Citrus Sinensis ID: 023301

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280----
Protein Sequence
MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCLA
Secondary Structure (PSIPRED)
ccccccEEEccccHHHHHHHHHHHcccccccEEEEEccccccHHHHHHHHccccccccEEEEcEEEEEHHHHHHHHHHccccccccHHHHHHHHHHHcEEEEEccccccHHHHHHHHHHHHHccccccEEEcccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccccHHHHHHHHHHHHHHccccEEEEccEEEEccccEEEEEEccccccccccccccccccccccEEEEEcccccHHHHHHHHHcHHc
Secondary Structure Prediction (SSPRO)
cccccEEEEccHHHHHHHHHHHHHHccccccEEEEEEEccccHHHHHHHHHHcHHHHHHEEEEEEEEEEEcccHHHHHHHcccccHHHHHHHHHHHHHEEEEcccccccHHHHHHHHHHHHHHccccEEEEcccccccHHHHHccccccHHHHHHcccccccccccccccccccccccccccccccccEEEEEEEEcccccHHHHHHHHHHHHHHHcccEEEEEEEEEEcccccHEEEEHHHHHHccccccccccccccccEEEEEcccccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mvnngclcctvRGDLVKMLLQLAKKKQGQFDHIVIEttglakpapvietFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVklakygsvdmdfvlgvggydleridsevhvdnshcathhhesahghheghhhnhmhdsavsSVTIvsegtldldEVDDWLERLIEEKGEDLYRMKGILsvsgseqqYVFQGVHstldgcpgkawgpdekrINKLVFIGRNLDETALRKGFKGCLA
Flexible Loop (DISEMBL)
mvnngclcctVRGDLVKMLLQLAKKKQGQFDHIVIettglakpapVIETFCTDELVSQYVKLDGVITLVDSKHAMQHlnevkprfvvNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIgrnldetalrkgfkgcla
Low Complexity Region (SEG)
MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNshcathhhesahghheghhhnhmhDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCLA
Disordered region (IsUnstruct)
***NGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCA************************SSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGF*****
Disordered Region (DISOPRED)
MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCLA
Disordered Region (DISEMBL)
MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCAT******************HDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCLA
Disordered Region (DISPRO)
**NNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSE**************************HMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCLA
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCLA
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	284	2.2.26 [Sep-21-2011]
Q8VEH6	393	COBW domain-containing pr	yes	no	0.933	0.674	0.344	1e-38
Q99MB4	394	COBW domain-containing pr	yes	no	0.933	0.672	0.337	2e-38
Q8IUF1	395	COBW domain-containing pr	yes	no	0.915	0.658	0.335	7e-38
Q9BRT8	395	COBW domain-containing pr	yes	no	0.915	0.658	0.335	8e-38
Q5RIA9	395	COBW domain-containing pr	yes	no	0.915	0.658	0.339	1e-37
Q5JTY5	395	COBW domain-containing pr	yes	no	0.915	0.658	0.339	1e-37
Q4V339	395	COBW domain-containing pr	yes	no	0.915	0.658	0.335	2e-37
P24203	318	Uncharacterized GTP-bindi	N/A	no	0.890	0.795	0.349	4e-35
O74310	411	COBW domain-containing pr	yes	no	0.911	0.630	0.312	5e-25
A6NM15	247	Putative COBW domain-cont	no	no	0.75	0.862	0.315	3e-24

>sp|Q8VEH6|CBWD1_MOUSE COBW domain-containing protein 1 OS=Mus musculus GN=Cbwd1 PE=2 SV=1

 Score =  159 bits (403), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 101/293 (34%), Positives = 158/293 (53%), Gaps = 28/293 (9%)

Query: 2   VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVK 61
           + NGCLCC+V+   ++ +  L +KK G+FD+I++ETTGLA P  V   F  D  +   + 
Sbjct: 101 LRNGCLCCSVKDSGLRAIENLMQKK-GKFDYILLETTGLADPGAVASMFWVDAELGSDIY 159

Query: 62  LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIK 121
           LDG+IT+VDSK+ ++HL E KP  +VNEA  QVA AD I++NK DLV+E EL +L   I+
Sbjct: 160 LDGIITVVDSKYGLKHLTEEKPDGLVNEATRQVALADMILINKTDLVSEEELNNLRTTIR 219

Query: 122 HINAMAPVKLAKYGSVDMDFVLGVGGYD-LERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
            IN +  V   +   V +  +L +  YD L  I  +  + +   A H             
Sbjct: 220 SINGLGKVLETQRSRVHLSNILDLHAYDILSGISLQKKLQHVSTAPH------------- 266

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKG--------EDLYRMKGILSVSGS 232
                D ++ +VT    G+   + ++ +++ L+ EK          ++ R+KG++S+   
Sbjct: 267 ----LDQSIVTVTFEVPGSAKEECLNVFIQNLLWEKNVKNKDGHCMEVIRLKGLVSIKDK 322

Query: 233 EQQYVFQGVHSTLDGCPGKA-WGPDEKRINKLVFIGRNLDETALRKGFKGCLA 284
            QQ + QG+H   D       W  D +R  +LVFIGRNLD+  L++ F   +A
Sbjct: 323 PQQMIVQGIHELYDLEESLVNWKDDAERACQLVFIGRNLDKDVLQQLFLTAVA 375

Mus musculus (taxid: 10090)

>sp|Q99MB4|CBWD1_RAT COBW domain-containing protein 1 OS=Rattus norvegicus GN=Cbwd1 PE=2 SV=2

 Score =  159 bits (403), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 99/293 (33%), Positives = 159/293 (54%), Gaps = 28/293 (9%)

Query: 2   VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVK 61
           + NGCLCC+V+ + +K +  L +KK G+FD+I++ETTGLA P  V   F  D  +   + 
Sbjct: 102 LRNGCLCCSVKDNGLKAIENLMQKK-GKFDYILLETTGLADPGAVASMFWVDAELGSDIY 160

Query: 62  LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIK 121
           LDG+IT+VDSK+ ++HL E KP  +VNEA  QVA AD I++NK DLV+E EL  L   I+
Sbjct: 161 LDGIITVVDSKYGLKHLTEEKPDGLVNEATRQVALADMILINKTDLVSEEELNKLRTTIR 220

Query: 122 HINAMAPVKLAKYGSVDMDFVLGVGGYD-LERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
            IN +  V   +     +  +L +  YD L  I  +  + +   A H             
Sbjct: 221 SINGLGKVLETQRSRTHLSNILDLHAYDTLSGISLQKKLQHVSTAPH------------- 267

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKG--------EDLYRMKGILSVSGS 232
                D ++ +VT    G+ + + ++ +++ L+ EK          ++ R+KG++S+   
Sbjct: 268 ----LDQSIVTVTFDVPGSAEEESLNVFIQNLLWEKNVKNKDGRCMEVIRLKGLVSIKDK 323

Query: 233 EQQYVFQGVHSTLDGCPGKA-WGPDEKRINKLVFIGRNLDETALRKGFKGCLA 284
            QQ + QG+H   +    +  W  D +R  +LVFIG+NLD+  L++ F   +A
Sbjct: 324 PQQMIVQGIHELYELEESRVNWKDDAERACQLVFIGKNLDKDILQQLFITAVA 376

Rattus norvegicus (taxid: 10116)

>sp|Q8IUF1|CBWD2_HUMAN COBW domain-containing protein 2 OS=Homo sapiens GN=CBWD2 PE=1 SV=1

 Score =  157 bits (397), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 97/289 (33%), Positives = 158/289 (54%), Gaps = 29/289 (10%)

Query: 2   VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVK 61
           + NGCLCC+V+ + ++ +  L +KK G+FD+I++ETTGLA P  V   F  D  +   + 
Sbjct: 103 LRNGCLCCSVKDNGLRAIENLMQKK-GKFDYILLETTGLADPGAVASMFWVDAELGSDIY 161

Query: 62  LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIK 121
           LDG+IT+VDSK+ ++HL E KP  ++NEA  QVA AD I++NK DLV E ++  L   I+
Sbjct: 162 LDGIITIVDSKYGLKHLAEEKPDGLINEATRQVALADAILINKTDLVPEEDVKKLRATIR 221

Query: 122 HINAMAPVKLAKYGSVDMDFVLGVGGYD-LERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
            IN +  +   +   VD+  VL +  +D L  I  +  +                H    
Sbjct: 222 SINGLGQILETQRSRVDLSNVLDLHAFDSLSGISLQKKL---------------QHVPGT 266

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKG--------EDLYRMKGILSVSGS 232
             H+ D ++ ++T    G    + ++ +++ L+ EK          ++ R+KG++S+   
Sbjct: 267 QPHL-DQSIVTITFEVPGNAKEEHLNMFIQNLLWEKNVRNKDNHCMEVIRLKGLVSIKDK 325

Query: 233 EQQYVFQGVHST--LDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGF 279
            QQ + QGVH    L+  P  +W  D +R N+LV +GRNLD+  L++ F
Sbjct: 326 SQQVIVQGVHELYDLEETP-VSWKDDTERTNRLVLLGRNLDKDILKQLF 373

Homo sapiens (taxid: 9606)

>sp|Q9BRT8|CBWD1_HUMAN COBW domain-containing protein 1 OS=Homo sapiens GN=CBWD1 PE=1 SV=1

 Score =  157 bits (397), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 97/289 (33%), Positives = 157/289 (54%), Gaps = 29/289 (10%)

Query: 2   VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVK 61
           + NGCLCC+V+   ++ +  L +KK G+FD+I++ETTGLA P  V   F  D  +   + 
Sbjct: 103 LRNGCLCCSVKDSGLRAIENLMQKK-GKFDYILLETTGLADPGAVASMFWVDAELGSDIY 161

Query: 62  LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIK 121
           LDG+IT+VDSK+ ++HL E KP  ++NEA  QVA AD I++NK DLV E ++  L   I+
Sbjct: 162 LDGIITIVDSKYGLKHLTEEKPDGLINEATRQVALADAILINKTDLVPEEDVKKLRTTIR 221

Query: 122 HINAMAPVKLAKYGSVDMDFVLGVGGYD-LERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
            IN +  +   +   VD+  VL +  +D L  I  +  +                H    
Sbjct: 222 SINGLGQILETQRSRVDLSNVLDLHAFDSLSGISLQKKL---------------QHVPGT 266

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKG--------EDLYRMKGILSVSGS 232
             H+ D ++ ++T    G    + ++ +++ L+ EK          ++ R+KG++S+   
Sbjct: 267 QPHL-DQSIVTITFEVPGNAKEEHLNMFIQNLLWEKNVRNKDNHCMEVIRLKGLVSIKDK 325

Query: 233 EQQYVFQGVHST--LDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGF 279
            QQ + QGVH    L+  P  +W  D +R N+LV +GRNLD+  L++ F
Sbjct: 326 SQQVIVQGVHELYDLEETP-VSWKDDTERTNRLVLLGRNLDKDILKQLF 373

Homo sapiens (taxid: 9606)

>sp|Q5RIA9|CBWD5_HUMAN COBW domain-containing protein 5 OS=Homo sapiens GN=CBWD5 PE=2 SV=1

 Score =  157 bits (396), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 98/289 (33%), Positives = 157/289 (54%), Gaps = 29/289 (10%)

Query: 2   VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVK 61
           + NGCLCC+V+ + ++ +  L +KK G+FD I++ETTGLA P  V   F  D  +   + 
Sbjct: 103 LRNGCLCCSVKDNGLRAIENLMQKK-GKFDDILLETTGLADPGAVTSMFWVDAELGSDIY 161

Query: 62  LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIK 121
           LDG+IT+VDSK+ ++HL E KP  ++NEA  QVA AD I++NK DLV E ++  L   I+
Sbjct: 162 LDGIITIVDSKYGLKHLTEEKPDGLINEATRQVALADIILINKTDLVPEEDVKKLRTTIR 221

Query: 122 HINAMAPVKLAKYGSVDMDFVLGVGGYD-LERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
            IN +  +   +   VD+  VL +  +D L  I  +  +                H    
Sbjct: 222 SINGLGQILETQRSRVDLSNVLDLHAFDSLSGISLQKKL---------------QHVPGT 266

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKG--------EDLYRMKGILSVSGS 232
             H+ D ++ ++T    G    + ++ +++ L+ EK          ++ R+KG++S+   
Sbjct: 267 QPHL-DQSIVTITFEVPGNAKEEHLNMFIQNLLWEKNVRNKDNHCMEVIRLKGLVSIKDK 325

Query: 233 EQQYVFQGVHST--LDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGF 279
            QQ + QGVH    L+  P  +W  D +R N+LV IGRNLD+  L++ F
Sbjct: 326 SQQVIVQGVHELYDLEETP-VSWKDDTERTNRLVLIGRNLDKDILKQLF 373

Homo sapiens (taxid: 9606)

>sp|Q5JTY5|CBWD3_HUMAN COBW domain-containing protein 3 OS=Homo sapiens GN=CBWD3 PE=2 SV=1

 Score =  157 bits (396), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 98/289 (33%), Positives = 157/289 (54%), Gaps = 29/289 (10%)

Query: 2   VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVK 61
           + NGCLCC+V+ + ++ +  L +KK G+FD I++ETTGLA P  V   F  D  +   + 
Sbjct: 103 LRNGCLCCSVKDNGLRAIENLMQKK-GKFDDILLETTGLADPGAVASMFWVDAELGSDIY 161

Query: 62  LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIK 121
           LDG+IT+VDSK+ ++HL E KP  ++NEA  QVA AD I++NK DLV E ++  L   I+
Sbjct: 162 LDGIITIVDSKYGLKHLTEEKPDGLINEATRQVALADIILINKTDLVPEEDVKKLRTTIR 221

Query: 122 HINAMAPVKLAKYGSVDMDFVLGVGGYD-LERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
            IN +  +   +   VD+  VL +  +D L  I  +  +                H    
Sbjct: 222 SINGLGQILETQRSRVDLSNVLDLHAFDSLSGISLQKKL---------------QHVPGT 266

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKG--------EDLYRMKGILSVSGS 232
             H+ D ++ ++T    G    + ++ +++ L+ EK          ++ R+KG++S+   
Sbjct: 267 QPHL-DQSIVTITFEVPGNAKEEHLNMFIQNLLWEKNVRNKDNHCMEVIRLKGLVSIKDK 325

Query: 233 EQQYVFQGVHST--LDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGF 279
            QQ + QGVH    L+  P  +W  D +R N+LV IGRNLD+  L++ F
Sbjct: 326 SQQVIVQGVHELYDLEETP-VSWKDDTERTNRLVLIGRNLDKDILKQLF 373

Homo sapiens (taxid: 9606)

>sp|Q4V339|CBWD6_HUMAN COBW domain-containing protein 6 OS=Homo sapiens GN=CBWD6 PE=2 SV=1

 Score =  155 bits (393), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 97/289 (33%), Positives = 157/289 (54%), Gaps = 29/289 (10%)

Query: 2   VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVK 61
           + NGCLCC+V+ + ++ +  L +KK G+FD I++ETTGLA P  V   F  D  +   + 
Sbjct: 103 LRNGCLCCSVKDNGLRAIENLMQKK-GKFDDILLETTGLADPGAVASMFWVDAELGSDIY 161

Query: 62  LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIK 121
           LDG+IT+VDSK+ ++HL E KP  ++NEA  QVA AD I++NK DLV E ++  L   ++
Sbjct: 162 LDGIITIVDSKYGLKHLTEEKPDGLINEATRQVALADIILINKTDLVPEEDVKKLRTTLR 221

Query: 122 HINAMAPVKLAKYGSVDMDFVLGVGGYD-LERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
            IN +  +   +   VD+  VL +  +D L  I  +  +                H    
Sbjct: 222 SINGLGQILETQRSRVDLSNVLDLHAFDSLSGISLQKKL---------------QHVPGT 266

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKG--------EDLYRMKGILSVSGS 232
             H+ D ++ ++T    G    + ++ +++ L+ EK          ++ R+KG++S+   
Sbjct: 267 QPHL-DQSIVTITFDVPGNAKEEHLNMFIQNLLWEKNVRNKDNHCMEVIRLKGLVSIKDK 325

Query: 233 EQQYVFQGVHST--LDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGF 279
            QQ + QGVH    L+  P  +W  D +R N+LV IGRNLD+  L++ F
Sbjct: 326 SQQVIVQGVHELCDLEETP-VSWKDDTERTNRLVLIGRNLDKDILKQLF 373

Homo sapiens (taxid: 9606)

>sp|P24203|YJIA_ECOLI Uncharacterized GTP-binding protein YjiA OS=Escherichia coli (strain K12) GN=yjiA PE=1 SV=3

 Score =  148 bits (374), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 99/283 (34%), Positives = 142/283 (50%), Gaps = 30/283 (10%)

Query: 2   VNNGCLCCTVRGDLVKMLLQLAK---KKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQ 58
           + NGC+CC+   +L   LL L     K   QFD +VIE TG+A P P+I+TF + E++ Q
Sbjct: 60  LTNGCICCSRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQ 119

Query: 59  YVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTE 118
              LDGVI LVD+ HA + +N+    F +  A  QV YADRI+L K D+  E E   L E
Sbjct: 120 RYLLDGVIALVDAVHADEQMNQ----FTI--AQSQVGYADRILLTKTDVAGEAE--KLHE 171

Query: 119 RIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEG 178
           R+  INA APV    +G +D+  +    G+ LE                  E+       
Sbjct: 172 RLARINARAPVYTVTHGDIDLGLLFNTNGFMLE------------------ENVVSTKPR 213

Query: 179 HHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVF 238
            H      + +SS+ +  +  +D+ EV   +E L+ E  + L R KG+L + G   + +F
Sbjct: 214 FHFIADKQNDISSIVVELDYPVDISEVSRVMENLLLESADKLLRYKGMLWIDGEPNRLLF 273

Query: 239 QGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKG 281
           QGV         + WG DEK  + +VFIG  L E  +R  F G
Sbjct: 274 QGVQRLYSADWDRPWG-DEKPHSTMVFIGIQLPEEEIRAAFAG 315

Binds GTP. May function as GTP-dependent regulator.

Escherichia coli (strain K12) (taxid: 83333)

>sp|O74310|YOG5_SCHPO COBW domain-containing protein C15D4.05 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC15D4.05 PE=3 SV=1

 Score =  114 bits (286), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 90/288 (31%), Positives = 149/288 (51%), Gaps = 29/288 (10%)

Query: 2   VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVK 61
           ++NGC+CCTV+ + +K L ++ ++K G+FD+IVIETTG+A P P+ +TF  D+ +   VK
Sbjct: 123 LSNGCMCCTVKDNGIKALEKIMRQK-GRFDNIVIETTGIANPGPLAQTFWLDDALKSDVK 181

Query: 62  LDGVITLVDSKHAMQHL-NEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
           LDG++T++D K+    L +E    F+      Q+++AD +ILNK DL++   L  + + I
Sbjct: 182 LDGIVTVIDCKNIDNILKDESDIGFI------QISHADCLILNKTDLISSEALSVVRQTI 235

Query: 121 KHINAMAPVKLAKYGSV-DMDFVLGVGGY------DLERIDSEVHVDNSHCATHHH-ESA 172
             IN +A +    YG + D+  +L +  Y      +LE      +  N +C+T    +  
Sbjct: 236 LKINCLAKIIETTYGRLDDISEILDLDAYGNENTSNLEWSIQRSNDSNINCSTCLDVDCQ 295

Query: 173 HGHHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIE---EKGED----LYRMKG 225
           H H    H   +         ++S+      +   W+   +    E+GED    +YR KG
Sbjct: 296 HLHSLDTHSLDISTHTFKLPPLMSKEV--FQQFLQWVRHTLWSCLEEGEDEEFMIYRSKG 353

Query: 226 ILSVSGSEQQYVFQGVHSTLDGCP--GKAWGPDEKRIN-KLVFIGRNL 270
           I +       Y+FQGV    +  P   K     EK I+ +++ IGRNL
Sbjct: 354 IFNKDDG-SWYIFQGVREVFEIMPLSEKPRAFLEKDIHPEIILIGRNL 400

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

>sp|A6NM15|CBWD7_HUMAN Putative COBW domain-containing protein 7 OS=Homo sapiens GN=CBWD7 PE=5 SV=3

 Score =  112 bits (281), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 76/241 (31%), Positives = 124/241 (51%), Gaps = 28/241 (11%)

Query: 50  FCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVT 109
           F  D  +   + LDG+IT+VDSK+ ++HL E KP  ++NEA  QVA AD I++NK DLV 
Sbjct: 2   FWVDAELGSDIYLDGIITIVDSKYGLKHLTEEKPDGLINEATRQVALADIILINKTDLVP 61

Query: 110 ETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYD-LERIDSEVHVDNSHCATHH 168
           E ++  L   I+ IN +  +   +   VD+  VL +  +D L  I  +  +         
Sbjct: 62  EEDVKKLRTTIRSINGLGQILETQRSRVDLSNVLDLHAFDSLSGISLQKKL--------- 112

Query: 169 HESAHGHHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKG--------EDL 220
                  H      H+ D ++ ++T    G    + ++ +++ L+ EK          ++
Sbjct: 113 ------QHVPGTQPHL-DQSIVTITFEVPGNAKEEHLNMFIQNLLWEKNVRNKDNHCMEV 165

Query: 221 YRMKGILSVSGSEQQYVFQGVHST--LDGCPGKAWGPDEKRINKLVFIGRNLDETALRKG 278
            R+KG++S+    QQ + QGVH    L+  P  +W  D +R N+LV IGRNLD+  L++ 
Sbjct: 166 IRLKGLVSIKDKSQQVIVQGVHELYDLEETPV-SWKDDTERTNRLVLIGRNLDKDILKQL 224

Query: 279 F 279
           F
Sbjct: 225 F 225

Homo sapiens (taxid: 9606)

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	284
224138328	420	predicted protein [Populus trichocarpa]	1.0	0.676	0.821	1e-132
255557855	413	prli-interacting factor l, putative [Ric	1.0	0.687	0.821	1e-132
225427419	415	PREDICTED: COBW domain-containing protei	0.996	0.681	0.855	1e-129
297804240	414	predicted protein [Arabidopsis lyrata su	0.996	0.683	0.777	1e-128
356559093	424	PREDICTED: COBW domain-containing protei	0.996	0.667	0.8	1e-125
449456911	424	PREDICTED: COBW domain-containing protei	0.992	0.665	0.802	1e-118
357165567	410	PREDICTED: COBW domain-containing protei	0.985	0.682	0.742	1e-113
326529359	406	predicted protein [Hordeum vulgare subsp	0.985	0.689	0.727	1e-109
115460306	411	Os04g0599700 [Oryza sativa Japonica Grou	0.992	0.686	0.727	1e-106
242074210	283	hypothetical protein SORBIDRAFT_06g02738	0.978	0.982	0.686	1e-103

>gi|224138328|ref|XP_002326575.1| predicted protein [Populus trichocarpa] gi|222833897|gb|EEE72374.1| predicted protein [Populus trichocarpa]

 Score =  478 bits (1231), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 240/292 (82%), Positives = 262/292 (89%), Gaps = 8/292 (2%)

Query: 1   MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
           MVNNGCLCCTVRGDLVKMLL+LAKK + +FDHIVIETTGLAKP PVIETFC+DELVS+YV
Sbjct: 129 MVNNGCLCCTVRGDLVKMLLELAKKNRDKFDHIVIETTGLAKPGPVIETFCSDELVSRYV 188

Query: 61  KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
           KLDGV+T+VDSKH +QHLNE+KPRFVVNEAVEQVAYADRIILNKIDLV+E EL  LT RI
Sbjct: 189 KLDGVVTMVDSKHVLQHLNELKPRFVVNEAVEQVAYADRIILNKIDLVSEEELKGLTMRI 248

Query: 121 KHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
           KHIN MAP+KLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNS  + H H +   HH+ HH
Sbjct: 249 KHINGMAPIKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSCSSMHQHGTTQEHHQRHH 308

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQ- 239
           HNH+HDSAVSSV+IV EG LDLDEVDDWLERLIEEKG+DLYRMKG+LSV+GS+Q+Y+FQ 
Sbjct: 309 HNHVHDSAVSSVSIVFEGMLDLDEVDDWLERLIEEKGDDLYRMKGVLSVTGSDQRYIFQI 368

Query: 240 -------GVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCLA 284
                  GVHS LDGCPGK WGPDEKRINKLVFIGRNLDETALRKGFKGCLA
Sbjct: 369 QTGYFLHGVHSLLDGCPGKTWGPDEKRINKLVFIGRNLDETALRKGFKGCLA 420

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255557855|ref|XP_002519957.1| prli-interacting factor l, putative [Ricinus communis] gi|223541003|gb|EEF42561.1| prli-interacting factor l, putative [Ricinus communis]

 Score =  476 bits (1225), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 239/291 (82%), Positives = 263/291 (90%), Gaps = 7/291 (2%)

Query: 1   MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
           MVNNGCLCCTVRGDLVKMLL+L KK++ +FDHIVIETTGLAKP PVIETFC+DELVS++V
Sbjct: 123 MVNNGCLCCTVRGDLVKMLLELVKKRRDKFDHIVIETTGLAKPGPVIETFCSDELVSRHV 182

Query: 61  KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
           KLDGV+T+VDSKHAMQHLNEVKPRFVVNEAVEQ+AYADRIILNKIDLV+E EL  LT RI
Sbjct: 183 KLDGVVTMVDSKHAMQHLNEVKPRFVVNEAVEQIAYADRIILNKIDLVSEAELQRLTNRI 242

Query: 121 KHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEG-- 178
           KHIN +APVKLAKYGSVDMDFVLGVGGYDLERIDSEV + NS   TH HE+A  HHEG  
Sbjct: 243 KHINGIAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVRIGNSCSGTHEHETAQEHHEGHH 302

Query: 179 -----HHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSE 233
                 HH+H+HDS VSSV+IVSEGTLDLDEVDDW ERLIEEKGEDLYRMKG+LSV+ S+
Sbjct: 303 HKECKSHHDHVHDSTVSSVSIVSEGTLDLDEVDDWFERLIEEKGEDLYRMKGVLSVTDSD 362

Query: 234 QQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCLA 284
           Q+Y+FQGVHSTLDGCPGK WGP+EKR+NKLVFIGRNLDETALRKGFKGCLA
Sbjct: 363 QRYIFQGVHSTLDGCPGKPWGPNEKRVNKLVFIGRNLDETALRKGFKGCLA 413

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225427419|ref|XP_002264766.1| PREDICTED: COBW domain-containing protein 2 [Vitis vinifera] gi|296088399|emb|CBI37390.3| unnamed protein product [Vitis vinifera]

 Score =  466 bits (1200), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 242/283 (85%), Positives = 268/283 (94%)

Query: 1   MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
           MVNNGCLCCTVRGDLVKMLL+L KKK+ +FDHIVIETTGLAKPAPVIETFCTDELVS+YV
Sbjct: 132 MVNNGCLCCTVRGDLVKMLLELVKKKRDKFDHIVIETTGLAKPAPVIETFCTDELVSRYV 191

Query: 61  KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
           KLDGV+TLVD+KHAMQHL+EVKPRFVVNEAVEQVAYADRIILNKIDLVTE +L  LT+RI
Sbjct: 192 KLDGVVTLVDAKHAMQHLDEVKPRFVVNEAVEQVAYADRIILNKIDLVTEADLERLTQRI 251

Query: 121 KHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
           KHIN MA +KLAK+G VDMDFVLGVGGYDLERIDSEV VD+SHCATH HE+  GHH+GHH
Sbjct: 252 KHINGMAQIKLAKFGCVDMDFVLGVGGYDLERIDSEVQVDSSHCATHQHETGKGHHKGHH 311

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQG 240
           H+H+HDSAVSSV+IVSEGTLDLDEVDDWLERL+EEKGEDLYRMKG+L V+GS+++YVFQG
Sbjct: 312 HDHVHDSAVSSVSIVSEGTLDLDEVDDWLERLLEEKGEDLYRMKGVLCVNGSDERYVFQG 371

Query: 241 VHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
           VHSTLDGCPGK W PDEKR++KLVFIGRNLDETALRKGF+GCL
Sbjct: 372 VHSTLDGCPGKTWEPDEKRVSKLVFIGRNLDETALRKGFRGCL 414

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297804240|ref|XP_002870004.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297315840|gb|EFH46263.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  462 bits (1189), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 224/288 (77%), Positives = 255/288 (88%), Gaps = 5/288 (1%)

Query: 1   MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
           MVNNGCLCCTVRGDLVKMLL L K K+ +FDHIVIETTGLAKP PVIETF +DEL+ +Y+
Sbjct: 126 MVNNGCLCCTVRGDLVKMLLDLVKNKRDKFDHIVIETTGLAKPGPVIETFNSDELLPRYI 185

Query: 61  KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTE-TELGSLTER 119
           KLDGV+TLVDSKHAM+HLNEVKPRFVVNEAVEQ+AYADRI+LNKIDLV+E +EL  LT+R
Sbjct: 186 KLDGVVTLVDSKHAMRHLNEVKPRFVVNEAVEQIAYADRIVLNKIDLVSEPSELEHLTKR 245

Query: 120 IKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCA----THHHESAHGH 175
           IK IN MAP+K  K+G VDMDFVLGVGGYDLERIDSEV+ D   CA     HHH+ +HG 
Sbjct: 246 IKQINCMAPIKHTKFGDVDMDFVLGVGGYDLERIDSEVNGDGLSCAEDHDHHHHQCSHGK 305

Query: 176 HEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQ 235
           H+ H H+H+HDSAV+SV+IVSEG LDLDEVDDWLERLIEEKG+DLYRMKG+LS+  S+Q+
Sbjct: 306 HKEHQHDHVHDSAVTSVSIVSEGKLDLDEVDDWLERLIEEKGDDLYRMKGVLSIDSSDQR 365

Query: 236 YVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
           Y+FQGVHS LDGCPGK+WGP+EKRINKLVFIGRNLDET LRKGFKGCL
Sbjct: 366 YIFQGVHSMLDGCPGKSWGPEEKRINKLVFIGRNLDETILRKGFKGCL 413

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356559093|ref|XP_003547836.1| PREDICTED: COBW domain-containing protein 2-like [Glycine max]

 Score =  453 bits (1165), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 228/285 (80%), Positives = 257/285 (90%), Gaps = 2/285 (0%)

Query: 1   MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
           MVNNGCLCCTVRGDLVKMLL+L +KK+ +FDHIVIETTGLAKPAPVIETFC+DELVSQ+V
Sbjct: 139 MVNNGCLCCTVRGDLVKMLLELVRKKRDKFDHIVIETTGLAKPAPVIETFCSDELVSQHV 198

Query: 61  KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
           KLDGV+TLVD KHAM+HLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTE+EL  LT++I
Sbjct: 199 KLDGVVTLVDCKHAMKHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTESELNILTKKI 258

Query: 121 KHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESA--HGHHEG 178
           KHIN MA +K AK+GSVDMDFVLGVGGYDLERI+SEV  +    ++H  +S   H  H  
Sbjct: 259 KHINGMAQIKQAKFGSVDMDFVLGVGGYDLERIESEVPGECPSSSSHQDDSGHEHKGHHH 318

Query: 179 HHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVF 238
           HHH+H+HDSAVSSV+IV+EGTLDLDEVDDWLER+IEEKG+DLYRMKG+LSV  S+Q+YVF
Sbjct: 319 HHHDHVHDSAVSSVSIVAEGTLDLDEVDDWLERVIEEKGDDLYRMKGVLSVDSSDQRYVF 378

Query: 239 QGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
           QGVHS LDGCPGK W P+EKRINKLVFIGRNLDETAL+KGFKGCL
Sbjct: 379 QGVHSMLDGCPGKTWEPNEKRINKLVFIGRNLDETALKKGFKGCL 423

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456911|ref|XP_004146192.1| PREDICTED: COBW domain-containing protein 2-like [Cucumis sativus] gi|449512950|ref|XP_004164186.1| PREDICTED: COBW domain-containing protein 2-like [Cucumis sativus]

 Score =  431 bits (1109), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 232/289 (80%), Positives = 257/289 (88%), Gaps = 7/289 (2%)

Query: 1   MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
           MVNNGCLCCTVRGDLVKMLL+L KKK+ +FDHIVIETTGLAKP PVIETFCTDELVS+YV
Sbjct: 136 MVNNGCLCCTVRGDLVKMLLELVKKKRDKFDHIVIETTGLAKPGPVIETFCTDELVSRYV 195

Query: 61  KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
           KLDGV+TLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRII+NKIDLV+  EL  LT++I
Sbjct: 196 KLDGVVTLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIIMNKIDLVSPEELEQLTQKI 255

Query: 121 KHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHES------AHG 174
           K INAMA VKL K+GSVD+DFVLGVGGYDL+RIDS+V   N+    H HE+       H 
Sbjct: 256 KRINAMAQVKLTKFGSVDIDFVLGVGGYDLDRIDSQVEA-NTCSGDHKHEAQHEHHKGHD 314

Query: 175 HHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQ 234
           HH  HHH+H+HDSAVSSV+IVSEG LDLDE+DDWLERLIEEKG+DLYRMKG+LSV+G +Q
Sbjct: 315 HHHHHHHDHVHDSAVSSVSIVSEGLLDLDEIDDWLERLIEEKGDDLYRMKGVLSVNGHDQ 374

Query: 235 QYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
           +YVFQGVHS LDGCPGKAWG DEKRINKLVFIG+NLDETALRKGFKGCL
Sbjct: 375 RYVFQGVHSILDGCPGKAWGSDEKRINKLVFIGKNLDETALRKGFKGCL 423

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357165567|ref|XP_003580428.1| PREDICTED: COBW domain-containing protein 1-like [Brachypodium distachyon]

 Score =  413 bits (1061), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 210/283 (74%), Positives = 240/283 (84%), Gaps = 3/283 (1%)

Query: 1   MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
           MVNNGCLCCTVRGDLVKMLL+L K+K  +FDHIVIETTGLAKP PVIETFC+DELVS+YV
Sbjct: 130 MVNNGCLCCTVRGDLVKMLLKLVKQKGDKFDHIVIETTGLAKPGPVIETFCSDELVSKYV 189

