEEEEEEECCC---CHHHHHHHH-HHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHCCTTSCEEEEEECGGGGGGCCSCH
T ss_pred             EEEEEEEECCCcchhHHHHHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECccccccCccCH
Confidence            4678899999932    112222 24699999999986432110         000112346799999999975421234


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+..+  .+++++||++|+|++++++++.+.
T Consensus       130 ~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~~~l~~~  164 (168)
T 1u8z_A          130 EEAKNRADQWN--VNYVETSAKTRANVDKVFFDLMRE  164 (168)
T ss_dssp             HHHHHHHHHHT--CEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC--CeEEEeCCCCCCCHHHHHHHHHHH
Confidence            45555665543  589999999999999999988654

>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=98.69  E-value=6.4e-09  Score=78.10  Aligned_cols=102  Identities=15%  Similarity=0.074  Sum_probs=67.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.|++|.|..-    ...+. ..+|.+++|+|+++......  .+..      .-..+-++|+||+|+.++.....+
T Consensus        71 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~iilV~d~~~~~s~~~~~~~~~~i~~~~~~~~piiiv~NK~Dl~~~~~v~~~  149 (192)
T 2fg5_A           71 LHKFLIWDTAGQERFHSLAPMYY-RGSAAAVIVYDITKQDSFYTLKKWVKELKEHGPENIVMAIAGNKCDLSDIREVPLK  149 (192)
T ss_dssp             EEEEEEEEECCSGGGGGGTHHHH-TTCSEEEEEEETTCTHHHHHHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHH
T ss_pred             EEEEEEEcCCCchhhHhhhHHhh-ccCCEEEEEEeCCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEECcccccccccCHH
Confidence            46789999999321    11111 24699999999987542211  0000      013467999999999753112345


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ...+..+..  +.+++++||++|+|+++++++|.+.+
T Consensus       150 ~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~i  184 (192)
T 2fg5_A          150 DAKEYAESI--GAIVVETSAKNAINIEELFQGISRQI  184 (192)
T ss_dssp             HHHHHHHTT--TCEEEECBTTTTBSHHHHHHHHHHTC
T ss_pred             HHHHHHHHc--CCEEEEEeCCCCcCHHHHHHHHHHHH
Confidence            566666554  36899999999999999999987653

>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=98.69  E-value=1.6e-08  Score=73.37  Aligned_cols=102  Identities=11%  Similarity=0.012  Sum_probs=66.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ++.+.+++|.|..    +...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.++.....
T Consensus        50 ~~~~~l~D~~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~  128 (167)
T 1c1y_A           50 QCMLEILDTAGTEQFTAMRDLYM-KNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGK  128 (167)
T ss_dssp             EEEEEEEEECSSCSSTTHHHHHH-HHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSCCCEEEEEECTTCGGGCCSCH
T ss_pred             EEEEEEEECCChHHHHHHHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCcCCCcEEEEEECccccccccCCH
Confidence            4678899999931    111122 24699999999986432110         000112345699999999975411223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+.. +..+++++||++|+|+++++++|.+.
T Consensus       129 ~~~~~~~~~~-~~~~~~~~Sa~~~~gi~~l~~~l~~~  164 (167)
T 1c1y_A          129 EQGQNLARQW-CNCAFLESSAKSKINVNEIFYDLVRQ  164 (167)
T ss_dssp             HHHHHHHHHT-TSCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHHc-cCCcEEEecCCCCCCHHHHHHHHHHH
Confidence            4445544443 45789999999999999999998764

>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=98.69  E-value=2.7e-08  Score=72.75  Aligned_cols=101  Identities=11%  Similarity=0.031  Sum_probs=61.9

Q ss_pred             CCCEEEEeCCcchh------hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDNL------AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~------~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~  137 (178)
                      .+.+.+++|.|..-      ...+ ...+|.+++|+|+++......         .....-..+-++|+||+|+.+....
T Consensus        51 ~~~~~~~D~~g~~~~~~~~~~~~~-~~~~~~~i~v~d~~~~~s~~~~~~~~~~l~~~~~~~~~piilv~NK~Dl~~~~~v  129 (175)
T 2nzj_A           51 DTTLVVVDTWEAEKLDKSWSQESC-LQGGSAYVIVYSIADRGSFESASELRIQLRRTHQADHVPIILVGNKADLARCREV  129 (175)
T ss_dssp             EEEEEEECCC-------CHHHHHT-TTSCSEEEEEEETTCHHHHHHHHHHHHHHHHCC----CCEEEEEECTTCTTTCCS
T ss_pred             EEEEEEEecCCCCccchhhhHHhh-cccCCEEEEEEECCCHHHHHHHHHHHHHHHHhhccCCCCEEEEEEChhhcccccc
Confidence            45788999999421      1111 124699999999986432110         0111113467999999999764112


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+......+..  +.+++++||++|+|+++++++|.+.
T Consensus       130 ~~~~~~~~~~~~--~~~~~~~Sa~~g~gi~~l~~~l~~~  166 (175)
T 2nzj_A          130 SVEEGRACAVVF--DCKFIETSATLQHNVAELFEGVVRQ  166 (175)
T ss_dssp             CHHHHHHHHHHH--TSEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHc--CCeEEEEecCCCCCHHHHHHHHHHH
Confidence            233344444443  3589999999999999999988654

>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=98.69  E-value=2.7e-08  Score=73.72  Aligned_cols=101  Identities=15%  Similarity=0.130  Sum_probs=66.2

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.+++|.|..-    ...+. ..+|.+++|+|+++......  .       ....-..+-++|+||+|+.++.....
T Consensus        69 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~  147 (195)
T 3bc1_A           69 RIHLQLWDTAGLERFRSLTTAFF-RDAMGFLLLFDLTNEQSFLNVRNWISQLQMHAYSENPDIVLCGNKSDLEDQRAVKE  147 (195)
T ss_dssp             EEEEEEEEECCSGGGHHHHHHTT-TTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSSSSSCCEEEEEECTTCGGGCCSCH
T ss_pred             EEEEEEEeCCCcHHHHHHHHHHH-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccCH
Confidence            46789999999421    11122 25799999999987532211  0       01112346799999999976311223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.+.+..+..  +.+++++||++|+|+++++++|.+.
T Consensus       148 ~~~~~~~~~~--~~~~~~~Sa~~~~~v~~l~~~l~~~  182 (195)
T 3bc1_A          148 EEARELAEKY--GIPYFETSAANGTNISHAIEMLLDL  182 (195)
T ss_dssp             HHHHHHHHHH--TCCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCCEEEEECCCCCCHHHHHHHHHHH
Confidence            4455555544  3589999999999999999988654

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=98.69  E-value=1.5e-08  Score=74.46  Aligned_cols=102  Identities=12%  Similarity=0.142  Sum_probs=63.7

Q ss_pred             CCCEEEEeCCcchh-hhc--ccccccceEEEEEeCCCCCCCCc----CCCCCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           73 KADLLLCESGGDNL-AAN--FSRELADYIIYIIDVSGGDKIPR----KGGPGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        73 ~~d~iiiEttG~~~-~~~--~~~~~ad~~I~VvD~~~~~~~~~----~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      +..+.+++|.|..- ...  .....+|.+++|+|++++.....    ........+-++|+||+|+.+.   ..+.+...
T Consensus        54 ~~~~~l~Dt~G~~~~~~~~~~~~~~~d~~i~v~d~~~~~~~~~~~~l~~~~~~~~p~ilv~nK~Dl~~~---~~~~~~~~  130 (178)
T 2lkc_A           54 DKKITFLDTPGHEAFTTMRARGAQVTDIVILVVAADDGVMPQTVEAINHAKAANVPIIVAINKMDKPEA---NPDRVMQE  130 (178)
T ss_dssp             TEEEEESCCCSSSSSSCSCCSSCCCCCEEEEEEETTCCCCHHHHHHHHHHGGGSCCEEEEEETTTSSCS---CHHHHHHH
T ss_pred             CceEEEEECCCCHHHHHHHHHHHhhCCEEEEEEECCCCCcHHHHHHHHHHHhCCCCEEEEEECccCCcC---CHHHHHHH
Confidence            35677899999311 111  11124689999999877432111    0001124467999999999865   22333444


Q ss_pred             HHhcCC-------CCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          146 ALRMRD-------GGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       146 l~~~np-------~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +++...       ..+++++||++|+|+++++++|.+.+
T Consensus       131 ~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~l~~~l~~~~  169 (178)
T 2lkc_A          131 LMEYNLVPEEWGGDTIFCKLSAKTKEGLDHLLEMILLVS  169 (178)
T ss_dssp             HTTTTCCBTTTTSSEEEEECCSSSSHHHHHHHHHHHHHH
T ss_pred             HHhcCcChhHcCCcccEEEEecCCCCCHHHHHHHHHHhh
Confidence            433221       24899999999999999999987653

>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=98.68  E-value=1.2e-08  Score=82.99  Aligned_cols=101  Identities=9%  Similarity=-0.041  Sum_probs=68.0

Q ss_pred             CCCCEEEEeCCcchh---------hh--cccccccceEEEEEeCCCCCCCCcC-C---CCCC--CceeEEEEecCCCCCc
Q 030407           72 FKADLLLCESGGDNL---------AA--NFSRELADYIIYIIDVSGGDKIPRK-G---GPGI--TQADLLVINKTDLASA  134 (178)
Q Consensus        72 ~~~d~iiiEttG~~~---------~~--~~~~~~ad~~I~VvD~~~~~~~~~~-~---~~qi--~~adiiviNK~Dl~~~  134 (178)
                      .+..++|++|.|..-         ..  ......+|.+++|+|++++...... .   ....  ..+.++|+||+|+.++
T Consensus        53 ~~~~l~l~DTpG~~~~~~~l~~~~~~~~~~~l~~ad~il~VvD~~~~~~~~~~~i~~~l~~~~~~~p~ilV~NK~Dl~~~  132 (301)
T 1wf3_A           53 GRRQIVFVDTPGLHKPMDALGEFMDQEVYEALADVNAVVWVVDLRHPPTPEDELVARALKPLVGKVPILLVGNKLDAAKY  132 (301)
T ss_dssp             TTEEEEEEECCCCCCCCSHHHHHHHHHHHHHTSSCSEEEEEEETTSCCCHHHHHHHHHHGGGTTTSCEEEEEECGGGCSS
T ss_pred             CCcEEEEecCccccchhhHHHHHHHHHHHHHHhcCCEEEEEEECCCCCChHHHHHHHHHHhhcCCCCEEEEEECcccCCc
Confidence            357899999999421         10  0112357999999999876432211 0   0112  4568999999999876


Q ss_pred             hhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          135 IGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       135 ~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                        .. + +.+.++++.+..+++++||++|.|++++++.+.+.
T Consensus       133 --~~-~-~~~~~~~~~~~~~~~~iSA~~g~gv~~l~~~l~~~  170 (301)
T 1wf3_A          133 --PE-E-AMKAYHELLPEAEPRMLSALDERQVAELKADLLAL  170 (301)
T ss_dssp             --HH-H-HHHHHHHTSTTSEEEECCTTCHHHHHHHHHHHHTT
T ss_pred             --hH-H-HHHHHHHhcCcCcEEEEeCCCCCCHHHHHHHHHHh
Confidence              33 0 23344444566789999999999999999998754

>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=98.68  E-value=6.3e-09  Score=79.26  Aligned_cols=102  Identities=16%  Similarity=0.115  Sum_probs=63.3

Q ss_pred             CCCEEEEeCCcch-----hhhcccccccceEEEEEeCCCCCCCCc----CC--------CCCCCceeEEEEecCCCCCch
Q 030407           73 KADLLLCESGGDN-----LAANFSRELADYIIYIIDVSGGDKIPR----KG--------GPGITQADLLVINKTDLASAI  135 (178)
Q Consensus        73 ~~d~iiiEttG~~-----~~~~~~~~~ad~~I~VvD~~~~~~~~~----~~--------~~qi~~adiiviNK~Dl~~~~  135 (178)
                      +..+.+++|.|..     +...+. ..+|.+++|+|+++......    .+        ......+-++|+||+|+.+. 
T Consensus        53 ~~~~~i~Dt~G~~~~~~~~~~~~~-~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~-  130 (214)
T 2fh5_B           53 GNSLTLIDLPGHESLRFQLLDRFK-SSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMA-  130 (214)
T ss_dssp             CCEEEEEECCCCHHHHHHHHHHHG-GGEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHTSTTCCEEEEEEECTTSTTC-
T ss_pred             ccEEEEEECCCChhHHHHHHHHHH-hhCCEEEEEEECCCcCHHHHHHHHHHHHHHhhhhhcccCCCEEEEEECCCCCCc-
Confidence            5779999999942     112222 35799999999976321100    00        01123567999999999865 


Q ss_pred             hHhHHHHHHHHHh------------------------cCC-------------CCCEEEEecccC------CCHHHHHHH
Q 030407          136 GADLAVMERDALR------------------------MRD-------------GGPFIFAQVGWV------IGIIFTLSI  172 (178)
Q Consensus       136 ~~~~~~~~~~l~~------------------------~np-------------~a~i~~~SA~~g------~gi~el~~~  172 (178)
                       ...+...+.+++                        ...             ..+++++||++|      +||+++|++
T Consensus       131 -~~~~~~~~~l~~~l~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~SAk~g~~~~~~~gv~~lf~~  209 (214)
T 2fh5_B          131 -KSAKLIQQQLEKELNTLRVTRSAAPSTLDSSSTAPAQLGKKGKEFEFSQLPLKVEFLECSAKGGRGDTGSADIQDLEKW  209 (214)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHHCC------------CCCSSCTTSCCCGGGSSSCEEEEECBCC-------CCBCHHHHHH
T ss_pred             -ccHHHHHHHHHHHHHHHhccchhccccccCCccccccccCCCCCcccccCCCcEEEEEeeccCCCccccccChHHHHHH
Confidence             333333333221                        111             457999999999      999999999


Q ss_pred             Hhhhh
Q 030407          173 THYIV  177 (178)
Q Consensus       173 l~~~~  177 (178)
                      |.+.+
T Consensus       210 l~~~~  214 (214)
T 2fh5_B          210 LAKIA  214 (214)
T ss_dssp             HHHHC
T ss_pred             HHHhC
Confidence            97753

>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=98.68  E-value=3.2e-08  Score=72.77  Aligned_cols=101  Identities=17%  Similarity=0.133  Sum_probs=64.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.+++|.|..    +...+. ..+|.+++|+|+++......  .+.      ..-..+-++|+||+|+.++.....+
T Consensus        59 ~~~~~~~Dt~G~~~~~~~~~~~~-~~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~  137 (180)
T 2g6b_A           59 KVKLQMWDTAGQERFRSVTHAYY-RDAHALLLLYDVTNKASFDNIQAWLTEIHEYAQHDVALMLLGNKVDSAHERVVKRE  137 (180)
T ss_dssp             EEEEEEEECCCC--------CCG-GGCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECCSTTSCCCSCHH
T ss_pred             EEEEEEEeCCCcHHHHHHHHHHc-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEECcccCcccccCHH
Confidence            4678899999932    111122 24699999999987532111  000      0123467999999999864212233


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  +.+++++||++|+|++++++++.+.
T Consensus       138 ~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  171 (180)
T 2g6b_A          138 DGEKLAKEY--GLPFMETSAKTGLNVDLAFTAIAKE  171 (180)
T ss_dssp             HHHHHHHHH--TCCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            444444444  3589999999999999999988654

>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=98.67  E-value=3e-08  Score=75.04  Aligned_cols=101  Identities=18%  Similarity=0.091  Sum_probs=65.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.|++|.|..-    ...+. ..+|.+++|+|+++......  .+.      ..-..+-++|+||+|+.++.....+
T Consensus        56 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~vilv~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~  134 (206)
T 2bcg_Y           56 TVKLQIWDTAGQERFRTITSSYY-RGSHGIIIVYDVTDQESFNGVKMWLQEIDRYATSTVLKLLVGNKCDLKDKRVVEYD  134 (206)
T ss_dssp             EEEEEEECCTTTTTTTCCCGGGG-TTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECTTCTTTCCSCHH
T ss_pred             EEEEEEEeCCChHHHHHHHHHhc-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCccccccCHH
Confidence            46789999999321    11122 24799999999987532111  000      0113456999999999864112234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  +.+++++||++|+|+++++++|.+.
T Consensus       135 ~~~~~~~~~--~~~~~~~Sa~~g~gi~~l~~~l~~~  168 (206)
T 2bcg_Y          135 VAKEFADAN--KMPFLETSALDSTNVEDAFLTMARQ  168 (206)
T ss_dssp             HHHHHHHHT--TCCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            444444443  3689999999999999999987654

>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=98.67  E-value=1.2e-08  Score=74.22  Aligned_cols=101  Identities=16%  Similarity=0.114  Sum_probs=65.5

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCCC------CCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGPG------ITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~q------i~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.+++|.|..    +...+. ..+|.+++|+|+++......  .+...      -..+-++|+||+|+.++.....+
T Consensus        54 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~  132 (170)
T 1z08_A           54 RVNLAIWDTAGQERFHALGPIYY-RDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEKERHVSIQ  132 (170)
T ss_dssp             EEEEEEEECCCC-------CCSS-TTCSEEEEEEETTCHHHHHHHHHHHHHHHHHHGGGSEEEEEEECGGGGGGCCSCHH
T ss_pred             EEEEEEEECCCcHhhhhhHHHHh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCeEEEEEECcccccccccCHH
Confidence            4678899999932    111122 24699999999987532111  00000      13456999999999764112344


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  +.+++++||++|+|+++++++|.+.
T Consensus       133 ~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  166 (170)
T 1z08_A          133 EAESYAESV--GAKHYHTSAKQNKGIEELFLDLCKR  166 (170)
T ss_dssp             HHHHHHHHT--TCEEEEEBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCeEEEecCCCCCCHHHHHHHHHHH
Confidence            555555554  3689999999999999999988654

>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=98.66  E-value=1.2e-08  Score=75.36  Aligned_cols=101  Identities=10%  Similarity=0.079  Sum_probs=66.8

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.|++|.|..    +...+. ..+|.+++|+|+++......         .+...-..+-++|+||+|+.++.....
T Consensus        65 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~  143 (187)
T 2a9k_A           65 EVQIDILDTAGQEDYAAIRDNYF-RSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSV  143 (187)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHH-HHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHCCTTCCEEEEEECGGGGGGCCSCH
T ss_pred             EEEEEEEECCCCcccHHHHHHHh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccCccCH
Confidence            3678899999932    111222 24699999999986432110         011112345699999999976421334


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.+.+..+..  ..+++++||++|+|+++++++|.+.
T Consensus       144 ~~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  178 (187)
T 2a9k_A          144 EEAKNRAEQW--NVNYVETSAKTRANVDKVFFDLMRE  178 (187)
T ss_dssp             HHHHHHHHHT--TCEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCeEEEeCCCCCCCHHHHHHHHHHH
Confidence            5566666654  3589999999999999999988654

>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=98.66  E-value=2.8e-08  Score=73.17  Aligned_cols=102  Identities=17%  Similarity=0.063  Sum_probs=66.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.|++|.|..-    ...+ ...+|.+++|+|+++......  .+.      ..-..+-++|+||+|+.++.....+
T Consensus        60 ~~~~~i~Dt~G~~~~~~~~~~~-~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~p~i~v~nK~Dl~~~~~~~~~  138 (181)
T 2efe_B           60 TVKFEIWDTAGQERYHSLAPMY-YRGAAAAIIVFDVTNQASFERAKKWVQELQAQGNPNMVMALAGNKSDLLDARKVTAE  138 (181)
T ss_dssp             EEEEEEEECCCSGGGGGGTHHH-HTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECTTCTTTCCSCHH
T ss_pred             EEEEEEEeCCCChhhhhhhHHH-hccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECCcccccccCCHH
Confidence            46789999999321    1111 124799999999976532111  000      0113457999999999754212334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .+.+..+..  ..+++++||++|+|+++++++|.+.+
T Consensus       139 ~~~~~~~~~--~~~~~~~Sa~~g~gi~~l~~~l~~~~  173 (181)
T 2efe_B          139 DAQTYAQEN--GLFFMETSAKTATNVKEIFYEIARRL  173 (181)
T ss_dssp             HHHHHHHHT--TCEEEECCSSSCTTHHHHHHHHHHTC
T ss_pred             HHHHHHHHc--CCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            555555543  46899999999999999999987643

>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=98.66  E-value=2.2e-08  Score=77.35  Aligned_cols=104  Identities=11%  Similarity=0.017  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCcchh----hh--------cccccccceEEEEEeCCCCCCCCc----C----CCCC-CCceeEEEEecCCC
Q 030407           73 KADLLLCESGGDNL----AA--------NFSRELADYIIYIIDVSGGDKIPR----K----GGPG-ITQADLLVINKTDL  131 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~--------~~~~~~ad~~I~VvD~~~~~~~~~----~----~~~q-i~~adiiviNK~Dl  131 (178)
                      +..+.|++|.|..-    ..        ......+|++++|+|+++......    .    .... -..+-++|+||+|+
T Consensus        75 ~~~~~l~DtpG~~~~~~~~~~~~~~~~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~l~~~~~~~piilv~nK~Dl  154 (228)
T 2qu8_A           75 LNKYQIIDTPGLLDRAFENRNTIEMTTITALAHINGVILFIIDISEQCGLTIKEQINLFYSIKSVFSNKSIVIGFNKIDK  154 (228)
T ss_dssp             TEEEEEEECTTTTTSCGGGCCHHHHHHHHHHHTSSEEEEEEEETTCTTSSCHHHHHHHHHHHHTCC-CCCEEEEEECGGG
T ss_pred             CCeEEEEECCCCcCcccchhhhHHHHHHHHhhccccEEEEEEecccccCcchHHHHHHHHHHHHhhcCCcEEEEEeCccc
Confidence            46789999999410    00        001224689999999987644321    0    0011 14567999999999


Q ss_pred             CCchh---HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          132 ASAIG---ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       132 ~~~~~---~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+...   ...+.+.+..+..++..+++++||++|+|+++++++|.+.
T Consensus       155 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~g~gi~~l~~~l~~~  202 (228)
T 2qu8_A          155 CNMDSLSIDNKLLIKQILDNVKNPIKFSSFSTLTGVGVEQAKITACEL  202 (228)
T ss_dssp             CC--CCCHHHHHHHHHHHHHCCSCEEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             CCchhhHHHHHHHHHHHHHhcCCCceEEEEecccCCCHHHHHHHHHHH
Confidence            76410   1112334444444344689999999999999999987654

>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=98.66  E-value=8.7e-08  Score=72.98  Aligned_cols=101  Identities=16%  Similarity=0.139  Sum_probs=66.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc------CCCCC---CCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR------KGGPG---ITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~------~~~~q---i~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.|++|.|..    +...+. ..+|.+++|+|+++......      .....   -..+-++|+||+|+.+......
T Consensus        83 ~~~l~l~Dt~G~~~~~~~~~~~~-~~~d~iilV~D~~~~~s~~~~~~~l~~i~~~~~~~~~piilV~NK~Dl~~~~~v~~  161 (217)
T 2f7s_A           83 KVHLQLWDTAGQERFRSLTTAFF-RDAMGFLLMFDLTSQQSFLNVRNWMSQLQANAYCENPDIVLIGNKADLPDQREVNE  161 (217)
T ss_dssp             EEEEEEEEEESHHHHHHHHHHHH-TTCCEEEEEEETTCHHHHHHHHHHHHTCCCCCTTTCCEEEEEEECTTCGGGCCSCH
T ss_pred             eEEEEEEECCCcHhHHhHHHHHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCcCCCCEEEEEECCccccccccCH
Confidence            4678999999931    111122 35799999999987532110      01111   2346799999999975311223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+..  ..+++++||++|+|+++++++|.+.
T Consensus       162 ~~~~~~~~~~--~~~~~~~Sa~~g~gi~~l~~~l~~~  196 (217)
T 2f7s_A          162 RQARELADKY--GIPYFETSAATGQNVEKAVETLLDL  196 (217)
T ss_dssp             HHHHHHHHHT--TCCEEEEBTTTTBTHHHHHHHHHHH
T ss_pred             HHHHHHHHHC--CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4455555544  3589999999999999999988654

>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=98.66  E-value=2.6e-08  Score=73.65  Aligned_cols=101  Identities=14%  Similarity=0.117  Sum_probs=58.3

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.|++|.|..    +...+. ..+|.+++|+|+++......  .+..      .-..+-++|+||+|+.++.....+
T Consensus        56 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~v~~~  134 (183)
T 2fu5_C           56 RIKLQIWDTAGQERFRTITTAYY-RGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKE  134 (183)
T ss_dssp             EEEEEEEEC---------CCTTT-TTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEEC--CCSCCCSCHH
T ss_pred             EEEEEEEcCCCChhhhhhHHHHH-hcCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECccCCccCcCCHH
Confidence            3678899999931    111122 24799999999987532111  0000      113467999999999764112234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  +.+++++||++|+|+++++++|.+.
T Consensus       135 ~~~~~~~~~--~~~~~~~Sa~~~~~i~~l~~~l~~~  168 (183)
T 2fu5_C          135 RGEKLALDY--GIKFMETSAKANINVENAFFTLARD  168 (183)
T ss_dssp             HHHHHHHHH--TCEEEECCC---CCHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            455555554  3589999999999999999988654

>3o47_A ADP-ribosylation factor GTPase-activating protein ribosylation factor 1; structural genomics consortium, GTPase activation; HET: GDP; 2.80A {Homo sapiens}

Probab=98.65  E-value=4.2e-08  Score=80.59  Aligned_cols=102  Identities=14%  Similarity=0.123  Sum_probs=66.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---C------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---K------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.|++|.|..    +...+. ..+|.+|+|+|+++......   .      ....-..+-++|+||+|+.+.  ...
T Consensus       208 ~~~l~i~Dt~G~~~~~~~~~~~~-~~ad~vilV~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilV~NK~Dl~~~--~~~  284 (329)
T 3o47_A          208 NISFTVWDVGGQDKIRPLWRHYF-QNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNA--MNA  284 (329)
T ss_dssp             TEEEEEEECC-----CCSHHHHH-TTEEEEEEEEETTCSSSHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC--CCH
T ss_pred             cEEEEEEECCCCHhHHHHHHHHh-ccCCEEEEEEECCchHHHHHHHHHHHHHHhhhccCCCeEEEEEECccCCcc--cCH
Confidence            5678899999931    111111 24699999999986543211   0      000113467999999999876  455


Q ss_pred             HHHHHHHHhcC---CCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDALRMR---DGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l~~~n---p~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +.+...+....   ...+++++||++|+||+++|+.|.+.+
T Consensus       285 ~~i~~~~~~~~~~~~~~~~~~vSAk~g~gi~el~~~l~~~l  325 (329)
T 3o47_A          285 AEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL  325 (329)
T ss_dssp             HHHHHHHTCTTCCSSCEEEEECBTTTTBTHHHHHHHHHHHH
T ss_pred             HHHHHHhchhhhhcCCCEEEEEECCCCcCHHHHHHHHHHHH
Confidence            55555554221   345799999999999999999887643

>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=98.65  E-value=5.8e-08  Score=72.28  Aligned_cols=100  Identities=20%  Similarity=0.128  Sum_probs=65.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.|++|.|..-    ...+. ..+|.+++|+|+++......         .+...-..+-++|+||+|+.+.. ...
T Consensus        63 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~p~ilv~nK~Dl~~~~-~~~  140 (195)
T 1x3s_A           63 KAKLAIWDTAGQERFRTLTPSYY-RGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKENRE-VDR  140 (195)
T ss_dssp             EEEEEEEEECSSGGGCCSHHHHH-TTCCEEEEEEETTCHHHHHTHHHHHHHHTTCCSCSCCEEEEEEECTTSSSCC-SCH
T ss_pred             EEEEEEEeCCCchhhhhhhHHHh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCcCCCcEEEEEECCcCcccc-cCH
Confidence            46789999999321    11111 24799999999987532110         11111234669999999996431 223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+..  ..+++++||++|+|+++++++|.+.
T Consensus       141 ~~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  175 (195)
T 1x3s_A          141 NEGLKFARKH--SMLFIEASAKTCDGVQCAFEELVEK  175 (195)
T ss_dssp             HHHHHHHHHT--TCEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCEEEEecCCCCCCHHHHHHHHHHH
Confidence            4455555544  4689999999999999999987653

>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=98.64  E-value=4.3e-08  Score=73.13  Aligned_cols=101  Identities=15%  Similarity=0.080  Sum_probs=65.6

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+.+++|.|..    +...+. ..+|.+++|+|+++......  .+..      .-..+-++|+||+|+.++.....+
T Consensus        70 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~  148 (189)
T 2gf9_A           70 RIKLQIWDTAGQERYRTITTAYY-RGAMGFLLMYDIANQESFAAVQDWATQIKTYSWDNAQVILVGNKCDLEDERVVPAE  148 (189)
T ss_dssp             EEEEEEEECCSCCSSCCSGGGGG-TTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHH
T ss_pred             EEEEEEEeCCCcHHHhhhHHHhc-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECcccccccCCCHH
Confidence            4678899999931    111222 24799999999976532111  0000      013467999999999754112234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..+  .+++++||++|+|+++++++|.+.
T Consensus       149 ~~~~~~~~~~--~~~~~~Sa~~g~gi~~l~~~l~~~  182 (189)
T 2gf9_A          149 DGRRLADDLG--FEFFEASAKENINVKQVFERLVDV  182 (189)
T ss_dssp             HHHHHHHHHT--CEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHcC--CeEEEEECCCCCCHHHHHHHHHHH
Confidence            4455555443  589999999999999999988654

>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=98.64  E-value=3.2e-08  Score=72.04  Aligned_cols=102  Identities=16%  Similarity=0.097  Sum_probs=64.4

Q ss_pred             CCCEEEEeCCcchhhhc-cc---ccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNLAAN-FS---RELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~-~~---~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.+++|.|..-... ..   ...+|.+++|+|+++......         .....-..+-++|+||+|+.+......
T Consensus        50 ~~~~~i~D~~g~~~~~~~~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~  129 (169)
T 3q85_A           50 EVTLIVYDIWEQGDAGGWLQDHCLQTGDAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVSL  129 (169)
T ss_dssp             EEEEEEECCCCC--------CHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHSTTSCCCEEEEEECTTCGGGCCSCH
T ss_pred             EEEEEEEECCCccccchhhhhhhhccCCEEEEEEECCChHHHHHHHHHHHHHHhcccCCCCCEEEEeeCcchhhcccCCH
Confidence            46778999999421111 11   123699999999987432111         001111356799999999974321233


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+..  ..+++++||++|+|++++|+.+.+.
T Consensus       130 ~~~~~~~~~~--~~~~~~~Sa~~~~~v~~l~~~l~~~  164 (169)
T 3q85_A          130 EEGRHLAGTL--SCKHIETSAALHHNTRELFEGAVRQ  164 (169)
T ss_dssp             HHHHHHHHHT--TCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCcEEEecCccCCCHHHHHHHHHHH
Confidence            4455555544  4599999999999999999987654

>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=98.64  E-value=4.3e-08  Score=72.45  Aligned_cols=100  Identities=15%  Similarity=0.095  Sum_probs=64.7

Q ss_pred             CCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           74 ADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        74 ~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      +.+-+++|.|..-    ...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.+......+
T Consensus        66 ~~l~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~v~~~  144 (183)
T 3kkq_A           66 AILDVLDTAGQEEFSAMREQYM-RTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTRD  144 (183)
T ss_dssp             EEEEEEECCSCGGGCSSHHHHH-HHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTSSCCCEEEEEECTTCSTTCCSCHH
T ss_pred             EEEEEEECCCchhhHHHHHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECCCchhccCcCHH
Confidence            4455699999321    11111 23699999999987532110         0001123456999999999763213344


Q ss_pred             HHHHHHHhcCCCCCEEEEecc-cCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVG-WVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~-~g~gi~el~~~l~~~  176 (178)
                      ...+..+..+  .+++++||+ +|+|++++|+.|.+.
T Consensus       145 ~~~~~~~~~~--~~~~~~Sa~~~~~~v~~l~~~l~~~  179 (183)
T 3kkq_A          145 QGKEMATKYN--IPYIETSAKDPPLNVDKTFHDLVRV  179 (183)
T ss_dssp             HHHHHHHHHT--CCEEEEBCSSSCBSHHHHHHHHHHH
T ss_pred             HHHHHHHHhC--CeEEEeccCCCCCCHHHHHHHHHHH
Confidence            5555555554  689999999 999999999988764

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=98.63  E-value=2e-08  Score=75.86  Aligned_cols=101  Identities=15%  Similarity=0.048  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.|++|.|..-    ...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.++.....
T Consensus        71 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~v~~  149 (201)
T 3oes_A           71 EFHLHLVDTAGQDEYSILPYSFI-IGVHGYVLVYSVTSLHSFQVIESLYQKLHEGHGKTRVPVVLVGNKADLSPEREVQA  149 (201)
T ss_dssp             CEEEEEEEECCCCTTCCCCGGGT-TTCCEEEEEEETTCHHHHHHHHHHHHHHHC-----CCCEEEEEECTTCGGGCCSCH
T ss_pred             EEEEEEEECCCccchHHHHHHHH-hcCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccCccccccCH
Confidence            57788999999321    11222 24799999999986432110         011112346799999999975421223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+..  +.+++++||++|+|++++|+.|.+.
T Consensus       150 ~~~~~~~~~~--~~~~~~~Sa~~~~~v~~l~~~l~~~  184 (201)
T 3oes_A          150 VEGKKLAESW--GATFMESSARENQLTQGIFTKVIQE  184 (201)
T ss_dssp             HHHHHHHHHH--TCEEEECCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHh--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            3444444544  3589999999999999999987654

>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=3.5e-08  Score=85.16  Aligned_cols=100  Identities=21%  Similarity=0.061  Sum_probs=62.0

Q ss_pred             CCCCEEEEeCCcchh----hh------cc-cccccceEEEEEeCCCCCCCC----c-CC-CCCCCceeEEEEecCCCCCc
Q 030407           72 FKADLLLCESGGDNL----AA------NF-SRELADYIIYIIDVSGGDKIP----R-KG-GPGITQADLLVINKTDLASA  134 (178)
Q Consensus        72 ~~~d~iiiEttG~~~----~~------~~-~~~~ad~~I~VvD~~~~~~~~----~-~~-~~qi~~adiiviNK~Dl~~~  134 (178)
                      .+..+.|++|.|..-    ..      +. ....+|.+++|+|++++....    . .+ ...-..+.++|+||+|+.+.
T Consensus       279 ~g~~l~liDT~G~~~~~~~ve~~gi~~~~~~~~~aD~vl~VvD~s~~~s~~~~~~~~~~l~~l~~~piIvV~NK~Dl~~~  358 (476)
T 3gee_A          279 DKTMFRLTDTAGLREAGEEIEHEGIRRSRMKMAEADLILYLLDLGTERLDDELTEIRELKAAHPAAKFLTVANKLDRAAN  358 (476)
T ss_dssp             TTEEEEEEC--------------------CCCSSCSEEEEEEETTTCSSGGGHHHHHHHHHHCTTSEEEEEEECTTSCTT
T ss_pred             CCeEEEEEECCCCCcchhHHHHHHHHHHHhhcccCCEEEEEEECCCCcchhhhHHHHHHHHhcCCCCEEEEEECcCCCCc
Confidence            356799999999411    00      01 123479999999998875431    0 00 00114578999999999877


Q ss_pred             hhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          135 IGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       135 ~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                        ...+.  +.+.+. +..+++++||++|+|+++++++|.+.
T Consensus       359 --~~~~~--~~l~~~-~~~~~i~vSAktg~GI~eL~~~i~~~  395 (476)
T 3gee_A          359 --ADALI--RAIADG-TGTEVIGISALNGDGIDTLKQHMGDL  395 (476)
T ss_dssp             --THHHH--HHHHHH-HTSCEEECBTTTTBSHHHHHHHHTHH
T ss_pred             --cchhH--HHHHhc-CCCceEEEEECCCCCHHHHHHHHHHH
Confidence              33322  223322 12589999999999999999998764

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=98.63  E-value=2.3e-08  Score=74.50  Aligned_cols=99  Identities=16%  Similarity=0.099  Sum_probs=65.6

Q ss_pred             CCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCCC----CCCceeEEEEecCCCCCchhHhHHHHH
Q 030407           74 ADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGGP----GITQADLLVINKTDLASAIGADLAVME  143 (178)
Q Consensus        74 ~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~----qi~~adiiviNK~Dl~~~~~~~~~~~~  143 (178)
                      ..+.|++|.|..-    ...+. ..+|.+++|+|++++.....  .+..    ....+-++|+||+|+... ....+.+.
T Consensus        93 ~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~D~~~~~s~~~~~~~~~~i~~~~~~piilv~NK~D~~~~-~~~~~~~~  170 (208)
T 3clv_A           93 IKFDIWDTAGQERYASIVPLYY-RGATCAIVVFDISNSNTLDRAKTWVNQLKISSNYIIILVANKIDKNKF-QVDILEVQ  170 (208)
T ss_dssp             EEEEEEECTTGGGCTTTHHHHH-TTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCCEEEEEEECTTCC-C-CSCHHHHH
T ss_pred             eEEEEEECCCcHHHHHHHHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCcccc-cCCHHHHH
Confidence            6889999999311    11111 24799999999987532211  0000    012567999999994321 13445666


Q ss_pred             HHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          144 RDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       144 ~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.++..  ..+++++||++|+|+++++++|.+.
T Consensus       171 ~~~~~~--~~~~~~~Sa~~~~~i~~l~~~l~~~  201 (208)
T 3clv_A          171 KYAQDN--NLLFIQTSAKTGTNIKNIFYMLAEE  201 (208)
T ss_dssp             HHHHHT--TCEEEEECTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHc--CCcEEEEecCCCCCHHHHHHHHHHH
Confidence            666654  3599999999999999999988654

>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=98.63  E-value=2.7e-08  Score=72.24  Aligned_cols=101  Identities=12%  Similarity=-0.007  Sum_probs=64.5

Q ss_pred             CCCEEEEeCCcchhh----hcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNLA----ANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~~----~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.+++|.|..--    ..+. ..+|.+++|+|+++......  .+.      ..-..+-++|+||+|+.++.....+
T Consensus        54 ~~~~~~~Dt~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~l~~~~~~~~~iilv~nK~Dl~~~~~v~~~  132 (170)
T 1z0j_A           54 LHKFLIWDTAGLERFRALAPMYY-RGSAAAIIVYDITKEETFSTLKNWVRELRQHGPPSIVVAIAGNKCDLTDVREVMER  132 (170)
T ss_dssp             EEEEEEEEECCSGGGGGGTHHHH-TTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTSEEEEEEECTTCGGGCCSCHH
T ss_pred             EEEEEEEcCCCchhhhcccHhhC-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCcEEEEEECCccccccccCHH
Confidence            467889999994211    1111 24699999999987532111  000      0113356888999999764111233


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ......+..  ..+++++||++|+|+++++++|.+.
T Consensus       133 ~~~~~~~~~--~~~~~~~Sa~~~~~i~~l~~~i~~~  166 (170)
T 1z0j_A          133 DAKDYADSI--HAIFVETSAKNAININELFIEISRR  166 (170)
T ss_dssp             HHHHHHHHT--TCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCEEEEEeCCCCcCHHHHHHHHHHH
Confidence            444444443  3689999999999999999988764

>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=98.63  E-value=7.4e-09  Score=75.17  Aligned_cols=101  Identities=15%  Similarity=0.071  Sum_probs=65.8

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCCCC-----CCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGGPG-----ITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~q-----i~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+.+.+++|.|..-    ...+. ..+|.+++|+|+++......  .+...     -..+-++|+||+|+.++.....+.
T Consensus        53 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~piilv~nK~Dl~~~~~~~~~~  131 (168)
T 1z2a_A           53 DVRLMLWDTAGQEEFDAITKAYY-RGAQACVLVFSTTDRESFEAISSWREKVVAEVGDIPTALVQNKIDLLDDSCIKNEE  131 (168)
T ss_dssp             EEEEEEECCTTGGGTTCCCHHHH-TTCCEEEEEEETTCHHHHHTHHHHHHHHHHHHCSCCEEEEEECGGGGGGCSSCHHH
T ss_pred             EEEEEEEcCCCcHhHHHHHHHHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCEEEEEECcccCcccccCHHH
Confidence            46889999999321    11111 24799999999987532111  01001     134679999999997631122344


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+..+..  +.+++++||++|+|+++++++|.+.
T Consensus       132 ~~~~~~~~--~~~~~~~Sa~~~~~i~~l~~~l~~~  164 (168)
T 1z2a_A          132 AEGLAKRL--KLRFYRTSVKEDLNVSEVFKYLAEK  164 (168)
T ss_dssp             HHHHHHHH--TCEEEECBTTTTBSSHHHHHHHHHH
T ss_pred             HHHHHHHc--CCeEEEEecCCCCCHHHHHHHHHHH
Confidence            55555544  3589999999999999999988653

>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=98.62  E-value=2.2e-08  Score=73.99  Aligned_cols=101  Identities=14%  Similarity=0.013  Sum_probs=65.4

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.+++|.|..-    ...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.++.....
T Consensus        53 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~  131 (181)
T 3t5g_A           53 EYHLQLVDTAGQDEYSIFPQTYS-IDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISY  131 (181)
T ss_dssp             EEEEEEEECCCCCTTCCCCGGGT-TTCSEEEEEEETTCHHHHHHHHHHHHHHHHHC----CCEEEEEECTTCTTTCCSCH
T ss_pred             EEEEEEEeCCCchhhhHHHHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccchhcceecH
Confidence            36778999999321    11222 24799999999986432111         011112346799999999965421234


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+..  +.+++++||++|+|++++|+.+.+.
T Consensus       132 ~~~~~~~~~~--~~~~~~~Sa~~~~~v~~l~~~l~~~  166 (181)
T 3t5g_A          132 EEGKALAESW--NAAFLESSAKENQTAVDVFRRIILE  166 (181)
T ss_dssp             HHHHHHHHHT--TCEEEECCTTSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHh--CCcEEEEecCCCCCHHHHHHHHHHH
Confidence            4555555554  4589999999999999999987654

>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=98.62  E-value=5.9e-08  Score=72.53  Aligned_cols=101  Identities=14%  Similarity=0.065  Sum_probs=65.3

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C------CCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K------GGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~------~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+.|++|.|..    +...+. ..+|.+++|+|++.......  .      ....-..+-++|+||+|+.+......+
T Consensus        73 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~vi~v~D~~~~~s~~~~~~~l~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~  151 (193)
T 2oil_A           73 AVKAQIWDTAGLERYRAITSAYY-RGAVGALLVFDLTKHQTYAVVERWLKELYDHAEATIVVMLVGNKSDLSQAREVPTE  151 (193)
T ss_dssp             EEEEEEEEESCCCTTCTTHHHHH-TTCCEEEEEEETTCHHHHHTHHHHHHHHHTTSCTTCEEEEEEECGGGGGGCCSCHH
T ss_pred             EEEEEEEeCCCchhhhhhhHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCeEEEEEECCCcccccccCHH
Confidence            4678899999931    111122 24699999999987532110  0      001124467999999999754112234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  +.+++++||++|+|+++++++|.+.
T Consensus       152 ~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  185 (193)
T 2oil_A          152 EARMFAENN--GLLFLETSALDSTNVELAFETVLKE  185 (193)
T ss_dssp             HHHHHHHHT--TCEEEEECTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            455555443  4689999999999999999987653

>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=98.62  E-value=3.1e-08  Score=73.34  Aligned_cols=100  Identities=12%  Similarity=0.014  Sum_probs=65.2

Q ss_pred             CCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CC------CCCCCceeEEEEecCCCCCchhHhHHH
Q 030407           74 ADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KG------GPGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        74 ~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~------~~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      +.+.+++|.|..-    ...+. ..+|.+++|+|+++......  .+      ...-..+-++|+||+|+.++.....+.
T Consensus        59 ~~~~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~~  137 (186)
T 2bme_A           59 VKLQIWDTAGQERFRSVTRSYY-RGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGNKKDLDADREVTFLE  137 (186)
T ss_dssp             EEEEEEEECCSGGGHHHHHTTS-TTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHHH
T ss_pred             EEEEEEeCCCcHHHHHHHHHHH-hcCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECcccccccccCHHH
Confidence            6788999999421    11222 24799999999987532111  00      001234679999999996531122344


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+..+..  ..+++++||++|+|++++++++.+.
T Consensus       138 ~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  170 (186)
T 2bme_A          138 ASRFAQEN--ELMFLETSALTGENVEEAFVQCARK  170 (186)
T ss_dssp             HHHHHHHT--TCEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHc--CCEEEEecCCCCCCHHHHHHHHHHH
Confidence            45555443  4689999999999999999987653

>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=98.62  E-value=3.2e-08  Score=85.41  Aligned_cols=102  Identities=14%  Similarity=0.118  Sum_probs=67.0

Q ss_pred             CCCEEEEeCCcch-hhh-cc-cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHH---
Q 030407           73 KADLLLCESGGDN-LAA-NF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVM---  142 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~-~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~---  142 (178)
                      +..+.|++|.|.. ... .. ....+|.+++|+|++++...+..    .......+.++++||+|+.++  +..+..   
T Consensus        72 ~~~i~iiDtPGh~~~~~~~~~~~~~aD~~ilVvda~~g~~~qt~e~l~~~~~~~ip~IvviNK~Dl~~~--~~~~~~~~~  149 (482)
T 1wb1_A           72 NYRITLVDAPGHADLIRAVVSAADIIDLALIVVDAKEGPKTQTGEHMLILDHFNIPIIVVITKSDNAGT--EEIKRTEMI  149 (482)
T ss_dssp             TEEEEECCCSSHHHHHHHHHHHTTSCCEEEEEEETTTCSCHHHHHHHHHHHHTTCCBCEEEECTTSSCH--HHHHHHHHH
T ss_pred             CEEEEEEECCChHHHHHHHHHHHhhCCEEEEEEecCCCccHHHHHHHHHHHHcCCCEEEEEECCCcccc--hhHHHHHHH
Confidence            4678999999931 011 11 11247999999999876432110    111233455999999999876  444433   


Q ss_pred             -HHHHHhc--CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          143 -ERDALRM--RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       143 -~~~l~~~--np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                       .+.++..  .+..+++++||++|+|+++|+++|.+.
T Consensus       150 l~~~l~~~~~~~~~~ii~vSA~~g~gI~~L~~~L~~~  186 (482)
T 1wb1_A          150 MKSILQSTHNLKNSSIIPISAKTGFGVDELKNLIITT  186 (482)
T ss_dssp             HHHHHHHSSSGGGCCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHhhhcccccceEEEEECcCCCCHHHHHHHHHHh
Confidence             3444332  235799999999999999999998764

>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=98.62  E-value=3.4e-08  Score=73.95  Aligned_cols=101  Identities=15%  Similarity=0.073  Sum_probs=64.8

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.|++|.|..-    ...+. ..+|.+++|+|+++......  .+.      ..-..+-++|+||+|+.+......+
T Consensus        69 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~ii~v~d~~~~~s~~~~~~~l~~i~~~~~~~~piilv~nK~Dl~~~~~v~~~  147 (191)
T 2a5j_A           69 QIKLQIWDTAGQESFRSITRSYY-RGAAGALLVYDITRRETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESRRDVKRE  147 (191)
T ss_dssp             EEEEEEECCTTGGGTSCCCHHHH-TTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHH
T ss_pred             EEEEEEEECCCchhhhhhHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECcccCCccccCHH
Confidence            46788999999321    11111 24799999999987432111  000      0113456999999999753112234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  ..+++++||++|+|++++|++|.+.
T Consensus       148 ~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  181 (191)
T 2a5j_A          148 EGEAFAREH--GLIFMETSAKTACNVEEAFINTAKE  181 (191)
T ss_dssp             HHHHHHHHH--TCEEEEECTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            445555544  3589999999999999999987653

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=98.62  E-value=2e-08  Score=75.46  Aligned_cols=102  Identities=19%  Similarity=0.079  Sum_probs=65.7

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.+++|.|..-    ...+. ..+|.+++|+|+++......  .+.      ..-..+-++|+||+|+.+......+
T Consensus        74 ~~~l~l~Dt~G~~~~~~~~~~~~-~~~d~iilV~D~~~~~s~~~~~~~~~~i~~~~~~~~piilV~NK~Dl~~~~~v~~~  152 (192)
T 2il1_A           74 KIRLQIWDTAGQERFNSITSAYY-RSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETDREITRQ  152 (192)
T ss_dssp             EEEEEEEEECCSGGGHHHHHHHH-HHCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHH
T ss_pred             EEEEEEEeCCCcHHHHHHHHHHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECcccccccccCHH
Confidence            46789999999321    11111 24699999999987542211  000      0113467999999999754112233


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+.. ...+++++||++|+|+++++++|.+.
T Consensus       153 ~~~~~~~~~-~~~~~~~~SA~~g~gi~~l~~~l~~~  187 (192)
T 2il1_A          153 QGEKFAQQI-TGMRFCEASAKDNFNVDEIFLKLVDD  187 (192)
T ss_dssp             HHHHHHHTS-TTCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHhc-CCCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            444444432 35689999999999999999988654

>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=98.61  E-value=3.5e-08  Score=71.56  Aligned_cols=102  Identities=15%  Similarity=0.090  Sum_probs=65.2

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CC-C-----CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KG-G-----PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~-~-----~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ++.+.+++|.|..-    ...+ ...+|.+++|+|+++......  .+ .     ..-..+-++|+||+|+.++.....+
T Consensus        54 ~~~~~~~D~~G~~~~~~~~~~~-~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilv~nK~Dl~~~~~~~~~  132 (170)
T 1r2q_A           54 TVKFEIWDTAGQERYHSLAPMY-YRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQ  132 (170)
T ss_dssp             EEEEEEEEECCSGGGGGGHHHH-HTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHH
T ss_pred             EEEEEEEeCCCcHHhhhhhHHh-ccCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECccCccccccCHH
Confidence            46788999999321    1111 124799999999987532111  00 0     0113456788899999754112234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ...+..+..  ..+++++||++|+|+++++++|.+.+
T Consensus       133 ~~~~~~~~~--~~~~~~~Sa~~g~gi~~l~~~i~~~~  167 (170)
T 1r2q_A          133 EAQSYADDN--SLLFMETSAKTSMNVNEIFMAIAKKL  167 (170)
T ss_dssp             HHHHHHHHT--TCEEEECCTTTCTTHHHHHHHHHHTS
T ss_pred             HHHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHHH
Confidence            455555443  46899999999999999999987643

>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=98.60  E-value=3.5e-08  Score=74.77  Aligned_cols=102  Identities=17%  Similarity=0.085  Sum_probs=65.6

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.|++|.|..    +...+. ..+|.+++|+|+++......  .+..      .-..+-++|+||+|+.+......+
T Consensus        77 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~d~iilv~D~~~~~s~~~~~~~~~~i~~~~~~~~piilv~NK~Dl~~~~~v~~~  155 (201)
T 2hup_A           77 RVKLQIWDTAGQERFRTITQSYY-RSANGAILAYDITKRSSFLSVPHWIEDVRKYAGSNIVQLLIGNKSDLSELREVSLA  155 (201)
T ss_dssp             EEEEEEECCTTCGGGHHHHHHHH-TTCSEEEEEEETTBHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHH
T ss_pred             EEEEEEEECCCcHhHHHHHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECCccccccccCHH
Confidence            3678899999942    111222 25799999999976432111  0000      123456999999999753112334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+..+.. ...+++++||++|+|+++++++|.+.
T Consensus       156 ~~~~~~~~~-~~~~~~~~SA~~g~gi~~l~~~l~~~  190 (201)
T 2hup_A          156 EAQSLAEHY-DILCAIETSAKDSSNVEEAFLRVATE  190 (201)
T ss_dssp             HHHHHHHHT-TCSEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHc-CCCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            555555544 22389999999999999999987654

>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=98.60  E-value=2.3e-08  Score=72.21  Aligned_cols=101  Identities=14%  Similarity=0.044  Sum_probs=64.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ++.+.+++|.|..    +...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.++.....
T Consensus        50 ~~~~~l~D~~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~  128 (167)
T 1kao_A           50 PSVLEILDTAGTEQFASMRDLYI-KNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRYEKVPVILVGNKVDLESEREVSS  128 (167)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHH-HHCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTTSCCCEEEEEECGGGGGGCCSCH
T ss_pred             EEEEEEEECCCchhhHHHHHHHh-ccCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCcccccccCCH
Confidence            3568899999931    111121 24699999999987432110         011112346799999999975411223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+..  +.+++++||++|+|+++++++|.+.
T Consensus       129 ~~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  163 (167)
T 1kao_A          129 SEGRALAEEW--GCPFMETSAKSKTMVDELFAEIVRQ  163 (167)
T ss_dssp             HHHHHHHHHH--TSCEEEECTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHh--CCCEEEecCCCCcCHHHHHHHHHHH
Confidence            3444444444  3589999999999999999988654

>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=98.60  E-value=5.3e-08  Score=70.09  Aligned_cols=100  Identities=14%  Similarity=0.125  Sum_probs=64.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+++.+++|.|..    +...+. ..+|.+++++|+++......  .       ....-..+-++|+||+|+.+.. ...
T Consensus        50 ~~~~~~~D~~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~~~~~~~~~~~~i~~~~~~~~~p~iiv~nK~Dl~~~~-~~~  127 (166)
T 2ce2_X           50 TCLLDILDTAGQEEYSAMRDQYM-RTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKSDLAART-VES  127 (166)
T ss_dssp             EEEEEEEECCCCSSCCHHHHHHH-HHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHTCSCCCEEEEEECTTCSCCC-SCH
T ss_pred             EEEEEEEECCCchhhhHHHHHhh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEEchhhhhcc-cCH
Confidence            4678899999932    111121 24699999999976432110  0       0011134679999999998631 223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..++.  ..+++++||++|+|++++++++.+.
T Consensus       128 ~~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  162 (166)
T 2ce2_X          128 RQAQDLARSY--GIPYIETSAKTRQGVEDAFYTLVRE  162 (166)
T ss_dssp             HHHHHHHHHH--TCCEEEECTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCeEEEecCCCCCCHHHHHHHHHHH
Confidence            4444444444  3589999999999999999988654

>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=98.60  E-value=4.8e-08  Score=82.30  Aligned_cols=101  Identities=16%  Similarity=0.108  Sum_probs=65.5

Q ss_pred             CCEEEEeCCcchh-h-hcc-cccccceEEEEEeCCCCCCCCc--CCC---CCCC-ceeEEEEecCCCCCchhHhHHHHHH
Q 030407           74 ADLLLCESGGDNL-A-ANF-SRELADYIIYIIDVSGGDKIPR--KGG---PGIT-QADLLVINKTDLASAIGADLAVMER  144 (178)
Q Consensus        74 ~d~iiiEttG~~~-~-~~~-~~~~ad~~I~VvD~~~~~~~~~--~~~---~qi~-~adiiviNK~Dl~~~~~~~~~~~~~  144 (178)
                      ..+.|++|.|-.- . .+. ....+|.+++|+|+.++.....  .+.   ..+. .+-++++||+|+.++  .+.+...+
T Consensus        75 ~~~~iiDtPGh~~~~~~~~~~~~~~D~~ilVvda~~~~~~~qt~~~~~~~~~~~~~~iivviNK~Dl~~~--~~~~~~~~  152 (403)
T 3sjy_A           75 RRISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSK--EEALSQYR  152 (403)
T ss_dssp             EEEEEEECCCCGGGHHHHHHHHTTCSEEEEEEETTSCSSCHHHHHHHHHHHHHTCCCEEEEEECGGGSCH--HHHHHHHH
T ss_pred             ceEEEEECCCcHHHHHHHHHHHhhCCEEEEEEECCCCCCcHHHHHHHHHHHHcCCCCEEEEEECccccch--HHHHHHHH
Confidence            5789999999310 1 110 1124699999999988652211  010   0111 245899999999987  44443333


Q ss_pred             HHHh----cC-CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          145 DALR----MR-DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       145 ~l~~----~n-p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+++    .. ...+++++||++|+|+++|++.|.+.
T Consensus       153 ~i~~~l~~~~~~~~~ii~vSA~~g~gi~~L~~~l~~~  189 (403)
T 3sjy_A          153 QIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEY  189 (403)
T ss_dssp             HHHHHHTTSTTTTCCEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHhhCCCCCEEEEEECCCCcChHHHHHHHHHh
Confidence            3332    22 35799999999999999999998763

>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=98.60  E-value=4.9e-08  Score=70.89  Aligned_cols=100  Identities=19%  Similarity=0.134  Sum_probs=64.2

Q ss_pred             CCCEEEEeCCcchhh----hcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNLA----ANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~~----~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.+++|.|..--    ..+. ..+|.+++|+|+++......  .+.      ..-..+-++|+||+|+.+.. ...+
T Consensus        51 ~~~~~l~D~~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~-~~~~  128 (170)
T 1g16_A           51 KVKLQIWDTAGQERFRTITTAYY-RGAMGIILVYDITDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRV-VTAD  128 (170)
T ss_dssp             EEEEEEECCTTGGGTSCCCHHHH-TTEEEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCTTCC-SCHH
T ss_pred             EEEEEEEeCCCChhhhhhHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECccCCcCc-cCHH
Confidence            467889999993211    1111 24689999999986532111  000      00134679999999995431 2233


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..++.  +.+++++||++|+|++++++++.+.
T Consensus       129 ~~~~~~~~~--~~~~~~~Sa~~~~gv~~l~~~l~~~  162 (170)
T 1g16_A          129 QGEALAKEL--GIPFIESSAKNDDNVNEIFFTLAKL  162 (170)
T ss_dssp             HHHHHHHHH--TCCEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            444444444  3589999999999999999988654

>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=98.59  E-value=7.9e-08  Score=71.07  Aligned_cols=100  Identities=16%  Similarity=0.136  Sum_probs=64.2

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.+++|.|..    +...+. ..+|.+++|+|+++......         .+...-..+-++|+||+|+.+.. ...
T Consensus        51 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~i~v~nK~Dl~~~~-~~~  128 (189)
T 4dsu_A           51 TCLLDILDTAGQEEYSAMRDQYM-RTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRT-VDT  128 (189)
T ss_dssp             EEEEEEEECCCC---CTTHHHHH-HHCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTCSCCCEEEEEECTTSSSCS-SCH
T ss_pred             EEEEEEEECCCcHHHHHHHHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECccCcccc-cCH
Confidence            3557789999932    111121 24699999999986432110         01111234679999999997541 223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+..  ..+++++||++|+|+++++++|.+.
T Consensus       129 ~~~~~~~~~~--~~~~~~~Sa~~g~gi~~l~~~l~~~  163 (189)
T 4dsu_A          129 KQAQDLARSY--GIPFIETSAKTRQGVDDAFYTLVRE  163 (189)
T ss_dssp             HHHHHHHHHH--TCCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            3444444444  3589999999999999999988654

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=98.59  E-value=3.5e-08  Score=71.72  Aligned_cols=102  Identities=12%  Similarity=0.037  Sum_probs=64.5

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CC--------CCCCCceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KG--------GPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~--------~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+.+.+++|.|..    +...+. ..+|.+++|+|+++......  .+        ...-..+-++|+||+|+.++....
T Consensus        50 ~~~~~~~Dt~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~~~~~~~~~~~~i~~~~~~~~~~pii~v~nK~Dl~~~~~v~  128 (172)
T 2erx_A           50 ICTLQITDTTGSHQFPAMQRLSI-SKGHAFILVYSITSRQSLEELKPIYEQICEIKGDVESIPIMLVGNKCDESPSREVQ  128 (172)
T ss_dssp             EEEEEEEECCSCSSCHHHHHHHH-HHCSEEEEEEETTCHHHHHTTHHHHHHHHHHHC---CCCEEEEEECGGGGGGCCSC
T ss_pred             EEEEEEEECCCchhhHHHHHHhc-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHHhCCCCCCCEEEEEEccccccccccC
Confidence            4678999999942    111122 24699999999986432111  00        000134679999999997541112


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .+......+..  ..+++++||++|+|+++++++|.+.+
T Consensus       129 ~~~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~~  165 (172)
T 2erx_A          129 SSEAEALARTW--KCAFMETSAKLNHNVKELFQELLNLE  165 (172)
T ss_dssp             HHHHHHHHHHH--TCEEEECBTTTTBSHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHh--CCeEEEecCCCCcCHHHHHHHHHHHH
Confidence            23334444433  35899999999999999999987654

>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=98.58  E-value=5.6e-08  Score=73.20  Aligned_cols=101  Identities=16%  Similarity=0.067  Sum_probs=66.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.|++|.|..    +...+. ..+|.+++|+|+++......  .+..      .-..+-++|+||+|+.+......+
T Consensus        56 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~  134 (203)
T 1zbd_A           56 RIKLQIWDTAGLERYRTITTAYY-RGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDMEDERVVSSE  134 (203)
T ss_dssp             EEEEEEEEECCSGGGHHHHHTTG-GGCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCSSCEEEEEEECTTCTTSCCSCHH
T ss_pred             EEEEEEEECCCchhhcchHHHhh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECcccCcccccCHH
Confidence            4678899999942    111222 24799999999987532110  0000      123467999999999764212234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..+  .+++++||++|+|+++++++|.+.
T Consensus       135 ~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~~~l~~~  168 (203)
T 1zbd_A          135 RGRQLADHLG--FEFFEASAKDNINVKQTFERLVDV  168 (203)
T ss_dssp             HHHHHHHHHT--CEEEECBTTTTBSSHHHHHHHHHH
T ss_pred             HHHHHHHHCC--CeEEEEECCCCCCHHHHHHHHHHH
Confidence            4455555443  589999999999999999987654

>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=98.58  E-value=4.9e-08  Score=84.38  Aligned_cols=99  Identities=14%  Similarity=0.063  Sum_probs=64.8

Q ss_pred             CCCEEEEeCCcch-hhh----------c-ccccccceEEEEEeCCCCCCCCcC-CCCCC-CceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDN-LAA----------N-FSRELADYIIYIIDVSGGDKIPRK-GGPGI-TQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~----------~-~~~~~ad~~I~VvD~~~~~~~~~~-~~~qi-~~adiiviNK~Dl~~~~~~~  138 (178)
                      +..+.|++|.|.. ...          . .....+|.+++|+|++++...... ..+.+ ..+.++|+||+|+.++  ..
T Consensus       290 g~~~~l~DTaG~~~~~~~~ve~~gi~~~~~~~~~aD~vl~VvD~s~~~s~~~~~il~~l~~~piivV~NK~DL~~~--~~  367 (482)
T 1xzp_A          290 GILFRIVDTAGVRSETNDLVERLGIERTLQEIEKADIVLFVLDASSPLDEEDRKILERIKNKRYLVVINKVDVVEK--IN  367 (482)
T ss_dssp             TEEEEEEESSCCCSSCCTTCCCCCHHHHHHHHHHCSEEEEEEETTSCCCHHHHHHHHHHTTSSEEEEEEECSSCCC--CC
T ss_pred             CeEEEEEECCCccccchhhHHHHHHHHHHHHhhcccEEEEEecCCCCCCHHHHHHHHHhcCCCEEEEEECcccccc--cC
Confidence            4678999999943 110          0 011246999999999876432110 00001 3467999999999765  33


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+.+..   ....+++++||++|+|+++++++|.+.
T Consensus       368 ~~~~~~~~---~~~~~~i~iSAktg~Gi~eL~~~l~~~  402 (482)
T 1xzp_A          368 EEEIKNKL---GTDRHMVKISALKGEGLEKLEESIYRE  402 (482)
T ss_dssp             HHHHHHHH---TCSTTEEEEEGGGTCCHHHHHHHHHHH
T ss_pred             HHHHHHHh---cCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            34444332   223689999999999999999988764

>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=98.57  E-value=3.9e-08  Score=74.41  Aligned_cols=101  Identities=12%  Similarity=0.012  Sum_probs=65.2

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.|++|.|..-    ...+. ..+|++++|+|+++......  .+.      ..-..+-++|+||+|+.++.....+
T Consensus        73 ~~~l~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~v~~~  151 (200)
T 2o52_A           73 TVKLQIWDTAGQERFRSVTRSYY-RGAAGALLVYDITSRETYNSLAAWLTDARTLASPNIVVILCGNKKDLDPEREVTFL  151 (200)
T ss_dssp             EEEEEEECCTTHHHHSCCCHHHH-TTCSEEEEEEETTCHHHHHTHHHHHHHHHHHTCTTCEEEEEEECGGGGGGCCSCHH
T ss_pred             eeEEEEEcCCCcHhHHHHHHHHh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECCCcccccccCHH
Confidence            36789999999321    11111 24799999999987532111  000      0123467999999999753112234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +..+..+..  ..+++++||++|+|+++++++|.+.
T Consensus       152 ~~~~~~~~~--~~~~~~~SA~~g~gi~~l~~~l~~~  185 (200)
T 2o52_A          152 EASRFAQEN--ELMFLETSALTGENVEEAFLKCART  185 (200)
T ss_dssp             HHHHHHHHT--TCEEEEECTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            444555443  4689999999999999999987653

>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=98.57  E-value=3.9e-08  Score=72.00  Aligned_cols=101  Identities=18%  Similarity=0.134  Sum_probs=65.2

Q ss_pred             CCCEEEEeCCcchh-h---hcccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL-A---ANFSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~-~---~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.+++|.|..- .   ..+. ..+|.+++|+|+++......  .+..      .-..+-++|+||+|+.++.....+
T Consensus        62 ~~~~~~~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~~~~~  140 (179)
T 2y8e_A           62 TVRLQLWDTAGQERFRSLIPSYI-RDSTVAVVVYDITNTNSFHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTE  140 (179)
T ss_dssp             EEEEEEEEECCSGGGGGGSHHHH-HTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTTSSEEEEEEECGGGGGGCCSCHH
T ss_pred             EEEEEEEECCCcHHHHHHHHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECCcccccCcCCHH
Confidence            35789999999321 1   1111 24699999999976432111  0000      013456999999999754112234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ......+..  ..+++++||++|+|+++++++|.+.
T Consensus       141 ~~~~~~~~~--~~~~~~~Sa~~~~~i~~l~~~l~~~  174 (179)
T 2y8e_A          141 EGERKAKEL--NVMFIETSAKAGYNVKQLFRRVAAA  174 (179)
T ss_dssp             HHHHHHHHH--TCEEEEEBTTTTBSHHHHHHHHHHT
T ss_pred             HHHHHHHHc--CCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            445555544  3589999999999999999998764

>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=98.57  E-value=3.3e-08  Score=74.00  Aligned_cols=102  Identities=15%  Similarity=0.076  Sum_probs=65.4

Q ss_pred             CCCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchhHhH
Q 030407           72 FKADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        72 ~~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ..+.+.|++|.|..    +...+. ..+|.+++|+|+++......  .+..      .-..+-++|+||+|+.+......
T Consensus        70 ~~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~~~~~  148 (191)
T 3dz8_A           70 KRVKLQIWDTAGQERYRTITTAYY-RGAMGFILMYDITNEESFNAVQDWATQIKTYSWDNAQVILVGNKCDMEEERVVPT  148 (191)
T ss_dssp             TTEEEEEECHHHHHHCHHHHHHHH-TTCCEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCH
T ss_pred             EEEEEEEEeCCChHHHHHHHHHHH-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCccccccCH
Confidence            35678999999932    111122 25799999999986432110  0000      01345699999999965421223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +......+..  +.+++++||++|+|++++|+++.+.
T Consensus       149 ~~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  183 (191)
T 3dz8_A          149 EKGQLLAEQL--GFDFFEASAKENISVRQAFERLVDA  183 (191)
T ss_dssp             HHHHHHHHHH--TCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3444444444  3589999999999999999987654

>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=98.57  E-value=7.6e-08  Score=73.28  Aligned_cols=101  Identities=14%  Similarity=0.057  Sum_probs=64.3

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.|++|.|..    +...+. ..+|.+++|+|+++......  .+.      ..-..+-++|+||+|+.+......+
T Consensus        74 ~~~l~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~D~~~~~s~~~~~~~~~~i~~~~~~~~piilv~NK~Dl~~~~~v~~~  152 (201)
T 2ew1_A           74 KVKLQIWDTAGQERFRSITQSYY-RSANALILTYDITCEESFRCLPEWLREIEQYASNKVITVLVGNKIDLAERREVSQQ  152 (201)
T ss_dssp             EEEEEEEEECCSGGGHHHHGGGS-TTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCSSCHH
T ss_pred             EEEEEEEECCCcHHHHHHHHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCccccccCHH
Confidence            3578899999942    111222 35799999999986532110  000      0113456899999999753112233


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+..+..  ..+++++||++|+|++++|+++.+.
T Consensus       153 ~~~~~~~~~--~~~~~~~Sa~~g~gv~~l~~~l~~~  186 (201)
T 2ew1_A          153 RAEEFSEAQ--DMYYLETSAKESDNVEKLFLDLACR  186 (201)
T ss_dssp             HHHHHHHHH--TCCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            444444433  3589999999999999999987653

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=98.56  E-value=3.3e-08  Score=72.56  Aligned_cols=100  Identities=16%  Similarity=0.077  Sum_probs=63.9