Query: 61  KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
           KLDGV+TLVD KHAM+HLNEVKPR+VVNEAVEQVAYADRIILNKIDLV + E   L  +I
Sbjct: 190 KLDGVVTLVDCKHAMKHLNEVKPRWVVNEAVEQVAYADRIILNKIDLVDDAEQEVLANKI 249

Query: 121 KHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
           K IN MA +K AK+G VDMDFVLG+GGYDL+RI+SEV  + S    H H        GHH
Sbjct: 250 KLINGMAQMKKAKFGDVDMDFVLGIGGYDLDRIESEVQSNESKETGHCHSGD---AHGHH 306

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQG 240
           H+H+HDSAV+SV+IVSEG LDLDEV+DWLERL++EKGEDLYR+KG++SV+ S  ++VFQG
Sbjct: 307 HDHVHDSAVTSVSIVSEGVLDLDEVNDWLERLVDEKGEDLYRLKGVISVNESTGRFVFQG 366

Query: 241 VHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
           VHS L+GCP K W PDEKRINKLVFIGRNLDE ALRK FKGCL
Sbjct: 367 VHSMLEGCPAKPWEPDEKRINKLVFIGRNLDEAALRKAFKGCL 409

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326529359|dbj|BAK01073.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  400 bits (1027), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 206/283 (72%), Positives = 239/283 (84%), Gaps = 3/283 (1%)

Query: 1   MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
           MVNNGCLCCTVRGDLVKMLL+L K+K  +FDHIVIETTGLAKP PVIETFC+DELVS+YV
Sbjct: 126 MVNNGCLCCTVRGDLVKMLLKLVKQKGDKFDHIVIETTGLAKPGPVIETFCSDELVSKYV 185

Query: 61  KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
           KLDGV+TLVD KHAMQHLNEVK R+VVNEAVEQVAYADRIILNK DLV E EL  LT +I
Sbjct: 186 KLDGVVTLVDCKHAMQHLNEVKARWVVNEAVEQVAYADRIILNKTDLVDEAELEVLTNKI 245

Query: 121 KHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
           K IN MA +K AK+G VDMDFVLG+GGYDL+R+++ V ++ +           GH  GHH
Sbjct: 246 KLINGMAEMKKAKFGDVDMDFVLGIGGYDLDRVEAAVQLNENK---ETGHCHSGHDHGHH 302

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQG 240
           H+H+HDSAV+SV+IVSEG LDLDEV+DWLERL++EKGEDLYR+KG++SV+ S  ++VFQG
Sbjct: 303 HDHVHDSAVTSVSIVSEGVLDLDEVNDWLERLVDEKGEDLYRLKGVVSVNESTGRFVFQG 362

Query: 241 VHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
           VHS L+GCP K W  DEKRI+KLVFIGRNLDE ALRK FKGCL
Sbjct: 363 VHSMLEGCPAKPWEDDEKRISKLVFIGRNLDEAALRKAFKGCL 405

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115460306|ref|NP_001053753.1| Os04g0599700 [Oryza sativa Japonica Group] gi|38345768|emb|CAE03469.2| OSJNBa0083N12.6 [Oryza sativa Japonica Group] gi|113565324|dbj|BAF15667.1| Os04g0599700 [Oryza sativa Japonica Group] gi|215694465|dbj|BAG89434.1| unnamed protein product [Oryza sativa Japonica Group] gi|218195492|gb|EEC77919.1| hypothetical protein OsI_17249 [Oryza sativa Indica Group] gi|222629477|gb|EEE61609.1| hypothetical protein OsJ_16026 [Oryza sativa Japonica Group]

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 206/283 (72%), Positives = 235/283 (83%), Gaps = 1/283 (0%)

Query: 1   MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
           MVNNGCLCCTVRGDLVKMLL+L K+K  +FDHIVIETTGLAKP PVIETFC+DELVS+YV
Sbjct: 129 MVNNGCLCCTVRGDLVKMLLKLVKQKGDKFDHIVIETTGLAKPGPVIETFCSDELVSRYV 188

Query: 61  KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
           KLDGV+T+VD KHAM+HLNEVK R+VVNEAVEQVAYADRIILNK DLV   EL  L  +I
Sbjct: 189 KLDGVVTMVDCKHAMKHLNEVKARWVVNEAVEQVAYADRIILNKTDLVDNAELEVLINKI 248

Query: 121 KHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
           K IN MA ++  K+G VDMDFVLG+GGYDL+RI+SEV +       H H +   H   HH
Sbjct: 249 KLINGMAQMRKTKFGDVDMDFVLGIGGYDLDRIESEVQLHERKETGHCH-AGEEHGHQHH 307

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQG 240
           H H+HDSAVSSV+IVSEG LDLDEV+DWLERL+EEKGEDLYR+KG++SV+ S  ++VFQG
Sbjct: 308 HGHVHDSAVSSVSIVSEGVLDLDEVNDWLERLVEEKGEDLYRLKGVISVNESTGRFVFQG 367

Query: 241 VHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
           VHS L+GCP K W PDEKR NKLVFIGRNLDE ALRK FKGCL
Sbjct: 368 VHSMLEGCPAKPWEPDEKRFNKLVFIGRNLDEAALRKAFKGCL 410

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242074210|ref|XP_002447041.1| hypothetical protein SORBIDRAFT_06g027386 [Sorghum bicolor] gi|241938224|gb|EES11369.1| hypothetical protein SORBIDRAFT_06g027386 [Sorghum bicolor]

 Score =  379 bits (973), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 197/287 (68%), Positives = 235/287 (81%), Gaps = 9/287 (3%)

Query: 1   MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKP----APVIETFCTDELV 56
           MVNNGCLCCTVRGDLVKMLL+L K+K  +FDHIVIETTG +       PVIETF +DELV
Sbjct: 1   MVNNGCLCCTVRGDLVKMLLKLVKQKGDKFDHIVIETTGKSYWNKVLCPVIETFSSDELV 60

Query: 57  SQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSL 116
           S+YVKLDGV+T+VD KHAM+HLNEVK R+VVNEAVEQVAYADRIILNK+DLV + EL +L
Sbjct: 61  SKYVKLDGVVTMVDCKHAMKHLNEVKARWVVNEAVEQVAYADRIILNKVDLVDDAELEAL 120

Query: 117 TERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHH 176
           T ++K IN MA +K AK+G VDMDFVLG+GGYDL+RI++EV       +   +   HG  
Sbjct: 121 TNKLKFINGMAQMKTAKFGDVDMDFVLGIGGYDLDRIEAEVQD-----SKETYHCHHGDE 175

Query: 177 EGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQY 236
            GHHH+H+HDSAV+SV+IVSEG LDLDEV+DWLERL++EKGEDLYR+KG++SV+ S  ++
Sbjct: 176 HGHHHDHVHDSAVTSVSIVSEGLLDLDEVNDWLERLVDEKGEDLYRLKGVISVNESTGRF 235

Query: 237 VFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
           +FQGVH  L+GCP K W PDEKRINKLVFI RNLDE ALRK F GCL
Sbjct: 236 MFQGVHCMLEGCPAKPWEPDEKRINKLVFICRNLDEAALRKAFNGCL 282

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	284
TAIR|locus:2198993	444	PTAC17 "plastid transcriptiona	0.996	0.637	0.545	3.2e-81
TAIR|locus:2036189	448	AT1G15730 [Arabidopsis thalian	0.996	0.631	0.523	3.4e-77
TAIR|locus:2197895	374	AT1G26520 "AT1G26520" [Arabido	0.933	0.708	0.362	3.5e-43
TIGR_CMR|BA_2021	316	BA_2021 "cobalamin synthesis p	0.461	0.414	0.436	1.1e-42
UNIPROTKB|Q4K5R5	323	yjiA "GTP-binding protein, Yji	0.496	0.436	0.444	1.4e-42
DICTYBASE|DDB_G0281589	396	DDB_G0281589 "COBW domain-cont	0.75	0.537	0.310	2.5e-41
ZFIN|ZDB-GENE-040426-2388	366	cbwd "COBW domain containing"	0.919	0.713	0.350	2.1e-38
UNIPROTKB|P24203	318	yjiA [Escherichia coli K-12 (t	0.5	0.446	0.424	2.8e-38
MGI|MGI:2385089	393	Cbwd1 "COBW domain containing	0.957	0.692	0.332	4.4e-36
RGD|708495	394	Cbwd1 "COBW domain containing	0.915	0.659	0.336	4.4e-36

TAIR|locus:2198993 PTAC17 "plastid transcriptionally active 17" [Arabidopsis thaliana (taxid:3702)]

 Score = 815 (292.0 bits), Expect = 3.2e-81, P = 3.2e-81
 Identities = 162/297 (54%), Positives = 208/297 (70%)

Query:     1 MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
             M+NNGCLCCTVRGDLV+M+ +L   K+G+FDHIVIETTGLA PAP+I+TF  +E +   V
Sbjct:   147 MLNNGCLCCTVRGDLVRMIGELVNTKKGKFDHIVIETTGLANPAPIIQTFYAEEEIFNDV 206

Query:    61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
             KLDGV+TLVD+KHA  HL+EVKP  VVNEAVEQ+AYADRII+NK DLV E ELGS+ +RI
Sbjct:   207 KLDGVVTLVDAKHARLHLDEVKPEGVVNEAVEQIAYADRIIVNKTDLVGEAELGSVVQRI 266

Query:   121 KHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNXXXXXXXXXXXXXXXXXX- 179
             K IN+MA +   KYG+VD+D+VLG+GG+DLERI+S V+ D+                   
Sbjct:   267 KTINSMAQMTRTKYGNVDLDYVLGIGGFDLERIESSVNEDDKGDHHDHDHDHHHDHNHDH 326

Query:   180 -------------XXXXXXDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGI 226
                                D  VSSV+IV EG+LDL++ + WL  L+ E+ ED+YRMKG+
Sbjct:   327 DHHHHDGHDHHHHSHDHTHDPGVSSVSIVCEGSLDLEKANMWLGTLLMERSEDIYRMKGL 386

Query:   227 LSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
             LSV   E+++VFQGVH    G P + WG +E+R+NK+VFIG+NL+   L KGFK CL
Sbjct:   387 LSVHTMEERFVFQGVHDIFQGSPDRLWGREEERVNKIVFIGKNLNREELEKGFKACL 443

GO:0009295 "nucleoid" evidence=IDA

GO:0009508 "plastid chromosome" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

TAIR|locus:2036189 AT1G15730 [Arabidopsis thaliana (taxid:3702)]

 Score = 777 (278.6 bits), Expect = 3.4e-77, P = 3.4e-77
 Identities = 156/298 (52%), Positives = 202/298 (67%)

Query:     1 MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
             M+NNGCLCCTVRGDLV+M+ ++ + K+G+FDHIVIETTGLA PAP+I+TF  ++ +   V
Sbjct:   150 MLNNGCLCCTVRGDLVRMISEMVQTKKGRFDHIVIETTGLANPAPIIQTFYAEDEIFNDV 209

Query:    61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
             KLDGV+TLVD+KHA  HL+EVKP   VNEAVEQ+AYADRII+NK DLV E EL S+ +RI
Sbjct:   210 KLDGVVTLVDAKHARLHLDEVKPEGYVNEAVEQIAYADRIIVNKTDLVGEPELASVMQRI 269

Query:   121 KHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEV----------HVDNXXXXX---- 166
             K IN+MA +K  KYG VD+D+VLG+GG+DLERI+S V          H D+         
Sbjct:   270 KTINSMAHMKRTKYGKVDLDYVLGIGGFDLERIESSVNEEEKEDREGHDDHHHGHDCHDH 329

Query:   167 -XXXXXXXXXXXXXXXXXXXDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKG 225
                                 D  V SV+IV EG LDL++ + WL  L+ ++ ED+YRMKG
Sbjct:   330 HNEHEHEHEHEHHHSHDHTHDPGVGSVSIVCEGDLDLEKANMWLGALLYQRSEDIYRMKG 389

Query:   226 ILSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
             ILSV   ++++VFQGVH   +G P + W  DE R NK+VFIG+NL+   L  GF+ CL
Sbjct:   390 ILSVQDMDERFVFQGVHEIFEGSPDRLWRKDETRTNKIVFIGKNLNREELEMGFRACL 447

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

TAIR|locus:2197895 AT1G26520 "AT1G26520" [Arabidopsis thaliana (taxid:3702)]

 Score = 456 (165.6 bits), Expect = 3.5e-43, P = 3.5e-43
 Identities = 102/281 (36%), Positives = 152/281 (54%)

Query:     4 NGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLD 63
             NGC+CCTV+  LV+ L QL ++K  + DHI++ETTGLA PAP+      D+ +   VKLD
Sbjct:   106 NGCVCCTVKHSLVQALEQLVQRKD-RLDHILLETTGLANPAPLASILWLDDQLESEVKLD 164

Query:    64 GVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHI 123
              ++T+VD+K+    LNE +      EA  Q+A+AD II+NK+DL+++ E   L + I  I
Sbjct:   165 CIVTVVDAKNLRFQLNERRDSSSFPEAFNQIAFADTIIMNKVDLISQEESDELEKEIHSI 224

Query:   124 NAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNXXXXXXXXXXXXXXXXXXXXXX 183
             N++A V  +    VD+  +L    YD        HV                        
Sbjct:   225 NSLANVIRSVRCQVDLSNILNCQAYD------STHVSRLESLLEANKSLTTTDLH----- 273

Query:   184 XXDSAVSSVTIVSEGTLDLDEVDDWLERLI-EEKGE-DLYRMKGILSVSGSEQQYVFQGV 241
               DS V ++ I     ++LD+V  WLE ++ ++K E D+YR K +LS+  S+Q ++ Q V
Sbjct:   274 --DSGVRTLCISEPQPINLDKVRLWLEEILWDKKSEMDVYRCKAVLSIQNSDQMHILQAV 331

Query:   242 HSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGC 282
                 +  P + W  +E R NK+VFIG  LDE  LR G + C
Sbjct:   332 RDIYEIVPARKWSEEENRTNKIVFIGHKLDEEVLRSGLRDC 372

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|BA_2021 BA_2021 "cobalamin synthesis protein/P47K family protein" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 275 (101.9 bits), Expect = 1.1e-42, Sum P(2) = 1.1e-42
 Identities = 62/142 (43%), Positives = 91/142 (64%)

Query:     2 VNNGCLCCTVRGDLVKMLLQLAK-KKQGQ--FDHIVIETTGLAKPAPVIETFCTDELVSQ 58
             + NGCLCCTVR DL+  L QL   K +G+  FD +VIETTGLA P P+I+TF  D ++  
Sbjct:    58 MTNGCLCCTVREDLLVALKQLLDVKAEGKMDFDGLVIETTGLANPGPIIQTFFLDPVIQS 117

Query:    59 YVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTE 118
               +++GV+T+VDS H  +H  +        EA EQ+A+AD I++NK+DL+ E+E  +L  
Sbjct:   118 AYQINGVVTVVDSYHIHKHFEKGL------EAKEQIAFADVILVNKLDLIEESEKENLLH 171

Query:   119 RIKHINAMAPVKLAKYGSVDMD 140
              ++ IN  A  KL +  + D+D
Sbjct:   172 ELQGINPTA--KLIQSTNCDVD 191

GO:0003824 "catalytic activity" evidence=ISS

GO:0009236 "cobalamin biosynthetic process" evidence=ISS

UNIPROTKB|Q4K5R5 yjiA "GTP-binding protein, YjiA family" [Pseudomonas protegens Pf-5 (taxid:220664)]

 Score = 310 (114.2 bits), Expect = 1.4e-42, Sum P(2) = 1.4e-42
 Identities = 68/153 (44%), Positives = 101/153 (66%)

Query:     2 VNNGCLCCTVRGDLVKML-LQLAKKKQGQ--FDHIVIETTGLAKPAPVIETFCTDE-LVS 57
             ++NGC+CCT+  DL K L L L +   G+  FD +VIE TGLA PAPV +TF  DE L  
Sbjct:    61 LSNGCVCCTIHTDLTKALYLLLERLDSGEIAFDRLVIECTGLADPAPVAQTFFIDEELRE 120

Query:    58 QYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLT 117
             +Y+ LDG+ITLVD+KHA  HL +      + +A  Q+ +ADR++++K DLV E    +L 
Sbjct:   121 RYI-LDGIITLVDAKHAEFHLTQT-----IAQA--QIGFADRLLVSKRDLVDEATFEALC 172

Query:   118 ERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDL 150
             +R+  IN  AP++L ++G +D+  +L V G++L
Sbjct:   173 QRLTRINRRAPIRLVEHGQIDLAELLDVRGFNL 205

GO:0005525 "GTP binding" evidence=ISS

DICTYBASE|DDB_G0281589 DDB_G0281589 "COBW domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 282 (104.3 bits), Expect = 2.5e-41, Sum P(2) = 2.5e-41
 Identities = 72/232 (31%), Positives = 121/232 (52%)

Query:    69 VDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTET----ELGSLTERIKHIN 124
             VD +    H  ++K  +   E   Q+A+AD I+LNKIDL+ ++    E+ ++TERIK IN
Sbjct:   166 VDDEDIEIHGTDIK--YYSTEVERQIAFADIILLNKIDLLDQSNLNNEIKTITERIKSIN 223

Query:   125 AMAPVKLAKYGSVDMDFVLGVGGYD---------LERIDSEVHVDNXXXXXXXXXXXXXX 175
              +A +   +   V +D VL V  Y+         L++     + +N              
Sbjct:   224 PIAKIITTERSVVPLDKVLDVKAYNPNIELLKEYLDQFQKGQNSNNQHQHQHNNNEESSS 283

Query:   176 XXXXXXXXXXDSA--VSSVTIVSEGTLDLDEVDDWLERLI-EEKGEDLYRMKGILSVSGS 232
                       + +  +++V I  +G +DL E + W+  L+ EEK + ++R KG++SV G 
Sbjct:   284 CKECSLTNTSNHSKFINTVCITEDGDIDLTEFNRWIGNLLWEEKKDCIFRCKGLISVKGQ 343

Query:   233 EQQYVFQGVHSTLDGCP-GKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
             +++Y+ QGV++T +  P G  W  DEKR NK+V IG +L++  L + FK  L
Sbjct:   344 DEKYILQGVYATFEVLPSGLLWSKDEKRHNKIVLIGESLNQNELEQSFKNKL 395

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

ZFIN|ZDB-GENE-040426-2388 cbwd "COBW domain containing" [Danio rerio (taxid:7955)]

 Score = 411 (149.7 bits), Expect = 2.1e-38, P = 2.1e-38
 Identities = 101/288 (35%), Positives = 158/288 (54%)

Query:     2 VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVK 61
             + NGCLCC+V+ + +K +  L +KK G+FD+I++ETTGLA P  V   F  D  +   V 
Sbjct:    85 LRNGCLCCSVKDNGLKAIENLMEKK-GKFDYILLETTGLADPGAVASMFWVDAELGSDVY 143

Query:    62 LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIK 121
             LDG++T++D+K+ +QHL E KP  ++NEA  Q+A AD  I+NK DLV ETEL  L + ++
Sbjct:   144 LDGIVTVIDAKYGLQHLTEEKPEGLINEAARQIALADLTIINKTDLVHETELLKLRDTVR 203

Query:   122 HINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNXXXXXXXXXXXXXXXXXXXX 181
              IN +  +   +   VD+  VL +  +D +  D E                         
Sbjct:   204 SINGLVKILETQKSRVDLSEVLDLHSFDTK--DGE-------------RLTKKLQLVKTS 248

Query:   182 XXXXDSAVSSVTIVSEGTLDLDEVDDWLERLIEEK------GEDL--YRMKGILSVSGSE 233
                 D ++ ++T    G++  D ++ +++ L+ EK      G  +   R+KGILS+   +
Sbjct:   249 QPHLDKSMLTITFEVPGSVSEDLLNIFIQELLWEKTFKNKAGLPMTVIRLKGILSLQQKQ 308

Query:   234 QQYVFQGVHST--LDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGF 279
             ++ + QGVH    L+  P + W   E R+N+LVFIGRNLD   L+K F
Sbjct:   309 KKVMLQGVHELYELEETP-EFWADQEPRLNRLVFIGRNLDGEILKKEF 355

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|P24203 yjiA [Escherichia coli K-12 (taxid:83333)]

 Score = 285 (105.4 bits), Expect = 2.8e-38, Sum P(2) = 2.8e-38
 Identities = 65/153 (42%), Positives = 90/153 (58%)

Query:     2 VNNGCLCCTVRGDLVKMLLQLAKK-KQG--QFDHIVIETTGLAKPAPVIETFCTDELVSQ 58
             + NGC+CC+   +L   LL L     +G  QFD +VIE TG+A P P+I+TF + E++ Q
Sbjct:    60 LTNGCICCSRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQ 119

Query:    59 YVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTE 118
                LDGVI LVD+ HA + +N+    F +  A  QV YADRI+L K D+  E E   L E
Sbjct:   120 RYLLDGVIALVDAVHADEQMNQ----FTI--AQSQVGYADRILLTKTDVAGEAE--KLHE 171

Query:   119 RIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLE 151
             R+  INA APV    +G +D+  +    G+ LE
Sbjct:   172 RLARINARAPVYTVTHGDIDLGLLFNTNGFMLE 204

GO:0006974 "response to DNA damage stimulus" evidence=IEP

GO:0005525 "GTP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:2385089 Cbwd1 "COBW domain containing 1" [Mus musculus (taxid:10090)]

 Score = 389 (142.0 bits), Expect = 4.4e-36, P = 4.4e-36
 Identities = 95/286 (33%), Positives = 147/286 (51%)

Query:     2 VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVK 61
             + NGCLCC+V+   ++ +  L +KK G+FD+I++ETTGLA P  V   F  D  +   + 
Sbjct:   101 LRNGCLCCSVKDSGLRAIENLMQKK-GKFDYILLETTGLADPGAVASMFWVDAELGSDIY 159

Query:    62 LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIK 121
             LDG+IT+VDSK+ ++HL E KP  +VNEA  QVA AD I++NK DLV+E EL +L   I+
Sbjct:   160 LDGIITVVDSKYGLKHLTEEKPDGLVNEATRQVALADMILINKTDLVSEEELNNLRTTIR 219

Query:   122 HINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNXXXXXXXXXXXXXXXXXXXX 181
              IN +  V   +   V +  +L +  YD   I S + +                      
Sbjct:   220 SINGLGKVLETQRSRVHLSNILDLHAYD---ILSGISLQKKLQHVSTAPHLDQSIVTVTF 276

Query:   182 XXXXDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGE--DLYRMKGILSVSGSEQQYVFQ 239
                  +    + +  +  L       W + +  + G   ++ R+KG++S+    QQ + Q
Sbjct:   277 EVPGSAKEECLNVFIQNLL-------WEKNVKNKDGHCMEVIRLKGLVSIKDKPQQMIVQ 329

Query:   240 GVHSTLDGCPGKA-WGPDEKRINKLVFIGRNLDETALRKGFKGCLA 284
             G+H   D       W  D +R  +LVFIGRNLD+  L++ F   +A
Sbjct:   330 GIHELYDLEESLVNWKDDAERACQLVFIGRNLDKDVLQQLFLTAVA 375

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

RGD|708495 Cbwd1 "COBW domain containing 1" [Rattus norvegicus (taxid:10116)]

 Score = 389 (142.0 bits), Expect = 4.4e-36, P = 4.4e-36
 Identities = 97/288 (33%), Positives = 156/288 (54%)

Query:     2 VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVK 61
             + NGCLCC+V+ + +K +  L +KK G+FD+I++ETTGLA P  V   F  D  +   + 
Sbjct:   102 LRNGCLCCSVKDNGLKAIENLMQKK-GKFDYILLETTGLADPGAVASMFWVDAELGSDIY 160

Query:    62 LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIK 121
             LDG+IT+VDSK+ ++HL E KP  +VNEA  QVA AD I++NK DLV+E EL  L   I+
Sbjct:   161 LDGIITVVDSKYGLKHLTEEKPDGLVNEATRQVALADMILINKTDLVSEEELNKLRTTIR 220

Query:   122 HINAMAPVKLAKYGSVDMDFVLGVGGYD-LERIDSEVHVDNXXXXXXXXXXXXXXXXXXX 180
              IN +  V   +     +  +L +  YD L  I  +  + +                   
Sbjct:   221 SINGLGKVLETQRSRTHLSNILDLHAYDTLSGISLQKKLQHVSTAPHL------------ 268

Query:   181 XXXXXDSAVSSVTIVSEGTLDLDEVDDWLERLIEEK------GE--DLYRMKGILSVSGS 232
                  D ++ +VT    G+ + + ++ +++ L+ EK      G   ++ R+KG++S+   
Sbjct:   269 -----DQSIVTVTFDVPGSAEEESLNVFIQNLLWEKNVKNKDGRCMEVIRLKGLVSIKDK 323

Query:   233 EQQYVFQGVHSTLDGCPGKA-WGPDEKRINKLVFIGRNLDETALRKGF 279
              QQ + QG+H   +    +  W  D +R  +LVFIG+NLD+  L++ F
Sbjct:   324 PQQMIVQGIHELYELEESRVNWKDDAERACQLVFIGKNLDKDILQQLF 371

GO:0005524 "ATP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

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

Your Input: gw1.29.49.1 hypothetical protein (392 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	284
COG0523	323	COG0523, COG0523, Putative GTPases (G3E family) [G	3e-82
PRK11537	318	PRK11537, PRK11537, putative GTP-binding protein Y	6e-53
cd03112	158	cd03112, CobW_like, The function of this protein f	5e-46
TIGR02475	341	TIGR02475, CobW, cobalamin biosynthesis protein Co	2e-37
pfam02492	178	pfam02492, cobW, CobW/HypB/UreG, nucleotide-bindin	1e-36
pfam07683	94	pfam07683, CobW_C, Cobalamin synthesis protein cob	2e-28
smart00833	92	smart00833, CobW_C, Cobalamin synthesis protein co	9e-16
PRK10019	279	PRK10019, PRK10019, nickel/cobalt efflux protein R	0.003

>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function prediction only]

 Score =  249 bits (639), Expect = 3e-82
 Identities = 106/284 (37%), Positives = 162/284 (57%), Gaps = 22/284 (7%)

Query: 3   NNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKL 62
            NGC+CCTVR DL+  L +L +++    D +VIETTGLA PAPVI+TF TD  ++  V+L
Sbjct: 59  TNGCICCTVRDDLLPALERLLRRRDR-PDRLVIETTGLADPAPVIQTFLTDPELADGVRL 117

Query: 63  DGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKH 122
           DGV+T+VD+ H ++ L+ +        A +Q+A+AD I+LNK DLV   EL +L  R++ 
Sbjct: 118 DGVVTVVDAAHFLEGLDAIA-----ELAEDQLAFADVIVLNKTDLVDAEELEALEARLRK 172

Query: 123 INAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGHHHN 182
           +N  A +    YG VD+  +L  G +DL+R             T    S H H   H   
Sbjct: 173 LNPRARIIETSYGDVDLAELLDEGLFDLDRDVGR---------TSPLFSDHQHDHEHDEG 223

Query: 183 HMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSV-SGSEQQYVFQGV 241
                 +SS ++ ++   D + ++ +L+ L+  +GE + R KGIL +  G  ++ VFQGV
Sbjct: 224 -----GISSFSVRADRPFDPERLEAFLDLLLSARGEKVLRAKGILWIAEGPPRRLVFQGV 278

Query: 242 HSTLDGCP-GKAWGPDEKRINKLVFIGRNLDETALRKGFKGCLA 284
               +  P G+ W  +  R ++LVFIGR+LD+ A+R+ F   L 
Sbjct: 279 GGVFEVPPAGREWPAEGDRKSRLVFIGRDLDDEAIREAFLAALL 322

Length = 323

>gnl|CDD|183183 PRK11537, PRK11537, putative GTP-binding protein YjiA; Provisional

 Score =  174 bits (443), Expect = 6e-53
 Identities = 98/281 (34%), Positives = 143/281 (50%), Gaps = 30/281 (10%)

Query: 4   NGCLCCTVRGDLVKMLLQL---AKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
           NGC+CC+   +L   LL L     K   QFD +VIE TG+A P P+I+TF + E++ Q  
Sbjct: 62  NGCICCSRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQRY 121

Query: 61  KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
            LDGVI LVD+ HA + +N    +F + ++  QV YADRI+L K D+  E E   L ER+
Sbjct: 122 LLDGVIALVDAVHADEQMN----QFTIAQS--QVGYADRILLTKTDVAGEAE--KLRERL 173

Query: 121 KHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGHH 180
             INA APV    +G +D+  +    G+ LE      +V ++    H             
Sbjct: 174 ARINARAPVYTVVHGDIDLSLLFNTNGFMLEE-----NVVSTKPRFHFIADK-------- 220

Query: 181 HNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQG 240
                 + +SS+ +  +  +D+ EV   +E L+ E  + L R KG+L + G   + +FQG
Sbjct: 221 -----QNDISSIVVELDYPVDISEVSRVMENLLLESADKLLRYKGMLWIDGEPNRLLFQG 275

Query: 241 VHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKG 281
           V         + WG DE   + LVFIG  L E  +R  F G
Sbjct: 276 VQRLYSADWDRPWG-DETPHSTLVFIGIQLPEEEIRAAFAG 315

Length = 318

>gnl|CDD|239386 cd03112, CobW_like, The function of this protein family is unkown

 Score =  151 bits (384), Expect = 5e-46
 Identities = 61/109 (55%), Positives = 77/109 (70%), Gaps = 9/109 (8%)

Query: 2   VNNGCLCCTVRGDLVKMLLQLAKKKQ---GQFDHIVIETTGLAKPAPVIETFCTDELVSQ 58
           +NNGC+CCTVRGDL++ LL L ++       FD IVIETTGLA P PV +TF  DE +++
Sbjct: 56  MNNGCICCTVRGDLIRALLDLLERLDAGKIAFDRIVIETTGLADPGPVAQTFFMDEELAE 115

Query: 59  YVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDL 107
              LDGVITLVD+KHA QHL++        EA  Q+A+ADRI+LNK DL
Sbjct: 116 RYLLDGVITLVDAKHANQHLDQ------QTEAQSQIAFADRILLNKTDL 158

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. Length = 158

>gnl|CDD|233883 TIGR02475, CobW, cobalamin biosynthesis protein CobW

 Score =  134 bits (340), Expect = 2e-37
 Identities = 95/297 (31%), Positives = 143/297 (48%), Gaps = 44/297 (14%)

Query: 4   NGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLD 63
           NGC+CCTV  D +  + +L  ++Q + DHI+IET+GLA P P+++ F   E+ S+ V +D
Sbjct: 68  NGCICCTVADDFIPTMTKLLARRQ-RPDHILIETSGLALPKPLVQAFQWPEIRSR-VTVD 125

Query: 64  GVITLVDS------------------KHAMQHLNEVKPRFVVNEAVE-QVAYADRIILNK 104
           GV+T+VD                   + A  +L+   P   + E  E Q+A AD +ILNK
Sbjct: 126 GVVTVVDGPAVAAGRFAADPDALDAQRAADDNLDHETP---LEELFEDQLACADLVILNK 182

Query: 105 IDLVTETELGSLTERIK-HINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSH 163
            DL+    L  +   I   +     +  A +G VD   +LG+G        +E  +DN  
Sbjct: 183 ADLLDAAGLARVRAEIAAELPRAVKIVEASHGEVDARVLLGLG------AAAEDDLDNR- 235

Query: 164 CATHHHESAHGHHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRM 223
             +HH        E H H+   DS V  +  V+    D   +   LERL EE   D+ R+
Sbjct: 236 -PSHHDFEGG---EEHDHDEF-DSVVVDLGEVA----DPAALRQRLERLAEE--HDVLRI 284

Query: 224 KGILSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIG-RNLDETALRKGF 279
           KG  +V G   + + QGV   +D    + W   E R  +LV IG  +LD+ A+R   
Sbjct: 285 KGFAAVPGKPMRLLVQGVGQRVDSYYDRPWQAAETRQTRLVVIGLHDLDQAAIRAAL 341

The family of proteins identified by this model is generally found proximal to the trimeric cobaltochelatase subunit CobN which is essential for vitamin B12 (cobalamin) biosynthesis. The protein contains an 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. A broader CobW family is delineated by two PFAM models which identify the N- and C-terminal domains (pfam02492 and pfam07683) [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 341

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

 Score =  128 bits (323), Expect = 1e-36
 Identities = 52/129 (40%), Positives = 75/129 (58%), Gaps = 10/129 (7%)

Query: 2   VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVK 61
           +NNGC+CCT+R DL  +L  L + K  + D + IETTGLA PAPV +TF + EL S  + 
Sbjct: 57  LNNGCICCTLREDLSMVLEALLELK-ERLDLLFIETTGLACPAPVAQTFLSPELRSD-LG 114

Query: 62  LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETE-LGSLTERI 120
           LDGV+T+VD               +  +A +Q+A+AD I++NK DL      L  L   +
Sbjct: 115 LDGVVTVVDVAETE-------GEDIPEKAPDQIAFADLIVINKTDLAPAVADLEKLEADL 167

Query: 121 KHINAMAPV 129
           + +N  AP+
Sbjct: 168 RRLNPEAPI 176

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|219512 pfam07683, CobW_C, Cobalamin synthesis protein cobW C-terminal domain

 Score =  103 bits (260), Expect = 2e-28
 Identities = 39/96 (40%), Positives = 52/96 (54%), Gaps = 3/96 (3%)

Query: 189 VSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQGVHSTLD-G 247
           +SS    ++   D + ++ WLE L     E + R KGIL ++G     VFQGV   L   
Sbjct: 1   ISSFVFRADRPFDPERLEAWLEDL--LLPEGILRAKGILWLAGRPDPLVFQGVGGRLSLE 58

Query: 248 CPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
             G+ W PDE R ++LVFIGR+LD  ALR     CL
Sbjct: 59  PAGRWWAPDEDRRSRLVFIGRDLDREALRAALDACL 94

This is a large and diverse family of putative metal chaperones that can be separated into up to 15 subgroups. In addition to known roles in cobalamin biosynthesis and the activation of the Fe-type nitrile hydratase, this family is also known to be involved in the response to zinc limitation. The CobW subgroup involved in cobalamin synthesis represents only a small sub-fraction of the family. Length = 94

>gnl|CDD|214844 smart00833, CobW_C, Cobalamin synthesis protein cobW C-terminal domain

 Score = 70.7 bits (174), Expect = 9e-16
 Identities = 28/96 (29%), Positives = 38/96 (39%), Gaps = 5/96 (5%)

Query: 189 VSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSV-SGSEQQYVFQGVHSTLDG 247
           +SS    +        +   L+ L     E + R KG   + S  +   V       L  
Sbjct: 1   ISSFVYRARRPFHPQRLLAALDEL----PEGVLRAKGFFWLASRPDLPGVLSQAGGRLRI 56

Query: 248 CPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL 283
            P  AW     R  +LVFIGR+LDE A+R     CL
Sbjct: 57  EPAGAWPAAGDRRTRLVFIGRDLDEEAIRAALDACL 92

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 the C-terminal domain found in CobW, as well as in P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression. Length = 92

>gnl|CDD|236641 PRK10019, PRK10019, nickel/cobalt efflux protein RcnA; Provisional

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 158 HVDNSHCATHHHESAHGHHEGHHHNHMHDSAVSS 191
              + H   H H+  H HH  H H+H H+   ++
Sbjct: 118 ENMHHHDHDHDHDHDHEHHHDHGHHHHHEHGATA 151

Length = 279

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	284
KOG2743	391	consensus Cobalamin synthesis protein [Coenzyme tr	100.0
COG0523	323	Putative GTPases (G3E family) [General function pr	100.0
PRK11537	318	putative GTP-binding protein YjiA; Provisional	100.0
TIGR02475	341	CobW cobalamin biosynthesis protein CobW. A broade	100.0
PF02492	178	cobW: CobW/HypB/UreG, nucleotide-binding domain; I	99.95
cd03112	158	CobW_like The function of this protein family is u	99.91
PF07683	94	CobW_C: Cobalamin synthesis protein cobW C-termina	99.79
smart00833	92	CobW_C Cobalamin synthesis protein cobW C-terminal	99.77
TIGR00101	199	ureG urease accessory protein UreG. This model rep	99.6
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	99.49
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	99.45
COG0378	202	HypB Ni2+-binding GTPase involved in regulation of	98.38
PRK09435	332	membrane ATPase/protein kinase; Provisional	98.33
COG2403	449	Predicted GTPase [General function prediction only	98.22
COG1159	298	Era GTPase [General function prediction only]	98.09
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	97.79
PRK00089	292	era GTPase Era; Reviewed	97.63
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	97.42
PRK13768	253	GTPase; Provisional	97.27
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	97.27
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	97.18
PRK15494	339	era GTPase Era; Provisional	96.82
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	96.81
cd01895	174	EngA2 EngA2 subfamily. This CD represents the seco	96.7
cd00881	189	GTP_translation_factor GTP translation factor fami	96.56
cd03114	148	ArgK-like The function of this protein family is u	96.49
cd04167	213	Snu114p Snu114p subfamily. Snu114p is one of sever	96.41
PRK09866	741	hypothetical protein; Provisional	96.34
cd00880	163	Era_like Era (E. coli Ras-like protein)-like. This	96.29
PRK00093	435	GTP-binding protein Der; Reviewed	96.06
TIGR03598	179	GTPase_YsxC ribosome biogenesis GTP-binding protei	95.65
PRK12298	390	obgE GTPase CgtA; Reviewed	95.59
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	95.56
TIGR03594	429	GTPase_EngA ribosome-associated GTPase EngA. EngA	95.49
COG1160	444	Predicted GTPases [General function prediction onl	95.34
cd01858	157	NGP_1 NGP-1. Autoantigen NGP-1 (Nucleolar G-protei	95.28
COG0218	200	Predicted GTPase [General function prediction only	95.03
COG2262	411	HflX GTPases [General function prediction only]	95.01
cd03115	173	SRP The signal recognition particle (SRP) mediates	94.96
cd04164	157	trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein	94.87
cd04178	172	Nucleostemin_like Nucleostemin-like. Nucleostemin	94.82
cd01888	203	eIF2_gamma eIF2-gamma (gamma subunit of initiation	94.7
PF02421	156	FeoB_N: Ferrous iron transport protein B; InterPro	94.68
PTZ00327	460	eukaryotic translation initiation factor 2 gamma s	94.65
PRK14974	336	cell division protein FtsY; Provisional	94.6
COG1084	346	Predicted GTPase [General function prediction only	94.57
cd01857	141	HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to t	94.57
cd01889	192	SelB_euk SelB subfamily. SelB is an elongation fac	94.54
cd01894	157	EngA1 EngA1 subfamily. This CD represents the firs	94.43
cd01884	195	EF_Tu EF-Tu subfamily. This subfamily includes ort	94.36
cd01898	170	Obg Obg subfamily. The Obg nucleotide binding prot	94.35
TIGR03156	351	GTP_HflX GTP-binding protein HflX. This protein fa	94.0
cd04105	203	SR_beta Signal recognition particle receptor, beta	93.94
cd01881	176	Obg_like The Obg-like subfamily consists of five w	93.82
cd01882	225	BMS1 Bms1. Bms1 is an essential, evolutionarily co	93.79
TIGR02729	329	Obg_CgtA Obg family GTPase CgtA. This model descri	93.78
PRK15467	158	ethanolamine utilization protein EutP; Provisional	93.78
PRK01889	356	GTPase RsgA; Reviewed	93.76
cd01876	170	YihA_EngB The YihA (EngB) subfamily. This subfamil	93.61
cd01879	158	FeoB Ferrous iron transport protein B (FeoB) subfa	93.47
TIGR00231	161	small_GTP small GTP-binding protein domain. This m	93.25
cd01849	155	YlqF_related_GTPase YlqF-related GTPases. These pr	93.23
PF00009	188	GTP_EFTU: Elongation factor Tu GTP binding domain;	93.04
PRK10512	614	selenocysteinyl-tRNA-specific translation factor;	93.03
cd04171	164	SelB SelB subfamily. SelB is an elongation factor	93.0
TIGR00064	272	ftsY signal recognition particle-docking protein F	92.93
PRK10416	318	signal recognition particle-docking protein FtsY;	92.88
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	92.85
PRK09554	772	feoB ferrous iron transport protein B; Reviewed	92.76
cd04165	224	GTPBP1_like GTPBP1-like. Mammalian GTP binding pro	92.73
KOG2484	435	consensus GTPase [General function prediction only	92.51
PRK12299	335	obgE GTPase CgtA; Reviewed	92.51
PRK00454	196	engB GTP-binding protein YsxC; Reviewed	92.27
cd01891	194	TypA_BipA TypA (tyrosine phosphorylated protein A)	92.25
cd00882	157	Ras_like_GTPase Ras-like GTPase superfamily. The R	92.21
cd01854	287	YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtil	92.13
cd04101	164	RabL4 RabL4 (Rab-like4) subfamily. RabL4s are nove	92.08
cd01883	219	EF1_alpha Eukaryotic elongation factor 1 (EF1) alp	91.99
cd04166	208	CysN_ATPS CysN_ATPS subfamily. CysN, together with	91.99
PRK00049	396	elongation factor Tu; Reviewed	91.97
TIGR00475	581	selB selenocysteine-specific elongation factor Sel	91.9
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	91.85
cd01887	168	IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryo	91.82
PRK12296	500	obgE GTPase CgtA; Reviewed	91.67
TIGR00959	428	ffh signal recognition particle protein. This mode	91.65
KOG1424	562	consensus Predicted GTP-binding protein MMR1 [Gene	91.52
cd01890	179	LepA LepA subfamily. LepA belongs to the GTPase fa	91.45
PLN03127	447	Elongation factor Tu; Provisional	91.03
KOG0462	650	consensus Elongation factor-type GTP-binding prote	90.99
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	90.96
PRK05124	474	cysN sulfate adenylyltransferase subunit 1; Provis	90.87
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	90.78
cd04142	198	RRP22 RRP22 subfamily. RRP22 (Ras-related protein	90.7
TIGR02528	142	EutP ethanolamine utilization protein, EutP. This	90.67
PRK10867	433	signal recognition particle protein; Provisional	90.67
cd01886	270	EF-G Elongation factor G (EF-G) subfamily. Translo	90.62
PRK04213	201	GTP-binding protein; Provisional	90.51
KOG0090	238	consensus Signal recognition particle receptor, be	90.46
cd04153	174	Arl5_Arl8 Arl5/Arl8 subfamily. Arl5 (Arf-like 5) a	90.43
PRK12289	352	GTPase RsgA; Reviewed	90.38
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	90.31
PF09439	181	SRPRB: Signal recognition particle receptor beta s	90.31
cd01859	156	MJ1464 MJ1464. This family represents archaeal GTP	90.25
PRK03003	472	GTP-binding protein Der; Reviewed	90.25
TIGR03596	276	GTPase_YlqF ribosome biogenesis GTP-binding protei	90.25
PRK12736	394	elongation factor Tu; Reviewed	90.22
cd04151	158	Arl1 Arl1 subfamily. Arl1 (Arf-like 1) localizes t	90.12
cd01885	222	EF2 EF2 (for archaea and eukarya). Translocation r	89.99
PRK04000	411	translation initiation factor IF-2 subunit gamma;	89.9
cd04154	173	Arl2 Arl2 subfamily. Arl2 (Arf-like 2) GTPases are	89.69
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	89.63
PRK05291	449	trmE tRNA modification GTPase TrmE; Reviewed	89.63
cd01856	171	YlqF YlqF. Proteins of the YlqF family contain all	89.56
PRK12735	396	elongation factor Tu; Reviewed	89.4
TIGR00437	591	feoB ferrous iron transporter FeoB. FeoB (773 amin	89.32
TIGR00485	394	EF-Tu translation elongation factor TU. This align	89.13
CHL00071	409	tufA elongation factor Tu	88.99
PRK09518	712	bifunctional cytidylate kinase/GTPase Der; Reviewe	88.99
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	88.97
PRK12297	424	obgE GTPase CgtA; Reviewed	88.62
KOG0780	483	consensus Signal recognition particle, subunit Srp	88.58
TIGR00157	245	ribosome small subunit-dependent GTPase A. The Aqu	88.49
PRK09563	287	rbgA GTPase YlqF; Reviewed	88.3
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	88.17
cd00878	158	Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-lik	88.03
COG3276	447	SelB Selenocysteine-specific translation elongatio	87.76
cd01860	163	Rab5_related Rab5-related subfamily. This subfamil	87.61
cd03110	179	Fer4_NifH_child This protein family's function is	87.38
smart00178	184	SAR Sar1p-like members of the Ras-family of small	87.24
COG1161	322	Predicted GTPases [General function prediction onl	87.19
cd04145	164	M_R_Ras_like M-Ras/R-Ras-like subfamily. This subf	87.15
cd04161	167	Arl2l1_Arl13_like Arl2l1/Arl13 subfamily. Arl2l1 (	87.03
cd00550	254	ArsA_ATPase Oxyanion-translocating ATPase (ArsA).	86.98
cd00154	159	Rab Rab family. Rab GTPases form the largest famil	86.7
TIGR02034	406	CysN sulfate adenylyltransferase, large subunit. H	86.32
PRK00098	298	GTPase RsgA; Reviewed	85.89
cd04158	169	ARD1 ARD1 subfamily. ARD1 (ADP-ribosylation factor	85.89
TIGR00483	426	EF-1_alpha translation elongation factor EF-1 alph	85.83
cd01852	196	AIG1 AIG1 (avrRpt2-induced gene 1). This represent	85.39
cd01864	165	Rab19 Rab19 subfamily. Rab19 proteins are associat	85.37
cd01869	166	Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in ev	85.33
TIGR00484	689	EF-G translation elongation factor EF-G. After pep	85.33
cd04150	159	Arf1_5_like Arf1-Arf5-like subfamily. This subfami	85.26
cd04110	199	Rab35 Rab35 subfamily. Rab35 is one of several Rab	85.21
PTZ00141	446	elongation factor 1- alpha; Provisional	85.11
cd01863	161	Rab18 Rab18 subfamily. Mammalian Rab18 is implicat	85.05
cd04149	168	Arf6 Arf6 subfamily. Arf6 (ADP ribosylation factor	84.95
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	84.81
cd04168	237	TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), T	84.65
PRK11058	426	GTPase HflX; Provisional	84.61
cd04170	268	EF-G_bact Elongation factor G (EF-G) subfamily. Tr	84.6
PRK00007	693	elongation factor G; Reviewed	83.95
COG1160	444	Predicted GTPases [General function prediction onl	83.86
PRK00771	437	signal recognition particle protein Srp54; Provisi	83.8
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	83.75
KOG1954	532	consensus Endocytosis/signaling protein EHD1 [Sign	83.72
PTZ00099	176	rab6; Provisional	83.42
COG5257	415	GCD11 Translation initiation factor 2, gamma subun	83.37
cd01850	276	CDC_Septin CDC/Septin. Septins are a conserved fam	83.27
cd04157	162	Arl6 Arl6 subfamily. Arl6 (Arf-like 6) forms a sub	83.24
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	83.19
PRK12739	691	elongation factor G; Reviewed	83.15
cd01866	168	Rab2 Rab2 subfamily. Rab2 is localized on cis-Golg	83.15
cd01893	166	Miro1 Miro1 subfamily. Miro (mitochondrial Rho) pr	83.1
PRK05506	632	bifunctional sulfate adenylyltransferase subunit 1	83.05
PLN03118	211	Rab family protein; Provisional	82.73
cd04156	160	ARLTS1 ARLTS1 subfamily. ARLTS1 (Arf-like tumor su	82.71
PF00025	175	Arf: ADP-ribosylation factor family The prints ent	82.71
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	82.54
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	82.47
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	82.42
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	82.41
TIGR03680	406	eif2g_arch translation initiation factor 2 subunit	82.35
smart00177	175	ARF ARF-like small GTPases; ARF, ADP-ribosylation	82.35
cd01897	168	NOG NOG1 is a nucleolar GTP-binding protein presen	82.21
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	81.72
TIGR01007	204	eps_fam capsular exopolysaccharide family. This mo	81.61
cd04104	197	p47_IIGP_like p47 (47-kDa) family. The p47 GTPase	81.58
cd01855	190	YqeH YqeH. YqeH is an essential GTP-binding protei	81.04
cd04124	161	RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily	80.97
PTZ00416	836	elongation factor 2; Provisional	80.92
cd04169	267	RF3 RF3 subfamily. Peptide chain release factor 3	80.78
cd04106	162	Rab23_lke Rab23-like subfamily. Rab23 is a member	80.75
PF00919	98	UPF0004: Uncharacterized protein family UPF0004; I	80.75
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	80.7
cd04115	170	Rab33B_Rab33A Rab33B/Rab33A subfamily. Rab33B is u	80.62
TIGR00503	527	prfC peptide chain release factor 3. This translat	80.62
PLN00116	843	translation elongation factor EF-2 subunit; Provis	80.59
COG1217	603	TypA Predicted membrane GTPase involved in stress	80.59
PLN03126	478	Elongation factor Tu; Provisional	80.57
cd01861	161	Rab6 Rab6 subfamily. Rab6 is involved in microtubu	80.43
cd04162	164	Arl9_Arfrp2_like Arl9/Arfrp2-like subfamily. Arl9	80.38
PTZ00133	182	ADP-ribosylation factor; Provisional	80.24
cd04137	180	RheB Rheb (Ras Homolog Enriched in Brain) subfamil	80.17

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

Probab=100.00  E-value=7.1e-55  Score=368.02  Aligned_cols=267  Identities=42%  Similarity=0.737  Sum_probs=235.8

Q ss_pred             CCCCceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhh
Q 023301            1 MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNE   80 (284)
Q Consensus         1 eL~~GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~   80 (284)
                      +|+|||+|||++++++.+|.++++ +++++|+|++||||+|+|+||+++||.+..+...+.|++||||||+.+....+++
T Consensus       118 ~L~NGClCCtVk~~gvraie~lvq-kkGkfD~IllETTGlAnPaPia~~Fw~dd~l~sdVkLDGIVTvvD~K~~~~~Lde  196 (391)
T KOG2743|consen  118 ELRNGCLCCTVKDNGVRAIENLVQ-KKGKFDHILLETTGLANPAPIASMFWLDDELGSDVKLDGIVTVVDAKHILKHLDE  196 (391)
T ss_pred             HhcCCeEEEEecchHHHHHHHHHh-cCCCcceEEEeccCCCCcHHHHHHHhhhhhhcCceeeeeEEEEEehhhHHhhhcc
Confidence            589999999999999999999999 5899999999999999999999999999999999999999999999999999998


Q ss_pred             cCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCCChhhhhcCCCCCccccccccccc
Q 023301           81 VKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVD  160 (284)
Q Consensus        81 ~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~~  160 (284)
                      ..+....+++..||++||.|++||+|+++++++..+++.|+.+|.-|+++.|.||++|+..+++...||...... ..+.
T Consensus       197 ~k~~g~i~EA~~QiA~AD~II~NKtDli~~e~~~~l~q~I~~INslA~m~~Tky~~vdlsnvLdi~ayds~ss~n-l~~k  275 (391)
T KOG2743|consen  197 EKPDGLINEATRQIALADRIIMNKTDLVSEEEVKKLRQRIRSINSLAQMIETKYSRVDLSNVLDIHAFDSESSIN-LDKK  275 (391)
T ss_pred             cCcccchHHHHHHHhhhheeeeccccccCHHHHHHHHHHHHHhhhHHHhhhhhhccccHHHhcccccccccccch-hhhh
Confidence            888777788999999999999999999999999999999999999999999999999999999999998652111 1110


Q ss_pred             CCcccccCCcCCCCCCCCCCCCCCCCCCeEEEEEEeCCCCCHHHHHHHHHHHHHH---hCCc----eEEEEEEEEecCCC
Q 023301          161 NSHCATHHHESAHGHHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEE---KGED----LYRMKGILSVSGSE  233 (284)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~l~~~l~~l~~~---~~~~----i~R~KG~v~~~~~~  233 (284)
                          ..|         .++. ..+++.++.|+++.+++-.+.+.+..||+.++|.   ....    |||+||++.+.+.+
T Consensus       276 ----~~~---------~~~~-~~h~d~~i~ti~~~~~~~~~~E~~n~wl~~lLw~~~~r~eD~~~evyR~KGllsi~d~~  341 (391)
T KOG2743|consen  276 ----LQH---------SGGT-QIHLDQSIGTITFEVPGLAKEEHLNMWLQNLLWEKNVRSEDNHMEVYRLKGLLSIKDKD  341 (391)
T ss_pred             ----hcc---------CCCC-CcccCCCcceEEEEeCCccCHHHHHHHHHHHHHhhhhcccccceeEEEeeeeEEeccCC
Confidence                000         1111 1223678999999999999999999999999987   3344    99999999998889


Q ss_pred             eeEEEEccceeeecCCCCCCCCCCCCccEEEEEecCCCHHHHHHHHhhhhC
Q 023301          234 QQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCLA  284 (284)
Q Consensus       234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lv~IG~~ld~~~l~~~l~~c~~  284 (284)
                      .++.||||...|+..| ..|+....+.++|||||++|+++.|+..|.+|+.
T Consensus       342 ~~~i~QGV~e~~e~~P-~~w~~d~~~~~kiVliGknL~re~le~~~~~~l~  391 (391)
T KOG2743|consen  342 QQVIFQGVHELYEETP-VSWKKDFERTNKIVLIGKNLDKEILEQLFRATLT  391 (391)
T ss_pred             eeEEeechhhhhccCc-ccccccccccceEEEEecccCHHHHHHHHHhhcC
Confidence            9999999999999988 7798777788899999999999999999999974

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

Probab=100.00  E-value=1.1e-53  Score=377.64  Aligned_cols=264  Identities=39%  Similarity=0.702  Sum_probs=222.3

Q ss_pred             CCCCceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhh
Q 023301            1 MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNE   80 (284)
Q Consensus         1 eL~~GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~   80 (284)
                      ||+|||||||+++++.+++.+|.+ ++.+||+|+|||||+|+|.++++++..++.++..+.|++|||||||.+|...+..
T Consensus        57 El~nGCICCT~r~dl~~~~~~L~~-~~~~~D~ivIEtTGlA~P~pv~~t~~~~~~l~~~~~ld~vvtvVDa~~~~~~~~~  135 (323)
T COG0523          57 ELTNGCICCTVRDDLLPALERLLR-RRDRPDRLVIETTGLADPAPVIQTFLTDPELADGVRLDGVVTVVDAAHFLEGLDA  135 (323)
T ss_pred             EeCCceEEEeccchhHHHHHHHHh-ccCCCCEEEEeCCCCCCCHHHHHHhccccccccceeeceEEEEEeHHHhhhhHHH
Confidence            789999999999999999999998 4567999999999999999999999887789999999999999999999987653


Q ss_pred             cCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCCChhhhhcCCCCCccccccccccc
Q 023301           81 VKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVD  160 (284)
Q Consensus        81 ~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~~  160 (284)
                           +..++.+||++||+||+||+|++++++++.+++.++++||.|+|+.+++|.++...+++.+.|+..+.....  .
T Consensus       136 -----~~~~~~~Qia~AD~ivlNK~Dlv~~~~l~~l~~~l~~lnp~A~i~~~~~~~~~~~~ll~~~~~~~~~~~~~~--~  208 (323)
T COG0523         136 -----IAELAEDQLAFADVIVLNKTDLVDAEELEALEARLRKLNPRARIIETSYGDVDLAELLDEGLFDLDRDVGRT--S  208 (323)
T ss_pred             -----HHHHHHHHHHhCcEEEEecccCCCHHHHHHHHHHHHHhCCCCeEEEccccCCCHHHhhcccccccccccccc--C
Confidence                 336779999999999999999999999999999999999999999999999999999998888765511100  0


Q ss_pred             CCcccccCCcCCCCCCCCCCCCCCCCCCeEEEEEEeCCCCCHHHHHHHHHHHHHHhCCceEEEEEEEEec-CCCeeEEEE
Q 023301          161 NSHCATHHHESAHGHHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVS-GSEQQYVFQ  239 (284)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~l~~~l~~l~~~~~~~i~R~KG~v~~~-~~~~~~~~~  239 (284)
                          . +.      +.++|.|.|.+ .++.|+++.+.+|+++++|..|+..+.+..+.+++|+||++|+. +.+.++.+|
T Consensus       209 ----~-~~------~~~~h~h~~~~-~~i~s~~~~~~~p~~~~~l~~~l~~l~~~~~~~v~R~KG~~~~~~~~~~~~~~~  276 (323)
T COG0523         209 ----P-LF------SDHQHDHEHDE-GGISSFSVRADRPFDPERLEAFLDLLLSARGEKVLRAKGILWIAEGPPRRLVFQ  276 (323)
T ss_pred             ----c-cc------cccCCCchhcc-cCceEEEEecCCCCCHHHHHHHHHHHHhhccCceEEEeeEEecCCCCCeEEEEe
Confidence                0 00      00011111111 26999999999999999999999999877778999999999998 566678899


Q ss_pred             ccceeeecCC-CCCCCCCCCCccEEEEEecCCCHHHHHHHHhhhhC
Q 023301          240 GVHSTLDGCP-GKAWGPDEKRINKLVFIGRNLDETALRKGFKGCLA  284 (284)
Q Consensus       240 ~~~~~~~~~~-~~~~~~~~~~~~~lv~IG~~ld~~~l~~~l~~c~~  284 (284)
                      +++..++... ...|++.+.+.+++||||++++...++..+.+|+.
T Consensus       277 ~v~~~~~~~~~~~~~~~~~~~~s~lv~Ig~~~~~~~~~~~~~~~~~  322 (323)
T COG0523         277 GVGGVFEVPPAGREWPAEGDRKSRLVFIGRDLDDEAIREAFLAALL  322 (323)
T ss_pred             cccccccccccccccccccCccceEEEEecCcchHHHHHHHHHHhc
Confidence            9999887643 34676667889999999999999999999988863

>PRK11537 putative GTP-binding protein YjiA; Provisional

Probab=100.00  E-value=2.3e-52  Score=371.01  Aligned_cols=256  Identities=37%  Similarity=0.609  Sum_probs=212.6

Q ss_pred             CCCCceeeeeeCchHHHHHHHHHHh-h--cCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHh
Q 023301            1 MVNNGCLCCTVRGDLVKMLLQLAKK-K--QGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQH   77 (284)
Q Consensus         1 eL~~GCiCCs~~~dl~~~l~~l~~~-~--~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~   77 (284)
                      ||+||||||+++++|..+|.++++. +  ..+||+|||||||+|+|.+|++.++.++.+...+.+++||||||+.++..+
T Consensus        59 eL~~GCiCCs~~~~l~~~l~~l~~~~~~~~~~~d~IvIEttG~a~p~~i~~~~~~~~~l~~~~~l~~vvtvvDa~~~~~~  138 (318)
T PRK11537         59 TLTNGCICCSRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQRYLLDGVIALVDAVHADEQ  138 (318)
T ss_pred             EECCCEEEEccCchHHHHHHHHHHHHhccCCCCCEEEEECCCccCHHHHHHHHhcChhhcccEEeccEEEEEEhhhhhhh
Confidence            5899999999999999999999863 1  136999999999999999999999777788899999999999999999887


Q ss_pred             hhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCCChhhhhcCCCCCcccccccc
Q 023301           78 LNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEV  157 (284)
Q Consensus        78 l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v~~~~l~~~~~~~~~~~~~~~  157 (284)
                      +.+.      ..+.+||++||+||+||+|++++.  +++++.++.+||.|+|+.+.+|++++..+++...|+........
T Consensus       139 ~~~~------~~~~~Qi~~AD~IvlnK~Dl~~~~--~~~~~~l~~lnp~a~i~~~~~~~v~~~~l~~~~~~~~~~~~~~~  210 (318)
T PRK11537        139 MNQF------TIAQSQVGYADRILLTKTDVAGEA--EKLRERLARINARAPVYTVVHGDIDLSLLFNTNGFMLEENVVST  210 (318)
T ss_pred             cccc------HHHHHHHHhCCEEEEeccccCCHH--HHHHHHHHHhCCCCEEEEeccCCCCHHHHhCCCCcCcccccccc
Confidence            6542      356899999999999999999854  78999999999999999999999999999887655422110000


Q ss_pred             cccCCcccccCCcCCCCCCCCCCCCCCCCCCeEEEEEEeCCCCCHHHHHHHHHHHHHHhCCceEEEEEEEEecCCCeeEE
Q 023301          158 HVDNSHCATHHHESAHGHHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYV  237 (284)
Q Consensus       158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~l~~~l~~l~~~~~~~i~R~KG~v~~~~~~~~~~  237 (284)
                      ..               +.+++   +.|++++.|++++.++|+++++|..||+.+++..+++|||+||++|+.+.+.++.
T Consensus       211 ~~---------------~~~~~---~~~~~~i~s~~~~~~~p~~~~~l~~~L~~l~~~~~~~i~R~KG~v~~~~~~~~~~  272 (318)
T PRK11537        211 KP---------------RFHFI---ADKQNDISSIVVELDYPVDISEVSRVMENLLLESADKLLRYKGMLWIDGEPNRLL  272 (318)
T ss_pred             Cc---------------ccccC---CcccCceEEEEEEcCCCCCHHHHHHHHHHHHHhCCCceEEeeeEEEeCCCCCEEE
Confidence            00               00000   1122479999999999999999999999999888899999999999988877889


Q ss_pred             EEccceeeecCCCCCCCCCCCCccEEEEEecCCCHHHHHHHHhhhh
Q 023301          238 FQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCL  283 (284)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~lv~IG~~ld~~~l~~~l~~c~  283 (284)
                      ||+|+..+.......|. .+++.++|||||+++|+++|++.|++|.
T Consensus       273 ~q~v~~~~~~~~~~~~~-~~~~~~~lVfIG~~ld~~~l~~~l~~l~  317 (318)
T PRK11537        273 FQGVQRLYSADWDRPWG-DETPHSTLVFIGIQLPEEEIRAAFAGLR  317 (318)
T ss_pred             EEEehhhcccCccccCC-CCCCceEEEEEcCCCCHHHHHHHHHhhc
Confidence            99999888655444674 4456789999999999999999998764

>TIGR02475 CobW cobalamin biosynthesis protein CobW

Probab=100.00  E-value=2.2e-50  Score=361.85  Aligned_cols=259  Identities=32%  Similarity=0.514  Sum_probs=205.7

Q ss_pred             CCCCceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhh
Q 023301            1 MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNE   80 (284)
Q Consensus         1 eL~~GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~   80 (284)
                      ||+|||||||++++|..+|.+++.. +.+||+|+|||||+|+|.+|+++|.. +.+...+.+++||||||+.++..+...
T Consensus        65 el~nGCiCCs~~~dl~~~l~~l~~~-~~~~d~IvIEtsG~a~P~~i~~~~~~-~~l~~~~~l~~vvtvVDa~~~~~~~~~  142 (341)
T TIGR02475        65 ELANGCICCTVADDFIPTMTKLLAR-RQRPDHILIETSGLALPKPLVQAFQW-PEIRSRVTVDGVVTVVDGPAVAAGRFA  142 (341)
T ss_pred             EeCCCCccccCcHHHHHHHHHHHhc-cCCCCEEEEeCCCCCCHHHHHHHhcC-ccccceEEeeeEEEEEECchhhhhccc
Confidence            5899999999999999999999862 57899999999999999999999854 678889999999999999987642110


Q ss_pred             c----------------CCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCC-CceeeeccCCCChhhhh
Q 023301           81 V----------------KPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAM-APVKLAKYGSVDMDFVL  143 (284)
Q Consensus        81 ~----------------~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~-a~i~~~~~g~v~~~~l~  143 (284)
                      .                ..+.+...+.+||++||+||+||+|++++++++.+++.|+++||. ++|+.+.+|++++..++
T Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~Qi~~AD~IvlnK~Dl~~~~~l~~~~~~l~~~~~~~a~i~~~~~~~v~~~~ll  222 (341)
T TIGR02475       143 ADPDALDAQRAADDNLDHETPLEELFEDQLACADLVILNKADLLDAAGLARVRAEIAAELPRAVKIVEASHGEVDARVLL  222 (341)
T ss_pred             cchhhhhhhccccccccccchHHHHHHHHHHhCCEEEEeccccCCHHHHHHHHHHHHHhCCCCCEEEEcccCCCCHHHHh
Confidence            0                011233466899999999999999999999999999999998885 68999999999999999


Q ss_pred             cCCCCCcccccccccccCCcccccCCcCCCCCCCCCCCCCCCCCCeEEEEEEeCCCCCHHHHHHHHHHHHHHhCCceEEE
Q 023301          144 GVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRM  223 (284)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~l~~~l~~l~~~~~~~i~R~  223 (284)
                      +...++......  .      ..+ ++.   +  .+ +.|.| +++.|++++.++|+++++|..||+.+++  +.+|||+
T Consensus       223 ~~~~~~~~~~~~--~------~~~-~~~---~--~~-~~~~~-~~i~s~~~~~~~p~~~~~~~~~L~~l~~--~~~i~R~  284 (341)
T TIGR02475       223 GLGAAAEDDLDN--R------PSH-HDF---E--GG-EEHDH-DEFDSVVVDLGEVADPAALRQRLERLAE--EHDVLRI  284 (341)
T ss_pred             CCCCcChhhhhc--C------ccc-ccc---c--CC-CCCCC-CCEEEEEEEcCCCCCHHHHHHHHHhhcc--cCceEEe
Confidence            875443211100  0      000 000   0  00 11222 4799999999999999999999999863  2579999


Q ss_pred             EEEEEecCCCeeEEEEccceeeecCCCCCCCCCCCCccEEEEEecC-CCHHHHHHHH
Q 023301          224 KGILSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGRN-LDETALRKGF  279 (284)
Q Consensus       224 KG~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lv~IG~~-ld~~~l~~~l  279 (284)
                      ||++|+.+.+.++.||+|+..++......|.+.+++.++|||||++ ++++.|++.|
T Consensus       285 KGiv~~~~~~~~~~~q~v~~~~~~~~~~~~~~~~~~~~~lV~IG~~~ld~~~l~~~l  341 (341)
T TIGR02475       285 KGFAAVPGKPMRLLVQGVGQRVDSYYDRPWQAAETRQTRLVVIGLHDLDQAAIRAAL  341 (341)
T ss_pred             eEEEEeCCCCcEEEEEcccceeccCcccCCCCCCCCCceEEEEecCCCCHHHHHhhC
Confidence            9999999888889999999988765555686555667899999999 9999998764

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

>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=99.95  E-value=1.5e-28  Score=202.13  Aligned_cols=119  Identities=41%  Similarity=0.710  Sum_probs=98.5

Q ss_pred             CCCCceeeeeeCchHHHHHHHHHHhhcC--CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhh
Q 023301            1 MVNNGCLCCTVRGDLVKMLLQLAKKKQG--QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHL   78 (284)
Q Consensus         1 eL~~GCiCCs~~~dl~~~l~~l~~~~~~--~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l   78 (284)
                      +|+|||+||+++++|..+|.++..  .+  +||+||||+||+++|.++  .+. .+.+...+.++.+|+||||.+|... 
T Consensus        56 ~l~~gcicc~~~~~~~~~l~~l~~--~~~~~~d~IiIE~sG~a~p~~l--~~~-~~~~~~~~~~~~iI~vVDa~~~~~~-  129 (178)
T PF02492_consen   56 ELNNGCICCTLRDDLVEALRRLLR--EYEERPDRIIIETSGLADPAPL--ILQ-DPPLKEDFRLDSIITVVDATNFDEL-  129 (178)
T ss_dssp             EECTTTESS-TTS-HHHHHHHHCC--CCHGC-SEEEEEEECSSGGGGH--HHH-SHHHHHHESESEEEEEEEGTTHGGH-
T ss_pred             EecCCCcccccHHHHHHHHHHHHH--hcCCCcCEEEECCccccccchh--hhc-cccccccccccceeEEecccccccc-
Confidence            478999999999999999999998  67  899999999999999998  222 5678889999999999999998433 


Q ss_pred             hhcCCccchHHHHHHHhhcCEEEEccCCCCChhH-HHHHHHHHHHhCCCCcee
Q 023301           79 NEVKPRFVVNEAVEQVAYADRIILNKIDLVTETE-LGSLTERIKHINAMAPVK  130 (284)
Q Consensus        79 ~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~-~~~~~~~l~~~np~a~i~  130 (284)
                      .+     ....+.+||++||+||+||+|++++++ ++++++.++++||.|+|+
T Consensus       130 ~~-----~~~~~~~Qi~~ADvIvlnK~D~~~~~~~i~~~~~~ir~lnp~a~Iv  177 (178)
T PF02492_consen  130 EN-----IPELLREQIAFADVIVLNKIDLVSDEQKIERVREMIRELNPKAPIV  177 (178)
T ss_dssp             TT-----HCHHHHHHHCT-SEEEEE-GGGHHHH--HHHHHHHHHHH-TTSEEE
T ss_pred             cc-----chhhhhhcchhcCEEEEeccccCChhhHHHHHHHHHHHHCCCCEEe
Confidence            22     236679999999999999999999884 599999999999999986

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.