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCCCC--------Cce-eEEEEecCCCCCchhHh
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGPGI--------TQA-DLLVINKTDLASAIGAD  138 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~qi--------~~a-diiviNK~Dl~~~~~~~  138 (178)
                      +.+.+++|.|..    +...+. ..+|.+++|+|+++......  .+...+        ..+ -++|+||+|+.+.....
T Consensus        56 ~~~~~~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~iilv~nK~Dl~~~~~~~  134 (178)
T 2hxs_A           56 VTLQIWDIGGQTIGGKMLDKYI-YGAQGVLLVYDITNYQSFENLEDWYTVVKKVSEESETQPLVALVGNKIDLEHMRTIK  134 (178)
T ss_dssp             EEEEEEECTTCCTTCTTHHHHH-TTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHHHHTCCCEEEEEEECGGGGGGCSSC
T ss_pred             EEEEEEECCCCccccchhhHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcccCCCCeEEEEEEccccccccccC
Confidence            678899999932    111222 24799999999987543211  000001        223 47899999997531122


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+...+..+..  +.+++++||++|+|+++++++|.+.
T Consensus       135 ~~~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  170 (178)
T 2hxs_A          135 PEKHLRFCQEN--GFSSHFVSAKTGDSVFLCFQKVAAE  170 (178)
T ss_dssp             HHHHHHHHHHH--TCEEEEECTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHc--CCcEEEEeCCCCCCHHHHHHHHHHH
Confidence            34444455544  3589999999999999999988654

>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=98.55  E-value=5.9e-08  Score=73.97  Aligned_cols=101  Identities=10%  Similarity=-0.027  Sum_probs=62.8

Q ss_pred             CCEEEEeCCcchhhhcc---cccccceEEEEEeCCCCCCCCc--CCCCC------CCceeEEEEecCCCCCchhHhHHHH
Q 030407           74 ADLLLCESGGDNLAANF---SRELADYIIYIIDVSGGDKIPR--KGGPG------ITQADLLVINKTDLASAIGADLAVM  142 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~~---~~~~ad~~I~VvD~~~~~~~~~--~~~~q------i~~adiiviNK~Dl~~~~~~~~~~~  142 (178)
                      +.+.+++|.|..-....   ....+|.+++|+|+++......  .+...      -..+-++|+||+|+.+......+..
T Consensus        61 ~~~~l~Dt~G~~~~~~~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~~~  140 (218)
T 4djt_A           61 IKFNVWDTAGQEKKAVLKDVYYIGASGAILFFDVTSRITCQNLARWVKEFQAVVGNEAPIVVCANKIDIKNRQKISKKLV  140 (218)
T ss_dssp             EEEEEEEECSGGGTSCCCHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCSSSCEEEEEECTTCC----CCHHHH
T ss_pred             EEEEEEecCCchhhchHHHHHhhcCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCccccccCHHHH
Confidence            67899999993211111   1124799999999987532211  00000      1346799999999976511222333


Q ss_pred             HHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          143 ERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       143 ~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+..+.  ...+++++||++|+|+++++++|.+.
T Consensus       141 ~~~~~~--~~~~~~~~Sa~~g~gv~~l~~~l~~~  172 (218)
T 4djt_A          141 MEVLKG--KNYEYFEISAKTAHNFGLPFLHLARI  172 (218)
T ss_dssp             HHHTTT--CCCEEEEEBTTTTBTTTHHHHHHHHH
T ss_pred             HHHHHH--cCCcEEEEecCCCCCHHHHHHHHHHH
Confidence            333332  35689999999999999999988764

>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=98.55  E-value=1.8e-08  Score=74.02  Aligned_cols=101  Identities=12%  Similarity=0.041  Sum_probs=64.0

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.+++|.|..-    ...+. ..+|.+++|+|+++......  .       ....-..+-++|+||+|+.+......
T Consensus        56 ~~~~~~~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~v~~  134 (181)
T 2fn4_A           56 PARLDILDTAGQEEFGAMREQYM-RAGHGFLLVFAINDRQSFNEVGKLFTQILRVKDRDDFPVVLVGNKADLESQRQVPR  134 (181)
T ss_dssp             EEEEEEEECCCTTTTSCCHHHHH-HHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHTSSCCCEEEEEECGGGGGGCCSCH
T ss_pred             EEEEEEEECCCchhhHHHHHHHH-hhCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccCH
Confidence            36788999999321    11111 23699999999987432110  0       00112345699999999976411122


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +......+..  ..+++++||++|+|+++++++|.+.
T Consensus       135 ~~~~~~~~~~--~~~~~~~Sa~~~~gv~~l~~~l~~~  169 (181)
T 2fn4_A          135 SEASAFGASH--HVAYFEASAKLRLNVDEAFEQLVRA  169 (181)
T ss_dssp             HHHHHHHHHT--TCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCeEEEecCCCCCCHHHHHHHHHHH
Confidence            3344444433  5689999999999999999988654

>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=98.54  E-value=4.5e-08  Score=74.35  Aligned_cols=101  Identities=15%  Similarity=0.033  Sum_probs=64.7

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchhHh--
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIGAD--  138 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~~~--  138 (178)
                      .+.+.|++|.|..-    ...+. ..+|.+++|+|+++......   .+...     -..+-++|+||+|+.+.  ..  
T Consensus        77 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~~  153 (204)
T 4gzl_A           77 PVNLGLWDTAGLEDYDRLRPLSY-PQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDD--KDTI  153 (204)
T ss_dssp             EEEEEEEEECCSGGGTTTGGGGC-TTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHCSSCCEEEEEECHHHHTC--HHHH
T ss_pred             EEEEEEEECCCchhhHHHHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEechhhccc--hhhh
Confidence            45677999999421    11122 25799999999987532211   11000     13467999999999765  22  


Q ss_pred             ------------HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          139 ------------LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       139 ------------~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                                  .+...+..+.. ...+++++||++|+|++++++++.+.+
T Consensus       154 ~~~~~~~~~~v~~~~~~~~~~~~-~~~~~~~~SA~~g~gi~~l~~~l~~~~  203 (204)
T 4gzl_A          154 EKLKEKKLTPITYPQGLAMAKEI-GAVKYLECSALTQRGLKTVFDEAIRAV  203 (204)
T ss_dssp             HHHHHTTCCCCCHHHHHHHHHHT-TCSEEEECCTTTCTTHHHHHHHHHHTT
T ss_pred             hhhhccccccccHHHHHHHHHhc-CCcEEEEeeCCCCCCHHHHHHHHHHHh
Confidence                        12233333333 335799999999999999999987643

>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=98.54  E-value=1.5e-07  Score=70.36  Aligned_cols=101  Identities=9%  Similarity=0.064  Sum_probs=64.3

Q ss_pred             CCCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCC--chhHhHHH
Q 030407           73 KADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLAS--AIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~--~~~~~~~~  141 (178)
                      .+.+-+++|.|..--. + ...+|.+++|+|+++......         .+...-..+-++|.||+|+.+  ......+.
T Consensus        66 ~~~l~i~Dt~G~~~~~-~-~~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~v~~~~  143 (184)
T 3ihw_A           66 SYLLLIRDEGGPPELQ-F-AAWVDAVVFVFSLEDEISFQTVYNYFLRLCSFRNASEVPMVLVGTQDAISAANPRVIDDSR  143 (184)
T ss_dssp             EEEEEEEECSSSCCHH-H-HHHCSEEEEEEETTCHHHHHHHHHHHHHHHTTSCGGGSCEEEEEECTTCBTTBCCCSCHHH
T ss_pred             EEEEEEEECCCChhhh-e-ecCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccccCHHH
Confidence            3567779999931111 2 224799999999987532211         011112345699999999942  11122344


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+..+.. ...+++++||++|+|++++|+++.+.
T Consensus       144 ~~~~~~~~-~~~~~~e~Sa~~~~gv~~lf~~l~~~  177 (184)
T 3ihw_A          144 ARKLSTDL-KRCTYYETCATYGLNVERVFQDVAQK  177 (184)
T ss_dssp             HHHHHHHT-TTCEEEEEBTTTTBTHHHHHHHHHHH
T ss_pred             HHHHHHHc-CCCeEEEecCCCCCCHHHHHHHHHHH
Confidence            55555544 34689999999999999999987654

>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=98.54  E-value=6.2e-08  Score=78.65  Aligned_cols=79  Identities=19%  Similarity=0.078  Sum_probs=53.8

Q ss_pred             ccceEEEEEeCCCCCCCCc---CCC---CCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHH
Q 030407           94 LADYIIYIIDVSGGDKIPR---KGG---PGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGII  167 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~---~~~---~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~  167 (178)
                      .+|.+++|+|+++......   .+.   ..-..+-++|+||+||.++  .+.++..++.+..+...+++++||++|+|++
T Consensus        84 ~ad~vilV~D~~~~~~s~~~l~~~l~~~~~~~~piilv~NK~DL~~~--~~v~~~~~~~~~~~~~~~~~~~SAktg~gv~  161 (301)
T 1u0l_A           84 NVDQVILVVTVKMPETSTYIIDKFLVLAEKNELETVMVINKMDLYDE--DDLRKVRELEEIYSGLYPIVKTSAKTGMGIE  161 (301)
T ss_dssp             SCCEEEEEECSSTTCCCHHHHHHHHHHHHHTTCEEEEEECCGGGCCH--HHHHHHHHHHHHHTTTSCEEECCTTTCTTHH
T ss_pred             cCCEEEEEEeCCCCCCCHHHHHHHHHHHHHCCCCEEEEEeHHHcCCc--hhHHHHHHHHHHHhhhCcEEEEECCCCcCHH
Confidence            5799999999987542111   111   0123467999999999876  4433344444443321689999999999999


Q ss_pred             HHHHHHh
Q 030407          168 FTLSITH  174 (178)
Q Consensus       168 el~~~l~  174 (178)
                      ++|+.+.
T Consensus       162 ~lf~~l~  168 (301)
T 1u0l_A          162 ELKEYLK  168 (301)
T ss_dssp             HHHHHHS
T ss_pred             HHHHHhc
Confidence            9998875

>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=98.54  E-value=1.2e-07  Score=70.61  Aligned_cols=100  Identities=14%  Similarity=0.080  Sum_probs=64.1

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+++.|++|.|..-    ...+. ..+|.+++|+|++.......  .       +...-..+-++|+||+|+.+.. ...
T Consensus        68 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~p~ilv~nK~Dl~~~~-~~~  145 (190)
T 3con_A           68 TCLLDILDTAGQEEYSAMRDQYM-RTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRT-VDT  145 (190)
T ss_dssp             EEEEEEEECCC-----------C-TTCSEEEEEEETTCHHHHHHHHHHHHHHHHHHTCSCCCEEEEEECTTCSCCC-SCH
T ss_pred             EEEEEEEECCChHHHHHHHHHhh-CcCCEEEEEEECcCHHHHHHHHHHHHHHHHHhCCCCCeEEEEEECCcCCccc-CCH
Confidence            46789999999321    11122 24799999999976532111  0       0011134569999999997631 233


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.+.+..+..+  .+++++||++|+|+++++++|.+.
T Consensus       146 ~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~~~l~~~  180 (190)
T 3con_A          146 KQAHELAKSYG--IPFIETSAKTRQGVEDAFYTLVRE  180 (190)
T ss_dssp             HHHHHHHHHHT--CCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC--CeEEEEeCCCCCCHHHHHHHHHHH
Confidence            44555555543  489999999999999999988654

>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=98.54  E-value=1.1e-07  Score=71.03  Aligned_cols=102  Identities=13%  Similarity=0.039  Sum_probs=64.8

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchh----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIG----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~----  136 (178)
                      .+.+.+++|.|..    +...+. ..+|.+++|+|+++......   .+...     -..+-++|+||+|+.+...    
T Consensus        65 ~~~~~i~D~~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~  143 (194)
T 2atx_A           65 QYLLGLYDTAGQEDYDRLRPLSY-PMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKTLAR  143 (194)
T ss_dssp             EEEEEEECCCCSSSSTTTGGGGC-TTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHSTTCCEEEEEECTTSTTCHHHHHH
T ss_pred             EEEEEEEECCCCcchhHHHHHhc-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEChhhcccccchhh
Confidence            3677899999942    112222 24799999999987532111   11000     1346799999999986410    


Q ss_pred             --------HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 --------ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 --------~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                              ...+...+..+..+ ..+++++||++|+|++++++++.+.
T Consensus       144 ~~~~~~~~v~~~~~~~~~~~~~-~~~~~~~Sa~~g~gi~~l~~~l~~~  190 (194)
T 2atx_A          144 LNDMKEKPICVEQGQKLAKEIG-ACCYVECSALTQKGLKTVFDEAIIA  190 (194)
T ss_dssp             HTTTTCCCCCHHHHHHHHHHHT-CSCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             cccccCcccCHHHHHHHHHHcC-CcEEEEeeCCCCCCHHHHHHHHHHH
Confidence                    11233444444442 2389999999999999999988654

>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=98.53  E-value=1.1e-07  Score=71.72  Aligned_cols=101  Identities=15%  Similarity=0.080  Sum_probs=64.8

Q ss_pred             CCCEEEEeCCcchh-----hhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDNL-----AANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~~-----~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+.+.+++|.|..-     ...+. ..+|.+++|+|+++......  .       ....-..+-++|+||+|+.+.....
T Consensus        71 ~~~l~i~Dt~g~~~~~~~~~~~~~-~~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~v~  149 (195)
T 3cbq_A           71 EVTLVVYDIWEQGDAGGWLRDHCL-QTGDAFLIVFSVTDRRSFSKVPETLLRLRAGRPHHDLPVILVGNKSDLARSREVS  149 (195)
T ss_dssp             EEEEEEECCCCCSGGGHHHHHHHH-HHCSEEEEEEETTCHHHHHTHHHHHHHHHHHSTTSCCCEEEEEECTTCTTTCCSC
T ss_pred             EEEEEEEecCCCccchhhhHHHhh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEeechhccccCCcC
Confidence            46678889999421     11111 24799999999986432110  0       0111234679999999997541123


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+...+..+..  ..+++++||++|+|++++|+.+.+.
T Consensus       150 ~~~~~~~a~~~--~~~~~e~Sa~~~~~v~~lf~~l~~~  185 (195)
T 3cbq_A          150 LEEGRHLAGTL--SCKHIETSAALHHNTRELFEGAVRQ  185 (195)
T ss_dssp             HHHHHHHHHHT--TCEEEEEBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh--CCEEEEEcCCCCCCHHHHHHHHHHH
Confidence            34445555444  3589999999999999999987654

>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=98.53  E-value=1.2e-07  Score=69.80  Aligned_cols=101  Identities=14%  Similarity=0.079  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCc--C-------CCC--CCCceeEEEEecCCCCC--chhHhH
Q 030407           73 KADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPR--K-------GGP--GITQADLLVINKTDLAS--AIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~--qi~~adiiviNK~Dl~~--~~~~~~  139 (178)
                      .+.+.+++|.|.. ...+. ..+|++++|+|+++......  .       ...  .-..+-++|+||+|+.+  ......
T Consensus        53 ~~~l~i~Dt~G~~-~~~~~-~~~d~~ilv~D~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~~~v~~  130 (178)
T 2iwr_A           53 THLVLIREEAGAP-DAKFS-GWADAVIFVFSLEDENSFQAVSRLHGQLSSLRGEGRGGLALALVGTQDRISASSPRVVGD  130 (178)
T ss_dssp             EEEEEEEECSSSC-CHHHH-HHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHCSSSCCCEEEEEEECTTCBTTBCCCSCH
T ss_pred             EEEEEEEECCCCc-hhHHH-HhCCEEEEEEECcCHHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccccCcCCH
Confidence            3567889999932 12222 24799999999987532110  0       000  12346799999999942  110223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+.. ...+++++||++|+|++++|+.+.+.
T Consensus       131 ~~~~~~~~~~-~~~~~~~~Sa~~~~~i~~lf~~l~~~  166 (178)
T 2iwr_A          131 ARARALXADM-KRCSYYETXATYGLNVDRVFQEVAQK  166 (178)
T ss_dssp             HHHHHHHHHH-SSEEEEEEBTTTTBTHHHHHHHHHHH
T ss_pred             HHHHHHHHhh-cCCeEEEEeccccCCHHHHHHHHHHH
Confidence            4444444443 24689999999999999999987653

>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=98.53  E-value=8e-08  Score=71.95  Aligned_cols=102  Identities=17%  Similarity=0.052  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCc--hhHh
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASA--IGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~--~~~~  138 (178)
                      .+.+.+++|.|..-    ...+. ..+|.+++|+|+++......   .+...     -..+-++|+||+|+.++  ....
T Consensus        70 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~~  148 (194)
T 3reg_A           70 EFILHLWDTAGQEEYDRLRPLSY-ADSDVVLLCFAVNNRTSFDNISTKWEPEIKHYIDTAKTVLVGLKVDLRKDGSDDVT  148 (194)
T ss_dssp             EEEEEEEEECCSGGGTTTGGGGC-TTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHCTTSEEEEEEECGGGCCTTTTCCC
T ss_pred             EEEEEEEECCCcHHHHHHhHhhc-cCCcEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEChhhccCCCCccc
Confidence            45678999999321    11122 24799999999987532211   11110     13467999999999752  1123


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+...+..+..+ ..+++++||++|+|++++|+.+.+.
T Consensus       149 ~~~~~~~~~~~~-~~~~~~~Sa~~~~gi~~l~~~l~~~  185 (194)
T 3reg_A          149 KQEGDDLCQKLG-CVAYIEASSVAKIGLNEVFEKSVDC  185 (194)
T ss_dssp             HHHHHHHHHHHT-CSCEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCEEEEeecCCCCCHHHHHHHHHHH
Confidence            344555555543 2349999999999999999987653

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C

Probab=98.52  E-value=7.3e-08  Score=72.45  Aligned_cols=101  Identities=20%  Similarity=0.172  Sum_probs=57.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--C-------CCC--CCCceeEEEEecCCCCC-chh
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--K-------GGP--GITQADLLVINKTDLAS-AIG  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~--qi~~adiiviNK~Dl~~-~~~  136 (178)
                      .+.+.|++|.|..-    ...+. ..+|++++|+|+++......  .       +..  .-..+-++|+||+|+.+ ...
T Consensus        72 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~~  150 (208)
T 2yc2_C           72 SVELFLLDTAGSDLYKEQISQYW-NGVYYAILVFDVSSMESFESCKAWFELLKSARPDRERPLRAVLVANKTDLPPQRHQ  150 (208)
T ss_dssp             EEEEEEEETTTTHHHHHHHSTTC-CCCCEEEEEEETTCHHHHHHHHHHHHHHHHHCSCTTSCCEEEEEEECC-------C
T ss_pred             EEEEEEEECCCcHHHHHHHHHHH-hhCcEEEEEEECCCHHHHHHHHHHHHHHHHhhcccccCCcEEEEEECcccchhhcc
Confidence            45789999999421    11222 35799999999987542111  0       000  12446799999999986 311


Q ss_pred             HhHHHHHHHHHhcCCCCCEEEEeccc-CCCHHHHHHHHhhh
Q 030407          137 ADLAVMERDALRMRDGGPFIFAQVGW-VIGIIFTLSITHYI  176 (178)
Q Consensus       137 ~~~~~~~~~l~~~np~a~i~~~SA~~-g~gi~el~~~l~~~  176 (178)
                      ...+...+..+..+  .+++++||++ |+|+++++++|.+.
T Consensus       151 v~~~~~~~~~~~~~--~~~~~~Sa~~~~~gi~~l~~~i~~~  189 (208)
T 2yc2_C          151 VRLDMAQDWATTNT--LDFFDVSANPPGKDADAPFLSIATT  189 (208)
T ss_dssp             CCHHHHHHHHHHTT--CEEEECCC-------CHHHHHHHHH
T ss_pred             CCHHHHHHHHHHcC--CEEEEeccCCCCcCHHHHHHHHHHH
Confidence            22355566666553  6899999999 99999999987653

>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=98.52  E-value=8.1e-08  Score=69.59  Aligned_cols=101  Identities=14%  Similarity=-0.016  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCc---hhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASA---IGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~---~~~  137 (178)
                      .+.+.+++|.|..-    ...+. ..+|.+++|+|+++......  .+.      ..-..+-++|+||+|+.++   ...
T Consensus        51 ~~~~~~~D~~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~v  129 (170)
T 1ek0_A           51 TVKFEIWDTAGQERFASLAPXYY-RNAQAALVVYDVTKPQSFIKARHWVKELHEQASKDIIIALVGNKIDXLQEGGERKV  129 (170)
T ss_dssp             EEEEEEEEECCSGGGGGGHHHHH-TTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECGGGGGSSCCCCS
T ss_pred             EEEEEEEECCCChhhhhhhhhhh-ccCcEEEEEEecCChHHHHHHHHHHHHHHHhcCCCCcEEEEEECCCccccccccCC
Confidence            46788999999321    11111 24699999999987532111  000      0123456899999999753   101


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+...+..+..  ..+++++||++|+|+++++++|.+.
T Consensus       130 ~~~~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  166 (170)
T 1ek0_A          130 AREEGEKLAEEK--GLLFFETSAKTGENVNDVFLGIGEK  166 (170)
T ss_dssp             CHHHHHHHHHHH--TCEEEECCTTTCTTHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            223333344433  3589999999999999999998764

>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=98.51  E-value=1.4e-07  Score=70.35  Aligned_cols=101  Identities=14%  Similarity=0.108  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcchh-----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDNL-----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~~-----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+.+.|++|.|..-     ...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.+.....
T Consensus        68 ~~~~~l~Dt~G~~~~~~~~~~~~~-~~~d~iilv~D~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~v~  146 (189)
T 1z06_A           68 RIKIQLWDTAGQERFRKSMVQHYY-RNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRILVGNKCDLRSAIQVP  146 (189)
T ss_dssp             EEEEEEEECCCSHHHHTTTHHHHH-TTCCEEEEEEETTCHHHHHTHHHHHHHHHHHCCCSCCCEEEEEECTTCGGGCCSC
T ss_pred             EEEEEEEECCCchhhhhhhhHHHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccceeC
Confidence            46789999999421     11111 24799999999986432111         01111234579999999997541122


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccC---CCHHHHHHHHhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWV---IGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g---~gi~el~~~l~~~  176 (178)
                      .+...+..+..  ..+++++||++|   +|++++|++|.+.
T Consensus       147 ~~~~~~~~~~~--~~~~~~~Sa~~~~~~~~i~~l~~~l~~~  185 (189)
T 1z06_A          147 TDLAQKFADTH--SMPLFETSAKNPNDNDHVEAIFMTLAHK  185 (189)
T ss_dssp             HHHHHHHHHHT--TCCEEECCSSSGGGGSCHHHHHHHHC--
T ss_pred             HHHHHHHHHHc--CCEEEEEeCCcCCcccCHHHHHHHHHHH
Confidence            33444444433  358999999999   9999999988653

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=98.50  E-value=6e-08  Score=74.56  Aligned_cols=101  Identities=13%  Similarity=-0.019  Sum_probs=62.6

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.|++|.|..    +...+. ..+|.+++|+|+++......  .+..      .-..+-++|+||+|+.+......+
T Consensus        61 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~vilV~D~~~~~s~~~~~~~l~~i~~~~~~~~piilv~nK~Dl~~~~~v~~~  139 (223)
T 3cpj_B           61 RIKAQIWDTAGQERYRAITSAYY-RGAVGALIVYDISKSSSYENCNHWLSELRENADDNVAVGLIGNKSDLAHLRAVPTE  139 (223)
T ss_dssp             EEEEEEECCTTTTTTTCCCGGGT-TTCCEEEEEEC-CCHHHHHHHHHHHHHHHHHCC--CEEEEEECCGGGGGGCCSCHH
T ss_pred             EEEEEEEECCCccchhhhHHHHh-ccCCEEEEEEeCCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccccCHH
Confidence            3678899999931    111222 24799999999987532211  0000      113456899999999753112234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...++.+..  ..+++++||++|+|++++|++|.+.
T Consensus       140 ~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  173 (223)
T 3cpj_B          140 ESKTFAQEN--QLLFTETSALNSENVDKAFEELINT  173 (223)
T ss_dssp             HHHHHHHHT--TCEEEECCCC-CCCHHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            445555543  3689999999999999999987654

>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=98.50  E-value=7.7e-08  Score=70.94  Aligned_cols=103  Identities=14%  Similarity=0.016  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchh----
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIG----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~----  136 (178)
                      .+.+.+++|.|..-    ...+. ..+|.+++|+|+++......   .+...     -..+-++|+||+|+.+...    
T Consensus        52 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~  130 (186)
T 1mh1_A           52 PVNLGLWDTAGQEDYDRLRPLSY-PQTDVSLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEK  130 (186)
T ss_dssp             EEEEEEECCCCSGGGTTTGGGGC-TTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHSTTSCEEEEEECHHHHTCHHHHHH
T ss_pred             EEEEEEEECCCCHhHHHHHHHhc-cCCcEEEEEEECCChhhHHHHHHHHHHHHHHhCCCCCEEEEeEcccccccchhhhh
Confidence            46677999999421    11122 24799999999987532211   11000     1446799999999976410    


Q ss_pred             --------HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          137 --------ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       137 --------~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                              ...+...+..+.. ...+++++||++|+|++++++.+.+.+
T Consensus       131 ~~~~~~~~v~~~~~~~~~~~~-~~~~~~~~Sa~~g~gi~~l~~~l~~~~  178 (186)
T 1mh1_A          131 LKEKKLTPITYPQGLAMAKEI-GAVKYLECSALTQRGLKTVFDEAIRAV  178 (186)
T ss_dssp             HHHTTCCCCCHHHHHHHHHHT-TCSEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             hcccccccCCHHHHHHHHHhc-CCcEEEEecCCCccCHHHHHHHHHHHH
Confidence                    0112233333333 224899999999999999999887643

>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=98.50  E-value=8.5e-08  Score=73.35  Aligned_cols=100  Identities=15%  Similarity=0.135  Sum_probs=60.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchhHhH-
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIGADL-  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~~~~-  139 (178)
                      .+.+.+++|.|..    +...+. ..+|.+++|+|+++......   .+...     -..+-++|+||+|+.+.  ... 
T Consensus        81 ~~~l~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~~  157 (214)
T 2j1l_A           81 PVHLHIWDTAGQDDYDRLRPLFY-PDASVLLLCFDVTSPNSFDNIFNRWYPEVNHFCKKVPIIVVGCKTDLRKD--KSLV  157 (214)
T ss_dssp             EEEEEEEEC----------------CEEEEEEEEETTCHHHHHHHHHTHHHHHHHHCSSCCEEEEEECGGGGSC--HHHH
T ss_pred             EEEEEEEECCCchhhhHHHHHHh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEChhhhcc--chhh
Confidence            4568899999931    111122 24699999999986532211   11000     13457999999999875  221 


Q ss_pred             -------------HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 -------------AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 -------------~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                                   ++..+..+.. ...+++++||++|+|++++|+.+.+.
T Consensus       158 ~~~~~~~~~~v~~~~~~~~~~~~-~~~~~~~~SA~~g~gi~el~~~l~~~  206 (214)
T 2j1l_A          158 NKLRRNGLEPVTYHRGQEMARSV-GAVAYLECSARLHDNVHAVFQEAAEV  206 (214)
T ss_dssp             HHHHHTTCCCCCHHHHHHHHHHT-TCSEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             hhhcccccCcccHHHHHHHHHhc-CCCEEEEecCCCCCCHHHHHHHHHHH
Confidence                         2233344433 23489999999999999999988654

>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=98.49  E-value=1.5e-07  Score=70.25  Aligned_cols=100  Identities=12%  Similarity=0.028  Sum_probs=64.6

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CC-------CC-CCCceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KG-------GP-GITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~-------~~-qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+.+.|++|.|..    +...+. ..+|++++|+|+++......  .+       .. .-..+-++|+||+|+.+.. ..
T Consensus        55 ~~~~~l~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~piilv~nK~Dl~~~~-~~  132 (199)
T 2gf0_A           55 VCTLQITDTTGSHQFPAMQRLSI-SKGHAFILVFSVTSKQSLEELGPIYKLIVQIKGSVEDIPVMLVGNKCDETQRE-VD  132 (199)
T ss_dssp             EEEEEEEECCGGGSCHHHHHHHH-HHCSEEEEEEETTCHHHHHTTHHHHHHHHHHHSCGGGSCEEEEEECTTCSSCS-SC
T ss_pred             EEEEEEEeCCChHHhHHHHHHhh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccCCccc-cC
Confidence            4578899999932    111121 24699999999976432110  00       00 0133569999999997641 22


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+......+..  ..+++++||++|+|+++++++|.+.
T Consensus       133 ~~~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  168 (199)
T 2gf0_A          133 TREAQAVAQEW--KCAFMETSAKMNYNVKELFQELLTL  168 (199)
T ss_dssp             HHHHHHHHHHH--TCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh--CCeEEEEecCCCCCHHHHHHHHHHH
Confidence            33444444444  3589999999999999999998764

>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=98.48  E-value=5.7e-08  Score=71.51  Aligned_cols=102  Identities=16%  Similarity=0.024  Sum_probs=62.5

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchhH---
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIGA---  137 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~~---  137 (178)
                      .+.+.+++|.|..    +...+. ..+|.+++|+|+++......   .+...     -..+-++|+||+|+.+....   
T Consensus        55 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~  133 (182)
T 3bwd_D           55 TVNLGLWDTAGQEDYNRLRPLSY-RGADVFILAFSLISKASYENVSKKWIPELKHYAPGVPIVLVGTKLDLRDDKQFFID  133 (182)
T ss_dssp             ---CEEECCCC-CTTTTTGGGGG-TTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHCTTCCEEEEEECHHHHTCHHHHHH
T ss_pred             EEEEEEEECCCChhhhhhHHhhc-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEechhhhcCcccccc
Confidence            4567799999931    111122 24799999999976532111   11000     13467999999999765211   


Q ss_pred             -------hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 -------DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 -------~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                             ..+...+..+..+ ..+++++||++|+|++++++.+.+.
T Consensus       134 ~~~~~~v~~~~~~~~~~~~~-~~~~~~~Sa~~~~gi~~l~~~l~~~  178 (182)
T 3bwd_D          134 HPGAVPITTVQGEELKKLIG-APAYIECSSKSQENVKGVFDAAIRV  178 (182)
T ss_dssp             C--CCCCCHHHHHHHHHHHT-CSEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             cccCCCCCHHHHHHHHHHcC-CCEEEEEECCCCCCHHHHHHHHHHH
Confidence                   1233444444432 2489999999999999999988664

>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=98.48  E-value=2.5e-07  Score=71.30  Aligned_cols=102  Identities=12%  Similarity=0.072  Sum_probs=61.8

Q ss_pred             CCCEEEEeCCcchh-h---hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL-A---ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~-~---~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.++++.|.|..- .   .......+++.++|+|.++......         .....-..+-++|.||+||.+......
T Consensus        86 ~~~l~~~Dt~g~~~~~~~l~~~~~~~a~~~ilVydvt~~~sf~~~~~~~~~l~~~~~~~~~piilVgNK~DL~~~r~v~~  165 (211)
T 2g3y_A           86 SATIILLDMWENKGENEWLHDHCMQVGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVSV  165 (211)
T ss_dssp             EEEEEEECCTTTTHHHHHHHHCCCCCCSEEEEEEETTCHHHHHHHHHHHHHHHTSGGGTTSCEEEEEECTTCGGGCCSCH
T ss_pred             eeEEEEeecCCCcchhhhHHHHHHhhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCcEEEEEEChHHhcCceEeH
Confidence            35567888888321 0   1112235799999999976432110         000011346799999999974311122


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +....+.+..  ..+++++||++|+||+++|+.+.+.
T Consensus       166 ~e~~~~a~~~--~~~~~e~SAk~g~~v~elf~~l~~~  200 (211)
T 2g3y_A          166 SEGRACAVVF--DCKFIETSAAVQHNVKELFEGIVRQ  200 (211)
T ss_dssp             HHHHHHHHHH--TCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            2333333333  3589999999999999999987653

>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=98.47  E-value=1e-07  Score=71.97  Aligned_cols=100  Identities=18%  Similarity=0.161  Sum_probs=63.6

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchhHhH-
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIGADL-  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~~~~-  139 (178)
                      .+.+.+++|.|..    +...+ ...+|.+++|+|++.......   .+...     -..+-++|+||+|+.+.  ... 
T Consensus        72 ~~~l~i~Dt~G~~~~~~~~~~~-~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~~  148 (201)
T 2gco_A           72 QVELALWDTAGQEDYDRLRPLS-YPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRQD--EHTR  148 (201)
T ss_dssp             EEEEEEECCCCSGGGTTTGGGG-CTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHSTTCCEEEEEECGGGTTC--HHHH
T ss_pred             EEEEEEEECCCchhHHHHHHHh-cCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEecHHhhcC--ccch
Confidence            4678899999932    11112 234799999999986432110   11000     13467999999999865  221 


Q ss_pred             -------------HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 -------------AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 -------------~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                                   +...+..+.. ...+++++||++|+|+++++++|.+.
T Consensus       149 ~~~~~~~~~~v~~~~~~~~~~~~-~~~~~~~~SA~~g~gi~~l~~~i~~~  197 (201)
T 2gco_A          149 RELAKMKQEPVRSEEGRDMANRI-SAFGYLECSAKTKEGVREVFEMATRA  197 (201)
T ss_dssp             HHHHTTTCCCCCHHHHHHHHHHT-TCSEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             hhhcccccCcCCHHHHHHHHHhC-CCcEEEEeeCCCCCCHHHHHHHHHHH
Confidence                         2223333332 22389999999999999999988764

>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=98.47  E-value=1.4e-07  Score=71.34  Aligned_cols=101  Identities=21%  Similarity=0.103  Sum_probs=63.9

Q ss_pred             CCCEEEEeCCcchhhhc---ccccccceEEEEEeCCCCCCCCc--CCCC------CCCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDNLAAN---FSRELADYIIYIIDVSGGDKIPR--KGGP------GITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~---~~~~~ad~~I~VvD~~~~~~~~~--~~~~------qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+.+.|++|.|..--..   .....+|.+++|+|+++......  .+..      .-..+-++|+||+|+.... ...+.
T Consensus        68 ~~~~~l~Dt~G~~~~~~~~~~~~~~~d~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~nK~Dl~~~~-~~~~~  146 (213)
T 3cph_A           68 KVKLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRV-VTADQ  146 (213)
T ss_dssp             EEEEEEECCTTGGGGTCCCHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHTTTCSEEEEEEECTTCSSCC-SCHHH
T ss_pred             EEEEEEEeCCCcHHHHHHHHHHhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCEEEEEECCCCcccc-cCHHH
Confidence            36789999999321111   11124799999999986532110  0000      0134679999999995331 22334


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+..+..  ..+++++||++|+|+++++++|.+.
T Consensus       147 ~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  179 (213)
T 3cph_A          147 GEALAKEL--GIPFIESSAKNDDNVNEIFFTLAKL  179 (213)
T ss_dssp             HHHHHHHH--TCCEEECBTTTTBSSHHHHHHHHHH
T ss_pred             HHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            44444444  3589999999999999999988654

>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=98.47  E-value=9.6e-08  Score=72.50  Aligned_cols=100  Identities=20%  Similarity=0.192  Sum_probs=62.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCC---cCCCCC-----CCceeEEEEecCCCCCchhHhH-
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIP---RKGGPG-----ITQADLLVINKTDLASAIGADL-  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~---~~~~~q-----i~~adiiviNK~Dl~~~~~~~~-  139 (178)
                      .+.+.+++|.|..    +...+. ..+|.+++|+|++......   ..+...     -..+-++|+||+|+.+.  ... 
T Consensus        72 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~~  148 (207)
T 2fv8_A           72 QVELALWDTAGQEDYDRLRPLSY-PDTDVILMCFSVDSPDSLENIPEKWVPEVKHFCPNVPIILVANKKDLRSD--EHVR  148 (207)
T ss_dssp             EEEEEEEECTTCTTCTTTGGGGC-TTCCEEEEEEETTCHHHHHHHHHTHHHHHHHHSTTCCEEEEEECGGGGGC--HHHH
T ss_pred             EEEEEEEECCCcHHHHHHHHhhc-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEchhhhcc--ccch
Confidence            4678899999942    111222 3479999999997643211   111000     13457999999999765  221 


Q ss_pred             -------------HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 -------------AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 -------------~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                                   +...+..+.. ...+++++||++|+|+++++++|.+.
T Consensus       149 ~~~~~~~~~~v~~~~~~~~~~~~-~~~~~~~~SA~~g~gi~el~~~l~~~  197 (207)
T 2fv8_A          149 TELARMKQEPVRTDDGRAMAVRI-QAYDYLECSAKTKEGVREVFETATRA  197 (207)
T ss_dssp             HHHHHTTCCCCCHHHHHHHHHHT-TCSEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             hhhhhcccCCCCHHHHHHHHHhc-CCCEEEEeeCCCCCCHHHHHHHHHHH
Confidence                         1222222222 22389999999999999999988654

>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=98.47  E-value=6.5e-08  Score=83.17  Aligned_cols=100  Identities=16%  Similarity=0.069  Sum_probs=61.5

Q ss_pred             CCCCEEEEeCCcchh----hhc------c-cccccceEEEEEeCCCCCCCCcC-CCCC-CCceeEEEEecCCCCCchhHh
Q 030407           72 FKADLLLCESGGDNL----AAN------F-SRELADYIIYIIDVSGGDKIPRK-GGPG-ITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        72 ~~~d~iiiEttG~~~----~~~------~-~~~~ad~~I~VvD~~~~~~~~~~-~~~q-i~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+..+.|++|.|..-    ...      . ....+|.+++|+|++++...... +... -..+.++|+||+|+.+.  ..
T Consensus       270 ~g~~v~liDT~G~~~~~~~ve~~gi~~~~~~~~~aD~vl~VvD~s~~~~~~~~~i~~~l~~~piivV~NK~Dl~~~--~~  347 (462)
T 3geh_A          270 GGIPVQVLDTAGIRETSDQVEKIGVERSRQAANTADLVLLTIDAATGWTTGDQEIYEQVKHRPLILVMNKIDLVEK--QL  347 (462)
T ss_dssp             TTEEEEECC--------------------CCCCSCSEEEEEEETTTCSCHHHHHHHHHHTTSCEEEEEECTTSSCG--GG
T ss_pred             CCEEEEEEECCccccchhHHHHHHHHHHhhhhhcCCEEEEEeccCCCCCHHHHHHHHhccCCcEEEEEECCCCCcc--hh
Confidence            457789999999410    011      1 12246999999999875432110 0000 12468999999999876  33


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ..    .++++....+++++||++|+|++++++.|.+.+
T Consensus       348 ~~----~~~~~~~~~~~i~iSAktg~Gi~eL~~~i~~~~  382 (462)
T 3geh_A          348 IT----SLEYPENITQIVHTAAAQKQGIDSLETAILEIV  382 (462)
T ss_dssp             ST----TCCCCTTCCCEEEEBTTTTBSHHHHHHHHHHHH
T ss_pred             hH----HHHHhccCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            22    222233456899999999999999999987653

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=98.46  E-value=7.4e-08  Score=72.44  Aligned_cols=102  Identities=15%  Similarity=0.130  Sum_probs=63.6

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchh----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIG----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~----  136 (178)
                      .+.+.+++|.|..    +...+. ..+|.+++|+|+++......   .+...     -..+-++|+||+|+.+...    
T Consensus        67 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~~  145 (201)
T 2q3h_A           67 PVRLQLCDTAGQDEFDKLRPLCY-TNTDIFLLCFSVVSPSSFQNVSEKWVPEIRCHCPKAPIILVGTQSDLREDVKVLIE  145 (201)
T ss_dssp             EEEEEEEECCCSTTCSSSGGGGG-TTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHCSSSCEEEEEECGGGGGCHHHHHH
T ss_pred             EEEEEEEECCCCHHHHHHhHhhc-CCCcEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEECHhhhhchhhhhh
Confidence            3567799999942    112222 24799999999987532211   11000     1346799999999975310    


Q ss_pred             --------HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 --------ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 --------~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                              ...+......+.. ...+++++||++|+|++++|+++.+.
T Consensus       146 ~~~~~~~~v~~~~~~~~~~~~-~~~~~~~~Sa~~g~gi~~l~~~l~~~  192 (201)
T 2q3h_A          146 LDKCKEKPVPEEAAKLLAEEI-KAASYIECSALTQKNLKEVFDAAIVA  192 (201)
T ss_dssp             HHTTTCCCCCHHHHHHHHHHH-TCSEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             hcccccccCCHHHHHHHHHhc-CCcEEEEEecCCCCCHHHHHHHHHHH
Confidence                    1123334444433 23489999999999999999987654

>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=98.46  E-value=9.6e-08  Score=71.73  Aligned_cols=101  Identities=12%  Similarity=0.033  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCcchh---hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNL---AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~---~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.+++|.|..-   ...+. ..+|.+++|+|+++......         .....-..+-++|+||+|+.+......+
T Consensus        75 ~~~~~l~Dt~G~~~~~~~~~~~-~~~d~iilv~D~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~NK~Dl~~~~~v~~~  153 (196)
T 2atv_A           75 VVSMEILDTAGQEDTIQREGHM-RWGEGFVLVYDITDRGSFEEVLPLKNILDEIKKPKNVTLILVGNKADLDHSRQVSTE  153 (196)
T ss_dssp             EEEEEEEECCCCCCCHHHHHHH-HHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTTSCCCEEEEEECGGGGGGCCSCHH
T ss_pred             EEEEEEEECCCCCcccchhhhh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhhCCCCCcEEEEEECcccccccccCHH
Confidence            46788999999321   11222 24699999999987432110         0001123457999999999753112234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCC-CHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVI-GIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~-gi~el~~~l~~~  176 (178)
                      ...+..+..  ..+++++||++|+ |++++|++|.+.
T Consensus       154 ~~~~~~~~~--~~~~~~~Sa~~g~~gi~~l~~~l~~~  188 (196)
T 2atv_A          154 EGEKLATEL--ACAFYECSACTGEGNITEIFYELCRE  188 (196)
T ss_dssp             HHHHHHHHH--TSEEEECCTTTCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHh--CCeEEEECCCcCCcCHHHHHHHHHHH
Confidence            444555544  3589999999999 999999987654

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=98.45  E-value=1.9e-07  Score=75.74  Aligned_cols=103  Identities=11%  Similarity=-0.045  Sum_probs=66.2

Q ss_pred             CCCCEEEEeCCcch-hhh-----cc------cccccceEEEEEeCCCCCCCCcC-CC---CCCCceeEEEEecCCCCCch
Q 030407           72 FKADLLLCESGGDN-LAA-----NF------SRELADYIIYIIDVSGGDKIPRK-GG---PGITQADLLVINKTDLASAI  135 (178)
Q Consensus        72 ~~~d~iiiEttG~~-~~~-----~~------~~~~ad~~I~VvD~~~~~~~~~~-~~---~qi~~adiiviNK~Dl~~~~  135 (178)
                      .+..+.|++|.|.. -..     .+      ....+|.+++|+|++. ...... ..   .....+.++++||+|+.+..
T Consensus        54 ~~~~i~~iDTpG~~~~~~~~l~~~~~~~~~~~l~~~D~vl~Vvd~~~-~~~~~~~i~~~l~~~~~P~ilvlNK~D~~~~~  132 (301)
T 1ega_A           54 GAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTR-WTPDDEMVLNKLREGKAPVILAVNKVDNVQEK  132 (301)
T ss_dssp             TTEEEEEESSSSCCHHHHHHHHHHHTCCTTSCCCCEEEEEEEEETTC-CCHHHHHHHHHHHSSSSCEEEEEESTTTCCCH
T ss_pred             CCeeEEEEECcCCCccchhhHHHHHHHHHHHHHhcCCEEEEEEeCCC-CCHHHHHHHHHHHhcCCCEEEEEECcccCccH
Confidence            35678999999943 100     01      1123689999999976 221111 10   11246789999999998721


Q ss_pred             hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          136 GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       136 ~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                       .......+.+.+..+..+++++||++|.|++++++.+.+.
T Consensus       133 -~~~~~~l~~l~~~~~~~~~i~iSA~~g~~v~~l~~~i~~~  172 (301)
T 1ega_A          133 -ADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKH  172 (301)
T ss_dssp             -HHHHHHHHHHHTTSCCSEEEECCTTTTTTHHHHHHHHHTT
T ss_pred             -HHHHHHHHHHHHhcCcCceEEEECCCCCCHHHHHHHHHHh
Confidence             3443334444444444579999999999999999988754

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=98.44  E-value=7.1e-08  Score=73.24  Aligned_cols=102  Identities=16%  Similarity=0.077  Sum_probs=65.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchhH---
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIGA---  137 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~~---  137 (178)
                      .+.+.+++|.|..    +...+. ..+|.+++|+|+++......   .+...     -..+-++|+||+|+.+....   
T Consensus        56 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~d~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~~  134 (212)
T 2j0v_A           56 IVNLGLWDTAGQEDYSRLRPLSY-RGADIFVLAFSLISKASYENVLKKWMPELRRFAPNVPIVLVGTKLDLRDDKGYLAD  134 (212)
T ss_dssp             EEEEEEECCCCCCCCCC--CGGG-TTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHCTTCCEEEEEECHHHHTCHHHHHT
T ss_pred             EEEEEEEECCCcHHHHHHHHhhc-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEeCHHhhhCcccccc
Confidence            4678899999931    111222 24799999999987532211   11000     13467999999999765110   


Q ss_pred             -----hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 -----DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 -----~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                           ..+...+..+..+ ..+++++||++|+|++++|+++.+.
T Consensus       135 ~~~~v~~~~~~~~~~~~~-~~~~~~~Sa~~g~gi~~l~~~l~~~  177 (212)
T 2j0v_A          135 HTNVITSTQGEELRKQIG-AAAYIECSSKTQQNVKAVFDTAIKV  177 (212)
T ss_dssp             CSSCCCHHHHHHHHHHHT-CSEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             ccCCCCHHHHHHHHHHcC-CceEEEccCCCCCCHHHHHHHHHHH
Confidence                 2344444444443 3489999999999999999987654

>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=97.82  E-value=2.3e-08  Score=75.60  Aligned_cols=102  Identities=14%  Similarity=0.059  Sum_probs=61.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCCC-----CceeEEEEecCCCCCchh----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPGI-----TQADLLVINKTDLASAIG----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~qi-----~~adiiviNK~Dl~~~~~----  136 (178)
                      .+.+.+++|.|..    +...+. ..+|.+++|+|+++......   .+...+     ..+-++|+||+|+.+...    
T Consensus        77 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~d~iilv~D~~~~~s~~~~~~~~~~~l~~~~~~~piilv~NK~Dl~~~~~~~~~  155 (204)
T 3th5_A           77 PVNLGLWDTAGQEDYDRLRPLSY-PQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEK  155 (204)
Confidence            4566689999932    111111 24699999999977543221   111111     345699999999976410    


Q ss_pred             --------HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 --------ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 --------~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                              ...+...+..+.. ...+++++||++|+|++++++.|.+.
T Consensus       156 ~~~~~~~~v~~~~~~~~~~~~-~~~~~~~vSA~~g~gi~~l~~~l~~~  202 (204)
T 3th5_A          156 LKEKKLTPITYPQGLAMAKEI-GAVKYLECSALTQRGLKTVFDEAIRA  202 (204)
Confidence                    1111222222222 12388999999999999999988654

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=98.44  E-value=3.7e-07  Score=75.63  Aligned_cols=100  Identities=21%  Similarity=0.071  Sum_probs=67.0

Q ss_pred             CCCEEEEeCCcchhhhc------------ccccccceEEEEEeCCCCCCC--Cc--CC----CCCC-CceeEEEEecCCC
Q 030407           73 KADLLLCESGGDNLAAN------------FSRELADYIIYIIDVSGGDKI--PR--KG----GPGI-TQADLLVINKTDL  131 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~------------~~~~~ad~~I~VvD~~~~~~~--~~--~~----~~qi-~~adiiviNK~Dl  131 (178)
                      +.++.+++|.|..-...            .....+|.+++|+|++.....  ..  .+    .... ..+-++|+||+|+
T Consensus       213 ~~~~~l~Dt~G~~~~~~~~~~~~~~~~~~~~~~~ad~illV~D~s~~~~~~~~~~~~~~~~i~~~~~~~piilV~NK~Dl  292 (357)
T 2e87_A          213 YFRYQIIDTPGLLDRPISERNEIEKQAILALRYLGNLIIYIFDPSEHCGFPLEEQIHLFEEVHGEFKDLPFLVVINKIDV  292 (357)
T ss_dssp             TEEEEEEECTTTSSSCSTTSCHHHHHHHHGGGGTCSEEEEEECTTCTTSSCHHHHHHHHHHHHHHTTTSCEEEEECCTTT
T ss_pred             CceEEEEeCCCccccchhhhhHHHHHHHHHHHhcCCEEEEEEeCCccccCCHHHHHHHHHHHHHhcCCCCEEEEEECccc
Confidence            46789999999410000            011246899999998765421  10  00    0001 4567999999999


Q ss_pred             CCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          132 ASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       132 ~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.  ...+...+.++..  ..+++++||++|+|++++++++.+.
T Consensus       293 ~~~--~~~~~~~~~~~~~--~~~~~~iSA~~g~gi~~l~~~i~~~  333 (357)
T 2e87_A          293 ADE--ENIKRLEKFVKEK--GLNPIKISALKGTGIDLVKEEIIKT  333 (357)
T ss_dssp             CCH--HHHHHHHHHHHHT--TCCCEECBTTTTBTHHHHHHHHHHH
T ss_pred             CCh--HHHHHHHHHHHhc--CCCeEEEeCCCCcCHHHHHHHHHHH
Confidence            877  5555566665543  4589999999999999999988654

>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=98.43  E-value=1.4e-07  Score=71.08  Aligned_cols=101  Identities=19%  Similarity=0.128  Sum_probs=62.8

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCch-----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAI-----  135 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~-----  135 (178)
                      .+.+.|++|.|..    +...+. ..+|.+++|+|+++......  .+.      ..-..+-++|+||+|+.+..     
T Consensus        76 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~d~iilv~d~~~~~s~~~~~~~~~~i~~~~~~~~piilv~NK~Dl~~~~~~~~~  154 (199)
T 2p5s_A           76 RTVLQLWDTAGQERFRSIAKSYF-RKADGVLLLYDVTCEKSFLNIREWVDMIEDAAHETVPIMLVGNKADIRDTAATEGQ  154 (199)
T ss_dssp             EEEEEEEECTTCTTCHHHHHHHH-HHCSEEEEEEETTCHHHHHTHHHHHHHHHHHC---CCEEEEEECGGGHHHHHHTTC
T ss_pred             EEEEEEEECCCCcchhhhHHHHH-hhCCEEEEEEECCChHHHHHHHHHHHHHHHhcCCCCCEEEEEECcccccccccccc
Confidence            3568899999932    111111 24699999999986532211  000      00134679999999996320     


Q ss_pred             -hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          136 -GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       136 -~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                       ....+...+..+..  ..+++++||++|+|+++++++|.+.
T Consensus       155 ~~v~~~~~~~~~~~~--~~~~~~~SA~~g~gv~el~~~l~~~  194 (199)
T 2p5s_A          155 KCVPGHFGEKLAMTY--GALFCETSAKDGSNIVEAVLHLARE  194 (199)
T ss_dssp             CCCCHHHHHHHHHHH--TCEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             cccCHHHHHHHHHHc--CCeEEEeeCCCCCCHHHHHHHHHHH
Confidence             01123334444444  3589999999999999999988764

>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=98.43  E-value=1.4e-07  Score=76.72  Aligned_cols=78  Identities=14%  Similarity=-0.041  Sum_probs=54.5

Q ss_pred             ccceEEEEEeCCCCCCCCc---CCC---CCCCceeEEEEecCCCCCchhHh---HHHHHHHHHhcCCCCCEEEEecccCC
Q 030407           94 LADYIIYIIDVSGGDKIPR---KGG---PGITQADLLVINKTDLASAIGAD---LAVMERDALRMRDGGPFIFAQVGWVI  164 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~---~~~---~qi~~adiiviNK~Dl~~~~~~~---~~~~~~~l~~~np~a~i~~~SA~~g~  164 (178)
                      .+|.++.|+|++++.....   .+.   .....+-++|+||+||.++  .+   .+...+..++.  +.+++++||++|+
T Consensus        79 naD~vliV~d~~~p~~s~~~l~~~l~~~~~~~~~~ilV~NK~DL~~~--~~v~~~~~~~~~~~~~--g~~~~~~SA~~g~  154 (302)
T 2yv5_A           79 NVDRVIIVETLKMPEFNNYLLDNMLVVYEYFKVEPVIVFNKIDLLNE--EEKKELERWISIYRDA--GYDVLKVSAKTGE  154 (302)
T ss_dssp             SCCEEEEEECSTTTTCCHHHHHHHHHHHHHTTCEEEEEECCGGGCCH--HHHHHHHHHHHHHHHT--TCEEEECCTTTCT
T ss_pred             hcCEEEEEEECCCCCCCHHHHHHHHHHHHhCCCCEEEEEEcccCCCc--cccHHHHHHHHHHHHC--CCeEEEEECCCCC
Confidence            4699999999987642211   111   0123456999999999876  42   44455555544  3589999999999


Q ss_pred             CHHHHHHHHhh
Q 030407          165 GIIFTLSITHY  175 (178)
Q Consensus       165 gi~el~~~l~~  175 (178)
                      |+++|++.+..
T Consensus       155 gi~~L~~~l~G  165 (302)
T 2yv5_A          155 GIDELVDYLEG  165 (302)
T ss_dssp             THHHHHHHTTT
T ss_pred             CHHHHHhhccC
Confidence            99999998753

>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=98.42  E-value=2.9e-07  Score=77.60  Aligned_cols=103  Identities=17%  Similarity=0.111  Sum_probs=60.3

Q ss_pred             CCEEEEeCCcch-hhhccc--ccccceEEEEEeCCCCC-CCCc-CC---CCCCCc-eeEEEEecCCCCCchh--HhHHHH
Q 030407           74 ADLLLCESGGDN-LAANFS--RELADYIIYIIDVSGGD-KIPR-KG---GPGITQ-ADLLVINKTDLASAIG--ADLAVM  142 (178)
Q Consensus        74 ~d~iiiEttG~~-~~~~~~--~~~ad~~I~VvD~~~~~-~~~~-~~---~~qi~~-adiiviNK~Dl~~~~~--~~~~~~  142 (178)
                      ..+.|++|.|-. ......  ...+|.+++|+|++++. ..+. .+   ...+.. .-++++||+|+.+...  ...+++
T Consensus        81 ~~i~iiDtPGh~~f~~~~~~~~~~~D~~ilVvda~~g~~~~qt~e~l~~~~~l~~~~iivv~NK~Dl~~~~~~~~~~~~i  160 (408)
T 1s0u_A           81 RRVSFVDSPGHETLMATMLSGASLMDGAILVIAANEPCPQPQTKEHLMALEILGIDKIIIVQNKIDLVDEKQAEENYEQI  160 (408)
T ss_dssp             EEEEEEECSSHHHHHHHHHTTCSCCSEEEEEEETTSCSSCHHHHHHHHHHHHTTCCCEEEEEECTTSSCTTTTTTHHHHH
T ss_pred             cEEEEEECCCHHHHHHHHHHhHhhCCEEEEEEECCCCCCCchhHHHHHHHHHcCCCeEEEEEEccCCCCHHHHHHHHHHH
Confidence            568999999921 111111  12469999999998764 1111 00   011222 3589999999987511  123455


Q ss_pred             HHHHHhcC-CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          143 ERDALRMR-DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       143 ~~~l~~~n-p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+++.. ...+++++||++|+|+++|+++|.+.
T Consensus       161 ~~~l~~~~~~~~~~i~vSA~~g~gi~~L~~~l~~~  195 (408)
T 1s0u_A          161 KEFVKGTIAENAPIIPISAHHEANIDVLLKAIQDF  195 (408)
T ss_dssp             HHHHTTSTTTTCCEEEC------CHHHHHHHHHHH
T ss_pred             HHHHhhcCCCCCeEEEeeCCCCCCHHHHHHHHHHh
Confidence            55555432 35799999999999999999998763

>3l0i_B RAS-related protein RAB-1A; GEF-GDF-RAB complex, GTP-binding, guanine-nucleotide exchang GDI-displacement factor; 2.85A {Homo sapiens}

Probab=98.41  E-value=2e-08  Score=75.83  Aligned_cols=102  Identities=19%  Similarity=0.139  Sum_probs=57.2

Q ss_pred             CCEEEEeCCcchhhh---cccccccceEEEEEeCCCCCCCCc--CC------CCCCCceeEEEEecCCCCCchhHhHHHH
Q 030407           74 ADLLLCESGGDNLAA---NFSRELADYIIYIIDVSGGDKIPR--KG------GPGITQADLLVINKTDLASAIGADLAVM  142 (178)
Q Consensus        74 ~d~iiiEttG~~~~~---~~~~~~ad~~I~VvD~~~~~~~~~--~~------~~qi~~adiiviNK~Dl~~~~~~~~~~~  142 (178)
                      +.+.|++|.|..--.   ......+|.+++|+|+++......  .+      ...-..+-++|+||+|+.+......+..
T Consensus        82 ~~~~i~Dt~G~~~~~~~~~~~~~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~p~ilv~nK~Dl~~~~~v~~~~~  161 (199)
T 3l0i_B           82 IKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTA  161 (199)
T ss_dssp             EEEEEECCTTCTTCCCCSCC--CCCSEEEECC-CCCSHHHHHHHHHHHHHHSCC-CCSEEEEC-CCSSCC--CCCCSCC-
T ss_pred             EEEEEEECCCcHhHHHHHHHHhhcCCEEEEEEECCCHHHHHHHHHHHHHHHHhccCCCCEEEEEECccCCccccCCHHHH
Confidence            578899999932111   111124799999999987542111  00      0011346799999999975411111223


Q ss_pred             HHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          143 ERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       143 ~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .+..+..  ..+++++||++|+|++++|++|.+.+
T Consensus       162 ~~~~~~~--~~~~~~vSA~~g~gv~~l~~~l~~~l  194 (199)
T 3l0i_B          162 KEFADSL--GIPFLETSAKNATNVEQSFMTMAAEI  194 (199)
T ss_dssp             CHHHHTT--TCCBCCCCC---HHHHHHHHHHTTTT
T ss_pred             HHHHHHc--CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3334433  46899999999999999999987653

>2hjg_A GTP-binding protein ENGA; GTPase ENGA KH-domain, hydrolase; HET: GDP; 2.50A {Bacillus subtilis}

Probab=98.41  E-value=1.5e-07  Score=80.10  Aligned_cols=83  Identities=16%  Similarity=0.079  Sum_probs=56.6

Q ss_pred             ccceEEEEEeCCCCCCCCcC-CC---CCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcC---CCCCEEEEecccCCCH
Q 030407           94 LADYIIYIIDVSGGDKIPRK-GG---PGITQADLLVINKTDLASAIGADLAVMERDALRMR---DGGPFIFAQVGWVIGI  166 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~-~~---~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~n---p~a~i~~~SA~~g~gi  166 (178)
                      .+|.+++|+|++++...+.. +.   .....+-++|+||+|+.+......+++.+.+++..   ..++++++||++|+|+
T Consensus       257 ~ad~~llv~D~~~~~s~~~~~~~~~~~~~~~~iiiv~NK~Dl~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~SA~tg~~v  336 (436)
T 2hjg_A          257 RSEVVAVVLDGEEGIIEQDKRIAGYAHEAGKAVVIVVNKWDAVDKDESTMKEFEENIRDHFQFLDYAPILFMSALTKKRI  336 (436)
T ss_dssp             HCSEEEEEEETTTCCCHHHHHHHHHHHHTTCEEEEEEECGGGSCCCTTHHHHHHHHHHHHCGGGTTSCEEECCTTTCTTG
T ss_pred             hCCEEEEEEcCCcCCcHHHHHHHHHHHHcCCcEEEEEECccCCCcchHHHHHHHHHHHHhcccCCCCCEEEEecccCCCH
Confidence            36899999999886543221 00   01245779999999998752122344444444332   4689999999999999


Q ss_pred             HHHHHHHhhh
Q 030407          167 IFTLSITHYI  176 (178)
Q Consensus       167 ~el~~~l~~~  176 (178)
                      +++++.+.+.
T Consensus       337 ~~l~~~i~~~  346 (436)
T 2hjg_A          337 HTLMPAIIKA  346 (436)
T ss_dssp             GGHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999887654

>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=98.41  E-value=2.6e-07  Score=77.87  Aligned_cols=101  Identities=14%  Similarity=0.081  Sum_probs=64.4

Q ss_pred             CCEEEEeCCcch-hhhccc--ccccceEEEEEeCCCCC-CCCc-CC---CCCCCc-eeEEEEecCCCCCchhHhH----H
Q 030407           74 ADLLLCESGGDN-LAANFS--RELADYIIYIIDVSGGD-KIPR-KG---GPGITQ-ADLLVINKTDLASAIGADL----A  140 (178)
Q Consensus        74 ~d~iiiEttG~~-~~~~~~--~~~ad~~I~VvD~~~~~-~~~~-~~---~~qi~~-adiiviNK~Dl~~~~~~~~----~  140 (178)
                      ..+.|++|.|-. ......  ...+|.+++|+|++++. ..+. .+   ...+.. .-++++||+|+.++  .+.    +
T Consensus        83 ~~i~iiDtPGh~~f~~~~~~~~~~~D~~ilVvda~~g~~~~qt~e~l~~~~~~~~~~iivviNK~Dl~~~--~~~~~~~~  160 (410)
T 1kk1_A           83 RRVSFIDAPGHEALMTTMLAGASLMDGAILVIAANEPCPRPQTREHLMALQIIGQKNIIIAQNKIELVDK--EKALENYR  160 (410)
T ss_dssp             EEEEEEECSSHHHHHHHHHHCGGGCSEEEEEEETTSCSSCHHHHHHHHHHHHHTCCCEEEEEECGGGSCH--HHHHHHHH
T ss_pred             cEEEEEECCChHHHHHHHHhhhhhCCEEEEEEECCCCCCChhHHHHHHHHHHcCCCcEEEEEECccCCCH--HHHHHHHH
Confidence            468999999931 111111  12469999999998764 2111 00   011121 34788999999876  332    3


Q ss_pred             HHHHHHHhc-CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRM-RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~-np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ++.+.++.. ....+++++||++|+|+++|+++|.+.
T Consensus       161 ~i~~~l~~~~~~~~~~i~vSA~~g~gi~~L~~~l~~~  197 (410)
T 1kk1_A          161 QIKEFIEGTVAENAPIIPISALHGANIDVLVKAIEDF  197 (410)
T ss_dssp             HHHHHHTTSTTTTCCEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHhcCcCCCeEEEeeCCCCCCHHHHHHHHHHh
Confidence            344444432 235799999999999999999998763

>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=98.41  E-value=1.6e-07  Score=72.00  Aligned_cols=102  Identities=15%  Similarity=0.103  Sum_probs=65.5

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCch-----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAI-----  135 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~-----  135 (178)
                      .+.+.|++|.|..    +...+. ..+|++++|+|+++......   .+...     -..+-++|+||+|+.++.     
T Consensus        74 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~i~~~~~~~piilv~nK~Dl~~~~~~~~~  152 (214)
T 3q3j_B           74 RVELSLWDTSGSPYYDNVRPLCY-SDSDAVLLCFDISRPETVDSALKKWRTEILDYCPSTRVLLIGCKTDLRTDLSTLME  152 (214)
T ss_dssp             EEEEEEEEECCSGGGTTTGGGGC-TTCSEEEEEEETTCTHHHHHHHTHHHHHHHHHCTTSEEEEEEECGGGGGCHHHHHH
T ss_pred             EEEEEEEECCCCHhHHHHHHHHc-CCCeEEEEEEECcCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEChhhccchhhhhh
Confidence            4678899999932    112222 24799999999987543211   11000     134679999999996520     


Q ss_pred             -------hHhHHHHHHHHHhcCCCCCEEEEecccCCC-HHHHHHHHhhh
Q 030407          136 -------GADLAVMERDALRMRDGGPFIFAQVGWVIG-IIFTLSITHYI  176 (178)
Q Consensus       136 -------~~~~~~~~~~l~~~np~a~i~~~SA~~g~g-i~el~~~l~~~  176 (178)
                             ....+...++.+..+ ..+++++||++|+| ++++|+.+.+.
T Consensus       153 ~~~~~~~~v~~~~~~~~~~~~~-~~~~~e~SA~~g~g~v~~lf~~l~~~  200 (214)
T 3q3j_B          153 LSHQKQAPISYEQGCAIAKQLG-AEIYLEGSAFTSEKSIHSIFRTASML  200 (214)
T ss_dssp             HHHTTCCCCCHHHHHHHHHHHT-CSEEEECCTTTCHHHHHHHHHHHHHH
T ss_pred             hcccccCccCHHHHHHHHHHcC-CCEEEEeccCCCcccHHHHHHHHHHH
Confidence                   022334445555442 23899999999999 99999988654

>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=98.40  E-value=1.8e-08  Score=80.14  Aligned_cols=99  Identities=20%  Similarity=0.099  Sum_probs=63.3

Q ss_pred             CCCEEEEeCCcch-hh-------------hccc-ccccceEEEEEeCCCCCCCCc--CCCCCCCceeEEEEecCCCCCch
Q 030407           73 KADLLLCESGGDN-LA-------------ANFS-RELADYIIYIIDVSGGDKIPR--KGGPGITQADLLVINKTDLASAI  135 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-------------~~~~-~~~ad~~I~VvD~~~~~~~~~--~~~~qi~~adiiviNK~Dl~~~~  135 (178)
                      +..+.|++|.|.. ..             ..+. ...+|.+++|+|+++......  .....+..+.++|+||+|+.+..
T Consensus        47 ~~~~~lvDtpG~~~~~~~~~~~~~~e~i~~~~~~~~~~d~vi~VvDas~~~~~~~l~~~l~~~~~pvilv~NK~Dl~~~~  126 (256)
T 3iby_A           47 EHLIEITDLPGVYSLVANAEGISQDEQIAAQSVIDLEYDCIINVIDACHLERHLYLTSQLFELGKPVVVALNMMDIAEHR  126 (256)
T ss_dssp             TEEEEEEECCCCSSCC------CHHHHHHHHHHHHSCCSEEEEEEEGGGHHHHHHHHHHHTTSCSCEEEEEECHHHHHHT
T ss_pred             CeEEEEEeCCCcccccccccCCCHHHHHHHHHHhhCCCCEEEEEeeCCCchhHHHHHHHHHHcCCCEEEEEEChhcCCcC
Confidence            4578999999941 11             1111 124699999999987321110  01112456789999999986541


Q ss_pred             h--HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          136 G--ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       136 ~--~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .  ...+.+.+.   +  +.+++++||++|+|++++++.+.+.
T Consensus       127 ~~~~~~~~l~~~---l--g~~vi~~SA~~g~gi~el~~~i~~~  164 (256)
T 3iby_A          127 GISIDTEKLESL---L--GCSVIPIQAHKNIGIPALQQSLLHC  164 (256)
T ss_dssp             TCEECHHHHHHH---H--CSCEEECBGGGTBSHHHHHHHHHTC
T ss_pred             CcHHHHHHHHHH---c--CCCEEEEECCCCCCHHHHHHHHHhh
Confidence            0  122333322   2  3699999999999999999998653

>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=98.40  E-value=2.7e-08  Score=76.21  Aligned_cols=99  Identities=10%  Similarity=-0.054  Sum_probs=63.6

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CCCCC-----CCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KGGPG-----ITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~q-----i~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      ++.+.|++|.|..-    ...+. ..+|.+++|+|+++......  .+...     -..+-++|+||+|+.+.  .....
T Consensus        63 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~--~~~~~  139 (221)
T 3gj0_A           63 PIKFNVWDTAGQEKFGGLRDGYY-IQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDR--KVKAK  139 (221)
T ss_dssp             EEEEEEEEECSGGGTSCCCHHHH-TTCCEEEEEEETTCHHHHHTHHHHHHHHHHHSTTCCEEEEEECTTSSSC--SSCGG
T ss_pred             EEEEEEEeCCChHHHhHHHHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCEEEEEECCccccc--cccHH
Confidence            46788999999321    11111 24799999999987532211  00000     13457999999999765  22222


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+..+..  ..+++++||++|.|++++|++|.+.
T Consensus       140 ~~~~~~~~--~~~~~~~Sa~~~~gi~~l~~~l~~~  172 (221)
T 3gj0_A          140 SIVFHRKK--NLQYYDISAKSNYNFEKPFLWLARK  172 (221)
T ss_dssp             GCCHHHHH--TCEEEECBGGGTBTTTHHHHHHHHH
T ss_pred             HHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            33333333  3589999999999999999987653

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=98.34  E-value=1.2e-07  Score=68.23  Aligned_cols=98  Identities=15%  Similarity=0.051  Sum_probs=62.1

Q ss_pred             CCCEEEEeCCcchh--------hhc--ccccccceEEEEEeCCCCCCCCcC-CC---CCCCceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDNL--------AAN--FSRELADYIIYIIDVSGGDKIPRK-GG---PGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~~--------~~~--~~~~~ad~~I~VvD~~~~~~~~~~-~~---~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      +..+.+++|.|..-        ...  .....+|.+++|+|+++....... ..   .....+-++|+||+|+.+.  .+
T Consensus        48 ~~~~~l~Dt~G~~~~~~~~~~~~~~~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~--~~  125 (161)
T 2dyk_A           48 RGRFLLVDTGGLWSGDKWEKKIQEKVDRALEDAEVVLFAVDGRAELTQADYEVAEYLRRKGKPVILVATKVDDPKH--EL  125 (161)
T ss_dssp             TEEEEEEECGGGCSSSSCCHHHHHHHHHHTTTCSEEEEEEESSSCCCHHHHHHHHHHHHHTCCEEEEEECCCSGGG--GG
T ss_pred             CceEEEEECCCCCCccchHHHHHHHHHHHHHhCCEEEEEEECCCcccHhHHHHHHHHHhcCCCEEEEEECcccccc--hH
Confidence            34788999999421        000  011246999999999875332110 00   0123467999999999765  21


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                        ...+.. +. ...+++++||++|+|++++++++.+.
T Consensus       126 --~~~~~~-~~-~~~~~~~~Sa~~~~gv~~l~~~l~~~  159 (161)
T 2dyk_A          126 --YLGPLY-GL-GFGDPIPTSSEHARGLEELLEAIWER  159 (161)
T ss_dssp             --GCGGGG-GG-SSCSCEECBTTTTBSHHHHHHHHHHH
T ss_pred             --hHHHHH-hC-CCCCeEEEecccCCChHHHHHHHHHh
Confidence              122222 22 23379999999999999999988764

>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=98.34  E-value=3.9e-07  Score=71.98  Aligned_cols=80  Identities=18%  Similarity=0.098  Sum_probs=54.5

Q ss_pred             ccceEEEEEeCCCC--CCCCc--CCCC-------CCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEeccc
Q 030407           94 LADYIIYIIDVSGG--DKIPR--KGGP-------GITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGW  162 (178)
Q Consensus        94 ~ad~~I~VvD~~~~--~~~~~--~~~~-------qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~  162 (178)
                      .+|++++|+|+++.  .....  .+..       .-..+-++|+||+|+.+.  ...+...+..+.. ...+++++||++
T Consensus       162 ~ad~vilV~D~t~~~~~s~~~~~~~l~~i~~~~~~~~~piilV~NK~Dl~~~--~~v~~~~~~~~~~-~~~~~~e~SAk~  238 (255)
T 3c5h_A          162 LVDGFLLGIDVSRGMNRNFDDQLKFVSNLYNQLAKTKKPIVVVLTKCDEGVE--RYIRDAHTFALSK-KNLQVVETSARS  238 (255)
T ss_dssp             ECCEEEEEEECBC----CHHHHHHHHHHHHHHHHHTTCCEEEEEECGGGBCH--HHHHHHHHHHHTS-SSCCEEECBTTT
T ss_pred             cCCEEEEEEECCCCchhhHHHHHHHHHHHHHHhccCCCCEEEEEEccccccc--HHHHHHHHHHHhc-CCCeEEEEECCC
Confidence            36999999999875  32211  0000       013457999999999765  4445555555432 356899999999


Q ss_pred             CCCHHHHHHHHhhh
Q 030407          163 VIGIIFTLSITHYI  176 (178)
Q Consensus       163 g~gi~el~~~l~~~  176 (178)
                      |+|++++|+.|.+.
T Consensus       239 g~gv~elf~~l~~~  252 (255)
T 3c5h_A          239 NVNVDLAFSTLVQL  252 (255)
T ss_dssp             TBSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999988654

>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=98.32  E-value=2.4e-07  Score=68.84  Aligned_cols=102  Identities=15%  Similarity=0.108  Sum_probs=64.6

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCch-----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAI-----  135 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~-----  135 (178)
                      .+.+.+++|.|..    +...+ ...+|.+++|+|+++......   .+...     -..+-++|+||+|+.++.     
T Consensus        54 ~~~~~i~Dt~G~~~~~~~~~~~-~~~~~~~i~v~d~~~~~s~~~~~~~~~~~i~~~~~~~piilv~nK~Dl~~~~~~~~~  132 (184)
T 1m7b_A           54 RIELSLWDTSGSPYYDNVRPLS-YPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDLRTDVSTLVE  132 (184)
T ss_dssp             EEEEEEEEECCSGGGTTTGGGG-CTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHCTTCEEEEEEECGGGGGCHHHHHH
T ss_pred             EEEEEEEECCCChhhhhhHHhh-cCCCcEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEcchhhcchhhHhh
Confidence            4678899999942    11112 235799999999986432211   11000     134679999999997430     


Q ss_pred             -------hHhHHHHHHHHHhcCCCCCEEEEecc-cCCCHHHHHHHHhhh
Q 030407          136 -------GADLAVMERDALRMRDGGPFIFAQVG-WVIGIIFTLSITHYI  176 (178)
Q Consensus       136 -------~~~~~~~~~~l~~~np~a~i~~~SA~-~g~gi~el~~~l~~~  176 (178)
                             ....+...+..++.+ ..+++++||+ +|+|++++|+.+.+.
T Consensus       133 ~~~~~~~~v~~~~~~~~~~~~~-~~~~~e~Sa~~~~~gi~~l~~~i~~~  180 (184)
T 1m7b_A          133 LSNHRQTPVSYDQGANMAKQIG-AATYIECSALQSENSVRDIFHVATLA  180 (184)
T ss_dssp             HHTTTCCCCCHHHHHHHHHHHT-CSEEEECBTTTBHHHHHHHHHHHHHH
T ss_pred             hhhcccCCCCHHHHHHHHHHcC-CcEEEEeeecCCCcCHHHHHHHHHHH
Confidence                   012233444454443 3589999999 699999999988764

>3j2k_7 ERF3, eukaryotic polypeptide chain release factor 3; rabbit 80S ribosome, ribosome-translation complex; 17.00A {Oryctolagus cuniculus}

Probab=98.31  E-value=9.6e-07  Score=75.27  Aligned_cols=98  Identities=11%  Similarity=0.029  Sum_probs=58.4

Q ss_pred             CCCEEEEeCCcch-hh-hc-ccccccceEEEEEeCCCCCCC-------Cc-CC---CCCCCce-eEEEEecCCCCCch--
Q 030407           73 KADLLLCESGGDN-LA-AN-FSRELADYIIYIIDVSGGDKI-------PR-KG---GPGITQA-DLLVINKTDLASAI--  135 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~-~~~~~ad~~I~VvD~~~~~~~-------~~-~~---~~qi~~a-diiviNK~Dl~~~~--  135 (178)
                      +..+.|+.|.|-. .. .+ .....+|.+++|+|++.+...       +. .+   ...+... -++++||+|+.+..  
T Consensus        94 ~~~~~iiDTPGh~~f~~~~~~~~~~aD~~ilVVDa~~g~~e~~~~~~~qt~e~l~~~~~~~v~~iIvviNK~Dl~~~~~~  173 (439)
T 3j2k_7           94 KKHFTILDAPGHKSFVPNMIGGASQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWS  173 (439)
T ss_pred             CeEEEEEECCChHHHHHHHHhhHhhCCEEEEEEECCCCccccccCCCchHHHHHHHHHHcCCCeEEEEeecCCCcccchH
Confidence            4578999999931 00 01 111247999999999887421       10 00   0113334 58999999996421  


Q ss_pred             hHhHHH----HHHHHHhcC--C--CCCEEEEecccCCCHHHHH
Q 030407          136 GADLAV----MERDALRMR--D--GGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus       136 ~~~~~~----~~~~l~~~n--p--~a~i~~~SA~~g~gi~el~  170 (178)
                      .+..+.    +.+.+++..  +  ..+++++||++|+|++++.
T Consensus       174 ~~~~~~i~~~~~~~l~~~g~~~~~~~~~i~iSA~~G~ni~~l~  216 (439)
T 3j2k_7          174 NERYEECKEKLVPFLKKVGFNPKKDIHFMPCSGLTGANLKEQS  216 (439)
T ss_pred             HHHHHHHHHHHHHHHHHhcccccCCeeEEEeeccCCccccccc
Confidence            022222    333333332  1  4689999999999999843

>3cnl_A YLQF, putative uncharacterized protein; circular permutation, GNP, signaling protein; HET: GNP; 2.00A {Thermotoga maritima} PDB: 3cnn_A* 3cno_A*

Probab=98.29  E-value=2.5e-06  Score=67.95  Aligned_cols=77  Identities=9%  Similarity=0.015  Sum_probs=56.5

Q ss_pred             ccceEEEEEeCCCCCCCCc-CCCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHH
Q 030407           94 LADYIIYIIDVSGGDKIPR-KGGPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSI  172 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~-~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~  172 (178)
                      .+|.++.|+|+..+..... ... .+..+-++|+||+||+++  +..+...++.++.  +.++ .+||++|.|+++|++.
T Consensus        21 ~~D~vl~VvDar~P~~~~~~~l~-ll~k~~iivlNK~DL~~~--~~~~~~~~~~~~~--g~~v-~iSa~~~~gi~~L~~~   94 (262)
T 3cnl_A           21 LVNTVVEVRDARAPFATSAYGVD-FSRKETIILLNKVDIADE--KTTKKWVEFFKKQ--GKRV-ITTHKGEPRKVLLKKL   94 (262)
T ss_dssp             TCSEEEEEEETTSTTTTSCTTSC-CTTSEEEEEEECGGGSCH--HHHHHHHHHHHHT--TCCE-EECCTTSCHHHHHHHH
T ss_pred             hCCEEEEEeeCCCCCcCcChHHH-hcCCCcEEEEECccCCCH--HHHHHHHHHHHHc--CCeE-EEECCCCcCHHHHHHH
Confidence            4699999999987654321 111 226678999999999987  5555555556543  3467 9999999999999998


Q ss_pred             Hhhh
Q 030407          173 THYI  176 (178)
Q Consensus       173 l~~~  176 (178)
                      +...
T Consensus        95 l~~~   98 (262)
T 3cnl_A           95 SFDR   98 (262)
T ss_dssp             CCCT
T ss_pred             HHHh
Confidence            7653

>3cb4_D GTP-binding protein LEPA; GTPase, OB-fold, membrane, nucleotide-binding, translation; 2.80A {Escherichia coli} PDB: 3deg_C*

Probab=98.28  E-value=1.3e-06  Score=77.30  Aligned_cols=100  Identities=14%  Similarity=0.101  Sum_probs=64.0

Q ss_pred             CCEEEEeCCcch-hhhcc--cccccceEEEEEeCCCCCCCCcC--C--CCCCCceeEEEEecCCCCCchhHhHHHHHHHH
Q 030407           74 ADLLLCESGGDN-LAANF--SRELADYIIYIIDVSGGDKIPRK--G--GPGITQADLLVINKTDLASAIGADLAVMERDA  146 (178)
Q Consensus        74 ~d~iiiEttG~~-~~~~~--~~~~ad~~I~VvD~~~~~~~~~~--~--~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l  146 (178)
                      +.+-||+|.|-. .....  ....+|++++|+|++++...+..  +  ......+-++++||+|+.+.  . .+...+.+
T Consensus        71 ~~l~liDTPGh~dF~~ev~~~l~~aD~aILVVDa~~gv~~qt~~~~~~~~~~~ipiIvViNKiDl~~a--~-~~~v~~ei  147 (599)
T 3cb4_D           71 YQLNFIDTPGHVDFSYEVSRSLAACEGALLVVDAGQGVEAQTLANCYTAMEMDLEVVPVLNKIDLPAA--D-PERVAEEI  147 (599)
T ss_dssp             EEEEEEECCCCGGGHHHHHHHHHHCSEEEEEEETTTCCCTHHHHHHHHHHHTTCEEEEEEECTTSTTC--C-HHHHHHHH
T ss_pred             EEEEEEECCCchHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEeeeccCcccc--c-HHHHHHHH
Confidence            567799999931 00000  11236999999999887543221  0  00123467999999999875  2 22333333


Q ss_pred             HhcC--CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          147 LRMR--DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       147 ~~~n--p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ++..  +..+++++||++|.|++++++.+.+.
T Consensus       148 ~~~lg~~~~~vi~vSAktg~GI~~Ll~~I~~~  179 (599)
T 3cb4_D          148 EDIVGIDATDAVRCSAKTGVGVQDVLERLVRD  179 (599)
T ss_dssp             HHHTCCCCTTCEEECTTTCTTHHHHHHHHHHH
T ss_pred             HHHhCCCcceEEEeecccCCCchhHHHHHhhc
Confidence            3332  22479999999999999999987654

>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=98.27  E-value=7.9e-07  Score=75.63  Aligned_cols=82  Identities=18%  Similarity=0.139  Sum_probs=55.2

Q ss_pred             cceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhc---CCCCCEEEEecccCCCHH
Q 030407           95 ADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERDALRM---RDGGPFIFAQVGWVIGII  167 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~---np~a~i~~~SA~~g~gi~  167 (178)
                      +|.+++++|++.+......    .......+-++|+||+|+.+......+++.+.+++.   .+.++++++||++|.|++
T Consensus       264 ad~vllv~d~~~~~~~~~~~i~~~l~~~~~~~ilv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~g~gv~  343 (439)
T 1mky_A          264 ADVVVIVLDATQGITRQDQRMAGLMERRGRASVVVFNKWDLVVHREKRYDEFTKLFREKLYFIDYSPLIFTSADKGWNID  343 (439)
T ss_dssp             CSEEEEEEETTTCCCHHHHHHHHHHHHTTCEEEEEEECGGGSTTGGGCHHHHHHHHHHHCGGGTTSCEEECBTTTTBSHH
T ss_pred             CCEEEEEEeCCCCCCHHHHHHHHHHHHcCCCEEEEEECccCCCchhhHHHHHHHHHHHHhccCCCCcEEEEECCCCCCHH
Confidence            5889999999875432211    011134578999999999865211244444444322   246799999999999999


Q ss_pred             HHHHHHhhh
Q 030407          168 FTLSITHYI  176 (178)
Q Consensus       168 el~~~l~~~  176 (178)
                      ++++.+.+.
T Consensus       344 ~l~~~i~~~  352 (439)
T 1mky_A          344 RMIDAMNLA  352 (439)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999988654

>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=98.27  E-value=9.9e-07  Score=78.06  Aligned_cols=100  Identities=21%  Similarity=0.149  Sum_probs=64.7

Q ss_pred             CCEEEEeCCcch-hhhcc--cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHHH
Q 030407           74 ADLLLCESGGDN-LAANF--SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERDA  146 (178)
Q Consensus        74 ~d~iiiEttG~~-~~~~~--~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l  146 (178)
                      +.+-||+|.|-. .....  ....+|++++|+|++++...+..    .......+-++++||+|+.+.  . .+...+.+
T Consensus        73 ~~inliDTPGh~dF~~ev~r~l~~aD~aILVVDa~~gv~~qt~~~~~~a~~~~ipiIvviNKiDl~~a--~-~~~v~~el  149 (600)
T 2ywe_A           73 YKLHLIDTPGHVDFSYEVSRALAACEGALLLIDASQGIEAQTVANFWKAVEQDLVIIPVINKIDLPSA--D-VDRVKKQI  149 (600)
T ss_dssp             EEEEEECCCCSGGGHHHHHHHHHTCSEEEEEEETTTBCCHHHHHHHHHHHHTTCEEEEEEECTTSTTC--C-HHHHHHHH
T ss_pred             EEEEEEECCCcHhHHHHHHHHHHhCCEEEEEEECCCCccHHHHHHHHHHHHCCCCEEEEEeccCcccc--C-HHHHHHHH
Confidence            567799999931 00000  11246999999999887543211    001134467999999999865  2 33344445


Q ss_pred             HhcCC--CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          147 LRMRD--GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       147 ~~~np--~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ++...  ..+++++||++|.|++++++.+.+.
T Consensus       150 ~~~lg~~~~~vi~vSAktg~GI~~Lle~I~~~  181 (600)
T 2ywe_A          150 EEVLGLDPEEAILASAKEGIGIEEILEAIVNR  181 (600)
T ss_dssp             HHTSCCCGGGCEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHhhCCCcccEEEEEeecCCCchHHHHHHHHh
Confidence            44322  2369999999999999999987653

>3tr5_A RF-3, peptide chain release factor 3; protein synthesis, translation; HET: GDP; 2.11A {Coxiella burnetii}

Probab=98.26  E-value=1.3e-06  Score=76.17  Aligned_cols=62  Identities=16%  Similarity=0.096  Sum_probs=39.4

Q ss_pred             CCCEEEEeCCcch-hh-hc-ccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-LA-AN-FSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~-~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      +..+.||.|.|.. .. .. .....+|++++|+|++.+......    .......+-++|+||+|+...
T Consensus        81 ~~~i~liDTPG~~df~~~~~~~l~~aD~allVvDa~~g~~~~t~~~~~~~~~~~iPiivviNK~Dl~~~  149 (528)
T 3tr5_A           81 DYLINLLDTPGHADFTEDTYRTLTAVDSALMVIDAAKGVEPRTIKLMEVCRLRHTPIMTFINKMDRDTR  149 (528)
T ss_dssp             TEEEEEECCCCSTTCCHHHHHGGGGCSEEEEEEETTTCSCHHHHHHHHHHHTTTCCEEEEEECTTSCCS
T ss_pred             CEEEEEEECCCchhHHHHHHHHHHhCCEEEEEEeCCCCCCHHHHHHHHHHHHcCCCEEEEEeCCCCccc
Confidence            5678999999931 00 11 111247999999999886543211    011134567999999999765

>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=98.25  E-value=1e-07  Score=75.72  Aligned_cols=99  Identities=17%  Similarity=0.107  Sum_probs=63.7

Q ss_pred             CCCEEEEeCCcch-h---------hhcccc-cccceEEEEEeCCCCCCCCcCC--CCCCCceeEEEEecCCCCCchh--H
Q 030407           73 KADLLLCESGGDN-L---------AANFSR-ELADYIIYIIDVSGGDKIPRKG--GPGITQADLLVINKTDLASAIG--A  137 (178)
Q Consensus        73 ~~d~iiiEttG~~-~---------~~~~~~-~~ad~~I~VvD~~~~~~~~~~~--~~qi~~adiiviNK~Dl~~~~~--~  137 (178)
                      +..+.|++|.|.. .         ...+.. ..+|.+++|+|+++........  ......+-++|+||+|+.+...  .
T Consensus        51 ~~~~~l~DtpG~~~~~~~~~~e~v~~~~~~~~~~d~ii~V~D~t~~~~~~~~~~~l~~~~~pvilv~NK~Dl~~~~~i~~  130 (258)
T 3a1s_A           51 GYTINLIDLPGTYSLGYSSIDEKIARDYLLKGDADLVILVADSVNPEQSLYLLLEILEMEKKVILAMTAIDEAKKTGMKI  130 (258)
T ss_dssp             TEEEEEEECCCCSSCCSSSHHHHHHHHHHHHSCCSEEEEEEETTSCHHHHHHHHHHHTTTCCEEEEEECHHHHHHTTCCB
T ss_pred             CeEEEEEECCCcCccCCCCHHHHHHHHHHhhcCCCEEEEEeCCCchhhHHHHHHHHHhcCCCEEEEEECcCCCCccchHH
Confidence            5789999999941 1         112221 2469999999998753221100  0113457799999999864310  1


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.+.+.   +.+  +.+++++||++|+|++++++.+.+.
T Consensus       131 ~~~~l~---~~l--g~~vi~~SA~~g~gi~el~~~i~~~  164 (258)
T 3a1s_A          131 DRYELQ---KHL--GIPVVFTSSVTGEGLEELKEKIVEY  164 (258)
T ss_dssp             CHHHHH---HHH--CSCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHH---HHc--CCCEEEEEeeCCcCHHHHHHHHHHH
Confidence            122332   333  3689999999999999999988664

>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=98.25  E-value=6.4e-07  Score=77.16  Aligned_cols=96  Identities=14%  Similarity=0.084  Sum_probs=56.5

Q ss_pred             CCCEEEEeCCcch-hhh--cccccccceEEEEEeCCCCCCCCcC-CCC----------CCCc-eeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDN-LAA--NFSRELADYIIYIIDVSGGDKIPRK-GGP----------GITQ-ADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~--~~~~~~ad~~I~VvD~~~~~~~~~~-~~~----------qi~~-adiiviNK~Dl~~~~~~  137 (178)
                      +..+.|++|.|.. ...  ......+|.+++|+|++.+...... ...          .+.. .-++|+||+|+.+....
T Consensus       110 ~~~~~iiDTPG~~~f~~~~~~~~~~aD~~llVvDa~~g~~~~~~~~~~qt~e~~~~~~~~~~~~iIvviNK~Dl~~~~~~  189 (483)
T 3p26_A          110 RANFTIVDAPGHRDFVPNAIMGISQADMAILCVDCSTNAFESGFDLDGQTKEHMLLASSLGIHNLIIAMNKMDNVDWSQQ  189 (483)
T ss_dssp             SCEEEEECCCCCGGGHHHHHHHHTTCSEEEEEEECCC------CCCCHHHHHHHHHHHHTTCCCEEEEEECGGGGTTCHH
T ss_pred             CceEEEEECCCcHHHHHHHHHhhhhCCEEEEEEECCCCccccccchhhhHHHHHHHHHHcCCCcEEEEEECcCcccchHH
Confidence            5689999999931 010  0111347999999999886321100 000          1222 36889999999873213


Q ss_pred             hHHHHHHHHHh----cC---CCCCEEEEecccCCCHHH
Q 030407          138 DLAVMERDALR----MR---DGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       138 ~~~~~~~~l~~----~n---p~a~i~~~SA~~g~gi~e  168 (178)
                      ..+.+.+.+++    ..   +..+++++||++|+|+++
T Consensus       190 ~~~~i~~~~~~~l~~~g~~~~~~~~i~iSA~~g~gi~e  227 (483)
T 3p26_A          190 RFEEIKSKLLPYLVDIGFFEDNINWVPISGFSGEGVYK  227 (483)
T ss_dssp             HHHHHHHHHHHHHHHHTCCGGGEEEEECCSSSCTTSSS
T ss_pred             HHHHHHHHHHHHHHHcCCCcccceEEEEeeecCCCccc
Confidence            33434433332    22   146899999999999975

>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=98.25  E-value=3.5e-08  Score=78.64  Aligned_cols=99  Identities=23%  Similarity=0.225  Sum_probs=62.6

Q ss_pred             CCCEEEEeCCcch----------hhhccc-ccccceEEEEEeCCCCCCCCcCCC--CCCC-ceeEEEEecCCCCCchh--
Q 030407           73 KADLLLCESGGDN----------LAANFS-RELADYIIYIIDVSGGDKIPRKGG--PGIT-QADLLVINKTDLASAIG--  136 (178)
Q Consensus        73 ~~d~iiiEttG~~----------~~~~~~-~~~ad~~I~VvD~~~~~~~~~~~~--~qi~-~adiiviNK~Dl~~~~~--  136 (178)
                      +..+.+++|.|..          +...+. ...+|.+++|+|++++........  .... .+.++|+||+|+.+...  
T Consensus        49 ~~~~~l~DtpG~~~~~~~~~~~~~~~~~~~~~~~d~vi~v~D~~~~~~~~~~~~~~~~~~~~p~ilv~NK~Dl~~~~~~~  128 (271)
T 3k53_A           49 EKEFLVVDLPGIYSLTAHSIDELIARNFILDGNADVIVDIVDSTCLMRNLFLTLELFEMEVKNIILVLNKFDLLKKKGAK  128 (271)
T ss_dssp             TEEEEEEECCCCSCCCSSCHHHHHHHHHHHTTCCSEEEEEEEGGGHHHHHHHHHHHHHTTCCSEEEEEECHHHHHHHTCC
T ss_pred             CceEEEEeCCCccccccCCHHHHHHHHhhhccCCcEEEEEecCCcchhhHHHHHHHHhcCCCCEEEEEEChhcCcccccH
Confidence            4568999999941          111111 124799999999987532111000  0122 56799999999864310  


Q ss_pred             HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 ~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...+.+.+   .+  +.+++++||++|+|++++++.+...
T Consensus       129 ~~~~~l~~---~l--g~~~~~~Sa~~g~gi~~l~~~i~~~  163 (271)
T 3k53_A          129 IDIKKMRK---EL--GVPVIPTNAKKGEGVEELKRMIALM  163 (271)
T ss_dssp             CCHHHHHH---HH--SSCEEECBGGGTBTHHHHHHHHHHH
T ss_pred             HHHHHHHH---Hc--CCcEEEEEeCCCCCHHHHHHHHHHH
Confidence            12233333   22  3689999999999999999988764

>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=98.24  E-value=2.3e-08  Score=80.04  Aligned_cols=100  Identities=16%  Similarity=0.138  Sum_probs=63.1

Q ss_pred             CCCEEEEeCCcchh-h-------------hccc-ccccceEEEEEeCCCCCCCCc--CCCCCCCceeEEEEecCCCCCch
Q 030407           73 KADLLLCESGGDNL-A-------------ANFS-RELADYIIYIIDVSGGDKIPR--KGGPGITQADLLVINKTDLASAI  135 (178)
Q Consensus        73 ~~d~iiiEttG~~~-~-------------~~~~-~~~ad~~I~VvD~~~~~~~~~--~~~~qi~~adiiviNK~Dl~~~~  135 (178)
                      +..+.++.|.|..- .             ..+. ...+|.+++|+|+++......  ........+.++|+||+|+.+..
T Consensus        49 ~~~~~liDtpG~~~~~~~~~~~~~~e~i~~~~~~~~~~d~ii~VvD~~~~~~~~~~~~~l~~~~~p~ivv~NK~Dl~~~~  128 (274)
T 3i8s_A           49 DHQVTLVDLPGTYSLTTISSQTSLDEQIACHYILSGDADLLINVVDASNLERNLYLTLQLLELGIPCIVALNMLDIAEKQ  128 (274)
T ss_dssp             SCEEEEEECCCCSCSCC----CCHHHHHHHHHHHHTCCSEEEEEEEGGGHHHHHHHHHHHHHHTCCEEEEEECHHHHHHT
T ss_pred             CCceEEEECcCCCccccccccCCHHHHHHHHHHhhcCCCEEEEEecCCChHHHHHHHHHHHhcCCCEEEEEECccchhhh
Confidence            56788999999411 0             0111 124699999999986322110  00011345789999999986541


Q ss_pred             h--HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          136 G--ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       136 ~--~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .  ...+.+.+   .+  +.+++++||++|+|++++++.+.+.+
T Consensus       129 ~~~~~~~~l~~---~l--g~~~i~~SA~~g~gi~el~~~i~~~~  167 (274)
T 3i8s_A          129 NIRIEIDALSA---RL--GCPVIPLVSTRGRGIEALKLAIDRYK  167 (274)
T ss_dssp             TEEECHHHHHH---HH--TSCEEECCCGGGHHHHHHHHHHHTCC
T ss_pred             hHHHHHHHHHH---hc--CCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            0  12233332   22  35899999999999999999987643

>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=98.24  E-value=3.9e-07  Score=69.43  Aligned_cols=103  Identities=15%  Similarity=0.106  Sum_probs=64.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCch-----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAI-----  135 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~-----  135 (178)
                      .+.+.|++|.|..    +...+. ..+|.+++|+|+++......   .+...     -..+-++|+||+|+.+..     
T Consensus        75 ~~~l~i~Dt~G~~~~~~~~~~~~-~~~d~~ilv~D~~~~~s~~~~~~~~~~~i~~~~~~~piilv~nK~Dl~~~~~~~~~  153 (205)
T 1gwn_A           75 RIELSLWDTSGSPYYDNVRPLSY-PDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDLRTDVSTLVE  153 (205)
T ss_dssp             EEEEEEEEECCSGGGTTTGGGGC-TTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHCTTCEEEEEEECGGGGGCHHHHHH
T ss_pred             EEEEEEEeCCCcHhhhHHHHhhc-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEechhhccchhhhhh
Confidence            4678899999932    111222 35799999999986432111   11000     134679999999997430     


Q ss_pred             -------hHhHHHHHHHHHhcCCCCCEEEEecc-cCCCHHHHHHHHhhhh
Q 030407          136 -------GADLAVMERDALRMRDGGPFIFAQVG-WVIGIIFTLSITHYIV  177 (178)
Q Consensus       136 -------~~~~~~~~~~l~~~np~a~i~~~SA~-~g~gi~el~~~l~~~~  177 (178)
                             ....+...+..+..+ ..+++++||+ +|+|++++|+.+.+.+
T Consensus       154 ~~~~~~~~v~~~~~~~~~~~~~-~~~~~e~SAk~~~~gv~~lf~~l~~~~  202 (205)
T 1gwn_A          154 LSNHRQTPVSYDQGANMAKQIG-AATYIECSALQSENSVRDIFHVATLAC  202 (205)
T ss_dssp             HHTTTCCCCCHHHHHHHHHHHT-CSEEEECCTTTCHHHHHHHHHHHHHHH
T ss_pred             hcccccCCCCHHHHHHHHHHcC-CCEEEEeeeccCCcCHHHHHHHHHHHH
Confidence                   011233444444443 3589999999 6899999999887643

>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=98.23  E-value=1.2e-06  Score=77.57  Aligned_cols=103  Identities=17%  Similarity=0.069  Sum_probs=62.2

Q ss_pred             CCEEEEeCCcch-hhhcc--cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchh----------
Q 030407           74 ADLLLCESGGDN-LAANF--SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIG----------  136 (178)
Q Consensus        74 ~d~iiiEttG~~-~~~~~--~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~----------  136 (178)
                      +.+.|+.|.|-. .....  ....+|.+|+|+|++++...+..    +......+-++++||+|+.+...          
T Consensus        70 ~~i~liDTPGhe~F~~~~~r~~~~aD~aILVvDa~~Gv~~qT~e~l~~l~~~~vPiIVViNKiDl~~~~~~~~~~~~~e~  149 (594)
T 1g7s_A           70 PGLFFIDTPGHEAFTTLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYRTPFVVAANKIDRIHGWRVHEGRPFMET  149 (594)
T ss_dssp             CEEEEECCCTTSCCTTSBCSSSBSCSEEEEEEETTTCCCHHHHHHHHHHHHTTCCEEEEEECGGGSTTCCCCTTCCHHHH
T ss_pred             CCEEEEECCCcHHHHHHHHHHHhhCCEEEEEEECCCCccHhHHHHHHHHHHcCCeEEEEecccccccccccccCCchHHH
Confidence            468999999921 11111  11246999999999986432210    01112346799999999974200          


Q ss_pred             -----Hh--------HHHHHHHHHhc-------------CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 -----AD--------LAVMERDALRM-------------RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 -----~~--------~~~~~~~l~~~-------------np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                           ..        +..+...+.+.             ....+++++||++|+|+++|++++...
T Consensus       150 sa~~~~~v~~~~~e~i~ei~~~L~e~gl~~e~~~~l~~~~~~vpvv~vSA~tG~GI~eLl~~I~~~  215 (594)
T 1g7s_A          150 FSKQDIQVQQKLDTKVYELVGKLHEEGFESERFDRVTDFASQVSIIPISAITGEGIPELLTMLMGL  215 (594)
T ss_dssp             HTTSCHHHHHHHHHHHHHHHHHHHHTTCEEEEGGGCSCTTTEEEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHcCcchHHHHHHHhccCcceEEEEeccCCCCchhHHHHHHhh
Confidence                 00        11122222221             123489999999999999999988653

>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=98.23  E-value=1.2e-06  Score=70.65  Aligned_cols=79  Identities=15%  Similarity=0.023  Sum_probs=56.1

Q ss_pred             ccceEEEEEeCCCCCCCCc-CCCCC-CCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHH
Q 030407           94 LADYIIYIIDVSGGDKIPR-KGGPG-ITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLS  171 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~-~~~~q-i~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~  171 (178)
                      .+|.++.|+|+..+..... ..... -..+-++|+||+||++.  +..+...++.++.  +.+++.+||++|.|++++++
T Consensus        23 ~aDvVl~VvDAr~p~~~~~~~l~~~l~~kp~ilVlNK~DL~~~--~~~~~~~~~~~~~--g~~~i~iSA~~~~gi~~L~~   98 (282)
T 1puj_A           23 LIDIVYELVDARIPMSSRNPMIEDILKNKPRIMLLNKADKADA--AVTQQWKEHFENQ--GIRSLSINSVNGQGLNQIVP   98 (282)
T ss_dssp             GCSEEEEEEETTSTTTTSCHHHHHHCSSSCEEEEEECGGGSCH--HHHHHHHHHHHTT--TCCEEECCTTTCTTGGGHHH
T ss_pred             hCCEEEEEEeCCCCCccCCHHHHHHHCCCCEEEEEECcccCCH--HHHHHHHHHHHhc--CCcEEEEECCCcccHHHHHH
Confidence            4699999999987654321 00011 13467999999999986  5555555555432  34899999999999999998


Q ss_pred             HHhhh
Q 030407          172 ITHYI  176 (178)
Q Consensus       172 ~l~~~  176 (178)
                      .+.+.
T Consensus        99 ~i~~~  103 (282)
T 1puj_A           99 ASKEI  103 (282)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77654

>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=98.22  E-value=7.7e-07  Score=74.88  Aligned_cols=103  Identities=13%  Similarity=0.053  Sum_probs=65.2

Q ss_pred             CCCEEEEeCCcch-hhh-cc-cccccceEEEEEeCCCCCCCCcC----CCCCCCce-eEEEEecCCCCCchhHhHH----
Q 030407           73 KADLLLCESGGDN-LAA-NF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQA-DLLVINKTDLASAIGADLA----  140 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~-~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~a-diiviNK~Dl~~~~~~~~~----  140 (178)
                      +..+.|++|.|.. ... +. ....+|.+++|+|++++...+..    .......+ -++++||+|+.+.. +..+    
T Consensus        74 ~~~~~iiDtpG~~~f~~~~~~~~~~aD~~ilVvda~~g~~~qt~~~l~~~~~~~ip~iivviNK~Dl~~~~-~~~~~~~~  152 (405)
T 2c78_A           74 KRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDP-ELLDLVEM  152 (405)
T ss_dssp             SCEEEEEECCCSGGGHHHHHHHHTTCSSEEEEEETTTCCCHHHHHHHHHHHHTTCCCEEEEEECGGGCCCH-HHHHHHHH
T ss_pred             CeEEEEEECCChHHHHHHHHHHHHHCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCEEEEEEECccccCcH-HHHHHHHH
Confidence            5789999999931 111 10 11246999999999886532211    01113345 36899999998531 2222    


Q ss_pred             HHHHHHHhcCC---CCCEEEEecccCCC------------------HHHHHHHHhhh
Q 030407          141 VMERDALRMRD---GGPFIFAQVGWVIG------------------IIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np---~a~i~~~SA~~g~g------------------i~el~~~l~~~  176 (178)
                      ++.+.++..+.   ..+++++||++|.|                  +++|++.|...
T Consensus       153 ~~~~~l~~~~~~~~~~~~i~~SA~~g~~v~~~~~~~~~~~~~~~~~i~~Ll~~l~~~  209 (405)
T 2c78_A          153 EVRDLLNQYEFPGDEVPVIRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAIDEY  209 (405)
T ss_dssp             HHHHHHHHTTSCTTTSCEEECCHHHHHHHHHHCTTCCTTSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcccccCCCEEEccHHHhhhhhccccccccCCCcccccHHHHHHHHHhh
Confidence            34455554432   47999999999987                  88888887653

>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=98.22  E-value=7.3e-07  Score=71.88  Aligned_cols=102  Identities=13%  Similarity=-0.002  Sum_probs=63.2

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchh----
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIG----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~----  136 (178)
                      .+.+.+++|.|..-    ...+ ...+|.+++|+|+++......   .+...     -..+-++|+||+|+.+...    
T Consensus       202 ~~~~~l~Dt~G~~~~~~~~~~~-~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~~  280 (332)
T 2wkq_A          202 PVNLGLWDTAGLEDYDRLRPLS-YPQTDVFLICFSLVSPASFHHVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEK  280 (332)
T ss_dssp             EEEEEEEEECCCGGGTTTGGGG-CTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHCTTSCEEEEEECHHHHTCHHHHHH
T ss_pred             EEEEEEEeCCCchhhhHHHHHh-ccCCCEEEEEEeCCCHHHHHHHHHHHHHHHHhhCCCCcEEEEEEchhcccccchhhh
Confidence            34566999999421    1112 224799999999987532211   00000     1456799999999965410    


Q ss_pred             --------HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 --------ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 --------~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                              ...+...++.+.. ...+++++||++|+|++++++.+.+.
T Consensus       281 ~~~~~~~~v~~~~~~~~~~~~-~~~~~~~~Sa~~~~gi~~l~~~l~~~  327 (332)
T 2wkq_A          281 LKEKKLTPITYPQGLAMAKEI-GAVKYLECSALTQRGLKTVFDEAIRA  327 (332)
T ss_dssp             HHHTTCCCCCHHHHHHHHHHT-TCSEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             ccccccccccHHHHHHHHHHc-CCcEEEEecCCCCcCHHHHHHHHHHH
Confidence                    1122333344433 22489999999999999999988654

>2elf_A Protein translation elongation factor 1A; tRNA, pyrrolysine, structural genomics, NPPSFA; HET: CIT; 1.70A {Methanosarcina mazei}

Probab=98.21  E-value=1.5e-06  Score=72.67  Aligned_cols=100  Identities=5%  Similarity=-0.009  Sum_probs=62.8

Q ss_pred             CCCEEEEeCCcch-h-hhcc-cccccceEEEEEeCCCCCCCCc-C---CCCCCCcee-EEEEe-cCCCCCchhHhHHH--
Q 030407           73 KADLLLCESGGDN-L-AANF-SRELADYIIYIIDVSGGDKIPR-K---GGPGITQAD-LLVIN-KTDLASAIGADLAV--  141 (178)
Q Consensus        73 ~~d~iiiEttG~~-~-~~~~-~~~~ad~~I~VvD~~~~~~~~~-~---~~~qi~~ad-iiviN-K~Dl~~~~~~~~~~--  141 (178)
                      +..+.|+.|.|-. . .... ....+|.+++|+| ..+...+. .   .......+. ++++| |+|+ ++  ...+.  
T Consensus        59 ~~~i~iiDtPGh~~f~~~~~~~~~~aD~ailVvd-~~g~~~qt~e~~~~~~~~~i~~~ivvvNNK~Dl-~~--~~~~~~~  134 (370)
T 2elf_A           59 GRNMVFVDAHSYPKTLKSLITALNISDIAVLCIP-PQGLDAHTGECIIALDLLGFKHGIIALTRSDST-HM--HAIDELK  134 (370)
T ss_dssp             SSEEEEEECTTTTTCHHHHHHHHHTCSEEEEEEC-TTCCCHHHHHHHHHHHHTTCCEEEEEECCGGGS-CH--HHHHHHH
T ss_pred             CeEEEEEECCChHHHHHHHHHHHHHCCEEEEEEc-CCCCcHHHHHHHHHHHHcCCCeEEEEEEeccCC-CH--HHHHHHH
Confidence            4569999999931 0 0000 1124799999999 65532211 0   011233455 89999 9999 65  44333  


Q ss_pred             --HHHHHHhcC-CCCCEEE--Eeccc---CCCHHHHHHHHhhh
Q 030407          142 --MERDALRMR-DGGPFIF--AQVGW---VIGIIFTLSITHYI  176 (178)
Q Consensus       142 --~~~~l~~~n-p~a~i~~--~SA~~---g~gi~el~~~l~~~  176 (178)
                        +.+.++... ...++++  +||++   |+|+++|++.|.+.
T Consensus       135 ~~i~~~l~~~~~~~~~ii~~~~SA~~~~~g~gi~~L~~~l~~~  177 (370)
T 2elf_A          135 AKLKVITSGTVLQDWECISLNTNKSAKNPFEGVDELKARINEV  177 (370)
T ss_dssp             HHHHHHTTTSTTTTCEEEECCCCTTSSSTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCceEEEecccccccCcCCCCHHHHHHHHHhh
Confidence              333333322 2469999  99999   99999999987654

>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=98.20  E-value=5.2e-07  Score=76.68  Aligned_cols=96  Identities=16%  Similarity=0.101  Sum_probs=59.1

Q ss_pred             CCCEEEEeCCcchh-hhc--ccccccceEEEEEeCCCCCCCCcC----CCCCCCc-eeEEEEecCCCCCchhHhH----H
Q 030407           73 KADLLLCESGGDNL-AAN--FSRELADYIIYIIDVSGGDKIPRK----GGPGITQ-ADLLVINKTDLASAIGADL----A  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~-~~~--~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~-adiiviNK~Dl~~~~~~~~----~  140 (178)
                      +..+.|++|.|..- ...  .....+|.+++|+|++++...+..    ....+.. .-++|+||+|+.+...+..    +
T Consensus       103 ~~~~~iiDtpGh~~f~~~~~~~~~~aD~~ilVvDa~~g~~~qt~~~l~~~~~~~~~~iIvviNK~Dl~~~~~~~~~~i~~  182 (434)
T 1zun_B          103 KRKFIIADTPGHEQYTRNMATGASTCDLAIILVDARYGVQTQTRRHSYIASLLGIKHIVVAINKMDLNGFDERVFESIKA  182 (434)
T ss_dssp             SEEEEEEECCCSGGGHHHHHHHHTTCSEEEEEEETTTCSCHHHHHHHHHHHHTTCCEEEEEEECTTTTTSCHHHHHHHHH
T ss_pred             CceEEEEECCChHHHHHHHHHHHhhCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCeEEEEEEcCcCCcccHHHHHHHHH
Confidence            35689999999310 100  011347999999999886432210    0111223 3588899999986311222    3


Q ss_pred             HHHHHHHhcC---CCCCEEEEecccCCCHHH
Q 030407          141 VMERDALRMR---DGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       141 ~~~~~l~~~n---p~a~i~~~SA~~g~gi~e  168 (178)
                      ++.+.++..+   +..+++++||++|+|+++
T Consensus       183 ~~~~~~~~~g~~~~~~~~i~vSA~~g~gi~~  213 (434)
T 1zun_B          183 DYLKFAEGIAFKPTTMAFVPMSALKGDNVVN  213 (434)
T ss_dssp             HHHHHHHTTTCCCSEEEEEECCTTTCTTTSS
T ss_pred             HHHHHHHHhCCCccCceEEEEeccCCCCccc
Confidence            3444445444   236899999999999987

>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=98.19  E-value=1.9e-06  Score=72.39  Aligned_cols=103  Identities=11%  Similarity=0.067  Sum_probs=65.4

Q ss_pred             CCCCEEEEeCCcch-hhh-c-ccccccceEEEEEeCCCCCCCCcC-C---CCCCCcee-EEEEecCCCCCchhHhH----
Q 030407           72 FKADLLLCESGGDN-LAA-N-FSRELADYIIYIIDVSGGDKIPRK-G---GPGITQAD-LLVINKTDLASAIGADL----  139 (178)
Q Consensus        72 ~~~d~iiiEttG~~-~~~-~-~~~~~ad~~I~VvD~~~~~~~~~~-~---~~qi~~ad-iiviNK~Dl~~~~~~~~----  139 (178)
                      .+..+.|++|.|.. ... + .....+|.+++|+|++++...+.. +   ......+. ++++||+|+.+.. +..    
T Consensus        64 ~~~~~~iiDtpG~~~f~~~~~~~~~~aD~~ilVvda~~g~~~qt~e~l~~~~~~~vp~iivviNK~Dl~~~~-~~~~~~~  142 (397)
T 1d2e_A           64 AARHYAHTDCPGHADYVKNMITGTAPLDGCILVVAANDGPMPQTREHLLLARQIGVEHVVVYVNKADAVQDS-EMVELVE  142 (397)
T ss_dssp             SSCEEEEEECSSHHHHHHHHHHTSSCCSEEEEEEETTTCSCHHHHHHHHHHHHTTCCCEEEEEECGGGCSCH-HHHHHHH
T ss_pred             CCeEEEEEECCChHHHHHHHHhhHhhCCEEEEEEECCCCCCHHHHHHHHHHHHcCCCeEEEEEECcccCCCH-HHHHHHH
Confidence            35789999999931 011 1 112247999999999886532210 0   01123443 6899999998531 222    


Q ss_pred             HHHHHHHHhcCC---CCCEEEEecccCCC----------HHHHHHHHhh
Q 030407          140 AVMERDALRMRD---GGPFIFAQVGWVIG----------IIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~np---~a~i~~~SA~~g~g----------i~el~~~l~~  175 (178)
                      +++.+.+++..-   ..+++++||++|.|          +++|++.|.+
T Consensus       143 ~~~~~~l~~~~~~~~~~~~i~~SA~~g~n~~~~~~~~g~i~~Ll~~l~~  191 (397)
T 1d2e_A          143 LEIRELLTEFGYKGEETPIIVGSALCALEQRDPELGLKSVQKLLDAVDT  191 (397)
T ss_dssp             HHHHHHHHHTTSCTTTSCEEECCHHHHHTTCCTTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcccCcEEEeehhhcccccCCCccCCcHHHHHHHHHH
Confidence            344455554431   46999999999774          9999998865

>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=98.18  E-value=1.5e-06  Score=71.87  Aligned_cols=100  Identities=22%  Similarity=0.198  Sum_probs=64.6

Q ss_pred             CCEEEEeCCcch--------hhhcccc--cccceEEEEEeCCCC---CCCC---------cCCCC-CCCceeEEEEecCC
Q 030407           74 ADLLLCESGGDN--------LAANFSR--ELADYIIYIIDVSGG---DKIP---------RKGGP-GITQADLLVINKTD  130 (178)
Q Consensus        74 ~d~iiiEttG~~--------~~~~~~~--~~ad~~I~VvD~~~~---~~~~---------~~~~~-qi~~adiiviNK~D  130 (178)
                      ..+.|++|.|..        +...|..  ..++.+++|+|++..   ....         ..+.+ ....+-++|+||+|
T Consensus       206 ~~~~l~DtPG~i~~a~~~~~l~~~fl~~i~~~d~ll~VvD~s~~~~~~~~~~~~~~~~eL~~~~~~l~~~p~ilV~NK~D  285 (342)
T 1lnz_A          206 RSFVMADLPGLIEGAHQGVGLGHQFLRHIERTRVIVHVIDMSGLEGRDPYDDYLTINQELSEYNLRLTERPQIIVANKMD  285 (342)
T ss_dssp             CEEEEEEHHHHHHHTTCTTTTHHHHHHHHHHCCEEEEEEESSCSSCCCHHHHHHHHHHHHHHSCSSTTTSCBCBEEECTT
T ss_pred             ceEEEecCCCCcccccccchhHHHHHHHHHhccEEEEEEECCcccccChHHHHHHHHHHHHHhhhhhcCCCEEEEEECcc
Confidence            568999999931        1112221  126899999999763   1110         01211 23456799999999


Q ss_pred             CCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          131 LASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       131 l~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +.+.  .  +.+.+..+.+....+++++||++|+|+++|+++|.+.+
T Consensus       286 l~~~--~--e~~~~l~~~l~~~~~v~~iSA~tg~gi~eL~~~l~~~l  328 (342)
T 1lnz_A          286 MPEA--A--ENLEAFKEKLTDDYPVFPISAVTREGLRELLFEVANQL  328 (342)
T ss_dssp             STTH--H--HHHHHHHHHCCSCCCBCCCSSCCSSTTHHHHHHHHHHH
T ss_pred             CCCC--H--HHHHHHHHHhhcCCCEEEEECCCCcCHHHHHHHHHHHH
Confidence            9865  3  22333334444336899999999999999999987654

>3dpu_A RAB family protein; roccor, G-domain, COR, GTP-binding, nucleotide-binding, SIGN protein; 2.90A {Chlorobaculum tepidum}

Probab=98.15  E-value=3e-07  Score=80.07  Aligned_cols=101  Identities=11%  Similarity=0.043  Sum_probs=62.2

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCcCCCCC-----CCceeEEEEecCCCCCchhHhHHHHH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPRKGGPG-----ITQADLLVINKTDLASAIGADLAVME  143 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~q-----i~~adiiviNK~Dl~~~~~~~~~~~~  143 (178)
                      +..+.++++.|..-    ...+. ..+|.+++|+|++....... +..+     -..+-++|+||+|+.+......+.+.
T Consensus        97 ~~~~~i~Dt~G~e~~~~~~~~~l-~~~d~ii~V~D~s~~~~~~~-~~~~l~~~~~~~pvilV~NK~Dl~~~~~v~~~~~~  174 (535)
T 3dpu_A           97 ECLFHFWDFGGQEIMHASHQFFM-TRSSVYMLLLDSRTDSNKHY-WLRHIEKYGGKSPVIVVMNKIDENPSYNIEQKKIN  174 (535)
T ss_dssp             TCEEEEECCCSCCTTTTTCHHHH-HSSEEEEEEECGGGGGGHHH-HHHHHHHHSSSCCEEEEECCTTTCTTCCCCHHHHH
T ss_pred             eEEEEEEECCcHHHHHHHHHHHc-cCCcEEEEEEeCCCchhHHH-HHHHHHHhCCCCCEEEEEECCCcccccccCHHHHH
Confidence            57899999999311    11122 24699999999976532211 0000     12467999999999865212344555


Q ss_pred             HHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          144 RDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       144 ~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +.....  ..+++++||++|+|++++++.+.+.+
T Consensus       175 ~~~~~~--~~~~~~vSA~~g~gi~eL~~~l~~~~  206 (535)
T 3dpu_A          175 ERFPAI--ENRFHRISCKNGDGVESIAKSLKSAV  206 (535)
T ss_dssp             HHCGGG--TTCEEECCC-----CTTHHHHHHHHH
T ss_pred             HHHHhc--CCceEEEecCcccCHHHHHHHHHHHH
Confidence            555544  35899999999999999999887643

>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=98.14  E-value=1.5e-06  Score=65.21  Aligned_cols=102  Identities=13%  Similarity=-0.061  Sum_probs=62.2

Q ss_pred             CCCCEEEEeCCcchh-hh-----cccccccceEEEEEeCCCCCCCC-cCCC--------CCCCceeEEEEecCCCCCchh
Q 030407           72 FKADLLLCESGGDNL-AA-----NFSRELADYIIYIIDVSGGDKIP-RKGG--------PGITQADLLVINKTDLASAIG  136 (178)
Q Consensus        72 ~~~d~iiiEttG~~~-~~-----~~~~~~ad~~I~VvD~~~~~~~~-~~~~--------~qi~~adiiviNK~Dl~~~~~  136 (178)
                      ....+.+++|.|..- ..     ......+|++++|+|+++..... ..+.        ..-..+-++|+||+|+.++  
T Consensus        67 ~~~~l~i~Dt~G~~~~~~~~~~~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~l~~~~~~~~~~piilv~nK~Dl~~~--  144 (196)
T 3llu_A           67 SFVNFQIWDFPGQMDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEVFIHKVDGLSD--  144 (196)
T ss_dssp             TSCCEEEEECCSSCCTTCTTCCHHHHHHTCSEEEEEEETTSCCHHHHHHHHHHHHHHHHHCTTCEEEEEEECGGGSCH--
T ss_pred             CeeEEEEEECCCCHHHHhhhhhcccccccCCEEEEEEECCCchHHHHHHHHHHHHHHHhcCCCCcEEEEEeccccCch--
Confidence            357899999999311 11     11122479999999998751000 0000        0113467999999999874  


Q ss_pred             HhH----HH-----HHHHHHhc--CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 ADL----AV-----MERDALRM--RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 ~~~----~~-----~~~~l~~~--np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ...    ..     ..+..+..  ....+++++||++ +|++++|+.+.+.
T Consensus       145 ~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~e~Sa~~-~~v~~~f~~l~~~  194 (196)
T 3llu_A          145 DHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYD-HSIFEAFSKVVQK  194 (196)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCTTSCEEEEEECTTS-THHHHHHHHHHHH
T ss_pred             hhhhHHHhHHHHHHHHHHHHhhhhcCCcceEEEEech-hhHHHHHHHHHHH
Confidence            211    11     11222211  2346899999999 9999999987653

>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=98.14  E-value=3.6e-07  Score=73.25  Aligned_cols=98  Identities=13%  Similarity=0.131  Sum_probs=62.9

Q ss_pred             CCCEEEEeCCcch----------hhhcccc-cccceEEEEEeCCCCCCCCcCCCCC---CCceeEEEEecCCCCCch--h
Q 030407           73 KADLLLCESGGDN----------LAANFSR-ELADYIIYIIDVSGGDKIPRKGGPG---ITQADLLVINKTDLASAI--G  136 (178)
Q Consensus        73 ~~d~iiiEttG~~----------~~~~~~~-~~ad~~I~VvD~~~~~~~~~~~~~q---i~~adiiviNK~Dl~~~~--~  136 (178)
                      +..+.++.|.|..          +...+.. ..+|.++.|+|+++..... .+..+   ...+.++++||+|+.+..  .
T Consensus        48 ~~~l~l~DtpG~~~~~~~~~~e~v~~~~~~~~~~d~vi~V~D~t~~e~~~-~~~~~l~~~~~p~ilv~NK~Dl~~~~~~~  126 (272)
T 3b1v_A           48 NKDLEIQDLPGIYSMSPYSPEAKVARDYLLSQRADSILNVVDATNLERNL-YLTTQLIETGIPVTIALNMIDVLDGQGKK  126 (272)
T ss_dssp             CTTEEEEECCCCSCSSCSSHHHHHHHHHHHTTCCSEEEEEEEGGGHHHHH-HHHHHHHHTCSCEEEEEECHHHHHHTTCC
T ss_pred             CCeEEEEECCCcCccCCCChHHHHHHHHHhcCCCCEEEEEecCCchHhHH-HHHHHHHhcCCCEEEEEEChhhCCcCCcH
Confidence            5689999999941          1112221 2479999999997643211 01111   345679999999986431  0


Q ss_pred             HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 ~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+.+.   +.+  +.+++++||++|+|++++++.+.+.
T Consensus       127 ~~~~~l~---~~l--g~~vi~~SA~~g~gi~el~~~i~~~  161 (272)
T 3b1v_A          127 INVDKLS---YHL--GVPVVATSALKQTGVDQVVKKAAHT  161 (272)
T ss_dssp             CCHHHHH---HHH--TSCEEECBTTTTBSHHHHHHHHHHS
T ss_pred             HHHHHHH---HHc--CCCEEEEEccCCCCHHHHHHHHHHH
Confidence            1223333   223  3589999999999999999988764

>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=98.13  E-value=2.1e-06  Score=64.46  Aligned_cols=100  Identities=12%  Similarity=0.080  Sum_probs=59.6

Q ss_pred             CCEEEEeCCcchh-----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           74 ADLLLCESGGDNL-----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        74 ~d~iiiEttG~~~-----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +.++++.|.|..-     ...+ ...+|+.++|+|.++......         .....-..+-++|.||+|+.+......
T Consensus        56 ~~l~~~Dt~~~~~~~~~~~~~~-~~~~~~~i~v~dv~~~~s~~~~~~~~~~l~~~~~~~~~piilV~NK~Dl~~~r~v~~  134 (192)
T 2cjw_A           56 ATIILLDMWENKGENEWLHDHC-MQVGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRXREVSV  134 (192)
T ss_dssp             EEEEEECCCCC----CTTGGGH-HHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTTSCCCEEEEEECTTCGGGCCSCH
T ss_pred             EEEEEEEeccCcchhhhHHHhh-cccCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCeEEEEEechhhhccccccH
Confidence            4567788888321     1111 124699999999976432110         000111345699999999964311122


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.........  ..+++++||++|+||+++|+.+.+.
T Consensus       135 ~~~~~~a~~~--~~~~~e~SA~~g~~v~~lf~~l~~~  169 (192)
T 2cjw_A          135 SEGRAXAVVF--DXKFIETSAAVQHNVKELFEGIVRQ  169 (192)
T ss_dssp             HHHHHHHHHT--TCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHHh--CCceEEeccccCCCHHHHHHHHHHH
Confidence            2222222332  3589999999999999999987653

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=98.13  E-value=3.9e-07  Score=72.83  Aligned_cols=102  Identities=16%  Similarity=0.022  Sum_probs=59.2

Q ss_pred             CCCEEEEeCCcchhh-----------------hcccccccceEE-EEEeCCCCCCCCcC--CCC---CCCceeEEEEecC
Q 030407           73 KADLLLCESGGDNLA-----------------ANFSRELADYII-YIIDVSGGDKIPRK--GGP---GITQADLLVINKT  129 (178)
Q Consensus        73 ~~d~iiiEttG~~~~-----------------~~~~~~~ad~~I-~VvD~~~~~~~~~~--~~~---qi~~adiiviNK~  129 (178)
                      .+++.|++|.|..-.                 ..+. ..++.++ +|+|++........  ...   ....+-++|+||+
T Consensus       124 ~~~l~lvDtpG~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~il~v~d~~~~~~~~~~~~~~~~~~~~~~~~i~V~NK~  202 (299)
T 2aka_B          124 VLNLTLVDLPGMTKVPVGDQPPDIEFQIRDMLMQFV-TKENCLILAVSPANSDLANSDALKIAKEVDPQGQRTIGVITKL  202 (299)
T ss_dssp             CCSEEEEECCCBCSSCCSSSCTTHHHHHHHHHHHHH-TSTTEEEEEEEESSSCGGGCHHHHHHHHHCTTCSSEEEEEECG
T ss_pred             CCCceEEeCCCCCCCcCCCCCchHHHHHHHHHHHHH-cCCCeEEEEEecCCcchhhhHHHHHHHHhCCCCCeEEEEEEcc
Confidence            379999999994210                 0111 1245454 79999765432211  111   1234679999999


Q ss_pred             CCCCchhHhHHHHHHHHHhcC-CCCCEEEEecccCCCHHHHHHHHhh
Q 030407          130 DLASAIGADLAVMERDALRMR-DGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       130 Dl~~~~~~~~~~~~~~l~~~n-p~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      |+.++.....+.+...+..+. +..+++++||++|+|++++++.+.+
T Consensus       203 Dl~~~~~~~~~~~~~~~~~~~~~~~~v~~~SA~~~~gi~~l~~~l~~  249 (299)
T 2aka_B          203 DLMDEGTDARDVLENKLLPLRRGYIGVVNRSQKDIDGKKDITAALAA  249 (299)
T ss_dssp             GGSCTTCCCHHHHTTCSSCCTTCEEECCCCCCBCTTSCBCHHHHHHH
T ss_pred             ccCCCCchHHHHHhCCcCcCCCCcEEEECCChhhccccccHHHHHHH
Confidence            998651111222221111111 2357899999999999999988653

>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=98.11  E-value=1.1e-07  Score=69.66  Aligned_cols=101  Identities=17%  Similarity=0.169  Sum_probs=61.0

Q ss_pred             CCCEEEEeCCcch----------hhhcccc-cccceEEEEEeCCCCCCCCcCCC--CCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----------LAANFSR-ELADYIIYIIDVSGGDKIPRKGG--PGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----------~~~~~~~-~~ad~~I~VvD~~~~~~~~~~~~--~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+-+++|.|..          +...+.. ..++.++.|+|+++.........  .....+-++|.||+|+....... 
T Consensus        49 ~~~l~i~Dt~G~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~D~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~-  127 (165)
T 2wji_A           49 GEKFKVVDLPGVYSLTANSIDEIIARDYIINEKPDLVVNIVDATALERNLYLTLQLMEMGANLLLALNKMDLAKSLGIE-  127 (165)
T ss_dssp             TEEEEEEECCCCSCSSSSSHHHHHHHHHHHHHCCSEEEEEEETTCHHHHHHHHHHHHHTTCCEEEEEECHHHHHHTTCC-
T ss_pred             CcEEEEEECCCcccCCCcchhHHHHHHHHhcCCCCEEEEEecCCchhHhHHHHHHHHhcCCCEEEEEEchHhccccChh-
Confidence            3567889999931          1111211 24689999999976432110000  01235679999999986431000 


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ....+..+..  +.+++++||++|+|++++|+++.+.
T Consensus       128 ~~~~~~~~~~--~~~~~~~SA~~~~~v~~l~~~l~~~  162 (165)
T 2wji_A          128 IDVDKLEKIL--GVKVVPLSAAKKMGIEELKKAISIA  162 (165)
T ss_dssp             CCHHHHHHHH--TSCEEECBGGGTBSHHHHHHHHHHH
T ss_pred             hHHHHHHHHh--CCCEEEEEcCCCCCHHHHHHHHHHH
Confidence            0122222333  2589999999999999999998764

>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=98.08  E-value=2.9e-07  Score=79.83  Aligned_cols=101  Identities=11%  Similarity=0.107  Sum_probs=61.8

Q ss_pred             CCCEEEEeCCcch-hhhccc--ccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           73 KADLLLCESGGDN-LAANFS--RELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~~~--~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      +..+.|++|.|-. ......  ...+|.+++|+|+.++...+..    +......+-++++||+|+.+....   ++.+.
T Consensus        50 ~~~i~~iDTPGhe~f~~~~~~~~~~aD~aILVVda~~g~~~qT~e~l~~~~~~~vPiIVviNKiDl~~~~~~---~v~~~  126 (501)
T 1zo1_I           50 NGMITFLDTPGHAAFTSMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAQVPVVVAVNKIDKPEADPD---RVKNE  126 (501)
T ss_dssp             SSCCCEECCCTTTCCTTSBCSSSBSCSSEEEEEETTTBSCTTTHHHHHHHHHTTCCEEEEEECSSSSTTCCC---CTTCC
T ss_pred             CEEEEEEECCCcHHHHHHHHHHHhhCCEEEEEeecccCccHHHHHHHHHHHhcCceEEEEEEeccccccCHH---HHHHH
Confidence            3467899999921 111111  1246999999999876433211    001123457999999999753111   11111


Q ss_pred             HH-------hcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          146 AL-------RMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       146 l~-------~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.       .+....+++++||++|+|+++|++++...
T Consensus       127 l~~~~~~~~~~~~~~~~v~vSAktG~gI~eLle~I~~~  164 (501)
T 1zo1_I          127 LSQYGILPEEWGGESQFVHVSAKAGTGIDELLDAILLQ  164 (501)
T ss_dssp             CCCCCCCTTCCSSSCEEEECCTTTCTTCTTHHHHTTTT
T ss_pred             HHHhhhhHHHhCCCccEEEEeeeeccCcchhhhhhhhh
Confidence            11       11123689999999999999999988643

>3izy_P Translation initiation factor IF-2, mitochondrial; E coli, RNA, ribosomal; 10.80A {Bos taurus}

Probab=98.08  E-value=2e-07  Score=81.51  Aligned_cols=105  Identities=12%  Similarity=0.065  Sum_probs=63.3

Q ss_pred             CCCEEEEeCCcch-hhhcc--cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhH-HHHHH
Q 030407           73 KADLLLCESGGDN-LAANF--SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADL-AVMER  144 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~~--~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~-~~~~~  144 (178)
                      +..+.|+.|.|-. .....  ....+|.+++|+|+.++...+..    +......+-++++||+|+.+...... +.+.+
T Consensus        51 g~~i~~iDTPGhe~f~~~~~~~~~~aD~vILVVDa~dg~~~qt~e~l~~~~~~~vPiIVViNKiDl~~~~~~~v~~~l~~  130 (537)
T 3izy_P           51 GEKITFLDTPGHAAFSAMRARGTQVTDIVILVVAADDGVMKQTVESIQHAKDAHVPIVLAINKCDKAEADPEKVKKELLA  130 (537)
T ss_dssp             SSCCBCEECSSSCCTTTSBBSSSBSBSSCEEECBSSSCCCHHHHHHHHHHHTTTCCEEECCBSGGGTTTSCCSSSSHHHH
T ss_pred             CCEEEEEECCChHHHHHHHHHHHccCCEEEEEEECCCCccHHHHHHHHHHHHcCCcEEEEEecccccccchHHHHHHHHh
Confidence            3467899999921 11111  11247999999999886543211    11112345799999999975411111 11111


Q ss_pred             H---HHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          145 D---ALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       145 ~---l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .   ...+....+++++||++|+|+++|++.+..++
T Consensus       131 ~~~~~e~~~~~~~iv~vSAktG~GI~eLle~I~~l~  166 (537)
T 3izy_P          131 YDVVCEDYGGDVQAVHVSALTGENMMALAEATIALA  166 (537)
T ss_dssp             TTSCCCCSSSSEEECCCCSSSSCSSHHHHHHHHHHH
T ss_pred             hhhhHHhcCCCceEEEEECCCCCCchhHHHHHHHhh
Confidence            1   11112235899999999999999999887653

>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=98.05  E-value=5.3e-06  Score=69.15  Aligned_cols=103  Identities=15%  Similarity=0.072  Sum_probs=63.2

Q ss_pred             CCEEEEeCCcc-h-----hhhcc-----cccccceEEEEEeCCCCC--CCC-----cC---CCCCCCceeEEEEecCCCC
Q 030407           74 ADLLLCESGGD-N-----LAANF-----SRELADYIIYIIDVSGGD--KIP-----RK---GGPGITQADLLVINKTDLA  132 (178)
Q Consensus        74 ~d~iiiEttG~-~-----~~~~~-----~~~~ad~~I~VvD~~~~~--~~~-----~~---~~~qi~~adiiviNK~Dl~  132 (178)
                      ..+.++.|.|. .     +...|     ....+|.+++|+|+++..  ...     ..   ....-..+-++|.||+|+.
T Consensus       226 ~~v~l~DT~G~i~~lp~~lve~f~~tl~~~~~aD~il~VvD~s~~~~~~~~~~~~~~~~L~~l~~~~~p~ilV~NK~Dl~  305 (364)
T 2qtf_A          226 RKIMLVDTVGFIRGIPPQIVDAFFVTLSEAKYSDALILVIDSTFSENLLIETLQSSFEILREIGVSGKPILVTLNKIDKI  305 (364)
T ss_dssp             EEEEEEECCCBCSSCCGGGHHHHHHHHHGGGGSSEEEEEEETTSCHHHHHHHHHHHHHHHHHHTCCSCCEEEEEECGGGC
T ss_pred             EEEEEEeCCCchhcCCHHHHHHHHHHHHHHHhCCEEEEEEECCCCcchHHHHHHHHHHHHHHhCcCCCCEEEEEECCCCC
Confidence            46788999993 1     01111     112469999999997754  110     00   0011234679999999998


Q ss_pred             CchhHh-HHHHHHHHHhc-CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          133 SAIGAD-LAVMERDALRM-RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       133 ~~~~~~-~~~~~~~l~~~-np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +....+ .+.+.+..+.+ .+..+++++||++|+|++++++.|.+.
T Consensus       306 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~SA~~g~gi~~L~~~I~~~  351 (364)
T 2qtf_A          306 NGDLYKKLDLVEKLSKELYSPIFDVIPISALKRTNLELLRDKIYQL  351 (364)
T ss_dssp             CSCHHHHHHHHHHHHHHHCSCEEEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHhcCCCCcEEEEECCCCcCHHHHHHHHHHH
Confidence            751011 11222233444 344578999999999999999998765

>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=98.05  E-value=6.1e-06  Score=60.85  Aligned_cols=55  Identities=15%  Similarity=0.022  Sum_probs=39.3

Q ss_pred             CceeEEEEecCCCCCchhHhHHHHHHHHHhcC-CC----CCEEEEecccCCCHHHHHHHHhhh
Q 030407          119 TQADLLVINKTDLASAIGADLAVMERDALRMR-DG----GPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       119 ~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~n-p~----a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+.++|+||+|+.+.  . .+...+..+..+ |.    .+++++||++|+|++++++++.+.
T Consensus       122 ~~piilv~nK~Dl~~~--~-~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~~v~~l~~~l~~~  181 (190)
T 2cxx_A          122 DIPTIVAVNKLDKIKN--V-QEVINFLAEKFEVPLSEIDKVFIPISAKFGDNIERLKNRIFEV  181 (190)
T ss_dssp             TCCEEEEEECGGGCSC--H-HHHHHHHHHHHTCCGGGHHHHEEECCTTTCTTHHHHHHHHHHH
T ss_pred             CCceEEEeehHhccCc--H-HHHHHHHHHHhhhhhhccCCcEEEEecCCCCCHHHHHHHHHHh
Confidence            4567999999999876  3 223333333333 21    358999999999999999988754

>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=98.04  E-value=1e-06  Score=65.08  Aligned_cols=94  Identities=16%  Similarity=0.121  Sum_probs=59.7

Q ss_pred             CCEEEEeCCcchh-----h-----hcc-cccccceEEEEEeCCCCCCCCcC-CCC------CCCceeEEEEecCCCCCch
Q 030407           74 ADLLLCESGGDNL-----A-----ANF-SRELADYIIYIIDVSGGDKIPRK-GGP------GITQADLLVINKTDLASAI  135 (178)
Q Consensus        74 ~d~iiiEttG~~~-----~-----~~~-~~~~ad~~I~VvD~~~~~~~~~~-~~~------qi~~adiiviNK~Dl~~~~  135 (178)
                      ..+.++.|.|..-     .     ... ....+|.+++|+|+++....... +..      ....+-++|+||+|+.++ 
T Consensus        52 ~~~~l~Dt~G~~~~~~~~~~~~~~~~~~~~~~ad~~i~v~D~~~~~s~~~~~~~~~~~~~~~~~~p~ilv~NK~Dl~~~-  130 (172)
T 2gj8_A           52 MPLHIIDTAGLREASDEVERIGIERAWQEIEQADRVLFMVDGTTTDAVDPAEIWPEFIARLPAKLPITVVRNKADITGE-  130 (172)
T ss_dssp             EEEEEEECCCCSCCSSHHHHHHHHHHHHHHHTCSEEEEEEETTTCCCCSHHHHCHHHHHHSCTTCCEEEEEECHHHHCC-
T ss_pred             eEEEEEECCCcccchhHHHHHHHHHHHHHHHhCCEEEEEEECCCCCCHHHHHHHHHHHHhcccCCCEEEEEECccCCcc-
Confidence            3477899999410     0     011 12347999999999876543210 000      012457999999999543 