>cd03112 CobW_like The function of this protein family is unkown

Probab=99.91  E-value=1.4e-24  Score=175.02  Aligned_cols=101  Identities=60%  Similarity=0.961  Sum_probs=89.1

Q ss_pred             CCCCceeeeeeCchHHHHHHHHHHh---hcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHh
Q 023301            1 MVNNGCLCCTVRGDLVKMLLQLAKK---KQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQH   77 (284)
Q Consensus         1 eL~~GCiCCs~~~dl~~~l~~l~~~---~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~   77 (284)
                      ||+|||+||+++++|..+|.++++.   +.++||+|||||||+++|.++++.++.++.+...+.++.+++|||+.++..+
T Consensus        55 ~l~~GCiCC~~~~~l~~~l~~l~~~~~~~~~~~d~I~IEt~G~~~p~~~~~~~~~~~~~~~~~~~d~vv~vvDa~~~~~~  134 (158)
T cd03112          55 EMNNGCICCTVRGDLIRALLDLLERLDAGKIAFDRIVIETTGLADPGPVAQTFFMDEELAERYLLDGVITLVDAKHANQH  134 (158)
T ss_pred             EeCCCEeEeeCchhHHHHHHHHHHHHHhccCCCCEEEEECCCcCCHHHHHHHHhhchhhhcceeeccEEEEEEhhHhHHH
Confidence            5899999999999999999766541   2578999999999999999999988766778889999999999999999998


Q ss_pred             hhhcCCccchHHHHHHHhhcCEEEEccCCC
Q 023301           78 LNEVKPRFVVNEAVEQVAYADRIILNKIDL  107 (284)
Q Consensus        78 l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~  107 (284)
                      ++++      +.+.+||++||+||+||+|+
T Consensus       135 ~~~~------~~~~~Qi~~ad~ivlnk~dl  158 (158)
T cd03112         135 LDQQ------TEAQSQIAFADRILLNKTDL  158 (158)
T ss_pred             hhcc------HHHHHHHHHCCEEEEecccC
Confidence            7653      46789999999999999996

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.

>PF07683 CobW_C: Cobalamin synthesis protein cobW C-terminal domain; InterPro: IPR011629 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt

Probab=99.79  E-value=5.4e-19  Score=130.08  Aligned_cols=91  Identities=41%  Similarity=0.719  Sum_probs=69.3

Q ss_pred             eEEEEEEeCCCCCHHHHHHHHHHHHHHhCCceEEEEEEEEecCCCeeEEEEccceeeecCCCCC-CCC--CCCCccEEEE
Q 023301          189 VSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQGVHSTLDGCPGKA-WGP--DEKRINKLVF  265 (284)
Q Consensus       189 ~~s~~~~~~~~~~~~~l~~~l~~l~~~~~~~i~R~KG~v~~~~~~~~~~~~~~~~~~~~~~~~~-~~~--~~~~~~~lv~  265 (284)
                      |.|+++..++|+++++|..||+.    .+++|||+||++++++.+..+.||++++.+++.+... |.+  ..++.++|||
T Consensus         1 i~s~~~~~~~p~~~~~l~~~l~~----~~~~vlR~KG~v~~~~~~~~~~~q~v~~~~~~~~~~~~~~~~~~~~~~~~lV~   76 (94)
T PF07683_consen    1 ISSVTFEFDRPFDPERLEAWLQE----LPGDVLRAKGIVWVADGPRRLVFQGVGGRYDIEPAGRWWPPMLGEDRDSRLVF   76 (94)
T ss_dssp             EEEEEEEESS-B-HHHHHHHHHH----TTTTEEEEEEEE-BTT-SEEEEEEEETTEEEEE-EEEE-TT---S---EEEEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHh----CCCCEEEEEEEEEeCCcCeEEEEEeeCCEEEecccccccccccCCCCCeEEEE
Confidence            67999999999999999999998    3599999999999998877899999999998876543 433  3567899999


Q ss_pred             EecCCCHHHHHHHHhhhh
Q 023301          266 IGRNLDETALRKGFKGCL  283 (284)
Q Consensus       266 IG~~ld~~~l~~~l~~c~  283 (284)
                      ||+++|+++|++.|++||
T Consensus        77 IG~~ld~~~l~~~l~~cl   94 (94)
T PF07683_consen   77 IGKNLDKEALREALDACL   94 (94)
T ss_dssp             EEES--HHHHHHHHHT--
T ss_pred             EECCCCHHHHHHHHHccC
Confidence            999999999999999997

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 the C-terminal domain found in CobW, as well as in P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [].; PDB: 1NIJ_A.

>smart00833 CobW_C Cobalamin synthesis protein cobW C-terminal domain

Probab=99.77  E-value=7e-18  Score=123.57  Aligned_cols=91  Identities=31%  Similarity=0.485  Sum_probs=80.1

Q ss_pred             eEEEEEEeCCCCCHHHHHHHHHHHHHHhCCceEEEEEEEEecCCC-eeEEEEccceeeecCCCCCCCCCCCCccEEEEEe
Q 023301          189 VSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSE-QQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIG  267 (284)
Q Consensus       189 ~~s~~~~~~~~~~~~~l~~~l~~l~~~~~~~i~R~KG~v~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lv~IG  267 (284)
                      +.|+++..+.|+++++|..||+.++    ++|+|+||++++.+.+ .++.||++++.++..+...|.+.+++.++|||||
T Consensus         1 ~~s~~~~~~~~~~~~~l~~~l~~l~----~~i~R~KG~v~~~~~~~~~~~~q~v~~~~~~~~~~~~~~~~~~~~~lV~IG   76 (92)
T smart00833        1 ISSFVYRARRPFHPQRLLAALDELP----EGVLRAKGFFWLASRPDLPGVLSGAGGRLRIEPAGAWPAAGDRRTRLVFIG   76 (92)
T ss_pred             CEEEEEecCCCCCHHHHHHHHHhcc----CCeEEEEEEEEeCCCCCeEEEEEccCCeeEcccCCCCCCCCCcceEEEEEe
Confidence            3678899999999999999999886    7899999999998765 6689999999988876667876556678999999


Q ss_pred             cCCCHHHHHHHHhhhh
Q 023301          268 RNLDETALRKGFKGCL  283 (284)
Q Consensus       268 ~~ld~~~l~~~l~~c~  283 (284)
                      +++|++.|++.|.+|+
T Consensus        77 ~~l~~~~l~~~l~~~~   92 (92)
T smart00833       77 RDLDEEAIRAALDACL   92 (92)
T ss_pred             CCCCHHHHHHHHHHhC
Confidence            9999999999999985

CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis PUBMED:12869542. 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 the C-terminal domain found in CobW, as well as in P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression PUBMED:7765511.

>TIGR00101 ureG urease accessory protein UreG

Probab=99.60  E-value=2.7e-15  Score=125.38  Aligned_cols=120  Identities=20%  Similarity=0.347  Sum_probs=88.9

Q ss_pred             CCceeeeeeCchHH---HHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhh
Q 023301            3 NNGCLCCTVRGDLV---KMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLN   79 (284)
Q Consensus         3 ~~GCiCCs~~~dl~---~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~   79 (284)
                      .|||+||+.++++.   .+|.++.. +..++|+|+||++|..    +...+  .+.+     .+.+|+|+|+.++.....
T Consensus        63 ~~g~~~~~~~~~~~~~~~~L~~l~~-~~~~~D~iiIEt~G~~----l~~~~--~~~l-----~~~~i~vvD~~~~~~~~~  130 (199)
T TIGR00101        63 TGGCPHTAIREDASMNLEAVAEMEA-RFPPLEMVFIESGGDN----LSATF--SPEL-----ADLTIFVIDVAAGDKIPR  130 (199)
T ss_pred             cCCCccceeccCHHHHHHHHHHHHh-cCCCCCEEEEECCCCC----ccccc--chhh-----hCcEEEEEEcchhhhhhh
Confidence            68999999999994   55666654 1347999999999962    22222  1222     356899999998765321


Q ss_pred             hcCCccchHHHHHHHhhcCEEEEccCCCCC--hhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301           80 EVKPRFVVNEAVEQVAYADRIILNKIDLVT--ETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus        80 ~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~--~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                               ....|+..||++++||+|+.+  +++++.+.+.++.+||.++++.++. .....+.++
T Consensus       131 ---------~~~~qi~~ad~~~~~k~d~~~~~~~~~~~~~~~~~~~~~~~~i~~~Sa~~g~gi~el~  188 (199)
T TIGR00101       131 ---------KGGPGITRSDLLVINKIDLAPMVGADLGVMERDAKKMRGEKPFIFTNLKTKEGLDTVI  188 (199)
T ss_pred             ---------hhHhHhhhccEEEEEhhhccccccccHHHHHHHHHHhCCCCCEEEEECCCCCCHHHHH
Confidence                     124799999999999999986  3678899999999999999998763 344455444

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.

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=99.49  E-value=7e-14  Score=121.78  Aligned_cols=119  Identities=20%  Similarity=0.223  Sum_probs=86.6

Q ss_pred             CCCCceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecCCC-CCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhh
Q 023301            1 MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGL-AKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLN   79 (284)
Q Consensus         1 eL~~GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG~-a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~   79 (284)
                      ++++||+||..+.++..++..|..   .+.|+||||++|. +.|..+        .+...+.+    +|++.......  
T Consensus       159 qi~tG~~Chl~a~mv~~Al~~L~~---~~~d~liIEnvGnLvcPa~f--------dlge~~~v----~vlsV~eg~dk--  221 (290)
T PRK10463        159 QVNTGKGCHLDAQMIADAAPRLPL---DDNGILFIENVGNLVCPASF--------DLGEKHKV----AVLSVTEGEDK--  221 (290)
T ss_pred             EecCCCCCcCcHHHHHHHHHHHhh---cCCcEEEEECCCCccCCCcc--------chhhceeE----EEEECcccccc--
Confidence            478999999999999999998865   5789999999995 677742        23333443    44444433211  


Q ss_pred             hcCCccchHHHHHHHhhcCEEEEccCCCCC--hhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301           80 EVKPRFVVNEAVEQVAYADRIILNKIDLVT--ETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus        80 ~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~--~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                         +    .....|++.||+|||||+|+++  ..+++.+.+.++++||.++|+.++. .....+.|.
T Consensus       222 ---p----lKyp~~f~~ADIVVLNKiDLl~~~~~dle~~~~~lr~lnp~a~I~~vSA~tGeGld~L~  281 (290)
T PRK10463        222 ---P----LKYPHMFAAASLMLLNKVDLLPYLNFDVEKCIACAREVNPEIEIILISATSGEGMDQWL  281 (290)
T ss_pred             ---c----hhccchhhcCcEEEEEhHHcCcccHHHHHHHHHHHHhhCCCCcEEEEECCCCCCHHHHH
Confidence               1    1124799999999999999987  4578889999999999999998653 334444443

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=99.45  E-value=2.3e-13  Score=114.61  Aligned_cols=119  Identities=23%  Similarity=0.259  Sum_probs=80.2

Q ss_pred             CCCCceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecCC-CCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhh
Q 023301            1 MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTG-LAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLN   79 (284)
Q Consensus         1 eL~~GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG-~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~   79 (284)
                      ++++||+||....++..++.++..   .++|+|+||||| +..|...        .+...+    .++|+|+......+.
T Consensus        77 ~l~~gcic~~~~~~~~~~l~~~~~---~~~d~IiIEt~G~l~~~~~~--------~~~~~~----~i~Vvd~~~~d~~~~  141 (207)
T TIGR00073        77 QINTGKECHLDAHMVAHALEDLPL---DDIDLLFIENVGNLVCPADF--------DLGEHM----RVVLLSVTEGDDKPL  141 (207)
T ss_pred             EEcCCCcccCChHHHHHHHHHhcc---CCCCEEEEecCCCcCCCccc--------ccccCe----EEEEEecCcccchhh
Confidence            478999999776666666765543   478999999999 4444311        111222    247888875432211


Q ss_pred             hcCCccchHHHHHHHhhcCEEEEccCCCCCh--hHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301           80 EVKPRFVVNEAVEQVAYADRIILNKIDLVTE--TELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus        80 ~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~--~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                               ....++..|++|++||+|+.+.  .+...+.+.++++||.++++.++. .......++
T Consensus       142 ---------~~~~~~~~a~iiv~NK~Dl~~~~~~~~~~~~~~l~~~~~~~~i~~~Sa~~g~gv~~l~  199 (207)
T TIGR00073       142 ---------KYPGMFKEADLIVINKADLAEAVGFDVEKMKADAKKINPEAEIILMSLKTGEGLDEWL  199 (207)
T ss_pred             ---------hhHhHHhhCCEEEEEHHHccccchhhHHHHHHHHHHhCCCCCEEEEECCCCCCHHHHH
Confidence                     1246788999999999999864  346778888999999999987753 333444443

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

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

Probab=98.38  E-value=6.9e-07  Score=72.95  Aligned_cols=98  Identities=19%  Similarity=0.280  Sum_probs=68.6

Q ss_pred             HHHHHHHHHHhhcCCCCEEEEecCC-CCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH
Q 023301           15 LVKMLLQLAKKKQGQFDHIVIETTG-LAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ   93 (284)
Q Consensus        15 l~~~l~~l~~~~~~~~d~iiIE~sG-~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q   93 (284)
                      ...++.++..+ ....|.+|||.-| ++.|..        |.+.+.+    -|+|+|...-.....-.+         .-
T Consensus        83 ~~~ai~~l~~~-~~~~Dll~iEs~GNL~~~~s--------p~L~d~~----~v~VidvteGe~~P~K~g---------P~  140 (202)
T COG0378          83 NLEAIEELVLD-FPDLDLLFIESVGNLVCPFS--------PDLGDHL----RVVVIDVTEGEDIPRKGG---------PG  140 (202)
T ss_pred             HHHHHHHHhhc-CCcCCEEEEecCcceecccC--------cchhhce----EEEEEECCCCCCCcccCC---------Cc
Confidence            36678888872 2237999999999 555532        4443323    588999987543211111         22


Q ss_pred             HhhcCEEEEccCCCCChhH--HHHHHHHHHHhCCCCceeeecc
Q 023301           94 VAYADRIILNKIDLVTETE--LGSLTERIKHINAMAPVKLAKY  134 (284)
Q Consensus        94 i~~Ad~ivlnK~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~  134 (284)
                      +..||++||||+|+++.-.  ++.+.+.+++.||+++|+.++.
T Consensus       141 i~~aDllVInK~DLa~~v~~dlevm~~da~~~np~~~ii~~n~  183 (202)
T COG0378         141 IFKADLLVINKTDLAPYVGADLEVMARDAKEVNPEAPIIFTNL  183 (202)
T ss_pred             eeEeeEEEEehHHhHHHhCccHHHHHHHHHHhCCCCCEEEEeC
Confidence            3349999999999987544  5889999999999999998863

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=98.33  E-value=5.4e-06  Score=74.37  Aligned_cols=104  Identities=19%  Similarity=0.250  Sum_probs=63.1

Q ss_pred             eeeeCc--hHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCcc
Q 023301            8 CCTVRG--DLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRF   85 (284)
Q Consensus         8 CCs~~~--dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~   85 (284)
                      ||.+.+  +......+++.  ...+|+|||||.|+......+-.           ..|.++.|+++..-.. +.      
T Consensus       127 ~~~l~~~a~~~~~~~~~~~--~~g~d~viieT~Gv~qs~~~i~~-----------~aD~vlvv~~p~~gd~-iq------  186 (332)
T PRK09435        127 SGTLGGVARKTRETMLLCE--AAGYDVILVETVGVGQSETAVAG-----------MVDFFLLLQLPGAGDE-LQ------  186 (332)
T ss_pred             cccccchHHHHHHHHHHHh--ccCCCEEEEECCCCccchhHHHH-----------hCCEEEEEecCCchHH-HH------
Confidence            788764  34444444555  57899999999999976543211           2344666766444222 11      


Q ss_pred             chHHHHHHHhhcCEEEEccCCCCChhHHHH----HHHHHHHhCCC-----Cceeeec
Q 023301           86 VVNEAVEQVAYADRIILNKIDLVTETELGS----LTERIKHINAM-----APVKLAK  133 (284)
Q Consensus        86 ~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~----~~~~l~~~np~-----a~i~~~~  133 (284)
                        .....+++.||++|+||+|+.+.....+    +++.++-.+|.     .+|+.++
T Consensus       187 --~~k~gi~E~aDIiVVNKaDl~~~~~a~~~~~el~~~L~l~~~~~~~w~~pVi~vS  241 (332)
T PRK09435        187 --GIKKGIMELADLIVINKADGDNKTAARRAAAEYRSALRLLRPKDPGWQPPVLTCS  241 (332)
T ss_pred             --HHHhhhhhhhheEEeehhcccchhHHHHHHHHHHHHHhcccccccCCCCCEEEEE
Confidence              1224599999999999999987544333    34444433332     4566544

>COG2403 Predicted GTPase [General function prediction only]

Probab=98.22  E-value=3.7e-06  Score=74.70  Aligned_cols=94  Identities=24%  Similarity=0.271  Sum_probs=74.7

Q ss_pred             chHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHH
Q 023301           13 GDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVE   92 (284)
Q Consensus        13 ~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~   92 (284)
                      .+|..-|.+-..    .-|.|+.|.+|-+.|-               +.-+..|+|+||.+....+.++-       -.-
T Consensus       212 vdy~~vlke~~~----~aD~IlwdGgnndfPf---------------vkpd~~Ivvvda~rpg~ei~~~p-------Ge~  265 (449)
T COG2403         212 VDYGTVLKEGEK----EADFILWDGGNNDFPF---------------VKPDLHIVVVDALRPGEEIGSFP-------GEL  265 (449)
T ss_pred             eeHHHHHHHHhh----hccEEEEeCCCCCCCc---------------ccCCeeEEEecCCCCchhhccCC-------Cce
Confidence            456666666654    2399999999988873               22334799999999776655431       135


Q ss_pred             HHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeee
Q 023301           93 QVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLA  132 (284)
Q Consensus        93 Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~  132 (284)
                      .|..||+|++||+|.+..+++.++.+.++++||+|.|+.+
T Consensus       266 ~irlAD~VIItkveea~~~kvrkI~~~I~~iNP~A~Vi~~  305 (449)
T COG2403         266 RIRLADLVIITKVEEAMAEKVRKIVRNIEEINPKAEVILA  305 (449)
T ss_pred             eeeeccEEEEecccccchHHHHHHHHHHHhhCCCcEEEec
Confidence            7889999999999999999999999999999999999877

>COG1159 Era GTPase [General function prediction only]

Probab=98.09  E-value=7.9e-06  Score=70.98  Aligned_cols=99  Identities=19%  Similarity=0.234  Sum_probs=77.6

Q ss_pred             CCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh---cCEEEEcc
Q 023301           28 GQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY---ADRIILNK  104 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~---Ad~ivlnK  104 (284)
                      .+.+.|||.|+|+..|..-+..++........-.++.+++|||+..-...    ++    ..+.+|+..   ..++++||
T Consensus        52 ~~~QiIfvDTPGih~pk~~l~~~m~~~a~~sl~dvDlilfvvd~~~~~~~----~d----~~il~~lk~~~~pvil~iNK  123 (298)
T COG1159          52 DNAQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGP----GD----EFILEQLKKTKTPVILVVNK  123 (298)
T ss_pred             CCceEEEEeCCCCCCcchHHHHHHHHHHHHHhccCcEEEEEEeccccCCc----cH----HHHHHHHhhcCCCeEEEEEc
Confidence            47899999999999999888877765555566789999999999883221    12    233566644   78999999


Q ss_pred             CCCCChhH-HHHHHHHHHHhCCCCceeeecc
Q 023301          105 IDLVTETE-LGSLTERIKHINAMAPVKLAKY  134 (284)
Q Consensus       105 ~D~~~~~~-~~~~~~~l~~~np~a~i~~~~~  134 (284)
                      +|.++++. +..+.+.++..-|..+++..+.
T Consensus       124 ID~~~~~~~l~~~~~~~~~~~~f~~ivpiSA  154 (298)
T COG1159         124 IDKVKPKTVLLKLIAFLKKLLPFKEIVPISA  154 (298)
T ss_pred             cccCCcHHHHHHHHHHHHhhCCcceEEEeec
Confidence            99998888 6788888888889999987764

>cd04163 Era Era subfamily

Probab=97.79  E-value=7.7e-05  Score=59.13  Aligned_cols=100  Identities=24%  Similarity=0.356  Sum_probs=63.4

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      +.++++++++|+.++...................+.++.|+|+.....+..    ..+. ....+.....++|+||+|+.
T Consensus        50 ~~~~~liDtpG~~~~~~~~~~~~~~~~~~~~~~~d~i~~v~d~~~~~~~~~----~~~~-~~~~~~~~~~iiv~nK~Dl~  124 (168)
T cd04163          50 DAQIIFVDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEPIGEGD----EFIL-ELLKKSKTPVILVLNKIDLV  124 (168)
T ss_pred             CeEEEEEECCCCCcchHHHHHHHHHHHHHHHHhCCEEEEEEECCCccCchH----HHHH-HHHHHhCCCEEEEEEchhcc
Confidence            457899999999988765433211111222346678999999988622111    1111 11223346789999999998


Q ss_pred             -ChhHHHHHHHHHHHhCCCCceeeec
Q 023301          109 -TETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       109 -~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                       +.+++....+.++..++..+++.++
T Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~s  150 (168)
T cd04163         125 KDKEDLLPLLEKLKELGPFAEIFPIS  150 (168)
T ss_pred             ccHHHHHHHHHHHHhccCCCceEEEE
Confidence             5667777778887777766776554

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.

>PRK00089 era GTPase Era; Reviewed

Probab=97.63  E-value=0.00021  Score=63.18  Aligned_cols=98  Identities=23%  Similarity=0.302  Sum_probs=63.8

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKI  105 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~  105 (284)
                      ..+.++++|+|+.++...+...............+.++.|+|+......    ..    ..+.+++   ....++|+||+
T Consensus        52 ~~qi~~iDTPG~~~~~~~l~~~~~~~~~~~~~~~D~il~vvd~~~~~~~----~~----~~i~~~l~~~~~pvilVlNKi  123 (292)
T PRK00089         52 DAQIIFVDTPGIHKPKRALNRAMNKAAWSSLKDVDLVLFVVDADEKIGP----GD----EFILEKLKKVKTPVILVLNKI  123 (292)
T ss_pred             CceEEEEECCCCCCchhHHHHHHHHHHHHHHhcCCEEEEEEeCCCCCCh----hH----HHHHHHHhhcCCCEEEEEECC
Confidence            4688999999999987554432221122233468889999999872111    00    1223333   45789999999


Q ss_pred             CCC-ChhHHHHHHHHHHHhCCCCceeeecc
Q 023301          106 DLV-TETELGSLTERIKHINAMAPVKLAKY  134 (284)
Q Consensus       106 D~~-~~~~~~~~~~~l~~~np~a~i~~~~~  134 (284)
                      |+. +.+++....+.+++..+..+++.++.
T Consensus       124 Dl~~~~~~l~~~~~~l~~~~~~~~i~~iSA  153 (292)
T PRK00089        124 DLVKDKEELLPLLEELSELMDFAEIVPISA  153 (292)
T ss_pred             cCCCCHHHHHHHHHHHHhhCCCCeEEEecC
Confidence            998 55666667777776667777876653

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

Probab=97.42  E-value=0.0012  Score=57.77  Aligned_cols=63  Identities=21%  Similarity=0.283  Sum_probs=40.9

Q ss_pred             cCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCC
Q 023301           27 QGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKID  106 (284)
Q Consensus        27 ~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D  106 (284)
                      -..+|.|||||.|++....-+-..           .+.++.|.=+.. -..        +...-..-++.||++||||.|
T Consensus       141 AaG~DvIIVETVGvGQsev~I~~~-----------aDt~~~v~~pg~-GD~--------~Q~iK~GimEiaDi~vINKaD  200 (323)
T COG1703         141 AAGYDVIIVETVGVGQSEVDIANM-----------ADTFLVVMIPGA-GDD--------LQGIKAGIMEIADIIVINKAD  200 (323)
T ss_pred             hcCCCEEEEEecCCCcchhHHhhh-----------cceEEEEecCCC-CcH--------HHHHHhhhhhhhheeeEeccC
Confidence            579999999999999976433221           233444443322 211        112235788999999999999


Q ss_pred             CCC
Q 023301          107 LVT  109 (284)
Q Consensus       107 ~~~  109 (284)
                      .-.
T Consensus       201 ~~~  203 (323)
T COG1703         201 RKG  203 (323)
T ss_pred             hhh
Confidence            644

>PRK13768 GTPase; Provisional

Probab=97.27  E-value=0.00083  Score=58.28  Aligned_cols=92  Identities=20%  Similarity=0.191  Sum_probs=52.6

Q ss_pred             cCCCCEEEEecCCCCCcHHH---HHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEc
Q 023301           27 QGQFDHIVIETTGLAKPAPV---IETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILN  103 (284)
Q Consensus        27 ~~~~d~iiIE~sG~a~p~~i---~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivln  103 (284)
                      ..+.|+|+|+++|..++...   ...+.  ..+.... -+.++.|+|+........-............+....-++|+|
T Consensus        94 ~~~~~~~~~d~~g~~~~~~~~~~~~~~~--~~l~~~~-~~~ii~liD~~~~~~~~d~~~~~~l~~~~~~~~~~~~i~v~n  170 (253)
T PRK13768         94 SLDADYVLVDTPGQMELFAFRESGRKLV--ERLSGSS-KSVVVFLIDAVLAKTPSDFVSLLLLALSVQLRLGLPQIPVLN  170 (253)
T ss_pred             hcCCCEEEEeCCcHHHHHhhhHHHHHHH--HHHHhcC-CeEEEEEechHHhCCHHHHHHHHHHHHHHHHHcCCCEEEEEE
Confidence            46679999999999887542   11111  1121111 567999999976432111000000000111245567789999


Q ss_pred             cCCCCChhHHHHHHHHHH
Q 023301          104 KIDLVTETELGSLTERIK  121 (284)
Q Consensus       104 K~D~~~~~~~~~~~~~l~  121 (284)
                      |+|+.+..+.+.+.+.++
T Consensus       171 K~D~~~~~~~~~~~~~l~  188 (253)
T PRK13768        171 KADLLSEEELERILKWLE  188 (253)
T ss_pred             hHhhcCchhHHHHHHHHh
Confidence            999998877666655444

>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=97.27  E-value=0.00079  Score=57.83  Aligned_cols=91  Identities=21%  Similarity=0.280  Sum_probs=48.1

Q ss_pred             HHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEE
Q 023301           21 QLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRI  100 (284)
Q Consensus        21 ~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~i  100 (284)
                      .++.  ...+|+|||||.|++.-.--+..+           .|.++.|+-|.. -..+..        .-..=++.||++
T Consensus       115 ~ll~--aaG~D~IiiETVGvGQsE~~I~~~-----------aD~~v~v~~Pg~-GD~iQ~--------~KaGimEiaDi~  172 (266)
T PF03308_consen  115 RLLD--AAGFDVIIIETVGVGQSEVDIADM-----------ADTVVLVLVPGL-GDEIQA--------IKAGIMEIADIF  172 (266)
T ss_dssp             HHHH--HTT-SEEEEEEESSSTHHHHHHTT-----------SSEEEEEEESST-CCCCCT--------B-TTHHHH-SEE
T ss_pred             HHHH--HcCCCEEEEeCCCCCccHHHHHHh-----------cCeEEEEecCCC-ccHHHH--------HhhhhhhhccEE
Confidence            3444  578999999999999976433221           233455555533 211111        113567789999


Q ss_pred             EEccCCCCChhH-HHHHHHHHHHhCC-----CCceeeec
Q 023301          101 ILNKIDLVTETE-LGSLTERIKHINA-----MAPVKLAK  133 (284)
Q Consensus       101 vlnK~D~~~~~~-~~~~~~~l~~~np-----~a~i~~~~  133 (284)
                      |+||+|....+. ...++..++-..+     ..+|+.++
T Consensus       173 vVNKaD~~gA~~~~~~l~~~l~l~~~~~~~W~ppV~~ts  211 (266)
T PF03308_consen  173 VVNKADRPGADRTVRDLRSMLHLLREREDGWRPPVLKTS  211 (266)
T ss_dssp             EEE--SHHHHHHHHHHHHHHHHHCSTSCTSB--EEEEEB
T ss_pred             EEeCCChHHHHHHHHHHHHHHhhccccccCCCCCEEEEE
Confidence            999999643333 3444555543332     23566554

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.

>TIGR00750 lao LAO/AO transport system ATPase

Probab=97.18  E-value=0.0058  Score=54.37  Aligned_cols=71  Identities=20%  Similarity=0.249  Sum_probs=43.4

Q ss_pred             HHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCE
Q 023301           20 LQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADR   99 (284)
Q Consensus        20 ~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~   99 (284)
                      .++++  ...+|+|||||+|++.+..  +.+         -..+.++.+.++... ..+..        ........+++
T Consensus       119 ~~~l~--~~g~D~viidT~G~~~~e~--~i~---------~~aD~i~vv~~~~~~-~el~~--------~~~~l~~~~~i  176 (300)
T TIGR00750       119 ILLLD--AAGYDVIIVETVGVGQSEV--DIA---------NMADTFVVVTIPGTG-DDLQG--------IKAGLMEIADI  176 (300)
T ss_pred             HHHHH--hCCCCEEEEeCCCCchhhh--HHH---------HhhceEEEEecCCcc-HHHHH--------HHHHHhhhccE
Confidence            33445  5789999999999996552  111         123445555544432 22221        11345678899


Q ss_pred             EEEccCCCCChhH
Q 023301          100 IILNKIDLVTETE  112 (284)
Q Consensus       100 ivlnK~D~~~~~~  112 (284)
                      ||+||+|+.+.+.
T Consensus       177 vv~NK~Dl~~~~~  189 (300)
T TIGR00750       177 YVVNKADGEGATN  189 (300)
T ss_pred             EEEEcccccchhH
Confidence            9999999987654

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.