Q ss_pred             hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          136 GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       136 ~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                       .. +    . .+ ....+++++||++|+|++++++.|.+.
T Consensus       131 -~~-~----~-~~-~~~~~~~~~SA~~g~gv~~l~~~l~~~  163 (172)
T 2gj8_A          131 -TL-G----M-SE-VNGHALIRLSARTGEGVDVLRNHLKQS  163 (172)
T ss_dssp             -CC-E----E-EE-ETTEEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             -hh-h----h-hh-ccCCceEEEeCCCCCCHHHHHHHHHHH
Confidence             11 0    0 01 124589999999999999999988764

>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=98.03  E-value=3.9e-06  Score=71.32  Aligned_cols=95  Identities=13%  Similarity=0.063  Sum_probs=57.6

Q ss_pred             CCCEEEEeCCcch-h---hhcccccccceEEEEEeCCCC-------CCCCc-CC---CCCCCc-eeEEEEecCCCCCch-
Q 030407           73 KADLLLCESGGDN-L---AANFSRELADYIIYIIDVSGG-------DKIPR-KG---GPGITQ-ADLLVINKTDLASAI-  135 (178)
Q Consensus        73 ~~d~iiiEttG~~-~---~~~~~~~~ad~~I~VvD~~~~-------~~~~~-~~---~~qi~~-adiiviNK~Dl~~~~-  135 (178)
                      +..+.|++|.|.. .   ...+ ...+|.+++|+|++++       ...+. .+   ..++.. .-++++||+|+.++. 
T Consensus        83 ~~~~~iiDtpG~~~f~~~~~~~-~~~aD~~ilVvDa~~gsfe~~~~~~~qt~~~~~~~~~~~~~~iivviNK~Dl~~~~~  161 (435)
T 1jny_A           83 KYFFTIIDAPGHRDFVKNMITG-ASQADAAILVVSAKKGEYEAGMSVEGQTREHIILAKTMGLDQLIVAVNKMDLTEPPY  161 (435)
T ss_dssp             SCEEEECCCSSSTTHHHHHHHT-SSCCSEEEEEEECSTTHHHHHHSTTCHHHHHHHHHHHTTCTTCEEEEECGGGSSSTT
T ss_pred             CeEEEEEECCCcHHHHHHHHhh-hhhcCEEEEEEECCCCccccccccchHHHHHHHHHHHcCCCeEEEEEEcccCCCccc
Confidence            5789999999931 0   1111 2357999999999875       11110 00   011222 247899999998720 


Q ss_pred             -hHh----HHHHHHHHHhcC--C-CCCEEEEecccCCCHHH
Q 030407          136 -GAD----LAVMERDALRMR--D-GGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       136 -~~~----~~~~~~~l~~~n--p-~a~i~~~SA~~g~gi~e  168 (178)
                       .+.    .+++.+.++...  + ..+++++||++|+|+.+
T Consensus       162 ~~~~~~~~~~~i~~~~~~~~~~~~~~~~i~iSA~~g~~v~e  202 (435)
T 1jny_A          162 DEKRYKEIVDQVSKFMRSYGFNTNKVRFVPVVAPSGDNITH  202 (435)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCCCTTCEEEECBTTTTBTTTB
T ss_pred             cHHHHHHHHHHHHHHHHHcCCCcCCceEEEeecccCccccc
Confidence             022    234445554433  2 36899999999999973

>3izq_1 HBS1P, elongation factor 1 alpha-like protein; NO-GO mRNA decay, ribosomal protein,hydrolase; 9.50A {Saccharomyces cerevisiae}

Probab=98.03  E-value=2.7e-06  Score=75.40  Aligned_cols=97  Identities=12%  Similarity=0.084  Sum_probs=57.4

Q ss_pred             CCCEEEEeCCcch--hhhc-ccccccceEEEEEeCCCCCC-------CCc-CC---CCCCCc-eeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDN--LAAN-FSRELADYIIYIIDVSGGDK-------IPR-KG---GPGITQ-ADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~-~~~~~ad~~I~VvD~~~~~~-------~~~-~~---~~qi~~-adiiviNK~Dl~~~~~~  137 (178)
                      +..+.|+.|.|..  ...+ .....+|.+++|+|++.+..       .+. .+   ...+.. .-++|+||+|+.+....
T Consensus       244 ~~~~~iiDTPG~e~f~~~~~~~~~~aD~~llVVDa~~g~~e~~~~~~~qt~e~l~~~~~lgi~~iIVVvNKiDl~~~~~~  323 (611)
T 3izq_1          244 RANFTIVDAPGHRDFVPNAIMGISQADMAILCVDCSTNAFESGFDLDGQTKEHMLLASSLGIHNLIIAMNKMDNVDWSQQ  323 (611)
T ss_dssp             SCEEEEEECCSSSCHHHHHTTTSSCCSEEEEEEECSHHHHHTTCCTTSHHHHHHHHHHTTTCCEEEEEEECTTTTTTCHH
T ss_pred             CceEEEEECCCCcccHHHHHHHHhhcCceEEEEECCCCcccccchhhhHHHHHHHHHHHcCCCeEEEEEecccccchhHH
Confidence            4578999999931  1111 11235799999999987420       000 00   011222 25888999999873112


Q ss_pred             hHHH----HHHHHHhcC---CCCCEEEEecccCCCHHHH
Q 030407          138 DLAV----MERDALRMR---DGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       138 ~~~~----~~~~l~~~n---p~a~i~~~SA~~g~gi~el  169 (178)
                      ..+.    +...++...   +..+++++||++|+|++++
T Consensus       324 ~~~ei~~~l~~~l~~~g~~~~~~~~i~vSA~tG~gI~el  362 (611)
T 3izq_1          324 RFEEIKSKLLPYLVDIGFFEDNINWVPISGFSGEGVYKI  362 (611)
T ss_dssp             HHHHHHHHHHHHHHHHTCCGGGCEEEECCTTTCTTTSSC
T ss_pred             HHHHHHHHHHHHHHhhcccccCccEEeeecccCCCcccc
Confidence            3333    333333332   1468999999999999854

>3h2y_A GTPase family protein; GTP-binding protein YQEH, possibly involved in replication initiation, csgid, IDP90222; HET: DGI; 1.80A {Bacillus anthracis str}

Probab=98.02  E-value=3.9e-06  Score=69.97  Aligned_cols=77  Identities=19%  Similarity=0.166  Sum_probs=50.7

Q ss_pred             cceEEEEEeCCCCCCCCcCCCCCC-----CceeEEEEecCCCCCchhHhHHHHHHH----HHhcC-CCCCEEEEecccCC
Q 030407           95 ADYIIYIIDVSGGDKIPRKGGPGI-----TQADLLVINKTDLASAIGADLAVMERD----ALRMR-DGGPFIFAQVGWVI  164 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~~~~~qi-----~~adiiviNK~Dl~~~~~~~~~~~~~~----l~~~n-p~a~i~~~SA~~g~  164 (178)
                      ++.++.|+|+++....   +...+     ..+-++|+||+||.+.. ...+.+.++    .++.+ +..+++.+||++|.
T Consensus        70 ~~~il~VvD~~d~~~~---~~~~l~~~~~~~p~ilV~NK~DL~~~~-~~~~~~~~~l~~~~~~~g~~~~~v~~iSA~~g~  145 (368)
T 3h2y_A           70 DALVVKIVDIFDFNGS---WLPGLHRFVGNNKVLLVGNKADLIPKS-VKHDKVKHWMRYSAKQLGLKPEDVFLISAAKGQ  145 (368)
T ss_dssp             CCEEEEEEETTSHHHH---CCTTHHHHSSSSCEEEEEECGGGSCTT-SCHHHHHHHHHHHHHHTTCCCSEEEECCTTTCT
T ss_pred             CcEEEEEEECCCCccc---HHHHHHHHhCCCcEEEEEEChhcCCcc-cCHHHHHHHHHHHHHHcCCCcccEEEEeCCCCc
Confidence            4789999999864311   11111     34568999999998651 122333333    33322 12379999999999


Q ss_pred             CHHHHHHHHhh
Q 030407          165 GIIFTLSITHY  175 (178)
Q Consensus       165 gi~el~~~l~~  175 (178)
                      |++++++.+.+
T Consensus       146 gi~~L~~~l~~  156 (368)
T 3h2y_A          146 GIAELADAIEY  156 (368)
T ss_dssp             THHHHHHHHHH
T ss_pred             CHHHHHhhhhh
Confidence            99999999865

>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=98.01  E-value=1e-05  Score=76.22  Aligned_cols=102  Identities=12%  Similarity=0.095  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCcch-hhh-c-ccccccceEEEEEeCCCCCCCCcC-C---CCCCCce-eEEEEecCCCCCchhHhH----H
Q 030407           73 KADLLLCESGGDN-LAA-N-FSRELADYIIYIIDVSGGDKIPRK-G---GPGITQA-DLLVINKTDLASAIGADL----A  140 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~-~-~~~~~ad~~I~VvD~~~~~~~~~~-~---~~qi~~a-diiviNK~Dl~~~~~~~~----~  140 (178)
                      +..+.|++|.|-. ... + .....+|.+|+|+|++++...+.. +   ......+ -++++||+|+.+.. +..    +
T Consensus       358 ~~kI~IIDTPGHedF~~~mi~gas~AD~aILVVDAtdGv~~QTrEhL~ll~~lgIP~IIVVINKiDLv~d~-e~le~i~e  436 (1289)
T 3avx_A          358 TRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDE-ELLELVEM  436 (1289)
T ss_dssp             SCEEEEEECCCHHHHHHHHHHTSCCCSEEEEEEETTTCSCTTHHHHHHHHHHHTCSCEEEEEECCTTCCCH-HHHHHHHH
T ss_pred             CEEEEEEECCChHHHHHHHHHHHhhCCEEEEEEcCCccCcHHHHHHHHHHHHcCCCeEEEEEeecccccch-hhHHHHHH
Confidence            4678999999931 010 1 112247999999999887533221 0   0112334 37899999998641 222    3


Q ss_pred             HHHHHHHhcC---CCCCEEEEecccC--------CCHHHHHHHHhh
Q 030407          141 VMERDALRMR---DGGPFIFAQVGWV--------IGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~n---p~a~i~~~SA~~g--------~gi~el~~~l~~  175 (178)
                      ++.+.+++..   ...+++++||++|        +|+++|++.|..
T Consensus       437 Ei~elLk~~G~~~~~vp~IpvSAktG~ng~~~w~eGI~eLleaL~~  482 (1289)
T 3avx_A          437 EVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDS  482 (1289)
T ss_dssp             HHHHHHHHTTSCTTTCCEEECCSTTTTTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccccccceeEEEEEeccCCCCCccccccchhhHhHHhh
Confidence            4445555443   2479999999999        579999998875

>3ec1_A YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase, signaling protein; HET: GDP; 2.36A {Geobacillus stearothermophilus}

Probab=98.01  E-value=9.2e-06  Score=67.72  Aligned_cols=81  Identities=16%  Similarity=0.013  Sum_probs=52.3

Q ss_pred             ccceEEEEEeCCCCCCCCcC-CCCCC-CceeEEEEecCCCCCchhHhHHHHHHH----HHhcC-CCCCEEEEecccCCCH
Q 030407           94 LADYIIYIIDVSGGDKIPRK-GGPGI-TQADLLVINKTDLASAIGADLAVMERD----ALRMR-DGGPFIFAQVGWVIGI  166 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~-~~~qi-~~adiiviNK~Dl~~~~~~~~~~~~~~----l~~~n-p~a~i~~~SA~~g~gi  166 (178)
                      .++.++.|+|+++....... ....+ ..+-++|+||+||.+.. ...+.+.++    .++.. +..+++.+||++|.|+
T Consensus        71 ~~~lil~VvD~~d~~~s~~~~l~~~l~~~piilV~NK~DLl~~~-~~~~~~~~~l~~~~~~~g~~~~~v~~iSA~~g~gi  149 (369)
T 3ec1_A           71 SKALVVNIVDIFDFNGSFIPGLPRFAADNPILLVGNKADLLPRS-VKYPKLLRWMRRMAEELGLCPVDVCLVSAAKGIGM  149 (369)
T ss_dssp             HCCEEEEEEETTCSGGGCCSSHHHHCTTSCEEEEEECGGGSCTT-CCHHHHHHHHHHHHHTTTCCCSEEEECBTTTTBTH
T ss_pred             cCcEEEEEEECCCCCCchhhHHHHHhCCCCEEEEEEChhcCCCc-cCHHHHHHHHHHHHHHcCCCcccEEEEECCCCCCH
Confidence            35789999999876532110 00011 34568999999998651 112333444    33322 1137999999999999


Q ss_pred             HHHHHHHhh
Q 030407          167 IFTLSITHY  175 (178)
Q Consensus       167 ~el~~~l~~  175 (178)
                      ++|++.+.+
T Consensus       150 ~~L~~~I~~  158 (369)
T 3ec1_A          150 AKVMEAINR  158 (369)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999999865

>2j69_A Bacterial dynamin-like protein; FZO, FZL, GTPase, hydrolase; 3.0A {Nostoc punctiforme} PDB: 2j68_A 2w6d_A*

Probab=97.99  E-value=1.1e-05  Score=72.55  Aligned_cols=103  Identities=10%  Similarity=-0.009  Sum_probs=63.4

Q ss_pred             CCEEEEeCCcchhhhc------ccccccceEEEEEeCCCCCCCCcC-----CCCCCCceeEEEEecCCCCCch---hH--
Q 030407           74 ADLLLCESGGDNLAAN------FSRELADYIIYIIDVSGGDKIPRK-----GGPGITQADLLVINKTDLASAI---GA--  137 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~------~~~~~ad~~I~VvD~~~~~~~~~~-----~~~qi~~adiiviNK~Dl~~~~---~~--  137 (178)
                      .++.||+|.|..-...      .....+|.+++|+|++++......     .......+.++|+||+|+.+..   .+  
T Consensus       174 ~~l~LiDTPGl~~~~~~~~~~~~~i~~aD~vL~Vvda~~~~s~~e~~~l~~~l~~~~~~iiiVlNK~Dl~~~~~~~~ee~  253 (695)
T 2j69_A          174 KGIEIVDSPGLNDTEARNELSLGYVNNCHAILFVMRASQPCTLGERRYLENYIKGRGLTVFFLVNAWDQVRESLIDPDDV  253 (695)
T ss_dssp             TTEEEEECCCHHHHHTCHHHHTHHHHSSSEEEEEEETTSTTCHHHHHHHHHHTTTSCCCEEEEEECGGGGGGGCSSTTCH
T ss_pred             CCeEEEECCCCCchhhHHHHHHHHHHhCCEEEEEEeCCCccchhHHHHHHHHHHhhCCCEEEEEECcccccccccChhhH
Confidence            5899999999432110      011247999999999876432110     1111234579999999997541   01  


Q ss_pred             -hHHH----HH----HHHHhcC-------CCCCEEEEecc--------------cCCCHHHHHHHHhhh
Q 030407          138 -DLAV----ME----RDALRMR-------DGGPFIFAQVG--------------WVIGIIFTLSITHYI  176 (178)
Q Consensus       138 -~~~~----~~----~~l~~~n-------p~a~i~~~SA~--------------~g~gi~el~~~l~~~  176 (178)
                       +++.    +.    ..+....       ...+++++||+              +|.|++++++.+.++
T Consensus       254 e~l~~~~~~i~~~~~~~l~~~~~~~g~~~~~~~v~~vSAk~al~~~~~~~~~~~~~~Gi~~L~~~L~~~  322 (695)
T 2j69_A          254 EELQASENRLRQVFNANLAEYCTVEGQNIYDERVFELSSIQALRRRLKNPQADLDGTGFPKFMDSLNTF  322 (695)
T ss_dssp             HHHHHHHHHHHHHHHHHHGGGGBSSSCBCGGGTEEECCHHHHHHHHHHCTTCCCTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhcccccccCCCcEEEEeChHHHHhhccCchhhhhccCHHHHHHHHHHH
Confidence             1221    22    1222221       23489999999              999999999988764

>3mca_A HBS1, elongation factor 1 alpha-like protein; protein protein complex, translation regulation; 2.74A {Schizosaccharomyces pombe}

Probab=97.98  E-value=4.1e-07  Score=80.37  Aligned_cols=104  Identities=14%  Similarity=0.097  Sum_probs=55.7

Q ss_pred             CCCEEEEeCCcch-hh-hc-ccccccceEEEEEeCCCCC-------CCCc-CC---CCCCCce-eEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDN-LA-AN-FSRELADYIIYIIDVSGGD-------KIPR-KG---GPGITQA-DLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~-~~~~~ad~~I~VvD~~~~~-------~~~~-~~---~~qi~~a-diiviNK~Dl~~~~~~  137 (178)
                      +..+.||.|.|.. .. .+ .....+|.+|+|+|++.+.       ..+. .+   ...+..+ -++|+||+|+.+...+
T Consensus       254 ~~~i~iiDTPGh~~f~~~~~~~~~~aD~alLVVDa~~g~~e~gi~~~~qt~e~l~~~~~lgip~iIvviNKiDl~~~~~~  333 (592)
T 3mca_A          254 KKIYEIGDAPGHRDFISGMIAGASSADFAVLVVDSSQNNFERGFLENGQTREHAYLLRALGISEIVVSVNKLDLMSWSED  333 (592)
T ss_dssp             -----CCEEESSSEEEEECCC-------CCSEEEEEECCSSTTSCSCSSHHHHHHHHHHSSCCCEEEEEECGGGGTTCHH
T ss_pred             CeEEEEEECCChHHHHHHHHHHHhhCCEEEEEEECCCCccccccccchHHHHHHHHHHHcCCCeEEEEEeccccccccHH
Confidence            4678899999921 00 00 1112469999999998753       1110 00   0112333 5779999999863114


Q ss_pred             hHHHHHHHHHhcC--------CCCCEEEEecccCCCHH--------------HHHHHHhhh
Q 030407          138 DLAVMERDALRMR--------DGGPFIFAQVGWVIGII--------------FTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~n--------p~a~i~~~SA~~g~gi~--------------el~~~l~~~  176 (178)
                      ..+.+.+.++...        ...+++++||++|.|+.              .|++.|..+
T Consensus       334 ~~~~i~~el~~~l~~~~g~~~~~~~ii~iSA~~G~gI~e~~~~~~~~w~~g~~Lle~l~~~  394 (592)
T 3mca_A          334 RFQEIKNIVSDFLIKMVGFKTSNVHFVPISAISGTNLIQKDSSDLYKWYKGPTLLSALDQL  394 (592)
T ss_dssp             HHHHHHHHHHHHHTTTSCCCGGGEEEEEECSSSCSSSCSCCCCGGGGTCCSCCHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHHhhCCCccceEEEEEecccCcccccccccccccccchHHHHHHHHhh
Confidence            4444444444322        13479999999999998              788887654

>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=97.96  E-value=4.3e-06  Score=71.03  Aligned_cols=98  Identities=15%  Similarity=0.037  Sum_probs=60.5

Q ss_pred             CCCEEEEeCCcchh----------hh--cccccccceEEEEEeCCCCCCCCcC-CCCC---CCceeEEEEecCCCCCchh
Q 030407           73 KADLLLCESGGDNL----------AA--NFSRELADYIIYIIDVSGGDKIPRK-GGPG---ITQADLLVINKTDLASAIG  136 (178)
Q Consensus        73 ~~d~iiiEttG~~~----------~~--~~~~~~ad~~I~VvD~~~~~~~~~~-~~~q---i~~adiiviNK~Dl~~~~~  136 (178)
                      +..+.++.|.|..-          ..  ......+|.+++|+|++.+...... ....   ...+-++|+||+|+.+.  
T Consensus        48 ~~~~~l~DT~G~~~~~~~~~~~~~~~~~~~~~~~ad~il~V~D~~~~~~~~d~~i~~~l~~~~~p~ilv~NK~D~~~~--  125 (439)
T 1mky_A           48 GKTFKLVDTCGVFDNPQDIISQKMKEVTLNMIREADLVLFVVDGKRGITKEDESLADFLRKSTVDTILVANKAENLRE--  125 (439)
T ss_dssp             TEEEEEEECTTTTSSGGGCCCHHHHHHHHHHHTTCSEEEEEEETTTCCCHHHHHHHHHHHHHTCCEEEEEESCCSHHH--
T ss_pred             CeEEEEEECCCccccccchHHHHHHHHHHHHHHhCCEEEEEEECCCCCCHHHHHHHHHHHHcCCCEEEEEeCCCCccc--
Confidence            34578999999421          00  0112357999999999876432210 1111   23457999999998532  


Q ss_pred             HhHHHH-HHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          137 ADLAVM-ERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       137 ~~~~~~-~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .. ... .+. .++ ...+++++||++|.|++++++.+.+
T Consensus       126 ~~-~~~~~~~-~~l-g~~~~~~iSA~~g~gv~~L~~~i~~  162 (439)
T 1mky_A          126 FE-REVKPEL-YSL-GFGEPIPVSAEHNINLDTMLETIIK  162 (439)
T ss_dssp             HH-HHTHHHH-GGG-SSCSCEECBTTTTBSHHHHHHHHHH
T ss_pred             cH-HHHHHHH-Hhc-CCCCEEEEeccCCCCHHHHHHHHHH
Confidence            11 222 222 222 2337899999999999999998754

>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation, GTP-binding domain, maturation enzyme, oxidoreductase; 2.99A {Thermotoga neapolitana}

Probab=97.95  E-value=6e-07  Score=76.35  Aligned_cols=98  Identities=12%  Similarity=-0.042  Sum_probs=61.6

Q ss_pred             CEEEEeCCcchhhhc----------ccccccceEEEEEeCCCCCCCCcCC---CCCCCceeEEEEecCCCCCchhHhHHH
Q 030407           75 DLLLCESGGDNLAAN----------FSRELADYIIYIIDVSGGDKIPRKG---GPGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        75 d~iiiEttG~~~~~~----------~~~~~ad~~I~VvD~~~~~~~~~~~---~~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+.|+.|.|..--..          .....+|.+++|+|+.. ......+   ......+-++|+||+|+.++  ...+.
T Consensus        84 ~l~liDTpG~~d~~~l~~~~~~~~~~~l~~aD~vllVvD~~~-~~~~~~~l~~l~~~~~piIvV~NK~Dl~~~--~~~~~  160 (423)
T 3qq5_A           84 PVTLVDTPGLDDVGELGRLRVEKARRVFYRADCGILVTDSAP-TPYEDDVVNLFKEMEIPFVVVVNKIDVLGE--KAEEL  160 (423)
T ss_dssp             EEEEEECSSTTCCCTTCCCCHHHHHHHHTSCSEEEEECSSSC-CHHHHHHHHHHHHTTCCEEEECCCCTTTTC--CCTHH
T ss_pred             eEEEEECcCCCcccchhHHHHHHHHHHHhcCCEEEEEEeCCC-hHHHHHHHHHHHhcCCCEEEEEeCcCCCCc--cHHHH
Confidence            688999999310000          01124799999999822 1111111   01124567999999999877  33322


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      . +.+.+. -+.+++++||++|+|++++++.|.+.+
T Consensus       161 ~-~~l~~~-~g~~v~~vSAktg~gI~eL~~~L~~~l  194 (423)
T 3qq5_A          161 K-GLYESR-YEAKVLLVSALQKKGFDDIGKTISEIL  194 (423)
T ss_dssp             H-HHSSCC-TTCCCCCCSSCCTTSTTTHHHHHHHHS
T ss_pred             H-HHHHHH-cCCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            2 222222 246899999999999999999987654

>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=97.95  E-value=6.8e-07  Score=70.31  Aligned_cols=103  Identities=6%  Similarity=0.006  Sum_probs=60.9

Q ss_pred             CCCEEEEeCCcchh------------hhcc--cccccceEEEEEeCCCCCCCCcC--------CCCCCCceeEEEEe-cC
Q 030407           73 KADLLLCESGGDNL------------AANF--SRELADYIIYIIDVSGGDKIPRK--------GGPGITQADLLVIN-KT  129 (178)
Q Consensus        73 ~~d~iiiEttG~~~------------~~~~--~~~~ad~~I~VvD~~~~~~~~~~--------~~~qi~~adiiviN-K~  129 (178)
                      +..+.|++|.|..-            ...+  ....+|++++|+|+++.......        +......+.++++| |+
T Consensus        70 ~~~i~iiDTpG~~~~~~~~~~~~~~i~~~~~~~~~~~d~il~V~d~~~~~~~~~~~~~~l~~~~~~~~~~~~i~vv~nK~  149 (260)
T 2xtp_A           70 NREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKE  149 (260)
T ss_dssp             TEEEEEEECCGGGGSSCCCHHHHHHHHHHHHHHTTCCSEEEEEEETTCCCHHHHHHHHHHHHHHCGGGGGGEEEEEECGG
T ss_pred             CCEEEEEECcCCCCCCCCHHHHHHHHHHHHHhcCCCCcEEEEEEeCCCCCHHHHHHHHHHHHHhCchhhccEEEEEEccc
Confidence            56799999999421            0000  11347999999999852211110        01112346788888 99


Q ss_pred             CCCCchhHh-H-----HHHHHHHHhcCC----CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          130 DLASAIGAD-L-----AVMERDALRMRD----GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       130 Dl~~~~~~~-~-----~~~~~~l~~~np----~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      |+.+..... +     +.+.+.++....    ..+ +++||++|.|++++++.+.+.
T Consensus       150 Dl~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~SA~~~~gv~~l~~~i~~~  205 (260)
T 2xtp_A          150 DLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNN-RAEGSNQDDQVKELMDCIEDL  205 (260)
T ss_dssp             GGTTCCHHHHHHHCCCHHHHHHHHHTTTCEEECCT-TCCHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCccHHHHHHhcchHHHHHHHHHhCCeEEEecC-cccccccHHHHHHHHHHHHHH
Confidence            998541010 0     112334444332    223 889999999999999988764

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=97.92  E-value=4.4e-06  Score=72.48  Aligned_cols=160  Identities=14%  Similarity=0.121  Sum_probs=88.6

Q ss_pred             HHHHHHhhc-CCcEEEEEecCC-C-chhHHH--HHHcCCCCccceeecccCCCcccccccccccCH-hHHHhhHhhCCCC
Q 030407            2 LALCKFLRD-KYSLAAVTNDIF-T-KEDGEF--LMRNGALPEERIRAVETGGCPHAAIREDISINL-GPLEELSNLFKAD   75 (178)
Q Consensus         2 ~~~~~~~~~-~~~vaVI~nd~g-~-~iD~~l--i~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l-~~l~~l~~~~~~d   75 (178)
                      .+++.++.+ ++|++++-.|.. . .+|..-  -...++    ++....++.        |....+ .++..+ ...++|
T Consensus       119 ~kLA~~l~~~G~kVllVd~D~~r~aa~~qL~~~~~~~~i----~v~~~~~~~--------dp~~i~~~al~~~-~~~~~D  185 (504)
T 2j37_W          119 SKLAYYYQRKGWKTCLICADTFRAGAFDQLKQNATKARI----PFYGSYTEM--------DPVIIASEGVEKF-KNENFE  185 (504)
T ss_dssp             HHHHHHHHHTTCCEEEEEECCSSSHHHHHHHHHHHHHTC----CEEECCCCS--------CHHHHHHHHHHHH-HHTTCC
T ss_pred             HHHHHHHHhCCCeEEEEeccccchhHHHHHHHHhhccCc----eEEccCCCC--------CHHHHHHHHHHHH-HHCCCc
Confidence            356666655 599999999987 4 233211  122233    333322211        111111 334433 236899


Q ss_pred             EEEEeCCcchhh-hcc--------cccccceEEEEEeCCCCCCCCcCCCCCCC--ce-eEEEEecCCCCCchhHhHHHHH
Q 030407           76 LLLCESGGDNLA-ANF--------SRELADYIIYIIDVSGGDKIPRKGGPGIT--QA-DLLVINKTDLASAIGADLAVME  143 (178)
Q Consensus        76 ~iiiEttG~~~~-~~~--------~~~~ad~~I~VvD~~~~~~~~~~~~~qi~--~a-diiviNK~Dl~~~~~~~~~~~~  143 (178)
                      ++||+|.|.... ..+        ....+|.+++|+|+..+.+... ....+.  .+ +.+|+||+|........+. +.
T Consensus       186 vvIIDTpG~~~~~~~l~~el~~~~~~i~pd~vllVvDa~~g~~~~~-~a~~~~~~~~i~gvVlNK~D~~~~~g~~l~-~~  263 (504)
T 2j37_W          186 IIIVDTSGRHKQEDSLFEEMLQVANAIQPDNIVYVMDASIGQACEA-QAKAFKDKVDVASVIVTKLDGHAKGGGALS-AV  263 (504)
T ss_dssp             EEEEEECCCCTTCHHHHHHHHHHHHHHCCSEEEEEEETTCCTTHHH-HHHHHHHHHCCCCEEEECTTSCCCCTHHHH-HH
T ss_pred             EEEEeCCCCcccchhHHHHHHHHHhhhcCceEEEEEeccccccHHH-HHHHHHhhcCceEEEEeCCccccchHHHHH-HH
Confidence            999999994211 010        0113588999999987643211 111121  23 5899999999765212222 22


Q ss_pred             HHH-------------HhcCCCCCEEEEecccCCC-HHHHHHHHhhh
Q 030407          144 RDA-------------LRMRDGGPFIFAQVGWVIG-IIFTLSITHYI  176 (178)
Q Consensus       144 ~~l-------------~~~np~a~i~~~SA~~g~g-i~el~~~l~~~  176 (178)
                      +..             ..+.|..+.+++|+++|.| +++|++++.+.
T Consensus       264 ~~~g~PI~fig~ge~~~dl~~f~~~~~vsal~G~Gdi~~Lie~i~e~  310 (504)
T 2j37_W          264 AATKSPIIFIGTGEHIDDFEPFKTQPFISKLLGMGDIEGLIDKVNEL  310 (504)
T ss_dssp             HHHCCCEEEEECSSSTTCEECCTHHHHHHCCCTTTTTTTTHHHHTTT
T ss_pred             HHhCCCeEEeccccchhhhhccCcceeeehhcCCCcHHHHHHHHHHH
Confidence            111             1223445667789999999 99999988754

>2hjg_A GTP-binding protein ENGA; GTPase ENGA KH-domain, hydrolase; HET: GDP; 2.50A {Bacillus subtilis}

Probab=97.91  E-value=3e-06  Score=71.96  Aligned_cols=98  Identities=16%  Similarity=0.099  Sum_probs=56.7

Q ss_pred             CCCEEEEeCCcch---------hhhc--ccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDN---------LAAN--FSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~---------~~~~--~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~  137 (178)
                      +..+.+++|.|..         +...  .....+|.+++|+|++.+......    .......+-++|+||+|+.+.  .
T Consensus        50 ~~~~~l~DT~G~~~~~~~~~~~~~~~~~~~~~~ad~il~vvD~~~~~~~~d~~~~~~l~~~~~pvilv~NK~D~~~~--~  127 (436)
T 2hjg_A           50 NYDFNLIDTGGIDIGDEPFLAQIRQQAEIAMDEADVIIFMVNGREGVTAADEEVAKILYRTKKPVVLAVNKLDNTEM--R  127 (436)
T ss_dssp             SSCCEEEC---------CHHHHHHHHHHHHHHHCSEEEEEEETTTCSCHHHHHHHHHHTTCCSCEEEEEECCCC------
T ss_pred             CceEEEEECCCCCCcchhHHHHHHHHHHHHHHhCCEEEEEEeCCCCCCHHHHHHHHHHHHcCCCEEEEEECccCccc--h
Confidence            4678999999942         1110  111247999999999876543211    111234567999999999754  2


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .  ...+.. ++ ...+++++||++|.|+++|++.+.+.
T Consensus       128 ~--~~~~~~-~l-g~~~~~~iSA~~g~gv~~L~~~i~~~  162 (436)
T 2hjg_A          128 A--NIYDFY-SL-GFGEPYPISGTHGLGLGDLLDAVAEH  162 (436)
T ss_dssp             ---CCCSSG-GG-SSCCCEECBTTTTBTHHHHHHHHHHT
T ss_pred             h--hHHHHH-Hc-CCCCeEEEeCcCCCChHHHHHHHHHh
Confidence            1  111111 22 22378999999999999999987653

>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=97.89  E-value=3.6e-06  Score=72.26  Aligned_cols=98  Identities=14%  Similarity=0.078  Sum_probs=56.7

Q ss_pred             CCCEEEEeCCcch-hhhcc--cccccceEEEEEeCCCCCC-------CCc-CC---CCCCCce-eEEEEecCCCCCch--
Q 030407           73 KADLLLCESGGDN-LAANF--SRELADYIIYIIDVSGGDK-------IPR-KG---GPGITQA-DLLVINKTDLASAI--  135 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~~--~~~~ad~~I~VvD~~~~~~-------~~~-~~---~~qi~~a-diiviNK~Dl~~~~--  135 (178)
                      +..+.|++|.|-. .....  ....+|.+|+|+|++++..       .+. .+   ......+ -++++||+|+.+..  
T Consensus       120 ~~~~~iiDtPGh~~f~~~~~~~~~~aD~~ilVvDa~~g~~e~sf~~~~qt~e~l~~~~~~~vp~iivviNK~Dl~~~~~~  199 (467)
T 1r5b_A          120 HRRFSLLDAPGHKGYVTNMINGASQADIGVLVISARRGEFEAGFERGGQTREHAVLARTQGINHLVVVINKMDEPSVQWS  199 (467)
T ss_dssp             SEEEEECCCCC-----------TTSCSEEEEEEECSTTHHHHTTSTTCCHHHHHHHHHHTTCSSEEEEEECTTSTTCSSC
T ss_pred             CeEEEEEECCCcHHHHHHHHhhcccCCEEEEEEeCCcCccccccCCCCcHHHHHHHHHHcCCCEEEEEEECccCCCcccc
Confidence            4568899999921 00111  1124699999999988631       010 00   0112334 58899999996420  


Q ss_pred             hHhH----HHHHHHHHhc-C-C---CCCEEEEecccCCCHHHHH
Q 030407          136 GADL----AVMERDALRM-R-D---GGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus       136 ~~~~----~~~~~~l~~~-n-p---~a~i~~~SA~~g~gi~el~  170 (178)
                      .+..    +++.+.++.. . +   ..+++++||++|+|+.+++
T Consensus       200 ~~~~~~i~~e~~~~l~~~~g~~~~~~~~~i~vSA~~g~~i~~l~  243 (467)
T 1r5b_A          200 EERYKECVDKLSMFLRRVAGYNSKTDVKYMPVSAYTGQNVKDRV  243 (467)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCCCHHHHEEEEECBTTTTBTTSSCC
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCccCCceEEeccccccccccccc
Confidence            0222    2344555443 1 1   4689999999999998643

>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=97.89  E-value=5.6e-06  Score=61.43  Aligned_cols=101  Identities=13%  Similarity=0.091  Sum_probs=58.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCC-CCc--CC-C---CC-CCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDK-IPR--KG-G---PG-ITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~-~~~--~~-~---~q-i~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+-+++|.|..    +...+. ..++.+++|+|.+++.. ...  .+ .   .. -..+-++|.||+|+.+.  ....
T Consensus        55 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~~s~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~~  131 (184)
T 2zej_A           55 DLVLNVWDFAGREEFYSTHPHFM-TQRALYLAVYDLSKGQAEVDAMKPWLFNIKARASSSPVILVGTHLDVSDE--KQRK  131 (184)
T ss_dssp             -CEEEEEEECSHHHHHTTSHHHH-HHSEEEEEEEEGGGCHHHHHTHHHHHHHHHHHCTTCEEEEEEECGGGCCH--HHHH
T ss_pred             ceEEEEEecCCCHHHHHhhHHHc-cCCcEEEEEEeCCcchhHHHHHHHHHHHHHhhCCCCcEEEEEECCCcccc--hhhH
Confidence            5678899999932    111111 23688889999877531 110  00 0   00 13456888899999765  3322


Q ss_pred             H-HHHHHHhcC--CCCC----EEEEecccCC-CHHHHHHHHhhh
Q 030407          141 V-MERDALRMR--DGGP----FIFAQVGWVI-GIIFTLSITHYI  176 (178)
Q Consensus       141 ~-~~~~l~~~n--p~a~----i~~~SA~~g~-gi~el~~~l~~~  176 (178)
                      . .....+.+.  -..+    ++++||++|. |+++|++.+.+.
T Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~~~~~~l~~~i~~~  175 (184)
T 2zej_A          132 ACMSKITKELLNKRGFPAIRDYHFVNATEESDALAKLRKTIINE  175 (184)
T ss_dssp             HHHHHHHHHTTTCTTSCEEEEEEECCTTSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCcchhheEEEecccCchhHHHHHHHHHHH
Confidence            1 111112221  1234    8999999996 999999987653

>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=97.84  E-value=4.5e-05  Score=59.20  Aligned_cols=82  Identities=7%  Similarity=-0.029  Sum_probs=53.1

Q ss_pred             ccceEEEEEeCCCCCCCCcC---------C-CCC-C-CceeEEEEecC-CCCCchhHhHHHHHHHHH--hcCCCCCEEEE
Q 030407           94 LADYIIYIIDVSGGDKIPRK---------G-GPG-I-TQADLLVINKT-DLASAIGADLAVMERDAL--RMRDGGPFIFA  158 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~---------~-~~q-i-~~adiiviNK~-Dl~~~~~~~~~~~~~~l~--~~np~a~i~~~  158 (178)
                      ..|++|+|||+++......+         . .+. + ..+-+|+.||. |+..+  -...++.+.+.  .+.....|..+
T Consensus       125 ~TdglIfVVDSsD~~R~eak~EL~eL~~mL~ee~~L~gapLLVlANKqqDlp~A--ms~~EI~e~L~L~~l~R~W~Iq~c  202 (227)
T 3l82_B          125 VVDGFIYVANAEAHKRHEWQDEFSHIMAMTDPAFGSSGRPLLVLSCISQGDVKR--MPCFYLAHELHLNLLNHPWLVQDT  202 (227)
T ss_dssp             HCSEEEEEEECBTTCCCCHHHHHHHHHHHSCTTSSCSCSCEEEEEEESSTTSCB--CCHHHHHHHTTGGGGCSCEEEEEE
T ss_pred             CCCEEEEEeccccHhHHHHHHHHHHHHHHhcchhhhCCCeEEEEeCCCcCccCC--CCHHHHHHHcCCcCCCCCEEEEEe
Confidence            47999999999865322110         0 111 2 23567777996 78655  33344444432  23334589999


Q ss_pred             ecccCCCHHHHHHHHhhhh
Q 030407          159 QVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       159 SA~~g~gi~el~~~l~~~~  177 (178)
                      ||++|+|+.|-++||.+.+
T Consensus       203 sA~TGeGL~EGLdWL~~~l  221 (227)
T 3l82_B          203 EAETLTGFLNGIEWILEEV  221 (227)
T ss_dssp             ETTTCTTHHHHHHHHTTTT
T ss_pred             ECCCCcCHHHHHHHHHHHH
Confidence            9999999999999997654

>1f60_A Elongation factor EEF1A; protein-protein complex, translation; 1.67A {Saccharomyces cerevisiae} SCOP: b.43.3.1 b.44.1.1 c.37.1.8 PDB: 1g7c_A* 1ije_A* 1ijf_A* 2b7b_A* 2b7c_A

Probab=97.83  E-value=2.2e-06  Score=73.38  Aligned_cols=96  Identities=15%  Similarity=0.035  Sum_probs=56.9

Q ss_pred             CCCEEEEeCCcch-hhh-c-ccccccceEEEEEeCCCCCCC-------Cc-CC---CCCCCce-eEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDN-LAA-N-FSRELADYIIYIIDVSGGDKI-------PR-KG---GPGITQA-DLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~-~-~~~~~ad~~I~VvD~~~~~~~-------~~-~~---~~qi~~a-diiviNK~Dl~~~~~~  137 (178)
                      +..+.|++|.|-. ... . .....+|.+++|+|++++...       +. .+   ......+ -++++||+|+.+...+
T Consensus        84 ~~~~~iiDtPGh~~f~~~~~~~~~~aD~~ilVvda~~g~~~~sf~~~~qt~~~~~~~~~~~v~~iivviNK~Dl~~~~~~  163 (458)
T 1f60_A           84 KYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDES  163 (458)
T ss_dssp             SEEEEEEECCCCTTHHHHHHHSSSCCSEEEEEEECSHHHHHHHTCTTSHHHHHHHHHHHTTCCEEEEEEECGGGGTTCHH
T ss_pred             CceEEEEECCCcHHHHHHHHhhhhhCCEEEEEEeCCcCccccccCcchhHHHHHHHHHHcCCCeEEEEEEccccccCCHH
Confidence            4679999999931 000 0 112347999999999865210       10 00   0112333 5788999999842113


Q ss_pred             hHH----HHHHHHHhcCC---CCCEEEEecccCCCHHH
Q 030407          138 DLA----VMERDALRMRD---GGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       138 ~~~----~~~~~l~~~np---~a~i~~~SA~~g~gi~e  168 (178)
                      ..+    ++.+.++...-   ..+++++||++|+|+.+
T Consensus       164 ~~~~i~~~~~~~l~~~g~~~~~~~~i~vSA~~g~nv~~  201 (458)
T 1f60_A          164 RFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIE  201 (458)
T ss_dssp             HHHHHHHHHHHHHHHHTCCGGGCCEEECCTTTCBTTTB
T ss_pred             HHHHHHHHHHHHHHHcCCCccCceEEEeecccCcCccc
Confidence            333    33444444331   37999999999999863

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=97.83  E-value=6.6e-07  Score=66.26  Aligned_cols=101  Identities=16%  Similarity=0.124  Sum_probs=61.7

Q ss_pred             CCCEEEEeCCcch----------hhhcccc-cccceEEEEEeCCCCCCCCcCC--CCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----------LAANFSR-ELADYIIYIIDVSGGDKIPRKG--GPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----------~~~~~~~-~~ad~~I~VvD~~~~~~~~~~~--~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.+++|.|..          +...+.. ..++.++.|+|++.........  ......+.++|+||+|+.+.  ...
T Consensus        53 ~~~~~l~Dt~G~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~--~~~  130 (188)
T 2wjg_A           53 GEKFKVVDLPGVYSLTANSIDEIIARDYIINEKPDLVVNIVDATALERNLYLTLQLMEMGANLLLALNKMDLAKS--LGI  130 (188)
T ss_dssp             TEEEEEEECCCCSCCSSSSHHHHHHHHHHHHHCCSEEEEEEEGGGHHHHHHHHHHHHTTTCCEEEEEECHHHHHH--TTC
T ss_pred             CcEEEEEECCCcCccccccHHHHHHHHHHhccCCCEEEEEecchhHHHHHHHHHHHHhcCCCEEEEEEhhhcccc--ccc
Confidence            4678899999941          1111211 1368999999987532111000  00123467999999998643  111


Q ss_pred             -HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 -AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 -~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                       +...+..+..+  .+++++||++|+|++++++++.+.+
T Consensus       131 ~~~~~~~~~~~~--~~~~~~Sa~~~~~v~~l~~~i~~~~  167 (188)
T 2wjg_A          131 EIDVDKLEKILG--VKVVPLSAAKKMGIEELKKAISIAV  167 (188)
T ss_dssp             CCCHHHHHHHHT--SCEEECBGGGTBSHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHhC--CCeEEEEecCCCCHHHHHHHHHHHH
Confidence             12222333332  5899999999999999999887653

>2qpt_A EH domain-containing protein-2; protein-nucleotide complex, membrane protein, endocytosis; HET: ANP; 3.10A {Mus musculus}

Probab=97.82  E-value=1.1e-05  Score=70.56  Aligned_cols=112  Identities=15%  Similarity=0.179  Sum_probs=61.1

Q ss_pred             EEEEEecCC-CchhHHHHHHcCCCCccceeec-------ccCC-CcccccccccccCHhHHHhhHhhCCCCEEEEeCCcc
Q 030407           14 LAAVTNDIF-TKEDGEFLMRNGALPEERIRAV-------ETGG-CPHAAIREDISINLGPLEELSNLFKADLLLCESGGD   84 (178)
Q Consensus        14 vaVI~nd~g-~~iD~~li~~~~~~~~~~~~~l-------~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~~~~d~iiiEttG~   84 (178)
                      .+++.|+++ +..|..++.....    .+.++       .+|| ||++  ++++          .    ..++||+|.|.
T Consensus       105 ~~i~~~~~~~i~~g~~l~~~~~~----~~~~L~~~g~~~~~~~~~~~~--~~~l----------l----~~l~lIDTPG~  164 (550)
T 2qpt_A          105 VAVMHGETEGTVPGNALVVDPEK----PFRKLNPFGNTFLNRFMCAQL--PNQV----------L----ESISIIDTPGI  164 (550)
T ss_dssp             EEEECCSSSEEECCC----------------------CCCTTEEEEEC--CCHH----------H----HHCEEEECCCB
T ss_pred             EEEEECCcccccCCceeeecCcc----cHHHHhhhcccccccceEEec--cccc----------c----CCEEEEECcCC
Confidence            577778877 6666655432211    23333       3789 8875  2211          1    14689999995


Q ss_pred             hhh------hc--c------cccccceEEEEEeCCCCCCCC--c---CCCCCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           85 NLA------AN--F------SRELADYIIYIIDVSGGDKIP--R---KGGPGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        85 ~~~------~~--~------~~~~ad~~I~VvD~~~~~~~~--~---~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      .-.      ..  +      ....+|.+++|+|+++.....  .   ....+...+.++|+||+|+.++  .++..+.+.
T Consensus       165 ~~~~~~~~~~~~~f~~~~~~~l~~aD~il~VvDa~~~~~~~~~~~~l~~l~~~~~pvilVlNK~Dl~~~--~el~~~~~~  242 (550)
T 2qpt_A          165 LSGAKQRVSRGYDFPAVLRWFAERVDLIILLFDAHKLEISDEFSEAIGALRGHEDKIRVVLNKADMVET--QQLMRVYGA  242 (550)
T ss_dssp             CC-------CCSCHHHHHHHHHHHCSEEEEEEETTSCCCCHHHHHHHHHTTTCGGGEEEEEECGGGSCH--HHHHHHHHH
T ss_pred             CCcchhHHHHHhhHHHHHHHHHHhCCEEEEEEeCCcCCCCHHHHHHHHHHHhcCCCEEEEEECCCccCH--HHHHHHHHH
Confidence            210      00  1      012369999999997632111  0   1112344578999999999987  666666655


Q ss_pred             HH
Q 030407          146 AL  147 (178)
Q Consensus       146 l~  147 (178)
                      ++
T Consensus       243 l~  244 (550)
T 2qpt_A          243 LM  244 (550)
T ss_dssp             HH
T ss_pred             hh
Confidence            53

>3t5d_A Septin-7; GTP-binding protein, cytoskeleton, signaling protein; HET: GDP; 3.30A {Homo sapiens} PDB: 3tw4_A*

Probab=97.81  E-value=1.5e-05  Score=63.28  Aligned_cols=78  Identities=12%  Similarity=-0.023  Sum_probs=41.4

Q ss_pred             cceEEEEEeCCC-CCCCCc-----CCCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhc--CCCCCEEEEecccCCCH
Q 030407           95 ADYIIYIIDVSG-GDKIPR-----KGGPGITQADLLVINKTDLASAIGADLAVMERDALRM--RDGGPFIFAQVGWVIGI  166 (178)
Q Consensus        95 ad~~I~VvD~~~-~~~~~~-----~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~--np~a~i~~~SA~~g~gi  166 (178)
                      +|.++++++++. +.....     ....  ..+-++|+||+|+.++  .+.+...+.+++.  ....+++.+||++|+|+
T Consensus       116 ~~~~l~~i~~~~~~~~~~d~~~l~~l~~--~~pvi~V~nK~D~~~~--~e~~~~~~~i~~~l~~~~i~v~~~sa~~~~~~  191 (274)
T 3t5d_A          116 VQCCLYFIAPSGHGLKPLDIEFMKRLHE--KVNIIPLIAKADTLTP--EECQQFKKQIMKEIQEHKIKIYEFPETDDEEE  191 (274)
T ss_dssp             CCEEEEEECSCCSSCCHHHHHHHHHHTT--TSCEEEEESSGGGSCH--HHHHHHHHHHHHHHHHTTCCCCCC--------
T ss_pred             eeEEEEEecCCCCCCCHHHHHHHHHHhc--cCCEEEEEeccCCCCH--HHHHHHHHHHHHHHHHcCCeEEcCCCCCChhH
Confidence            468888887654 221111     0111  4567999999999877  5665544433322  23468999999999999


Q ss_pred             HHHHHHHhhh
Q 030407          167 IFTLSITHYI  176 (178)
Q Consensus       167 ~el~~~l~~~  176 (178)
                      +++++.|...
T Consensus       192 ~~l~~~l~~~  201 (274)
T 3t5d_A          192 NKLVKKIKDR  201 (274)
T ss_dssp             ---CHHHHHT
T ss_pred             HHHHHHHhcC
Confidence            9999988653

>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=97.81  E-value=1.1e-05  Score=60.05  Aligned_cols=101  Identities=13%  Similarity=-0.018  Sum_probs=64.0

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc--CCCC----C-----CCceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR--KGGP----G-----ITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~--~~~~----q-----i~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+.+.|++|.|..--   ..+. ..+|.+++|+|+++......  .+..    .     -..+-++|+||+|+.+.....
T Consensus        68 ~~~l~i~Dt~G~~~~~~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~v~  146 (187)
T 3c5c_A           68 PVHLRVMDTADLDTPRNCERYL-NWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNKLDMAQYRQVT  146 (187)
T ss_dssp             EEEEEEEECCC---CCCTHHHH-TTCSEEEEEEETTCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECGGGGGGCSSC
T ss_pred             EEEEEEEECCCCCcchhHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhhccCCCCCEEEEEECcchhhcCccC
Confidence            466788999993210   1111 24799999999986432211  0000    0     134569999999996531122


Q ss_pred             HHHHHHHHHhcCCCCCEEEEec-ccCCCHHHHHHHHhhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQV-GWVIGIIFTLSITHYI  176 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA-~~g~gi~el~~~l~~~  176 (178)
                      .+...+..++.+  .+++++|| ++|+|++++|+.+.+.
T Consensus       147 ~~~~~~~~~~~~--~~~~e~Sa~~~g~gv~~lf~~l~~~  183 (187)
T 3c5c_A          147 KAEGVALAGRFG--CLFFEVSACLDFEHVQHVFHEAVRE  183 (187)
T ss_dssp             HHHHHHHHHHHT--CEEEECCSSSCSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcC--CcEEEEeecCccccHHHHHHHHHHH
Confidence            344555555553  58999999 8999999999988654

>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=97.76  E-value=8.8e-06  Score=65.46  Aligned_cols=104  Identities=13%  Similarity=-0.011  Sum_probs=58.0

Q ss_pred             CCCEEEEeCCcchhhh----------cc------cccccceEEEEEeCCC-CCCCCc--C---CCCCCCceeEEEEecCC
Q 030407           73 KADLLLCESGGDNLAA----------NF------SRELADYIIYIIDVSG-GDKIPR--K---GGPGITQADLLVINKTD  130 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~----------~~------~~~~ad~~I~VvD~~~-~~~~~~--~---~~~qi~~adiiviNK~D  130 (178)
                      .++++|++|.|..-.+          .+      ....+|.+++|+|+.. +.....  .   .......+.++|+||+|
T Consensus       130 ~~~~~lvDTpG~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~iilvvd~~~~~~~~~~~~~i~~~~~~~~~~~i~v~NK~D  209 (315)
T 1jwy_B          130 VVNLTLVDLPGITKVPVGDQPTDIEQQIRRMVMAYIKKQNAIIVAVTPANTDLANSDALQLAKEVDPEGKRTIGVITKLD  209 (315)
T ss_dssp             SCSEEEEECCCCC---------CSHHHHHHHHHHHHHSTTEEEEEEEESSSCSTTCSHHHHHHHHCSSCSSEEEEEECTT
T ss_pred             CCCcEEEECCCCccCCCCCCchhHHHHHHHHHHHHHcCCCeEEEEEEecCcchhhhHHHHHHHHhCCCCCcEEEEEcCcc
Confidence            4789999999942100          01      1124689999999743 221111  0   11123456799999999


Q ss_pred             CCCchhHhHHHHHHHHHhc-CCCCCEEEEeccc---CCCHHHHHHHHhhh
Q 030407          131 LASAIGADLAVMERDALRM-RDGGPFIFAQVGW---VIGIIFTLSITHYI  176 (178)
Q Consensus       131 l~~~~~~~~~~~~~~l~~~-np~a~i~~~SA~~---g~gi~el~~~l~~~  176 (178)
                      +.++.....+.+...+... .+..++..+||++   |.|++++++.+.++
T Consensus       210 l~~~~~~~~~~~~~~~~~~~~~~~~v~~~sa~~~~~~~gv~~l~~~~~~~  259 (315)
T 1jwy_B          210 LMDKGTDAMEVLTGRVIPLTLGFIGVINRSQEDIIAKKSIRESLKSEILY  259 (315)
T ss_dssp             SSCSSCCCHHHHTTSSSCCTTCEEECCCCCHHHHSSSCCHHHHHHHHHHH
T ss_pred             cCCcchHHHHHHhCCCccCCCCeEEEecCChhhhccCCCHHHHHHHHHHH
Confidence            9876211122222111111 1223555567777   89999999887654

>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=97.73  E-value=2.9e-06  Score=70.09  Aligned_cols=99  Identities=12%  Similarity=-0.069  Sum_probs=58.0

Q ss_pred             CCCEEEEeCCcchh-----------------hhcccccccceEEEEEeCCCCCCCCcC--CCC---CCCceeEEEEecCC
Q 030407           73 KADLLLCESGGDNL-----------------AANFSRELADYIIYIIDVSGGDKIPRK--GGP---GITQADLLVINKTD  130 (178)
Q Consensus        73 ~~d~iiiEttG~~~-----------------~~~~~~~~ad~~I~VvD~~~~~~~~~~--~~~---qi~~adiiviNK~D  130 (178)
                      .+++.||+|.|..-                 ...|.....+.+++|+|+.........  ...   ....+-++|+||+|
T Consensus       129 ~~~l~lvDTPG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiL~v~~a~~~~~~~~~~~i~~~~~~~~~~~i~V~NK~D  208 (353)
T 2x2e_A          129 VLNLTLVDLPGMTKVPVGDQPPDIEFQIRDMLMQFVTKENCLILAVSPANSDLANSDALKVAKEVDPQGQRTIGVITKLD  208 (353)
T ss_dssp             CCSEEEEECCCBCSSCCTTCCTTHHHHHHHHHHHHHTSTTEEEEEEEETTSCGGGCHHHHHHHHHCTTCTTEEEEEECGG
T ss_pred             CCCcEEEECCCCCCCccCCCchhHHHHHHHHHHHHHcCCCeEEEEEecCCCccchhHHHHHHHHhCcCCCceEEEecccc
Confidence            47899999999521                 011122223566777887653222110  100   11335699999999


Q ss_pred             CCCchhHhHHHHHHHHHh-cCC----CCCEEEEecccCCCHHHHHHHHhh
Q 030407          131 LASAIGADLAVMERDALR-MRD----GGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       131 l~~~~~~~~~~~~~~l~~-~np----~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +.++  ...  ....++. ..+    ..+++.+||++|+|++++++.+.+
T Consensus       209 l~~~--~~~--~~~~~~~~~~~l~~~~~~v~~~SA~~~~~i~~l~~~l~~  254 (353)
T 2x2e_A          209 LMDE--GTD--ARDVLENKLLPLRRGYIGVVNRSQKDIDGKKDITAALAA  254 (353)
T ss_dssp             GSCT--TCC--CHHHHTTCSSCCTTCEEECCCCCHHHHHTTCCHHHHHHH
T ss_pred             ccCc--chh--HHHHHhCCcccccCCceEEEeCCcccccccccHHHHHHH
Confidence            9865  220  1112221 112    347889999999999999988754

>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=97.72  E-value=5.7e-06  Score=67.53  Aligned_cols=75  Identities=11%  Similarity=0.036  Sum_probs=51.8

Q ss_pred             cceEEEEEeCCCCCCCCcCCCC------CCCceeEEEEecCCCCCchhHh----HHHHHHHHHhcCCCCCEEEEecccCC
Q 030407           95 ADYIIYIIDVSGGDKIPRKGGP------GITQADLLVINKTDLASAIGAD----LAVMERDALRMRDGGPFIFAQVGWVI  164 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~~~~~------qi~~adiiviNK~Dl~~~~~~~----~~~~~~~l~~~np~a~i~~~SA~~g~  164 (178)
                      +|.++.|+|+..+.........      .-...-+||+||+||.++  .+    ++.+.+..+..  +.+++.+||++|.
T Consensus        87 vD~v~~V~~~~~p~~~~~~i~r~L~~~~~~~~~~vivlnK~DL~~~--~~~~~~~~~~~~~y~~~--g~~v~~~sa~~~~  162 (307)
T 1t9h_A           87 VDQAVLVFSAVQPSFSTALLDRFLVLVEANDIQPIICITKMDLIED--QDTEDTIQAYAEDYRNI--GYDVYLTSSKDQD  162 (307)
T ss_dssp             CCEEEEEEESTTTTCCHHHHHHHHHHHHTTTCEEEEEEECGGGCCC--HHHHHHHHHHHHHHHHH--TCCEEECCHHHHT
T ss_pred             CCEEEEEEeCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCccCch--hhhHHHHHHHHHHHHhC--CCeEEEEecCCCC
Confidence            5999999999866533221111      123356999999999987  44    34455555443  4589999999999


Q ss_pred             CHHHHHHHH
Q 030407          165 GIIFTLSIT  173 (178)
Q Consensus       165 gi~el~~~l  173 (178)
                      |+++|++..
T Consensus       163 g~~~L~~~~  171 (307)
T 1t9h_A          163 SLADIIPHF  171 (307)
T ss_dssp             TCTTTGGGG
T ss_pred             CHHHHHhhc
Confidence            999887654

>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=97.72  E-value=2.9e-05  Score=58.38  Aligned_cols=82  Identities=10%  Similarity=-0.043  Sum_probs=54.9

Q ss_pred             ccceEEEEEeCCCCCCCCc-C---CCCCCCceeEEEEecCCCCCchhHhH----HHHHHHHHhcCCCCCEEEEecccCCC
Q 030407           94 LADYIIYIIDVSGGDKIPR-K---GGPGITQADLLVINKTDLASAIGADL----AVMERDALRMRDGGPFIFAQVGWVIG  165 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~-~---~~~qi~~adiiviNK~Dl~~~~~~~~----~~~~~~l~~~np~a~i~~~SA~~g~g  165 (178)
                      ..+.+++++|+..+..... .   +......+.+++.||+|+.+.  .+.    +.+.+.+++......++++||+++.|
T Consensus       108 ~~~~~~~v~d~~~~~~~~~~~~~~~~~~~~~~~~~v~nK~D~~s~--~~~~~~~~~~~~~~~~~~~~~~~~~~Sal~~~~  185 (210)
T 1pui_A          108 SLQGLVVLMDIRHPLKDLDQQMIEWAVDSNIAVLVLLTKADKLAS--GARKAQLNMVREAVLAFNGDVQVETFSSLKKQG  185 (210)
T ss_dssp             TEEEEEEEEETTSCCCHHHHHHHHHHHHTTCCEEEEEECGGGSCH--HHHHHHHHHHHHHHGGGCSCEEEEECBTTTTBS
T ss_pred             cccEEEEEEECCCCCchhHHHHHHHHHHcCCCeEEEEecccCCCc--hhHHHHHHHHHHHHHhcCCCCceEEEeecCCCC
Confidence            4578899999977543211 0   111123456888999999876  432    33444454433346789999999999


Q ss_pred             HHHHHHHHhhhh
Q 030407          166 IIFTLSITHYIV  177 (178)
Q Consensus       166 i~el~~~l~~~~  177 (178)
                      ++++++.|.+..
T Consensus       186 ~~~l~~~l~~~~  197 (210)
T 1pui_A          186 VDKLRQKLDTWF  197 (210)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999987653

>1dar_A EF-G, elongation factor G; ribosomal translocase, translational GTPase; HET: GDP; 2.40A {Thermus thermophilus} SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 PDB: 1elo_A 1ktv_A 2om7_L* 2wri_Y* 2wrk_Y* 2xsy_Y* 2xuy_Y* 2j7k_A* 2efg_A* 1jqm_B 1efg_A* 1fnm_A* 1pn6_A 2bm1_A* 2bm0_A* 2bv3_A* 3izp_E 1zn0_B 1jqs_C 2bcw_C ...

Probab=97.70  E-value=3.6e-05  Score=69.12  Aligned_cols=62  Identities=18%  Similarity=0.199  Sum_probs=39.9

Q ss_pred             CCCEEEEeCCcch-hhhcc--cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-LAANF--SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~~--~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      ++.+.||+|.|.. .....  ....+|.+++|+|++.+......    .......+.++++||+|+...
T Consensus        76 ~~~i~liDTPG~~df~~~~~~~l~~aD~~ilVvDa~~g~~~~t~~~~~~~~~~~~p~ivviNKiD~~~~  144 (691)
T 1dar_A           76 DHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGA  144 (691)
T ss_dssp             TEEEEEECCCSSTTCHHHHHHHHHHCSEEEEEEETTTCSCHHHHHHHHHHHHTTCCEEEEEECTTSTTC
T ss_pred             CeEEEEEECcCccchHHHHHHHHHHCCEEEEEEECCCCcchhhHHHHHHHHHcCCCEEEEEECCCcccC
Confidence            5789999999931 11110  11246999999999887543211    111234567999999999765

>3r7w_A Gtpase1, GTP-binding protein GTR1; RAG gtpases, GTR1P, GTR2P, MTOR, protein transport; HET: GNP; 2.77A {Saccharomyces cerevisiae} PDB: 4arz_A*

Probab=97.67  E-value=2.9e-05  Score=62.90  Aligned_cols=99  Identities=12%  Similarity=0.099  Sum_probs=62.1

Q ss_pred             CCCEEEEeCCcch-hhhcc-------cccccceEEEEEeCCCCCCCCc--CCC---CC-----CCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-LAANF-------SRELADYIIYIIDVSGGDKIPR--KGG---PG-----ITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~~-------~~~~ad~~I~VvD~~~~~~~~~--~~~---~q-----i~~adiiviNK~Dl~~~  134 (178)
                      +..+.+++|.|.. ....+       ....+|++++|+|+++......  .+.   ..     -..+-++|+||+|+.++
T Consensus        51 ~~~l~i~Dt~G~~~~~~~~~~~~~~~~~~~ad~vi~V~D~t~~~s~~~l~~~~~~l~~l~~~~~~~piilv~NK~Dl~~~  130 (307)
T 3r7w_A           51 NMTLNLWDCGGQDVFMENYFTKQKDHIFQMVQVLIHVFDVESTEVLKDIEIFAKALKQLRKYSPDAKIFVLLHKMDLVQL  130 (307)
T ss_dssp             TEEEEEEEECCSHHHHHHHHTTTHHHHHTTCSEEEEEEETTCSCHHHHHHHHHHHHHHHHHHCTTCEEEEEEECGGGSCH
T ss_pred             ceEEEEEECCCcHHHhhhhhhhHHHHHhccCCEEEEEEECCChhhHHHHHHHHHHHHHHHHhCCCCeEEEEEecccccch
Confidence            5778999999942 10100       1124799999999987642211  000   00     13567999999999874


Q ss_pred             hhHhH--------HHHHHHHHhcC-CCCCEEEEecccCCCHHHHHHHHh
Q 030407          135 IGADL--------AVMERDALRMR-DGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       135 ~~~~~--------~~~~~~l~~~n-p~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                        ...        +.+.+..+..+ |..+++++||++ .|+.+.|..+.
T Consensus       131 --~~r~~~~~v~~~~~~~~~~~~g~~~~~~~~tSa~~-~~i~e~~~~iv  176 (307)
T 3r7w_A          131 --DKREELFQIMMKNLSETSSEFGFPNLIGFPTSIWD-ESLYKAWSQIV  176 (307)
T ss_dssp             --HHHHHHHHHHHHHHHHHHHTTTCCSCEEEECCTTS-SHHHHHHHHHH
T ss_pred             --hhhhHHHHHHHHHHHHHHHHcCCCCeEEEEeeecC-ChHHHHHHHHH
Confidence              222        33444444432 247999999999 78888876543

>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=97.66  E-value=7.3e-06  Score=74.31  Aligned_cols=99  Identities=13%  Similarity=-0.031  Sum_probs=63.2

Q ss_pred             CCCEEEEeCCcchhhh-----------------cccccccceEEEEEeCCCCCCCCcC--CC---CCCCceeEEEEecCC
Q 030407           73 KADLLLCESGGDNLAA-----------------NFSRELADYIIYIIDVSGGDKIPRK--GG---PGITQADLLVINKTD  130 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~-----------------~~~~~~ad~~I~VvD~~~~~~~~~~--~~---~qi~~adiiviNK~D  130 (178)
                      .++++||.|.|..-..                 .|....+|.+++|+|++.+....+.  ..   .....+-++|+||+|
T Consensus       149 ~~qL~LVDTPGi~~~~~~~qp~di~~~i~~lv~~yi~~~aDlIL~VVDAs~~~~~~d~l~ll~~L~~~g~pvIlVlNKiD  228 (772)
T 3zvr_A          149 VLNLTLVDLPGMTKVPVGDQPPDIEFQIRDMLMQFVTKENCLILAVSPANSDLANSDALKIAKEVDPQGQRTIGVITKLD  228 (772)
T ss_dssp             CCSEEEEECCCCCCCCSSCCCCHHHHHHHHHHHHHHTSTTEEEEEEEETTSCSSSCHHHHHHHHHCTTCSSEEEEEECTT
T ss_pred             CCceEEEECCCcccCCCCCCcHHHHHHHHHHHHHHHhcCCcEEEEEEcCCCCcchhHHHHHHHHHHhcCCCEEEEEeCcc
Confidence            4679999999942110                 1111246899999999875433221  11   112356799999999


Q ss_pred             CCCchhHhH-HHHHHHHHhc----CCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          131 LASAIGADL-AVMERDALRM----RDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       131 l~~~~~~~~-~~~~~~l~~~----np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ++++  ... ..+.+  .+.    .++.+++++||++|.|+++|++.+.+
T Consensus       229 lv~~--~~~~~~il~--~~~~~l~lg~~~VV~iSA~~G~GvdeL~eaI~~  274 (772)
T 3zvr_A          229 LMDE--GTDARDVLE--NKLLPLRRGYIGVVNRSQKDIDGKKDITAALAA  274 (772)
T ss_dssp             SSCT--TCCSHHHHT--TCSSCCSSCEEECCCCCCEESSSSEEHHHHHHH
T ss_pred             cCCc--chhhHHHHH--HHhhhhhccCCceEEecccccccchhHHHHHHH
Confidence            9876  221 11111  111    13467899999999999999988764

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=97.65  E-value=4.8e-05  Score=64.96  Aligned_cols=146  Identities=12%  Similarity=0.128  Sum_probs=79.3

Q ss_pred             HHHHHHhhcC-CcEEEEEecCC-CchhHHHHH---HcCCCCccceeecccCCCcccccccccccCH-hHHHhhHhhCCCC
Q 030407            2 LALCKFLRDK-YSLAAVTNDIF-TKEDGEFLM---RNGALPEERIRAVETGGCPHAAIREDISINL-GPLEELSNLFKAD   75 (178)
Q Consensus         2 ~~~~~~~~~~-~~vaVI~nd~g-~~iD~~li~---~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l-~~l~~l~~~~~~d   75 (178)
                      .+++.++.++ +|++++..|.. .+--.++-.   ..|+    ++.....+.        |....+ .++..+ ...++|
T Consensus       118 ~kLA~~l~~~G~kVllv~~D~~R~aa~eqL~~~~~~~gv----pv~~~~~~~--------dp~~i~~~al~~a-~~~~~D  184 (443)
T 3dm5_A          118 AKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHI----EVFGNPQEK--------DAIKLAKEGVDYF-KSKGVD  184 (443)
T ss_dssp             HHHHHHHHTTTCCEEEEECCCSSTHHHHHHHHHHGGGTC----EEECCTTCC--------CHHHHHHHHHHHH-HHTTCS
T ss_pred             HHHHHHHHHCCCeEEEEeCCCcchhHHHHHHHHHHhcCC----cEEecCCCC--------CHHHHHHHHHHHH-HhCCCC
Confidence            3566777664 99999999988 533222211   1232    233222221        111112 333333 356799


Q ss_pred             EEEEeCCcchhh---------hcccccccceEEEEEeCCCCCCCCcC---CCCCCCceeEEEEecCCCCCchhHhHHHHH
Q 030407           76 LLLCESGGDNLA---------ANFSRELADYIIYIIDVSGGDKIPRK---GGPGITQADLLVINKTDLASAIGADLAVME  143 (178)
Q Consensus        76 ~iiiEttG~~~~---------~~~~~~~ad~~I~VvD~~~~~~~~~~---~~~qi~~adiiviNK~Dl~~~~~~~~~~~~  143 (178)
                      +|||+|.|....         ........|.+++|+|+..+.+....   +.+.+ ..+.+|+||+|....  .  ..+.
T Consensus       185 vVIIDTaGrl~~d~~lm~el~~i~~~~~pd~vlLVvDA~~gq~a~~~a~~f~~~~-~i~gVIlTKlD~~~~--g--G~~l  259 (443)
T 3dm5_A          185 IIIVDTAGRHKEDKALIEEMKQISNVIHPHEVILVIDGTIGQQAYNQALAFKEAT-PIGSIIVTKLDGSAK--G--GGAL  259 (443)
T ss_dssp             EEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHHHHHHHHHHSC-TTEEEEEECCSSCSS--H--HHHH
T ss_pred             EEEEECCCcccchHHHHHHHHHHHHhhcCceEEEEEeCCCchhHHHHHHHHHhhC-CCeEEEEECCCCccc--c--cHHH
Confidence            999999994110         00111124889999999875432110   11111 235799999999765  2  1223


Q ss_pred             HHHHhcCCCCCEEEEecccCCCHHHH
Q 030407          144 RDALRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       144 ~~l~~~np~a~i~~~SA~~g~gi~el  169 (178)
                      .....  .+.|+.+++.  |+++++|
T Consensus       260 s~~~~--~g~PI~fig~--Ge~vddL  281 (443)
T 3dm5_A          260 SAVAA--TGAPIKFIGT--GEKIDDI  281 (443)
T ss_dssp             HHHHT--TCCCEEEEEC--SSSTTCE
T ss_pred             HHHHH--HCCCEEEEEc--CCChHHh
Confidence            33332  3568888884  8888654

>2h5e_A Peptide chain release factor RF-3; beta barrel, translation; HET: GDP; 2.80A {Escherichia coli} PDB: 2o0f_A 3sfs_W* 3zvo_Y* 3uoq_W*

Probab=97.64  E-value=0.00014  Score=63.33  Aligned_cols=61  Identities=16%  Similarity=0.108  Sum_probs=39.6

Q ss_pred             CCCEEEEeCCcch-h---hhcccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-L---AANFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-~---~~~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      +..+.|++|.|.. .   ...+ ...+|++|+|+|++.+...+..    .......+-++++||+|+.+.
T Consensus        81 ~~~i~liDTPG~~df~~~~~~~-l~~aD~~IlVvDa~~g~~~~t~~~~~~~~~~~ipiivviNK~Dl~~~  149 (529)
T 2h5e_A           81 DCLVNLLDTPGHEDFSEDTYRT-LTAVDCCLMVIDAAKGVEDRTRKLMEVTRLRDTPILTFMNKLDRDIR  149 (529)
T ss_dssp             TEEEEEECCCCSTTCCHHHHHG-GGGCSEEEEEEETTTCSCHHHHHHHHHHTTTTCCEEEEEECTTSCCS
T ss_pred             CeEEEEEECCCChhHHHHHHHH-HHHCCEEEEEEeCCccchHHHHHHHHHHHHcCCCEEEEEcCcCCccc
Confidence            5789999999931 0   1111 1247999999999887532211    111234457999999999865

>2rdo_7 EF-G, elongation factor G; elongation factor G, EF-G, RRF, GDPNP, 50S subunit, cryo-EM, REAL-space refinement, ribonucleoprotein; 9.10A {Escherichia coli} PDB: 3j0e_H

Probab=97.62  E-value=0.00011  Score=66.19  Aligned_cols=62  Identities=15%  Similarity=0.184  Sum_probs=39.3

Q ss_pred             CCCEEEEeCCcch-hhhcc--cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-LAANF--SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~~--~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      .+++.||+|.|-. .....  ....+|++|+|+|++.+...+..    .......+-++++||+|+...
T Consensus        81 ~~~i~liDTPG~~df~~~~~~~l~~aD~aIlVvDa~~gv~~qt~~~~~~~~~~~ip~ilviNKiD~~~~  149 (704)
T 2rdo_7           81 PHRINIIDTPGHVDFTIEVERSMRVLDGAVMVYCAVGGVQPQSETVWRQANKYKVPRIAFVNKMDRMGA  149 (704)
T ss_pred             ceeEEEEeCCCccchHHHHHHHHHHCCEEEEEEeCCCCCcHHHHHHHHHHHHcCCCEEEEEeCCCcccc
Confidence            4889999999931 11110  11246999999999887543211    111124467999999999764

>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=97.62  E-value=2.6e-05  Score=64.77  Aligned_cols=103  Identities=14%  Similarity=0.077  Sum_probs=62.5

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCC----------Cc---------CCCCCCCceeEEEEecC
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKI----------PR---------KGGPGITQADLLVINKT  129 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~----------~~---------~~~~qi~~adiiviNK~  129 (178)
                      +..+-++.+.|..    +...+. ..++++|+|+|.++.+..          ..         .....-..+-++++||+
T Consensus       192 ~~~l~iwDt~GQe~~r~~w~~yf-~~a~~iIfV~dls~~d~~l~ed~~~nr~~e~~~~~~~i~~~~~~~~~piiLv~NK~  270 (353)
T 1cip_A          192 DLHFKMFDVGGQRSERKKWIHCF-EGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKK  270 (353)
T ss_dssp             TEEEEEEEECCSGGGGGGGGGGC-TTCSEEEEEEEGGGGGCEETTEEEEEHHHHHHHHHHHHHTCGGGTTSEEEEEEECH
T ss_pred             CeeEEEEeCCCchhhhHHHHHHH-hcCCEEEEEEECccccccccccchhhhHHHHHHHHHHHHcCccccCCcEEEEEECc
Confidence            3456678888831    112222 357999999999874321          00         00001235679999999


Q ss_pred             CCCCch---------------hHhHHHHHHHHH----hcC-----CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          130 DLASAI---------------GADLAVMERDAL----RMR-----DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       130 Dl~~~~---------------~~~~~~~~~~l~----~~n-----p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ||..+.               ....+...++++    +++     ...++++|||++|+||+++|+++...
T Consensus       271 DL~~~ki~~~~l~~~fp~~~g~~~~~e~~~~~~~~f~~l~~~~~~~~~~~~etSA~~~~nV~~vF~~v~~~  341 (353)
T 1cip_A          271 DLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDV  341 (353)
T ss_dssp             HHHHHHHTTSCGGGTCTTCCSCSCHHHHHHHHHHHHHTTCSCTTTCCEEEEECCTTCHHHHHHHHHHHHHH
T ss_pred             CchhhhccccchhhcccccCCCCCHHHHHHHHHHHHHHhhcccCCCceEEEEEECcCchhHHHHHHHHHHH
Confidence            985220               012334444444    332     24578899999999999999987653

>4dcu_A GTP-binding protein ENGA; GTPase, GDP, protein binding, hydrolase; HET: GDP; 2.00A {Bacillus subtilis} PDB: 4dct_A* 4dcs_A* 4dcv_A* 2hjg_A*

Probab=97.61  E-value=3.2e-05  Score=65.95  Aligned_cols=98  Identities=18%  Similarity=0.116  Sum_probs=56.6

Q ss_pred             CCCEEEEeCCcchh-----hh------cccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDNL-----AA------NFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~-----~~------~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~  137 (178)
                      +..+.++.|.|...     ..      ......+|.+++|+|+..+......    +......+-++|+||+|+.+.  .
T Consensus        70 ~~~~~liDT~G~~~~~~~~~~~~~~~~~~~~~~ad~il~VvD~~~~~~~~d~~l~~~l~~~~~pvilV~NK~D~~~~--~  147 (456)
T 4dcu_A           70 NYDFNLIDTGGIDIGDEPFLAQIRQQAEIAMDEADVIIFMVNGREGVTAADEEVAKILYRTKKPVVLAVNKLDNTEM--R  147 (456)
T ss_dssp             SSCCEEECCCC------CCHHHHHHHHHHHHHHCSEEEEEEESSSCSCHHHHHHHHHHTTCCSCEEEEEECC--------
T ss_pred             CceEEEEECCCCCCcchHHHHHHHHHHHhhHhhCCEEEEEEeCCCCCChHHHHHHHHHHHcCCCEEEEEECccchhh--h
Confidence            56788999999321     00      0111247999999998775432211    111234567999999998754  2


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                        +...+.. ++ ...+.+++||++|.|+.++++.+.+.
T Consensus       148 --~~~~e~~-~l-g~~~~~~iSA~~g~gv~~L~~~i~~~  182 (456)
T 4dcu_A          148 --ANIYDFY-SL-GFGEPYPISGTHGLGLGDLLDAVAEH  182 (456)
T ss_dssp             -----CCSG-GG-SSSSEEECCTTTCTTHHHHHHHHHTT
T ss_pred             --hhHHHHH-Hc-CCCceEEeecccccchHHHHHHHHhh
Confidence              1111111 12 23467899999999999999987653

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=97.54  E-value=0.00014  Score=54.18  Aligned_cols=76  Identities=17%  Similarity=0.085  Sum_probs=38.3

Q ss_pred             HHHHHHhhcC-CcEEEEEecCC-Cch------hHHHHHHcCCCCccceeecccCCCcccccc-cccccCHhHHHhhHhhC
Q 030407            2 LALCKFLRDK-YSLAAVTNDIF-TKE------DGEFLMRNGALPEERIRAVETGGCPHAAIR-EDISINLGPLEELSNLF   72 (178)
Q Consensus         2 ~~~~~~~~~~-~~vaVI~nd~g-~~i------D~~li~~~~~~~~~~~~~l~~GcCc~l~i~-~dl~~~l~~l~~l~~~~   72 (178)
                      .++++.+.++ .|+++|.+|++ ..+      |..++...|.   +.+...++||||.. .+ .++.  ...+.++....
T Consensus        22 ~~L~~~l~~~g~~v~~ik~~~~~~diD~~~g~D~~r~~~aGa---~~v~~~s~~~~~~~-~~~~~~~--~~~~~~ll~~~   95 (169)
T 1xjc_A           22 EKWVAAAVREGWRVGTVKHHGHGGEPARPEGVDSVRHERAGA---VATAVEGDGLLQLH-LRRPLWR--LDDVLALYAPL   95 (169)
T ss_dssp             HHHHHHHHHTTCCEEEEECCC--------------------C---SEEEEEETTEEEEE-ECCSCCC--HHHHHHHHGGG
T ss_pred             HHHHHhhHhcCCeeeEEEeCCCCcccccCCChhHHHHHhcCC---CeEEeccCCEEEEE-ecccccc--hHHHHHHHHhc
Confidence            4677777654 99999999988 544      4666665564   24555666663322 11 0111  12233333223


Q ss_pred             CCCEEEEeCCc
Q 030407           73 KADLLLCESGG   83 (178)
Q Consensus        73 ~~d~iiiEttG   83 (178)
                      ++|+||||++|
T Consensus        96 ~~D~vlVEg~~  106 (169)
T 1xjc_A           96 RLDLVLVEGYK  106 (169)
T ss_dssp             CCSEEEEECCT
T ss_pred             CCCEEEEeCCC
Confidence            89999999999

>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=97.52  E-value=9.3e-05  Score=61.41  Aligned_cols=103  Identities=13%  Similarity=-0.005  Sum_probs=58.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcC-------------C----C-CC-CCceeEEEEecC
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRK-------------G----G-PG-ITQADLLVINKT  129 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~-------------~----~-~q-i~~adiiviNK~  129 (178)
                      ++.+-++.|.|..    +...+. ..++++|+|+|.+..+.....             +    . .. -..+-++|+||+
T Consensus       182 ~v~l~iwDtaGQe~~r~~~~~y~-~~~~~iI~v~dis~ydq~l~e~~~~~s~~~~~~~~~~i~~~~~~~~~piiLvgNK~  260 (354)
T 2xtz_A          182 GEVYRLFDVGGQRNERRKWIHLF-EGVTAVIFCAAISEYDQTLFEDEQKNRMMETKELFDWVLKQPCFEKTSFMLFLNKF  260 (354)
T ss_dssp             --EEEEEEECCSTTGGGGTGGGC-TTEEEEEEEEEGGGTTCBCSSCTTSBHHHHHHHHHHHHHTCGGGSSCEEEEEEECH
T ss_pred             ceeeEEEECCCchhhhHHHHHHh-CCCCEEEEEEECcccccccccccchhHHHHHHHHHHHHHhccccCCCeEEEEEECc
Confidence            3556778888831    112222 357999999999743221100             0    0 00 134679999999


Q ss_pred             CCCCch---------------------hHhHHHHHHHHHh----c---C--C-----CCCEEEEecccCCCHHHHHHHHh
Q 030407          130 DLASAI---------------------GADLAVMERDALR----M---R--D-----GGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       130 Dl~~~~---------------------~~~~~~~~~~l~~----~---n--p-----~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      ||.++.                     +...++..+++++    +   |  |     ...+++|||++|+||+++|+.+.
T Consensus       261 DL~~~k~~~v~l~~~~~fp~y~~~~~~~~~~~~a~~~~~~~f~~l~~~~~~~~~~~~~~~~~eTSA~d~~nV~~vF~~v~  340 (354)
T 2xtz_A          261 DIFEKKVLDVPLNVCEWFRDYQPVSSGKQEIEHAYEFVKKKFEELYYQNTAPDRVDRVFKIYRTTALDQKLVKKTFKLVD  340 (354)
T ss_dssp             HHHHHHTTTSCGGGSGGGTTCCCCSSHHHHHHHHHHHHHHHHHHHHHHTCCTTTTTSCEEEEECCTTCHHHHHHHHHHHH
T ss_pred             chhhhhcccccccccccccccccccCCCcCHHHHHHHHHHHHHHhhhccccccccCcceEEEEEEeecchhHHHHHHHHH
Confidence            984210                     0113344444332    1   2  2     12468999999999999999876


Q ss_pred             hh
Q 030407          175 YI  176 (178)
Q Consensus       175 ~~  176 (178)
                      +.
T Consensus       341 ~~  342 (354)
T 2xtz_A          341 ET  342 (354)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

>2xex_A Elongation factor G; GTPase, translation, biosynthetic protein; 1.90A {Staphylococcus aureus}

Probab=97.47  E-value=8.4e-05  Score=66.75  Aligned_cols=62  Identities=15%  Similarity=0.214  Sum_probs=39.4

Q ss_pred             CCCEEEEeCCcch-hhhcc--cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDN-LAANF--SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~~--~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      +..+.||+|.|.. .....  ....+|.+++|+|++++......    .......+.++|+||+|+...
T Consensus        74 ~~~i~liDTPG~~df~~~~~~~l~~aD~~llVvDa~~g~~~~~~~~~~~~~~~~~p~ilviNK~Dl~~~  142 (693)
T 2xex_A           74 GHRVNIIDTPGHVDFTVEVERSLRVLDGAVTVLDAQSGVEPQTETVWRQATTYGVPRIVFVNKMDKLGA  142 (693)
T ss_dssp             TEEEEEECCCCCSSCCHHHHHHHHHCSEEEEEEETTTBSCHHHHHHHHHHHHTTCCEEEEEECTTSTTC
T ss_pred             CeeEEEEECcCCcchHHHHHHHHHHCCEEEEEECCCCCCcHHHHHHHHHHHHcCCCEEEEEECCCcccc
Confidence            5779999999931 00000  11236999999999876543211    111134567999999999865

>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=97.46  E-value=5.2e-05  Score=63.10  Aligned_cols=103  Identities=15%  Similarity=0.082  Sum_probs=61.2

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCC------cC-------C----C-CC-CCceeEEEEecC
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIP------RK-------G----G-PG-ITQADLLVINKT  129 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~------~~-------~----~-~q-i~~adiiviNK~  129 (178)
                      +..+-++.|.|..    ....+. ..++++|+|+|.++.+...      ..       +    . +. -..+-++++||+
T Consensus       200 ~~~l~i~Dt~Gq~~~r~~w~~~f-~~~~~iIfv~dls~~dq~l~ed~~~n~~~es~~~~~~i~~~~~~~~~piILv~NK~  278 (362)
T 1zcb_A          200 NVPFKMVDVGGQRSERKRWFECF-DSVTSILFLVSSSEFDQVLMEDRQTNRLTESLNIFETIVNNRVFSNVSIILFLNKT  278 (362)
T ss_dssp             TEEEEEEEECC-------CTTSC-TTCCEEEEEEETTCTTCEETTEEEEEHHHHHHHHHHHHHTCGGGTTSEEEEEEECH
T ss_pred             CeEEEEEeccchhhhhhhHHHHh-CCCCEEEEEEECccccccccccccccHHHHHHHHHHHHhcchhhCCCCEEEEEECh
Confidence            3567788888831    111222 3579999999998843210      00       0    0 01 234679999999


Q ss_pred             CCCCch----------------hHhHHHHHHHHH----hcC-----CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          130 DLASAI----------------GADLAVMERDAL----RMR-----DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       130 Dl~~~~----------------~~~~~~~~~~l~----~~n-----p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ||..+.                ....+...++++    .++     ....+++|||++|+||+++|+.+...
T Consensus       279 DL~~~ki~~~~l~~~fp~y~g~~~~~~e~~~~~~~~f~~l~~~~~~~~~~~~~tSA~d~~nV~~vF~~v~~~  350 (362)
T 1zcb_A          279 DLLEEKVQVVSIKDYFLEFEGDPHCLRDVQKFLVECFRGKRRDQQQRPLYHHFTTAINTENIRLVFRDVKDT  350 (362)
T ss_dssp             HHHHHHTTTCCGGGTCTTCCSCTTCHHHHHHHHHHHHHTTCSSCC--CCEEEECCTTCHHHHHHHHHHHHHH
T ss_pred             hhhhhhccccchhhcCccccCCCCCHHHHHHHHHHHHHHhhcccCCCceEEEEEecCCchhHHHHHHHHHHH
Confidence            985210                012344444442    222     23578899999999999999987653

>3vqt_A RF-3, peptide chain release factor 3; translation, GTPase; HET: GDP; 1.80A {Desulfovibrio vulgaris} PDB: 3vr1_A*

Probab=97.43  E-value=0.00012  Score=63.97  Aligned_cols=60  Identities=15%  Similarity=0.140  Sum_probs=39.1

Q ss_pred             CCCEEEEeCCcchhhhc----cc-ccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDNLAAN----FS-RELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~----~~-~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      +..+=||.|.|  .+..    .. ...+|+.|+|||+..|...+..    .......+-++++||+|....
T Consensus        99 ~~~iNlIDTPG--HvDF~~Ev~raL~~~DgAvlVvda~~GV~~qT~~v~~~a~~~~lp~i~fINK~Dr~~a  167 (548)
T 3vqt_A           99 DRVVNLLDTPG--HQDFSEDTYRVLTAVDSALVVIDAAKGVEAQTRKLMDVCRMRATPVMTFVNKMDREAL  167 (548)
T ss_dssp             TEEEEEECCCC--GGGCSHHHHHHHHSCSEEEEEEETTTBSCHHHHHHHHHHHHTTCCEEEEEECTTSCCC
T ss_pred             CEEEEEEeCCC--cHHHHHHHHHHHHhcCceEEEeecCCCcccccHHHHHHHHHhCCceEEEEecccchhc
Confidence            45677899999  2211    10 1236999999999998754321    111234466999999999765

>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=97.40  E-value=0.00026  Score=59.97  Aligned_cols=97  Identities=19%  Similarity=0.246  Sum_probs=64.1

Q ss_pred             CCEEEEeCCcch--------hhhcccc--cccceEEEEEeCCCCCCCCcC----------CCC-CCCceeEEEEecCCCC
Q 030407           74 ADLLLCESGGDN--------LAANFSR--ELADYIIYIIDVSGGDKIPRK----------GGP-GITQADLLVINKTDLA  132 (178)
Q Consensus        74 ~d~iiiEttG~~--------~~~~~~~--~~ad~~I~VvD~~~~~~~~~~----------~~~-qi~~adiiviNK~Dl~  132 (178)
                      ..+.+.++.|..        +...+..  ..++.++.++|.+  ......          +.. ....+.++++||+|+.
T Consensus       205 ~~~~l~DtpGli~~a~~~~~L~~~fl~~~era~~lL~vvDls--~~~~~~ls~g~~el~~la~aL~~~P~ILVlNKlDl~  282 (416)
T 1udx_A          205 ERFTLADIPGIIEGASEGKGLGLEFLRHIARTRVLLYVLDAA--DEPLKTLETLRKEVGAYDPALLRRPSLVALNKVDLL  282 (416)
T ss_dssp             CEEEEEECCCCCCCGGGSCCSCHHHHHHHTSSSEEEEEEETT--SCHHHHHHHHHHHHHHHCHHHHHSCEEEEEECCTTS
T ss_pred             ceEEEEeccccccchhhhhhhhHHHHHHHHHHHhhhEEeCCc--cCCHHHHHHHHHHHHHHhHHhhcCCEEEEEECCChh
Confidence            457788999841        1111111  2368899999997  111100          110 1245789999999998


Q ss_pred             CchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          133 SAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       133 ~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.  ...+.+.+.+++.  ..+++.+||++++|+++|++.+.+.
T Consensus       283 ~~--~~~~~l~~~l~~~--g~~vi~iSA~~g~gi~eL~~~i~~~  322 (416)
T 1udx_A          283 EE--EAVKALADALARE--GLAVLPVSALTGAGLPALKEALHAL  322 (416)
T ss_dssp             CH--HHHHHHHHHHHTT--TSCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             hH--HHHHHHHHHHHhc--CCeEEEEECCCccCHHHHHHHHHHH
Confidence            66  5556666655533  4589999999999999999988764

>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=97.35  E-value=0.00019  Score=58.15  Aligned_cols=82  Identities=10%  Similarity=0.054  Sum_probs=53.3

Q ss_pred             ccceEEEEEeCCCCCCCCcCC---------CC--CC-CceeEEEEec-CCCCCchhHhHHHHHHHHH--hcCCCCCEEEE
Q 030407           94 LADYIIYIIDVSGGDKIPRKG---------GP--GI-TQADLLVINK-TDLASAIGADLAVMERDAL--RMRDGGPFIFA  158 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~~---------~~--qi-~~adiiviNK-~Dl~~~~~~~~~~~~~~l~--~~np~a~i~~~  158 (178)
                      ..|++|+|||+++.+....+.         .+  .+ ..+-+|+.|| -|+..+  ....++.+.+.  .+...-.|..+
T Consensus       210 ~tdglIfVVDSsDreRleak~EL~eL~~mL~e~~~l~~apLLVfANKkQDlp~A--ms~~EI~e~L~L~~l~r~W~Iq~c  287 (312)
T 3l2o_B          210 VVDGFIYVANAEAHKRHEWQDEFSHIMAMTDPAFGSSGRPLLVLSCISQGDVKR--MPCFYLAHELHLNLLNHPWLVQDT  287 (312)
T ss_dssp             HCSEEEECCBCBTTCCCCHHHHHHHHHHHHCHHHHCTTCCEEEEEEESSTTSCB--CCHHHHHHHTTGGGGCSCEEEEEE
T ss_pred             CCCEEEEEecCCcHhHHHHHHHHHHHHHHhcchhhcCCCeEEEEeCCcccccCC--CCHHHHHHHcCCccCCCcEEEEec
Confidence            479999999998765322110         00  12 2345677797 588765  33344444432  23334579999


Q ss_pred             ecccCCCHHHHHHHHhhhh
Q 030407          159 QVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       159 SA~~g~gi~el~~~l~~~~  177 (178)
                      ||+||+|+.|-+++|.+.+
T Consensus       288 sA~tGeGL~EGldWL~~~l  306 (312)
T 3l2o_B          288 EAETLTGFLNGIEWILEEV  306 (312)
T ss_dssp             ETTTCTTHHHHHHHHHHHS
T ss_pred             ccCCCcCHHHHHHHHHHHH
Confidence            9999999999999987654

>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=97.33  E-value=0.00017  Score=64.40  Aligned_cols=60  Identities=15%  Similarity=0.222  Sum_probs=36.9

Q ss_pred             CCCEEEEeCCcch-hhhc--ccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCC
Q 030407           73 KADLLLCESGGDN-LAAN--FSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLA  132 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~~--~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~  132 (178)
                      ....-|+.|.|.. ....  .....+|..++|+|++.+...+..    .......+-++++||+|+.
T Consensus        73 ~~~~nliDTpG~~~f~~~~~~~l~~ad~~ilVvD~~~g~~~qt~~~~~~~~~~~ip~ilv~NKiD~~  139 (665)
T 2dy1_A           73 GHRVFLLDAPGYGDFVGEIRGALEAADAALVAVSAEAGVQVGTERAWTVAERLGLPRMVVVTKLDKG  139 (665)
T ss_dssp             TEEEEEEECCCSGGGHHHHHHHHHHCSEEEEEEETTTCSCHHHHHHHHHHHHTTCCEEEEEECGGGC
T ss_pred             CEEEEEEeCCCccchHHHHHHHHhhcCcEEEEEcCCcccchhHHHHHHHHHHccCCEEEEecCCchh
Confidence            4667888999931 1110  011246999999999877543211    0011244679999999997

>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=97.21  E-value=0.0004  Score=51.84  Aligned_cols=100  Identities=12%  Similarity=-0.019  Sum_probs=61.9

Q ss_pred             CCEEEEeCCcchhh----hcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHHH
Q 030407           74 ADLLLCESGGDNLA----ANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        74 ~d~iiiEttG~~~~----~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      +.+.++++.|....    ..+. ..++.+++|+|.+.......  .+.      ..-..+-++++||+|+.+......+.
T Consensus        54 ~~~~i~Dt~g~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~i~~v~nK~Dl~~~~~~~~~~  132 (199)
T 2f9l_A           54 IKAQIWDTAGQERYRRITSAYY-RGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDE  132 (199)
T ss_dssp             EEEEEEECSSGGGTTCCCHHHH-TTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHHH
T ss_pred             EEEEEEECCCchhhhhhhHHHH-hcCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCeEEEEEECcccccccCcCHHH
Confidence            45667888883211    1111 24688999999876432111  000      01234568999999996531112233


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+..+  .|...++.+||+++.|++++++.+.+.
T Consensus       133 a~~l~~--~~~~~~~d~Sal~~~~i~~l~~~l~~~  165 (199)
T 2f9l_A          133 ARAFAE--KNNLSFIETSALDSTNVEEAFKNILTE  165 (199)
T ss_dssp             HHHHHH--HTTCEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHH--HcCCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            444444  356789999999999999999988654

>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=97.20  E-value=0.0005  Score=57.12  Aligned_cols=52  Identities=15%  Similarity=0.088  Sum_probs=37.4

Q ss_pred             ceeEEEEecCCCCCchhHhHHHHHHHHHhc-CCCCCEEEEecccCCCHHHHHHHH
Q 030407          120 QADLLVINKTDLASAIGADLAVMERDALRM-RDGGPFIFAQVGWVIGIIFTLSIT  173 (178)
Q Consensus       120 ~adiiviNK~Dl~~~~~~~~~~~~~~l~~~-np~a~i~~~SA~~g~gi~el~~~l  173 (178)
                      ..-+||+||+||+++  +..+.+.+++... ..+.+++.+||++|.|++++...+
T Consensus       161 ~~~iivlNK~DL~~~--~~~~~~~~~~~~y~~~G~~v~~~Sa~~~~gl~~L~~~~  213 (358)
T 2rcn_A          161 VEPLIVLNKIDLLDD--EGMDFVNEQMDIYRNIGYRVLMVSSHTQDGLKPLEEAL  213 (358)
T ss_dssp             CEEEEEEECGGGCCH--HHHHHHHHHHHHHHTTTCCEEECBTTTTBTHHHHHHHH
T ss_pred             CCEEEEEECccCCCc--hhHHHHHHHHHHHHhCCCcEEEEecCCCcCHHHHHHhc
Confidence            345999999999987  4433333333322 235689999999999999998764

>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=97.19  E-value=0.00021  Score=60.32  Aligned_cols=24  Identities=13%  Similarity=-0.244  Sum_probs=20.1

Q ss_pred             CCEEEEecccCCCHHHHHHHHhhh
Q 030407          153 GPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       153 a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..++.|||++++||+++|+.+...
T Consensus       359 ~~~~~TSA~d~~nV~~vF~~v~~~  382 (402)
T 1azs_C          359 CYPHFTCAVDTENIRRVFNDCRDI  382 (402)
T ss_dssp             EEEEECCTTCHHHHHHHHHHHHHH
T ss_pred             cEEEEEEeecCcCHHHHHHHHHHH
Confidence            356789999999999999987653

>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=97.18  E-value=0.00026  Score=54.65  Aligned_cols=100  Identities=8%  Similarity=0.067  Sum_probs=57.7

Q ss_pred             CCCEEEEeCCcch------------hhhcc--cccccceEEEEEeCCCCCCCCcCCC--------CCCCceeEEEEecCC
Q 030407           73 KADLLLCESGGDN------------LAANF--SRELADYIIYIIDVSGGDKIPRKGG--------PGITQADLLVINKTD  130 (178)
Q Consensus        73 ~~d~iiiEttG~~------------~~~~~--~~~~ad~~I~VvD~~~~~~~~~~~~--------~qi~~adiiviNK~D  130 (178)
                      +..+.|++|.|..            +...+  ....+|.+++|+|+++.........        .....+-++|+||+|
T Consensus        77 ~~~i~liDTpG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~d~~~~~~~~~~~l~~~~~~~~~~~~~~~iiv~nK~D  156 (239)
T 3lxx_A           77 ETELVVVDTPGIFDTEVPNAETSKEIIRCILLTSPGPHALLLVVPLGRYTEEEHKATEKILKMFGERARSFMILIFTRKD  156 (239)
T ss_dssp             TEEEEEEECCSCC-----CHHHHHHHHHHHHHTTTCCSEEEEEEETTCCSSHHHHHHHHHHHHHHHHHGGGEEEEEECGG
T ss_pred             CceEEEEECCCccCCCCCHHHHHHHHHHHHHhcCCCCcEEEEEeeCCCCCHHHHHHHHHHHHHhhhhccceEEEEEeCCc
Confidence            4578999999941            11111  1124699999999875433111100        011235799999999


Q ss_pred             CCCchhHhHH--------HHHHHHHhcCCCCCEEEEecc-----cCCCHHHHHHHHhhh
Q 030407          131 LASAIGADLA--------VMERDALRMRDGGPFIFAQVG-----WVIGIIFTLSITHYI  176 (178)
Q Consensus       131 l~~~~~~~~~--------~~~~~l~~~np~a~i~~~SA~-----~g~gi~el~~~l~~~  176 (178)
                      +.+.  ..++        .+.+.+++...  +++..++.     ++.|+.+|++.+.+.
T Consensus       157 ~~~~--~~~~~~i~~~~~~l~~l~~~~~~--~~~~~~~~~~~~~~~~~v~~ll~~i~~~  211 (239)
T 3lxx_A          157 DLGD--TNLHDYLREAPEDIQDLMDIFGD--RYCALNNKATGAEQEAQRAQLLGLIQRV  211 (239)
T ss_dssp             GC--------------CHHHHHHHHHHSS--SEEECCTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCc--ccHHHHHHhchHHHHHHHHHcCC--EEEEEECCCCccccHHHHHHHHHHHHHH
Confidence            9865  3333        34555555533  56666655     347999999887654

>3j25_A Tetracycline resistance protein TETM; antibiotic resistance, translation; HET: GCP; 7.20A {Enterococcus faecalis}

Probab=97.12  E-value=0.00011  Score=65.35  Aligned_cols=61  Identities=15%  Similarity=0.250  Sum_probs=38.0

Q ss_pred             CCCEEEEeCCcchh--h-hccc-ccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           73 KADLLLCESGGDNL--A-ANFS-RELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        73 ~~d~iiiEttG~~~--~-~~~~-~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      ++.+=||.|.| ..  . .... ...+|+.|+|||+..|...+..    .......+-++++||+|....
T Consensus        66 ~~~iNlIDTPG-H~DF~~Ev~raL~~~DgavlVVDa~~GV~~qT~~v~~~a~~~~lp~i~~INKmDr~~a  134 (638)
T 3j25_A           66 NTKVNIIDTPG-HMDFLAEVYRSLSVLDGAILLISAKDGVQAQTRILFHALRKMGIPTIFFINKIDQNGI  134 (638)
T ss_dssp             SCBCCCEECCC-SSSTHHHHHHHHTTCSEEECCEESSCTTCSHHHHHHHHHHHHTCSCEECCEECCSSSC
T ss_pred             CEEEEEEECCC-cHHHHHHHHHHHHHhCEEEEEEeCCCCCcHHHHHHHHHHHHcCCCeEEEEeccccccC
Confidence            45567899999 21  1 1110 1246999999999988755421    111123355999999998654

>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=97.02  E-value=0.00055  Score=56.17  Aligned_cols=101  Identities=17%  Similarity=0.106  Sum_probs=58.3

Q ss_pred             CEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcC-------------C-----CCC-CCceeEEEEecCCC
Q 030407           75 DLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRK-------------G-----GPG-ITQADLLVINKTDL  131 (178)
Q Consensus        75 d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~-------------~-----~~q-i~~adiiviNK~Dl  131 (178)
                      .+-++++.|--    +...+. ..++++|+|+|.++.+.....             +     .+. -..+-++++||+|+
T Consensus       168 ~l~iwDtgGQe~~R~~w~~yf-~~~~~iIfV~dls~ydq~l~d~~~~nr~~es~~~~~~i~~~~~~~~~~iiL~~NK~DL  246 (327)
T 3ohm_A          168 IFRMVDVGGQRSERRKWIHCF-ENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNSSVILFLNKKDL  246 (327)
T ss_dssp             EEEEEEECCSHHHHTTGGGGC-SSCSEEEEEEEGGGGGCBCSSCTTSBHHHHHHHHHHHHHTSGGGTTCEEEEEEECHHH
T ss_pred             eeEEEEcCCchhHHHHHHHHh-CCCCEEEEEEECccccccccccccHhHHHHHHHHHHHHhhhhccCCceEEEEEECchh
Confidence            34566777721    112232 357999999987643221100             0     001 13467999999998


Q ss_pred             CCch----------------hHhHHHHHHHHH----hcCC----CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          132 ASAI----------------GADLAVMERDAL----RMRD----GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       132 ~~~~----------------~~~~~~~~~~l~----~~np----~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+.                ....+...++++    ++++    ....+.|||+++++|+++|+.+...
T Consensus       247 ~~~ki~~~~l~~~fp~y~g~~~~~e~a~~fi~~~F~~~~~~~~~~i~~~~TsA~d~~nV~~vF~~v~~~  315 (327)
T 3ohm_A          247 LEEKIMYSHLVDYFPEYDGPQRDAQAAREFILKMFVDLNPDSDKIIYSHFTCATDTENIRFVFAAVKDT  315 (327)
T ss_dssp             HHHHTTTSCGGGTCTTCCSCSSCHHHHHHHHHHHHHSSCTTTTSCEEEEECCTTCHHHHHHHHHHHHHH
T ss_pred             hhhhhccchHhhhchhccCCCCCHHHHHHHHHHHHHhhcccccCCcEEEEEEeecCHHHHHHHHHHHHH
Confidence            5421                012334444433    3332    2357889999999999999987653

>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=97.02  E-value=0.0006  Score=50.72  Aligned_cols=100  Identities=13%  Similarity=0.024  Sum_probs=60.3

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CCC------CCCCceeEEEEecCCCCCchhHhHHH
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KGG------PGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~~------~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      +...++++.|..    +...+. ..++..++|+|.........  .+.      .....+-++++||+|+.+......+.
T Consensus        78 ~~~~i~Dt~g~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~i~~v~nK~Dl~~~~~~~~~~  156 (191)
T 1oix_A           78 IKAQIWDTAGLERYRAITSAYY-RGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDE  156 (191)
T ss_dssp             EEEEEEEECSCCSSSCCCHHHH-TTCCEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHHH
T ss_pred             EEEEEEECCCCcchhhhhHHHh-hcCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECcccccccccCHHH
Confidence            344567777731    111111 23578899999875422110  000      11234568999999996531112333


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .++..+  .|...++.+||+++.|++++++.|.+.
T Consensus       157 a~~l~~--~~~~~~ld~Sald~~~v~~l~~~l~~~  189 (191)
T 1oix_A          157 ARAFAE--KNGLSFIETSALDSTNVEAAFQTILTE  189 (191)
T ss_dssp             HHHHHH--HTTCEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHH--HcCCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            444444  356789999999999999999998764

>3r7w_B Gtpase2, GTP-binding protein GTR2; RAG gtpases, GTR1P, GTR2P, MTOR, protein transport; HET: GNP; 2.77A {Saccharomyces cerevisiae} PDB: 4arz_B*

Probab=96.92  E-value=0.0009  Score=55.02  Aligned_cols=98  Identities=14%  Similarity=0.009  Sum_probs=59.6

Q ss_pred             CCCEEEEeCCcch-h------hhcccccccceEEEEEeCCCCCCC-CcCCCC--------CCCceeEEEEecCCCCCchh
Q 030407           73 KADLLLCESGGDN-L------AANFSRELADYIIYIIDVSGGDKI-PRKGGP--------GITQADLLVINKTDLASAIG  136 (178)
Q Consensus        73 ~~d~iiiEttG~~-~------~~~~~~~~ad~~I~VvD~~~~~~~-~~~~~~--------qi~~adiiviNK~Dl~~~~~  136 (178)
                      ...+-++.|.|.- .      ...+. ..++++|+|+|+++.... ...+..        .-..+-++++||+||.++  
T Consensus        45 ~v~LqIWDTAGQErf~~~~l~~~~yy-r~a~~~IlV~Ditd~~~~~~~~l~~~l~~~~~~~~~ipillvgNK~DL~~~--  121 (331)
T 3r7w_B           45 LIDLAVMELPGQLNYFEPSYDSERLF-KSVGALVYVIDSQDEYINAITNLAMIIEYAYKVNPSINIEVLIHKVDGLSE--  121 (331)
T ss_dssp             SSCEEEEECCSCSSSCCCSHHHHHHH-TTCSEEEEECCCSSCTTHHHHHHHHHHHHHHHHCTTCEEEEECCCCCSSCS--
T ss_pred             EEEEEEEECCCchhccchhhhhhhhc-cCCCEEEEEEECCchHHHHHHHHHHHHHHHhhcCCCCcEEEEEECcccCch--
Confidence            4788999999931 1      11222 368999999999875100 001100        013456899999999876  


Q ss_pred             HhH----HHHHHH-HHhcC------CCCCEEEEecccCCCHHHHHHHHh
Q 030407          137 ADL----AVMERD-ALRMR------DGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       137 ~~~----~~~~~~-l~~~n------p~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      .+.    ..+.+. .+++.      -+.++++|||++ .+|.+.|..+.
T Consensus       122 ~~R~~~~R~V~~~~~~~la~~~~~~~~i~f~eTSAkd-~nV~eAFs~iv  169 (331)
T 3r7w_B          122 DFKVDAQRDIMQRTGEELLELGLDGVQVSFYLTSIFD-HSIYEAFSRIV  169 (331)
T ss_dssp             HHHHHHHHHHHHHHHHTTSSSSCSCCCEEEECCCSSS-SHHHHHHHHHH
T ss_pred             hhhhhHHHHhhHHHHHHHHhhcccccCceEEEeccCC-CcHHHHHHHHH
Confidence            332    122222 22222      246899999998 58999987654

>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=96.87  E-value=0.0011  Score=54.74  Aligned_cols=102  Identities=14%  Similarity=0.051  Sum_probs=60.1

Q ss_pred             CCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcC-------------C-----CCC-CCceeEEEEecCC
Q 030407           74 ADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRK-------------G-----GPG-ITQADLLVINKTD  130 (178)
Q Consensus        74 ~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~-------------~-----~~q-i~~adiiviNK~D  130 (178)
                      ..+-++.+.|--    +...+. ..++++|+|+|.++.+.....             +     .+. -..+-++++||+|
T Consensus       161 v~l~iwDtaGQe~~R~~w~~yy-~~a~~iIfV~diS~ydq~l~e~~~~nr~~es~~~~~~i~~~~~~~~~piiLv~NK~D  239 (340)
T 4fid_A          161 IPFHLIDVGGQRSERKXWVSFF-SDVDCAIFVTSLAEYDMKLYEDGNTSRLTESIAVFKDIMTNEFLKGAVKLIFLNKMD  239 (340)
T ss_dssp             CEEEEEECCSCHHHHHHHHTTS-CSCSEEEEEEEGGGTTCBCC--CCSBHHHHHHHHHHHHHHCGGGTTSEEEEEEECHH
T ss_pred             eeeccccCCCcccccccHHHHh-ccCCEEEEEEECCccccccccccccchHHHHHHHHHHHhhhhccCCCeEEEEEECch
Confidence            456677787731    112233 367999999999843321100             0     001 1346799999999


Q ss_pred             CCCch---------------hHhHHHHHHHHHhcC-------------------------CCCCEEEEecccCCCHHHHH
Q 030407          131 LASAI---------------GADLAVMERDALRMR-------------------------DGGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus       131 l~~~~---------------~~~~~~~~~~l~~~n-------------------------p~a~i~~~SA~~g~gi~el~  170 (178)
                      |..+.               +...+...++++..+                         ....++.|||+++.+|+.+|
T Consensus       240 L~~eki~~~~l~~~fp~y~g~~~~e~a~~~i~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~iy~h~TsA~dt~nv~~vF  319 (340)
T 4fid_A          240 LFEEKLTKVPLNTIFPEYTGGDNAVMGAQYIQQLFTGKLQTEEMNISGADGTANIEGAVNEKVYTNPTNATDGSNIKRVF  319 (340)
T ss_dssp             HHHHHHHHSCGGGTCTTCCCTTCHHHHHHHHHHHHHTTSEEEESCC--------------CEEEEEEECTTCHHHHHHHH
T ss_pred             hhhhhcCcchHHHhhhhhcCCCCHHHHHHHHHHhcccccchhhhhccccccccccccccCcceEEEEEEeeCcHHHHHHH
Confidence            85320               011233434443322                         12467899999999999999


Q ss_pred             HHHhhh
Q 030407          171 SITHYI  176 (178)
Q Consensus       171 ~~l~~~  176 (178)
                      +.+...
T Consensus       320 ~~v~~~  325 (340)
T 4fid_A          320 MLAVDV  325 (340)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877653

>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=96.66  E-value=7.2e-05  Score=56.57  Aligned_cols=62  Identities=16%  Similarity=0.246  Sum_probs=37.4

Q ss_pred             CCCEEEEeCCcchh----hhcccc---cccceEEEEEeCC-CCCCCCc--C-CCC---------CCCceeEEEEecCCCC
Q 030407           73 KADLLLCESGGDNL----AANFSR---ELADYIIYIIDVS-GGDKIPR--K-GGP---------GITQADLLVINKTDLA  132 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~---~~ad~~I~VvD~~-~~~~~~~--~-~~~---------qi~~adiiviNK~Dl~  132 (178)
                      ...+.+++|.|..-    ...+..   ..+|.+++|+|++ .......  . ...         .-..+-++|+||+|+.
T Consensus        54 ~~~~~l~Dt~G~~~~~~~~~~~~~~~~~~~~~~i~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~  133 (218)
T 1nrj_B           54 GSGVTLVDFPGHVKLRYKLSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELF  133 (218)
T ss_dssp             GSSCEEEECCCCGGGTHHHHHHHHHHGGGEEEEEEEEETTSCTTCCHHHHHHHHHHHHHHHHHSTTCCCEEEEEECTTST
T ss_pred             CceEEEEECCCcHHHHHHHHHHHHhccccCCEEEEEEECCCChHHHHHHHHHHHHHHhcccccccCCCCEEEEEEchHhc
Confidence            56889999999421    112221   1268999999998 3322211  0 000         0134579999999998


Q ss_pred             Cc
Q 030407          133 SA  134 (178)
Q Consensus       133 ~~  134 (178)
                      ++
T Consensus       134 ~~  135 (218)
T 1nrj_B          134 TA  135 (218)
T ss_dssp             TC
T ss_pred             cc
Confidence            76

>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=96.38  E-value=0.00074  Score=55.56  Aligned_cols=97  Identities=15%  Similarity=0.121  Sum_probs=55.6

Q ss_pred             CCCEEEEeCCcchhh-----------------hcccccccceEEEEEeCCCCCCCCc------CCCCCCCceeEEEEecC
Q 030407           73 KADLLLCESGGDNLA-----------------ANFSRELADYIIYIIDVSGGDKIPR------KGGPGITQADLLVINKT  129 (178)
Q Consensus        73 ~~d~iiiEttG~~~~-----------------~~~~~~~ad~~I~VvD~~~~~~~~~------~~~~qi~~adiiviNK~  129 (178)
                      .+++.||.|.|..-.                 ..+ ...+|.+++++|+...+....      .........-++|+||+
T Consensus       135 ~~~l~lvDtPG~~~~~~~~q~~~~~~~~~~~~~~~-i~~~d~iilvv~~~~~~~~~~~~~~l~~~~~~~~~~~i~V~nK~  213 (360)
T 3t34_A          135 VVNLTLIDLPGLTKVAVDGQSDSIVKDIENMVRSY-IEKPNCIILAISPANQDLATSDAIKISREVDPSGDRTFGVLTKI  213 (360)
T ss_dssp             SCSEEEEECCCBCSSCCTTCCSSHHHHHHHHHHHH-HHSSSEEEEEEEETTSCGGGCHHHHHHHHSCTTCTTEEEEEECG
T ss_pred             CCCeEEEECCCCCcCCcCCCchhHHHHHHHHHHHH-hhcCCeEEEEeecccCCcCCHHHHHHHHHhcccCCCEEEEEeCC
Confidence            468999999994210                 011 123688999998754321110      00111233579999999


Q ss_pred             CCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHH
Q 030407          130 DLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSI  172 (178)
Q Consensus       130 Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~  172 (178)
                      |++++.....+.+...  ...-..+++.+|++++.|+++.+..
T Consensus       214 Dl~~~~~~~~~~~~~~--~~~~~~~~~~v~~~s~~~i~~~~~~  254 (360)
T 3t34_A          214 DLMDKGTDAVEILEGR--SFKLKYPWVGVVNRSQADINKNVDM  254 (360)
T ss_dssp             GGCCTTCCSHHHHTTS--SSCCSSCCEEECCCCHHHHHTTCCH
T ss_pred             ccCCCcccHHHHHcCc--cccccCCeEEEEECChHHhccCCCH
Confidence            9986521112222211  1123468899999999988876543

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=96.35  E-value=0.0012  Score=53.16  Aligned_cols=50  Identities=8%  Similarity=-0.147  Sum_probs=29.1

Q ss_pred             eeEEEEecCCCCCchhHhH----HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          121 ADLLVINKTDLASAIGADL----AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       121 adiiviNK~Dl~~~~~~~~----~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .-++|+||.|+.+.  .++    +++.+.++..  +.+++++||++| |++++|+.+.+
T Consensus       157 ~iilV~~K~Dl~~~--~e~~~~~~~~~~~~~~~--~~~~~e~Sa~~~-~v~e~f~~l~~  210 (301)
T 2qnr_A          157 NIVPVIAKADTLTL--KERERLKKRILDEIEEH--NIKIYHLPDAES-DEDEDFKEQTR  210 (301)
T ss_dssp             CEEEEECCGGGSCH--HHHHHHHHHHHHHHHHT--TCCCCCCC----------CHHHHH
T ss_pred             CEEEEEEeCCCCCH--HHHHHHHHHHHHHHHHc--CCeEEecCCccc-cccHHHHHHHH
Confidence            56999999999876  443    3445555544  468999999999 99999877654

>4fn5_A EF-G 1, elongation factor G 1; translation, translation-antibiotic compl; HET: 0UO; 2.90A {Pseudomonas aeruginosa}

Probab=96.27  E-value=0.0039  Score=56.01  Aligned_cols=58  Identities=12%  Similarity=0.112  Sum_probs=36.3

Q ss_pred             CEEEEeCCcchhhhc---cc--ccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCc
Q 030407           75 DLLLCESGGDNLAAN---FS--RELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        75 d~iiiEttG~~~~~~---~~--~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~  134 (178)
                      -+=||.|.|  .+..   ..  ....|++|+|||+..|...+..    .......+-++++||+|....
T Consensus        86 ~iNlIDTPG--HvDF~~Ev~~aLr~~DgavlvVDaveGV~~qT~~v~~~a~~~~lp~i~~iNKiDr~~a  152 (709)
T 4fn5_A           86 RVNVIDTPG--HVDFTIEVERSLRVLDGAVVVFCGTSGVEPQSETVWRQANKYGVPRIVYVNKMDRQGA  152 (709)
T ss_dssp             EEEEECCCS--CTTCHHHHHHHHHHCSEEEEEEETTTCSCHHHHHHHHHHHHHTCCEEEEEECSSSTTC
T ss_pred             EEEEEeCCC--CcccHHHHHHHHHHhCeEEEEEECCCCCchhHHHHHHHHHHcCCCeEEEEccccccCc
Confidence            344899999  2210   01  1136999999999998754321    111123456999999998643

>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=96.13  E-value=0.0023  Score=52.94  Aligned_cols=50  Identities=10%  Similarity=-0.102  Sum_probs=26.7

Q ss_pred             ceeEEEEecCCCCCchhHhHHHHHHHHHhcC--CCCCEEEEecccCCCHHHHHHH
Q 030407          120 QADLLVINKTDLASAIGADLAVMERDALRMR--DGGPFIFAQVGWVIGIIFTLSI  172 (178)
Q Consensus       120 ~adiiviNK~Dl~~~~~~~~~~~~~~l~~~n--p~a~i~~~SA~~g~gi~el~~~  172 (178)
                      .+-++|+||+|+.+.  .++..+.+.+++..  .+.+++++||++|.| ++.+..
T Consensus       175 ~piIlV~NK~Dl~~~--~ev~~~k~~i~~~~~~~~i~~~~~Sa~~~~~-~e~~~~  226 (361)
T 2qag_A          175 VNIVPVIAKADTLTL--KERERLKKRILDEIEEHNIKIYHLPDAESDE-DEDFKE  226 (361)
T ss_dssp             SCEEEEEECCSSSCH--HHHHHHHHHHHHHTTCC-CCSCCCC----------CHH
T ss_pred             CCEEEEEECCCCCCH--HHHHHHHHHHHHHHHHCCCCEEeCCCcCCCc-chhHHH
Confidence            457999999999877  55544433343321  246899999999998 555443

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=96.09  E-value=0.00023  Score=60.56  Aligned_cols=103  Identities=18%  Similarity=0.169  Sum_probs=56.0

Q ss_pred             CCCCEEEEeCCcchh-----hh---cc-cccccceEEEEEeCCCCCCCCc---CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           72 FKADLLLCESGGDNL-----AA---NF-SRELADYIIYIIDVSGGDKIPR---KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        72 ~~~d~iiiEttG~~~-----~~---~~-~~~~ad~~I~VvD~~~~~~~~~---~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .++|+|||+|.|..-     ..   .. ....+|.+++|+|+..+.+...   .+...+.....+|+||+|........+
T Consensus       179 ~~~D~vIIDT~G~~~~~~~l~~~l~~i~~~~~~d~vllVvda~~g~~~~~~~~~~~~~~~~i~gvVlnK~D~~~~~g~~l  258 (432)
T 2v3c_C          179 KKADVLIIDTAGRHKEEKGLLEEMKQIKEITNPDEIILVIDGTIGQQAGIQAKAFKEAVGEIGSIIVTKLDGSAKGGGAL  258 (432)
T ss_dssp             SSCSEEEEECCCSCSSHHHHHHHHHHTTSSSCCSEEEEEEEGGGGGGHHHHHHHHHTTSCSCEEEEEECSSSCSTTHHHH
T ss_pred             hCCCEEEEcCCCCccccHHHHHHHHHHHHHhcCcceeEEeeccccHHHHHHHHHHhhcccCCeEEEEeCCCCccchHHHH
Confidence            579999999999421     00   01 1112588999999976642211   011111012789999999865411111


Q ss_pred             HHHHHHH-------------HhcCCCCCEEEEecccCCC-HHHHHHHHhh
Q 030407          140 AVMERDA-------------LRMRDGGPFIFAQVGWVIG-IIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l-------------~~~np~a~i~~~SA~~g~g-i~el~~~l~~  175 (178)
                      . +....             ..+.|..+..++|+..|.| +..|++.+.+
T Consensus       259 ~-~~~~~~~pi~~ig~Ge~~~dl~~f~~~~~~s~l~g~gdi~~L~e~~~~  307 (432)
T 2v3c_C          259 S-AVAETKAPIKFIGIGEGIDDLEPFDPKKFISRLLGMGDLESLLEKAED  307 (432)
T ss_dssp             H-HHHHSSCCEEEECCSSSSSSCCBCCHHHHHHHHTCSSCSSTTSSTTTS
T ss_pred             H-HHHHHCCCEEEeecCccccccccCCHHHHHHHHcCCCcHHHHHHHHHH
Confidence            1 21111             1112344455668888888 7777665543

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=95.88  E-value=0.0071  Score=51.41  Aligned_cols=143  Identities=17%  Similarity=0.173  Sum_probs=75.0

Q ss_pred             HHHHHhhc-CCcEEEEEecCC-C-chhHHHH--HHcCCCCccceeecccCCCcccccccccccCH-hHHHhhHhhCCCCE
Q 030407            3 ALCKFLRD-KYSLAAVTNDIF-T-KEDGEFL--MRNGALPEERIRAVETGGCPHAAIREDISINL-GPLEELSNLFKADL   76 (178)
Q Consensus         3 ~~~~~~~~-~~~vaVI~nd~g-~-~iD~~li--~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l-~~l~~l~~~~~~d~   76 (178)
                      +++.++.+ ++||.++.-|.. . .++....  +..|+    ++....++...        .... .++..+. ..++|+
T Consensus       116 kLA~~l~~~G~kVllv~~D~~r~~a~eqL~~~~~~~gv----~~~~~~~~~dp--------~~i~~~al~~a~-~~~~Dv  182 (433)
T 3kl4_A          116 KLAYFYKKRGYKVGLVAADVYRPAAYDQLLQLGNQIGV----QVYGEPNNQNP--------IEIAKKGVDIFV-KNKMDI  182 (433)
T ss_dssp             HHHHHHHHTTCCEEEEEECCSCHHHHHHHHHHHHTTTC----CEECCTTCSCH--------HHHHHHHHHHTT-TTTCSE
T ss_pred             HHHHHHHHcCCeEEEEecCccchhHHHHHHHHHHhcCC----ceeeccccCCH--------HHHHHHHHHHHH-hcCCCE
Confidence            45666655 499999999977 3 3332221  11232    22222211111        1111 3333332 457999


Q ss_pred             EEEeCCcchh---hhccc--------ccccceEEEEEeCCCCCCCCc---CCCCCCCceeEEEEecCCCCCchhHhHHHH
Q 030407           77 LLCESGGDNL---AANFS--------RELADYIIYIIDVSGGDKIPR---KGGPGITQADLLVINKTDLASAIGADLAVM  142 (178)
Q Consensus        77 iiiEttG~~~---~~~~~--------~~~ad~~I~VvD~~~~~~~~~---~~~~qi~~adiiviNK~Dl~~~~~~~~~~~  142 (178)
                      |||+|.|...   ...+.        ....+.+++|+|+..+.+...   .+.+.+ ....+|+||.|.....    ..+
T Consensus       183 vIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~a~~~a~~f~~~~-~~~gVIlTKlD~~a~~----G~a  257 (433)
T 3kl4_A          183 IIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLASRFHQAS-PIGSVIITKMDGTAKG----GGA  257 (433)
T ss_dssp             EEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGGGGGGHHHHHHHHHHC-SSEEEEEECGGGCSCH----HHH
T ss_pred             EEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCccchHHHHHHHHHhccc-CCcEEEEecccccccc----hHH
Confidence            9999999311   11010        011378999999987643211   011111 2478999999987552    222


Q ss_pred             HHHHHhcCCCCCEEEEecccCCCHH
Q 030407          143 ERDALRMRDGGPFIFAQVGWVIGII  167 (178)
Q Consensus       143 ~~~l~~~np~a~i~~~SA~~g~gi~  167 (178)
                      .+.....  +.|+.+++.  |++++
T Consensus       258 ls~~~~~--g~Pi~fig~--Ge~v~  278 (433)
T 3kl4_A          258 LSAVVAT--GATIKFIGT--GEKID  278 (433)
T ss_dssp             HHHHHHH--TCEEEEEEC--CSSSS
T ss_pred             HHHHHHH--CCCEEEEEC--CCChH
Confidence            2233322  468888875  88774

>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=94.98  E-value=0.0043  Score=52.02  Aligned_cols=47  Identities=17%  Similarity=0.146  Sum_probs=35.9

Q ss_pred             ceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHH
Q 030407          120 QADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus       120 ~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~  170 (178)
                      .+.++|+||+|+...  ..++.+.+.....  .++++++||+.+.|+.+++
T Consensus       215 kP~i~v~NK~D~~~~--~~l~~l~~~~~~~--~~~vv~iSA~~e~~l~~L~  261 (397)
T 1wxq_A          215 KPMVIAANKADAASD--EQIKRLVREEEKR--GYIVIPTSAAAELTLRKAA  261 (397)
T ss_dssp             SCEEEEEECGGGSCH--HHHHHHHHHHHHT--TCEEEEECHHHHHHHHSCS
T ss_pred             CCEEEEEeCccccch--HHHHHHHHHHhhc--CCcEEEEeccchhhHHHHH
Confidence            678999999999844  5566666555432  4689999999999998764

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=94.92  E-value=0.0038  Score=45.82  Aligned_cols=72  Identities=14%  Similarity=0.181  Sum_probs=40.9

Q ss_pred             CCCEEEEeCCcchh----hhcccc---cccceEEEEEeCC-CCCCCCc---CCCC---------CCCceeEEEEecCCCC
Q 030407           73 KADLLLCESGGDNL----AANFSR---ELADYIIYIIDVS-GGDKIPR---KGGP---------GITQADLLVINKTDLA  132 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~---~~ad~~I~VvD~~-~~~~~~~---~~~~---------qi~~adiiviNK~Dl~  132 (178)
                      ...+.+++|.|..-    ...+..   ..+|++++|+|++ .......   .+..         .-..+-++|+||+|+.
T Consensus        90 ~~~~~l~Dt~G~~~~~~~~~~~~~~~~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~  169 (193)
T 2ged_A           90 GSGVTLVDFPGHVKLRYKLSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELF  169 (193)
T ss_dssp             CTTCSEEEETTCCBSSCCHHHHHHHHGGGEEEEEEEEETTCCHHHHHHHHHHHHHHHHHHHHHSTTCCCEEEEEECTTST
T ss_pred             CCeEEEEECCCCchHHHHHHHHHHhhcccCCEEEEEEECCCCchhHHHHHHHHHHHHhhhhhccccCCCEEEEEEchHhc
Confidence            56788999999411    111111   1268999999998 3211100   0000         0134679999999998


Q ss_pred             CchhHhHHHHHHHH
Q 030407          133 SAIGADLAVMERDA  146 (178)
Q Consensus       133 ~~~~~~~~~~~~~l  146 (178)
                      ++  ...+.+.+.+
T Consensus       170 ~~--~~~~~~~~~l  181 (193)
T 2ged_A          170 TA--RPPSKIKDAL  181 (193)
T ss_dssp             TC--CCHHHHHHHH
T ss_pred             CC--CCHHHHHHHH
Confidence            76  4444444443

>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=94.74  E-value=0.011  Score=50.02  Aligned_cols=53  Identities=6%  Similarity=-0.183  Sum_probs=26.1

Q ss_pred             CceeEEEEecCCCCCchhHhHHH----HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          119 TQADLLVINKTDLASAIGADLAV----MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       119 ~~adiiviNK~Dl~~~~~~~~~~----~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ..+-++|+||+|+.++  .++..    +.+.+...  +.+++.+||++++++++++..+..
T Consensus       167 ~v~iIlVinK~Dll~~--~ev~~~k~~i~~~~~~~--~i~~~~~sa~~~~~v~~~~~~l~~  223 (418)
T 2qag_C          167 KVNIIPLIAKADTLTP--EECQQFKKQIMKEIQEH--KIKIYEFPETDDEEENKLVKKIKD  223 (418)
T ss_dssp             TSEEEEEEESTTSSCH--HHHHHHHHHHHHHHHHH--TCCCCCCC----------------
T ss_pred             cCcEEEEEEcccCccH--HHHHHHHHHHHHHHHHc--CCeEEeCCCCCCcCHHHHHHHHHh
Confidence            3567999999999876  55543    44444443  568999999999999988776543

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=94.02  E-value=0.13  Score=41.31  Aligned_cols=145  Identities=15%  Similarity=0.140  Sum_probs=75.1

Q ss_pred             HHHHHhhc-CCcEEEEEecCC-CchhHH---HHHHcCCCCccceeecccCCCcccccccccccCH-hHHHhhHhhCCCCE
Q 030407            3 ALCKFLRD-KYSLAAVTNDIF-TKEDGE---FLMRNGALPEERIRAVETGGCPHAAIREDISINL-GPLEELSNLFKADL   76 (178)
Q Consensus         3 ~~~~~~~~-~~~vaVI~nd~g-~~iD~~---li~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l-~~l~~l~~~~~~d~   76 (178)
                      ++...+.. +.|+.++--|+. ..--.+   +.+..|+    ++..-..+.        |....+ ..+..+ +..++|+
T Consensus       117 ~la~~~~~~g~~v~l~~~D~~r~~a~~ql~~~~~~~~v----~v~~~~~~~--------~p~~~~~~~l~~~-~~~~~D~  183 (297)
T 1j8m_F          117 KLAYFYKKKGFKVGLVGADVYRPAALEQLQQLGQQIGV----PVYGEPGEK--------DVVGIAKRGVEKF-LSEKMEI  183 (297)
T ss_dssp             HHHHHHHHTTCCEEEEECCCSSSHHHHHHHHHHHHHTC----CEECCTTCC--------CHHHHHHHHHHHH-HHTTCSE
T ss_pred             HHHHHHHHCCCeEEEEecCCCCHHHHHHHHHHhccCCe----EEEecCCCC--------CHHHHHHHHHHHH-HhCCCCE
Confidence            44455544 489999998877 432211   1223344    333321111        111112 233333 2368999


Q ss_pred             EEEeCCcchh--h-hccc--------ccccceEEEEEeCCCCCCCCcCCCCCC--Cce-eEEEEecCCCCCchhHhHHHH
Q 030407           77 LLCESGGDNL--A-ANFS--------RELADYIIYIIDVSGGDKIPRKGGPGI--TQA-DLLVINKTDLASAIGADLAVM  142 (178)
Q Consensus        77 iiiEttG~~~--~-~~~~--------~~~ad~~I~VvD~~~~~~~~~~~~~qi--~~a-diiviNK~Dl~~~~~~~~~~~  142 (178)
                      |||.|.|...  . ....        ...+|.+++|+|+..+.+..... ..+  ... ..+|+||+|....  .  ..+
T Consensus       184 ViIDTpg~~~~~~~~~l~~el~~i~~~~~~d~vllVvda~~g~~~~~~~-~~~~~~~~i~gvVlnk~D~~~~--~--g~~  258 (297)
T 1j8m_F          184 IIVDTAGRHGYGEEAALLEEMKNIYEAIKPDEVTLVIDASIGQKAYDLA-SKFNQASKIGTIIITKMDGTAK--G--GGA  258 (297)
T ss_dssp             EEEECCCSCCTTCHHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHHHHH-HHHHHTCTTEEEEEECGGGCTT--H--HHH
T ss_pred             EEEeCCCCcccccHHHHHHHHHHHHHHhcCCEEEEEeeCCchHHHHHHH-HHHHhhCCCCEEEEeCCCCCcc--h--HHH
Confidence            9999999422  1 0111        11358899999987542211100 011  122 5789999998644  2  223


Q ss_pred             HHHHHhcCCCCCEEEEecccCCCHHHH
Q 030407          143 ERDALRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       143 ~~~l~~~np~a~i~~~SA~~g~gi~el  169 (178)
                      .+.....  +.|+.+++  +|++++++
T Consensus       259 ~~~~~~~--~~pi~~i~--~Ge~v~dl  281 (297)
T 1j8m_F          259 LSAVAAT--GATIKFIG--TGEKIDEL  281 (297)
T ss_dssp             HHHHHTT--TCCEEEEE--CSSSTTCE
T ss_pred             HHHHHHH--CcCEEEEe--CCCChhhc
Confidence            3333332  46888876  68887654

>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=94.00  E-value=0.011  Score=54.07  Aligned_cols=59  Identities=22%  Similarity=0.206  Sum_probs=38.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCC
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLA  132 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~  132 (178)
                      ++.+-||+|.|..    ....+. ..+|++|+|+|++++...+..    .......+-++++||+|+.
T Consensus        97 ~~~i~liDTPG~~df~~~~~~~l-~~aD~ailVvDa~~g~~~qt~~~~~~~~~~~~p~ilviNK~D~~  163 (842)
T 1n0u_A           97 SFLINLIDSPGHVDFSSEVTAAL-RVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRA  163 (842)
T ss_dssp             EEEEEEECCCCCCSSCHHHHHHH-HTCSEEEEEEETTTBSCHHHHHHHHHHHHTTCEEEEEEECHHHH
T ss_pred             CceEEEEECcCchhhHHHHHHHH-HhCCEEEEEEeCCCCCCHHHHHHHHHHHHcCCCeEEEEECCCcc
Confidence            5678899999931    111111 247999999999987543221    0011234679999999986

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=91.85  E-value=0.25  Score=36.43  Aligned_cols=25  Identities=12%  Similarity=-0.013  Sum_probs=16.3

Q ss_pred             HHHHHHhhc-CCcEEEEEecCC-Cchh
Q 030407            2 LALCKFLRD-KYSLAAVTNDIF-TKED   26 (178)
Q Consensus         2 ~~~~~~~~~-~~~vaVI~nd~g-~~iD   26 (178)
                      .++++.+.+ ++++++|.++++ ..+|
T Consensus        24 ~~l~~~l~~~g~~v~~i~~~~~~~~id   50 (174)
T 1np6_A           24 KKLIPALCARGIRPGLIKHTHHDMDVD   50 (174)
T ss_dssp             HHHHHHHHHTTCCEEEEEECCC-----
T ss_pred             HHHHHhccccCCceeEEeeCCCccccC
Confidence            456666655 489999999987 6676

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=90.50  E-value=0.46  Score=36.95  Aligned_cols=63  Identities=13%  Similarity=0.138  Sum_probs=36.4

Q ss_pred             CCCCEEEEeCCcchhh----h----c---c-cccccceEEEEEeCCCCCCC-Cc-CC--------CCCCCceeEEEEecC
Q 030407           72 FKADLLLCESGGDNLA----A----N---F-SRELADYIIYIIDVSGGDKI-PR-KG--------GPGITQADLLVINKT  129 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~----~----~---~-~~~~ad~~I~VvD~~~~~~~-~~-~~--------~~qi~~adiiviNK~  129 (178)
                      .+..+.|+.|.|..-.    .    .   + ....+|.+++|+|+...... .. .+        ...+..+-++|+||+
T Consensus        85 ~~~~l~iiDTpG~~~~~~~~~~~~~~i~~~~~~~~~d~il~v~~~d~~~~~~~~~~~~~~l~~~~~~~~~~~iivV~nK~  164 (270)
T 1h65_A           85 AGFTLNIIDTPGLIEGGYINDMALNIIKSFLLDKTIDVLLYVDRLDAYRVDNLDKLVAKAITDSFGKGIWNKAIVALTHA  164 (270)
T ss_dssp             TTEEEEEEECCCSEETTEECHHHHHHHHHHTTTCEECEEEEEEESSCCCCCHHHHHHHHHHHHHHCGGGGGGEEEEEECC
T ss_pred             CCeEEEEEECCCCCCCccchHHHHHHHHHHhhcCCCCEEEEEEeCCCCcCCHHHHHHHHHHHHHhCcccccCEEEEEECc
Confidence            3568999999994100    0    0   1 11246999999887542111 00 00        111113679999999


Q ss_pred             CCCCc
Q 030407          130 DLASA  134 (178)
Q Consensus       130 Dl~~~  134 (178)
                      |+.++
T Consensus       165 Dl~~~  169 (270)
T 1h65_A          165 QFSPP  169 (270)
T ss_dssp             SCCCG
T ss_pred             ccCCc
Confidence            99865

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=87.40  E-value=0.3  Score=39.50  Aligned_cols=89  Identities=13%  Similarity=0.062  Sum_probs=48.6

Q ss_pred             hCCCCEEEEeCCcchhhh---------------cccccccceEEEEEeCCCCCCCCc---CCCCCCCceeEEEEecCCCC
Q 030407           71 LFKADLLLCESGGDNLAA---------------NFSRELADYIIYIIDVSGGDKIPR---KGGPGITQADLLVINKTDLA  132 (178)
Q Consensus        71 ~~~~d~iiiEttG~~~~~---------------~~~~~~ad~~I~VvD~~~~~~~~~---~~~~qi~~adiiviNK~Dl~  132 (178)
                      ..++|+|||.|.|.....               ...+...|.+++|+|+..+.+...   .+.+.+. -.-+|+||.|-.
T Consensus       189 ~~~yD~VIIDTpg~l~~~~~l~~eL~~~~~vi~~~~p~~~d~vllVl~a~~~~~~l~~~~~~~~~~~-i~GvVltk~d~~  267 (320)
T 1zu4_A          189 EQNYDLLLIDTAGRLQNKTNLMAELEKMNKIIQQVEKSAPHEVLLVIDATTGQNGVIQAEEFSKVAD-VSGIILTKMDST  267 (320)
T ss_dssp             HTTCSEEEEECCCCGGGHHHHHHHHHHHHHHHHTTCTTCCSEEEEEEEGGGTHHHHHHHHHHTTTSC-CCEEEEECGGGC
T ss_pred             hcCCCEEEEcCCCcccccHHHHHHHHHHHHHHhcccCCCCceEEEEEECCCcHHHHHHHHHHhhcCC-CcEEEEeCCCCC
Confidence            468999999999942110               011222478899999875421111   1111111 235899999975