>PRK15494 era GTPase Era; Provisional

Probab=96.82  E-value=0.0025  Score=57.72  Aligned_cols=108  Identities=17%  Similarity=0.227  Sum_probs=62.3

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVT  109 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~  109 (284)
                      .+.+|++|+|+.++..-+........+...-..+.+++|+|+........    ..+.. ...+....-++|+||+|+.+
T Consensus       100 ~qi~~~DTpG~~~~~~~l~~~~~r~~~~~l~~aDvil~VvD~~~s~~~~~----~~il~-~l~~~~~p~IlViNKiDl~~  174 (339)
T PRK15494        100 TQVILYDTPGIFEPKGSLEKAMVRCAWSSLHSADLVLLIIDSLKSFDDIT----HNILD-KLRSLNIVPIFLLNKIDIES  174 (339)
T ss_pred             eEEEEEECCCcCCCcccHHHHHHHHHHHHhhhCCEEEEEEECCCCCCHHH----HHHHH-HHHhcCCCEEEEEEhhcCcc
Confidence            45689999999876432222111111122346788999999876322111    11111 12333456789999999965


Q ss_pred             hhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          110 ETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       110 ~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      . .+..+.+.++..++...++.++. .....+.++
T Consensus       175 ~-~~~~~~~~l~~~~~~~~i~~iSAktg~gv~eL~  208 (339)
T PRK15494        175 K-YLNDIKAFLTENHPDSLLFPISALSGKNIDGLL  208 (339)
T ss_pred             c-cHHHHHHHHHhcCCCcEEEEEeccCccCHHHHH
Confidence            4 45667777777777777877654 223444444

>TIGR00436 era GTP-binding protein Era

Probab=96.81  E-value=0.0041  Score=54.44  Aligned_cols=105  Identities=15%  Similarity=0.139  Sum_probs=58.7

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~ivlnK~D  106 (284)
                      ...+|++|+|+..+..-+............-..+.++.|+|+.......         ..+..++.   ..-++|+||+|
T Consensus        48 ~qii~vDTPG~~~~~~~l~~~~~~~~~~~l~~aDvvl~VvD~~~~~~~~---------~~i~~~l~~~~~p~ilV~NK~D  118 (270)
T TIGR00436        48 SQIIFIDTPGFHEKKHSLNRLMMKEARSAIGGVDLILFVVDSDQWNGDG---------EFVLTKLQNLKRPVVLTRNKLD  118 (270)
T ss_pred             cEEEEEECcCCCCCcchHHHHHHHHHHHHHhhCCEEEEEEECCCCCchH---------HHHHHHHHhcCCCEEEEEECee
Confidence            4578999999987632221111101111223677899999998743210         11233443   34588999999


Q ss_pred             CCChhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          107 LVTETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       107 ~~~~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +.+.+++......+....+..+++.+|. .....+.++
T Consensus       119 l~~~~~~~~~~~~~~~~~~~~~v~~iSA~~g~gi~~L~  156 (270)
T TIGR00436       119 NKFKDKLLPLIDKYAILEDFKDIVPISALTGDNTSFLA  156 (270)
T ss_pred             CCCHHHHHHHHHHHHhhcCCCceEEEecCCCCCHHHHH
Confidence            9876555444444444445456776653 233454444

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

>cd01895 EngA2 EngA2 subfamily

Probab=96.70  E-value=0.0056  Score=48.77  Aligned_cols=100  Identities=18%  Similarity=0.255  Sum_probs=57.1

Q ss_pred             CCCEEEEecCCCCCcHHHHHHh---cccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccC
Q 023301           29 QFDHIVIETTGLAKPAPVIETF---CTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKI  105 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l---~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~  105 (284)
                      ..++.+|+++|..++...-..+   .....+...-..+.++.|+|+.+......    ..+. ....+....-++++||+
T Consensus        49 ~~~~~iiDtpG~~~~~~~~~~~e~~~~~~~~~~~~~~d~vi~v~d~~~~~~~~~----~~~~-~~~~~~~~~~iiv~nK~  123 (174)
T cd01895          49 GKKYTLIDTAGIRRKGKVEEGIEKYSVLRTLKAIERADVVLLVIDATEGITEQD----LRIA-GLILEEGKALVIVVNKW  123 (174)
T ss_pred             CeeEEEEECCCCccccchhccHHHHHHHHHHHHHhhcCeEEEEEeCCCCcchhH----HHHH-HHHHhcCCCEEEEEecc
Confidence            3567899999998764321111   00001111235678999999977533211    0010 11222345678899999


Q ss_pred             CCCCh--hHHHHHHHHHHHhCC---CCceeeec
Q 023301          106 DLVTE--TELGSLTERIKHINA---MAPVKLAK  133 (284)
Q Consensus       106 D~~~~--~~~~~~~~~l~~~np---~a~i~~~~  133 (284)
                      |+.+.  ...+.+.+.+++..+   ..+++.++
T Consensus       124 Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~S  156 (174)
T cd01895         124 DLVEKDSKTMKEFKKEIRRKLPFLDYAPIVFIS  156 (174)
T ss_pred             ccCCccHHHHHHHHHHHHhhcccccCCceEEEe
Confidence            99876  567777777776654   35565554

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.

>cd00881 GTP_translation_factor GTP translation factor family

Probab=96.56  E-value=0.0081  Score=48.75  Aligned_cols=82  Identities=22%  Similarity=0.227  Sum_probs=50.0

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      ..+.+|++++|..+........     +   -..+.++.|+|+.........    ... ....+....-++++||+|+.
T Consensus        61 ~~~~~liDtpG~~~~~~~~~~~-----~---~~~d~~i~v~d~~~~~~~~~~----~~~-~~~~~~~~~i~iv~nK~D~~  127 (189)
T cd00881          61 DRRVNFIDTPGHEDFSSEVIRG-----L---SVSDGAILVVDANEGVQPQTR----EHL-RIAREGGLPIIVAINKIDRV  127 (189)
T ss_pred             CEEEEEEeCCCcHHHHHHHHHH-----H---HhcCEEEEEEECCCCCcHHHH----HHH-HHHHHCCCCeEEEEECCCCc
Confidence            3578999999987754432221     1   257789999999764321100    010 11233456779999999998


Q ss_pred             ChhHHHHHHHHHHHh
Q 023301          109 TETELGSLTERIKHI  123 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~  123 (284)
                      +++++....+.+++.
T Consensus       128 ~~~~~~~~~~~~~~~  142 (189)
T cd00881         128 GEEDLEEVLREIKEL  142 (189)
T ss_pred             chhcHHHHHHHHHHH
Confidence            866655555555543

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.

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

Probab=96.49  E-value=0.019  Score=45.51  Aligned_cols=66  Identities=18%  Similarity=0.331  Sum_probs=40.3

Q ss_pred             HHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC
Q 023301           19 LLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD   98 (284)
Q Consensus        19 l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad   98 (284)
                      +.+.++  ..++|+||||+.|+....  ...+.         .-+-+|.|+.+.-.-.|         .-.-..-++.||
T Consensus        83 ~~~~~~--~~~~D~iiIDtaG~~~~~--~~~~~---------~Ad~~ivv~tpe~~D~y---------~~~k~~~~~~~~  140 (148)
T cd03114          83 VIRVLD--AAGFDVIIVETVGVGQSE--VDIAS---------MADTTVVVMAPGAGDDI---------QAIKAGIMEIAD  140 (148)
T ss_pred             HHHHHH--hcCCCEEEEECCccChhh--hhHHH---------hCCEEEEEECCCchhHH---------HHhhhhHhhhcC
Confidence            334454  458999999999987433  22221         12235666666622111         011246788899


Q ss_pred             EEEEccCC
Q 023301           99 RIILNKID  106 (284)
Q Consensus        99 ~ivlnK~D  106 (284)
                      ++++||+|
T Consensus       141 ~~~~~k~~  148 (148)
T cd03114         141 IVVVNKAD  148 (148)
T ss_pred             EEEEeCCC
Confidence            99999997

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.

>cd04167 Snu114p Snu114p subfamily

Probab=96.41  E-value=0.0033  Score=52.92  Aligned_cols=90  Identities=18%  Similarity=0.203  Sum_probs=58.4

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC-
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV-  108 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~-  108 (284)
                      ....++.++|..+.......        .....+.+++|+|+.........    ..... ..+...+.++|+||+|++ 
T Consensus        71 ~~i~iiDtpG~~~f~~~~~~--------~~~~aD~~llVvD~~~~~~~~~~----~~~~~-~~~~~~p~iiviNK~D~~~  137 (213)
T cd04167          71 YLFNIIDTPGHVNFMDEVAA--------ALRLSDGVVLVVDVVEGVTSNTE----RLIRH-AILEGLPIVLVINKIDRLI  137 (213)
T ss_pred             EEEEEEECCCCcchHHHHHH--------HHHhCCEEEEEEECCCCCCHHHH----HHHHH-HHHcCCCEEEEEECcccCc
Confidence            56688999998875432211        12356789999999764322110    01011 122236789999999986 


Q ss_pred             ------ChhHHHHHHHHHHHhCCCCceeee
Q 023301          109 ------TETELGSLTERIKHINAMAPVKLA  132 (284)
Q Consensus       109 ------~~~~~~~~~~~l~~~np~a~i~~~  132 (284)
                            +.+..+++.+.++++||.+..+..
T Consensus       138 ~~~~l~~~~~~~~l~~~i~~~n~~~~~~~~  167 (213)
T cd04167         138 LELKLPPNDAYFKLRHIIDEVNNIIASFST  167 (213)
T ss_pred             ccccCCHHHHHHHHHHHHHHHHHHHHHhcC
Confidence                  445678899999999998776543

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.

>PRK09866 hypothetical protein; Provisional

Probab=96.34  E-value=0.014  Score=56.50  Aligned_cols=104  Identities=11%  Similarity=0.068  Sum_probs=60.3

Q ss_pred             CCCCEEEEecCCCCCcHHH-HHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh-----cCEEE
Q 023301           28 GQFDHIVIETTGLAKPAPV-IETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY-----ADRII  101 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~~i-~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~-----Ad~iv  101 (284)
                      ...+.|||.|+|+..|..- +......    ..-..+.|++|||+.+....    .++    .+.+.++.     .-++|
T Consensus       228 ~~~QIIFVDTPGIhk~~~~~L~k~M~e----qL~eADvVLFVVDat~~~s~----~De----eIlk~Lkk~~K~~PVILV  295 (741)
T PRK09866        228 YPGQLTLLDTPGPNEAGQPHLQKMLNQ----QLARASAVLAVLDYTQLKSI----SDE----EVREAILAVGQSVPLYVL  295 (741)
T ss_pred             ccCCEEEEECCCCCCccchHHHHHHHH----HHhhCCEEEEEEeCCCCCCh----hHH----HHHHHHHhcCCCCCEEEE
Confidence            4678999999999987422 3222221    23356889999999874321    111    12333332     55678


Q ss_pred             EccCCCCChhH--HHHHHHHHHHh-----CCCCceeeecc-CCCChhhhh
Q 023301          102 LNKIDLVTETE--LGSLTERIKHI-----NAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       102 lnK~D~~~~~~--~~~~~~~l~~~-----np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +||+|..+.+.  .+.+++.++..     .+...|+..|. -....+.++
T Consensus       296 VNKIDl~dreeddkE~Lle~V~~~L~q~~i~f~eIfPVSAlkG~nid~LL  345 (741)
T PRK09866        296 VNKFDQQDRNSDDADQVRALISGTLMKGCITPQQIFPVSSMWGYLANRAR  345 (741)
T ss_pred             EEcccCCCcccchHHHHHHHHHHHHHhcCCCCceEEEEeCCCCCCHHHHH
Confidence            99999976222  45555555432     24677887653 233444443

>cd00880 Era_like Era (E

Probab=96.29  E-value=0.011  Score=45.94  Aligned_cols=99  Identities=20%  Similarity=0.139  Sum_probs=59.2

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      ..+.++++++|...+......... ......-..+.+++|+|+.........    . ......+....-++|+||+|++
T Consensus        44 ~~~~~~~Dt~g~~~~~~~~~~~~~-~~~~~~~~~d~il~v~~~~~~~~~~~~----~-~~~~~~~~~~~~ivv~nK~D~~  117 (163)
T cd00880          44 LGPVVLIDTPGIDEAGGLGREREE-LARRVLERADLILFVVDADLRADEEEE----K-LLELLRERGKPVLLVLNKIDLL  117 (163)
T ss_pred             CCcEEEEECCCCCccccchhhHHH-HHHHHHHhCCEEEEEEeCCCCCCHHHH----H-HHHHHHhcCCeEEEEEEccccC
Confidence            568899999999886543221000 000012246779999999986543211    0 0112345566779999999998


Q ss_pred             ChhHHHHHH---HHHHHhCCCCceeeec
Q 023301          109 TETELGSLT---ERIKHINAMAPVKLAK  133 (284)
Q Consensus       109 ~~~~~~~~~---~~l~~~np~a~i~~~~  133 (284)
                      .+.......   .......+.++++..+
T Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s  145 (163)
T cd00880         118 PEEEEEELLELRLLILLLLLGLPVIAVS  145 (163)
T ss_pred             ChhhHHHHHHHHHhhcccccCCceEEEe
Confidence            876665542   2334445667777654

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

>PRK00093 GTP-binding protein Der; Reviewed

Probab=96.06  E-value=0.02  Score=53.61  Aligned_cols=110  Identities=18%  Similarity=0.246  Sum_probs=62.9

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcc---cccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCT---DELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKI  105 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~---~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~  105 (284)
                      ..++.+++|+|+.....+-..+..   ...+...-..+.++.|+|+..-.....    ..+.. ...+-..+-+|++||+
T Consensus       220 ~~~~~lvDT~G~~~~~~~~~~~e~~~~~~~~~~~~~ad~~ilViD~~~~~~~~~----~~i~~-~~~~~~~~~ivv~NK~  294 (435)
T PRK00093        220 GQKYTLIDTAGIRRKGKVTEGVEKYSVIRTLKAIERADVVLLVIDATEGITEQD----LRIAG-LALEAGRALVIVVNKW  294 (435)
T ss_pred             CeeEEEEECCCCCCCcchhhHHHHHHHHHHHHHHHHCCEEEEEEeCCCCCCHHH----HHHHH-HHHHcCCcEEEEEECc
Confidence            346899999999876554321110   001111224578999999986432111    01100 1122236779999999


Q ss_pred             CCCChhHHHHHHHHHHHhC---CCCceeeecc-CCCChhhhh
Q 023301          106 DLVTETELGSLTERIKHIN---AMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       106 D~~~~~~~~~~~~~l~~~n---p~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+.+++....+.+.++...   +.++++.++. ....+..++
T Consensus       295 Dl~~~~~~~~~~~~~~~~l~~~~~~~i~~~SA~~~~gv~~l~  336 (435)
T PRK00093        295 DLVDEKTMEEFKKELRRRLPFLDYAPIVFISALTGQGVDKLL  336 (435)
T ss_pred             cCCCHHHHHHHHHHHHHhcccccCCCEEEEeCCCCCCHHHHH
Confidence            9997777777777777544   3567776653 233444443

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

Probab=95.65  E-value=0.052  Score=44.11  Aligned_cols=97  Identities=20%  Similarity=0.302  Sum_probs=49.9

Q ss_pred             CEEEEecCCCCCcHH---H---HHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAP---V---IETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~---i---~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK  104 (284)
                      +.+++.++|......   .   ...+. ...+...-.++.++.|+|+.+-.....    ..+.. ...+....=++++||
T Consensus        65 ~~~liDtpG~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~ii~vvd~~~~~~~~~----~~~~~-~~~~~~~pviiv~nK  138 (179)
T TIGR03598        65 GFRLVDLPGYGYAKVSKEEKEKWQKLI-EEYLEKRENLKGVVLLMDIRHPLKELD----LEMLE-WLRERGIPVLIVLTK  138 (179)
T ss_pred             cEEEEeCCCCccccCChhHHHHHHHHH-HHHHHhChhhcEEEEEecCCCCCCHHH----HHHHH-HHHHcCCCEEEEEEC
Confidence            468999999865321   0   11110 011222224678999999987322111    01111 122333455788899


Q ss_pred             CCCCChhHHHHHHHHHHH----hCCCCceeeec
Q 023301          105 IDLVTETELGSLTERIKH----INAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~~~~~~~~l~~----~np~a~i~~~~  133 (284)
                      +|+.++++.+...+.+++    ..+..+++.++
T Consensus       139 ~D~~~~~~~~~~~~~i~~~l~~~~~~~~v~~~S  171 (179)
T TIGR03598       139 ADKLKKSELNKQLKKIKKALKKDADDPSVQLFS  171 (179)
T ss_pred             cccCCHHHHHHHHHHHHHHHhhccCCCceEEEE
Confidence            999876655444444443    32234566554

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.

>PRK12298 obgE GTPase CgtA; Reviewed

Probab=95.59  E-value=0.037  Score=51.07  Aligned_cols=106  Identities=16%  Similarity=0.210  Sum_probs=56.0

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH--HhhhhcCCccchHHHHHHHh--------hcCEE
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM--QHLNEVKPRFVVNEAVEQVA--------YADRI  100 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~--~~l~~~~~~~~~~~~~~Qi~--------~Ad~i  100 (284)
                      ..+|+.++|+..+...-..|- ...++..-..+.++.|||+..+.  ..+.+.      ..+..++.        ..-+|
T Consensus       208 ~i~~vDtPGi~~~a~~~~~Lg-~~~l~~i~radvlL~VVD~s~~~~~d~~e~~------~~l~~eL~~~~~~L~~kP~Il  280 (390)
T PRK12298        208 SFVVADIPGLIEGASEGAGLG-IRFLKHLERCRVLLHLIDIAPIDGSDPVENA------RIIINELEKYSPKLAEKPRWL  280 (390)
T ss_pred             EEEEEeCCCccccccchhhHH-HHHHHHHHhCCEEEEEeccCcccccChHHHH------HHHHHHHHhhhhhhcCCCEEE
Confidence            379999999987653211010 01122334678899999987321  111110      11223332        46799


Q ss_pred             EEccCCCCChhHHHHHHHHHHHhCC-CCceeeecc-CCCChhhhh
Q 023301          101 ILNKIDLVTETELGSLTERIKHINA-MAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       101 vlnK~D~~~~~~~~~~~~~l~~~np-~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+||+|+.+.+++....+.+++..+ ..+++.++. ....+..++
T Consensus       281 VlNKiDl~~~~el~~~l~~l~~~~~~~~~Vi~ISA~tg~GIdeLl  325 (390)
T PRK12298        281 VFNKIDLLDEEEAEERAKAIVEALGWEGPVYLISAASGLGVKELC  325 (390)
T ss_pred             EEeCCccCChHHHHHHHHHHHHHhCCCCCEEEEECCCCcCHHHHH
Confidence            9999999876665544444443333 235665443 333444443

>cd01878 HflX HflX subfamily

Probab=95.56  E-value=0.04  Score=45.73  Aligned_cols=79  Identities=23%  Similarity=0.450  Sum_probs=46.0

Q ss_pred             CCEEEEecCCCCC--cHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC---EEEEcc
Q 023301           30 FDHIVIETTGLAK--PAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD---RIILNK  104 (284)
Q Consensus        30 ~d~iiIE~sG~a~--p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad---~ivlnK  104 (284)
                      ..+.|++++|..+  +......+..  .+......+.++.|+|+....... +.  ... ..+..++...+   +||+||
T Consensus        89 ~~~~i~Dt~G~~~~~~~~~~~~~~~--~~~~~~~~d~ii~v~D~~~~~~~~-~~--~~~-~~~l~~~~~~~~~viiV~NK  162 (204)
T cd01878          89 REVLLTDTVGFIRDLPHQLVEAFRS--TLEEVAEADLLLHVVDASDPDYEE-QI--ETV-EKVLKELGAEDIPMILVLNK  162 (204)
T ss_pred             ceEEEeCCCccccCCCHHHHHHHHH--HHHHHhcCCeEEEEEECCCCChhh-HH--HHH-HHHHHHcCcCCCCEEEEEEc
Confidence            3788999999854  3333333321  122234678899999997643211 00  001 12345555445   889999


Q ss_pred             CCCCChhHHH
Q 023301          105 IDLVTETELG  114 (284)
Q Consensus       105 ~D~~~~~~~~  114 (284)
                      +|+.+.....
T Consensus       163 ~Dl~~~~~~~  172 (204)
T cd01878         163 IDLLDDEELE  172 (204)
T ss_pred             cccCChHHHH
Confidence            9998765543

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.

>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA

Probab=95.49  E-value=0.03  Score=52.22  Aligned_cols=99  Identities=18%  Similarity=0.281  Sum_probs=57.9

Q ss_pred             CEEEEecCCCCCcHHHHHHh---cccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETF---CTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l---~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~  107 (284)
                      .+.+++|+|+.....+-+.+   .....+...-..+.++.|+|+..-.....    ..+.. ...+-..+-+||+||+|+
T Consensus       221 ~~~liDT~G~~~~~~~~~~~e~~~~~~~~~~~~~ad~~ilV~D~~~~~~~~~----~~~~~-~~~~~~~~iiiv~NK~Dl  295 (429)
T TIGR03594       221 KYLLIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEGITEQD----LRIAG-LILEAGKALVIVVNKWDL  295 (429)
T ss_pred             EEEEEECCCccccccchhhHHHHHHHHHHHHHHhCCEEEEEEECCCCccHHH----HHHHH-HHHHcCCcEEEEEECccc
Confidence            57899999987655432111   00011112235678999999986332211    00101 112234678999999999


Q ss_pred             C-ChhHHHHHHHHHHHhCC---CCceeeecc
Q 023301          108 V-TETELGSLTERIKHINA---MAPVKLAKY  134 (284)
Q Consensus       108 ~-~~~~~~~~~~~l~~~np---~a~i~~~~~  134 (284)
                      . +.+..+.+.+.++...+   .++++.++.
T Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~vi~~SA  326 (429)
T TIGR03594       296 VKDEKTREEFKKELRRKLPFLDFAPIVFISA  326 (429)
T ss_pred             CCCHHHHHHHHHHHHHhcccCCCCceEEEeC
Confidence            8 66667777777776553   467776653

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.

>COG1160 Predicted GTPases [General function prediction only]

Probab=95.34  E-value=0.025  Score=52.28  Aligned_cols=102  Identities=17%  Similarity=0.301  Sum_probs=68.8

Q ss_pred             CCCCEEEEecCCCCCcHHHHHHhccc---ccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEcc
Q 023301           28 GQFDHIVIETTGLAKPAPVIETFCTD---ELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNK  104 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~~i~~~l~~~---~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK  104 (284)
                      ..-.+.+|+|-|+=.-..|.+.+..-   ..++..-..+.++.|+||..-....+.    .+ .-+..-..-|.+||+||
T Consensus       224 ~~~~~~liDTAGiRrk~ki~e~~E~~Sv~rt~~aI~~a~vvllviDa~~~~~~qD~----~i-a~~i~~~g~~~vIvvNK  298 (444)
T COG1160         224 DGRKYVLIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDL----RI-AGLIEEAGRGIVIVVNK  298 (444)
T ss_pred             CCeEEEEEECCCCCcccccccceEEEeehhhHhHHhhcCEEEEEEECCCCchHHHH----HH-HHHHHHcCCCeEEEEEc
Confidence            34567999999999888777654321   122334466778999999884432111    11 12356677899999999


Q ss_pred             CCCCCh--hHHHHHHHHHHHhCC---CCceeeecc
Q 023301          105 IDLVTE--TELGSLTERIKHINA---MAPVKLAKY  134 (284)
Q Consensus       105 ~D~~~~--~~~~~~~~~l~~~np---~a~i~~~~~  134 (284)
                      +|+++.  ...+.+++.++...|   .|+++..+.
T Consensus       299 WDl~~~~~~~~~~~k~~i~~~l~~l~~a~i~~iSA  333 (444)
T COG1160         299 WDLVEEDEATMEEFKKKLRRKLPFLDFAPIVFISA  333 (444)
T ss_pred             cccCCchhhHHHHHHHHHHHHhccccCCeEEEEEe
Confidence            999886  667788888887655   477776653

>cd01858 NGP_1 NGP-1

Probab=95.28  E-value=0.044  Score=43.61  Aligned_cols=56  Identities=21%  Similarity=0.208  Sum_probs=34.2

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-----hcCEEEEccCCCCChhHHHHHHHHHHHhC
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-----YADRIILNKIDLVTETELGSLTERIKHIN  124 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-----~Ad~ivlnK~D~~~~~~~~~~~~~l~~~n  124 (284)
                      ..|.++.|+|+......    .++    .+.+.+.     ..-++|+||+|+.+++++....+.+++..
T Consensus         8 ~aD~il~VvD~~~p~~~----~~~----~i~~~l~~~~~~~p~ilVlNKiDl~~~~~~~~~~~~~~~~~   68 (157)
T cd01858           8 SSDVVIQVLDARDPMGT----RCK----HVEEYLKKEKPHKHLIFVLNKCDLVPTWVTARWVKILSKEY   68 (157)
T ss_pred             hCCEEEEEEECCCCccc----cCH----HHHHHHHhccCCCCEEEEEEchhcCCHHHHHHHHHHHhcCC
Confidence            46779999999875321    111    2233332     23489999999988766555555554433

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.

>COG0218 Predicted GTPase [General function prediction only]

Probab=95.03  E-value=0.081  Score=43.81  Aligned_cols=86  Identities=19%  Similarity=0.337  Sum_probs=61.6

Q ss_pred             CEEEEecCCCCCc---HHHHHHhc--ccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccC
Q 023301           31 DHIVIETTGLAKP---APVIETFC--TDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKI  105 (284)
Q Consensus        31 d~iiIE~sG~a~p---~~i~~~l~--~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~  105 (284)
                      ...+|.-+|.+.-   .+.-+...  ....+..+-.|..+|.+||+++.....+.    .+ ..+..+...+=+||+||+
T Consensus        71 ~~~lVDlPGYGyAkv~k~~~e~w~~~i~~YL~~R~~L~~vvlliD~r~~~~~~D~----em-~~~l~~~~i~~~vv~tK~  145 (200)
T COG0218          71 ELRLVDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDR----EM-IEFLLELGIPVIVVLTKA  145 (200)
T ss_pred             cEEEEeCCCcccccCCHHHHHHHHHHHHHHHhhchhheEEEEEEECCCCCcHHHH----HH-HHHHHHcCCCeEEEEEcc
Confidence            3679999998873   33222211  12466777789999999999998765432    12 245688888899999999


Q ss_pred             CCCChhHHHHHHHHHH
Q 023301          106 DLVTETELGSLTERIK  121 (284)
Q Consensus       106 D~~~~~~~~~~~~~l~  121 (284)
                      |.++..+..+....++
T Consensus       146 DKi~~~~~~k~l~~v~  161 (200)
T COG0218         146 DKLKKSERNKQLNKVA  161 (200)
T ss_pred             ccCChhHHHHHHHHHH
Confidence            9999877766666666

>COG2262 HflX GTPases [General function prediction only]

Probab=95.01  E-value=0.11  Score=47.60  Aligned_cols=105  Identities=20%  Similarity=0.417  Sum_probs=68.4

Q ss_pred             CCCEEEEecCCCCC--cHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC---EEEEc
Q 023301           29 QFDHIVIETTGLAK--PAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD---RIILN  103 (284)
Q Consensus        29 ~~d~iiIE~sG~a~--p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad---~ivln  103 (284)
                      ....++-+|.|.-.  |..++.+|.+  .|.+...-|.++.|||+... ......   .....+..+|...+   ++|+|
T Consensus       239 g~~vlLtDTVGFI~~LP~~LV~AFks--TLEE~~~aDlllhVVDaSdp-~~~~~~---~~v~~vL~el~~~~~p~i~v~N  312 (411)
T COG2262         239 GRKVLLTDTVGFIRDLPHPLVEAFKS--TLEEVKEADLLLHVVDASDP-EILEKL---EAVEDVLAEIGADEIPIILVLN  312 (411)
T ss_pred             CceEEEecCccCcccCChHHHHHHHH--HHHHhhcCCEEEEEeecCCh-hHHHHH---HHHHHHHHHcCCCCCCEEEEEe
Confidence            35588889999877  9999999864  67788899999999999886 222221   11233456665444   78899


Q ss_pred             cCCCCChhHHHHHHHHHHHhCCCCceeeeccCCCChhhhh
Q 023301          104 KIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVL  143 (284)
Q Consensus       104 K~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v~~~~l~  143 (284)
                      |+|+++++.   ....+....| .+|..+......++.|.
T Consensus       313 KiD~~~~~~---~~~~~~~~~~-~~v~iSA~~~~gl~~L~  348 (411)
T COG2262         313 KIDLLEDEE---ILAELERGSP-NPVFISAKTGEGLDLLR  348 (411)
T ss_pred             cccccCchh---hhhhhhhcCC-CeEEEEeccCcCHHHHH
Confidence            999987665   2333333335 45544444444455544

>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=94.96  E-value=0.14  Score=41.38  Aligned_cols=73  Identities=23%  Similarity=0.381  Sum_probs=46.5

Q ss_pred             cCCCCEEEEecCCCCC-cHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccC
Q 023301           27 QGQFDHIVIETTGLAK-PAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKI  105 (284)
Q Consensus        27 ~~~~d~iiIE~sG~a~-p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~  105 (284)
                      ....|+|||++.|... ....+..+.   .+.....-+.++.|+|+....+.+..      ...+.++.. .+.+|+||.
T Consensus        80 ~~~~d~viiDt~g~~~~~~~~l~~l~---~l~~~~~~~~~~lVv~~~~~~~~~~~------~~~~~~~~~-~~~viltk~  149 (173)
T cd03115          80 EENFDVVIVDTAGRLQIDENLMEELK---KIKRVVKPDEVLLVVDAMTGQDAVNQ------AKAFNEALG-ITGVILTKL  149 (173)
T ss_pred             hCCCCEEEEECcccchhhHHHHHHHH---HHHhhcCCCeEEEEEECCCChHHHHH------HHHHHhhCC-CCEEEEECC
Confidence            4688999999999874 334444442   22233457789999999654433221      122234444 689999999


Q ss_pred             CCCC
Q 023301          106 DLVT  109 (284)
Q Consensus       106 D~~~  109 (284)
                      |...
T Consensus       150 D~~~  153 (173)
T cd03115         150 DGDA  153 (173)
T ss_pred             cCCC
Confidence            9865

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.

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

Probab=94.87  E-value=0.035  Score=43.38  Aligned_cols=77  Identities=19%  Similarity=0.268  Sum_probs=44.3

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVT  109 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~  109 (284)
                      ....+++++|..+.....+...........-..+.++.|+|+.+......       .......-...-++|+||+|+.+
T Consensus        49 ~~~~i~DtpG~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~d~~~~~~~~~-------~~~~~~~~~~~vi~v~nK~D~~~  121 (157)
T cd04164          49 IPVRLIDTAGIRETEDEIEKIGIERAREAIEEADLVLFVIDASRGLDEED-------LEILELPADKPIIVVLNKSDLLP  121 (157)
T ss_pred             EEEEEEECCCcCCCcchHHHHHHHHHHHHHhhCCEEEEEEECCCCCCHHH-------HHHHHhhcCCCEEEEEEchhcCC
Confidence            45689999998775433221110011112236778999999997332211       01112234566789999999987


Q ss_pred             hhHH
Q 023301          110 ETEL  113 (284)
Q Consensus       110 ~~~~  113 (284)
                      ....
T Consensus       122 ~~~~  125 (157)
T cd04164         122 DSEL  125 (157)
T ss_pred             cccc
Confidence            5543

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.

>cd04178 Nucleostemin_like Nucleostemin-like

Probab=94.82  E-value=0.059  Score=43.88  Aligned_cols=54  Identities=19%  Similarity=0.256  Sum_probs=35.0

Q ss_pred             ceEEEEEcccchHHhhhhcCCccchHHHHHH--H---hhcCEEEEccCCCCChhHHHHHHHHHHHhC
Q 023301           63 DGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ--V---AYADRIILNKIDLVTETELGSLTERIKHIN  124 (284)
Q Consensus        63 ~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q--i---~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~n  124 (284)
                      |.|+.|+|+.......    .    ..+.+.  +   .-.-++|+||+|+++++.+..+.+.+++..
T Consensus         1 DvVl~VvDar~p~~~~----~----~~i~~~~~l~~~~kp~IlVlNK~DL~~~~~l~~~~~~~~~~~   59 (172)
T cd04178           1 DVILEVLDARDPLGCR----C----PQVEEAVLQAGGNKKLVLVLNKIDLVPKENVEKWLKYLRREF   59 (172)
T ss_pred             CEEEEEEECCCCCCCC----C----HHHHHHHHhccCCCCEEEEEehhhcCCHHHHHHHHHHHHhhC
Confidence            4689999998753221    1    112222  2   245699999999999887776666666554

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

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

Probab=94.70  E-value=0.1  Score=43.54  Aligned_cols=92  Identities=22%  Similarity=0.277  Sum_probs=48.7

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC-EEEEccCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDLV  108 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~~  108 (284)
                      ..+.|++++|-.+   +...     .+...-.++.++.|+|+...... ..  ....... .......- +||+||+|+.
T Consensus        83 ~~i~~iDtPG~~~---~~~~-----~~~~~~~~D~~llVvd~~~~~~~-~~--t~~~l~~-~~~~~~~~iiivvNK~Dl~  150 (203)
T cd01888          83 RHVSFVDCPGHEI---LMAT-----MLSGAAVMDGALLLIAANEPCPQ-PQ--TSEHLAA-LEIMGLKHIIIVQNKIDLV  150 (203)
T ss_pred             cEEEEEECCChHH---HHHH-----HHHhhhcCCEEEEEEECCCCCCC-cc--hHHHHHH-HHHcCCCcEEEEEEchhcc
Confidence            4578999999422   2222     12233467889999999862100 00  0000011 12222233 5699999998


Q ss_pred             ChhHHHHHHHHHHHhC-----CCCceeeec
Q 023301          109 TETELGSLTERIKHIN-----AMAPVKLAK  133 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~n-----p~a~i~~~~  133 (284)
                      +.+++....+.+++..     ...+++.++
T Consensus       151 ~~~~~~~~~~~i~~~~~~~~~~~~~i~~vS  180 (203)
T cd01888         151 KEEQALENYEQIKKFVKGTIAENAPIIPIS  180 (203)
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCcEEEEe
Confidence            7665544444444432     245566554

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

>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=94.68  E-value=0.0066  Score=48.58  Aligned_cols=94  Identities=15%  Similarity=0.184  Sum_probs=50.2

Q ss_pred             CCCEEEEecCCCCCcHHHH--HHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCC
Q 023301           29 QFDHIVIETTGLAKPAPVI--ETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKID  106 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~--~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D  106 (284)
                      .-.+.+|.++|+..+.+.-  +.+.. ..+. .-..+.+|.|+||.++...+.      + -....++...=++++||+|
T Consensus        46 ~~~~~lvDlPG~ysl~~~s~ee~v~~-~~l~-~~~~D~ii~VvDa~~l~r~l~------l-~~ql~e~g~P~vvvlN~~D  116 (156)
T PF02421_consen   46 DQQVELVDLPGIYSLSSKSEEERVAR-DYLL-SEKPDLIIVVVDATNLERNLY------L-TLQLLELGIPVVVVLNKMD  116 (156)
T ss_dssp             TEEEEEEE----SSSSSSSHHHHHHH-HHHH-HTSSSEEEEEEEGGGHHHHHH------H-HHHHHHTTSSEEEEEETHH
T ss_pred             CceEEEEECCCcccCCCCCcHHHHHH-HHHh-hcCCCEEEEECCCCCHHHHHH------H-HHHHHHcCCCEEEEEeCHH
Confidence            4578999999988765321  11111 1111 125788999999999765431      0 1123455677789999999


Q ss_pred             CCChhHHHH-HHHHHHHhCCCCceeeec
Q 023301          107 LVTETELGS-LTERIKHINAMAPVKLAK  133 (284)
Q Consensus       107 ~~~~~~~~~-~~~~l~~~np~a~i~~~~  133 (284)
                      ++....+.- ..+.-+.+  ..+++.++
T Consensus       117 ~a~~~g~~id~~~Ls~~L--g~pvi~~s  142 (156)
T PF02421_consen  117 EAERKGIEIDAEKLSERL--GVPVIPVS  142 (156)
T ss_dssp             HHHHTTEEE-HHHHHHHH--TS-EEEEB
T ss_pred             HHHHcCCEECHHHHHHHh--CCCEEEEE
Confidence            876543211 22222223  35777665

FeoB has been identified as part of this transport system and may play a role in the transport of ferrous iron. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent [].; GO: 0005525 GTP binding, 0015093 ferrous iron transmembrane transporter activity, 0015684 ferrous iron transport, 0016021 integral to membrane; PDB: 3TAH_B 3B1X_A 3SS8_A 3B1W_C 3B1V_A 3LX5_A 3B1Y_A 3LX8_A 3B1Z_A 3K53_B ....

>PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional

Probab=94.65  E-value=0.13  Score=48.46  Aligned_cols=89  Identities=22%  Similarity=0.333  Sum_probs=52.6

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccch--HHhhhhcCCccchHHHHHHHhhcC-EEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHA--MQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~--~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~  107 (284)
                      .+.||+++|-.   .++...     +...-..+.++.|||+...  ..+..+    .+  .+.+.+.... +|++||+|+
T Consensus       118 ~i~~IDtPGH~---~fi~~m-----~~g~~~~D~alLVVda~~g~~~~qT~e----hl--~i~~~lgi~~iIVvlNKiDl  183 (460)
T PTZ00327        118 HVSFVDCPGHD---ILMATM-----LNGAAVMDAALLLIAANESCPQPQTSE----HL--AAVEIMKLKHIIILQNKIDL  183 (460)
T ss_pred             eEeeeeCCCHH---HHHHHH-----HHHHhhCCEEEEEEECCCCccchhhHH----HH--HHHHHcCCCcEEEEEecccc
Confidence            56899999943   333332     2223467889999999862  111111    11  1234444444 579999999


Q ss_pred             CChhHHHHHHHHHHHh-----CCCCceeeec
Q 023301          108 VTETELGSLTERIKHI-----NAMAPVKLAK  133 (284)
Q Consensus       108 ~~~~~~~~~~~~l~~~-----np~a~i~~~~  133 (284)
                      ++.+.+.+..+.++++     ...++++..+
T Consensus       184 v~~~~~~~~~~ei~~~l~~~~~~~~~iipVS  214 (460)
T PTZ00327        184 VKEAQAQDQYEEIRNFVKGTIADNAPIIPIS  214 (460)
T ss_pred             cCHHHHHHHHHHHHHHHHhhccCCCeEEEee
Confidence            9876655555555443     2456787765

>PRK14974 cell division protein FtsY; Provisional

Probab=94.60  E-value=0.34  Score=43.78  Aligned_cols=95  Identities=20%  Similarity=0.250  Sum_probs=58.1

Q ss_pred             CCCCEEEEecCCCCC-cHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCC
Q 023301           28 GQFDHIVIETTGLAK-PAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKID  106 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~-p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D  106 (284)
                      .+.|+|||+|.|... ...++..|..   +.....-+.++.|+|+..-...+..       .....+....|-+|+||.|
T Consensus       221 ~~~DvVLIDTaGr~~~~~~lm~eL~~---i~~~~~pd~~iLVl~a~~g~d~~~~-------a~~f~~~~~~~giIlTKlD  290 (336)
T PRK14974        221 RGIDVVLIDTAGRMHTDANLMDELKK---IVRVTKPDLVIFVGDALAGNDAVEQ-------AREFNEAVGIDGVILTKVD  290 (336)
T ss_pred             CCCCEEEEECCCccCCcHHHHHHHHH---HHHhhCCceEEEeeccccchhHHHH-------HHHHHhcCCCCEEEEeeec
Confidence            568999999999986 5666666532   2233445668899999764322211       0112234457999999999


Q ss_pred             CCChhHHHHHHHHHHHhCCCCceeeeccCC
Q 023301          107 LVTETELGSLTERIKHINAMAPVKLAKYGS  136 (284)
Q Consensus       107 ~~~~~~~~~~~~~l~~~np~a~i~~~~~g~  136 (284)
                      ...  ..-.+...+...  +.||.....|+
T Consensus       291 ~~~--~~G~~ls~~~~~--~~Pi~~i~~Gq  316 (336)
T PRK14974        291 ADA--KGGAALSIAYVI--GKPILFLGVGQ  316 (336)
T ss_pred             CCC--CccHHHHHHHHH--CcCEEEEeCCC
Confidence            854  233444444444  46776666663

>COG1084 Predicted GTPase [General function prediction only]

Probab=94.57  E-value=0.034  Score=49.32  Aligned_cols=92  Identities=18%  Similarity=0.192  Sum_probs=55.1

Q ss_pred             CEEEEecCCCCC-cHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCC
Q 023301           31 DHIVIETTGLAK-PAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVT  109 (284)
Q Consensus        31 d~iiIE~sG~a~-p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~  109 (284)
                      .+=+|.|+|+-| |.+=...+.....++-..-=+.|++++|+.....|--+.+ ..+......-+...=++|+||+|.++
T Consensus       216 R~QvIDTPGlLDRPl~ErN~IE~qAi~AL~hl~~~IlF~~D~Se~cgy~lE~Q-~~L~~eIk~~f~~p~v~V~nK~D~~~  294 (346)
T COG1084         216 RIQVIDTPGLLDRPLEERNEIERQAILALRHLAGVILFLFDPSETCGYSLEEQ-ISLLEEIKELFKAPIVVVINKIDIAD  294 (346)
T ss_pred             eEEEecCCcccCCChHHhcHHHHHHHHHHHHhcCeEEEEEcCccccCCCHHHH-HHHHHHHHHhcCCCeEEEEecccccc
Confidence            456899999998 5433333322122221222345779999987655422111 11223344555545778889999999


Q ss_pred             hhHHHHHHHHHHHh
Q 023301          110 ETELGSLTERIKHI  123 (284)
Q Consensus       110 ~~~~~~~~~~l~~~  123 (284)
                      .+.++++...+...
T Consensus       295 ~e~~~~~~~~~~~~  308 (346)
T COG1084         295 EEKLEEIEASVLEE  308 (346)
T ss_pred             hhHHHHHHHHHHhh
Confidence            98888888776544

>cd01857 HSR1_MMR1 HSR1/MMR1

Probab=94.57  E-value=0.084  Score=41.22  Aligned_cols=65  Identities=26%  Similarity=0.329  Sum_probs=37.7

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHHHHH--hhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeee
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV--AYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLA  132 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi--~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~  132 (284)
                      ..+.++.|+|+.......    +..+. ....+.  ...-++|+||+|+.+++++..+.+.++...  .+++..
T Consensus        11 ~aD~vl~ViD~~~p~~~~----~~~l~-~~l~~~~~~k~~iivlNK~DL~~~~~~~~~~~~~~~~~--~~ii~i   77 (141)
T cd01857          11 RSDIVVQIVDARNPLLFR----PPDLE-RYVKEVDPRKKNILLLNKADLLTEEQRKAWAEYFKKEG--IVVVFF   77 (141)
T ss_pred             hCCEEEEEEEccCCcccC----CHHHH-HHHHhccCCCcEEEEEechhcCCHHHHHHHHHHHHhcC--CeEEEE
Confidence            456789999997643211    11111 112222  334678889999988777666666665444  345544

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.

>cd01889 SelB_euk SelB subfamily

Probab=94.54  E-value=0.3  Score=40.05  Aligned_cols=91  Identities=19%  Similarity=0.311  Sum_probs=48.9

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-hhcCEEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-AYADRIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-~~Ad~ivlnK~D~  107 (284)
                      .....+++++|...   +....     +...-..+.++.|+|+.........    .  .....+. ...=++++||+|+
T Consensus        67 ~~~~~i~DtpG~~~---~~~~~-----~~~~~~~d~vi~VvD~~~~~~~~~~----~--~~~~~~~~~~~~iiv~NK~Dl  132 (192)
T cd01889          67 NLQITLVDCPGHAS---LIRTI-----IGGAQIIDLMLLVVDATKGIQTQTA----E--CLVIGEILCKKLIVVLNKIDL  132 (192)
T ss_pred             CceEEEEECCCcHH---HHHHH-----HHHHhhCCEEEEEEECCCCccHHHH----H--HHHHHHHcCCCEEEEEECccc
Confidence            56778999999732   22222     1122346789999999763211000    0  0111222 2334688899999


Q ss_pred             CChhHHH----HHHHHHHHh-----CCCCceeeec
Q 023301          108 VTETELG----SLTERIKHI-----NAMAPVKLAK  133 (284)
Q Consensus       108 ~~~~~~~----~~~~~l~~~-----np~a~i~~~~  133 (284)
                      .+.++.+    .+++.++..     +...+++.++
T Consensus       133 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~vi~iS  167 (192)
T cd01889         133 IPEEERERKIEKMKKKLQKTLEKTRFKNSPIIPVS  167 (192)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhcCcCCCCEEEEe
Confidence            8655543    333333322     3456777665

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

>cd01894 EngA1 EngA1 subfamily

Probab=94.43  E-value=0.18  Score=39.24  Aligned_cols=79  Identities=14%  Similarity=0.225  Sum_probs=43.8

Q ss_pred             CCCEEEEecCCCCCcHH-HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAP-VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~-i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~  107 (284)
                      +....+++++|..+-.. +...+.. ......-..+.++.|+|+.......    ...+ .....+....=++|+||+|+
T Consensus        44 ~~~~~i~DtpG~~~~~~~~~~~~~~-~~~~~~~~~d~ii~v~d~~~~~~~~----~~~~-~~~~~~~~~piiiv~nK~D~  117 (157)
T cd01894          44 GREFILIDTGGIEPDDEGISKEIRE-QAELAIEEADVILFVVDGREGLTPA----DEEI-AKYLRKSKKPVILVVNKVDN  117 (157)
T ss_pred             CeEEEEEECCCCCCchhHHHHHHHH-HHHHHHHhCCEEEEEEeccccCCcc----HHHH-HHHHHhcCCCEEEEEECccc
Confidence            35678999999988654 2221111 0111123467899999997632110    0111 11122334556889999999


Q ss_pred             CChhHH
Q 023301          108 VTETEL  113 (284)
Q Consensus       108 ~~~~~~  113 (284)
                      .+.+..
T Consensus       118 ~~~~~~  123 (157)
T cd01894         118 IKEEDE  123 (157)
T ss_pred             CChHHH
Confidence            875543

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.

>cd01884 EF_Tu EF-Tu subfamily

Probab=94.36  E-value=0.097  Score=43.48  Aligned_cols=81  Identities=21%  Similarity=0.283  Sum_probs=43.7

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC-EEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~  107 (284)
                      +..+.||+|+|..+.   +...     ....-..+.++.|||+..-....    .+.... ...+....- ++++||+|+
T Consensus        64 ~~~i~~iDtPG~~~~---~~~~-----~~~~~~~D~~ilVvda~~g~~~~----~~~~~~-~~~~~~~~~iIvviNK~D~  130 (195)
T cd01884          64 NRHYAHVDCPGHADY---IKNM-----ITGAAQMDGAILVVSATDGPMPQ----TREHLL-LARQVGVPYIVVFLNKADM  130 (195)
T ss_pred             CeEEEEEECcCHHHH---HHHH-----HHHhhhCCEEEEEEECCCCCcHH----HHHHHH-HHHHcCCCcEEEEEeCCCC
Confidence            346799999998542   2221     22234678899999997632110    011111 122333332 467899999


Q ss_pred             CChhH-HHHHHHHHHH
Q 023301          108 VTETE-LGSLTERIKH  122 (284)
Q Consensus       108 ~~~~~-~~~~~~~l~~  122 (284)
                      ++.++ .+.+.+.++.
T Consensus       131 ~~~~~~~~~~~~~i~~  146 (195)
T cd01884         131 VDDEELLELVEMEVRE  146 (195)
T ss_pred             CCcHHHHHHHHHHHHH
Confidence            75443 3334444443

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.

>cd01898 Obg Obg subfamily

Probab=94.35  E-value=0.11  Score=41.32  Aligned_cols=74  Identities=20%  Similarity=0.302  Sum_probs=40.2

Q ss_pred             CEEEEecCCCCCcH----HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH--------hhcC
Q 023301           31 DHIVIETTGLAKPA----PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV--------AYAD   98 (284)
Q Consensus        31 d~iiIE~sG~a~p~----~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi--------~~Ad   98 (284)
                      ...+++++|+.+-.    .+...+     +...-..+.++.|+|+......+.+.      ....+++        ...-
T Consensus        49 ~~~l~DtpG~~~~~~~~~~~~~~~-----~~~~~~~d~vi~v~D~~~~~~~~~~~------~~~~~~l~~~~~~~~~~p~  117 (170)
T cd01898          49 SFVVADIPGLIEGASEGKGLGHRF-----LRHIERTRLLLHVIDLSGDDDPVEDY------KTIRNELELYNPELLEKPR  117 (170)
T ss_pred             eEEEEecCcccCcccccCCchHHH-----HHHHHhCCEEEEEEecCCCCCHHHHH------HHHHHHHHHhCcccccccc
Confidence            66799999975321    111111     11122467899999998641111111      1111222        3445


Q ss_pred             EEEEccCCCCChhHHHH
Q 023301           99 RIILNKIDLVTETELGS  115 (284)
Q Consensus        99 ~ivlnK~D~~~~~~~~~  115 (284)
                      ++|+||+|+.+......
T Consensus       118 ivv~NK~Dl~~~~~~~~  134 (170)
T cd01898         118 IVVLNKIDLLDEEELFE  134 (170)
T ss_pred             EEEEEchhcCCchhhHH
Confidence            89999999977655433

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.

>TIGR03156 GTP_HflX GTP-binding protein HflX

Probab=94.00  E-value=0.18  Score=45.87  Aligned_cols=79  Identities=20%  Similarity=0.412  Sum_probs=47.9

Q ss_pred             CCCEEEEecCCC-CC-cHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC---EEEEc
Q 023301           29 QFDHIVIETTGL-AK-PAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD---RIILN  103 (284)
Q Consensus        29 ~~d~iiIE~sG~-a~-p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad---~ivln  103 (284)
                      ....+|++|.|. .+ |..+++.+..  .+......+.++.|+|+...... .+.  ..+ ..+..++...+   ++|+|
T Consensus       236 ~~~i~l~DT~G~~~~l~~~lie~f~~--tle~~~~ADlil~VvD~s~~~~~-~~~--~~~-~~~L~~l~~~~~piIlV~N  309 (351)
T TIGR03156       236 GGEVLLTDTVGFIRDLPHELVAAFRA--TLEEVREADLLLHVVDASDPDRE-EQI--EAV-EKVLEELGAEDIPQLLVYN  309 (351)
T ss_pred             CceEEEEecCcccccCCHHHHHHHHH--HHHHHHhCCEEEEEEECCCCchH-HHH--HHH-HHHHHHhccCCCCEEEEEE
Confidence            346789999998 33 7777766532  23334467889999999764321 110  000 12334554333   88999


Q ss_pred             cCCCCChhHH
Q 023301          104 KIDLVTETEL  113 (284)
Q Consensus       104 K~D~~~~~~~  113 (284)
                      |+|+.+.+++
T Consensus       310 K~Dl~~~~~v  319 (351)
T TIGR03156       310 KIDLLDEPRI  319 (351)
T ss_pred             eecCCChHhH
Confidence            9999875443

This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial members are designated HflX, following the naming convention in Escherichia coli where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function. Over large numbers of other bacterial genomes, the pairing with hfq is more significant than with hflK and hlfC. The gene from Homo sapiens in this family has been named PGPL (pseudoautosomal GTP-binding protein-like).

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

Probab=93.94  E-value=0.15  Score=42.58  Aligned_cols=84  Identities=19%  Similarity=0.244  Sum_probs=46.7

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHH-HHH---hhcCEEEEccC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAV-EQV---AYADRIILNKI  105 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~-~Qi---~~Ad~ivlnK~  105 (284)
                      ..+.|++++|-.........     .+...  ++++|+|+|+......+.... .++...+. .+.   ...=+|+.||+
T Consensus        48 ~~~~l~D~pG~~~~~~~~~~-----~~~~~--~~~vV~VvD~~~~~~~~~~~~-~~l~~il~~~~~~~~~~pvliv~NK~  119 (203)
T cd04105          48 KKFRLVDVPGHPKLRDKLLE-----TLKNS--AKGIVFVVDSATFQKNLKDVA-EFLYDILTDLEKVKNKIPVLIACNKQ  119 (203)
T ss_pred             ceEEEEECCCCHHHHHHHHH-----HHhcc--CCEEEEEEECccchhHHHHHH-HHHHHHHHHHhhccCCCCEEEEecch
Confidence            45678899997654432221     22222  689999999998743333210 11111111 222   23446777999


Q ss_pred             CCCChhHHHHHHHHHH
Q 023301          106 DLVTETELGSLTERIK  121 (284)
Q Consensus       106 D~~~~~~~~~~~~~l~  121 (284)
                      |+.+....+.+++.+.
T Consensus       120 Dl~~a~~~~~i~~~le  135 (203)
T cd04105         120 DLFTAKPAKKIKEQLE  135 (203)
T ss_pred             hhcccCCHHHHHHHHH
Confidence            9976555555555554

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

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

Probab=93.82  E-value=0.16  Score=40.52  Aligned_cols=102  Identities=21%  Similarity=0.179  Sum_probs=51.1

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH-----HhhhhcCCccchHHHHH-H--------H
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM-----QHLNEVKPRFVVNEAVE-Q--------V   94 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~-----~~l~~~~~~~~~~~~~~-Q--------i   94 (284)
                      .....+++++|..+-....+.+.. ..+...-..+.++.|+|+....     ....+..  .....+.. +        .
T Consensus        43 ~~~~~i~DtpG~~~~~~~~~~~~~-~~~~~~~~~d~ii~v~d~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~  119 (176)
T cd01881          43 GARIQVADIPGLIEGASEGRGLGN-QFLAHIRRADAILHVVDASEDDDIGGVDPLEDYE--ILNAELKLYDLETILGLLT  119 (176)
T ss_pred             CCeEEEEeccccchhhhcCCCccH-HHHHHHhccCEEEEEEeccCCccccccCHHHHHH--HHHHHHHHhhhhhHHHHHh
Confidence            455688999998532111111100 0011122467899999998752     1111110  00011111 1        3


Q ss_pred             hhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeec
Q 023301           95 AYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus        95 ~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ...-++|+||+|+.+..................+++.++
T Consensus       120 ~~p~ivv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~S  158 (176)
T cd01881         120 AKPVIYVLNKIDLDDAEELEEELVRELALEEGAEVVPIS  158 (176)
T ss_pred             hCCeEEEEEchhcCchhHHHHHHHHHHhcCCCCCEEEEe
Confidence            567899999999987766554422222333445565554

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

>cd01882 BMS1 Bms1

Probab=93.79  E-value=0.31  Score=41.38  Aligned_cols=95  Identities=18%  Similarity=0.178  Sum_probs=51.5

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEE-EEccCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRI-ILNKIDLV  108 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~i-vlnK~D~~  108 (284)
                      -.+.+++|+|-.  ..+++.+         -..+.++.|+|+.......    +..+...+.. .....+| |+||+|+.
T Consensus        83 ~~i~~vDtPg~~--~~~l~~a---------k~aDvVllviDa~~~~~~~----~~~i~~~l~~-~g~p~vi~VvnK~D~~  146 (225)
T cd01882          83 RRLTFIECPNDI--NAMIDIA---------KVADLVLLLIDASFGFEME----TFEFLNILQV-HGFPRVMGVLTHLDLF  146 (225)
T ss_pred             ceEEEEeCCchH--HHHHHHH---------HhcCEEEEEEecCcCCCHH----HHHHHHHHHH-cCCCeEEEEEeccccC
Confidence            345788888732  3333321         2457789999997532110    0111111112 2334555 99999997


Q ss_pred             Ch-hHHHHHHHHHHH-----hCCCCceeeec---cCCCChh
Q 023301          109 TE-TELGSLTERIKH-----INAMAPVKLAK---YGSVDMD  140 (284)
Q Consensus       109 ~~-~~~~~~~~~l~~-----~np~a~i~~~~---~g~v~~~  140 (284)
                      ++ +.++.+.+.++.     +.+.++|+..+   .+.++..
T Consensus       147 ~~~~~~~~~~~~l~~~~~~~~~~~~ki~~iSa~~~~~~~~~  187 (225)
T cd01882         147 KKNKTLRKTKKRLKHRFWTEVYQGAKLFYLSGIVHGRYPKT  187 (225)
T ss_pred             CcHHHHHHHHHHHHHHHHHhhCCCCcEEEEeeccCCCCCHH
Confidence            43 335555544433     55788888776   4444443

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.

>TIGR02729 Obg_CgtA Obg family GTPase CgtA

Probab=93.78  E-value=0.21  Score=45.07  Aligned_cols=92  Identities=21%  Similarity=0.308  Sum_probs=51.2

Q ss_pred             CCEEEEecCCCCCcHH----HHHHhcccccccceeeeceEEEEEcccchH--HhhhhcCCccchHHHHHHH--------h
Q 023301           30 FDHIVIETTGLAKPAP----VIETFCTDELVSQYVKLDGVITLVDSKHAM--QHLNEVKPRFVVNEAVEQV--------A   95 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~----i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~--~~l~~~~~~~~~~~~~~Qi--------~   95 (284)
                      ..+.|++++|+-+...    +-..+     ++..-..+.++.|+|+....  ..+.+.      ..+..++        .
T Consensus       205 ~~~~i~D~PGli~~a~~~~gLg~~f-----lrhierad~ll~VvD~s~~~~~~~~e~l------~~l~~EL~~~~~~l~~  273 (329)
T TIGR02729       205 RSFVIADIPGLIEGASEGAGLGHRF-----LKHIERTRVLLHLIDISPLDGRDPIEDY------EIIRNELKKYSPELAE  273 (329)
T ss_pred             eEEEEEeCCCcccCCcccccHHHHH-----HHHHHhhCEEEEEEcCccccccCHHHHH------HHHHHHHHHhhhhhcc
Confidence            4578889999854321    11111     22223567899999998641  111111      1122222        3


Q ss_pred             hcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeec
Q 023301           96 YADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus        96 ~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ..-+||+||+|+.+.+..+.+.+.+.+... .+++.++
T Consensus       274 kp~IIV~NK~DL~~~~~~~~~~~~l~~~~~-~~vi~iS  310 (329)
T TIGR02729       274 KPRIVVLNKIDLLDEEELAELLKELKKALG-KPVFPIS  310 (329)
T ss_pred             CCEEEEEeCccCCChHHHHHHHHHHHHHcC-CcEEEEE
Confidence            456899999999877666655555543332 4566554

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.

>PRK15467 ethanolamine utilization protein EutP; Provisional

Probab=93.78  E-value=0.14  Score=40.80  Aligned_cols=97  Identities=11%  Similarity=0.094  Sum_probs=55.0

Q ss_pred             EEecCCCCCcHH-HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhH
Q 023301           34 VIETTGLAKPAP-VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETE  112 (284)
Q Consensus        34 iIE~sG~a~p~~-i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~  112 (284)
                      +|.++|.....+ ....+.     ...-..+.++.|+|+......+.    ..   .........-++++||+|+.+ ..
T Consensus        41 ~iDtpG~~~~~~~~~~~~~-----~~~~~ad~il~v~d~~~~~s~~~----~~---~~~~~~~~~ii~v~nK~Dl~~-~~  107 (158)
T PRK15467         41 DIDTPGEYFSHPRWYHALI-----TTLQDVDMLIYVHGANDPESRLP----AG---LLDIGVSKRQIAVISKTDMPD-AD  107 (158)
T ss_pred             cccCCccccCCHHHHHHHH-----HHHhcCCEEEEEEeCCCcccccC----HH---HHhccCCCCeEEEEEccccCc-cc
Confidence            578888744332 222211     11236688999999986532211    11   111111234689999999865 34


Q ss_pred             HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          113 LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       113 ~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      .+.+.+++++.....+++.++. ..-..+.++
T Consensus       108 ~~~~~~~~~~~~~~~p~~~~Sa~~g~gi~~l~  139 (158)
T PRK15467        108 VAATRKLLLETGFEEPIFELNSHDPQSVQQLV  139 (158)
T ss_pred             HHHHHHHHHHcCCCCCEEEEECCCccCHHHHH
Confidence            5667777777765568877653 344555555

>PRK01889 GTPase RsgA; Reviewed

Probab=93.76  E-value=0.081  Score=48.27  Aligned_cols=69  Identities=16%  Similarity=0.230  Sum_probs=39.8

Q ss_pred             eeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeecc
Q 023301           60 VKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKY  134 (284)
Q Consensus        60 ~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~  134 (284)
                      -.+|.++.|+++..-.+.  ..-++++.  +......--+||+||+|++++.  +...+.++.+++..+|+.++.
T Consensus       111 ANvD~vliV~s~~p~~~~--~~ldr~L~--~a~~~~i~piIVLNK~DL~~~~--~~~~~~~~~~~~g~~Vi~vSa  179 (356)
T PRK01889        111 ANVDTVFIVCSLNHDFNL--RRIERYLA--LAWESGAEPVIVLTKADLCEDA--EEKIAEVEALAPGVPVLAVSA  179 (356)
T ss_pred             EeCCEEEEEEecCCCCCh--hHHHHHHH--HHHHcCCCEEEEEEChhcCCCH--HHHHHHHHHhCCCCcEEEEEC
Confidence            578889999988531110  00112221  1233333458999999998752  233455666677788886553

>cd01876 YihA_EngB The YihA (EngB) subfamily

Probab=93.61  E-value=0.51  Score=36.93  Aligned_cols=97  Identities=20%  Similarity=0.316  Sum_probs=51.2

Q ss_pred             CEEEEecCCCCCc------HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEcc
Q 023301           31 DHIVIETTGLAKP------APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p------~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK  104 (284)
                      ...+++++|++..      ..-...+. ...+...-.++.++.|+|..........    .+ ...........++++||
T Consensus        46 ~~~~~D~~g~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~d~~~~~~~~~~----~~-~~~l~~~~~~vi~v~nK  119 (170)
T cd01876          46 KFRLVDLPGYGYAKVSKEVKEKWGKLI-EEYLENRENLKGVVLLIDSRHGPTEIDL----EM-LDWLEELGIPFLVVLTK  119 (170)
T ss_pred             eEEEecCCCccccccCHHHHHHHHHHH-HHHHHhChhhhEEEEEEEcCcCCCHhHH----HH-HHHHHHcCCCEEEEEEc
Confidence            5678999998773      11111111 1112222346678889998754211100    01 11223334455889999


Q ss_pred             CCCCChhHHHHHHHHHHH----hCCCCceeeec
Q 023301          105 IDLVTETELGSLTERIKH----INAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~~~~~~~~l~~----~np~a~i~~~~  133 (284)
                      +|+.++++.......++.    ..+..+++.++
T Consensus       120 ~D~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~S  152 (170)
T cd01876         120 ADKLKKSELAKALKEIKKELKLFEIDPPIILFS  152 (170)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhccCCCceEEEe
Confidence            999877766555444442    23445666544

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.

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

Probab=93.47  E-value=0.21  Score=39.09  Aligned_cols=93  Identities=16%  Similarity=0.217  Sum_probs=48.7

Q ss_pred             CCEEEEecCCCCCcHHH--HHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPV--IETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i--~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~  107 (284)
                      .+..+++|+|..+....  -..+.. ..+.. -..+.++.|+|+........      .... ..+....=++|+||+|+
T Consensus        43 ~~~~liDtpG~~~~~~~~~~~~~~~-~~~~~-~~~d~vi~v~d~~~~~~~~~------~~~~-~~~~~~~~iiv~NK~Dl  113 (158)
T cd01879          43 KEIEIVDLPGTYSLSPYSEDEKVAR-DFLLG-EKPDLIVNVVDATNLERNLY------LTLQ-LLELGLPVVVALNMIDE  113 (158)
T ss_pred             eEEEEEECCCccccCCCChhHHHHH-HHhcC-CCCcEEEEEeeCCcchhHHH------HHHH-HHHcCCCEEEEEehhhh
Confidence            46789999998764321  000100 01111 25778999999987432211      0011 12234556889999999


Q ss_pred             CChhHHHH-HHHHHHHhCCCCceeeec
Q 023301          108 VTETELGS-LTERIKHINAMAPVKLAK  133 (284)
Q Consensus       108 ~~~~~~~~-~~~~l~~~np~a~i~~~~  133 (284)
                      .+.+.+.. ..+..+.++  .+++.++
T Consensus       114 ~~~~~~~~~~~~~~~~~~--~~~~~iS  138 (158)
T cd01879         114 AEKRGIKIDLDKLSELLG--VPVVPTS  138 (158)
T ss_pred             cccccchhhHHHHHHhhC--CCeEEEE
Confidence            76544332 222223333  4566544

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.

>TIGR00231 small_GTP small GTP-binding protein domain

Probab=93.25  E-value=0.52  Score=36.17  Aligned_cols=94  Identities=16%  Similarity=0.223  Sum_probs=50.4

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH--hhcCEEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV--AYADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi--~~Ad~ivlnK~D~  107 (284)
                      ....+++++|..+...+...... ....-.+..+.++.|+|+........        ..+..+.  ...-++++||+|+
T Consensus        50 ~~~~~~D~~G~~~~~~~~~~~~~-~~~~~i~~~d~~~~v~~~~~~~~~~~--------~~~~~~~~~~~p~ivv~nK~D~  120 (161)
T TIGR00231        50 YKFNLLDTAGQEDYRAIRRLYYR-AVESSLRVFDIVILVLDVEEILEKQT--------KEIIHHAESNVPIILVGNKIDL  120 (161)
T ss_pred             EEEEEEECCCcccchHHHHHHHh-hhhEEEEEEEEeeeehhhhhHhHHHH--------HHHHHhcccCCcEEEEEEcccC
Confidence            45678899997666554433221 11222345555566666655442111        1111111  4567899999999


Q ss_pred             CChhHHHHHHHHHHHhCCCCceeeec
Q 023301          108 VTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       108 ~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ..........+.++.++. .+++.++
T Consensus       121 ~~~~~~~~~~~~~~~~~~-~~~~~~s  145 (161)
T TIGR00231       121 RDAKLKTHVAFLFAKLNG-EPIIPLS  145 (161)
T ss_pred             CcchhhHHHHHHHhhccC-CceEEee
Confidence            875545555555555443 3455544

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.

>cd01849 YlqF_related_GTPase YlqF-related GTPases

Probab=93.23  E-value=0.28  Score=38.88  Aligned_cols=66  Identities=15%  Similarity=0.174  Sum_probs=35.2

Q ss_pred             ceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeec
Q 023301           63 DGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus        63 ~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      |.++.|+|+.......    ...+.......-.-.-++|+||+|+++.+++......+++..+ ..++..+
T Consensus         1 Dvvl~VvD~~~p~~~~----~~~i~~~~~~~~~~p~IiVlNK~Dl~~~~~~~~~~~~~~~~~~-~~ii~vS   66 (155)
T cd01849           1 DVILEVLDARDPLGTR----SPDIERVLIKEKGKKLILVLNKADLVPKEVLRKWLAYLRHSYP-TIPFKIS   66 (155)
T ss_pred             CEEEEEEeccCCcccc----CHHHHHHHHhcCCCCEEEEEechhcCCHHHHHHHHHHHHhhCC-ceEEEEe
Confidence            3578999997653221    1111100111223356888999999887665544444444433 4555443

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.

>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=93.04  E-value=0.27  Score=40.24  Aligned_cols=79  Identities=27%  Similarity=0.324  Sum_probs=44.4

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      .....+|.++|-.+...  ...      ......+.+|.|||+.........    .. -....+....=+|++||+|+.
T Consensus        69 ~~~i~~iDtPG~~~f~~--~~~------~~~~~~D~ailvVda~~g~~~~~~----~~-l~~~~~~~~p~ivvlNK~D~~  135 (188)
T PF00009_consen   69 NRKITLIDTPGHEDFIK--EMI------RGLRQADIAILVVDANDGIQPQTE----EH-LKILRELGIPIIVVLNKMDLI  135 (188)
T ss_dssp             SEEEEEEEESSSHHHHH--HHH------HHHTTSSEEEEEEETTTBSTHHHH----HH-HHHHHHTT-SEEEEEETCTSS
T ss_pred             ccceeecccccccceee--ccc------ceecccccceeeeecccccccccc----cc-cccccccccceEEeeeeccch
Confidence            44678899999654221  111      112356789999999864321110    00 112344455578999999998


Q ss_pred             ChhHHHHHHHHHH
Q 023301          109 TETELGSLTERIK  121 (284)
Q Consensus       109 ~~~~~~~~~~~l~  121 (284)
                       ..++.++.+.++
T Consensus       136 -~~~~~~~~~~~~  147 (188)
T PF00009_consen  136 -EKELEEIIEEIK  147 (188)
T ss_dssp             -HHHHHHHHHHHH
T ss_pred             -hhhHHHHHHHHH
Confidence             545555544444

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 ....