Q ss_pred             CchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHH
Q 030407          133 SAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       133 ~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                      ..  .  ..+.+.....  +.|+.+++  +|+++++
T Consensus       268 ~~--~--g~~~~~~~~~--~~Pi~~i~--~Ge~~~d  295 (320)
T 1zu4_A          268 SK--G--GIGLAIKELL--NIPIKMIG--VGEKVDD  295 (320)
T ss_dssp             SC--T--THHHHHHHHH--CCCEEEEE--CSSSTTC
T ss_pred             Cc--h--hHHHHHHHHH--CcCEEEEe--CCCCccc
Confidence            44  1  2333344433  34676664  4666644

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=87.23  E-value=1.3  Score=35.93  Aligned_cols=145  Identities=17%  Similarity=0.249  Sum_probs=74.5

Q ss_pred             HHHHhhc-CCcEEEEEecCC-Cc-hhHHH--HHHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCCCCEEE
Q 030407            4 LCKFLRD-KYSLAAVTNDIF-TK-EDGEF--LMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADLLL   78 (178)
Q Consensus         4 ~~~~~~~-~~~vaVI~nd~g-~~-iD~~l--i~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~~d~ii   78 (178)
                      +...+++ +.+|.+.-.|.. .+ .+...  -++.|+    .+..-..+......+       .+.+. +....++|+++
T Consensus       149 Lag~l~~~~g~V~l~g~D~~r~~a~eql~~~~~~~gv----~~v~q~~~~~p~~~v-------~e~l~-~~~~~~~d~vl  216 (328)
T 3e70_C          149 LANWLKNHGFSVVIAASDTFRAGAIEQLEEHAKRIGV----KVIKHSYGADPAAVA-------YDAIQ-HAKARGIDVVL  216 (328)
T ss_dssp             HHHHHHHTTCCEEEEEECCSSTTHHHHHHHHHHHTTC----EEECCCTTCCHHHHH-------HHHHH-HHHHHTCSEEE
T ss_pred             HHHHHHhcCCEEEEEeecccccchHHHHHHHHHHcCc----eEEeccccCCHHHHH-------HHHHH-HHHhccchhhH
Confidence            4444544 378888888876 32 33211  123343    233332232332211       12222 22234789999


Q ss_pred             EeCCcchh-hhc----c----cccccceEEEEEeCCCCCCCCcCCCCCC---CceeEEEEecCCCCCchhHhHHHHHHHH
Q 030407           79 CESGGDNL-AAN----F----SRELADYIIYIIDVSGGDKIPRKGGPGI---TQADLLVINKTDLASAIGADLAVMERDA  146 (178)
Q Consensus        79 iEttG~~~-~~~----~----~~~~ad~~I~VvD~~~~~~~~~~~~~qi---~~adiiviNK~Dl~~~~~~~~~~~~~~l  146 (178)
                      ++|.|..- ...    .    .....|-.+.++|+..+.+..... ..+   .....+++||.|-....    ..+...+
T Consensus       217 iDtaG~~~~~~~l~~eL~~i~ral~~de~llvLDa~t~~~~~~~~-~~~~~~~~it~iilTKlD~~a~~----G~~l~~~  291 (328)
T 3e70_C          217 IDTAGRSETNRNLMDEMKKIARVTKPNLVIFVGDALAGNAIVEQA-RQFNEAVKIDGIILTKLDADARG----GAALSIS  291 (328)
T ss_dssp             EEECCSCCTTTCHHHHHHHHHHHHCCSEEEEEEEGGGTTHHHHHH-HHHHHHSCCCEEEEECGGGCSCC----HHHHHHH
T ss_pred             HhhccchhHHHHHHHHHHHHHHHhcCCCCEEEEecHHHHHHHHHH-HHHHHhcCCCEEEEeCcCCccch----hHHHHHH
Confidence            99999421 100    0    001137788999987664221100 001   12468999999975432    2233344


Q ss_pred             HhcCCCCCEEEEecccCCCHHHH
Q 030407          147 LRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       147 ~~~np~a~i~~~SA~~g~gi~el  169 (178)
                      ...  +.|+.+++  +|++++++
T Consensus       292 ~~~--~~pi~~i~--~Ge~v~dl  310 (328)
T 3e70_C          292 YVI--DAPILFVG--VGQGYDDL  310 (328)
T ss_dssp             HHH--TCCEEEEE--CSSSTTCE
T ss_pred             HHH--CCCEEEEe--CCCCcccc
Confidence            433  35888888  78887654

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=86.72  E-value=1.9  Score=36.32  Aligned_cols=118  Identities=19%  Similarity=0.211  Sum_probs=60.0

Q ss_pred             HHHHHhhc--CCcEEEEEecCC-C-chhHHH--HHHcCCCCccceeecccCCCcccccccccccCH-hHHHhhHhhCCCC
Q 030407            3 ALCKFLRD--KYSLAAVTNDIF-T-KEDGEF--LMRNGALPEERIRAVETGGCPHAAIREDISINL-GPLEELSNLFKAD   75 (178)
Q Consensus         3 ~~~~~~~~--~~~vaVI~nd~g-~-~iD~~l--i~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l-~~l~~l~~~~~~d   75 (178)
                      +++.++.+  ++||.++--|+. . .+|...  -...++    ++.....+.        |....+ ..+..+ +..++|
T Consensus       119 ~LA~~l~~~~G~kVllvd~D~~r~~a~~ql~~~~~~~~l----~v~~~~~~~--------dp~~i~~~~l~~~-~~~~~D  185 (433)
T 2xxa_A          119 KLGKFLREKHKKKVLVVSADVYRPAAIKQLETLAEQVGV----DFFPSDVGQ--------KPVDIVNAALKEA-KLKFYD  185 (433)
T ss_dssp             HHHHHHHHTSCCCEEEEECCCSSTTHHHHHHHHHHHHTC----EECCCCSSS--------CHHHHHHHHHHHH-HHTTCS
T ss_pred             HHHHHHHHhcCCeEEEEecCCCCccHHHHHHhhcccCCe----eEEeCCCCC--------CHHHHHHHHHHHH-HhCCCC
Confidence            45556643  689999999987 4 344211  112233    332221111        111111 233333 235899


Q ss_pred             EEEEeCCcchh-----hhc---cc-ccccceEEEEEeCCCCCCCCcC---CCCCCCceeEEEEecCCCCCc
Q 030407           76 LLLCESGGDNL-----AAN---FS-RELADYIIYIIDVSGGDKIPRK---GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        76 ~iiiEttG~~~-----~~~---~~-~~~ad~~I~VvD~~~~~~~~~~---~~~qi~~adiiviNK~Dl~~~  134 (178)
                      +|||+|.|..-     ...   .. ....+.+++|+|+..+.+....   +.+.+.. .-+|+||.|....
T Consensus       186 ~VIIDTpG~l~~~~~l~~~L~~~~~~~~p~~vllVvda~~g~~~~~~~~~f~~~l~i-~gvVlnK~D~~~~  255 (433)
T 2xxa_A          186 VLLVDTAGRLHVDEAMMDEIKQVHASINPVETLFVVDAMTGQDAANTAKAFNEALPL-TGVVLTKVDGDAR  255 (433)
T ss_dssp             EEEEECCCCCTTCHHHHHHHHHHHHHSCCSEEEEEEETTBCTTHHHHHHHHHHHSCC-CCEEEECTTSSSC
T ss_pred             EEEEECCCcccccHHHHHHHHHHHHhhcCcceeEEeecchhHHHHHHHHHHhccCCC-eEEEEecCCCCcc
Confidence            99999999311     000   00 1124788999999765322110   1001111 3579999998654

>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=85.38  E-value=0.3  Score=40.40  Aligned_cols=49  Identities=14%  Similarity=0.177  Sum_probs=33.3

Q ss_pred             ceeEEEEecCC--CCCc-hhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHH
Q 030407          120 QADLLVINKTD--LASA-IGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus       120 ~adiiviNK~D--l~~~-~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~  170 (178)
                      .+-+++.||.|  +.+. .....+.++++.+..  +++++++||++++++.+|.
T Consensus       202 KPvi~v~N~~e~d~~~~~~n~~~~~v~~~a~~~--g~~vv~iSAk~E~el~eL~  253 (368)
T 2dby_A          202 KPVIYVANVAEEDLPDGRGNPQVEAVRRKALEE--GAEVVVVSARLEAELAELS  253 (368)
T ss_dssp             SCEEEEEECCGGGTTTCTTCHHHHHHHHHHHHH--TCEEEEECHHHHHHHHTSC
T ss_pred             CCeEEeccccHHhhcccchhhHHHHHHHHHHHc--CCeEEEeechhHHHHHHhc
Confidence            57899999997  3331 014566777766654  3699999999866655543

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=81.94  E-value=2.4  Score=32.61  Aligned_cols=62  Identities=13%  Similarity=0.155  Sum_probs=34.7

Q ss_pred             CCCEEEEeCCcch----h--------hhcccccccceEEEEEeCCCCCCC--CcCC--------CCCCCceeEEEEecCC
Q 030407           73 KADLLLCESGGDN----L--------AANFSRELADYIIYIIDVSGGDKI--PRKG--------GPGITQADLLVINKTD  130 (178)
Q Consensus        73 ~~d~iiiEttG~~----~--------~~~~~~~~ad~~I~VvD~~~~~~~--~~~~--------~~qi~~adiiviNK~D  130 (178)
                      +..+.|+.|.|..    .        ...+....+|.+++|+|.......  ....        ......+-++|+||+|
T Consensus        83 ~~~l~liDTpG~~~~~~~~~~~~~~i~~~l~~~~~~~il~V~~~d~~~~~~~~~~~~~~l~~~~~~~~~~~~ivv~nK~D  162 (262)
T 3def_A           83 GFTINIIDTPGLVEAGYVNHQALELIKGFLVNRTIDVLLYVDRLDVYAVDELDKQVVIAITQTFGKEIWCKTLLVLTHAQ  162 (262)
T ss_dssp             TEEEEEEECCCSEETTEECHHHHHHHHHHTTTCEECEEEEEEESSCSCCCHHHHHHHHHHHHHHCGGGGGGEEEEEECTT
T ss_pred             CeeEEEEECCCCCCcccchHHHHHHHHHHHhcCCCCEEEEEEcCCCCCCCHHHHHHHHHHHHHhchhhhcCEEEEEeCcc
Confidence            4578999999941    0        011111245889999877543211  0000        1111225689999999


Q ss_pred             CCCc
Q 030407          131 LASA  134 (178)
Q Consensus       131 l~~~  134 (178)
                      +.++
T Consensus       163 l~~~  166 (262)
T 3def_A          163 FSPP  166 (262)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            9643

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=81.83  E-value=1.3  Score=37.24  Aligned_cols=56  Identities=11%  Similarity=-0.065  Sum_probs=36.6

Q ss_pred             CceeEEEEecCCCC---------CchhHhHHHHHHHHHhc---------CCCCCEEEEec--ccCCCHHHHHHHHhhh
Q 030407          119 TQADLLVINKTDLA---------SAIGADLAVMERDALRM---------RDGGPFIFAQV--GWVIGIIFTLSITHYI  176 (178)
Q Consensus       119 ~~adiiviNK~Dl~---------~~~~~~~~~~~~~l~~~---------np~a~i~~~SA--~~g~gi~el~~~l~~~  176 (178)
                      ..+-++|+||.|+.         ++  ...+++.+.++++         .+..+++.+|+  +++.|++++.+.+.+.
T Consensus       175 ~~p~~lV~tkpdlllLDEPtsgLD~--~~~~~l~~~l~~l~~~~l~~~g~~~~~iiliSsh~l~~~~~e~L~d~I~~~  250 (413)
T 1tq4_A          175 KKEFYFVRTKVDSDITNEADGEPQT--FDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISD  250 (413)
T ss_dssp             TCEEEEEECCHHHHHHHHHTTCCTT--CCHHHHHHHHHHHHHHHHHHTTCSSCCEEECCTTCTTSTTHHHHHHHHHHH
T ss_pred             CCCeEEEEecCcccccCcccccCCH--HHHHHHHHHHHHHHHHHHHhcCCCCCcEEEEecCcCCccCHHHHHHHHHHh
Confidence            44679999999975         11  1223333333332         24568999999  6677899999988653

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	178
d2qm8a1	323	c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylo	4e-15
d2p67a1	327	c.37.1.10 (A:1-327) LAO/AO transport system kinase	2e-09

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]} Length = 323

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

 Score = 69.5 bits (169), Expect = 4e-15
 Identities = 25/176 (14%), Positives = 53/176 (30%), Gaps = 6/176 (3%)

Query: 1   MLALCKFLRD-KYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGGCPHAAIREDIS 59
           + AL   L    + +A +  D  +   G  ++ +                P  +      
Sbjct: 68  IDALGSLLTAAGHKVAVLAVDPSSTRTGGSILGDKTRMARLAIDRNAFIRPSPSSGTLGG 127

Query: 60  INLGPLE--ELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPG 117
           +     E   L      D++L E+ G   +     +L D+ + ++    GD++       
Sbjct: 128 VAAKTRETMLLCEAAGFDVILVETVGVGQSETAVADLTDFFLVLMLPGAGDELQGIKKGI 187

Query: 118 ITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSIT 173
              AD++ +NK D         A        +    P       W   ++    + 
Sbjct: 188 FELADMIAVNKADDGDGERRASAAASEYRAALHILTP---PSATWTPPVVTISGLH 240

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]} Length = 327

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

 Score = 53.3 bits (127), Expect = 2e-09
 Identities = 30/153 (19%), Positives = 53/153 (34%), Gaps = 4/153 (2%)

Query: 1   MLALCKFLRDKY-SLAAVTNDIFTKEDGEFLMRNGALPEE--RIRAVETGGCPHAAIRED 57
           + A    L  +   +A +  D  +   G  ++ +     +  R  A      P +     
Sbjct: 71  LEAFGMLLIREGLKVAVIAVDPSSPVTGGSILGDKTRMNDLARAEAAFIRPVPSSGHLGG 130

Query: 58  ISINLGPLEELSNLFKADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPG 117
            S     L  L      D+++ E+ G   +      + D  I +    GGD +       
Sbjct: 131 ASQRARELMLLCEAAGYDVVIVETVGVGQSETEVARMVDCFISLQIAGGGDDLQGIKKGL 190

Query: 118 ITQADLLVINKTDLASAIGADLAVME-RDALRM 149
           +  ADL+VINK D  +     +A      AL +
Sbjct: 191 MEVADLIVINKDDGDNHTNVAIARHMYESALHI 223

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	178
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	99.93
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	99.88
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	99.84
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	99.5
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	98.91
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	98.89
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	98.78
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	98.77
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	98.74
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	98.73
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	98.72
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	98.72
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	98.71
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	98.68
d1kk1a3	195	Initiation factor eIF2 gamma subunit, N-terminal (	98.65
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	98.65
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	98.64
d2qn6a3	205	Initiation factor eIF2 gamma subunit, N-terminal (	98.64
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	98.63
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	98.62
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	98.61
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	98.6
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	98.58
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	98.57
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	98.57
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	98.57
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	98.56
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	98.55
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	98.55
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	98.54
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	98.53
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	98.52
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	98.52
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	98.5
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	98.5
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	98.48
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	98.48
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	98.48
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	98.48
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	98.47
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	98.44
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	98.43
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	98.42
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	98.41
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	98.4
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	98.4
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	98.4
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	98.38
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	98.37
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	98.35
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	98.35
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	98.34
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	98.34
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	98.33
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	98.33
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	98.33
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	98.32
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	98.32
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	98.31
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	98.25
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	98.22
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	98.21
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	98.21
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	98.17
d1d2ea3	196	Elongation factor Tu (EF-Tu), N-terminal (G) domai	98.15
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	98.14
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	98.13
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	98.11
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	98.07
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	98.05
d1zunb3	222	Sulfate adenylate transferase subunit cysN/C, EF-T	98.04
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	97.98
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	97.98
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	97.89
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	97.75
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	97.75
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	97.63
d1r5ba3	245	Eukaryotic peptide chain release factor ERF2, G do	97.6
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	97.17
d1jnya3	224	Elongation factor eEF-1alpha, N-terminal (G) domai	97.16
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.14
d1f60a3	239	Elongation factor eEF-1alpha, N-terminal (G) domai	97.08
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	96.84
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	96.72
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.67
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.51
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.33
d1okkd2	207	GTPase domain of the signal recognition particle r	96.12
d2fh5b1	207	Signal recognition particle receptor beta-subunit	96.0
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	95.76
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	95.46
d1ls1a2	207	GTPase domain of the signal sequence recognition p	94.54
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	92.14
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	90.3
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	88.95

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, 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: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.93  E-value=4.6e-28  Score=188.75  Aligned_cols=157  Identities=19%  Similarity=0.264  Sum_probs=110.4

Q ss_pred             HHHHHHhhcCCcEEEEEecCC-CchhHHHHHHcCCCCccceeecccCC-CcccccccccccCHhH-HHhhHh-hCCCCEE
Q 030407            2 LALCKFLRDKYSLAAVTNDIF-TKEDGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGP-LEELSN-LFKADLL   77 (178)
Q Consensus         2 ~~~~~~~~~~~~vaVI~nd~g-~~iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~-l~~l~~-~~~~d~i   77 (178)
                      ++++++ .+++|+|||+|||| +++|+.++...+.    .++++.+|| ||+.  ++++...+.. +.++.. ..+||+|
T Consensus        21 ~~lL~~-~~~~riaVI~Ne~g~~~iD~~~~~~~~~----~~~el~~gcicc~~--~~~~~~~l~~~~~~~~~~~~~~d~i   93 (222)
T d1nija1          21 RHILNE-QHGYKIAVIENEFGEVSVDDQLIGDRAT----QIKTLTNGCICCSR--SNELEDALLDLLDNLDKGNIQFDRL   93 (222)
T ss_dssp             HHHHHS-CCCCCEEEECSSCCSCCEEEEEECTTSC----EEEEETTSCEEECT--TSCHHHHHHHHHHHHHHTSCCCSEE
T ss_pred             HHHHhc-CCCCcEEEEEecccchhhhhhhhccccc----ceEEecCCcceecc--chhHHHHHHHHHHHHhhccCCccee
Confidence            345543 23589999999999 9999998876554    789999999 9985  5555444322 223322 2369999


Q ss_pred             EEeCCcchh----hhcccc-------cccceEEEEEeCCCCCCCCcC---CCCCCCceeEEEEecCCCCCchhHhHHHHH
Q 030407           78 LCESGGDNL----AANFSR-------ELADYIIYIIDVSGGDKIPRK---GGPGITQADLLVINKTDLASAIGADLAVME  143 (178)
Q Consensus        78 iiEttG~~~----~~~~~~-------~~ad~~I~VvD~~~~~~~~~~---~~~qi~~adiiviNK~Dl~~~~~~~~~~~~  143 (178)
                      +|||||++-    ...+..       ...+.+|+|+|+.++......   +..|++.||+||+||+|++++  .  ++++
T Consensus        94 iIE~sG~~~p~~l~~~~~~~~~~~~~~~l~~vi~vVDa~~~~~~~~~~~~~~~Qi~~AD~ivlNK~Dl~~~--~--~~~~  169 (222)
T d1nija1          94 VIECTGMADPGPIIQTFFSHEVLCQRYLLDGVIALVDAVHADEQMNQFTIAQSQVGYADRILLTKTDVAGE--A--EKLH  169 (222)
T ss_dssp             EEEEETTCCHHHHHHHHHHSHHHHHHEEEEEEEEEEETTTHHHHHHHCHHHHHHHHTCSEEEEECTTTCSC--T--HHHH
T ss_pred             EEeecccchhhHHHHHHHhhhcccccccccchhhhhhhhhhhhhhhhhHHHHHHHHhCCcccccccccccH--H--HHHH
Confidence            999999531    111110       113789999999887644332   335899999999999999876  3  4788


Q ss_pred             HHHHhcCCCCCEEEEecccCCCHHHHH
Q 030407          144 RDALRMRDGGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus       144 ~~l~~~np~a~i~~~SA~~g~gi~el~  170 (178)
                      +.++++||.++|+.+| .-...++.|+
T Consensus       170 ~~l~~lNP~a~Ii~~~-~g~v~~~~ll  195 (222)
T d1nija1         170 ERLARINARAPVYTVT-HGDIDLGLLF  195 (222)
T ss_dssp             HHHHHHCSSSCEEECC-SSCCCGGGGS
T ss_pred             HHHHHHhCCCeEEEee-CCccCHHHhh
Confidence            8999999999999877 2234555443

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=99.88  E-value=4.2e-23  Score=168.62  Aligned_cols=170  Identities=15%  Similarity=0.111  Sum_probs=111.4

Q ss_pred             CHHHHHHhhc-CCcEEEEEecCCCchhHHHHHHcCCCCccceeecccCC-Cc--cccccccc---ccCHhHHHhhHhhCC
Q 030407            1 MLALCKFLRD-KYSLAAVTNDIFTKEDGEFLMRNGALPEERIRAVETGG-CP--HAAIREDI---SINLGPLEELSNLFK   73 (178)
Q Consensus         1 ~~~~~~~~~~-~~~vaVI~nd~g~~iD~~li~~~~~~~~~~~~~l~~Gc-Cc--~l~i~~dl---~~~l~~l~~l~~~~~   73 (178)
                      ++++++++.+ ++|+|||.||+++++++..+-....    .+.++..++ ||  +..-|+.+   .........+.+..+
T Consensus        68 i~~l~~~~~~~g~~vaViavDpss~~~gg~llgdr~----rm~~~~~~~~~~ir~~~~~~~~gg~~~~~~~~i~~~~~~g  143 (323)
T d2qm8a1          68 IDALGSLLTAAGHKVAVLAVDPSSTRTGGSILGDKT----RMARLAIDRNAFIRPSPSSGTLGGVAAKTRETMLLCEAAG  143 (323)
T ss_dssp             HHHHHHHHHHTTCCEEEEEECGGGGSSCCCSSCCGG----GSTTGGGCTTEEEECCCCCSSHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhhcCCceeeeecccccHHHHhccccchh----hHHHHhcccceeeccccccccccchhHHHHHHHHhhccCC
Confidence            3578887765 5999999999997664322211111    334444333 22  11111221   111223334555679


Q ss_pred             CCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHhHH-HH----HHHHHh
Q 030407           74 ADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLA-VM----ERDALR  148 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~~~-~~----~~~l~~  148 (178)
                      ||+|||||+|+++...+....+|..++|+.+..|++.+..++.+++.||++|+||+|+.+.  .... .+    ...++.
T Consensus       144 ~d~iiiETVG~gq~e~~~~~~~D~~v~v~~p~~GD~iQ~~k~gilE~aDi~vvNKaD~~~~--~~~~~~~~~~~~~~l~~  221 (323)
T d2qm8a1         144 FDVILVETVGVGQSETAVADLTDFFLVLMLPGAGDELQGIKKGIFELADMIAVNKADDGDG--ERRASAAASEYRAALHI  221 (323)
T ss_dssp             CCEEEEEECSSSSCHHHHHTTSSEEEEEECSCC------CCTTHHHHCSEEEEECCSTTCC--HHHHHHHHHHHHHHHTT
T ss_pred             CCeEEEeehhhhhhhhhhhcccceEEEEeeccchhhhhhhhhhHhhhhheeeEeccccccc--hHHHHHHHHHHHHHhhc
Confidence            9999999999877777776778999999999999999999999999999999999999876  3322 12    222222


Q ss_pred             cC-----CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          149 MR-----DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       149 ~n-----p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..     +..|++.+||++|+|+++|++++.+.
T Consensus       222 ~~~~~~~~~p~V~~~Sa~~g~Gi~el~~~I~~~  254 (323)
T d2qm8a1         222 LTPPSATWTPPVVTISGLHGKGLDSLWSRIEDH  254 (323)
T ss_dssp             BCCSBTTBCCCEEEEBTTTTBSHHHHHHHHHHH
T ss_pred             ccccccCCCCceEEEEecCCCCHHHHHHHHHHH
Confidence            22     44699999999999999999998764

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {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: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=99.84  E-value=2.9e-21  Score=157.85  Aligned_cols=168  Identities=20%  Similarity=0.136  Sum_probs=105.6

Q ss_pred             HHHHHHhhc-CCcEEEEEecCCCchhH-------HHHHHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCC
Q 030407            2 LALCKFLRD-KYSLAAVTNDIFTKEDG-------EFLMRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFK   73 (178)
Q Consensus         2 ~~~~~~~~~-~~~vaVI~nd~g~~iD~-------~li~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~   73 (178)
                      +++++++.+ ++||||+.+|++++.++       .+|...+..+...++++.++|  ++   +.+.........+.+..+
T Consensus        72 ~~l~~~~~~~g~~vavlavDpss~~~ggailgdr~rm~~~~~~~~~~ir~~~~~g--~l---gg~~~~~~~~~~~~~~~g  146 (327)
T d2p67a1          72 EAFGMLLIREGLKVAVIAVDPSSPVTGGSILGDKTRMNDLARAEAAFIRPVPSSG--HL---GGASQRARELMLLCEAAG  146 (327)
T ss_dssp             HHHHHHHHHTTCCEEEEEECCC---------------CTTTTCTTEEEEEECC----------CHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhcCCceeeecCCCceeeeccccccchhHHHHhccccccccccccccc--cc---ccchhhhhHHHHHHHhcC
Confidence            567777766 49999999999976643       333322222223444444333  21   011222233345556779


Q ss_pred             CCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCcCCCCCCCceeEEEEecCCCCCchhHhHH----HHHHHHHhc
Q 030407           74 ADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPRKGGPGITQADLLVINKTDLASAIGADLA----VMERDALRM  149 (178)
Q Consensus        74 ~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~~qi~~adiiviNK~Dl~~~~~~~~~----~~~~~l~~~  149 (178)
                      +|+|||||+|+.+........+|.+++|+++..|++.+..+...++.||++|+||+|+...  ....    .+...++..
T Consensus       147 ~d~iliEtvG~gq~e~~i~~~aD~~l~v~~P~~Gd~iq~~k~gi~e~aDi~VvNKaD~~~~--~~~~~~~~~~~~al~~~  224 (327)
T d2p67a1         147 YDVVIVETVGVGQSETEVARMVDCFISLQIAGGGDDLQGIKKGLMEVADLIVINKDDGDNH--TNVAIARHMYESALHIL  224 (327)
T ss_dssp             CSEEEEEEECCTTHHHHHHTTCSEEEEEECC------CCCCHHHHHHCSEEEECCCCTTCH--HHHHHHHHHHHHHHHHS
T ss_pred             CCeEEEeeccccccchhhhhccceEEEEecCCCchhhhhhchhhhccccEEEEEeecccch--HHHHHHHHHHHHHhhhc
Confidence            9999999999777666555578999999999999988877777889999999999999876  3322    233333322


Q ss_pred             C-----CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          150 R-----DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       150 n-----p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .     +..||+.|||++|+||++|++.|.++
T Consensus       225 ~~~~~~w~p~V~~~SA~~g~Gi~eL~~~I~~~  256 (327)
T d2p67a1         225 RRKYDEWQPRVLTCSALEKRGIDEIWHAIIDF  256 (327)
T ss_dssp             CCSBTTBCCEEEECBGGGTBSHHHHHHHHHHH
T ss_pred             ccCCCCCcceeEEEEeeCCCCHHHHHHHHHHH
Confidence            2     23589999999999999999998764

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=99.50  E-value=6e-16  Score=118.84  Aligned_cols=167  Identities=12%  Similarity=0.010  Sum_probs=98.2

Q ss_pred             HHHHHHhhcCCcEEEEEecCC-C------chhHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhH--hh
Q 030407            2 LALCKFLRDKYSLAAVTNDIF-T------KEDGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELS--NL   71 (178)
Q Consensus         2 ~~~~~~~~~~~~vaVI~nd~g-~------~iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~--~~   71 (178)
                      .++++++..++++|+|-+|+| .      .+|...+.+..... .......+|| ||+-.+    ...+..+....  ..
T Consensus        18 ~~ll~~~~~~~~~~ivn~d~~~~~~~~~~~id~~~~~~~~~~~-~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~   92 (244)
T d1yrba1          18 GEFGRYLEDNYKVAYVNLDTGVKELPYEPSIDVREFVTVEEIM-REGYGPNGAIVESYDRL----MEKFNEYLNKILRLE   92 (244)
T ss_dssp             HHHHHHHTTTSCEEEEECCSSCSCCSSCCSEEGGGTCCHHHHH-TTTCCHHHHHHHHHHHH----HTTHHHHHHHHHHHH
T ss_pred             HHHHHHHhhCCeEEEEecCcccccCCCcccchHHHHHHHHHHh-HhhhccCCchhhhhHhH----HhhHHHHHHHHHhhc
Confidence            466777766688998887877 3      34544321100000 1224555677 443211    22332222211  12


Q ss_pred             CCCCEEEEeCCcchhh-------hccc-ccccceEEEEEeCCCCCCCCcC---------CCCCCCceeEEEEecCCCCCc
Q 030407           72 FKADLLLCESGGDNLA-------ANFS-RELADYIIYIIDVSGGDKIPRK---------GGPGITQADLLVINKTDLASA  134 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~-------~~~~-~~~ad~~I~VvD~~~~~~~~~~---------~~~qi~~adiiviNK~Dl~~~  134 (178)
                      ..++++++++.|..-.       ..+. ....+.+++++|+..+...+..         ...|+..++++++||+|+.++
T Consensus        93 ~~~~~~~id~~g~~~~~~~~~~~~~~~~~~~~~~~v~vvd~~~~~~~~~~~~~~l~~~~~~~~~~~~~ivvinK~D~~~~  172 (244)
T d1yrba1          93 KENDYVLIDTPGQMETFLFHEFGVRLMENLPYPLVVYISDPEILKKPNDYCFVRFFALLIDLRLGATTIPALNKVDLLSE  172 (244)
T ss_dssp             HHCSEEEEECCSSHHHHHHSHHHHHHHHTSSSCEEEEEECGGGCCSHHHHHHHHHHHHHHHHHHTSCEEEEECCGGGCCH
T ss_pred             cccceeeeccccchhHHHHHHHHHHHHhhccCceEEEEeccccccCchhHhhHHHHHHHHHHHhCCCceeeeeccccccH
Confidence            3689999999994210       0011 1123678999998776543221         112567899999999999986


Q ss_pred             hhHhHHHHHHH----------------------------HHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          135 IGADLAVMERD----------------------------ALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       135 ~~~~~~~~~~~----------------------------l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                        .+.+....+                            +++..+..+++++||++|+|+++|++.|.+
T Consensus       173 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vSa~~geGi~~L~~~l~e  239 (244)
T d1yrba1         173 --EEKERHRKYFEDIDYLTARLKLDPSMQGLMAYKMCSMMTEVLPPVRVLYLSAKTREGFEDLETLAYE  239 (244)
T ss_dssp             --HHHHHHHHHHHCHHHHHHHHHHCCSHHHHHHHHHHHHHHHHSCCCCCEECCTTTCTTHHHHHHHHHH
T ss_pred             --HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCCcEEEEECCCCCCHHHHHHHHHH
Confidence              443332211                            122345679999999999999999999876

>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=98.91  E-value=5e-10  Score=82.37  Aligned_cols=102  Identities=16%  Similarity=0.122  Sum_probs=64.3

Q ss_pred             CCCEEEEeCCcch-h-hhc-ccccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           73 KADLLLCESGGDN-L-AAN-FSRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        73 ~~d~iiiEttG~~-~-~~~-~~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      ++.+.++.+.|.. . ... .....+|.+++++|+..+...+..    .......+-++|+||+|+++.  ++.+.....
T Consensus        58 ~~~~~~~d~~g~~~~~~~~~~~l~~~d~~ilv~d~~~g~~~~~~~~~~~~~~~~~p~iiv~NKiD~~~~--~~~~~~~~~  135 (179)
T d1wb1a4          58 NYRITLVDAPGHADLIRAVVSAADIIDLALIVVDAKEGPKTQTGEHMLILDHFNIPIIVVITKSDNAGT--EEIKRTEMI  135 (179)
T ss_dssp             TEEEEECCCSSHHHHHHHHHHHTTSCCEEEEEEETTTCSCHHHHHHHHHHHHTTCCBCEEEECTTSSCH--HHHHHHHHH
T ss_pred             CccccccccccccccccchhhhhhhccccccccccccccchhhhhhhhhhhhcCCcceeccccccccCH--HHHHHHHHH
Confidence            3456666777721 0 011 111246999999999887543211    011134567999999999987  544333322


Q ss_pred             HHh----c--CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          146 ALR----M--RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       146 l~~----~--np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.    .  .+..+++++||++|+|+++|++.|.+.
T Consensus       136 ~~~~~~~~~~~~~~~iv~iSA~~g~gi~eL~~~I~~~  172 (179)
T d1wb1a4         136 MKSILQSTHNLKNSSIIPISAKTGFGVDELKNLIITT  172 (179)
T ss_dssp             HHHHHHHSSSGGGCCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHhhcCCCCeEEEEEccCCcCHHHHHHHHHhc
Confidence            222    1  134699999999999999999988654

>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=98.89  E-value=6.5e-10  Score=82.37  Aligned_cols=81  Identities=7%  Similarity=-0.024  Sum_probs=58.0

Q ss_pred             cceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHh---cCCCCCEEEEecccCCCHH
Q 030407           95 ADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERDALR---MRDGGPFIFAQVGWVIGII  167 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~---~np~a~i~~~SA~~g~gi~  167 (178)
                      ++.+++++|+.++......    +......+-++|+||+|+.++  .+.+...+.+++   .++..+++++||++|+|++
T Consensus       106 ~~~vi~viD~~~~~~~~~~~~~~~l~~~~~piivv~NK~D~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~SA~~~~gi~  183 (195)
T d1svia_         106 LKAVVQIVDLRHAPSNDDVQMYEFLKYYGIPVIVIATKADKIPK--GKWDKHAKVVRQTLNIDPEDELILFSSETKKGKD  183 (195)
T ss_dssp             EEEEEEEEETTSCCCHHHHHHHHHHHHTTCCEEEEEECGGGSCG--GGHHHHHHHHHHHHTCCTTSEEEECCTTTCTTHH
T ss_pred             hhhhhhhhhccccccccccccccccccccCcceechhhccccCH--HHHHHHHHHHHHHhcccCCCCEEEEeCCCCCCHH
Confidence            4789999999876432210    111234467999999999876  555554444432   3577899999999999999


Q ss_pred             HHHHHHhhhh
Q 030407          168 FTLSITHYIV  177 (178)
Q Consensus       168 el~~~l~~~~  177 (178)
                      +|+++|.+..
T Consensus       184 el~~~i~~~l  193 (195)
T d1svia_         184 EAWGAIKKMI  193 (195)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999998765

>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=98.78  E-value=1.1e-08  Score=74.68  Aligned_cols=103  Identities=15%  Similarity=0.147  Sum_probs=64.8

Q ss_pred             CCCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHh
Q 030407           72 FKADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        72 ~~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      .+..+.++++.|..-    ...+. ..++.+++++|.++......         .....-..+-+|+.||+|+.+.  ..
T Consensus        59 ~~~~~~i~D~~g~~~~~~~~~~~~-~~~~~ii~v~d~~d~~s~~~~~~~l~~~~~~~~~~~~piliv~NK~Dl~~~--~~  135 (182)
T d1moza_          59 KNLKLNVWDLGGQTSIRPYWRCYY-ADTAAVIFVVDSTDKDRMSTASKELHLMLQEEELQDAALLVFANKQDQPGA--LS  135 (182)
T ss_dssp             TTEEEEEEEEC----CCTTGGGTT-TTEEEEEEEEETTCTTTHHHHHHHHHHHTTSSTTSSCEEEEEEECTTSTTC--CC
T ss_pred             CCEEEEEEecccccccchhHHhhh-ccceeEEEEeeecccccchhHHHHHHHHHHhhccCCcceEEEEEeeccccc--cC
Confidence            356788899999421    11222 25799999999987643211         0111123467889999999765  34


Q ss_pred             HHHHHHHHH--hcC-CCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          139 LAVMERDAL--RMR-DGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       139 ~~~~~~~l~--~~n-p~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      .+++.+.+.  ... ...+++++||++|+|+++++++|.+.+
T Consensus       136 ~~~i~~~~~~~~~~~~~~~~~e~SA~~g~gv~e~~~~l~~~i  177 (182)
T d1moza_         136 ASEVSKELNLVELKDRSWSIVASSAIKGEGITEGLDWLIDVI  177 (182)
T ss_dssp             HHHHHHHTTTTTCCSSCEEEEEEBGGGTBTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhCCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            444444432  112 235799999999999999999887653

>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=98.77  E-value=1e-08  Score=74.41  Aligned_cols=104  Identities=15%  Similarity=0.106  Sum_probs=67.3

Q ss_pred             CCCCEEEEeCCcchhhhc---ccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           72 FKADLLLCESGGDNLAAN---FSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~~~---~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ..+.+.++++.|..-...   .....++.+++|+|++.......         .....-..+-++++||+|+.++  ...
T Consensus        54 ~~~~~~i~D~~g~~~~~~~~~~~~~~~~~ii~v~D~s~~~~~~~~~~~l~~~~~~~~~~~~piiiv~NK~Dl~~~--~~~  131 (173)
T d1e0sa_          54 KNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDA--MKP  131 (173)
T ss_dssp             TTEEEEEEEESCCGGGHHHHGGGTTTCCEEEEEEETTCGGGHHHHHHHHHHHHTSGGGTTCEEEEEEECTTSTTC--CCH
T ss_pred             cceeeEEecCCCcchhhhHHHhhhcccceEEEEEecccchhHHHHHHHHHHHhhhcccccceeeeeeeccccccc--ccH
Confidence            357888999999432111   11235799999999976543211         0111123567999999999765  333


Q ss_pred             HHHHHHH--HhcC-CCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDA--LRMR-DGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l--~~~n-p~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ..+...+  .... ...+++++||++|+||+|+|++|.+.+
T Consensus       132 ~~i~~~~~~~~~~~~~~~~~e~SA~tg~gv~e~~~~l~~~~  172 (173)
T d1e0sa_         132 HEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY  172 (173)
T ss_dssp             HHHHHHTTGGGCCSSCEEEEECBTTTTBTHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhCCCEEEEeeCCCCcCHHHHHHHHHHhc
Confidence            4444433  2222 234789999999999999999998754

>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=98.74  E-value=4.4e-09  Score=76.70  Aligned_cols=100  Identities=10%  Similarity=0.002  Sum_probs=68.1

Q ss_pred             CCCEEEEeCCcchhh---------hcc--cccccceEEEEEeCCCCCCCCcC-CC----CC-CCceeEEEEecCCCCCch
Q 030407           73 KADLLLCESGGDNLA---------ANF--SRELADYIIYIIDVSGGDKIPRK-GG----PG-ITQADLLVINKTDLASAI  135 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---------~~~--~~~~ad~~I~VvD~~~~~~~~~~-~~----~q-i~~adiiviNK~Dl~~~~  135 (178)
                      +..+.++.|.|....         ...  ....+|.+++|+|++++...... ..    .. -..+-++|+||+|+.+. 
T Consensus        52 ~~~~~~~DtpG~~~~~~~~~~~~~~~~~~~~~~ad~il~v~D~~~~~~~~~~~i~~~l~~~~~~~piilv~NK~Dl~~~-  130 (178)
T d1wf3a1          52 RRQIVFVDTPGLHKPMDALGEFMDQEVYEALADVNAVVWVVDLRHPPTPEDELVARALKPLVGKVPILLVGNKLDAAKY-  130 (178)
T ss_dssp             TEEEEEEECCCCCCCCSHHHHHHHHHHHHHTSSCSEEEEEEETTSCCCHHHHHHHHHHGGGTTTSCEEEEEECGGGCSS-
T ss_pred             eeeeeecccccccccccccchhcccccccccccccceeeeechhhhhcccccchhhheeccccchhhhhhhcccccccC-
Confidence            567899999994110         000  11247999999999876432211 00    00 13356999999999876 


Q ss_pred             hHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          136 GADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       136 ~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                       .+  ...+.+++..+..+++++||++|+|+++|++.|.+.
T Consensus       131 -~~--~~~~~~~~~~~~~~~~~iSA~~~~gi~~L~~~i~~~  168 (178)
T d1wf3a1         131 -PE--EAMKAYHELLPEAEPRMLSALDERQVAELKADLLAL  168 (178)
T ss_dssp             -HH--HHHHHHHHTSTTSEEEECCTTCHHHHHHHHHHHHTT
T ss_pred             -HH--HHHHHHHhhcccCceEEEecCCCCCHHHHHHHHHHh
Confidence             32  334555666778899999999999999999998765

>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=98.73  E-value=1.5e-08  Score=72.66  Aligned_cols=103  Identities=13%  Similarity=0.032  Sum_probs=65.2

Q ss_pred             hCCCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHh
Q 030407           71 LFKADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        71 ~~~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      ..++.+.++++.|..--   .......++.+++++|+++......         .....-..+-++|.||+|+.+.  ..
T Consensus        43 ~~~~~~~~~D~~G~~~~~~~~~~~~~~~~~~i~v~d~~d~~~~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~--~~  120 (165)
T d1ksha_          43 HRGFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATLLIFANKQDLPGA--LS  120 (165)
T ss_dssp             ETTEEEEEEEECCSHHHHTTGGGGCTTCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC--CC
T ss_pred             ccccceeeeecCcchhhhhHHHhhhhhhhcceeeeecccchhHHHHHHhhhhhhhhcccCCCceEEEEeccccccc--cC
Confidence            34678999999994211   1111224699999999876432211         0011122467899999999865  34


Q ss_pred             HHHHHHHHH--hc-CCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          139 LAVMERDAL--RM-RDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       139 ~~~~~~~l~--~~-np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+.....+.  .+ ....+++++||++|+|+++++++|.+
T Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~e~~~~l~~  160 (165)
T d1ksha_         121 CNAIQEALELDSIRSHHWRIQGCSAVTGEDLLPGIDWLLD  160 (165)
T ss_dssp             HHHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhhcCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            444443332  11 23457999999999999999998754

>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=98.72  E-value=1.5e-08  Score=73.29  Aligned_cols=103  Identities=17%  Similarity=0.045  Sum_probs=66.3

Q ss_pred             CCCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           72 FKADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .++.+.+.++.|..-.   .......+|.+++++|+++......         .....-..+-++++||+|+.++  ...
T Consensus        58 ~~~~~~i~d~~g~~~~~~~~~~~~~~~~~ii~v~d~~d~~s~~~~~~~~~~~~~~~~~~~~pillv~nK~Dl~~~--~~~  135 (176)
T d1fzqa_          58 QGFKLNVWDIGGQRKIRPYWRSYFENTDILIYVIDSADRKRFEETGQELTELLEEEKLSCVPVLIFANKQDLLTA--APA  135 (176)
T ss_dssp             TTEEEEEEECSSCGGGHHHHHHHHTTCSEEEEEEETTCGGGHHHHHHHHHHHTTCGGGTTCCEEEEEECTTSTTC--CCH
T ss_pred             CCeeEeEeeccccccchhHHHHHhhccceeEEeeccccccchhhhhhhhhhhhhhhccCCCeEEEEEEecccccc--ccH
Confidence            3567888888883211   1112235799999999986532211         0001112456889999999876  455


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.+.+.+...   ....+++++||++|+|++|+|++|.+.
T Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~SA~tg~gv~e~~~~l~~~  175 (176)
T d1fzqa_         136 SEIAEGLNLHTIRDRVWQIQSCSALTGEGVQDGMNWVCKN  175 (176)
T ss_dssp             HHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhcCCEEEEEeCCCCCCHHHHHHHHHhc
Confidence            5555444311   123579999999999999999998653

>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=98.72  E-value=6.8e-09  Score=75.86  Aligned_cols=82  Identities=18%  Similarity=0.139  Sum_probs=58.0

Q ss_pred             cceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcC---CCCCEEEEecccCCCHH
Q 030407           95 ADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIGADLAVMERDALRMR---DGGPFIFAQVGWVIGII  167 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~n---p~a~i~~~SA~~g~gi~  167 (178)
                      +|.+++|+|+..+......    .......+.++|+||+|+..........+.+.+++..   +..+++++||++|.|++
T Consensus        92 ~dvii~v~d~~~~~~~~~~~~~~~~~~~~~~~i~v~nK~D~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vSa~~g~gv~  171 (186)
T d1mkya2          92 ADVVVIVLDATQGITRQDQRMAGLMERRGRASVVVFNKWDLVVHREKRYDEFTKLFREKLYFIDYSPLIFTSADKGWNID  171 (186)
T ss_dssp             CSEEEEEEETTTCCCHHHHHHHHHHHHTTCEEEEEEECGGGSTTGGGCHHHHHHHHHHHCGGGTTSCEEECBTTTTBSHH
T ss_pred             CCEEEEeecccccchhhHHHHHHHHHHcCCceeeeccchhhhcchhhhhhhHHHHHHHHhcccCCCeEEEEeCCCCCCHH
Confidence            5899999999876443221    1112345679999999998663233455555555432   46799999999999999


Q ss_pred             HHHHHHhhh
Q 030407          168 FTLSITHYI  176 (178)
Q Consensus       168 el~~~l~~~  176 (178)
                      +|++.|.+.
T Consensus       172 ~L~~~i~~~  180 (186)
T d1mkya2         172 RMIDAMNLA  180 (186)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999998764

>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=98.71  E-value=8.1e-09  Score=73.55  Aligned_cols=98  Identities=13%  Similarity=0.080  Sum_probs=66.4

Q ss_pred             CCCEEEEeCCcchhh-----------hccc-ccccceEEEEEeCCCCCCCCcC--CCCCCCceeEEEEecCCCCCchhHh
Q 030407           73 KADLLLCESGGDNLA-----------ANFS-RELADYIIYIIDVSGGDKIPRK--GGPGITQADLLVINKTDLASAIGAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~~~-----------~~~~-~~~ad~~I~VvD~~~~~~~~~~--~~~qi~~adiiviNK~Dl~~~~~~~  138 (178)
                      +..+.+++|.|....           .... ...+|.+++|+|++++......  ........-++++||+|+.+.  ..
T Consensus        47 ~~~~~~~Dt~G~~~~~~~~~~~~~~~~~~~~~~~ad~ii~v~d~~~~~~~~~~~~~~~~~~~~~i~~~~k~d~~~~--~~  124 (160)
T d1xzpa2          47 GILFRIVDTAGVRSETNDLVERLGIERTLQEIEKADIVLFVLDASSPLDEEDRKILERIKNKRYLVVINKVDVVEK--IN  124 (160)
T ss_dssp             TEEEEEEESSCCCSSCCTTCCCCCHHHHHHHHHHCSEEEEEEETTSCCCHHHHHHHHHHTTSSEEEEEEECSSCCC--CC
T ss_pred             CeeEEeccccccccCCccHHHHHHHHHHHHHHHhCCEEEEEEeCCCCcchhhhhhhhhcccccceeeeeeccccch--hh
Confidence            566778888884111           0000 1236999999999876532211  001123456899999999987  55


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+.+.+.   +.+..+++++||++|+||++|++.|.+
T Consensus       125 ~~~~~~~---~~~~~~~~~vSA~~g~gi~~L~~~I~k  158 (160)
T d1xzpa2         125 EEEIKNK---LGTDRHMVKISALKGEGLEKLEESIYR  158 (160)
T ss_dssp             HHHHHHH---HTCSTTEEEEEGGGTCCHHHHHHHHHH
T ss_pred             hHHHHHH---hCCCCcEEEEECCCCCCHHHHHHHHHh
Confidence            5555443   456779999999999999999999865

>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=98.68  E-value=7.4e-09  Score=74.93  Aligned_cols=100  Identities=14%  Similarity=0.121  Sum_probs=63.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.++++.|..    +...+. ..+|++++|+|+++......         .....-..+-++|.||+|+.+......
T Consensus        47 ~~~l~i~D~~g~e~~~~~~~~~~-~~~d~~ilv~d~t~~~s~~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~~~v~~  125 (168)
T d2gjsa1          47 EASLMVYDIWEQDGGRWLPGHCM-AMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVSV  125 (168)
T ss_dssp             EEEEEEEECC-------CHHHHH-TSCSEEEEEEETTCHHHHHHHHHHHHHHHHHCC--CCCEEEEEECTTCGGGCCSCH
T ss_pred             ccceeeeecccccccceecccch-hhhhhhceeccccccccccccccccchhhcccccccceEEEeecccchhhhcchhH
Confidence            5788899999931    112222 25799999999987532211         011112235689999999975411123


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ...++..+..  +.+++++||++|.||+++|+.+.+
T Consensus       126 ~~~~~~~~~~--~~~~~e~Sak~~~~v~~~f~~l~~  159 (168)
T d2gjsa1         126 DEGRACAVVF--DCKFIETSAALHHNVQALFEGVVR  159 (168)
T ss_dssp             HHHHHHHHHH--TSEEEECBTTTTBSHHHHHHHHHH
T ss_pred             HHHHHHHHhc--CCEEEEEeCCCCcCHHHHHHHHHH
Confidence            3444444544  458999999999999999998754

>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=98.65  E-value=2e-08  Score=74.54  Aligned_cols=101  Identities=15%  Similarity=0.105  Sum_probs=64.2

Q ss_pred             CCEEEEeCCcch-hhhcc--cccccceEEEEEeCCCCCCCCc--CC---CCCCCce-eEEEEecCCCCCchhHhH----H
Q 030407           74 ADLLLCESGGDN-LAANF--SRELADYIIYIIDVSGGDKIPR--KG---GPGITQA-DLLVINKTDLASAIGADL----A  140 (178)
Q Consensus        74 ~d~iiiEttG~~-~~~~~--~~~~ad~~I~VvD~~~~~~~~~--~~---~~qi~~a-diiviNK~Dl~~~~~~~~----~  140 (178)
                      +-+.||.|.|-. .....  ....+|..+.|+|+..+...+.  .+   ...+... -++++||+|+.++  .+.    +
T Consensus        78 ~~~~~iDtPGh~~f~~~~~~~~~~~d~~ilvvda~~g~~~~~t~e~~~~~~~~~~~~iiv~inK~D~~d~--~~~~~~~~  155 (195)
T d1kk1a3          78 RRVSFIDAPGHEALMTTMLAGASLMDGAILVIAANEPCPRPQTREHLMALQIIGQKNIIIAQNKIELVDK--EKALENYR  155 (195)
T ss_dssp             EEEEEEECSSHHHHHHHHHHCGGGCSEEEEEEETTSCSSCHHHHHHHHHHHHHTCCCEEEEEECGGGSCH--HHHHHHHH
T ss_pred             eeEeeeccchhhhhhHHhhcccccccccccccchhhhhhhhhhHHHHHHHHHhcCccceeeeecccchhh--HHHHHHHH
Confidence            347899999921 11111  1124699999999988743211  00   0011223 3678999999976  332    3


Q ss_pred             HHHHHHHhcC-CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMR-DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~n-p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+.++..+ ..++++++||++|+||++|++.+.+.
T Consensus       156 ~~~~~~~~~~~~~~~iIpiSA~~G~ni~~Ll~~I~~~  192 (195)
T d1kk1a3         156 QIKEFIEGTVAENAPIIPISALHGANIDVLVKAIEDF  192 (195)
T ss_dssp             HHHHHHTTSTTTTCCEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHhccccCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3444444433 34789999999999999999988764

>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=98.65  E-value=1.8e-08  Score=72.85  Aligned_cols=101  Identities=17%  Similarity=0.104  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C------CCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K------GGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~------~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+-+++|.|..    +...+. ..+|++|+|+|.++......  .      ....-..+-+++.||+|+........+
T Consensus        53 ~~~l~~wDt~G~e~~~~~~~~~~-~~ad~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~iivv~nK~D~~~~~~v~~~  131 (169)
T d3raba_          53 RIKLQIWDTAGQERYRTITTAYY-RGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDMEDERVVSSE  131 (169)
T ss_dssp             EEEEEEEEECCSGGGHHHHHTTT-TTCCEEEEEEETTCHHHHHTHHHHHHHHHHHCCSCCEEEEEEECTTCGGGCCSCHH
T ss_pred             eEEEEEEECCCchhhHHHHHHHH-hcCCEEEEEEECccchhhhhhhhhhhhhhcccCCcceEEEEEeecccccccccchh
Confidence            3567789999932    122232 35799999999987532211  0      001123456788899998654212234


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..++..++.  +.+++++||++|+||+++|+.+.+.
T Consensus       132 ~~~~~~~~~--~~~~~e~Sak~g~gv~e~f~~l~~~  165 (169)
T d3raba_         132 RGRQLADHL--GFEFFEASAKDNINVKQTFERLVDV  165 (169)
T ss_dssp             HHHHHHHHH--TCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             hhHHHHHHc--CCEEEEecCCCCcCHHHHHHHHHHH
Confidence            445555554  3689999999999999999987654

>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=98.64  E-value=9e-09  Score=74.36  Aligned_cols=103  Identities=13%  Similarity=0.064  Sum_probs=65.3

Q ss_pred             CCCEEEEeCCcchh---hhcccccccceEEEEEeCCCCCCCCc--C--------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL---AANFSRELADYIIYIIDVSGGDKIPR--K--------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~---~~~~~~~~ad~~I~VvD~~~~~~~~~--~--------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+-+.++.|...   ........+|++++|+|+++......  .        ....-..+-++|.||+|+........
T Consensus        49 ~~~l~~~d~~g~~~~~~~~~~~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~piilVgnK~Dl~~~~~v~~  128 (171)
T d2erxa1          49 ICTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIKGDVESIPIMLVGNKCDESPSREVQS  128 (171)
T ss_dssp             EEEEEEEECCSCSSCHHHHHHHHHHCSEEEEEEETTCHHHHHTTHHHHHHHHHHHC---CCCEEEEEECGGGGGGCCSCH
T ss_pred             cceeccccccccccccccccccccceeEEEEEeecccccchhcccchhhhhhhhhccCCCCcEEEEeecccccccccccH
Confidence            46778889999421   01111234799999999986432211  0        01112235689999999964311223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ++.++..++.  +.++++|||++|+||+++|+.|.+++
T Consensus       129 ~e~~~~~~~~--~~~~~e~Sak~~~~v~e~f~~l~~~~  164 (171)
T d2erxa1         129 SEAEALARTW--KCAFMETSAKLNHNVKELFQELLNLE  164 (171)
T ss_dssp             HHHHHHHHHH--TCEEEECBTTTTBSHHHHHHHHHHTC
T ss_pred             HHHHHHHHHc--CCeEEEEcCCCCcCHHHHHHHHHHHH
Confidence            4455555554  35899999999999999999887764

>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=98.64  E-value=2.8e-08  Score=74.31  Aligned_cols=100  Identities=16%  Similarity=0.092  Sum_probs=62.5

Q ss_pred             CEEEEeCCcch-h-hhcc-cccccceEEEEEeCCCCC-CCCcC-C---CCCCCc-eeEEEEecCCCCCchhHhHHH----
Q 030407           75 DLLLCESGGDN-L-AANF-SRELADYIIYIIDVSGGD-KIPRK-G---GPGITQ-ADLLVINKTDLASAIGADLAV----  141 (178)
Q Consensus        75 d~iiiEttG~~-~-~~~~-~~~~ad~~I~VvD~~~~~-~~~~~-~---~~qi~~-adiiviNK~Dl~~~~~~~~~~----  141 (178)
                      .+-+|.|.|-. . ..+. ....+|.+|+|+|+..+. ..+.+ +   ...+.. .-+|++||+|+.++  .+...    
T Consensus        87 ~~~iiD~PGH~df~~~~~~~~~~ad~ailvVda~~gi~~~~t~e~~~~~~~~~i~~iIV~vNK~Dl~~~--~~~~~~~~~  164 (205)
T d2qn6a3          87 RISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSK--EEALSQYRQ  164 (205)
T ss_dssp             EEEEEECSCHHHHHHHHHHTSSCCSEEEEEEETTSCSSCHHHHHHHHHHHHTTCCCEEEEEECGGGSCH--HHHHHHHHH
T ss_pred             EEEEeccchHHHHHhhhhcceeccccccccccccccccchhHHHHHHHHHHcCCceeeeccccCCCccc--hHHHHHHHH
Confidence            36799999921 1 1111 112469999999998874 21110 0   001222 34777999999876  43333    


Q ss_pred             HHHHHHhcC-CCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMR-DGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~n-p~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+.++..+ ...+++++||++|.||++|++.+...
T Consensus       165 ~~~~l~~~~~~~~p~ipiSA~~g~nI~~L~e~i~~~  200 (205)
T d2qn6a3         165 IKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEY  200 (205)
T ss_dssp             HHHHHTTSTTTTCCEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHhccccCCCCeEEEEeCCCCCChHHHHHHHHhh
Confidence            333333333 24799999999999999999987654

>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=98.63  E-value=5.1e-09  Score=79.85  Aligned_cols=106  Identities=16%  Similarity=0.038  Sum_probs=64.5

Q ss_pred             CCCCEEEEeCCcch-hh-hcc-cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCCchh--------
Q 030407           72 FKADLLLCESGGDN-LA-ANF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLASAIG--------  136 (178)
Q Consensus        72 ~~~d~iiiEttG~~-~~-~~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~~~~--------  136 (178)
                      ....+.||.|.|-. .. ... ....+|.+|+|+|+.++...+..    .......+-++++||+|+.+...        
T Consensus        68 ~~~~~~~iDtPGh~~f~~~~~~~~~~~D~~ilVvda~~g~~~~~~~~~~~~~~~~~p~iivlNK~D~~~~~~~~~~~~~~  147 (227)
T d1g7sa4          68 TLPGLFFIDTPGHEAFTTLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYRTPFVVAANKIDRIHGWRVHEGRPFM  147 (227)
T ss_dssp             TCCEEEEECCCTTSCCTTSBCSSSBSCSEEEEEEETTTCCCHHHHHHHHHHHHTTCCEEEEEECGGGSTTCCCCTTCCHH
T ss_pred             cccccccccccceecccccchhcccccceEEEEEecccCcccchhHHHHHhhcCCCeEEEEEECccCCCchhhhhhHHHH
Confidence            35678999999921 11 111 11246999999999887543321    11113456799999999975410        


Q ss_pred             ------------HhHHHHHHHHHhc----------------CCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          137 ------------ADLAVMERDALRM----------------RDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       137 ------------~~~~~~~~~l~~~----------------np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                                  .....+.+....+                ....+++++||++|+|+++|++.|...+
T Consensus       148 ~~~~~~~~~v~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~pvSa~~G~gid~Ll~~l~~l~  216 (227)
T d1g7sa4         148 ETFSKQDIQVQQKLDTKVYELVGKLHEEGFESERFDRVTDFASQVSIIPISAITGEGIPELLTMLMGLA  216 (227)
T ss_dssp             HHHTTSCHHHHHHHHHHHHHHHHHHHHTTCEEEEGGGCSCTTTEEEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             HhhhcchHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccccccCCCeEEEeeCCCCCCHHHHHHHHHHHH
Confidence                        0001111111111                1125799999999999999999886653

>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=98.62  E-value=3e-08  Score=72.19  Aligned_cols=101  Identities=17%  Similarity=0.190  Sum_probs=68.1

Q ss_pred             CCCEEEEeCCcchhhhc--------cc--ccccceEEEEEeCCCCCCCCc----C-----CCCCCCceeEEEEecCCCCC
Q 030407           73 KADLLLCESGGDNLAAN--------FS--RELADYIIYIIDVSGGDKIPR----K-----GGPGITQADLLVINKTDLAS  133 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~--------~~--~~~ad~~I~VvD~~~~~~~~~----~-----~~~qi~~adiiviNK~Dl~~  133 (178)
                      +..+.++.|.|..-...        +.  ...++.++.++|.........    .     .......+-++|+||+|+.+
T Consensus        48 ~~~~~~~DtpG~~~~~~~~~~~~~~~l~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~p~iiv~NK~D~~~  127 (180)
T d1udxa2          48 EERFTLADIPGIIEGASEGKGLGLEFLRHIARTRVLLYVLDAADEPLKTLETLRKEVGAYDPALLRRPSLVALNKVDLLE  127 (180)
T ss_dssp             SCEEEEEECCCCCCCGGGSCCSCHHHHHHHTSSSEEEEEEETTSCHHHHHHHHHHHHHHHCHHHHHSCEEEEEECCTTSC
T ss_pred             CCeEEEcCCCeeecCchHHHHHHHHHHHHHHhhhhhhhhcccccccccchhhhhhhhhccccccchhhhhhhhhhhhhhh
Confidence            56788999999311000        00  123588899999865321100    0     00112345799999999998


Q ss_pred             chhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          134 AIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       134 ~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      +  .+.+.+.+.++.  ...+++++||++|+|+++|++.|.+.+
T Consensus       128 ~--~~~~~~~~~~~~--~~~~~~~iSA~tg~gid~L~~~i~~~l  167 (180)
T d1udxa2         128 E--EAVKALADALAR--EGLAVLPVSALTGAGLPALKEALHALV  167 (180)
T ss_dssp             H--HHHHHHHHHHHT--TTSCEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             H--HHHHHHHHHHHh--cCCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            8  777777777764  356999999999999999999987653

>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=98.61  E-value=5.5e-08  Score=71.07  Aligned_cols=101  Identities=16%  Similarity=0.134  Sum_probs=64.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ....-+.+|+|..    +...+. ..+|++|+|+|.+.......         .....-..+-++|.||+|+........
T Consensus        63 ~~~~~i~dt~G~e~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~iilv~nK~Dl~~~~~v~~  141 (186)
T d2f7sa1          63 KVHLQLWDTAGQERFRSLTTAFF-RDAMGFLLMFDLTSQQSFLNVRNWMSQLQANAYCENPDIVLIGNKADLPDQREVNE  141 (186)
T ss_dssp             EEEEEEEEEESHHHHHHHHHHHH-TTCCEEEEEEETTCHHHHHHHHHHHHTCCCCCTTTCCEEEEEEECTTCGGGCCSCH
T ss_pred             eEEeccccCCcchhhHHHHHHHH-hcCCEEEEEEeccccccceeeeeccchhhhhccCCCceEEEEeeeccchhhhcchH
Confidence            3556778888831    112222 35799999999976432110         111112235689999999965421223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..++.  +.+++++||++|+||+++|+.+.+.
T Consensus       142 ~e~~~~~~~~--~~~~~e~Sak~~~~i~e~f~~l~~~  176 (186)
T d2f7sa1         142 RQARELADKY--GIPYFETSAATGQNVEKAVETLLDL  176 (186)
T ss_dssp             HHHHHHHHHT--TCCEEEEBTTTTBTHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            4455566654  4689999999999999999987654

>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=98.60  E-value=6.7e-08  Score=69.77  Aligned_cols=102  Identities=13%  Similarity=0.066  Sum_probs=61.0

Q ss_pred             CCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc--CC----------CCCCCceeEEEEecCCCCCchh-H
Q 030407           74 ADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR--KG----------GPGITQADLLVINKTDLASAIG-A  137 (178)
Q Consensus        74 ~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~--~~----------~~qi~~adiiviNK~Dl~~~~~-~  137 (178)
                      ..+.+..|.|..-.   .......++.+++++|.+.......  .+          ...-..+-++++||+|+.+... .
T Consensus        52 ~~~~~~d~~g~~~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~piilv~nK~Dl~~~~~~v  131 (175)
T d1ky3a_          52 ATMQVWDTAGQERFQSLGVAFYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANVNSPETFPFVILGNKIDAEESKKIV  131 (175)
T ss_dssp             EEEEEECCC----------CCSTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSCTTTCCEEEEEECTTSCGGGCCS
T ss_pred             ccceeeccCCchhhhhHHHHHhhccceEEEEeecccccccchhhhcchhhhhhhhhcccccCcEEEEecccchhhhhcch
Confidence            45667888883111   1111235799999999976432111  00          0111346799999999975410 1


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+..++..++. ...+++++||++|+||+++|+.|.+.
T Consensus       132 ~~~~~~~~~~~~-~~~~~~e~SA~~g~gv~e~f~~l~~~  169 (175)
T d1ky3a_         132 SEKSAQELAKSL-GDIPLFLTSAKNAINVDTAFEEIARS  169 (175)
T ss_dssp             CHHHHHHHHHHT-TSCCEEEEBTTTTBSHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHc-CCCeEEEEeCCCCcCHHHHHHHHHHH
Confidence            123344444443 45689999999999999999987653

>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=98.58  E-value=5.8e-08  Score=70.90  Aligned_cols=101  Identities=12%  Similarity=0.091  Sum_probs=63.2

Q ss_pred             CCCEEEEeCCcchhhh---cccccccceEEEEEeCCCCCCCCc--CC--------CC--CCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDNLAA---NFSRELADYIIYIIDVSGGDKIPR--KG--------GP--GITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~---~~~~~~ad~~I~VvD~~~~~~~~~--~~--------~~--qi~~adiiviNK~Dl~~~~~~  137 (178)
                      .+.+.+.++.|..-..   ......++++++++|.+.......  .+        ..  .-..+-++|.||+|+.+.. .
T Consensus        50 ~~~~~~~d~~g~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~~~~~~i~~~~~~~~~~~ip~ilv~nK~Dl~~~~-~  128 (184)
T d1vg8a_          50 LVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQ-V  128 (184)
T ss_dssp             EEEEEEEEECSSGGGSCSCCGGGTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSSGGGSCEEEEEECTTSSCCC-S
T ss_pred             eEEEEeeecCCcccccccccccccCccEEEEeecccchhhhhcchhhHHHHHHHhccccccCCCEEEEEEeecccccc-h
Confidence            4677888999932111   111234799999999976432110  00        00  1123569999999987641 2


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ..+...+.... ....++++|||++|.||+++|+.|.+
T Consensus       129 ~~~~~~~~~~~-~~~~~~~e~Sak~~~gI~e~f~~l~~  165 (184)
T d1vg8a_         129 ATKRAQAWCYS-KNNIPYFETSAKEAINVEQAFQTIAR  165 (184)
T ss_dssp             CHHHHHHHHHH-TTSCCEEECBTTTTBSHHHHHHHHHH
T ss_pred             hHHHHHHHHHH-hcCCeEEEEcCCCCcCHHHHHHHHHH
Confidence            22333333333 34679999999999999999998754

>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=98.57  E-value=3e-08  Score=71.66  Aligned_cols=99  Identities=14%  Similarity=0.053  Sum_probs=63.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CC-----CCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KG-----GPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~-----~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.+++|.|..    +...+. ..++.+++|+|.++......   .+     ...-..+-++|.||+|+........+
T Consensus        53 ~~~l~i~Dt~G~e~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~ilvgnK~D~~~~~~v~~~  131 (171)
T d2ew1a1          53 KVKLQIWDTAGQERFRSITQSYY-RSANALILTYDITCEESFRCLPEWLREIEQYASNKVITVLVGNKIDLAERREVSQQ  131 (171)
T ss_dssp             EEEEEEEEECCSGGGHHHHGGGS-TTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCSSCHH
T ss_pred             EEEEEEEECCCchhhHHHHHHHH-hccceEEEeeecccchhhhhhhhhhhhhcccccccccEEEEEeecccccccchhhh
Confidence            4678889999931    112222 35799999999876432211   00     01113456888999998654212344


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~  174 (178)
                      ...+..+..  +.+++++||++|+||+++|..|.
T Consensus       132 ~~~~~~~~~--~~~~~~~SAktg~gV~e~f~~l~  163 (171)
T d2ew1a1         132 RAEEFSEAQ--DMYYLETSAKESDNVEKLFLDLA  163 (171)
T ss_dssp             HHHHHHHHH--TCCEEECCTTTCTTHHHHHHHHH
T ss_pred             HHHHHHHhC--CCEEEEEccCCCCCHHHHHHHHH
Confidence            555555544  35899999999999999987654

>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=98.57  E-value=2.7e-08  Score=71.60  Aligned_cols=100  Identities=14%  Similarity=0.088  Sum_probs=65.5

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C------CCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K------GGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~------~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.+.++.|..    +...+. ..+|++++|+|.++......  .      ....-..+-+++.||+|+........+
T Consensus        52 ~~~l~i~D~~g~~~~~~~~~~~~-~~~d~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilvgnK~Dl~~~~~~~~~  130 (166)
T d1z0fa1          52 KIKLQIWDTAGQERFRAVTRSYY-RGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIILIGNKADLEAQRDVTYE  130 (166)
T ss_dssp             EEEEEEEECTTGGGTCHHHHHHH-HTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHH
T ss_pred             EEEEEEeccCCchhHHHHHHHHh-cCCcEEEEEeccCchHHHHHHHHHHHHHHhhccccceEEEEcccccchhhcccHHH
Confidence            4678889999932    112222 24799999999976532211  0      001123456888999999654223334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ..++..++.  ..+++++||++|+||+++|+.|.+
T Consensus       131 ~~~~~~~~~--~~~~~e~Saktg~~v~e~f~~i~~  163 (166)
T d1z0fa1         131 EAKQFAEEN--GLLFLEASAKTGENVEDAFLEAAK  163 (166)
T ss_dssp             HHHHHHHHT--TCEEEECCTTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCEEEEEeCCCCCCHHHHHHHHHH
Confidence            556666654  468999999999999999987754

>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=98.57  E-value=2.2e-08  Score=71.78  Aligned_cols=102  Identities=18%  Similarity=0.082  Sum_probs=66.6

Q ss_pred             CCCEEEEeCCcchhhh---cccccccceEEEEEeCCCCCCCCc---CCC-----CCCCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDNLAA---NFSRELADYIIYIIDVSGGDKIPR---KGG-----PGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~---~~~~~~ad~~I~VvD~~~~~~~~~---~~~-----~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+.+-++++.|...-.   ......++.+++++|.++......   .+.     ..-..+-++|.||+|+.+......+.
T Consensus        48 ~~~~~i~d~~g~~~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~i~~~~~~~~~~~~~~~~iilvgnK~Dl~~~~~~~~~~  127 (164)
T d1yzqa1          48 TIRLQLWDTAGQERFRSLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQVSIEE  127 (164)
T ss_dssp             EEEEEEEEECCSGGGGGGHHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTTSSEEEEEEECTTCGGGCCSCHHH
T ss_pred             ceeeeecccCCcchhccchHHHhhccceEEEeeccccccchhhhHhhHHHHHHhcCCCceEEEEecccchhhhhhhhHHH
Confidence            4566788898832111   111224799999999977543211   000     01234578889999997542234455


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+..++.  +++++++||++|+||+++|+.|.+.
T Consensus       128 ~~~~~~~~--~~~~~e~SAk~g~~v~e~f~~i~~~  160 (164)
T d1yzqa1         128 GERKAKEL--NVMFIETSAKAGYNVKQLFRRVAAA  160 (164)
T ss_dssp             HHHHHHHT--TCEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHc--CCEEEEecCCCCcCHHHHHHHHHHh
Confidence            66666655  4689999999999999999988764

>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=98.56  E-value=5.4e-08  Score=69.77  Aligned_cols=102  Identities=18%  Similarity=0.060  Sum_probs=65.9

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      +..+.++|+.|...    ...+ ...++.+++|+|++.......         .....-..+-++|.||.|+...  ...
T Consensus        46 ~~~~~i~D~~G~~~~~~~~~~~-~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~pi~lv~nK~Dl~~~--~~~  122 (164)
T d1zd9a1          46 NVTIKLWDIGGQPRFRSMWERY-CRGVSAIVYMVDAADQEKIEASKNELHNLLDKPQLQGIPVLVLGNKRDLPGA--LDE  122 (164)
T ss_dssp             TEEEEEEEECCSHHHHTTHHHH-HTTCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCCEEEEEECTTSTTC--CCH
T ss_pred             eEEEEEeecccccccccccccc-ccccchhhcccccccccccchhhhhhhhhhhhhcccCCcEEEEEeccccchh--hhH
Confidence            46678899999321    1111 134799999999976432211         0001113467899999999765  344


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                      ..+.+.+...   ....+++++||++|+|++++|++|.+.+
T Consensus       123 ~~i~~~~~~~~~~~~~~~~~e~Sa~~g~gv~e~~~~l~~~~  163 (164)
T d1zd9a1         123 KELIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHS  163 (164)
T ss_dssp             HHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHhCCCEEEEEeCcCCcCHHHHHHHHHHcc
Confidence            4444444211   2346889999999999999999987754

>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=98.55  E-value=1.9e-08  Score=72.53  Aligned_cols=101  Identities=16%  Similarity=0.103  Sum_probs=65.1

Q ss_pred             CCCEEEEeCCcchhhh---cccccccceEEEEEeCCCCCCCCc--C-CC-----CCCCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDNLAA---NFSRELADYIIYIIDVSGGDKIPR--K-GG-----PGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~---~~~~~~ad~~I~VvD~~~~~~~~~--~-~~-----~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+.+-+.++.|..-..   ......+|++++|+|.++......  . +.     ......-+++.||+|+........++
T Consensus        51 ~~~~~~~d~~g~~~~~~~~~~~~~~~~~~i~v~d~~~~~Sf~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~~~v~~~e  130 (167)
T d1z08a1          51 RVNLAIWDTAGQERFHALGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEKERHVSIQE  130 (167)
T ss_dssp             EEEEEEEECCCC-------CCSSTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHHGGGSEEEEEEECGGGGGGCCSCHHH
T ss_pred             cceeeeeccCCcceecccchhhccCCceeEEEEeCCchhHHHhhhhhhhhcccccccccceeeeccccccccccccchHH
Confidence            4778889999942111   111235799999999987543211  0 00     01233567889999997542123455


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .++..++.  +.+++++||++|+||+++|+.|.+
T Consensus       131 ~~~~a~~~--~~~~~e~Sak~~~~v~e~F~~l~~  162 (167)
T d1z08a1         131 AESYAESV--GAKHYHTSAKQNKGIEELFLDLCK  162 (167)
T ss_dssp             HHHHHHHT--TCEEEEEBTTTTBSHHHHHHHHHH
T ss_pred             HHHHHHHc--CCeEEEEecCCCcCHHHHHHHHHH
Confidence            66666655  468999999999999999987654

>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=98.55  E-value=3.6e-08  Score=70.97  Aligned_cols=100  Identities=14%  Similarity=0.053  Sum_probs=63.6

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C------CCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K------GGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~------~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+.+.++.|..    +...+ ...++++++++|.+.......  .      ....-..+-++|.||+|+.+......+
T Consensus        52 ~~~~~i~d~~g~~~~~~~~~~~-~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilvgnK~Dl~~~~~v~~~  130 (167)
T d1z0ja1          52 LHKFLIWDTAGLERFRALAPMY-YRGSAAAIIVYDITKEETFSTLKNWVRELRQHGPPSIVVAIAGNKCDLTDVREVMER  130 (167)
T ss_dssp             EEEEEEEEECCSGGGGGGTHHH-HTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTSEEEEEEECTTCGGGCCSCHH
T ss_pred             ccceeeeecCCchhhhHHHHHH-HhhccceEEEeeechhhhhhhHHHhhhhhhhccCCcceEEEecccchhccccchhHH
Confidence            3456678888831    11112 234799999999876432211  0      001123466899999999653212334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ..++..+..  +.+++++||++|+||+++|..|.+
T Consensus       131 ~~~~~~~~~--~~~~~e~SAk~~~nV~e~f~~l~~  163 (167)
T d1z0ja1         131 DAKDYADSI--HAIFVETSAKNAININELFIEISR  163 (167)
T ss_dssp             HHHHHHHHT--TCEEEECBTTTTBSHHHHHHHHHH
T ss_pred             HHHHHHHHc--CCEEEEEecCCCCCHHHHHHHHHH
Confidence            455555554  468999999999999999998755

>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=98.54  E-value=1.3e-08  Score=73.51  Aligned_cols=79  Identities=16%  Similarity=0.109  Sum_probs=52.6

Q ss_pred             ccceEEEEEeCCCCCCCCcC-CCC---CCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHH
Q 030407           94 LADYIIYIIDVSGGDKIPRK-GGP---GITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~-~~~---qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el  169 (178)
                      .+|.+++++|+..+...... ...   ....+-++|+||+|+.++  .+. +..+.+.+. +..+++++||++|.||++|
T Consensus        80 ~ad~i~~~~~~~~~~~~~~~~~~~~l~~~~~pviiv~NK~Dl~~~--~~~-~~~~~~~~~-~~~~~i~iSAk~g~gid~L  155 (171)
T d1mkya1          80 EADLVLFVVDGKRGITKEDESLADFLRKSTVDTILVANKAENLRE--FER-EVKPELYSL-GFGEPIPVSAEHNINLDTM  155 (171)
T ss_dssp             TCSEEEEEEETTTCCCHHHHHHHHHHHHHTCCEEEEEESCCSHHH--HHH-HTHHHHGGG-SSCSCEECBTTTTBSHHHH
T ss_pred             cCcEEEEeecccccccccccccccccccccccccccchhhhhhhh--hhh-HHHHHHHhc-CCCCeEEEecCCCCCHHHH
Confidence            46889999998765432211 101   123356999999999765  333 333333333 3457899999999999999


Q ss_pred             HHHHhhh
Q 030407          170 LSITHYI  176 (178)
Q Consensus       170 ~~~l~~~  176 (178)
                      +++|.+.
T Consensus       156 ~~~i~~~  162 (171)
T d1mkya1         156 LETIIKK  162 (171)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9988754

>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=98.53  E-value=2.2e-08  Score=72.59  Aligned_cols=100  Identities=10%  Similarity=-0.070  Sum_probs=65.8

Q ss_pred             hCCCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCcC---CCC----CCCceeEEEEecCCCCCchhHhH
Q 030407           71 LFKADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPRK---GGP----GITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        71 ~~~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~~---~~~----qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ...+.+.++++.|...    ...+. ..++++++|+|+++.......   +..    .-..+-++|.||+|+...  ...
T Consensus        49 ~~~~~l~i~D~~g~~~~~~~~~~~~-~~~~~~ilv~d~~~~~Sf~~~~~~~~~~~~~~~~~piilvgnK~Dl~~~--~~~  125 (170)
T d1i2ma_          49 RGPIKFNVWDTAGQEKFGGLRDGYY-IQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDR--KVK  125 (170)
T ss_dssp             TCCEEEEEEECTTHHHHSSCGGGGT-TTCCEEEEEEETTSGGGGTTHHHHHHHHHHHHCSCCEEEEEECCCCSCS--CCT
T ss_pred             cccccccccccccccccceecchhc-ccccchhhccccccccccchhHHHHHHHhhccCCCceeeecchhhhhhh--hhh
Confidence            3467889999999321    12222 257999999999886543210   000    013456999999999765  222


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ++.....+.  .+.+++++||++|+||+++|+.|.+
T Consensus       126 ~~~~~~~~~--~~~~~~e~Sak~~~~v~e~f~~l~~  159 (170)
T d1i2ma_         126 AKSIVFHRK--KNLQYYDISAKSNYNFEKPFLWLAR  159 (170)
T ss_dssp             TTSHHHHSS--CSSEEEEEBTTTTBTTTHHHHHHHH
T ss_pred             hHHHHHHHH--cCCEEEEEeCCCCCCHHHHHHHHHH
Confidence            333333333  3568999999999999999988754

>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=98.52  E-value=1.5e-08  Score=72.84  Aligned_cols=101  Identities=15%  Similarity=0.061  Sum_probs=64.5

Q ss_pred             CCCEEEEeCCcchhhhcc---cccccceEEEEEeCCCCCCCCc--CCCCC-----CCceeEEEEecCCCCCchhHhHHHH
Q 030407           73 KADLLLCESGGDNLAANF---SRELADYIIYIIDVSGGDKIPR--KGGPG-----ITQADLLVINKTDLASAIGADLAVM  142 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~---~~~~ad~~I~VvD~~~~~~~~~--~~~~q-----i~~adiiviNK~Dl~~~~~~~~~~~  142 (178)
                      .+.+.++.|.|..-....   ....++.+++|+|.++......  .+..+     -..+-++|.||+|+.++.....++.
T Consensus        50 ~~~~~i~d~~g~~~~~~~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~iilVgnK~Dl~~~~~v~~~~~  129 (164)
T d1z2aa1          50 DVRLMLWDTAGQEEFDAITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAEVGDIPTALVQNKIDLLDDSCIKNEEA  129 (164)
T ss_dssp             EEEEEEECCTTGGGTTCCCHHHHTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHHCSCCEEEEEECGGGGGGCSSCHHHH
T ss_pred             eeeeeeeccCCccchhhhhhhhhccCceEEEEEeccchhhhhhcccccccccccCCCceEEEeeccCCcccceeeeehhh
Confidence            467888899983211111   1234799999999987543211  00000     1234688899999975421223445


Q ss_pred             HHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          143 ERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       143 ~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ++..++.+  .+++++||++|.||+++|+.|.+
T Consensus       130 ~~~~~~~~--~~~~e~Sak~g~~v~e~f~~l~~  160 (164)
T d1z2aa1         130 EGLAKRLK--LRFYRTSVKEDLNVSEVFKYLAE  160 (164)
T ss_dssp             HHHHHHHT--CEEEECBTTTTBSSHHHHHHHHH
T ss_pred             HHHHHHcC--CEEEEeccCCCcCHHHHHHHHHH
Confidence            55566553  58999999999999999998754

>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=98.52  E-value=7.1e-08  Score=69.68  Aligned_cols=101  Identities=15%  Similarity=0.044  Sum_probs=66.5

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---C------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---K------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---~------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ...+-++++.|..-    ...+. ..+|++++|+|.++......   .      ....-..+-+++.||+|+........
T Consensus        51 ~~~~~i~d~~g~~~~~~~~~~~~-~~~~~~llv~d~~d~~Sf~~~~~~~~~i~~~~~~~~~p~ilvgnK~Dl~~~~~v~~  129 (169)
T d1x1ra1          51 WAILDVLDTAGQEEFSAMREQYM-RTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDRESFPMILVANKVDLMHLRKVTR  129 (169)
T ss_dssp             EEEEEEEECCSCGGGCSSHHHHH-HHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTSSCCCEEEEEECTTCSTTCCSCH
T ss_pred             cccccccccccccccccchhhhh-hhccEEEEecccccchhhhccchhhHHHHhhccccCccEEEEecccchhhhceeeh
Confidence            46677889999321    11122 24799999999987532211   0      11112334689999999976522334


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCC-CHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVI-GIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~-gi~el~~~l~~~  176 (178)
                      ++..++.++.+  .+++++|||+|. ||+++|+.|.+.
T Consensus       130 e~~~~~~~~~~--~~~~e~Sak~~~~nV~~~F~~l~~~  165 (169)
T d1x1ra1         130 DQGKEMATKYN--IPYIETSAKDPPLNVDKTFHDLVRV  165 (169)
T ss_dssp             HHHHHHHHHHT--CCEEEEBCSSSCBSHHHHHHHHHHH
T ss_pred             hhHHHHHHHcC--CEEEEEcCCCCCcCHHHHHHHHHHH
Confidence            56667777664  589999999986 999999977653

>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=98.50  E-value=4.5e-08  Score=70.97  Aligned_cols=102  Identities=12%  Similarity=0.077  Sum_probs=62.1

Q ss_pred             CCCEEEEeCCcch-hh---hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN-LA---ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~---~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+...+++..|.. ..   .......+|++|+|+|+++......         .....-..+-++|.||+|+.+......
T Consensus        52 ~~~~~~~d~~~~~g~e~~~~~~~~~~~~~~ilvfd~t~~~s~~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~~~v~~  131 (172)
T d2g3ya1          52 SATIILLDMWENKGENEWLHDHCMQVGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVSV  131 (172)
T ss_dssp             EEEEEEECCTTTTHHHHHHHHCCCCCCSEEEEEEETTCHHHHHHHHHHHHHHHTSGGGTTSCEEEEEECTTCGGGCCSCH
T ss_pred             eeeeeeeccccccccccccccccccccceeeeeecccccchhhhhhhhhhhhhhccccCCceEEEEeccccccccccccH
Confidence            4556677754421 11   1112235799999999987532210         010111345699999999865421223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +..++..+..  +.+++++||++|+||+++|+.|.+.
T Consensus       132 ~~~~~~a~~~--~~~~~e~Sak~g~~i~~~f~~l~~~  166 (172)
T d2g3ya1         132 SEGRACAVVF--DCKFIETSAAVQHNVKELFEGIVRQ  166 (172)
T ss_dssp             HHHHHHHHHH--TCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CCeEEEEeCCCCcCHHHHHHHHHHH
Confidence            3444444444  3689999999999999999987653

>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=98.50  E-value=2.6e-08  Score=71.99  Aligned_cols=100  Identities=10%  Similarity=0.048  Sum_probs=64.1

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CC-------CCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KG-------GPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~-------~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.++++.|..-    ...+. ..+|++++|+|..+......  .+       ...-..+-++|.||+|+.+......
T Consensus        51 ~~~l~i~d~~g~~~~~~~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piiivgnK~Dl~~~~~v~~  129 (168)
T d1u8za_          51 EVQIDILDTAGQEDYAAIRDNYF-RSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSV  129 (168)
T ss_dssp             EEEEEEEECCC---CHHHHHHHH-HHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHCCTTSCEEEEEECGGGGGGCCSCH
T ss_pred             cccccccccccccchhhhhhhcc-cccceeEEEeeccchhhhhhHHHHHHHHHHhhCCCCCcEEEEeccccccccccccH
Confidence            57778899999321    11122 24799999999977432211  00       0011335689999999864311233


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +..+++.++.+  .+++++||++|+||+++|+.|.+
T Consensus       130 ~~~~~~~~~~~--~~~~e~Sak~g~gv~e~f~~l~~  163 (168)
T d1u8za_         130 EEAKNRADQWN--VNYVETSAKTRANVDKVFFDLMR  163 (168)
T ss_dssp             HHHHHHHHHHT--CEEEECCTTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHHcC--CeEEEEcCCCCcCHHHHHHHHHH
Confidence            55666666653  68999999999999999997654

>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=98.48  E-value=5.7e-08  Score=70.15  Aligned_cols=101  Identities=12%  Similarity=0.118  Sum_probs=64.3

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+..-++++.|..    ....+. ..+|.+++|+|.+.......  .       ....-..+-++|.||+|+........
T Consensus        52 ~~~~~~~d~~g~~~~~~~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ilvgnK~Dl~~~~~v~~  130 (171)
T d2erya1          52 AARLDILDTAGQEEFGAMREQYM-RTGEGFLLVFSVTDRGSFEEIYKFQRQILRVKDRDEFPMILIGNKADLDHQRQVTQ  130 (171)
T ss_dssp             EEEEEEEECC----CCHHHHHHH-HHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTSSCCSEEEEEECTTCTTSCSSCH
T ss_pred             ccccccccccccccccccccccc-cccceEEEeeccccccchhhHHHHhHHHHhhcccCCCCEEEEEeccchhhhccchH
Confidence            4567788888831    111122 24799999999877532211  0       00112345689999999975421233


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...++.++.+  .+++++||++|+||+++|+.|.+.
T Consensus       131 ~~~~~~~~~~~--~~~~e~Sak~~~~i~e~f~~l~~~  165 (171)
T d2erya1         131 EEGQQLARQLK--VTYMEASAKIRMNVDQAFHELVRV  165 (171)
T ss_dssp             HHHHHHHHHTT--CEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC--CEEEEEcCCCCcCHHHHHHHHHHH
Confidence            45666666653  589999999999999999988654

>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=98.48  E-value=1.9e-07  Score=67.11  Aligned_cols=102  Identities=13%  Similarity=0.075  Sum_probs=63.5

Q ss_pred             CCCEEEEeCCcchhhhcc---cccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNLAANF---SRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~---~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      +....+....|.......   ....++.++.++|.++......         .....-..+-++|+||+|+...  ...+
T Consensus        58 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~i~v~d~~d~~~~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~--~~~~  135 (177)
T d1zj6a1          58 NTRFLMWDIGGQESLRSSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKEC--MTVA  135 (177)
T ss_dssp             TEEEEEEECCC----CGGGHHHHTTCCEEEEEEETTCTTTHHHHHHHHHHHHTSGGGTTCEEEEEEECTTSTTC--CCHH
T ss_pred             ceEEEEeccccccccccchhhhhccceeeeeecccccccchhhhhhhhhhhhhcccccceEEEEEEEccccccc--CcHH
Confidence            456677777663111111   1124688999999876543211         0111234567999999999766  4444


Q ss_pred             HHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .+.+..+..   ....+++++||++|+|++|++++|.+.
T Consensus       136 ~i~~~~~~~~~~~~~~~~~~~Sa~tg~Gi~e~~~~L~~~  174 (177)
T d1zj6a1         136 EISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSR  174 (177)
T ss_dssp             HHHHHHTGGGCCSSCEEEEECBTTTTBTHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhHhcCCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            444444321   234589999999999999999998764

>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=98.48  E-value=3.3e-08  Score=71.72  Aligned_cols=101  Identities=12%  Similarity=0.038  Sum_probs=64.9

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc--CC-------CCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR--KG-------GPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~--~~-------~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+-++++.|..-    ...+. ..++++++|+|.+.......  .+       ...-..+-++|.||+|+........
T Consensus        53 ~~~l~~~d~~g~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~p~ilvgnK~Dl~~~~~~~~  131 (173)
T d2fn4a1          53 PARLDILDTAGQEEFGAMREQYM-RAGHGFLLVFAINDRQSFNEVGKLFTQILRVKDRDDFPVVLVGNKADLESQRQVPR  131 (173)
T ss_dssp             EEEEEEEECCCTTTTSCCHHHHH-HHCSEEEEEEETTCHHHHHHHHHHHHHHHHHHTSSCCCEEEEEECGGGGGGCCSCH
T ss_pred             eeeeeccccccccccccccchhh-ccceeeeeecccccccccchhhhhhHHHHHHhccCCCceEEEEEeechhhccccch
Confidence            46778889999311    11121 24799999999987542211  00       0111335689999999865421223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +...+..+..  +.++++|||++|+||+++|+.|.+.
T Consensus       132 ~~~~~~~~~~--~~~~~e~Sak~g~gv~e~f~~l~~~  166 (173)
T d2fn4a1         132 SEASAFGASH--HVAYFEASAKLRLNVDEAFEQLVRA  166 (173)
T ss_dssp             HHHHHHHHHT--TCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             hhhhHHHHhc--CCEEEEEeCCCCcCHHHHHHHHHHH
Confidence            4455555544  4689999999999999999987653

>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=98.48  E-value=3.2e-08  Score=71.18  Aligned_cols=100  Identities=14%  Similarity=0.022  Sum_probs=64.9

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+-+.++.|..-    ...+. ..+|.+++|+|.++......         .....-..+-++|.||+|+..+.....
T Consensus        51 ~~~l~i~d~~g~~~~~~~~~~~~-~~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~r~v~~  129 (167)
T d1xtqa1          51 EYHLQLVDTAGQDEYSIFPQTYS-IDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISY  129 (167)
T ss_dssp             EEEEEEEECCCCCTTCCCCGGGT-SSCCEEEEEEETTCHHHHHHHHHHHHHHHHHHCSSCCCEEEEEECTTCGGGCCSCH
T ss_pred             EEEeeecccccccccccccchhh-hhhhhhhhhcccchhhhhhhhhhhhhhhhhcccccccceeeeccccccccccchhH
Confidence            46677888888321    11222 24799999999987543211         001112346689999999965411223


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +..+++.++.+  .+++++||++|+||+++|+.|.+
T Consensus       130 ~~~~~~a~~~~--~~~~e~Sak~~~~v~~~f~~li~  163 (167)
T d1xtqa1         130 EEGKALAESWN--AAFLESSAKENQTAVDVFRRIIL  163 (167)
T ss_dssp             HHHHHHHHHHT--CEEEECCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC--CEEEEEecCCCCCHHHHHHHHHH
Confidence            45555666553  58999999999999999997654

>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=98.47  E-value=1.3e-07  Score=69.28  Aligned_cols=101  Identities=13%  Similarity=0.047  Sum_probs=63.1

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCC-----CCCceeEEEEecCCCCCchh----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGP-----GITQADLLVINKTDLASAIG----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~-----qi~~adiiviNK~Dl~~~~~----  136 (178)
                      .+.+-++++.|..    +...+ ...+|++++|+|+++......   .+..     .-..+-++|.||+|+.+...    
T Consensus        56 ~~~l~i~D~~g~e~~~~~~~~~-~~~a~~~ilv~d~t~~~Sf~~~~~~~~~~~~~~~~~~~~ilvgnK~Dl~~~~~~~~~  134 (185)
T d2atxa1          56 QYLLGLYDTAGQEDYDRLRPLS-YPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKTLAR  134 (185)
T ss_dssp             EEEEEEECCCCSSSSTTTGGGG-CTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHSTTCCEEEEEECTTSTTCHHHHHH
T ss_pred             eEEeecccccccchhhhhhhhc-ccccceeeeccccchHHHHHHHHHHHHHHHHhcCCCCCeeEeeeccccccchhhhhh
Confidence            4667789999931    11222 235799999999987543211   1000     11235689999999976410    


Q ss_pred             --------HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          137 --------ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       137 --------~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                              ...++..+..++.+ ..++++|||++|+||+++|+.+.+
T Consensus       135 ~~~~~~r~v~~~~~~~~a~~~~-~~~~~E~SAk~~~gv~e~F~~li~  180 (185)
T d2atxa1         135 LNDMKEKPICVEQGQKLAKEIG-ACCYVECSALTQKGLKTVFDEAII  180 (185)
T ss_dssp             HTTTTCCCCCHHHHHHHHHHHT-CSCEEECCTTTCTTHHHHHHHHHH
T ss_pred             hhhcccccccHHHHHHHHHHcC-CCEEEEecCCCCcCHHHHHHHHHH
Confidence                    01223344444443 358899999999999999997654

>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=98.44  E-value=7.4e-08  Score=69.24  Aligned_cols=102  Identities=11%  Similarity=0.003  Sum_probs=65.3

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CC------CCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KG------GPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~------~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ...+-+.++.|..    +...+. ..+|++++++|.++......   .+      ...-..+-++|.||+|+........
T Consensus        50 ~~~~~~~d~~g~~~~~~~~~~~~-~~~~~~ilv~d~~~~~sf~~~~~~~~~~~~~~~~~~~p~ilvgnK~Dl~~~~~~~~  128 (167)
T d1c1ya_          50 QCMLEILDTAGTEQFTAMRDLYM-KNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGK  128 (167)
T ss_dssp             EEEEEEEEECSSCSSTTHHHHHH-HHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHCCSCCCEEEEEECTTCGGGCCSCH
T ss_pred             EEEeccccccCcccccccccccc-cccceeEEeeeccchhhhHhHHHHHHHHHHhcCCCCCeEEEEEEecCcccccccch
Confidence            4677788888831    112222 24799999999987532211   00      0011235699999999975422233


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +......++. ...+++++||++|+||+++|+.|.+.
T Consensus       129 ~~~~~~~~~~-~~~~~~e~Sak~g~gv~e~F~~l~~~  164 (167)
T d1c1ya_         129 EQGQNLARQW-CNCAFLESSAKSKINVNEIFYDLVRQ  164 (167)
T ss_dssp             HHHHHHHHHT-TSCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             hHHHHHHHHh-CCCEEEEEcCCCCcCHHHHHHHHHHH
Confidence            4444444443 45789999999999999999987654

>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=98.43  E-value=1.8e-07  Score=67.39  Aligned_cols=100  Identities=16%  Similarity=0.131  Sum_probs=65.7

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C------CCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K------GGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~------~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+-|++|.|..    +...+ ...+|.+++++|.++......  .      ....-..+-+++.||.|+........+
T Consensus        55 ~~~l~i~Dt~G~e~~~~~~~~~-~~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilv~~k~d~~~~~~v~~~  133 (170)
T d2g6ba1          55 KVKLQMWDTAGQERFRSVTHAY-YRDAHALLLLYDVTNKASFDNIQAWLTEIHEYAQHDVALMLLGNKVDSAHERVVKRE  133 (170)
T ss_dssp             EEEEEEEECCCC--------CC-GGGCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECCSTTSCCCSCHH
T ss_pred             EEEEEEEECCCchhhHHHHHHh-hcCCceeEEEecCCcccchhhhhhhhhhhhhccCCCceEEEEEeeechhhcccccHH
Confidence            3567788999931    11122 235799999999976542211  0      001123467889999999875323345


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +..+..+..+  .+++++||++|+||+++|+.|.+
T Consensus       134 ~~~~~~~~~~--~~~~e~Sak~g~gi~e~f~~l~~  166 (170)
T d2g6ba1         134 DGEKLAKEYG--LPFMETSAKTGLNVDLAFTAIAK  166 (170)
T ss_dssp             HHHHHHHHHT--CCEEECCTTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHcC--CEEEEEeCCCCcCHHHHHHHHHH
Confidence            5566666553  69999999999999999998764

>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=98.42  E-value=4.1e-08  Score=70.55  Aligned_cols=102  Identities=13%  Similarity=-0.004  Sum_probs=64.8

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+-++++.|....   .......++.+++++|.++......         .....-..+-++|.||+|+.+......+
T Consensus        50 ~~~l~~~d~~g~~~~~~~~~~~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilvgnK~Dl~~~~~~~~~  129 (167)
T d1kaoa_          50 PSVLEILDTAGTEQFASMRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRYEKVPVILVGNKVDLESEREVSSS  129 (167)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHHHCSEEEEEEETTCHHHHHHHHHHHHHHHHHTTTSCCCEEEEEECGGGGGGCCSCHH
T ss_pred             eEeeccccCCCccccccchHHHhhcccceeeeeeecchhhhhhhhchhhhhhhhccCCCCCEEEEEEccchhhcccchHH
Confidence            467778888883211   1111224799999999986432211         0011123456899999998754212334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      +.....++.+  .+++++||++|+||+++|+.+.+.
T Consensus       130 ~~~~~~~~~~--~~~~e~Sak~g~~i~e~f~~i~~~  163 (167)
T d1kaoa_         130 EGRALAEEWG--CPFMETSAKSKTMVDELFAEIVRQ  163 (167)
T ss_dssp             HHHHHHHHHT--SCEEEECTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcC--CeEEEECCCCCcCHHHHHHHHHHH
Confidence            4455555543  589999999999999999987653

>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=98.41  E-value=7.8e-08  Score=69.78  Aligned_cols=102  Identities=18%  Similarity=0.123  Sum_probs=63.8

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchhH---
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIGA---  137 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~~---  137 (178)
                      .+.+-+.++.|..    +...+. ..+|.+++|+|.++......   .+...     -..+-++|.||+|+.+....   
T Consensus        49 ~~~l~i~D~~g~~~~~~~~~~~~-~~~~~~ilv~d~~~~~Sf~~~~~~~~~~~~~~~~~~piilvgnK~Dl~~~~~~~~~  127 (177)
T d1kmqa_          49 QVELALWDTAGLEDYDRLRPLSY-PDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRE  127 (177)
T ss_dssp             EEEEEEEEECCSGGGTTTGGGGC-TTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHSTTSCEEEEEECGGGTTCHHHHHH
T ss_pred             ceeeeccccCccchhcccchhhc-ccchhhhhhcccchhHHHHHHHHHHHHHHHHhCCCCceEEeeecccccchhhHHHH
Confidence            4678889999932    112222 35799999999987542211   11000     12456899999999765110   


Q ss_pred             ---------hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          138 ---------DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       138 ---------~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                               ..++..++.++. ...++++|||++|+||+++|+.+.+.
T Consensus       128 ~~~~~~~~v~~~e~~~~a~~~-~~~~~~E~SAkt~~gi~e~F~~i~~~  174 (177)
T d1kmqa_         128 LAKMKQEPVKPEEGRDMANRI-GAFGYMECSAKTKDGVREVFEMATRA  174 (177)
T ss_dssp             HHHTTCCCCCHHHHHHHHHHT-TCSEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             HHHhhcccccHHHHHHHHHHc-CCcEEEEecCCCCcCHHHHHHHHHHH
Confidence                     112233344433 23589999999999999999987664

>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=98.40  E-value=8.8e-08  Score=69.02  Aligned_cols=101  Identities=16%  Similarity=0.106  Sum_probs=64.9

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--CC------CCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--KG------GPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~~------~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+.++.+.|..    +...+. ..++.+++++|.++......  .+      ...-..+-++|.||+|+..+.....+
T Consensus        54 ~~~~~~~d~~g~~~~~~~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilvgnK~Dl~~~~~v~~e  132 (170)
T d1r2qa_          54 TVKFEIWDTAGQERYHSLAPMYY-RGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQ  132 (170)
T ss_dssp             EEEEEEEEECCSGGGGGGHHHHH-TTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHH
T ss_pred             EEEEEeccCCCchhhhhhHHHHh-hCcceEEEEeccchhhHHHHHHHHhhhhhhccCCCceEEeecccccccccccccHH
Confidence            4677888888832    111222 25799999999877542211  00      00113456899999998654222344


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..++..+..  ..+++++||++|+||+++|+.|.+.
T Consensus       133 ~~~~~~~~~--~~~~~e~SAk~g~~V~e~f~~l~~~  166 (170)
T d1r2qa_         133 EAQSYADDN--SLLFMETSAKTSMNVNEIFMAIAKK  166 (170)
T ss_dssp             HHHHHHHHT--TCEEEECCTTTCTTHHHHHHHHHHT
T ss_pred             HHHHHHHhc--CCEEEEeeCCCCCCHHHHHHHHHHH
Confidence            555555544  4689999999999999999987543

>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=98.40  E-value=1.4e-07  Score=68.12  Aligned_cols=100  Identities=12%  Similarity=0.026  Sum_probs=64.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C-C-----CCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K-G-----GPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~-~-----~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      ...+.++++.|..    +...+. ..++++++++|.++......  . .     ...-..+-++|.||+|+.+......+
T Consensus        53 ~~~~~i~D~~G~~~~~~~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piivv~nK~D~~~~~~~~~~  131 (174)
T d2bmea1          53 YVKLQIWDTAGQERFRSVTRSYY-RGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIILCGNKKDLDADREVTFL  131 (174)
T ss_dssp             EEEEEEEEECCSGGGHHHHHTTS-TTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECGGGGGGCCSCHH
T ss_pred             ceeEEEEECCCchhhhhhHHHHh-hhCCEEEEEEecccchhHHHHhhhhcccccccCCceEEEEEEecccccchhchhhh
Confidence            4567889999931    112222 25799999999986532211  0 0     01123567999999998654212223


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ...+..+..  ..+++++||++|+||+++|+.+.+
T Consensus       132 ~~~~~~~~~--~~~~~e~Sak~~~gi~e~f~~l~~  164 (174)
T d2bmea1         132 EASRFAQEN--ELMFLETSALTGENVEEAFVQCAR  164 (174)
T ss_dssp             HHHHHHHHT--TCEEEECCTTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHhC--CCEEEEeeCCCCcCHHHHHHHHHH
Confidence            444444443  468999999999999999987644

>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=98.40  E-value=7.6e-08  Score=69.40  Aligned_cols=100  Identities=13%  Similarity=0.057  Sum_probs=64.6

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc--C-------CCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR--K-------GGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+-++++.|....   ..+. ..++++++|+|.++......  .       ....-..+-++|.||+|+.++.....+
T Consensus        49 ~~~l~i~D~~g~~~~~~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~piilvgnK~Dl~~~r~V~~~  127 (168)
T d2atva1          49 VVSMEILDTAGQEDTIQREGHM-RWGEGFVLVYDITDRGSFEEVLPLKNILDEIKKPKNVTLILVGNKADLDHSRQVSTE  127 (168)
T ss_dssp             EEEEEEEECCCCCCCHHHHHHH-HHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTTSCCCEEEEEECGGGGGGCCSCHH
T ss_pred             ceEEEEeecccccccccchhhh-cccccceeecccCCccchhhhhhhcccccccccccCcceeeeccchhhhhhccCcHH
Confidence            467889999994211   1122 24799999999987532211  0       011123467999999999643112334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCC-HHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIG-IIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~g-i~el~~~l~~  175 (178)
                      +..+..++.+  .++++|||++|+| |+++|..+.+
T Consensus       128 e~~~~a~~~~--~~~~e~Saktg~gnV~e~F~~l~~  161 (168)
T d2atva1         128 EGEKLATELA--CAFYECSACTGEGNITEIFYELCR  161 (168)
T ss_dssp             HHHHHHHHHT--SEEEECCTTTCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHhC--CeEEEEccccCCcCHHHHHHHHHH
Confidence            5555556553  5899999999996 9999987654

>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=98.38  E-value=4.6e-07  Score=65.58  Aligned_cols=99  Identities=20%  Similarity=0.134  Sum_probs=65.4

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.+++|.|..-    ...+. ..+|++++|+|.++......         ........+-+++.||.|..... ...
T Consensus        55 ~~~~~i~Dt~G~~~~~~~~~~~~-~~~~~ii~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~i~~~~nk~d~~~~~-v~~  132 (177)
T d1x3sa1          55 KAKLAIWDTAGQERFRTLTPSYY-RGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKENRE-VDR  132 (177)
T ss_dssp             EEEEEEEEECSSGGGCCSHHHHH-TTCCEEEEEEETTCHHHHHTHHHHHHHHTTCCSCSCCEEEEEEECTTSSSCC-SCH
T ss_pred             ccEEEEEECCCchhhHHHHHHHH-hcCCEEEEEEECCCccccccchhhhhhhcccccccceeeEEEeecccccccc-ccH
Confidence            46788899999321    11111 24699999999876432111         11222345668999999987542 333


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +...+..+..+  .+++++||++|+|++++|+++.+
T Consensus       133 ~~~~~~~~~~~--~~~~e~Sa~tg~gv~e~f~~l~~  166 (177)
T d1x3sa1         133 NEGLKFARKHS--MLFIEASAKTCDGVQCAFEELVE  166 (177)
T ss_dssp             HHHHHHHHHTT--CEEEECCTTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHHCC--CEEEEEeCCCCCCHHHHHHHHHH
Confidence            45555666543  58999999999999999987654

>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=98.37  E-value=2e-07  Score=66.84  Aligned_cols=100  Identities=14%  Similarity=0.073  Sum_probs=63.3

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc--CCC-------CCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR--KGG-------PGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~--~~~-------~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+-+.++.|....   .+.....++.+++|+|.++......  .+.       .--..+-++|.||+|+.... ...+
T Consensus        50 ~~~l~~~d~~~~~~~~~~~~~~~~~~~~~iiv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~-~~~~  128 (166)
T d1ctqa_          50 TCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAART-VESR  128 (166)
T ss_dssp             EEEEEEEEECCCGGGHHHHHHHHHHCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTCSSCCEEEEEECTTCSCCC-SCHH
T ss_pred             eeeeeeeeccCccccccchhhhhhcccccceeecccccccHHHHHHHHHHHHHhcCCCCCeEEEEeccccccccc-ccHH
Confidence            356777788883211   1111224689999999976532211  000       00123579999999997642 2334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ...++.+..  +.+++++||++|+||+++|+.+.+
T Consensus       129 ~~~~~~~~~--~~~~~e~Sak~g~gi~e~f~~i~~  161 (166)
T d1ctqa_         129 QAQDLARSY--GIPYIETSAKTRQGVEDAFYTLVR  161 (166)
T ss_dssp             HHHHHHHHH--TCCEEECCTTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHh--CCeEEEEcCCCCcCHHHHHHHHHH
Confidence            555555554  358999999999999999987754

>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=98.35  E-value=6.1e-07  Score=62.84  Aligned_cols=103  Identities=13%  Similarity=0.065  Sum_probs=65.1

Q ss_pred             CCCCEEEEeCCcchhhh---cccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           72 FKADLLLCESGGDNLAA---NFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~~---~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      ....+.+.++.|.....   ......++.+++++|..+......         .....-..+-+++.||.|+.+.  ...
T Consensus        42 ~~~~~~~~d~~g~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~k~d~~~~--~~~  119 (160)
T d1r8sa_          42 KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNA--MNA  119 (160)
T ss_dssp             SSCEEEEEECCCCGGGHHHHHHHTTTCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC--CCH
T ss_pred             eeEEEEEecCCCcccchhhhhhhhccceeEEEEEEecChHHHHHHHHHHHHHHHhhcccCceEEEEeeccccccc--ccH
Confidence            46788889999942211   111224689999999876432211         0011123456899999999876  333


Q ss_pred             HHHHHHHHhc---CCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          140 AVMERDALRM---RDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       140 ~~~~~~l~~~---np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .++.......   ....+++++||++|+||+++|++|.+.
T Consensus       120 ~~i~~~~~~~~~~~~~~~~~~~SAktg~gi~e~~~~l~~~  159 (160)
T d1r8sa_         120 AEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQ  159 (160)
T ss_dssp             HHHHHHTTGGGCSSCCEEEEECBTTTTBTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhCCCEEEEeECCCCCCHHHHHHHHHhc
Confidence            3433332211   234689999999999999999998753

>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=98.35  E-value=7.5e-07  Score=64.16  Aligned_cols=101  Identities=7%  Similarity=-0.010  Sum_probs=64.1

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc--CC----------CCCCCceeEEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR--KG----------GPGITQADLLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~--~~----------~~qi~~adiiviNK~Dl~~~~~~  137 (178)
                      .+.+-+.++.|..-.   .+.....++.+++++|.+.......  .+          ...-..+-++|.||+|+.+.. .
T Consensus        54 ~~~~~i~d~~g~~~~~~~~~~~~~~~~~~i~~~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~piilVgnK~Dl~~~~-v  132 (174)
T d1wmsa_          54 FVTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDISERQ-V  132 (174)
T ss_dssp             EEEEEEEECCCCGGGHHHHGGGGTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHHTCSCTTTSCEEEEEECTTCSSCS-S
T ss_pred             eeeEeeecccCcceehhhhhhhhhccceEEEEEeeecccccchhhhHHHHHHHHhccccCCCceEEEeccccchhhcc-C
Confidence            456678888883211   1222234699999999976432110  00          001124579999999997531 2


Q ss_pred             hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          138 DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       138 ~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ..+..+++.++. ...++++|||++|+||+++|+.+.+
T Consensus       133 ~~~~~~~~~~~~-~~~~~~e~Sak~~~gI~e~f~~l~~  169 (174)
T d1wmsa_         133 STEEAQAWCRDN-GDYPYFETSAKDATNVAAAFEEAVR  169 (174)
T ss_dssp             CHHHHHHHHHHT-TCCCEEECCTTTCTTHHHHHHHHHH
T ss_pred             cHHHHHHHHHHc-CCCeEEEEcCCCCcCHHHHHHHHHH
Confidence            344556666654 3468999999999999999987643

>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=98.34  E-value=3.2e-07  Score=67.57  Aligned_cols=100  Identities=18%  Similarity=0.126  Sum_probs=65.0

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc--C------CCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR--K------GGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~--~------~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      .+.+-+++|.|..    +...+. ..++++|+|+|++.......  .      ....-..+-++|.||+|+.+......+
T Consensus        54 ~~~l~i~Dt~G~e~~~~~~~~~~-~~a~~~i~v~d~t~~~s~~~~~~~~~~~~~~~~~~~~iilv~nK~D~~~~~~~~~~  132 (194)
T d2bcgy1          54 TVKLQIWDTAGQERFRTITSSYY-RGSHGIIIVYDVTDQESFNGVKMWLQEIDRYATSTVLKLLVGNKCDLKDKRVVEYD  132 (194)
T ss_dssp             EEEEEEECCTTTTTTTCCCGGGG-TTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECTTCTTTCCSCHH
T ss_pred             EEEEEEEECCCchhhHHHHHHHh-ccCCEEEEEEeCcchhhhhhHhhhhhhhhhcccCCceEEEEEeccccccccchhHH
Confidence            5678888999931    112222 25799999999976432211  0      001123356999999999865323334


Q ss_pred             HHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ......+..  ..+++++||++|.||+++|+.+.+
T Consensus       133 ~~~~~~~~~--~~~~~e~SAk~g~gi~e~f~~l~~  165 (194)
T d2bcgy1         133 VAKEFADAN--KMPFLETSALDSTNVEDAFLTMAR  165 (194)
T ss_dssp             HHHHHHHHT--TCCEEECCTTTCTTHHHHHHHHHH
T ss_pred             HHhhhhhcc--CcceEEEecCcCccHHHHHHHHHH
Confidence            444444443  468999999999999999998754

>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=98.34  E-value=2.2e-07  Score=66.33  Aligned_cols=100  Identities=14%  Similarity=0.090  Sum_probs=63.8

Q ss_pred             CCCEEEEeCCcchhh----hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhH
Q 030407           73 KADLLLCESGGDNLA----ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~~----~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      .+.+.+..+.|....    .......+|++++|+|.++......         ++...-..+-++|.||+|+.++.....
T Consensus        50 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~pi~lvgnK~Dl~~~~~v~~  129 (165)
T d1z06a1          50 RIKIQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRILVGNKCDLRSAIQVPT  129 (165)
T ss_dssp             EEEEEEEECCCSHHHHTTTHHHHHTTCCEEEEEEETTCHHHHHTHHHHHHHHHHHCCCSCCCEEEEEECTTCGGGCCSCH
T ss_pred             ceEEEEEeccCchhhccccceeeecCCCceEEEEEeehhhhhhhhhhhhHHHHhhccCCCCeEEEEeccccchhccchhH
Confidence            467778888883211    1111235799999999987532211         011111345789999999965421234


Q ss_pred             HHHHHHHHhcCCCCCEEEEeccc---CCCHHHHHHHHh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGW---VIGIIFTLSITH  174 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~---g~gi~el~~~l~  174 (178)
                      +..+++.++.  +.+++++|||+   |+||+++|+.|.
T Consensus       130 ~~~~~~~~~~--~~~~~e~SAkt~~~~~~V~e~F~~lA  165 (165)
T d1z06a1         130 DLAQKFADTH--SMPLFETSAKNPNDNDHVEAIFMTLA  165 (165)
T ss_dssp             HHHHHHHHHT--TCCEEECCSSSGGGGSCHHHHHHHHC
T ss_pred             HHHHHHHHHC--CCEEEEEecccCCcCcCHHHHHHHhC
Confidence            4556666655  35899999997   569999998763

>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=98.33  E-value=1.4e-07  Score=68.64  Aligned_cols=100  Identities=20%  Similarity=0.130  Sum_probs=61.7

Q ss_pred             CCCEEEEeCCcchhhhc--------cc--ccccceEEEEEeCCCCCCCCc-------------CCCCCCCceeEEEEecC
Q 030407           73 KADLLLCESGGDNLAAN--------FS--RELADYIIYIIDVSGGDKIPR-------------KGGPGITQADLLVINKT  129 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~--------~~--~~~ad~~I~VvD~~~~~~~~~-------------~~~~qi~~adiiviNK~  129 (178)
                      +..+.++.|.|..-...        +.  ...++.+..+++.........             ........+.++|+||+
T Consensus        48 ~~~~~~~DtpG~~~~~~~~~~~~~~~l~~~~~~~~i~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kp~ivv~NK~  127 (185)
T d1lnza2          48 GRSFVMADLPGLIEGAHQGVGLGHQFLRHIERTRVIVHVIDMSGLEGRDPYDDYLTINQELSEYNLRLTERPQIIVANKM  127 (185)
T ss_dssp             SCEEEEEEHHHHHHHTTCTTTTHHHHHHHHHHCCEEEEEEESSCSSCCCHHHHHHHHHHHHHHSCSSTTTSCBCBEEECT
T ss_pred             CcEEEEecCCCcccCchHHHHHHHHHHHHHHHhhhhhheeeecccccchhhhhhhhhhhccchhhhhccCCcchhhcccc
Confidence            34578889999311000        10  012466777777654332211             00112345679999999


Q ss_pred             CCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          130 DLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       130 Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      |+.+.  .  +.+....+.+....+++++||++|+||++|++.+.+.
T Consensus       128 Dl~~~--~--~~~~~~~~~~~~~~~v~~iSA~~g~Gi~~L~~~i~~~  170 (185)
T d1lnza2         128 DMPEA--A--ENLEAFKEKLTDDYPVFPISAVTREGLRELLFEVANQ  170 (185)
T ss_dssp             TSTTH--H--HHHHHHHHHCCSCCCBCCCSSCCSSTTHHHHHHHHHH
T ss_pred             chHhH--H--HHHHHHHHHhccCCcEEEEECCCCCCHHHHHHHHHHh
Confidence            99865  3  2333334455567899999999999999999988654

>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=98.33  E-value=2.3e-07  Score=67.00  Aligned_cols=102  Identities=14%  Similarity=0.087  Sum_probs=57.8

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc--C------CCCCCCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR--K------GGPGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~--~------~~~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+.+-++++.|...-   .......+|++|+|+|+++......  .      .......+-++|.||.|+........+.
T Consensus        54 ~~~l~i~D~~G~e~~~~~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilv~~k~D~~~~~~~~~~~  133 (173)
T d2fu5c1          54 RIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKER  133 (173)
T ss_dssp             EEEEEEEEC---------CCTTTTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEEC--CCSCCCSCHHH
T ss_pred             EEEEEEEECCCchhhHHHHHHhccCCCEEEEEEECCChhhHHHHHHHHHHhhhhccCCceEEEEEecccchhhcccHHHH
Confidence            356667899993110   1111234799999999987532110  0      0112335678999999998652233344


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+..+..  +.+++++||++|+||+++|++|.+.
T Consensus       134 ~~~~~~~~--~~~~~e~Sa~~g~gv~e~f~~l~~~  166 (173)
T d2fu5c1         134 GEKLALDY--GIKFMETSAKANINVENAFFTLARD  166 (173)
T ss_dssp             HHHHHHHH--TCEEEECCC---CCHHHHHHHHHHH
T ss_pred             HHHHHHhc--CCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            44455443  5789999999999999999987653

>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=98.33  E-value=2e-06  Score=59.93  Aligned_cols=101  Identities=12%  Similarity=0.045  Sum_probs=62.7

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHH
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLA  140 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~  140 (178)
                      +.-..+..+.|..-.   .......++..++++|..+......         ........+.+++.||.|+...  ....
T Consensus        43 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~~~k~d~~~~--~~~~  120 (166)
T d2qtvb1          43 NIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIAELKDVPFVILGNKIDAPNA--VSEA  120 (166)
T ss_dssp             TCCEEEEECCCSGGGGGGGGGGCTTCSEEEEEEETTCGGGHHHHHHHHHHHHTCTTTTTCCEEEEEECTTSSSC--CCHH
T ss_pred             CeeEEEEeeccchhhhhhHhhhhhheeeeeeeccccchhhhhhhhHHHHhhhhhhccCCceEEEEecccccccc--CCHH
Confidence            455666667773111   1111224688999999876433211         1222344567899999999765  3344


Q ss_pred             HHHHHHHhcC----------CCCCEEEEecccCCCHHHHHHHHhh
Q 030407          141 VMERDALRMR----------DGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       141 ~~~~~l~~~n----------p~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ++.+.++..+          ...+++++||++|+|++|+|++|.+
T Consensus       121 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~SA~tg~Gv~e~~~~l~~  165 (166)
T d2qtvb1         121 ELRSALGLLNTTGSQRIEGQRPVEVFMCSVVMRNGYLEAFQWLSQ  165 (166)
T ss_dssp             HHHHHHTCSSCCC---CCSSCCEEEEEEBTTTTBSHHHHHHHHTT
T ss_pred             HHHHHhhhhhhhHHHhhcccCCCEEEEeeCCCCCCHHHHHHHHhC
Confidence            4444443211          1236899999999999999999976

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {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 GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=98.32  E-value=3.6e-07  Score=65.71  Aligned_cols=58  Identities=12%  Similarity=-0.024  Sum_probs=45.0

Q ss_pred             CceeEEEEecCCCCCchhHhH----HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhhhC
Q 030407          119 TQADLLVINKTDLASAIGADL----AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYIVS  178 (178)
Q Consensus       119 ~~adiiviNK~Dl~~~~~~~~----~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~~~  178 (178)
                      ....++++||+|+++.  ...    +.+.+.++...+..+++++||++|+||++|++.|.++-|
T Consensus       127 ~~~~~~v~~k~D~~~~--~~~~~~~~~~~~~l~~~~~~~~~i~vSA~~g~Gid~L~~~i~~~~~  188 (188)
T d1puia_         127 NIAVLVLLTKADKLAS--GARKAQLNMVREAVLAFNGDVQVETFSSLKKQGVDKLRQKLDTWFS  188 (188)
T ss_dssp             TCCEEEEEECGGGSCH--HHHHHHHHHHHHHHGGGCSCEEEEECBTTTTBSHHHHHHHHHHHHC
T ss_pred             cccccchhhhhhccCH--HHHHHHHHHHHHHHHhhCCCCcEEEEeCCCCCCHHHHHHHHHHHhC
Confidence            4467999999999886  443    344455555566779999999999999999999987643

>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=98.32  E-value=2.3e-07  Score=67.01  Aligned_cols=101  Identities=15%  Similarity=0.061  Sum_probs=63.1

Q ss_pred             CCCEEEEeCCcchhhhcc---cccccceEEEEEeCCCCCCCCc--C-C-----CCCCCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDNLAANF---SRELADYIIYIIDVSGGDKIPR--K-G-----GPGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~---~~~~ad~~I~VvD~~~~~~~~~--~-~-----~~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+.+.+.++.|.-.-...   ....+|++|+|+|.++......  . +     ...-..+-++|.||+|+........+.
T Consensus        51 ~~~~~i~d~~g~~~~~~~~~~~~~~~d~~ilv~d~~~~~sf~~~~~~~~~~~~~~~~~~piilv~nK~D~~~~~~~~~~~  130 (173)
T d2a5ja1          51 QIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESRRDVKREE  130 (173)
T ss_dssp             EEEEEEECCTTGGGTSCCCHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHHH
T ss_pred             EEEEEeecccCccchhhHHHHHhhccCEEEEEEeecChHHHHhHHHHHHHHHHhCCCCCeEEEEecCCchhhhhhhHHHH
Confidence            467778888883111111   1124699999999977532211  0 0     001234668999999986432133344


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .....++.  ..+++++||++|.||+++|..+.+
T Consensus       131 ~~~~a~~~--~~~~~e~Sa~tg~~V~e~f~~i~~  162 (173)
T d2a5ja1         131 GEAFAREH--GLIFMETSAKTACNVEEAFINTAK  162 (173)
T ss_dssp             HHHHHHHH--TCEEEEECTTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHc--CCEEEEecCCCCCCHHHHHHHHHH
Confidence            55555544  468999999999999999987654

>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=98.31  E-value=2.6e-07  Score=66.81  Aligned_cols=101  Identities=12%  Similarity=-0.058  Sum_probs=62.0

Q ss_pred             CCCEEEEeCCcchhhhcc---cccccceEEEEEeCCCCCCCCc---CCC-----CCCCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDNLAANF---SRELADYIIYIIDVSGGDKIPR---KGG-----PGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~---~~~~ad~~I~VvD~~~~~~~~~---~~~-----~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+.+-+.++.|..--...   ....++++++|+|.++......   .+.     ..-..+-++|.||+|+.+......+.
T Consensus        52 ~~~~~i~d~~g~e~~~~~~~~~~~~~~~~i~v~d~~~~~S~~~~~~~~~~i~~~~~~~~piilvgnK~Dl~~~~~~~~~~  131 (175)
T d2f9la1          52 TIKAQIWDTAGQERYRRITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDE  131 (175)
T ss_dssp             EEEEEEEECSSGGGTTCCCHHHHTTCSEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCGGGCCSCHHH
T ss_pred             EEEEEecccCCcHHHHHHHHHHhhccCeEEEEEECCCcccchhHHHHHHHHHHhcCCCCcEEEEEeeecccccccchHHH
Confidence            467788899993110010   1124699999999987532211   000     00124678899999997542122233


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .....+..  ..+++++||++|+|++++|+.+.+
T Consensus       132 ~~~~~~~~--~~~~~e~Sa~~g~~i~e~f~~l~~  163 (175)
T d2f9la1         132 ARAFAEKN--NLSFIETSALDSTNVEEAFKNILT  163 (175)
T ss_dssp             HHHHHHHT--TCEEEECCTTTCTTHHHHHHHHHH
T ss_pred             HHHhhccc--CceEEEEecCCCcCHHHHHHHHHH
Confidence            34444433  468999999999999999987543

>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=98.25  E-value=9.4e-08  Score=67.87  Aligned_cols=73  Identities=15%  Similarity=0.076  Sum_probs=50.2

Q ss_pred             ccceEEEEEeCCCCCCCCcC--CCC-----CCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCH
Q 030407           94 LADYIIYIIDVSGGDKIPRK--GGP-----GITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGI  166 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~--~~~-----qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi  166 (178)
                      .+|.+++++|+.........  +..     .-..+.++|+||+|+.++  ...      +++ .+..+++++||++|+||
T Consensus        80 ~~d~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~iilv~NK~Dl~~~--~~~------~~~-~~~~~~~~iSAk~~~gi  150 (161)
T d2gj8a1          80 QADRVLFMVDGTTTDAVDPAEIWPEFIARLPAKLPITVVRNKADITGE--TLG------MSE-VNGHALIRLSARTGEGV  150 (161)
T ss_dssp             TCSEEEEEEETTTCCCCSHHHHCHHHHHHSCTTCCEEEEEECHHHHCC--CCE------EEE-ETTEEEEECCTTTCTTH
T ss_pred             hccccceeeccccccchhhhhhhhhhhhhcccccceeeccchhhhhhh--HHH------HHH-hCCCcEEEEECCCCCCH
Confidence            46899999999875432210  000     013467999999999765  210      112 24568999999999999


Q ss_pred             HHHHHHHhh
Q 030407          167 IFTLSITHY  175 (178)
Q Consensus       167 ~el~~~l~~  175 (178)
                      ++|+++|.+
T Consensus       151 ~~L~~~l~~  159 (161)
T d2gj8a1         151 DVLRNHLKQ  159 (161)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999999865

>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=98.22  E-value=6.2e-07  Score=68.25  Aligned_cols=79  Identities=19%  Similarity=0.094  Sum_probs=56.3

Q ss_pred             cceEEEEEeCCCCCCCCc---CC---CCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHH
Q 030407           95 ADYIIYIIDVSGGDKIPR---KG---GPGITQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~---~~---~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                      .|.++.|+.+.+++....   ++   .......-+||+||+||.++  ++.+.+........+..+++.+||++|+|+++
T Consensus        11 iD~vliV~s~~~P~~~~~~ldR~Lv~a~~~~i~pvIvlnK~DL~~~--~~~~~~~~~~~~~~~~~~v~~vSa~~~~g~~~   88 (225)
T d1u0la2          11 VDQVILVVTVKMPETSTYIIDKFLVLAEKNELETVMVINKMDLYDE--DDLRKVRELEEIYSGLYPIVKTSAKTGMGIEE   88 (225)
T ss_dssp             CCEEEEEECSSTTCCCHHHHHHHHHHHHHTTCEEEEEECCGGGCCH--HHHHHHHHHHHHHTTTSCEEECCTTTCTTHHH
T ss_pred             CCEEEEEEeCCCCCCCHHHHHHHHHHHHHcCCCEEEEEeCcccCCH--HHHHHHHHhhcccccceeEEEeccccchhHhh
Confidence            477888887755432211   11   01123356999999999988  67777776666555667999999999999999


Q ss_pred             HHHHHhh
Q 030407          169 TLSITHY  175 (178)
Q Consensus       169 l~~~l~~  175 (178)
                      |.+++..
T Consensus        89 L~~~l~~   95 (225)
T d1u0la2          89 LKEYLKG   95 (225)
T ss_dssp             HHHHHSS
T ss_pred             HHHHhcC
Confidence            9988753

>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=98.21  E-value=7.4e-07  Score=63.66  Aligned_cols=101  Identities=19%  Similarity=0.123  Sum_probs=65.6

Q ss_pred             CCCEEEEeCCcchhhhcc---cccccceEEEEEeCCCCCCCCcC--------CCCCCCceeEEEEecCCCCCchhHhHHH
Q 030407           73 KADLLLCESGGDNLAANF---SRELADYIIYIIDVSGGDKIPRK--------GGPGITQADLLVINKTDLASAIGADLAV  141 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~---~~~~ad~~I~VvD~~~~~~~~~~--------~~~qi~~adiiviNK~Dl~~~~~~~~~~  141 (178)
                      .+.+-+++|.|..--...   ....++++++|+|..+.......        ....-..+.+++.||.|+.+.. ...+.
T Consensus        50 ~~~~~i~Dt~G~~~~~~~~~~~~~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~i~~~~k~d~~~~~-~~~~~  128 (166)
T d1g16a_          50 KVKLQIWDTAGQERFRTITTAYYRGAMGIILVYDITDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRV-VTADQ  128 (166)
T ss_dssp             EEEEEEECCTTGGGTSCCCHHHHTTEEEEEEEEETTCHHHHHTHHHHHHHHHHHSCTTCEEEEEEECTTCTTCC-SCHHH
T ss_pred             EEEEEEEECCCchhhHHHHHHHHhcCCEEEEEEECCCccCHHHHHhhhhhhhccccCcceeeeecchhhhhhhh-hhHHH
Confidence            466778999993211111   11347999999999875422110        0112334678899999987652 22344


Q ss_pred             HHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          142 MERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       142 ~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      ..+..++.  +.+++++||++|+||+++|+.|.+.
T Consensus       129 ~~~~~~~~--~~~~~~~Sa~~~~~v~e~f~~l~~~  161 (166)
T d1g16a_         129 GEALAKEL--GIPFIESSAKNDDNVNEIFFTLAKL  161 (166)
T ss_dssp             HHHHHHHH--TCCEEECBTTTTBSHHHHHHHHHHH
T ss_pred             HHHHHHhc--CCeEEEECCCCCCCHHHHHHHHHHH
Confidence            45555544  4699999999999999999988654

>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=98.21  E-value=4.3e-07  Score=65.17  Aligned_cols=101  Identities=14%  Similarity=-0.037  Sum_probs=65.1

Q ss_pred             CCCEEEEeCCcchhhh---cccccccceEEEEEeCCCCCCCCc---CC-----CCCCCceeEEEEecCCCCCch---hHh
Q 030407           73 KADLLLCESGGDNLAA---NFSRELADYIIYIIDVSGGDKIPR---KG-----GPGITQADLLVINKTDLASAI---GAD  138 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~---~~~~~~ad~~I~VvD~~~~~~~~~---~~-----~~qi~~adiiviNK~Dl~~~~---~~~  138 (178)
                      .+++-+.++.|...-.   ......+|.+++|+|.++......   .+     ...-..+-+++.||+|+.+..   ...
T Consensus        51 ~~~l~i~d~~g~~~~~~~~~~~~~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~v~nk~d~~~~~~~~~v~  130 (170)
T d1ek0a_          51 TVKFEIWDTAGQERFASLAPMYYRNAQAALVVYDVTKPQSFIKARHWVKELHEQASKDIIIALVGNKIDMLQEGGERKVA  130 (170)
T ss_dssp             EEEEEEEEECCSGGGGGGHHHHHTTCSEEEEEEETTCHHHHHHHHHHHHHHHHHSCTTCEEEEEEECGGGGGSSCCCCSC
T ss_pred             cccccccccCCchhHHHHHHHHHhccceEEEEEeCCcccchhhhhhhhhhhccccccccceeeeecccccccccchhhhh
Confidence            4678889999942111   111235799999999987532211   00     011234678999999985431   122


Q ss_pred             HHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          139 LAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       139 ~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      .+...+..+..  +.+++++||++|+||+++|+.|.+
T Consensus       131 ~~~~~~~~~~~--~~~~~e~Sak~g~gV~e~F~~i~~  165 (170)
T d1ek0a_         131 REEGEKLAEEK--GLLFFETSAKTGENVNDVFLGIGE  165 (170)
T ss_dssp             HHHHHHHHHHH--TCEEEECCTTTCTTHHHHHHHHHT
T ss_pred             HHHHHHHHHHc--CCEEEEecCCCCcCHHHHHHHHHH
Confidence            34455556655  358999999999999999998754

>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=98.17  E-value=6.7e-07  Score=65.54  Aligned_cols=101  Identities=16%  Similarity=0.077  Sum_probs=63.4

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCC-----CCCceeEEEEecCCCCCchh----
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGP-----GITQADLLVINKTDLASAIG----  136 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~-----qi~~adiiviNK~Dl~~~~~----  136 (178)
                      .+.+-++++.|..    +...+. ..+|++++|+|.++......   .+..     .-..+-++|.||+|+.+...    
T Consensus        50 ~~~l~i~D~~g~~~~~~~~~~~~-~~~~~~ilv~d~~~~~Sf~~~~~~~~~~~~~~~~~~~i~lvgnK~Dl~~~~~~~~~  128 (191)
T d2ngra_          50 PYTLGLFDTAGQEDYDRLRPLSY-PQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEK  128 (191)
T ss_dssp             EEEEEEEEECCSGGGTTTGGGGC-TTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHCTTCCEEEEEECGGGGGCHHHHHH
T ss_pred             eeeeeccccccchhhhhhhhhcc-cccceeecccccchHHHHHHHHHHHHHHHhhcCCCCceEEEeccccccccchhhhh
Confidence            4677889999942    112222 25799999999987643211   1100     01345689999999864410    


Q ss_pred             --------HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          137 --------ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       137 --------~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                              ...+...++.++.+ ..+++++||++|+||+++|+.+.+
T Consensus       129 ~~~~~~~~v~~~~~~~~~~~~~-~~~~~e~SAk~~~~V~e~f~~l~~  174 (191)
T d2ngra_         129 LAKNKQKPITPETAEKLARDLK-AVKYVECSALTQKGLKNVFDEAIL  174 (191)
T ss_dssp             HHTTTCCCCCHHHHHHHHHHTT-CSCEEECCTTTCTTHHHHHHHHHH
T ss_pred             hhhcccccccHHHHHHHHHHcC-CCeEEEEeCCCCcCHHHHHHHHHH
Confidence                    11223344444443 358999999999999999987654

>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=98.15  E-value=9.9e-07  Score=65.64  Aligned_cols=103  Identities=11%  Similarity=0.074  Sum_probs=64.8

Q ss_pred             CCCEEEEeCCcch--hhhccc-ccccceEEEEEeCCCCCCCCcC-CC---CCCCc-eeEEEEecCCCCCchhHhHHH---
Q 030407           73 KADLLLCESGGDN--LAANFS-RELADYIIYIIDVSGGDKIPRK-GG---PGITQ-ADLLVINKTDLASAIGADLAV---  141 (178)
Q Consensus        73 ~~d~iiiEttG~~--~~~~~~-~~~ad~~I~VvD~~~~~~~~~~-~~---~qi~~-adiiviNK~Dl~~~~~~~~~~---  141 (178)
                      +..+-++.|.|-.  ...+.. ...+|.+++|+|+..|...+.+ +.   ..+.. .-++++||+|++++. +..+.   
T Consensus        65 ~~~~~~iDtPGh~~f~~~~~~~~~~aD~allVVda~~G~~~QT~~~~~~a~~~~~~~iIv~iNK~D~~~~~-~~~~~i~~  143 (196)
T d1d2ea3          65 ARHYAHTDCPGHADYVKNMITGTAPLDGCILVVAANDGPMPQTREHLLLARQIGVEHVVVYVNKADAVQDS-EMVELVEL  143 (196)
T ss_dssp             SCEEEEEECSSHHHHHHHHHHTSSCCSEEEEEEETTTCSCHHHHHHHHHHHHTTCCCEEEEEECGGGCSCH-HHHHHHHH
T ss_pred             eeeEEeecCcchHHHHHHHHHHHhhcCeEEEEEEcCCCCchhHHHHHHHHHHhcCCcEEEEEecccccccH-HHHHHHHH
Confidence            5678999999921  111111 1246999999999988654321 11   11222 246779999998651 22233   


Q ss_pred             -HHHHHHhcC--C-CCCEEEEecccC----------CCHHHHHHHHhhh
Q 030407          142 -MERDALRMR--D-GGPFIFAQVGWV----------IGIIFTLSITHYI  176 (178)
Q Consensus       142 -~~~~l~~~n--p-~a~i~~~SA~~g----------~gi~el~~~l~~~  176 (178)
                       +...+...+  | .+|++++||++|          .|+++|++.+.+.
T Consensus       144 ~i~~~l~~~~~~~~~~pii~iSa~~g~~~~~~~~~~~~~~~Lldai~~~  192 (196)
T d1d2ea3         144 EIRELLTEFGYKGEETPIIVGSALCALEQRDPELGLKSVQKLLDAVDTY  192 (196)
T ss_dssp             HHHHHHHHTTSCTTTSCEEECCHHHHHTTCCTTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCcccCEEEEEEccccccccCcccccCCHHHHHHHHHhh
Confidence             334444332  2 378999999999          5999999988664

>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=98.14  E-value=1.5e-06  Score=62.31  Aligned_cols=104  Identities=11%  Similarity=-0.038  Sum_probs=64.4

Q ss_pred             CCCCEEEEeCCcchhh------h---c---ccccccceEEEEEeCCCCCCCCcCC---CCCCCceeEEEEecCCCCCchh
Q 030407           72 FKADLLLCESGGDNLA------A---N---FSRELADYIIYIIDVSGGDKIPRKG---GPGITQADLLVINKTDLASAIG  136 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~------~---~---~~~~~ad~~I~VvD~~~~~~~~~~~---~~qi~~adiiviNK~Dl~~~~~  136 (178)
                      .....+.+.+.|....      .   .   .....++.++++.|+..........   ...-...-++++||+|..... 
T Consensus        51 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~~~~~~~~~~~~l~~~~~~~i~v~~k~d~~~~~-  129 (179)
T d1egaa1          51 GAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEK-  129 (179)
T ss_dssp             TTEEEEEESSSSCCHHHHHHHHHHHTCCTTSCCCCEEEEEEEEETTCCCHHHHHHHHHHHSSSSCEEEEEESTTTCCCH-
T ss_pred             CCceeEeecCCCceecchhhhhhhhhhccccchhhcceeEEEEecCccchhHHHHHHHhhhccCceeeeeeeeeccchh-
Confidence            3556777788884211      0   0   0112347788888876543221100   001123469999999988762 


Q ss_pred             HhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhhh
Q 030407          137 ADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       137 ~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      .++....+.+....+..+++++||++|+||++|++.|.+.
T Consensus       130 ~~~~~~~~~~~~~~~~~~~~~vSA~~g~gi~~L~~~i~~~  169 (179)
T d1egaa1         130 ADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKH  169 (179)
T ss_dssp             HHHHHHHHHHHTTSCCSEEEECCTTTTTTHHHHHHHHHTT
T ss_pred             hhhhhHhhhhhhhcCCCCEEEEeCcCCCCHHHHHHHHHHh
Confidence            3344444555555566799999999999999999998653