>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional

Probab=93.03  E-value=0.46  Score=46.59  Aligned_cols=89  Identities=16%  Similarity=0.234  Sum_probs=50.4

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC-EEEEccCCCCCh
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDLVTE  110 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~~~~  110 (284)
                      +-||.++|-..   .+...     +...-.++.++.|||+..-.+.  ..  +... .+...+.... +||+||+|++++
T Consensus        53 i~~IDtPGhe~---fi~~m-----~~g~~~~D~~lLVVda~eg~~~--qT--~ehl-~il~~lgi~~iIVVlNKiDlv~~  119 (614)
T PRK10512         53 LGFIDVPGHEK---FLSNM-----LAGVGGIDHALLVVACDDGVMA--QT--REHL-AILQLTGNPMLTVALTKADRVDE  119 (614)
T ss_pred             EEEEECCCHHH---HHHHH-----HHHhhcCCEEEEEEECCCCCcH--HH--HHHH-HHHHHcCCCeEEEEEECCccCCH
Confidence            35889999633   22221     1223457889999999763211  00  0010 1123333344 589999999987


Q ss_pred             hHHHHHHHHHHHh----C-CCCceeeec
Q 023301          111 TELGSLTERIKHI----N-AMAPVKLAK  133 (284)
Q Consensus       111 ~~~~~~~~~l~~~----n-p~a~i~~~~  133 (284)
                      +.++.+.+.+++.    + ..++++.+|
T Consensus       120 ~~~~~v~~ei~~~l~~~~~~~~~ii~VS  147 (614)
T PRK10512        120 ARIAEVRRQVKAVLREYGFAEAKLFVTA  147 (614)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCcEEEEe
Confidence            7766655555543    2 246777665

>cd04171 SelB SelB subfamily

Probab=93.00  E-value=0.69  Score=36.24  Aligned_cols=90  Identities=22%  Similarity=0.231  Sum_probs=45.6

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH-HhhhhcCCccchHHHHHHHhh-cCEEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM-QHLNEVKPRFVVNEAVEQVAY-ADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~-~~l~~~~~~~~~~~~~~Qi~~-Ad~ivlnK~D~  107 (284)
                      ....+++|+|.-...   ...     .......+.++.|+|+..-. ....+     .. ....+... .=++++||+|+
T Consensus        51 ~~~~~~DtpG~~~~~---~~~-----~~~~~~ad~ii~V~d~~~~~~~~~~~-----~~-~~~~~~~~~~~ilv~NK~Dl  116 (164)
T cd04171          51 KRLGFIDVPGHEKFI---KNM-----LAGAGGIDLVLLVVAADEGIMPQTRE-----HL-EILELLGIKRGLVVLTKADL  116 (164)
T ss_pred             cEEEEEECCChHHHH---HHH-----HhhhhcCCEEEEEEECCCCccHhHHH-----HH-HHHHHhCCCcEEEEEECccc
Confidence            345678899864321   111     11123577899999997511 11000     00 11233333 34688899999


Q ss_pred             CChhHHH----HHHHHHHHhC-CCCceeeec
Q 023301          108 VTETELG----SLTERIKHIN-AMAPVKLAK  133 (284)
Q Consensus       108 ~~~~~~~----~~~~~l~~~n-p~a~i~~~~  133 (284)
                      .+.+.+.    ++.+.++... ...+++.++
T Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~S  147 (164)
T cd04171         117 VDEDWLELVEEEIRELLAGTFLADAPIFPVS  147 (164)
T ss_pred             cCHHHHHHHHHHHHHHHHhcCcCCCcEEEEe
Confidence            8764333    3334443321 235666554

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

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=92.93  E-value=1.2  Score=39.13  Aligned_cols=100  Identities=18%  Similarity=0.310  Sum_probs=57.3

Q ss_pred             CCCCEEEEecCCCCCcHH-HHHHhccccccccee------eeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEE
Q 023301           28 GQFDHIVIETTGLAKPAP-VIETFCTDELVSQYV------KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRI  100 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~~-i~~~l~~~~~l~~~~------~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~i  100 (284)
                      .++|+|||+|.|...... +++.|..   +....      .-+.++.|+|+..-.+.+...       ....+....+-+
T Consensus       153 ~~~D~ViIDT~G~~~~d~~~~~el~~---~~~~~~~~~~~~~~~~~LVl~a~~~~~~~~~~-------~~f~~~~~~~g~  222 (272)
T TIGR00064       153 RNIDVVLIDTAGRLQNKVNLMDELKK---IKRVIKKVDKDAPDEVLLVLDATTGQNALEQA-------KVFNEAVGLTGI  222 (272)
T ss_pred             CCCCEEEEeCCCCCcchHHHHHHHHH---HHHHHhcccCCCCceEEEEEECCCCHHHHHHH-------HHHHhhCCCCEE
Confidence            679999999999986432 2222211   11111      256789999997643332210       111223357899


Q ss_pred             EEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCCChhhh
Q 023301          101 ILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFV  142 (284)
Q Consensus       101 vlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v~~~~l  142 (284)
                      |+||.|....  .-.+.......  ..||...+.|+- ++.|
T Consensus       223 IlTKlDe~~~--~G~~l~~~~~~--~~Pi~~~~~Gq~-~~dl  259 (272)
T TIGR00064       223 ILTKLDGTAK--GGIILSIAYEL--KLPIKFIGVGEK-IDDL  259 (272)
T ss_pred             EEEccCCCCC--ccHHHHHHHHH--CcCEEEEeCCCC-hHhC
Confidence            9999998542  33444444444  367777667654 3443

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.

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=92.88  E-value=1.1  Score=40.22  Aligned_cols=98  Identities=18%  Similarity=0.230  Sum_probs=56.8

Q ss_pred             cCCCCEEEEecCCCCCcH-HHHHHhccccc-ccc--eeeeceEEEEEcccchHHhhhhcCCccchHHHHH--HHhhcCEE
Q 023301           27 QGQFDHIVIETTGLAKPA-PVIETFCTDEL-VSQ--YVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVE--QVAYADRI  100 (284)
Q Consensus        27 ~~~~d~iiIE~sG~a~p~-~i~~~l~~~~~-l~~--~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~--Qi~~Ad~i  100 (284)
                      ..++|+|||+|.|..... ..++.|..-.. ...  ...-..++.|+|+..-...+..         +..  +....+-+
T Consensus       194 ~~~~D~ViIDTaGr~~~~~~l~~eL~~~~~v~~~~~~~~p~~~~LVl~a~~g~~~~~~---------a~~f~~~~~~~gi  264 (318)
T PRK10416        194 ARGIDVLIIDTAGRLHNKTNLMEELKKIKRVIKKADPDAPHEVLLVLDATTGQNALSQ---------AKAFHEAVGLTGI  264 (318)
T ss_pred             hCCCCEEEEeCCCCCcCCHHHHHHHHHHHHHHhhhcCCCCceEEEEEECCCChHHHHH---------HHHHHhhCCCCEE
Confidence            467999999999997633 22222211000 000  1123458999999874433221         122  23357789


Q ss_pred             EEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCC
Q 023301          101 ILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSV  137 (284)
Q Consensus       101 vlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v  137 (284)
                      |+||.|...  ..-.+...+...  ..||.....|+-
T Consensus       265 IlTKlD~t~--~~G~~l~~~~~~--~~Pi~~v~~Gq~  297 (318)
T PRK10416        265 ILTKLDGTA--KGGVVFAIADEL--GIPIKFIGVGEG  297 (318)
T ss_pred             EEECCCCCC--CccHHHHHHHHH--CCCEEEEeCCCC
Confidence            999999754  344555555555  577777777753

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=92.85  E-value=0.51  Score=37.35  Aligned_cols=82  Identities=15%  Similarity=0.201  Sum_probs=45.0

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH---HhhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ---VAYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q---i~~Ad~ivlnK~D  106 (284)
                      ....+++++|...-..+.....        -..+.+|.|+|+..... +.... ..+ ..+..+   -...=+|++||+|
T Consensus        50 ~~~~l~Dt~G~~~~~~~~~~~~--------~~~~~~v~vvd~~~~~~-~~~~~-~~~-~~~~~~~~~~~~p~ilv~NK~D  118 (167)
T cd04160          50 ARLKFWDLGGQESLRSLWDKYY--------AECHAIIYVIDSTDRER-FEESK-SAL-EKVLRNEALEGVPLLILANKQD  118 (167)
T ss_pred             EEEEEEECCCChhhHHHHHHHh--------CCCCEEEEEEECchHHH-HHHHH-HHH-HHHHhChhhcCCCEEEEEEccc
Confidence            5567889999876544333221        13467999999977432 11110 011 111111   1245588889999


Q ss_pred             CCChhHHHHHHHHHHH
Q 023301          107 LVTETELGSLTERIKH  122 (284)
Q Consensus       107 ~~~~~~~~~~~~~l~~  122 (284)
                      +.+......+.+.++.
T Consensus       119 ~~~~~~~~~~~~~~~~  134 (167)
T cd04160         119 LPDALSVEEIKEVFQD  134 (167)
T ss_pred             cccCCCHHHHHHHhcc
Confidence            8665444555555443

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.

>PRK09554 feoB ferrous iron transport protein B; Reviewed

Probab=92.76  E-value=0.17  Score=50.93  Aligned_cols=97  Identities=13%  Similarity=0.141  Sum_probs=51.9

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccce----eeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEcc
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQY----VKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNK  104 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~----~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK  104 (284)
                      ..+..+++++|..+..........++.....    -..+.++.|+|+.+....+.      .. ....+....-++++||
T Consensus        49 ~~~i~lvDtPG~ysl~~~~~~~s~~E~i~~~~l~~~~aD~vI~VvDat~ler~l~------l~-~ql~e~giPvIvVlNK  121 (772)
T PRK09554         49 DHQVTLVDLPGTYSLTTISSQTSLDEQIACHYILSGDADLLINVVDASNLERNLY------LT-LQLLELGIPCIVALNM  121 (772)
T ss_pred             ceEEEEEECCCccccccccccccHHHHHHHHHHhccCCCEEEEEecCCcchhhHH------HH-HHHHHcCCCEEEEEEc
Confidence            3467899999998754321100000111111    15688999999998654321      10 1123345677999999


Q ss_pred             CCCCChhHHHHHHHHHHHhCCCCceeeec
Q 023301          105 IDLVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +|+........-.+.+++.. ..+++.++
T Consensus       122 ~Dl~~~~~i~id~~~L~~~L-G~pVvpiS  149 (772)
T PRK09554        122 LDIAEKQNIRIDIDALSARL-GCPVIPLV  149 (772)
T ss_pred             hhhhhccCcHHHHHHHHHHh-CCCEEEEE
Confidence            99875433322223333322 24666554

>cd04165 GTPBP1_like GTPBP1-like

Probab=92.73  E-value=0.61  Score=39.61  Aligned_cols=84  Identities=14%  Similarity=0.124  Sum_probs=48.5

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      ..-+-+|.++|..+...  .++.   .+.. ...+.++.|||+..-.....    +... .+..+....=+||+||+|++
T Consensus        83 ~~~i~liDtpG~~~~~~--~~~~---~~~~-~~~D~~llVvda~~g~~~~d----~~~l-~~l~~~~ip~ivvvNK~D~~  151 (224)
T cd04165          83 SKLVTFIDLAGHERYLK--TTLF---GLTG-YAPDYAMLVVAANAGIIGMT----KEHL-GLALALNIPVFVVVTKIDLA  151 (224)
T ss_pred             CcEEEEEECCCcHHHHH--HHHH---hhcc-cCCCEEEEEEECCCCCcHHH----HHHH-HHHHHcCCCEEEEEECcccc
Confidence            45678899999754322  1111   1111 24567899999876332111    1111 11233334458999999999


Q ss_pred             ChhHHHHHHHHHHHh
Q 023301          109 TETELGSLTERIKHI  123 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~  123 (284)
                      +.+++....+.+++.
T Consensus       152 ~~~~~~~~~~~l~~~  166 (224)
T cd04165         152 PANILQETLKDLKRI  166 (224)
T ss_pred             CHHHHHHHHHHHHHH
Confidence            887777777766654

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

>KOG2484 consensus GTPase [General function prediction only]

Probab=92.51  E-value=0.28  Score=44.74  Aligned_cols=64  Identities=25%  Similarity=0.310  Sum_probs=47.0

Q ss_pred             eceEEEEEcccchHHhhhhcCCccchHHHHHHHhhc-----CEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeec
Q 023301           62 LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYA-----DRIILNKIDLVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus        62 l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~A-----d~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      -|.|+-|+||+-....      +  ...+.+|+..|     =++||||+|+++.+.++....+++.-.|.......+
T Consensus       147 sDVVleVlDARDPlgt------R--~~~vE~~V~~~~gnKkLILVLNK~DLVPrEv~e~Wl~YLr~~~ptv~fkast  215 (435)
T KOG2484|consen  147 SDVVLEVLDARDPLGT------R--CPEVEEAVLQAHGNKKLILVLNKIDLVPREVVEKWLVYLRREGPTVAFKAST  215 (435)
T ss_pred             hheEEEeeeccCCCCC------C--ChhHHHHHHhccCCceEEEEeehhccCCHHHHHHHHHHHHhhCCcceeeccc
Confidence            4567899999886542      1  13456666433     267889999999999999999999998876664433

>PRK12299 obgE GTPase CgtA; Reviewed

Probab=92.51  E-value=0.36  Score=43.67  Aligned_cols=108  Identities=19%  Similarity=0.238  Sum_probs=51.9

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHH---H-HhhcCEEEEccC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVE---Q-VAYADRIILNKI  105 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~---Q-i~~Ad~ivlnK~  105 (284)
                      ...++++++|+-+-..--..|.. ..++..-..+.++.|+|+.... .+.+.  ..+..++..   . ....-+||+||+
T Consensus       206 ~~~~i~D~PGli~ga~~~~gLg~-~flrhie~a~vlI~ViD~s~~~-s~e~~--~~~~~EL~~~~~~L~~kp~IIV~NKi  281 (335)
T PRK12299        206 KSFVIADIPGLIEGASEGAGLGH-RFLKHIERTRLLLHLVDIEAVD-PVEDY--KTIRNELEKYSPELADKPRILVLNKI  281 (335)
T ss_pred             cEEEEEeCCCccCCCCccccHHH-HHHHHhhhcCEEEEEEcCCCCC-CHHHH--HHHHHHHHHhhhhcccCCeEEEEECc
Confidence            35789999998653221001100 1122222456799999998532 11111  001111111   1 234678999999


Q ss_pred             CCCChhHHH--HHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          106 DLVTETELG--SLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       106 D~~~~~~~~--~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+.+.++..  ......+..  ..+++.++. ....++.++
T Consensus       282 DL~~~~~~~~~~~~~~~~~~--~~~i~~iSAktg~GI~eL~  320 (335)
T PRK12299        282 DLLDEEEEREKRAALELAAL--GGPVFLISAVTGEGLDELL  320 (335)
T ss_pred             ccCCchhHHHHHHHHHHHhc--CCCEEEEEcCCCCCHHHHH
Confidence            997654432  122222222  256666553 233444444

>PRK00454 engB GTP-binding protein YsxC; Reviewed

Probab=92.27  E-value=0.8  Score=37.33  Aligned_cols=98  Identities=18%  Similarity=0.235  Sum_probs=49.3

Q ss_pred             CCEEEEecCCCCCc---HHHH---HHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEc
Q 023301           30 FDHIVIETTGLAKP---APVI---ETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILN  103 (284)
Q Consensus        30 ~d~iiIE~sG~a~p---~~i~---~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivln  103 (284)
                      .+..|+.++|....   ....   ..+. ...+...-.++.++.|+|+..-.....    ..+ ..........-++++|
T Consensus        70 ~~l~l~DtpG~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~d~~~~~~~~~----~~i-~~~l~~~~~~~iiv~n  143 (196)
T PRK00454         70 DKLRLVDLPGYGYAKVSKEEKEKWQKLI-EEYLRTRENLKGVVLLIDSRHPLKELD----LQM-IEWLKEYGIPVLIVLT  143 (196)
T ss_pred             CeEEEeCCCCCCCcCCCchHHHHHHHHH-HHHHHhCccceEEEEEEecCCCCCHHH----HHH-HHHHHHcCCcEEEEEE
Confidence            35678999997532   1111   1111 112222234566788888765221110    001 1112223333478899


Q ss_pred             cCCCCChhHHHHHHHHHHHhC-C-CCceeeec
Q 023301          104 KIDLVTETELGSLTERIKHIN-A-MAPVKLAK  133 (284)
Q Consensus       104 K~D~~~~~~~~~~~~~l~~~n-p-~a~i~~~~  133 (284)
                      |+|+.+..+.+.+.+.++... . ..+++.++
T Consensus       144 K~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~~S  175 (196)
T PRK00454        144 KADKLKKGERKKQLKKVRKALKFGDDEVILFS  175 (196)
T ss_pred             CcccCCHHHHHHHHHHHHHHHHhcCCceEEEE
Confidence            999988777666555554432 2 35666554

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

Probab=92.25  E-value=0.89  Score=37.31  Aligned_cols=67  Identities=25%  Similarity=0.375  Sum_probs=39.2

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVT  109 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~  109 (284)
                      ....+++++|..+.........        -..+.++.|+|+..-...  .  ...+... ..+....-+|++||+|+..
T Consensus        65 ~~~~l~DtpG~~~~~~~~~~~~--------~~~d~~ilV~d~~~~~~~--~--~~~~~~~-~~~~~~p~iiv~NK~Dl~~  131 (194)
T cd01891          65 TKINIVDTPGHADFGGEVERVL--------SMVDGVLLLVDASEGPMP--Q--TRFVLKK-ALELGLKPIVVINKIDRPD  131 (194)
T ss_pred             EEEEEEECCCcHHHHHHHHHHH--------HhcCEEEEEEECCCCccH--H--HHHHHHH-HHHcCCCEEEEEECCCCCC
Confidence            4557899999877554333221        245788999999762110  0  0011011 1233456789999999964

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

>cd00882 Ras_like_GTPase Ras-like GTPase superfamily

Probab=92.21  E-value=0.26  Score=37.38  Aligned_cols=96  Identities=18%  Similarity=0.156  Sum_probs=54.0

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCcc--chHHHHHHHhhcCEEEEccCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRF--VVNEAVEQVAYADRIILNKID  106 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~--~~~~~~~Qi~~Ad~ivlnK~D  106 (284)
                      ..+..+++++|...........        .-..+.++.|+|+....... ... ..  ........-...-++++||+|
T Consensus        44 ~~~~~l~D~~g~~~~~~~~~~~--------~~~~~~~i~v~d~~~~~~~~-~~~-~~~~~~~~~~~~~~~~~ivv~nk~D  113 (157)
T cd00882          44 KVKLQIWDTAGQERFRSLRRLY--------YRGADGIILVYDVTDRESFE-NVK-EWLLLILINKEGENIPIILVGNKID  113 (157)
T ss_pred             EEEEEEEecCChHHHHhHHHHH--------hcCCCEEEEEEECcCHHHHH-HHH-HHHHHHHHhhccCCCcEEEEEeccc
Confidence            5567899999987755432211        12456789999998855321 110 00  000112333455688889999


Q ss_pred             CCChhHHHHHH-HHHHHhCCCCceeeecc
Q 023301          107 LVTETELGSLT-ERIKHINAMAPVKLAKY  134 (284)
Q Consensus       107 ~~~~~~~~~~~-~~l~~~np~a~i~~~~~  134 (284)
                      +.+........ ..........+++.++.
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s~  142 (157)
T cd00882         114 LPEERVVSEEELAEQLAKELGVPYFETSA  142 (157)
T ss_pred             cccccchHHHHHHHHHHhhcCCcEEEEec
Confidence            98765544432 22233345677776653

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

>cd01854 YjeQ_engC YjeQ/EngC

Probab=92.13  E-value=0.31  Score=43.02  Aligned_cols=115  Identities=22%  Similarity=0.225  Sum_probs=55.7

Q ss_pred             CceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhc-ccccccc----------eeeeceEEEEEccc
Q 023301            4 NGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFC-TDELVSQ----------YVKLDGVITLVDSK   72 (284)
Q Consensus         4 ~GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~-~~~~l~~----------~~~l~~vv~vvD~~   72 (284)
                      +|=+-|.+++.|...     ....---|+|.+|..+ .+. .++..+. ....+.+          .-.++.++.|+|+.
T Consensus        17 ~~~~~~~~~g~~~~~-----~~~~~vGD~V~~~~~~-~~~-~~i~~i~~R~~~l~R~~~~~~~~~i~anvD~vllV~d~~   89 (287)
T cd01854          17 GGELRCRARGKLRKK-----GIKPVVGDWVEVEPDD-DGE-GVIVRVLPRKNLLSRPAAGGREQVIAANVDQLVIVVSLN   89 (287)
T ss_pred             CeEEEEEeccccccC-----CCCccCCCEEEEEecC-CCc-EEEEEEECCCceEEccCCCCcceeEEEeCCEEEEEEEcC
Confidence            344567777766421     1001234999998754 111 1121111 1111111          34788899999997


Q ss_pred             chHHhhhhcCCccchHHHHHHHhhcC---EEEEccCCCCChhHHHHHHHHHHHhCCCCceeeec
Q 023301           73 HAMQHLNEVKPRFVVNEAVEQVAYAD---RIILNKIDLVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus        73 ~~~~~l~~~~~~~~~~~~~~Qi~~Ad---~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ...-....     + +.....+..++   +||+||+|+.++.+........  .+...+++.++
T Consensus        90 ~p~~s~~~-----l-dr~L~~~~~~~ip~iIVlNK~DL~~~~~~~~~~~~~--~~~g~~v~~vS  145 (287)
T cd01854          90 EPFFNPRL-----L-DRYLVAAEAAGIEPVIVLTKADLLDDEEEELELVEA--LALGYPVLAVS  145 (287)
T ss_pred             CCCCCHHH-----H-HHHHHHHHHcCCCEEEEEEHHHCCChHHHHHHHHHH--HhCCCeEEEEE
Confidence            64300000     0 11122233333   8899999998764322222222  23446766554

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.

>cd04101 RabL4 RabL4 (Rab-like4) subfamily

Probab=92.08  E-value=0.63  Score=36.65  Aligned_cols=68  Identities=15%  Similarity=0.252  Sum_probs=38.6

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-----hcCEEEEcc
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-----YADRIILNK  104 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-----~Ad~ivlnK  104 (284)
                      .+..+.+++|.-....+....     +   -..+.++.|+|..+.... .+.      ..+..++.     ..-++|.||
T Consensus        52 ~~l~i~Dt~G~~~~~~~~~~~-----~---~~~d~ii~v~d~~~~~s~-~~~------~~~~~~~~~~~~~~p~ilv~nK  116 (164)
T cd04101          52 VELFIFDSAGQELYSDMVSNY-----W---ESPSVFILVYDVSNKASF-ENC------SRWVNKVRTASKHMPGVLVGNK  116 (164)
T ss_pred             EEEEEEECCCHHHHHHHHHHH-----h---CCCCEEEEEEECcCHHHH-HHH------HHHHHHHHHhCCCCCEEEEEEC
Confidence            455677888864443332221     1   245789999999875432 111      11223332     345888899


Q ss_pred             CCCCChhH
Q 023301          105 IDLVTETE  112 (284)
Q Consensus       105 ~D~~~~~~  112 (284)
                      +|+.+..+
T Consensus       117 ~Dl~~~~~  124 (164)
T cd04101         117 MDLADKAE  124 (164)
T ss_pred             cccccccC
Confidence            99976543

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.

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

Probab=91.99  E-value=0.27  Score=41.46  Aligned_cols=84  Identities=12%  Similarity=0.223  Sum_probs=42.2

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHH--hhhhcCCccchH-HHHHHHhhcC-EEEEcc
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQ--HLNEVKPRFVVN-EAVEQVAYAD-RIILNK  104 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~--~l~~~~~~~~~~-~~~~Qi~~Ad-~ivlnK  104 (284)
                      .+...+++++|..+..   ...     ....-..+.+|.|||+.....  .+.. ....... .....+...- +|++||
T Consensus        76 ~~~i~liDtpG~~~~~---~~~-----~~~~~~~d~~i~VvDa~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~iiivvNK  146 (219)
T cd01883          76 KYRFTILDAPGHRDFV---PNM-----ITGASQADVAVLVVDARKGEFEAGFEK-GGQTREHALLARTLGVKQLIVAVNK  146 (219)
T ss_pred             CeEEEEEECCChHHHH---HHH-----HHHhhhCCEEEEEEECCCCcccccccc-ccchHHHHHHHHHcCCCeEEEEEEc
Confidence            5677899999964321   111     112235678999999986310  0000 0000000 1122223233 459999


Q ss_pred             CCCCC----hhHHHHHHHHHH
Q 023301          105 IDLVT----ETELGSLTERIK  121 (284)
Q Consensus       105 ~D~~~----~~~~~~~~~~l~  121 (284)
                      +|+..    ++..+.+.+.++
T Consensus       147 ~Dl~~~~~~~~~~~~i~~~l~  167 (219)
T cd01883         147 MDDVTVNWSEERYDEIKKELS  167 (219)
T ss_pred             cccccccccHHHHHHHHHHHH
Confidence            99973    344455555443

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

>cd04166 CysN_ATPS CysN_ATPS subfamily

Probab=91.99  E-value=0.61  Score=38.94  Aligned_cols=68  Identities=22%  Similarity=0.283  Sum_probs=36.8

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEE-EEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRI-ILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~i-vlnK~D~  107 (284)
                      +..+.|+.|+|..+..   ...     ....-..+.++.|+|+..-....    .... ..+..+.....+| |+||+|+
T Consensus        76 ~~~~~liDTpG~~~~~---~~~-----~~~~~~ad~~llVvD~~~~~~~~----~~~~-~~~~~~~~~~~iIvviNK~D~  142 (208)
T cd04166          76 KRKFIIADTPGHEQYT---RNM-----VTGASTADLAILLVDARKGVLEQ----TRRH-SYILSLLGIRHVVVAVNKMDL  142 (208)
T ss_pred             CceEEEEECCcHHHHH---HHH-----HHhhhhCCEEEEEEECCCCccHh----HHHH-HHHHHHcCCCcEEEEEEchhc
Confidence            3467899999974422   111     11123567899999997632110    0000 1122333334445 7999999


Q ss_pred             CC
Q 023301          108 VT  109 (284)
Q Consensus       108 ~~  109 (284)
                      .+
T Consensus       143 ~~  144 (208)
T cd04166         143 VD  144 (208)
T ss_pred             cc
Confidence            74

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.

>PRK00049 elongation factor Tu; Reviewed

Probab=91.97  E-value=0.94  Score=41.95  Aligned_cols=92  Identities=20%  Similarity=0.280  Sum_probs=48.5

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCE-EEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADR-IILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~-ivlnK~D~  107 (284)
                      +..++||+|+|..   ..+....     ...-..+.++.|||+..-...  .  .+... .+.......-+ |++||+|+
T Consensus        74 ~~~i~~iDtPG~~---~f~~~~~-----~~~~~aD~~llVVDa~~g~~~--q--t~~~~-~~~~~~g~p~iiVvvNK~D~  140 (396)
T PRK00049         74 KRHYAHVDCPGHA---DYVKNMI-----TGAAQMDGAILVVSAADGPMP--Q--TREHI-LLARQVGVPYIVVFLNKCDM  140 (396)
T ss_pred             CeEEEEEECCCHH---HHHHHHH-----hhhccCCEEEEEEECCCCCch--H--HHHHH-HHHHHcCCCEEEEEEeecCC
Confidence            4468999999974   3333322     123467889999999763211  0  00110 11222233444 47899999


Q ss_pred             CChhH-HH----HHHHHHHHhC---CCCceeeec
Q 023301          108 VTETE-LG----SLTERIKHIN---AMAPVKLAK  133 (284)
Q Consensus       108 ~~~~~-~~----~~~~~l~~~n---p~a~i~~~~  133 (284)
                      ++.++ .+    ++.+.++.+.   ..++++..+
T Consensus       141 ~~~~~~~~~~~~~i~~~l~~~~~~~~~~~iv~iS  174 (396)
T PRK00049        141 VDDEELLELVEMEVRELLSKYDFPGDDTPIIRGS  174 (396)
T ss_pred             cchHHHHHHHHHHHHHHHHhcCCCccCCcEEEee
Confidence            86433 33    3334444332   246666544

>TIGR00475 selB selenocysteine-specific elongation factor SelB

Probab=91.90  E-value=0.94  Score=44.19  Aligned_cols=89  Identities=17%  Similarity=0.217  Sum_probs=50.5

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHH-hhhhcCCccchHHHHHHHhhc-CEEEEccCCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQ-HLNEVKPRFVVNEAVEQVAYA-DRIILNKIDLV  108 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~-~l~~~~~~~~~~~~~~Qi~~A-d~ivlnK~D~~  108 (284)
                      ...||+++|-..   .....     +......+.++.|||+..-.+ +..+    .+  .....+... =+|++||+|++
T Consensus        51 ~v~~iDtPGhe~---f~~~~-----~~g~~~aD~aILVVDa~~G~~~qT~e----hl--~il~~lgi~~iIVVlNK~Dlv  116 (581)
T TIGR00475        51 RLGFIDVPGHEK---FISNA-----IAGGGGIDAALLVVDADEGVMTQTGE----HL--AVLDLLGIPHTIVVITKADRV  116 (581)
T ss_pred             EEEEEECCCHHH---HHHHH-----HhhhccCCEEEEEEECCCCCcHHHHH----HH--HHHHHcCCCeEEEEEECCCCC
Confidence            446889999532   22221     222346888999999986321 1110    01  112334444 57888999999


Q ss_pred             ChhHHHHHHHHHHH----hC--CCCceeeec
Q 023301          109 TETELGSLTERIKH----IN--AMAPVKLAK  133 (284)
Q Consensus       109 ~~~~~~~~~~~l~~----~n--p~a~i~~~~  133 (284)
                      +.+.++.+.+.+++    ..  +.++++.+|
T Consensus       117 ~~~~~~~~~~ei~~~l~~~~~~~~~~ii~vS  147 (581)
T TIGR00475       117 NEEEIKRTEMFMKQILNSYIFLKNAKIFKTS  147 (581)
T ss_pred             CHHHHHHHHHHHHHHHHHhCCCCCCcEEEEe
Confidence            87766554444443    21  357887765

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.

>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=91.85  E-value=2.7  Score=34.93  Aligned_cols=96  Identities=20%  Similarity=0.293  Sum_probs=56.9

Q ss_pred             cCCCCEEEEecCCCCCcHH-HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccC
Q 023301           27 QGQFDHIVIETTGLAKPAP-VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKI  105 (284)
Q Consensus        27 ~~~~d~iiIE~sG~a~p~~-i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~  105 (284)
                      ..+.|+|+|.|+|...-.+ .++.+.   .+.....-..++.|+|+..-.+.+...       ....+.-.-+-+|++|.
T Consensus        81 ~~~~D~vlIDT~Gr~~~d~~~~~el~---~~~~~~~~~~~~LVlsa~~~~~~~~~~-------~~~~~~~~~~~lIlTKl  150 (196)
T PF00448_consen   81 KKGYDLVLIDTAGRSPRDEELLEELK---KLLEALNPDEVHLVLSATMGQEDLEQA-------LAFYEAFGIDGLILTKL  150 (196)
T ss_dssp             HTTSSEEEEEE-SSSSTHHHHHHHHH---HHHHHHSSSEEEEEEEGGGGGHHHHHH-------HHHHHHSSTCEEEEEST
T ss_pred             hcCCCEEEEecCCcchhhHHHHHHHH---HHhhhcCCccceEEEecccChHHHHHH-------HHHhhcccCceEEEEee
Confidence            3679999999999997542 233332   122233455689999998866554321       11223333578999999


Q ss_pred             CCCChhHHHHHHHHHHHhCCCCceeeeccCC
Q 023301          106 DLVTETELGSLTERIKHINAMAPVKLAKYGS  136 (284)
Q Consensus       106 D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~  136 (284)
                      |...  ..-.+...+.+..  .||-..+.|+
T Consensus       151 Det~--~~G~~l~~~~~~~--~Pi~~it~Gq  177 (196)
T PF00448_consen  151 DETA--RLGALLSLAYESG--LPISYITTGQ  177 (196)
T ss_dssp             TSSS--TTHHHHHHHHHHT--SEEEEEESSS
T ss_pred             cCCC--CcccceeHHHHhC--CCeEEEECCC
Confidence            9855  2344555554443  5666566653

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 ....

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

Probab=91.82  E-value=0.83  Score=36.02  Aligned_cols=69  Identities=16%  Similarity=0.042  Sum_probs=40.5

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      ..+..+++|+|......+....        .-..+.++.|+|+......  ..  ..... ...+....-+||+||+|+.
T Consensus        49 ~~~~~iiDtpG~~~~~~~~~~~--------~~~~d~il~v~d~~~~~~~--~~--~~~~~-~~~~~~~p~ivv~NK~Dl~  115 (168)
T cd01887          49 IPGITFIDTPGHEAFTNMRARG--------ASLTDIAILVVAADDGVMP--QT--IEAIK-LAKAANVPFIVALNKIDKP  115 (168)
T ss_pred             cceEEEEeCCCcHHHHHHHHHH--------HhhcCEEEEEEECCCCccH--HH--HHHHH-HHHHcCCCEEEEEEceecc
Confidence            4678999999976544322211        1245678999999763211  00  00001 1234555678999999987


Q ss_pred             Ch
Q 023301          109 TE  110 (284)
Q Consensus       109 ~~  110 (284)
                      +.
T Consensus       116 ~~  117 (168)
T cd01887         116 NA  117 (168)
T ss_pred             cc
Confidence            43

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.