>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=98.13  E-value=6.9e-07  Score=64.97  Aligned_cols=101  Identities=14%  Similarity=0.035  Sum_probs=60.4

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCc---CCCC-----CCCceeEEEEecCCCCCchhH---
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPR---KGGP-----GITQADLLVINKTDLASAIGA---  137 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~-----qi~~adiiviNK~Dl~~~~~~---  137 (178)
                      .+.+-+..+.|..    +...+. ..+|++++|+|.++......   .+..     .-..+-++|.||+|+.++...   
T Consensus        52 ~~~~~~~d~~g~~~~~~~~~~~~-~~~~~~ilv~d~~~~~sf~~i~~~~~~~~~~~~~~~piilvgnK~Dl~~~~~~~~~  130 (183)
T d1mh1a_          52 PVNLGLWDTAGQEDYDRLRPLSY-PQTDVSLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEK  130 (183)
T ss_dssp             EEEEEEECCCCSGGGTTTGGGGC-TTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHSTTSCEEEEEECHHHHTCHHHHHH
T ss_pred             ceEEEeecccccccchhhhhhcc-cccceeeeeeccchHHHHHHHHHHHHHHHHHhCCCCcEEEEeecccchhhhhhhhh
Confidence            3555667777731    112222 35799999999986542211   0000     012467899999998654100   


Q ss_pred             ---------hHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          138 ---------DLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       138 ---------~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                               .........+.. ...++++|||++|+||+++|+.+.+
T Consensus       131 ~~~~~~~~~~~~~~~~~a~~~-~~~~~~E~SAk~~~~V~e~F~~l~~  176 (183)
T d1mh1a_         131 LKEKKLTPITYPQGLAMAKEI-GAVKYLECSALTQRGLKTVFDEAIR  176 (183)
T ss_dssp             HHHTTCCCCCHHHHHHHHHHT-TCSEEEECCTTTCTTHHHHHHHHHH
T ss_pred             hhhccccchhhHHHHHHHHHc-CCceEEEcCCCCCcCHHHHHHHHHH
Confidence                     011222333333 2368999999999999999997764

>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=98.11  E-value=3.1e-06  Score=59.43  Aligned_cols=80  Identities=15%  Similarity=0.070  Sum_probs=52.9

Q ss_pred             cceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHh---cCCCCCEEEEeccc
Q 030407           95 ADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLAVMERDALR---MRDGGPFIFAQVGW  162 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~---~np~a~i~~~SA~~  162 (178)
                      .+..+.++|.........         .....-..+-+++.||.|+...  .....+...+..   .+...+++++||++
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iv~nk~Dl~~~--~~~~~i~~~~~~~~~~~~~~~~~~~SA~~  150 (169)
T d1upta_          73 TDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQA--MTSSEMANSLGLPALKDRKWQIFKTSATK  150 (169)
T ss_dssp             CSEEEEEEETTCCTTHHHHHHHHHHHHTCGGGTTCEEEEEEECTTSTTC--CCHHHHHHHHTGGGCTTSCEEEEECCTTT
T ss_pred             hhhhhhhhhhhhcchhhhccchhhhhhhhhccccceEEEEEeecccccc--ccHHHHHHHHHHHHHhcCCCEEEEEeCCC
Confidence            588899999875443211         0011123356899999999876  444444444321   23456899999999


Q ss_pred             CCCHHHHHHHHhhh
Q 030407          163 VIGIIFTLSITHYI  176 (178)
Q Consensus       163 g~gi~el~~~l~~~  176 (178)
                      |+||+++|++|.+.
T Consensus       151 g~gv~e~~~~l~~~  164 (169)
T d1upta_         151 GTGLDEAMEWLVET  164 (169)
T ss_dssp             CTTHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999988654

>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=98.07  E-value=3e-06  Score=61.45  Aligned_cols=100  Identities=14%  Similarity=0.082  Sum_probs=62.6

Q ss_pred             CCCEEEEeCCcchhhhcccccccceEEEEEeCCCCCCCCc--C-------CC--CCCCceeEEEEecCCCCCch--hHhH
Q 030407           73 KADLLLCESGGDNLAANFSRELADYIIYIIDVSGGDKIPR--K-------GG--PGITQADLLVINKTDLASAI--GADL  139 (178)
Q Consensus        73 ~~d~iiiEttG~~~~~~~~~~~ad~~I~VvD~~~~~~~~~--~-------~~--~qi~~adiiviNK~Dl~~~~--~~~~  139 (178)
                      .+.+-+.+|.| .....|.. .+|++|+|+|.++......  .       ..  ..-..+-++|+||.|+....  ....
T Consensus        51 ~~~l~i~Dt~g-~~~~~~~~-~ad~~ilVfd~~~~~Sf~~~~~~~~~i~~~~~~~~~~~pi~lV~~k~d~d~~~~~~v~~  128 (175)
T d2bmja1          51 THLVLIREEAG-APDAKFSG-WADAVIFVFSLEDENSFQAVSRLHGQLSSLRGEGRGGLALALVGTQDRISASSPRVVGD  128 (175)
T ss_dssp             EEEEEEEECSS-CCCHHHHH-HCSEEEEEEETTCHHHHHHHHHHHHHHHHHCC--CCCCEEEEEEECTTCCSSSCCCSCH
T ss_pred             EEEEEEeeccc-cccccccc-ccceeEEEeecccchhhhhhHHHHHHHHHHhhcccCCccEEEEeeecCcchhhhcchhH
Confidence            46777889999 23333332 5799999999987532111  0       01  11123568899998874321  0112


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHHHHHHhh
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      ++..++.++. ...+++++||++|.|++++|..+.+
T Consensus       129 ~~~~~~~~~~-~~~~~~e~SAk~~~~v~~~F~~l~~  163 (175)
T d2bmja1         129 ARARALCADM-KRCSYYETCATYGLNVDRVFQEVAQ  163 (175)
T ss_dssp             HHHHHHHHTS-TTEEEEEEBTTTTBTHHHHHHHHHH
T ss_pred             HHHHHHHHHh-CCCeEEEeCCCCCcCHHHHHHHHHH
Confidence            3344444443 3468999999999999999987654

>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=98.05  E-value=1.5e-06  Score=62.60  Aligned_cols=83  Identities=11%  Similarity=0.027  Sum_probs=50.8

Q ss_pred             ccceEEEEEeCCCCCCCCc-----CCC----------CCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcC--CCCCEE
Q 030407           94 LADYIIYIIDVSGGDKIPR-----KGG----------PGITQADLLVINKTDLASAIGADLAVMERDALRMR--DGGPFI  156 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~-----~~~----------~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~n--p~a~i~  156 (178)
                      .+|.+++|+|+........     ...          .....+-++|+||+|+++......+.+.+.++...  +..+++
T Consensus        81 ~~d~~~~vvD~~~~~~~~~~~~~~~~~~~d~~~~~~l~~~~~p~iiv~NK~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (184)
T d2cxxa1          81 NIDVAVLVVDGKAAPEIIKRWEKRGEIPIDVEFYQFLRELDIPTIVAVNKLDKIKNVQEVINFLAEKFEVPLSEIDKVFI  160 (184)
T ss_dssp             GCCEEEEEEETTHHHHHHHHHHHTTCCCHHHHHHHHHHHTTCCEEEEEECGGGCSCHHHHHHHHHHHHTCCGGGHHHHEE
T ss_pred             ccchheeeeeccccchhhhhhhhccccHHHHHHHHHHHHcCCCEEEEEeeeehhhhHHHHHHHHHHHhcccccccCCeEE
Confidence            3589999999864321000     000          01234569999999998762122222322222111  124689


Q ss_pred             EEecccCCCHHHHHHHHhhh
Q 030407          157 FAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       157 ~~SA~~g~gi~el~~~l~~~  176 (178)
                      ++||++|+||++|++.|.+.
T Consensus       161 ~vSA~~g~gi~~L~~~i~~~  180 (184)
T d2cxxa1         161 PISAKFGDNIERLKNRIFEV  180 (184)
T ss_dssp             ECCTTTCTTHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            99999999999999998765

>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=98.04  E-value=8.3e-07  Score=67.32  Aligned_cols=93  Identities=14%  Similarity=0.088  Sum_probs=55.7

Q ss_pred             CCEEEEeCCcch-hh-hcc-cccccceEEEEEeCCCCCCCCcC----CCCCCC-ceeEEEEecCCCCCchhHhH----HH
Q 030407           74 ADLLLCESGGDN-LA-ANF-SRELADYIIYIIDVSGGDKIPRK----GGPGIT-QADLLVINKTDLASAIGADL----AV  141 (178)
Q Consensus        74 ~d~iiiEttG~~-~~-~~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~-~adiiviNK~Dl~~~~~~~~----~~  141 (178)
                      ..+-||.|.|-. .. .+. ....+|.+++|+|+..|...+..    ....+. ..-++++||+|+.+......    +.
T Consensus        89 ~~~~iiD~PGH~dfv~~~~~g~~~aD~ailVvda~~G~~~Qt~e~~~~~~~~gv~~iiv~vNK~D~~~~~~~~~~~~~~~  168 (222)
T d1zunb3          89 RKFIIADTPGHEQYTRNMATGASTCDLAIILVDARYGVQTQTRRHSYIASLLGIKHIVVAINKMDLNGFDERVFESIKAD  168 (222)
T ss_dssp             EEEEEEECCCSGGGHHHHHHHHTTCSEEEEEEETTTCSCHHHHHHHHHHHHTTCCEEEEEEECTTTTTSCHHHHHHHHHH
T ss_pred             eEEEEEeccchhhhhhhhccccccCceEEEEeccccCcccchHHHHHHHHHcCCCEEEEEEEccccccccceehhhhHHH
Confidence            457899999921 11 111 11246999999999887654321    001122 12588999999987521222    23


Q ss_pred             HHHHHHhcC--C-CCCEEEEecccCCCH
Q 030407          142 MERDALRMR--D-GGPFIFAQVGWVIGI  166 (178)
Q Consensus       142 ~~~~l~~~n--p-~a~i~~~SA~~g~gi  166 (178)
                      +...+++..  + ..+++++||++|+|+
T Consensus       169 l~~~~~~~~~~~~~i~~IPiSA~~G~ni  196 (222)
T d1zunb3         169 YLKFAEGIAFKPTTMAFVPMSALKGDNV  196 (222)
T ss_dssp             HHHHHHTTTCCCSEEEEEECCTTTCTTT
T ss_pred             HhhhhHhhccCCCceEEEEEEcccCccC
Confidence            344444442  2 247799999999998

>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=97.98  E-value=1.7e-06  Score=62.84  Aligned_cols=104  Identities=15%  Similarity=0.124  Sum_probs=63.9

Q ss_pred             CCCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCc---CCCCC-----CCceeEEEEecCCCCCchh----
Q 030407           72 FKADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPR---KGGPG-----ITQADLLVINKTDLASAIG----  136 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~---~~~~q-----i~~adiiviNK~Dl~~~~~----  136 (178)
                      ..+.+-++++.|..--   .+.....+|.+++|+|.++......   .+...     -..+-++|.||+|+.+...    
T Consensus        48 ~~~~~~i~D~~g~~~~~~~~~~~~~~~~~~ilv~d~~~~~Sf~~~~~~~~~~~~~~~~~~~iilVgnK~Dl~~~~~~~~~  127 (179)
T d1m7ba_          48 QRIELSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDLRTDVSTLVE  127 (179)
T ss_dssp             CEEEEEEEEECCSGGGTTTGGGGCTTCSEEEEEEETTCHHHHHHHHHTHHHHHHHHCTTCEEEEEEECGGGGGCHHHHHH
T ss_pred             eEEeeccccccccccccccccchhhhhhhhheeeecccCCCHHHHHHHHHHHHhccCCcceEEEEEecccccccchhhHH
Confidence            3577778899993211   1122235799999999987543211   11000     1345699999999864310    


Q ss_pred             --------HhHHHHHHHHHhcCCCCCEEEEecccCC-CHHHHHHHHhhh
Q 030407          137 --------ADLAVMERDALRMRDGGPFIFAQVGWVI-GIIFTLSITHYI  176 (178)
Q Consensus       137 --------~~~~~~~~~l~~~np~a~i~~~SA~~g~-gi~el~~~l~~~  176 (178)
                              ...++..+..++.+ ..++++|||++|+ |++++|+.+.+.
T Consensus       128 ~~~~~~~~V~~~e~~~~a~~~~-~~~y~E~SAk~~~n~i~~~F~~~~~~  175 (179)
T d1m7ba_         128 LSNHRQTPVSYDQGANMAKQIG-AATYIECSALQSENSVRDIFHVATLA  175 (179)
T ss_dssp             HHTTTCCCCCHHHHHHHHHHHT-CSEEEECBTTTBHHHHHHHHHHHHHH
T ss_pred             HhhhhcCcchHHHHHHHHHHhC-CCeEEEEeCCCCCcCHHHHHHHHHHH
Confidence                    11233444445443 3578999999998 699999976543

>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=97.98  E-value=3.5e-06  Score=60.05  Aligned_cols=82  Identities=11%  Similarity=0.003  Sum_probs=53.9

Q ss_pred             ccceEEEEEeCCCCCCCCc---------CCCCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhcC--------------
Q 030407           94 LADYIIYIIDVSGGDKIPR---------KGGPGITQADLLVINKTDLASAIGADLAVMERDALRMR--------------  150 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~---------~~~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~n--------------  150 (178)
                      ..+.++.++|.+.......         .....-..+.+++.||.|+...  .....+.+.+....              
T Consensus        80 ~~~~~~~~~d~~d~~~~~~~~~~~~~~~~~~~~~~~~~li~~~K~D~~~~--~~~~~i~~~~~~~~~~~~~~~~~~~~~~  157 (186)
T d1f6ba_          80 AINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEA--ISEERLREMFGLYGQTTGKGSVSLKELN  157 (186)
T ss_dssp             GCSEEEEEEETTCGGGHHHHHHHHHHHHTCGGGTTSCEEEEEECTTSTTC--CCHHHHHHHHTCTTTCCCSSCCCTTTCC
T ss_pred             ccceeeeeeeccCccchHHHHHHHHHhhcccccCCCceEEEEeccCcccc--CCHHHHHHHHhhcccchhhhhhhHHHhh
Confidence            3588999999876432110         0111123567999999999775  44444544443211              


Q ss_pred             -CCCCEEEEecccCCCHHHHHHHHhhhh
Q 030407          151 -DGGPFIFAQVGWVIGIIFTLSITHYIV  177 (178)
Q Consensus       151 -p~a~i~~~SA~~g~gi~el~~~l~~~~  177 (178)
                       ...+++++||++|+||+|+|++|.+++
T Consensus       158 ~~~~~~~~~SA~tg~Gi~e~~~~l~~~i  185 (186)
T d1f6ba_         158 ARPLEVFMCSVLKRQGYGEGFRWMAQYI  185 (186)
T ss_dssp             SCCEEEEECBTTTTBSHHHHHHHHHTTC
T ss_pred             cCCCEEEEEeCCCCCCHHHHHHHHHHhh
Confidence             113689999999999999999998764

>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=97.89  E-value=5.1e-06  Score=64.47  Aligned_cols=78  Identities=14%  Similarity=0.030  Sum_probs=55.6

Q ss_pred             ccceEEEEEeCCCCCCCCcC-CCCCC-CceeEEEEecCCCCCchhHhHHHHHHHHHhcCCCCCEEEEecccCCCHHHHHH
Q 030407           94 LADYIIYIIDVSGGDKIPRK-GGPGI-TQADLLVINKTDLASAIGADLAVMERDALRMRDGGPFIFAQVGWVIGIIFTLS  171 (178)
Q Consensus        94 ~ad~~I~VvD~~~~~~~~~~-~~~qi-~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~np~a~i~~~SA~~g~gi~el~~  171 (178)
                      .+|.++.|+|+..+...... ....+ ..+-++|+||+||++.  ...+...++.+..  ..+.+.+|++++.|..++.+
T Consensus        15 ~~DvIl~V~DaR~P~ss~~~~l~~~~~~Kp~IlVlNK~DLv~~--~~~~~w~~~f~~~--~~~~i~isa~~~~~~~~~~~   90 (273)
T d1puja_          15 LIDIVYELVDARIPMSSRNPMIEDILKNKPRIMLLNKADKADA--AVTQQWKEHFENQ--GIRSLSINSVNGQGLNQIVP   90 (273)
T ss_dssp             GCSEEEEEEETTSTTTTSCHHHHHHCSSSCEEEEEECGGGSCH--HHHHHHHHHHHTT--TCCEEECCTTTCTTGGGHHH
T ss_pred             hCCEEEEEEECCCCCCCCCHHHHHHHcCCCeEEEEECccCCch--HHHHHHHHHHHhc--CCccceeecccCCCccccch
Confidence            46999999999876543221 00011 3467999999999988  6666666666644  45789999999999988877


Q ss_pred             HHhh
Q 030407          172 ITHY  175 (178)
Q Consensus       172 ~l~~  175 (178)
                      .+.+
T Consensus        91 ~~~~   94 (273)
T d1puja_          91 ASKE   94 (273)
T ss_dssp             HHHH
T ss_pred             hhhh
Confidence            6544

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.75  E-value=2.3e-05  Score=55.62  Aligned_cols=78  Identities=21%  Similarity=0.128  Sum_probs=44.6

Q ss_pred             CHHHHHHhhcC-CcEEEEEecCC-Cc------hhHHHHHHcCCCCccceeecccCC-CcccccccccccCHhHHHhhHhh
Q 030407            1 MLALCKFLRDK-YSLAAVTNDIF-TK------EDGEFLMRNGALPEERIRAVETGG-CPHAAIREDISINLGPLEELSNL   71 (178)
Q Consensus         1 ~~~~~~~~~~~-~~vaVI~nd~g-~~------iD~~li~~~~~~~~~~~~~l~~Gc-Cc~l~i~~dl~~~l~~l~~l~~~   71 (178)
                      +.+++++|+++ .|+|+|.||.+ ..      -|..++...|.    ....+.++| ||..  .++....+.....+...
T Consensus        18 i~~l~~~L~~~g~~v~vik~d~~~~~~~~~~~~ds~r~~~~g~----~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~   91 (165)
T d1xjca_          18 MEKWVAAAVREGWRVGTVKHHGHGGEPARPEGVDSVRHERAGA----VATAVEGDGLLQLH--LRRPLWRLDDVLALYAP   91 (165)
T ss_dssp             HHHHHHHHHHTTCCEEEEECCC--------------------C----SEEEEEETTEEEEE--ECCSCCCHHHHHHHHGG
T ss_pred             HHHHHHHHHhCCCeEEEEEeccCccccchhhccccHHHHhhcc----ccccccChHHHHHH--hhccccchhhHHHHHhh
Confidence            36788888765 99999999976 43      35555555554    566777888 5543  23223334333334445


Q ss_pred             CCCCEEEEeCCcc
Q 030407           72 FKADLLLCESGGD   84 (178)
Q Consensus        72 ~~~d~iiiEttG~   84 (178)
                      ..+|+|++|+.+.
T Consensus        92 ~~~D~iivEg~~~  104 (165)
T d1xjca_          92 LRLDLVLVEGYKQ  104 (165)
T ss_dssp             GCCSEEEEECCTT
T ss_pred             cccCeEeeecccc
Confidence            6899999999994

>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=97.75  E-value=7.4e-06  Score=60.96  Aligned_cols=91  Identities=13%  Similarity=0.101  Sum_probs=53.0

Q ss_pred             CCCCEEEEeCCcch-hh-hccc-ccccceEEEEEeCCCCCCCCcC----CCCCCCcee-EEEEecCCCCCchhHhHHHHH
Q 030407           72 FKADLLLCESGGDN-LA-ANFS-RELADYIIYIIDVSGGDKIPRK----GGPGITQAD-LLVINKTDLASAIGADLAVME  143 (178)
Q Consensus        72 ~~~d~iiiEttG~~-~~-~~~~-~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~ad-iiviNK~Dl~~~~~~~~~~~~  143 (178)
                      .+..+.||.|.|-. .. .+.. ...+|.+|+|+|+..|...+..    +......+- ++++||+|+++.. +..+.+.
T Consensus        65 ~~~~i~iiDtPGh~df~~~~~~~~~~aD~avlVvda~~Gv~~qt~~~~~~~~~~gi~~iiv~iNK~D~~~~~-~~~~~~~  143 (204)
T d2c78a3          65 AKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDP-ELLDLVE  143 (204)
T ss_dssp             SSCEEEEEECCCSGGGHHHHHHHHTTCSSEEEEEETTTCCCHHHHHHHHHHHHTTCCCEEEEEECGGGCCCH-HHHHHHH
T ss_pred             CCeEEEEEeCCCchhhHHHHHHHHHHCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCeEEEEEEecccCCCH-HHHHHHH
Confidence            36789999999921 11 1111 1246999999999988654321    111123343 5569999998751 2233333


Q ss_pred             ----HHHHhcC-C--CCCEEEEecccC
Q 030407          144 ----RDALRMR-D--GGPFIFAQVGWV  163 (178)
Q Consensus       144 ----~~l~~~n-p--~a~i~~~SA~~g  163 (178)
                          ..+.... |  ..++++.||..|
T Consensus       144 ~~i~~~l~~~~~~~~~i~~i~~sa~~~  170 (204)
T d2c78a3         144 MEVRDLLNQYEFPGDEVPVIRGSALLA  170 (204)
T ss_dssp             HHHHHHHHHTTSCTTTSCEEECCHHHH
T ss_pred             HHHHHHHHhcCCCcccceeeeeechhh
Confidence                3333322 2  368899998643

>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=97.63  E-value=4.3e-06  Score=63.72  Aligned_cols=78  Identities=9%  Similarity=-0.049  Sum_probs=49.3

Q ss_pred             cceEEEEEeCCCCCCCCc---CC---CCCCCceeEEEEecCCCCCchhHhHHHHHHHHHhc--CCCCCEEEEecccCCCH
Q 030407           95 ADYIIYIIDVSGGDKIPR---KG---GPGITQADLLVINKTDLASAIGADLAVMERDALRM--RDGGPFIFAQVGWVIGI  166 (178)
Q Consensus        95 ad~~I~VvD~~~~~~~~~---~~---~~qi~~adiiviNK~Dl~~~~~~~~~~~~~~l~~~--np~a~i~~~SA~~g~gi  166 (178)
                      .|.+++|+.+.+++....   ++   ...-...-+||+||+||.++  .+.+...+.+.+.  ..+.+++.+||++|+|+
T Consensus        11 iD~~~iV~s~~~P~~~~~~idR~Lv~a~~~~i~pvIvlnK~DL~~~--~~~~~~~~~~~~~y~~~g~~v~~~Sa~~~~gl   88 (231)
T d1t9ha2          11 VDQAVLVFSAVQPSFSTALLDRFLVLVEANDIQPIICITKMDLIED--QDTEDTIQAYAEDYRNIGYDVYLTSSKDQDSL   88 (231)
T ss_dssp             CCEEEEEEESTTTTCCHHHHHHHHHHHHTTTCEEEEEEECGGGCCC--HHHHHHHHHHHHHHHHHTCCEEECCHHHHTTC
T ss_pred             cCEEEEEEECCCCCCCHHHHHHHHHHHHHcCCCEEEEEeccccccc--HHHHHHHHHHHHHHhhccccceeeecCChhHH
Confidence            477888888765532211   11   11123356999999999987  4433322222111  12579999999999999


Q ss_pred             HHHHHHHh
Q 030407          167 IFTLSITH  174 (178)
Q Consensus       167 ~el~~~l~  174 (178)
                      ++|.+++.
T Consensus        89 ~~L~~~l~   96 (231)
T d1t9ha2          89 ADIIPHFQ   96 (231)
T ss_dssp             TTTGGGGT
T ss_pred             HHHHHhhc
Confidence            99987765

>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=97.60  E-value=8.6e-06  Score=62.36  Aligned_cols=98  Identities=14%  Similarity=0.084  Sum_probs=55.3

Q ss_pred             CCCEEEEeCCcch-hh-hccc-ccccceEEEEEeCCCCCCCCc-CCCCC----------CCce-eEEEEecCCCCCch--
Q 030407           73 KADLLLCESGGDN-LA-ANFS-RELADYIIYIIDVSGGDKIPR-KGGPG----------ITQA-DLLVINKTDLASAI--  135 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~~~-~~~ad~~I~VvD~~~~~~~~~-~~~~q----------i~~a-diiviNK~Dl~~~~--  135 (178)
                      ...+-|+.|.|-. .. .... ...+|.+++|||+.+|...+. ....|          +... -++++||+|+++..  
T Consensus       101 ~~~i~~iDtPGH~df~~~~~~g~~~aD~ailVVda~~G~~~~~~~~~~QT~e~l~l~~~~~i~~iiv~iNKmD~~~~~~~  180 (245)
T d1r5ba3         101 HRRFSLLDAPGHKGYVTNMINGASQADIGVLVISARRGEFEAGFERGGQTREHAVLARTQGINHLVVVINKMDEPSVQWS  180 (245)
T ss_dssp             SEEEEECCCCC-----------TTSCSEEEEEEECSTTHHHHTTSTTCCHHHHHHHHHHTTCSSEEEEEECTTSTTCSSC
T ss_pred             cceeeeecccccccchhhhhhhhhhhcceeeEEEcCCCccCCccccccchHHHHHHHHHcCCCeEEEEEEcCCCCccchh
Confidence            3568889999921 11 1111 124699999999988642111 11112          1222 36889999997431  


Q ss_pred             hHh----HHHHHHHHHhc---CC--CCCEEEEecccCCCHHHHH
Q 030407          136 GAD----LAVMERDALRM---RD--GGPFIFAQVGWVIGIIFTL  170 (178)
Q Consensus       136 ~~~----~~~~~~~l~~~---np--~a~i~~~SA~~g~gi~el~  170 (178)
                      ...    .+++...++++   ++  ..+++++||++|+||.+++
T Consensus       181 e~~~~ei~~~l~~~l~~i~~~~~~~~v~~VPiSA~~G~nI~~~~  224 (245)
T d1r5ba3         181 EERYKECVDKLSMFLRRVAGYNSKTDVKYMPVSAYTGQNVKDRV  224 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCCCHHHHEEEEECBTTTTBTTSSCC
T ss_pred             HHHHHHHHHHHHHHHHHHhCcCcccCCEEEEeeccCCCCcccch
Confidence            011    22333333333   22  2479999999999998753

>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=97.17  E-value=0.00034  Score=54.19  Aligned_cols=61  Identities=15%  Similarity=0.139  Sum_probs=38.6

Q ss_pred             CCCEEEEeCCcch-hh-hccc-ccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCCC
Q 030407           73 KADLLLCESGGDN-LA-ANFS-RELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLAS  133 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~~~-~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~~  133 (178)
                      +..+-|+.|.|-. .. .... ...+|..|+|+|+..|...+..    .......+-++++||.|...
T Consensus        70 ~~~~n~iDtPG~~dF~~e~~~~l~~~D~avlVvda~~Gv~~~T~~~w~~a~~~~lP~i~fINKmDr~~  137 (276)
T d2bv3a2          70 DHRINIIDAPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTG  137 (276)
T ss_dssp             TEEEEEECCCSSSSCSTTHHHHHHHCCEEEEEEETTTSSCHHHHHHHHHHHTTTCCEEEEEECTTSTT
T ss_pred             CeEEEEecCCchhhhHHHHHHHHHhhhheEEeccccCCcchhHHHHHHHHHHcCCCEEEEEecccccc
Confidence            5678899999921 00 0100 1136999999999998754321    11224556799999999853

>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=97.16  E-value=0.00013  Score=54.60  Aligned_cols=96  Identities=13%  Similarity=0.092  Sum_probs=54.5

Q ss_pred             CCCEEEEeCCcch-hhh-cc-cccccceEEEEEeCCCCCCCCc-CCCCC----------CCc-eeEEEEecCCCCCch--
Q 030407           73 KADLLLCESGGDN-LAA-NF-SRELADYIIYIIDVSGGDKIPR-KGGPG----------ITQ-ADLLVINKTDLASAI--  135 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~~-~~-~~~~ad~~I~VvD~~~~~~~~~-~~~~q----------i~~-adiiviNK~Dl~~~~--  135 (178)
                      ++.+-||.|.|-. ... +. ....+|+.++|||+.+|...+. ...+|          +.. .-++++||+|+..+.  
T Consensus        80 ~~~i~iiDtPGH~df~~~~~~g~~~~D~allVVda~~G~~~~t~~~~~qt~e~l~~~~~~~~~~iIv~iNK~D~~~~~~~  159 (224)
T d1jnya3          80 KYFFTIIDAPGHRDFVKNMITGASQADAAILVVSAKKGEYEAGMSVEGQTREHIILAKTMGLDQLIVAVNKMDLTEPPYD  159 (224)
T ss_dssp             SCEEEECCCSSSTTHHHHHHHTSSCCSEEEEEEECSTTHHHHHHSTTCHHHHHHHHHHHTTCTTCEEEEECGGGSSSTTC
T ss_pred             CceeEEeeCCCcHHHHHHHHHHHHhhceEEEEEecccCcccccccccchhHHHHHHHHHhCCCceEEEEEcccCCCcccc
Confidence            4667889999921 111 11 1124699999999998742110 01111          112 237779999997531  


Q ss_pred             hHhHHHHHHHHHh----cC---CCCCEEEEecccCCCHHH
Q 030407          136 GADLAVMERDALR----MR---DGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       136 ~~~~~~~~~~l~~----~n---p~a~i~~~SA~~g~gi~e  168 (178)
                      ....+.+...++.    ..   ...+++++||.+|.|+.+
T Consensus       160 ~~~~~~v~~~i~~~~~~~~~~~~~i~~IPISA~~G~NV~~  199 (224)
T d1jnya3         160 EKRYKEIVDQVSKFMRSYGFNTNKVRFVPVVAPSGDNITH  199 (224)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCTTCEEEECBTTTTBTTTB
T ss_pred             HHHHHHHHHHHHhHHHhcCCCcccCeEEEEEccCCCCccc
Confidence            1223333333332    21   345789999999999854

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=97.14  E-value=0.00029  Score=52.51  Aligned_cols=147  Identities=15%  Similarity=0.089  Sum_probs=81.7

Q ss_pred             HHHHHHhhcC-CcEEEEEecCC-C-chhHHHH--HHcCCCCccceeecccCCCcccccccccccCH-hHHHhhHhhCCCC
Q 030407            2 LALCKFLRDK-YSLAAVTNDIF-T-KEDGEFL--MRNGALPEERIRAVETGGCPHAAIREDISINL-GPLEELSNLFKAD   75 (178)
Q Consensus         2 ~~~~~~~~~~-~~vaVI~nd~g-~-~iD~~li--~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l-~~l~~l~~~~~~d   75 (178)
                      .++..+++++ +||++|..|.. . .++....  +..|+    ++....+..        |+...+ +++. .....++|
T Consensus        30 AKLA~~~~~~g~kV~lit~Dt~R~ga~eQL~~~a~~l~v----~~~~~~~~~--------~~~~~~~~a~~-~~~~~~~d   96 (211)
T d1j8yf2          30 GKLAYFYKKKGFKVGLVGADVYRPAALEQLQQLGQQIGV----PVYGEPGEK--------DVVGIAKRGVE-KFLSEKME   96 (211)
T ss_dssp             HHHHHHHHHTTCCEEEEECCCSSHHHHHHHHHHHHHHTC----CEECCTTCC--------CHHHHHHHHHH-HHHHTTCS
T ss_pred             HHHHHHHHHCCCceEEEEeeccccchhHHHHHhccccCc----ceeecccch--------hhhHHHHHHHH-HhhccCCc
Confidence            3566667654 99999999988 4 5544221  22244    333332222        222222 2332 22356899


Q ss_pred             EEEEeCCcchhhh-------c---c-cccccceEEEEEeCCCCCCCCcCCCCC--CCceeEEEEecCCCCCchhHhHHHH
Q 030407           76 LLLCESGGDNLAA-------N---F-SRELADYIIYIIDVSGGDKIPRKGGPG--ITQADLLVINKTDLASAIGADLAVM  142 (178)
Q Consensus        76 ~iiiEttG~~~~~-------~---~-~~~~ad~~I~VvD~~~~~~~~~~~~~q--i~~adiiviNK~Dl~~~~~~~~~~~  142 (178)
                      +|||.|.|.+-..       .   + .....+-+++|+|++.+.+........  ....+-++++|.|-...    ...+
T Consensus        97 ~IlIDTaGr~~~~~~~~~~~el~~~~~~~~~~~~~LVl~a~~~~~~~~~~~~~~~~~~~~~lI~TKlDet~~----~G~~  172 (211)
T d1j8yf2          97 IIIVDTAGRHGYGEEAALLEEMKNIYEAIKPDEVTLVIDASIGQKAYDLASKFNQASKIGTIIITKMDGTAK----GGGA  172 (211)
T ss_dssp             EEEEECCCSCCTTCHHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHHHHHHHHHHHCTTEEEEEECTTSCSC----HHHH
T ss_pred             eEEEecCCcCccchhhHHHHHHHHHHhhcCCceEEEEEecccCcchHHHHhhhhcccCcceEEEecccCCCc----ccHH
Confidence            9999999942100       0   0 001136788999997764332111000  11235688999998655    3455


Q ss_pred             HHHHHhcCCCCCEEEEecccCCCHHHH
Q 030407          143 ERDALRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       143 ~~~l~~~np~a~i~~~SA~~g~gi~el  169 (178)
                      .+...+.  ..|+.++|  +|+++++|
T Consensus       173 l~~~~~~--~lPi~~it--~Gq~v~DL  195 (211)
T d1j8yf2         173 LSAVAAT--GATIKFIG--TGEKIDEL  195 (211)
T ss_dssp             HHHHHTT--TCCEEEEE--CSSSTTCE
T ss_pred             HHHHHHH--CcCEEEEe--CCCCcccC
Confidence            5555543  46888887  58888653

>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=97.08  E-value=4.3e-05  Score=58.13  Aligned_cols=94  Identities=14%  Similarity=0.047  Sum_probs=54.4

Q ss_pred             CCCEEEEeCCcch-hh-hcc-cccccceEEEEEeCCCCCC-------CCc-C---CCCCCCcee-EEEEecCCCCCchhH
Q 030407           73 KADLLLCESGGDN-LA-ANF-SRELADYIIYIIDVSGGDK-------IPR-K---GGPGITQAD-LLVINKTDLASAIGA  137 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~~-~~~~ad~~I~VvD~~~~~~-------~~~-~---~~~qi~~ad-iiviNK~Dl~~~~~~  137 (178)
                      +..+.||+|.|-. .. .+. ....+|..|+|+|+..|..       .+. .   ....+...- ++++||+|+.+...+
T Consensus        83 ~~~i~iiDtPGH~df~~~~~~g~~~~D~ailvvda~~G~~e~g~~~~~QT~eh~~~~~~~gv~~iiv~iNKmD~~~~d~~  162 (239)
T d1f60a3          83 KYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDES  162 (239)
T ss_dssp             SEEEEEEECCCCTTHHHHHHHSSSCCSEEEEEEECSHHHHHHHTCTTSHHHHHHHHHHHTTCCEEEEEEECGGGGTTCHH
T ss_pred             CEEEEEEECCCcHHHHHHHHHHHHHhCEEEEEEECCCCccccccCchHhHHHHHHHHHHcCCCeEEEEEECCCCCCCCHH
Confidence            3468999999920 11 111 1123699999999987521       110 0   011123333 668999999875222


Q ss_pred             hH----HHHHHHHHhcCC---CCCEEEEecccCCCH
Q 030407          138 DL----AVMERDALRMRD---GGPFIFAQVGWVIGI  166 (178)
Q Consensus       138 ~~----~~~~~~l~~~np---~a~i~~~SA~~g~gi  166 (178)
                      ..    +.+...+.....   ..+++++||++|.|+
T Consensus       163 ~~~~~~~el~~~l~~~~~~~~~i~~ipiSa~~G~ni  198 (239)
T d1f60a3         163 RFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNM  198 (239)
T ss_dssp             HHHHHHHHHHHHHHHHTCCGGGCCEEECCTTTCBTT
T ss_pred             HHHHHHHHHHHHHHhcCCCCCcEEEEEEEccCCCcc
Confidence            22    334444443332   367899999999987

>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=96.84  E-value=0.00057  Score=52.64  Aligned_cols=60  Identities=15%  Similarity=0.206  Sum_probs=37.8

Q ss_pred             CCCEEEEeCCcch-hh-hccc-ccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCC
Q 030407           73 KADLLLCESGGDN-LA-ANFS-RELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLA  132 (178)
Q Consensus        73 ~~d~iiiEttG~~-~~-~~~~-~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~  132 (178)
                      +..+-||.|.|-. .. .+.. ...+|+.|+|+|+..|...+..    ...+...+-++++||+|..
T Consensus        66 ~~~~n~iDtPGh~dF~~e~~~al~~~D~avlvvda~~Gv~~~t~~~~~~~~~~~~p~~i~iNk~D~~  132 (267)
T d2dy1a2          66 GHRVFLLDAPGYGDFVGEIRGALEAADAALVAVSAEAGVQVGTERAWTVAERLGLPRMVVVTKLDKG  132 (267)
T ss_dssp             TEEEEEEECCCSGGGHHHHHHHHHHCSEEEEEEETTTCSCHHHHHHHHHHHHTTCCEEEEEECGGGC
T ss_pred             ccceeEEccCchhhhhhhhhhhhcccCceEEEeeccCCccchhHHHHHhhhhccccccccccccccc
Confidence            3457899999921 11 1111 1236999999999988654321    1122345679999999975

>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=96.72  E-value=0.0015  Score=46.21  Aligned_cols=103  Identities=15%  Similarity=0.106  Sum_probs=58.4

Q ss_pred             CCCEEEEeCCcch----hhhcccccccceEEEEEeCCCCCCCCcCCC------------------C-CCCceeEEEEecC
Q 030407           73 KADLLLCESGGDN----LAANFSRELADYIIYIIDVSGGDKIPRKGG------------------P-GITQADLLVINKT  129 (178)
Q Consensus        73 ~~d~iiiEttG~~----~~~~~~~~~ad~~I~VvD~~~~~~~~~~~~------------------~-qi~~adiiviNK~  129 (178)
                      .+..-+.++.|..    +...+. ..++++++++|.+..........                  . .-..+-+++.||+
T Consensus        41 ~~~~~i~D~~Gq~~~~~~~~~~~-~~~~~~i~v~d~~~~~~~~~~~~~~~~~~e~~~~~~~i~~~~~~~~~~~~lv~Nk~  119 (195)
T d1svsa1          41 DLHFKMFDVGGQRSERKKWIHCF-EGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKK  119 (195)
T ss_dssp             TEEEEEEEECCSGGGGGGGGGGC-TTCSEEEEEEEGGGGGCBCSSCTTSBHHHHHHHHHHHHHTCGGGTTSEEEEEEECH
T ss_pred             eeeeeeeccccccccccchhhcc-cCCceeeeEEeecccchHHHHhhhhHHHHHHHHHHHHHhcccccCCCCEEEEeccc
Confidence            4556678888831    112222 35799999999876543221000                  0 1123679999999


Q ss_pred             CCCCc-------------------hhHhHHHHHHHHHhcCC-----CCCEEEEecccCCCHHHHHHHHhhh
Q 030407          130 DLASA-------------------IGADLAVMERDALRMRD-----GGPFIFAQVGWVIGIIFTLSITHYI  176 (178)
Q Consensus       130 Dl~~~-------------------~~~~~~~~~~~l~~~np-----~a~i~~~SA~~g~gi~el~~~l~~~  176 (178)
                      |+...                   ..+....+.....+.+.     ..++++|||++|++|+++|+.+...
T Consensus       120 d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~tSA~~~~nv~~~F~~v~~~  190 (195)
T d1svsa1         120 DLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDV  190 (195)
T ss_dssp             HHHHHHTTTSCGGGTCTTCCSCSSHHHHHHHHHHHHHTTCSCTTTCCEEEEECCTTCHHHHHHHHHHHHHH
T ss_pred             hhhhhhccchHHHHHhhhhcCcccHHHHHHHHHHHHHHHhcccCCCcceeEEEEeECCHhHHHHHHHHHHH
Confidence            96311                   00111122233333321     1245679999999999999987654

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=96.67  E-value=0.0013  Score=48.95  Aligned_cols=148  Identities=17%  Similarity=0.114  Sum_probs=82.2

Q ss_pred             HHHHHHhhcC-CcEEEEEecCC-C-chhHHHH--HHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCCCCE
Q 030407            2 LALCKFLRDK-YSLAAVTNDIF-T-KEDGEFL--MRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADL   76 (178)
Q Consensus         2 ~~~~~~~~~~-~~vaVI~nd~g-~-~iD~~li--~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~~d~   76 (178)
                      .++..+++++ +||++|.-|-. . .++....  +..|+    ++....++        +|+...+....+..+..++|+
T Consensus        27 AKLA~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v----~~~~~~~~--------~d~~~~l~~~~~~a~~~~~d~   94 (211)
T d2qy9a2          27 GKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNNI----PVIAQHTG--------ADSASVIFDAIQAAKARNIDV   94 (211)
T ss_dssp             HHHHHHHHTTTCCEEEECCCTTCHHHHHHHHHHHHHTTC----CEECCSTT--------CCHHHHHHHHHHHHHHTTCSE
T ss_pred             HHHHHHHHHCCCcEEEEecccccccchhhhhhhhhhcCC----cccccccC--------CCHHHHHHHHHHHHHHcCCCE
Confidence            4666677654 99999999987 4 5665422  23344    33333322        222222222222233568999


Q ss_pred             EEEeCCcchhh-----h-------cc---cccccceEEEEEeCCCCCCCCcCCCCC--CCceeEEEEecCCCCCchhHhH
Q 030407           77 LLCESGGDNLA-----A-------NF---SRELADYIIYIIDVSGGDKIPRKGGPG--ITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        77 iiiEttG~~~~-----~-------~~---~~~~ad~~I~VvD~~~~~~~~~~~~~q--i~~adiiviNK~Dl~~~~~~~~  139 (178)
                      |||.|.|-+..     .       ..   .....+-.++|+|++.+.+........  .-..+-++++|.|-....    
T Consensus        95 ilIDTaGr~~~d~~~~~el~~l~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~~~~~~~~~~~~lIlTKlDe~~~~----  170 (211)
T d2qy9a2          95 LIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQAKLFHEAVGLTGITLTKLDGTAKG----  170 (211)
T ss_dssp             EEECCCCCGGGHHHHHHHHHHHHHHHTTTCTTCCSEEEEEEEGGGTHHHHHHHHHHHHHSCCCEEEEECCTTCTTT----
T ss_pred             EEeccCCCccccHHHHHHHHHHHHHHhhhcccCcceeeeehhcccCcchHHHHhhhhhccCCceEEEeecCCCCCc----
Confidence            99999994211     0       00   000125788999998764321110000  112478999999986542    


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHH
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el  169 (178)
                      ..+.....+.  ..|+.+++  +|+++++|
T Consensus       171 G~~l~~~~~~--~~Pi~~i~--~Gq~v~Dl  196 (211)
T d2qy9a2         171 GVIFSVADQF--GIPIRYIG--VGERIEDL  196 (211)
T ss_dssp             THHHHHHHHH--CCCEEEEE--CSSSGGGE
T ss_pred             cHHHHHHHHH--CCCEEEEe--CCCCcccC
Confidence            3344444433  45888888  78888553

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {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: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=96.51  E-value=0.0013  Score=45.57  Aligned_cols=81  Identities=11%  Similarity=-0.013  Sum_probs=38.3

Q ss_pred             HHHHHHhhcC-CcEEEEEecCC-CchhHHHHHHcCCC--CccceeecccCC-CcccccccccccCH-hHHHhhHhhCCCC
Q 030407            2 LALCKFLRDK-YSLAAVTNDIF-TKEDGEFLMRNGAL--PEERIRAVETGG-CPHAAIREDISINL-GPLEELSNLFKAD   75 (178)
Q Consensus         2 ~~~~~~~~~~-~~vaVI~nd~g-~~iD~~li~~~~~~--~~~~~~~l~~Gc-Cc~l~i~~dl~~~l-~~l~~l~~~~~~d   75 (178)
                      ++++++|.++ .|++++.||++ ...|.....+....  ..+.+.....++ ||......+..... ..+..+ ....+|
T Consensus        20 ~~L~~~l~~~g~~v~v~~~d~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~d   98 (170)
T d1np6a_          20 KKLIPALCARGIRPGLIKHTHHDMDVDKPGKDSYELRKAGAAQTIVASQQRWALMTETPDEEELDLQFLASRM-DTSKLD   98 (170)
T ss_dssp             HHHHHHHHHTTCCEEEEEECCC------------CHHHHTCSEEEEECSSEEEEEEECSSSCCCCHHHHHHHS-CGGGCS
T ss_pred             HHHHHHHHHCCCeEEEecccccccccccccCccHHHHHhhhhheeeecCcceEEEeecccccccchHHHHHHh-cccccC
Confidence            5778888664 99999999999 66655443321110  012444554444 33321111111111 222222 234689


Q ss_pred             EEEEeCCc
Q 030407           76 LLLCESGG   83 (178)
Q Consensus        76 ~iiiEttG   83 (178)
                      ++++|+.+
T Consensus        99 ~~~ve~~~  106 (170)
T d1np6a_          99 LILVEGFK  106 (170)
T ss_dssp             EEEEESCS
T ss_pred             ceeEeecc
Confidence            99999998

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=96.33  E-value=0.0025  Score=47.27  Aligned_cols=148  Identities=15%  Similarity=0.077  Sum_probs=80.1

Q ss_pred             HHHHHHhhc-CCcEEEEEecCC-C-chhHHHH--HHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCCCCE
Q 030407            2 LALCKFLRD-KYSLAAVTNDIF-T-KEDGEFL--MRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADL   76 (178)
Q Consensus         2 ~~~~~~~~~-~~~vaVI~nd~g-~-~iD~~li--~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~~d~   76 (178)
                      .++..++.+ ++||++|.-|-- . .++....  +..++    ++....++        +|+...+.....+....++|+
T Consensus        29 AKLAa~~~~~~~kV~lit~Dt~R~gA~eQL~~~a~~l~i----~~~~~~~~--------~d~~~~~~~~~~~~~~~~~d~   96 (213)
T d1vmaa2          29 GKLAKMFVDEGKSVVLAAADTFRAAAIEQLKIWGERVGA----TVISHSEG--------ADPAAVAFDAVAHALARNKDV   96 (213)
T ss_dssp             HHHHHHHHHTTCCEEEEEECTTCHHHHHHHHHHHHHHTC----EEECCSTT--------CCHHHHHHHHHHHHHHTTCSE
T ss_pred             HHHHHHHHHCCCceEEEeecccccchhHHHHHHhhhcCc----cccccCCC--------CcHHHHHHHHHHHHHHcCCCE
Confidence            356666655 499999999977 4 5554322  22343    33332222        122221222223333568999


Q ss_pred             EEEeCCcchhh---------hc------ccccccceEEEEEeCCCCCCCCcCCC--CCCCceeEEEEecCCCCCchhHhH
Q 030407           77 LLCESGGDNLA---------AN------FSRELADYIIYIIDVSGGDKIPRKGG--PGITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        77 iiiEttG~~~~---------~~------~~~~~ad~~I~VvD~~~~~~~~~~~~--~qi~~adiiviNK~Dl~~~~~~~~  139 (178)
                      |||.|.|.+..         ..      ..+...+-.++|+|++.+........  .+.-..+-++++|.|-....    
T Consensus        97 ilIDTaGr~~~d~~~~~el~~~~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~~~~~~~~~~~~lI~TKlDe~~~~----  172 (213)
T d1vmaa2          97 VIIDTAGRLHTKKNLMEELRKVHRVVKKKIPDAPHETLLVIDATTGQNGLVQAKIFKEAVNVTGIILTKLDGTAKG----  172 (213)
T ss_dssp             EEEEECCCCSCHHHHHHHHHHHHHHGGGTCTTCCSEEEEEEEGGGHHHHHHHHHHHHHHSCCCEEEEECGGGCSCT----
T ss_pred             EEEeccccccchHHHHHHHHHHHhhhhhccccccceeEEeeccccCcchhhhhhhhccccCCceEEEecccCCCcc----
Confidence            99999994210         00      01111256889999976532111000  01123578999999976542    


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHHH
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIFT  169 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~el  169 (178)
                      ..+.....+.  ..|+.+++  +|+++++|
T Consensus       173 G~~l~~~~~~--~~Pi~~i~--~Gq~v~Dl  198 (213)
T d1vmaa2         173 GITLAIAREL--GIPIKFIG--VGEKAEDL  198 (213)
T ss_dssp             THHHHHHHHH--CCCEEEEE--CSSSGGGE
T ss_pred             cHHHHHHHHH--CCCEEEEe--CCCCcccC
Confidence            3344444433  45888887  68887553

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=96.12  E-value=0.0031  Score=46.53  Aligned_cols=147  Identities=13%  Similarity=0.038  Sum_probs=79.6

Q ss_pred             HHHHHHhhc-CCcEEEEEecCC-C-chhHHHH--HHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCCCCE
Q 030407            2 LALCKFLRD-KYSLAAVTNDIF-T-KEDGEFL--MRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADL   76 (178)
Q Consensus         2 ~~~~~~~~~-~~~vaVI~nd~g-~-~iD~~li--~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~~d~   76 (178)
                      .++..++.+ ++||++|.-|.. . .++....  +..|+    ++....++.        |+...+.......+..++|+
T Consensus        24 aKLA~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~i----~~~~~~~~~--------d~~~~~~~~~~~~~~~~~d~   91 (207)
T d1okkd2          24 AKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSI----PVIQGPEGT--------DPAALAYDAVQAMKARGYDL   91 (207)
T ss_dssp             HHHHHHHHTTTCCEEEECCCCSSTTHHHHHHHHHHHHTC----CEECCCTTC--------CHHHHHHHHHHHHHHHTCSE
T ss_pred             HHHHHHHHHCCCcEEEEEeccccccchhhHhhcccccCc----eEEeccCCc--------cHHHHHHHHHHHHHHCCCCE
Confidence            356677765 499999999977 4 6665422  22243    333333222        22221211122233457999


Q ss_pred             EEEeCCcchhh-----h---cc-------cccccceEEEEEeCCCCCCCCcCCCCC--CCceeEEEEecCCCCCchhHhH
Q 030407           77 LLCESGGDNLA-----A---NF-------SRELADYIIYIIDVSGGDKIPRKGGPG--ITQADLLVINKTDLASAIGADL  139 (178)
Q Consensus        77 iiiEttG~~~~-----~---~~-------~~~~ad~~I~VvD~~~~~~~~~~~~~q--i~~adiiviNK~Dl~~~~~~~~  139 (178)
                      |||.|.|.+..     .   .+       .....+-.++|+|++.+.+........  .-..+-++++|.|-....    
T Consensus        92 ilIDTaGr~~~d~~l~~el~~~~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~~~~~~~~~~~~lI~TKlDet~~~----  167 (207)
T d1okkd2          92 LFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAKKFHEAVGLTGVIVTKLDGTAKG----  167 (207)
T ss_dssp             EEECCCCCCTTCHHHHHHHHHHHHHHHHHCTTCCSEEEEEEETTBCTHHHHHHHHHHHHHCCSEEEEECTTSSCCC----
T ss_pred             EEcCccccchhhHHHHHHHHHHHHHhhhcccCCCceEEEEeecccCchHHHHHHHhhhccCCceEEEeccCCCCCc----
Confidence            99999994211     0   01       011125689999998765322111000  112478999999976542    


Q ss_pred             HHHHHHHHhcCCCCCEEEEecccCCCHHH
Q 030407          140 AVMERDALRMRDGGPFIFAQVGWVIGIIF  168 (178)
Q Consensus       140 ~~~~~~l~~~np~a~i~~~SA~~g~gi~e  168 (178)
                      ..+.+...+.  ..|+.++|  +|++.++
T Consensus       168 G~~l~~~~~~--~~Pi~~i~--~Gq~p~D  192 (207)
T d1okkd2         168 GVLIPIVRTL--KVPIKFVG--VGEGPDD  192 (207)
T ss_dssp             TTHHHHHHHH--CCCEEEEE--CSSSTTC
T ss_pred             cHHHHHHHHH--CCCEEEEe--CCCChHh
Confidence            2333344433  45787777  4776543

>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=96.00  E-value=0.0033  Score=45.34  Aligned_cols=104  Identities=15%  Similarity=0.068  Sum_probs=55.3

Q ss_pred             CCCCEEEEeCCcch-hhh---cccccccceEEEEEeCCCCCCCCc----CC-------C-CCCCceeEEEEecCCCCCch
Q 030407           72 FKADLLLCESGGDN-LAA---NFSRELADYIIYIIDVSGGDKIPR----KG-------G-PGITQADLLVINKTDLASAI  135 (178)
Q Consensus        72 ~~~d~iiiEttG~~-~~~---~~~~~~ad~~I~VvD~~~~~~~~~----~~-------~-~qi~~adiiviNK~Dl~~~~  135 (178)
                      ....+-++.+.|.. ...   ......++.+++|+|++.......    ..       . ..-..+-+|++||+|+.++ 
T Consensus        45 ~~~~~~~~d~~g~~~~~~~~~~~~~~~~~~~i~v~D~~d~~~~~~~~~~~l~~~l~~~~~~~~~~pilvv~NK~Dl~~a-  123 (207)
T d2fh5b1          45 RGNSLTLIDLPGHESLRFQLLDRFKSSARAVVFVVDSAAFQREVKDVAEFLYQVLIDSMALKNSPSLLIACNKQDIAMA-  123 (207)
T ss_dssp             TCCEEEEEECCCCHHHHHHHHHHHGGGEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHTSTTCCEEEEEEECTTSTTC-
T ss_pred             eeeeeeeeeccccccccchhhhhhhhhccccceEEEcccccccHHHHHHHHHHHHHhHHHhhcCCcEEEEEECcccCCC-
Confidence            35667778888831 111   111234688999999976432100    00       0 0012356788999999865 


Q ss_pred             hHhHHHHHHHHH----hc---------------------------------CCCCCEEEEecccCCC------HHHHHHH
Q 030407          136 GADLAVMERDAL----RM---------------------------------RDGGPFIFAQVGWVIG------IIFTLSI  172 (178)
Q Consensus       136 ~~~~~~~~~~l~----~~---------------------------------np~a~i~~~SA~~g~g------i~el~~~  172 (178)
                       ...+.+.+.++    ..                                 .....++..|+++|.|      ++++-+|
T Consensus       124 -~~~~~i~~~l~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~S~~~~~~~~~~~~i~~~~~w  202 (207)
T d2fh5b1         124 -KSAKLIQQQLEKELNTLRVTRSAAPSTLDSSSTAPAQLGKKGKEFEFSQLPLKVEFLECSAKGGRGDTGSADIQDLEKW  202 (207)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHHCC------------CCCSSCTTSCCCGGGSSSCEEEEECBCC-------CCBCHHHHHH
T ss_pred             -CCHHHHHHHHHHHhhhhhhccccccceeehhhhhhhhhcccchhhhHHhccCCcEEEEeeecCCCcccccccHHHHHHH
Confidence             22222222221    10                                 0112578899999998      8888888


Q ss_pred             Hhhhh
Q 030407          173 THYIV  177 (178)
Q Consensus       173 l~~~~  177 (178)
                      |.++|
T Consensus       203 l~~~a  207 (207)
T d2fh5b1         203 LAKIA  207 (207)
T ss_dssp             HHHHC
T ss_pred             HHHhC
Confidence            87765

>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=95.76  E-value=0.0039  Score=44.09  Aligned_cols=102  Identities=15%  Similarity=0.079  Sum_probs=57.4

Q ss_pred             CCCEEEEeCCcchh----hhcccccccceEEEEEeCCCCCCCCcC-------------------CCCCCCceeEEEEecC
Q 030407           73 KADLLLCESGGDNL----AANFSRELADYIIYIIDVSGGDKIPRK-------------------GGPGITQADLLVINKT  129 (178)
Q Consensus        73 ~~d~iiiEttG~~~----~~~~~~~~ad~~I~VvD~~~~~~~~~~-------------------~~~qi~~adiiviNK~  129 (178)
                      ....-+.++.|...    ...+. ..++.++.++|.+........                   ....-..+-+++.||.
T Consensus        44 ~~~~~~~d~~g~~~~~~~~~~~~-~~~~~~i~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~l~~~~~~~~~~~~v~NK~  122 (200)
T d2bcjq2          44 SVIFRMVDVGGQRSERRKWIHCF-ENVTSIMFLVALSEYDQVLVESDNENRMEESKALFRTIITYPWFQNSSVILFLNKK  122 (200)
T ss_dssp             SCEEEEEECCCSTTGGGGGGGGC-SSCSEEEEEEEGGGGGCBCSSCTTSBHHHHHHHHHHHHHHCGGGSSSEEEEEEECH
T ss_pred             ceeeeeccccccccccccccccc-cccceeeEeeeccchhhhhhhhccccchHHHHHHHHHHHhhhhccCccEEEecchh
Confidence            45566777877311    12222 246889999998764321110                   0001234679999999


Q ss_pred             CCCCchh----------------HhHH----HHHHHHHhcCCC----CCEEEEecccCCCHHHHHHHHhh
Q 030407          130 DLASAIG----------------ADLA----VMERDALRMRDG----GPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       130 Dl~~~~~----------------~~~~----~~~~~l~~~np~----a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      |+.....                ...+    .+.....+.++.    ..+++|||++|+||+++|+.+.+
T Consensus       123 Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~f~~~~~~~~~~~~~~~tSAk~~~ni~~vF~~i~~  192 (200)
T d2bcjq2         123 DLLEEKIMYSHLVDYFPEYDGPQRDAQAAREFILKMFVDLNPDSDKIIYSHFTCATDTENIRFVFAAVKD  192 (200)
T ss_dssp             HHHHHHTTTSCHHHHSTTCCSCSSCHHHHHHHHHHHHHTTCSCTTSCEEEEECCTTCHHHHHHHHHHHHH
T ss_pred             hhhhhcccchHHHHhcccccCCchhHHHHHHHHHHHHHHhcccCCCceEEEEeEEEcCHhHHHHHHHHHH
Confidence            9842200                0111    122222233321    23678999999999999988754

>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=95.46  E-value=0.0028  Score=45.12  Aligned_cols=103  Identities=15%  Similarity=0.035  Sum_probs=56.0

Q ss_pred             CCCEEEEeCCcchhh---hcccccccceEEEEEeCCCCCCCCcC-------------------CCCCCCceeEEEEecCC
Q 030407           73 KADLLLCESGGDNLA---ANFSRELADYIIYIIDVSGGDKIPRK-------------------GGPGITQADLLVINKTD  130 (178)
Q Consensus        73 ~~d~iiiEttG~~~~---~~~~~~~ad~~I~VvD~~~~~~~~~~-------------------~~~qi~~adiiviNK~D  130 (178)
                      ...+-++.+.|...-   .......++.++.++|.++.......                   ....-..+-++++||+|
T Consensus        43 ~~~~~~~D~~gq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~piilv~NK~D  122 (200)
T d1zcba2          43 NVPFKMVDVGGQRSERKRWFECFDSVTSILFLVSSSEFDQVLMEDRQTNRLTESLNIFETIVNNRVFSNVSIILFLNKTD  122 (200)
T ss_dssp             TEEEEEEEECC-------CTTSCTTCCEEEEEEETTCTTCEETTEEEEEHHHHHHHHHHHHHTCGGGTTSEEEEEEECHH
T ss_pred             eeeeeeecccceeeecccccccccccceeEEEEEcCCcceeeeecccchhhhHHHHHHHHHhhChhhcCceEEEEeccch
Confidence            345666677772111   01112246889999998875432110                   00012346799999999


Q ss_pred             CCCch----------------hHhHHH----HHHHHHhcCC---C--CCEEEEecccCCCHHHHHHHHhh
Q 030407          131 LASAI----------------GADLAV----MERDALRMRD---G--GPFIFAQVGWVIGIIFTLSITHY  175 (178)
Q Consensus       131 l~~~~----------------~~~~~~----~~~~l~~~np---~--a~i~~~SA~~g~gi~el~~~l~~  175 (178)
                      +.+..                +...+.    +.+..+..++   .  ...+.|||+++++|+++|+.+..
T Consensus       123 l~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~iy~~~TsA~d~~ni~~vf~~v~d  192 (200)
T d1zcba2         123 LLEEKVQVVSIKDYFLEFEGDPHCLRDVQKFLVECFRGKRRDQQQRPLYHHFTTAINTENIRLVFRDVKD  192 (200)
T ss_dssp             HHHHHTTTCCGGGTCTTCCSCTTCHHHHHHHHHHHHHTTCSSCC--CCEEEECCTTCHHHHHHHHHHHHH
T ss_pred             hhhhhccccHHHHhCccccCCcchHHHHHHHHHHHHHHhccCCCCCceEEEEeeeeCcHHHHHHHHHHHH
Confidence            84210                011222    2233332221   1  23457999999999999988754

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=94.54  E-value=0.011  Score=43.53  Aligned_cols=146  Identities=18%  Similarity=0.116  Sum_probs=74.7

Q ss_pred             HHHHHHhhcC-CcEEEEEecCC-C-chhHHHH--HHcCCCCccceeecccCCCcccccccccccCHhHHHhhHhhCCCCE
Q 030407            2 LALCKFLRDK-YSLAAVTNDIF-T-KEDGEFL--MRNGALPEERIRAVETGGCPHAAIREDISINLGPLEELSNLFKADL   76 (178)
Q Consensus         2 ~~~~~~~~~~-~~vaVI~nd~g-~-~iD~~li--~~~~~~~~~~~~~l~~GcCc~l~i~~dl~~~l~~l~~l~~~~~~d~   76 (178)
                      .+|..++.++ +|+++|.-|.. . .++....  +..++    ++....+.        +|+.........+.+..++|+
T Consensus        28 aKLA~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v----~~~~~~~~--------~~~~~~~~~~~~~~~~~~~d~   95 (207)
T d1ls1a2          28 AKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGV----PVLEVMDG--------ESPESIRRRVEEKARLEARDL   95 (207)
T ss_dssp             HHHHHHHHHTTCCEEEEECCSSCHHHHHHHHHHHHHHTC----CEEECCTT--------CCHHHHHHHHHHHHHHHTCCE
T ss_pred             HHHHHHHHHCCCcEEEEecccccchHHHHHHHHHHhcCC----cccccccc--------chhhHHHHHHHHHHhhccCcc
Confidence            3566667654 99999999977 4 5554322  22243    33333221        122111112223444568999


Q ss_pred             EEEeCCcchhh---------hcccccccceEEEEEeCCCCCCCCcCCCC--CCCceeEEEEecCCCCCchhHhHHHHHHH
Q 030407           77 LLCESGGDNLA---------ANFSRELADYIIYIIDVSGGDKIPRKGGP--GITQADLLVINKTDLASAIGADLAVMERD  145 (178)
Q Consensus        77 iiiEttG~~~~---------~~~~~~~ad~~I~VvD~~~~~~~~~~~~~--qi~~adiiviNK~Dl~~~~~~~~~~~~~~  145 (178)
                      |||.|.|.+..         ........+-+++|+|++.+.+.......  ..-..+-++++|.|-...    ...+...
T Consensus        96 vlIDTaGr~~~d~~~~~el~~~~~~~~~~~~llv~~a~~~~~~~~~~~~f~~~~~~~~~I~TKlDe~~~----~G~~l~~  171 (207)
T d1ls1a2          96 ILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDAR----GGAALSA  171 (207)
T ss_dssp             EEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTHHHHHHHHHHHHHTCCCEEEEECGGGCSS----CHHHHHH
T ss_pred             eeecccccchhhhhhHHHHHHHHhhcCCceEEEEeccccchhHHHHHHHHHhhCCCCeeEEeecCcccc----chHHHHH
Confidence            99999994211         00111123778999998776432211000  001236799999997544    3344444


Q ss_pred             HHhcCCCCCEEEEecccCCCHH
Q 030407          146 ALRMRDGGPFIFAQVGWVIGII  167 (178)
Q Consensus       146 l~~~np~a~i~~~SA~~g~gi~  167 (178)
                      ....  ..|+.+++  +|+..+
T Consensus       172 ~~~~--~~Pi~~i~--~Gq~pe  189 (207)
T d1ls1a2         172 RHVT--GKPIYFAG--VSEKPE  189 (207)
T ss_dssp             HHHH--CCCEEEEC--------
T ss_pred             HHHH--CCCEEEEe--CCCChh
Confidence            4444  35777765  355444

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.14  E-value=0.1  Score=41.56  Aligned_cols=104  Identities=10%  Similarity=-0.065  Sum_probs=57.4

Q ss_pred             CCCCEEEEeCCcchhh----hc----ccccccceEEEEEeCCCCCCCCcC---CCCCCCceeEEEEecCCCCCch-----
Q 030407           72 FKADLLLCESGGDNLA----AN----FSRELADYIIYIIDVSGGDKIPRK---GGPGITQADLLVINKTDLASAI-----  135 (178)
Q Consensus        72 ~~~d~iiiEttG~~~~----~~----~~~~~ad~~I~VvD~~~~~~~~~~---~~~qi~~adiiviNK~Dl~~~~-----  135 (178)
                      ..+.++|+.|.|..-.    ..    ......|.++++.|..- ......   .......+-++|+||+|...+.     
T Consensus       105 ~~~~~~l~DtPG~~~~~~~~~~~~~~~~~~~~d~~l~~~~~~~-~~~d~~l~~~l~~~~k~~~~V~nK~D~~~~~~~~~~  183 (400)
T d1tq4a_         105 NIPNVVFWDLPGIGSTNFPPDTYLEKMKFYEYDFFIIISATRF-KKNDIDIAKAISMMKKEFYFVRTKVDSDITNEADGE  183 (400)
T ss_dssp             SCTTEEEEECCCGGGSSCCHHHHHHHTTGGGCSEEEEEESSCC-CHHHHHHHHHHHHTTCEEEEEECCHHHHHHHHHTTC
T ss_pred             CCCeEEEEeCCCcccccccHHHHHHHhhhhcceEEEEecCCCC-CHHHHHHHHHHHHcCCCEEEEEeCcccccchhhhcc
Confidence            3577999999995321    00    11122477777766421 111101   1112456789999999964110     


Q ss_pred             ------hHhHHHHH----HHHHhc-CCCCCEEEEeccc--CCCHHHHHHHHhhh
Q 030407          136 ------GADLAVME----RDALRM-RDGGPFIFAQVGW--VIGIIFTLSITHYI  176 (178)
Q Consensus       136 ------~~~~~~~~----~~l~~~-np~a~i~~~SA~~--g~gi~el~~~l~~~  176 (178)
                            ...++.++    +.++.. .+..++|.+|..+  ..|+++|.+.+.+.
T Consensus       184 ~~~~~~e~~l~~ir~~~~~~l~~~~~~~~~vflvS~~~~~~~d~~~L~~~l~~~  237 (400)
T d1tq4a_         184 PQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISD  237 (400)
T ss_dssp             CTTCCHHHHHHHHHHHHHHHHHHTTCSSCCEEECCTTCTTSTTHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCCEEEecCCcccccCHHHHHHHHHHH
Confidence                  01222332    333332 2456899999765  45899999987654

>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=90.30  E-value=0.06  Score=39.10  Aligned_cols=20  Identities=10%  Similarity=-0.228  Sum_probs=16.8

Q ss_pred             EEEEecccCCCHHHHHHHHh
Q 030407          155 FIFAQVGWVIGIIFTLSITH  174 (178)
Q Consensus       155 i~~~SA~~g~gi~el~~~l~  174 (178)
                      .+.|||+++++|+.+|+.+.
T Consensus       191 ~h~T~A~Dt~ni~~vf~~v~  210 (221)
T d1azta2         191 PHFTCAVDTENIRRVFNDCR  210 (221)
T ss_dssp             EEECCTTCHHHHHHHHHTTH
T ss_pred             eeecceeccHHHHHHHHHHH
Confidence            45799999999999997654

>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=88.95  E-value=0.042  Score=43.20  Aligned_cols=57  Identities=23%  Similarity=0.300  Sum_probs=35.1

Q ss_pred             EEEEeCCcc-hhh-hcc-cccccceEEEEEeCCCCCCCCcC----CCCCCCceeEEEEecCCCC
Q 030407           76 LLLCESGGD-NLA-ANF-SRELADYIIYIIDVSGGDKIPRK----GGPGITQADLLVINKTDLA  132 (178)
Q Consensus        76 ~iiiEttG~-~~~-~~~-~~~~ad~~I~VvD~~~~~~~~~~----~~~qi~~adiiviNK~Dl~  132 (178)
                      +=||.|.|- ... ... ....+|++++|||+.+|...+..    .......+-++++||+|..
T Consensus        98 inliDtPGh~dF~~ev~~al~~~D~allVVda~eGv~~qT~~~~~~a~~~~~p~i~viNKiDr~  161 (341)
T d1n0ua2          98 INLIDSPGHVDFSSEVTAALRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRA  161 (341)
T ss_dssp             EEEECCCCCCSSCHHHHHHHHTCSEEEEEEETTTBSCHHHHHHHHHHHHTTCEEEEEEECHHHH
T ss_pred             EEEEcCCCcHHHHHHHHHHHhhcCceEEEEecccCcchhHHHHHHHHHHcCCCeEEEEECcccc
Confidence            446999992 011 110 11246999999999988654321    1112344679999999974