>PRK12296 obgE GTPase CgtA; Reviewed

Probab=91.67  E-value=0.58  Score=44.56  Aligned_cols=107  Identities=15%  Similarity=0.140  Sum_probs=52.9

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---------------
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---------------   94 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---------------   94 (284)
                      ..++|++++|+-+.+.--..|-. ..++..-..+.+|.|||+.......   .+..-...+..+|               
T Consensus       206 ~~f~laDtPGliegas~g~gLg~-~fLrhieradvLv~VVD~s~~e~~r---dp~~d~~~i~~EL~~y~~~l~~~~~~~~  281 (500)
T PRK12296        206 TRFTVADVPGLIPGASEGKGLGL-DFLRHIERCAVLVHVVDCATLEPGR---DPLSDIDALEAELAAYAPALDGDLGLGD  281 (500)
T ss_pred             eEEEEEECCCCccccchhhHHHH-HHHHHHHhcCEEEEEECCccccccc---CchhhHHHHHHHHHHhhhcccccchhhh
Confidence            35788999998654322111110 1122233567899999997632100   0000001111122               


Q ss_pred             --hhcCEEEEccCCCCChhHHH-HHHHHHHHhCCCCceeeecc-CCCChhhh
Q 023301           95 --AYADRIILNKIDLVTETELG-SLTERIKHINAMAPVKLAKY-GSVDMDFV  142 (284)
Q Consensus        95 --~~Ad~ivlnK~D~~~~~~~~-~~~~~l~~~np~a~i~~~~~-g~v~~~~l  142 (284)
                        ...-+||+||+|+.+..++. .+.+.++..  ..+|+.+|. ....+..+
T Consensus       282 l~~kP~IVVlNKiDL~da~el~e~l~~~l~~~--g~~Vf~ISA~tgeGLdEL  331 (500)
T PRK12296        282 LAERPRLVVLNKIDVPDARELAEFVRPELEAR--GWPVFEVSAASREGLREL  331 (500)
T ss_pred             hcCCCEEEEEECccchhhHHHHHHHHHHHHHc--CCeEEEEECCCCCCHHHH
Confidence              24568999999997654432 333344333  356776653 23344444

>TIGR00959 ffh signal recognition particle protein

Probab=91.65  E-value=1.9  Score=40.37  Aligned_cols=95  Identities=18%  Similarity=0.332  Sum_probs=56.3

Q ss_pred             cCCCCEEEEecCCCCCc-HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccC
Q 023301           27 QGQFDHIVIETTGLAKP-APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKI  105 (284)
Q Consensus        27 ~~~~d~iiIE~sG~a~p-~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~  105 (284)
                      ...+|+|||+|.|.... ..++..+.   .+...+.-+.++.|+|+..-......      ...+.+.+. -+-||+||.
T Consensus       180 ~~~~DvVIIDTaGr~~~d~~l~~eL~---~i~~~~~p~e~lLVvda~tgq~~~~~------a~~f~~~v~-i~giIlTKl  249 (428)
T TIGR00959       180 ENGFDVVIVDTAGRLQIDEELMEELA---AIKEILNPDEILLVVDAMTGQDAVNT------AKTFNERLG-LTGVVLTKL  249 (428)
T ss_pred             hcCCCEEEEeCCCccccCHHHHHHHH---HHHHhhCCceEEEEEeccchHHHHHH------HHHHHhhCC-CCEEEEeCc
Confidence            36799999999997653 34455442   23345566788999999764332211      122233443 468889999


Q ss_pred             CCCChhHHHHHHHHHHHhCCCCceeeeccC
Q 023301          106 DLVTETELGSLTERIKHINAMAPVKLAKYG  135 (284)
Q Consensus       106 D~~~~~~~~~~~~~l~~~np~a~i~~~~~g  135 (284)
                      |...  ..-.+.......+  .||.....|
T Consensus       250 D~~~--~~G~~lsi~~~~~--~PI~fi~~G  275 (428)
T TIGR00959       250 DGDA--RGGAALSVRSVTG--KPIKFIGVG  275 (428)
T ss_pred             cCcc--cccHHHHHHHHHC--cCEEEEeCC
Confidence            9633  1222444444444  666655555

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.

>KOG1424 consensus Predicted GTP-binding protein MMR1 [General function prediction only]

Probab=91.52  E-value=0.35  Score=45.49  Aligned_cols=60  Identities=20%  Similarity=0.247  Sum_probs=41.1

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-hcCEEEEccCCCCChhHHHHHHHHHHHhC
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-YADRIILNKIDLVTETELGSLTERIKHIN  124 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-~Ad~ivlnK~D~~~~~~~~~~~~~l~~~n  124 (284)
                      .=|-||-+|||++..-+..    ..+..-+.+-.. -+.++++||+|++++++.....+.-+.-|
T Consensus       174 rSDivvqIVDARnPllfr~----~dLe~Yvke~d~~K~~~LLvNKaDLl~~~qr~aWa~YF~~~n  234 (562)
T KOG1424|consen  174 RSDIVVQIVDARNPLLFRS----PDLEDYVKEVDPSKANVLLVNKADLLPPEQRVAWAEYFRQNN  234 (562)
T ss_pred             hcceEEEEeecCCccccCC----hhHHHHHhccccccceEEEEehhhcCCHHHHHHHHHHHHhcC
Confidence            3456899999999764321    111111222223 57899999999999999988888887766

>cd01890 LepA LepA subfamily

Probab=91.45  E-value=1.1  Score=35.94  Aligned_cols=68  Identities=18%  Similarity=0.213  Sum_probs=39.1

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      +....|++|+|..+........     +   -..+.+|.|+|+...... ...  ... .. ..+-...-++|+||+|+.
T Consensus        66 ~~~~~l~Dt~G~~~~~~~~~~~-----~---~~ad~~i~v~D~~~~~~~-~~~--~~~-~~-~~~~~~~iiiv~NK~Dl~  132 (179)
T cd01890          66 EYLLNLIDTPGHVDFSYEVSRS-----L---AACEGALLLVDATQGVEA-QTL--ANF-YL-ALENNLEIIPVINKIDLP  132 (179)
T ss_pred             cEEEEEEECCCChhhHHHHHHH-----H---HhcCeEEEEEECCCCccH-hhH--HHH-HH-HHHcCCCEEEEEECCCCC
Confidence            4456689999998765544332     1   246788999999763211 000  000 01 111223458899999986


Q ss_pred             C
Q 023301          109 T  109 (284)
Q Consensus       109 ~  109 (284)
                      +
T Consensus       133 ~  133 (179)
T cd01890         133 S  133 (179)
T ss_pred             c
Confidence            4

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.

>PLN03127 Elongation factor Tu; Provisional

Probab=91.03  E-value=0.48  Score=44.62  Aligned_cols=70  Identities=21%  Similarity=0.293  Sum_probs=39.6

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC-EEEEccCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDLV  108 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~~  108 (284)
                      ..++||+|+|..+.   +.....     .....+.++.|||+..-...  +  .+... .+...+.... ++++||+|++
T Consensus       124 ~~i~~iDtPGh~~f---~~~~~~-----g~~~aD~allVVda~~g~~~--q--t~e~l-~~~~~~gip~iIvviNKiDlv  190 (447)
T PLN03127        124 RHYAHVDCPGHADY---VKNMIT-----GAAQMDGGILVVSAPDGPMP--Q--TKEHI-LLARQVGVPSLVVFLNKVDVV  190 (447)
T ss_pred             eEEEEEECCCccch---HHHHHH-----HHhhCCEEEEEEECCCCCch--h--HHHHH-HHHHHcCCCeEEEEEEeeccC
Confidence            46799999998652   222211     12347889999999753211  0  11111 1123334444 4679999998


Q ss_pred             ChhH
Q 023301          109 TETE  112 (284)
Q Consensus       109 ~~~~  112 (284)
                      +.++
T Consensus       191 ~~~~  194 (447)
T PLN03127        191 DDEE  194 (447)
T ss_pred             CHHH
Confidence            6444

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

Probab=90.99  E-value=0.51  Score=44.86  Aligned_cols=98  Identities=20%  Similarity=0.218  Sum_probs=60.5

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHH-HHHHHhhcCEEEEccCCCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNE-AVEQVAYADRIILNKIDLVT  109 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~-~~~Qi~~Ad~ivlnK~D~~~  109 (284)
                      -.=+|.|+|=.|.+.=.        -+..-..++++.||||..-...  +    .+.+. +.-+...+=+.||||+|+-+
T Consensus       126 lLNLIDTPGHvDFs~EV--------sRslaac~G~lLvVDA~qGvqA--Q----T~anf~lAfe~~L~iIpVlNKIDlp~  191 (650)
T KOG0462|consen  126 LLNLIDTPGHVDFSGEV--------SRSLAACDGALLVVDASQGVQA--Q----TVANFYLAFEAGLAIIPVLNKIDLPS  191 (650)
T ss_pred             EEEeecCCCccccccee--------hehhhhcCceEEEEEcCcCchH--H----HHHHHHHHHHcCCeEEEeeeccCCCC
Confidence            34478999988865311        1123367899999999875432  1    11122 23455667899999999943


Q ss_pred             hhHHHHHHHHHHHhC--CCCceeeecc-CCCChhhhh
Q 023301          110 ETELGSLTERIKHIN--AMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       110 ~~~~~~~~~~l~~~n--p~a~i~~~~~-g~v~~~~l~  143 (284)
                       ++.++++..+..+.  |.++++..+. .....+.++
T Consensus       192 -adpe~V~~q~~~lF~~~~~~~i~vSAK~G~~v~~lL  227 (650)
T KOG0462|consen  192 -ADPERVENQLFELFDIPPAEVIYVSAKTGLNVEELL  227 (650)
T ss_pred             -CCHHHHHHHHHHHhcCCccceEEEEeccCccHHHHH
Confidence             45677777777764  6677765543 234444443

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=90.96  E-value=1.5  Score=38.43  Aligned_cols=84  Identities=20%  Similarity=0.345  Sum_probs=48.0

Q ss_pred             HHHHHHHHhhcCCCCEEEEecCCCCC------cHHH-HHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHH
Q 023301           17 KMLLQLAKKKQGQFDHIVIETTGLAK------PAPV-IETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNE   89 (284)
Q Consensus        17 ~~l~~l~~~~~~~~d~iiIE~sG~a~------p~~i-~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~   89 (284)
                      +++.++++++...+|+++|.|+|=-+      +..| .++|.+      .+. ..|+.|||..+-....     -+.++.
T Consensus       103 dqv~~~iek~~~~~~~~liDTPGQIE~FtWSAsGsIIte~las------s~p-tvv~YvvDt~rs~~p~-----tFMSNM  170 (366)
T KOG1532|consen  103 DQVIELIEKRAEEFDYVLIDTPGQIEAFTWSASGSIITETLAS------SFP-TVVVYVVDTPRSTSPT-----TFMSNM  170 (366)
T ss_pred             HHHHHHHHHhhcccCEEEEcCCCceEEEEecCCccchHhhHhh------cCC-eEEEEEecCCcCCCch-----hHHHHH
Confidence            34556666545679999999999533      3333 333322      121 2378999987632110     011111


Q ss_pred             -----HHHHHhhcCEEEEccCCCCChhH
Q 023301           90 -----AVEQVAYADRIILNKIDLVTETE  112 (284)
Q Consensus        90 -----~~~Qi~~Ad~ivlnK~D~~~~~~  112 (284)
                           +.-.-+..=+|++||+|+.+.+-
T Consensus       171 lYAcSilyktklp~ivvfNK~Dv~d~~f  198 (366)
T KOG1532|consen  171 LYACSILYKTKLPFIVVFNKTDVSDSEF  198 (366)
T ss_pred             HHHHHHHHhccCCeEEEEecccccccHH
Confidence                 22334556789999999987543

>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional

Probab=90.87  E-value=0.8  Score=43.51  Aligned_cols=92  Identities=17%  Similarity=0.199  Sum_probs=49.8

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC-EEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~  107 (284)
                      +..++||+|+|-.   .+.....     ...-..+.++.|||+..-...  .  .+.. ..+...+.... +|++||+|+
T Consensus       106 ~~~i~~iDTPGh~---~f~~~~~-----~~l~~aD~allVVDa~~G~~~--q--t~~~-~~l~~~lg~~~iIvvvNKiD~  172 (474)
T PRK05124        106 KRKFIIADTPGHE---QYTRNMA-----TGASTCDLAILLIDARKGVLD--Q--TRRH-SFIATLLGIKHLVVAVNKMDL  172 (474)
T ss_pred             CcEEEEEECCCcH---HHHHHHH-----HHHhhCCEEEEEEECCCCccc--c--chHH-HHHHHHhCCCceEEEEEeecc
Confidence            4578999999943   2222211     123467789999999763211  0  0000 01223333233 569999999


Q ss_pred             CC--hhHHHHHHHHHHH----h--CCCCceeeec
Q 023301          108 VT--ETELGSLTERIKH----I--NAMAPVKLAK  133 (284)
Q Consensus       108 ~~--~~~~~~~~~~l~~----~--np~a~i~~~~  133 (284)
                      ++  .+.+..+++.++.    +  .+.++++..+
T Consensus       173 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~iipvS  206 (474)
T PRK05124        173 VDYSEEVFERIREDYLTFAEQLPGNLDIRFVPLS  206 (474)
T ss_pred             ccchhHHHHHHHHHHHHHHHhcCCCCCceEEEEE
Confidence            74  3345555555543    2  2456777654

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=90.78  E-value=1.2  Score=41.61  Aligned_cols=94  Identities=19%  Similarity=0.323  Sum_probs=55.4

Q ss_pred             CCCCEEEEecCCCCCcH-HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCC
Q 023301           28 GQFDHIVIETTGLAKPA-PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKID  106 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~-~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D  106 (284)
                      ..+|+|||.|.|-.... .+++.+.   .+.....-+.++.|+|+..-......      . ....+...-+-+|+||.|
T Consensus       181 ~~~DvViIDTaGr~~~d~~lm~El~---~i~~~~~p~e~lLVlda~~Gq~a~~~------a-~~F~~~~~~~g~IlTKlD  250 (429)
T TIGR01425       181 ENFDIIIVDTSGRHKQEDSLFEEML---QVAEAIQPDNIIFVMDGSIGQAAEAQ------A-KAFKDSVDVGSVIITKLD  250 (429)
T ss_pred             CCCCEEEEECCCCCcchHHHHHHHH---HHhhhcCCcEEEEEeccccChhHHHH------H-HHHHhccCCcEEEEECcc
Confidence            57899999999988764 3444432   22234455678999999764332111      1 112334457889999999


Q ss_pred             CCChhHHHHHHHHHHHhCCCCceeeeccC
Q 023301          107 LVTETELGSLTERIKHINAMAPVKLAKYG  135 (284)
Q Consensus       107 ~~~~~~~~~~~~~l~~~np~a~i~~~~~g  135 (284)
                      ....  .-.+.......  ..||.....|
T Consensus       251 ~~ar--gG~aLs~~~~t--~~PI~fig~G  275 (429)
T TIGR01425       251 GHAK--GGGALSAVAAT--KSPIIFIGTG  275 (429)
T ss_pred             CCCC--ccHHhhhHHHH--CCCeEEEcCC
Confidence            8542  22233333333  4666666555

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.

>cd04142 RRP22 RRP22 subfamily

Probab=90.70  E-value=1.8  Score=35.88  Aligned_cols=107  Identities=9%  Similarity=-0.025  Sum_probs=52.9

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---------hcCEE
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---------YADRI  100 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---------~Ad~i  100 (284)
                      ....+++++|..........-+.+......-..+.+|.|+|+.+.... ...      ..+.+++.         ..-+|
T Consensus        49 ~~l~i~Dt~G~~~~~~~~~~e~~~~~~~~~~~ad~iilv~D~~~~~S~-~~~------~~~~~~i~~~~~~~~~~~piii  121 (198)
T cd04142          49 YDLHILDVPNMQRYPGTAGQEWMDPRFRGLRNSRAFILVYDICSPDSF-HYV------KLLRQQILETRPAGNKEPPIVV  121 (198)
T ss_pred             EEEEEEeCCCcccCCccchhHHHHHHHhhhccCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhcccCCCCCCEEE
Confidence            345588999975421111100000011112357889999999874332 211      12223332         23478


Q ss_pred             EEccCCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhhc
Q 023301          101 ILNKIDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVLG  144 (284)
Q Consensus       101 vlnK~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~~  144 (284)
                      |.||+|+.....  .+...++.++. -.+++++++. .......++.
T Consensus       122 vgNK~Dl~~~~~~~~~~~~~~~~~~-~~~~~~e~Sak~g~~v~~lf~  167 (198)
T cd04142         122 VGNKRDQQRHRFAPRHVLSVLVRKS-WKCGYLECSAKYNWHILLLFK  167 (198)
T ss_pred             EEECccccccccccHHHHHHHHHHh-cCCcEEEecCCCCCCHHHHHH
Confidence            899999954321  12222222222 2467777764 4456666663

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.

>TIGR02528 EutP ethanolamine utilization protein, EutP

Probab=90.67  E-value=0.84  Score=35.08  Aligned_cols=64  Identities=13%  Similarity=0.120  Sum_probs=37.6

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChh-HHHHHHHHHHHhCCCCceeeec
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTET-ELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~-~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ..+.++.|+|+.+......        ..+...+...-++|+||+|+.+.+ ..+...++++..+. .+++.++
T Consensus        62 ~ad~vilv~d~~~~~s~~~--------~~~~~~~~~p~ilv~NK~Dl~~~~~~~~~~~~~~~~~~~-~~~~~~S  126 (142)
T TIGR02528        62 DADVIALVQSATDPESRFP--------PGFASIFVKPVIGLVTKIDLAEADVDIERAKELLETAGA-EPIFEIS  126 (142)
T ss_pred             cCCEEEEEecCCCCCcCCC--------hhHHHhccCCeEEEEEeeccCCcccCHHHHHHHHHHcCC-CcEEEEe
Confidence            6778999999977554311        112233344778899999986532 23444555554432 3555554

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.

>PRK10867 signal recognition particle protein; Provisional

Probab=90.67  E-value=3.1  Score=38.97  Aligned_cols=95  Identities=18%  Similarity=0.277  Sum_probs=53.8

Q ss_pred             cCCCCEEEEecCCCCCc-HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccC
Q 023301           27 QGQFDHIVIETTGLAKP-APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKI  105 (284)
Q Consensus        27 ~~~~d~iiIE~sG~a~p-~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~  105 (284)
                      ...+|+|||+|.|.... ..+++.+.   .+...+.-+.++.|+|+..-......      ...+.+.+ .-+-+|+||.
T Consensus       181 ~~~~DvVIIDTaGrl~~d~~lm~eL~---~i~~~v~p~evllVlda~~gq~av~~------a~~F~~~~-~i~giIlTKl  250 (433)
T PRK10867        181 ENGYDVVIVDTAGRLHIDEELMDELK---AIKAAVNPDEILLVVDAMTGQDAVNT------AKAFNEAL-GLTGVILTKL  250 (433)
T ss_pred             hcCCCEEEEeCCCCcccCHHHHHHHH---HHHHhhCCCeEEEEEecccHHHHHHH------HHHHHhhC-CCCEEEEeCc
Confidence            46799999999997653 44454442   23334455678999999764332211      11122223 2467899999


Q ss_pred             CCCChhHHHHHHHHHHHhCCCCceeeeccC
Q 023301          106 DLVTETELGSLTERIKHINAMAPVKLAKYG  135 (284)
Q Consensus       106 D~~~~~~~~~~~~~l~~~np~a~i~~~~~g  135 (284)
                      |....  .-.+.......+  .||.....|
T Consensus       251 D~~~r--gG~alsi~~~~~--~PI~fig~G  276 (433)
T PRK10867        251 DGDAR--GGAALSIRAVTG--KPIKFIGTG  276 (433)
T ss_pred             cCccc--ccHHHHHHHHHC--cCEEEEeCC
Confidence            96331  222344444444  566655544

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

Probab=90.62  E-value=0.81  Score=40.06  Aligned_cols=81  Identities=17%  Similarity=0.237  Sum_probs=46.1

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      +..+.+|.|+|..+...-...        ..-..+.++.|||+..-...-.    ..+. ....+....-++++||+|+.
T Consensus        63 ~~~i~liDTPG~~df~~~~~~--------~l~~aD~ailVVDa~~g~~~~t----~~~~-~~~~~~~~p~ivviNK~D~~  129 (270)
T cd01886          63 DHRINIIDTPGHVDFTIEVER--------SLRVLDGAVAVFDAVAGVEPQT----ETVW-RQADRYNVPRIAFVNKMDRT  129 (270)
T ss_pred             CEEEEEEECCCcHHHHHHHHH--------HHHHcCEEEEEEECCCCCCHHH----HHHH-HHHHHcCCCEEEEEECCCCC
Confidence            457789999998764432111        1234578999999977432100    1111 11234445678999999986


Q ss_pred             ChhHHHHHHHHHHHh
Q 023301          109 TETELGSLTERIKHI  123 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~  123 (284)
                      +. ..+.+.+.++..
T Consensus       130 ~a-~~~~~~~~l~~~  143 (270)
T cd01886         130 GA-DFFRVVEQIREK  143 (270)
T ss_pred             CC-CHHHHHHHHHHH
Confidence            43 233444445443

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

>PRK04213 GTP-binding protein; Provisional

Probab=90.51  E-value=0.94  Score=37.24  Aligned_cols=80  Identities=14%  Similarity=0.202  Sum_probs=39.6

Q ss_pred             CEEEEecCCCCCcH-------HHHHHhccccccc-ceeeeceEEEEEcccchHHhhhhc---CCccchHHHHH---HHhh
Q 023301           31 DHIVIETTGLAKPA-------PVIETFCTDELVS-QYVKLDGVITLVDSKHAMQHLNEV---KPRFVVNEAVE---QVAY   96 (284)
Q Consensus        31 d~iiIE~sG~a~p~-------~i~~~l~~~~~l~-~~~~l~~vv~vvD~~~~~~~l~~~---~~~~~~~~~~~---Qi~~   96 (284)
                      +..+++++|.+...       +-+..++. ..+. ..-.++.++.|+|+..+.......   +.......+..   ....
T Consensus        53 ~~~l~Dt~G~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~vi~v~d~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  131 (201)
T PRK04213         53 DFILTDLPGFGFMSGVPKEVQEKIKDEIV-RYIEDNADRILAAVLVVDGKSFIEIIERWEGRGEIPIDVEMFDFLRELGI  131 (201)
T ss_pred             ceEEEeCCccccccccCHHHHHHHHHHHH-HHHHhhhhhheEEEEEEeCccccccccccccCCCcHHHHHHHHHHHHcCC
Confidence            57889999975421       22222211 1111 123456789999997653211100   00000011112   2234


Q ss_pred             cCEEEEccCCCCChh
Q 023301           97 ADRIILNKIDLVTET  111 (284)
Q Consensus        97 Ad~ivlnK~D~~~~~  111 (284)
                      .=+||+||+|+.+..
T Consensus       132 p~iiv~NK~Dl~~~~  146 (201)
T PRK04213        132 PPIVAVNKMDKIKNR  146 (201)
T ss_pred             CeEEEEECccccCcH
Confidence            558999999997543

>KOG0090 consensus Signal recognition particle receptor, beta subunit (small G protein superfamily) [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.46  E-value=0.93  Score=38.02  Aligned_cols=62  Identities=18%  Similarity=0.244  Sum_probs=39.6

Q ss_pred             ccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhc--------CEEEEccCCCCChhHHHHHHHHH
Q 023301           54 ELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYA--------DRIILNKIDLVTETELGSLTERI  120 (284)
Q Consensus        54 ~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~A--------d~ivlnK~D~~~~~~~~~~~~~l  120 (284)
                      +.+...+.+.++|+|||+..|.....+     ++..+.+=+..+        =+|.-||.|+....--+.|++.+
T Consensus       101 e~~~~~~~akaiVFVVDSa~f~k~vrd-----vaefLydil~~~~~~~~~~~vLIaCNKqDl~tAkt~~~Ir~~L  170 (238)
T KOG0090|consen  101 EYLKHNYSAKAIVFVVDSATFLKNVRD-----VAEFLYDILLDSRVKKNKPPVLIACNKQDLFTAKTAEKIRQQL  170 (238)
T ss_pred             HHccccccceeEEEEEeccccchhhHH-----HHHHHHHHHHhhccccCCCCEEEEecchhhhhcCcHHHHHHHH
Confidence            345566889999999999999876543     333334444444        25666999997644433444333

>cd04153 Arl5_Arl8 Arl5/Arl8 subfamily

Probab=90.43  E-value=1.9  Score=34.64  Aligned_cols=66  Identities=20%  Similarity=0.179  Sum_probs=36.4

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh------cCEEEEc
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY------ADRIILN  103 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~------Ad~ivln  103 (284)
                      ....+++++|..........     .+   -..+.+|.|+|+...... ...     ...+...+..      .=+|++|
T Consensus        59 ~~~~l~D~~G~~~~~~~~~~-----~~---~~~d~vi~V~D~s~~~~~-~~~-----~~~l~~~~~~~~~~~~p~viv~N  124 (174)
T cd04153          59 IRFLMWDIGGQESLRSSWNT-----YY---TNTDAVILVIDSTDRERL-PLT-----KEELYKMLAHEDLRKAVLLVLAN  124 (174)
T ss_pred             eEEEEEECCCCHHHHHHHHH-----Hh---hcCCEEEEEEECCCHHHH-HHH-----HHHHHHHHhchhhcCCCEEEEEE
Confidence            45678889997543322221     11   246789999999874322 111     0112222222      2278889


Q ss_pred             cCCCCC
Q 023301          104 KIDLVT  109 (284)
Q Consensus       104 K~D~~~  109 (284)
                      |+|+..
T Consensus       125 K~Dl~~  130 (174)
T cd04153         125 KQDLKG  130 (174)
T ss_pred             CCCCCC
Confidence            999864

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.

>PRK12289 GTPase RsgA; Reviewed

Probab=90.38  E-value=0.44  Score=43.40  Aligned_cols=80  Identities=19%  Similarity=0.240  Sum_probs=42.6

Q ss_pred             eeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeecc-CCC
Q 023301           59 YVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKY-GSV  137 (284)
Q Consensus        59 ~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~-g~v  137 (284)
                      .-.++.++.|+|+......... -++++.  ........=+||+||+|++++++.+.+.+.++..+  .+++.++. ...
T Consensus        87 ~aNvD~vLlV~d~~~p~~~~~~-LdR~L~--~a~~~~ip~ILVlNK~DLv~~~~~~~~~~~~~~~g--~~v~~iSA~tg~  161 (352)
T PRK12289         87 VANADQILLVFALAEPPLDPWQ-LSRFLV--KAESTGLEIVLCLNKADLVSPTEQQQWQDRLQQWG--YQPLFISVETGI  161 (352)
T ss_pred             hhcCCEEEEEEECCCCCCCHHH-HHHHHH--HHHHCCCCEEEEEEchhcCChHHHHHHHHHHHhcC--CeEEEEEcCCCC
Confidence            3478889999998642200000 011111  01122334478889999998776665555554433  35555442 233


Q ss_pred             Chhhhh
Q 023301          138 DMDFVL  143 (284)
Q Consensus       138 ~~~~l~  143 (284)
                      ..+.|+
T Consensus       162 GI~eL~  167 (352)
T PRK12289        162 GLEALL  167 (352)
T ss_pred             CHHHHh
Confidence            455554

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=90.31  E-value=3.6  Score=36.04  Aligned_cols=108  Identities=19%  Similarity=0.259  Sum_probs=62.7

Q ss_pred             hHHHHHHHHHHhhcCCCCEEEEecCCCCCc-HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHH
Q 023301           14 DLVKMLLQLAKKKQGQFDHIVIETTGLAKP-APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVE   92 (284)
Q Consensus        14 dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p-~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~   92 (284)
                      ++..++..+.+  ..++|+|||.+.|-..- .+.++.+..   +.....-+.++.|+||..-...+.+.     ... ..
T Consensus       141 ~l~~~l~~l~~--~~~~D~ViIDt~Gr~~~~~~~l~el~~---~~~~~~~~~~~LVl~a~~~~~d~~~~-----~~~-f~  209 (270)
T PRK06731        141 AMTRALTYFKE--EARVDYILIDTAGKNYRASETVEEMIE---TMGQVEPDYICLTLSASMKSKDMIEI-----ITN-FK  209 (270)
T ss_pred             HHHHHHHHHHh--cCCCCEEEEECCCCCcCCHHHHHHHHH---HHhhhCCCeEEEEEcCccCHHHHHHH-----HHH-hC
Confidence            45555555543  35799999999999852 333443321   11223334588999997644332221     011 11


Q ss_pred             HHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCC
Q 023301           93 QVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSV  137 (284)
Q Consensus        93 Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v  137 (284)
                      . ..-|-+|++|.|...  ..-.+...+...  +.||...+.|+-
T Consensus       210 ~-~~~~~~I~TKlDet~--~~G~~l~~~~~~--~~Pi~~it~Gq~  249 (270)
T PRK06731        210 D-IHIDGIVFTKFDETA--SSGELLKIPAVS--SAPIVLMTDGQD  249 (270)
T ss_pred             C-CCCCEEEEEeecCCC--CccHHHHHHHHH--CcCEEEEeCCCC
Confidence            2 467999999999865  344455555444  467777777643

>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=90.31  E-value=1  Score=37.00  Aligned_cols=86  Identities=16%  Similarity=0.222  Sum_probs=45.3

Q ss_pred             CCCEEEEecCCCCCcHH-HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHH-HH---HhhcCEEEEc
Q 023301           29 QFDHIVIETTGLAKPAP-VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAV-EQ---VAYADRIILN  103 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~-i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~-~Q---i~~Ad~ivln  103 (284)
                      ...+-+|+.+|=..... +++.+.      ..-.+.+||+|||+..+...+.+. ..++.+.+. .+   -...=+|+.|
T Consensus        48 ~~~~~lvD~PGH~rlr~~~~~~~~------~~~~~k~IIfvvDSs~~~~~~~~~-Ae~Ly~iL~~~~~~~~~~piLIacN  120 (181)
T PF09439_consen   48 GKKLRLVDIPGHPRLRSKLLDELK------YLSNAKGIIFVVDSSTDQKELRDV-AEYLYDILSDTEVQKNKPPILIACN  120 (181)
T ss_dssp             GTCECEEEETT-HCCCHHHHHHHH------HHGGEEEEEEEEETTTHHHHHHHH-HHHHHHHHHHHHCCTT--EEEEEEE
T ss_pred             CCEEEEEECCCcHHHHHHHHHhhh------chhhCCEEEEEEeCccchhhHHHH-HHHHHHHHHhhhhccCCCCEEEEEe
Confidence            34567888888777553 222211      123588999999999877655442 112222221 11   2334457779


Q ss_pred             cCCCCChhHHHHHHHHHH
Q 023301          104 KIDLVTETELGSLTERIK  121 (284)
Q Consensus       104 K~D~~~~~~~~~~~~~l~  121 (284)
                      |.|+........+++.|.
T Consensus       121 K~Dl~~A~~~~~Ik~~LE  138 (181)
T PF09439_consen  121 KQDLFTAKPPKKIKKLLE  138 (181)
T ss_dssp             -TTSTT---HHHHHHHHH
T ss_pred             CccccccCCHHHHHHHHH
Confidence            999977554555555554

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.

>cd01859 MJ1464 MJ1464

Probab=90.25  E-value=0.91  Score=35.79  Aligned_cols=65  Identities=26%  Similarity=0.299  Sum_probs=33.8

Q ss_pred             eceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeec
Q 023301           62 LDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus        62 l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      .+.++.|+|+......    ....+.. ........-++|+||+|+.+.+....... +.. ....+++.++
T Consensus        13 aD~vl~V~D~~~~~~~----~~~~l~~-~~~~~~~p~iiv~NK~Dl~~~~~~~~~~~-~~~-~~~~~~~~iS   77 (156)
T cd01859          13 SDVVLEVLDARDPELT----RSRKLER-YVLELGKKLLIVLNKADLVPKEVLEKWKS-IKE-SEGIPVVYVS   77 (156)
T ss_pred             CCEEEEEeeCCCCccc----CCHHHHH-HHHhCCCcEEEEEEhHHhCCHHHHHHHHH-HHH-hCCCcEEEEE
Confidence            6779999999764321    1111111 11112334588899999987655443332 222 1335565544

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.

>PRK03003 GTP-binding protein Der; Reviewed

Probab=90.25  E-value=2.1  Score=40.56  Aligned_cols=102  Identities=19%  Similarity=0.185  Sum_probs=53.1

Q ss_pred             CEEEEecCCCCCc------HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEE
Q 023301           31 DHIVIETTGLAKP------APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRII  101 (284)
Q Consensus        31 d~iiIE~sG~a~p------~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~iv  101 (284)
                      .+.++.|.|+-.-      .+.+..+..   ....-..+.+|.|+|+..-.....      .  ....++   ...=+||
T Consensus       260 ~~~l~DTaG~~~~~~~~~~~e~~~~~~~---~~~i~~ad~vilV~Da~~~~s~~~------~--~~~~~~~~~~~piIiV  328 (472)
T PRK03003        260 TWRFVDTAGLRRRVKQASGHEYYASLRT---HAAIEAAEVAVVLIDASEPISEQD------Q--RVLSMVIEAGRALVLA  328 (472)
T ss_pred             EEEEEECCCccccccccchHHHHHHHHH---HHHHhcCCEEEEEEeCCCCCCHHH------H--HHHHHHHHcCCCEEEE
Confidence            3578899997321      122222111   011125778999999976322110      0  112232   2345788


Q ss_pred             EccCCCCChhHHHHHHHHHHHhC---CCCceeeecc-CCCChhhhh
Q 023301          102 LNKIDLVTETELGSLTERIKHIN---AMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       102 lnK~D~~~~~~~~~~~~~l~~~n---p~a~i~~~~~-g~v~~~~l~  143 (284)
                      +||+|+.+.+....+.+.++...   +.++++.++. .......++
T Consensus       329 ~NK~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~~~SAk~g~gv~~lf  374 (472)
T PRK03003        329 FNKWDLVDEDRRYYLEREIDRELAQVPWAPRVNISAKTGRAVDKLV  374 (472)
T ss_pred             EECcccCChhHHHHHHHHHHHhcccCCCCCEEEEECCCCCCHHHHH
Confidence            89999987554444444444321   3467776653 334455554

>TIGR03596 GTPase_YlqF ribosome biogenesis GTP-binding protein YlqF

Probab=90.25  E-value=0.75  Score=40.33  Aligned_cols=72  Identities=17%  Similarity=0.154  Sum_probs=39.8

Q ss_pred             CCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-hcCEEEEccCCCCChhHHHHHHHH
Q 023301           41 AKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-YADRIILNKIDLVTETELGSLTER  119 (284)
Q Consensus        41 a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-~Ad~ivlnK~D~~~~~~~~~~~~~  119 (284)
                      +.|..+.+++..  .....-..|.|+.|+|+......    ..    ..+.+.+. ..-++|+||+|+++.++.....+.
T Consensus         3 WfpgHm~k~~~~--~~~~l~~aDvVl~V~Dar~p~~~----~~----~~i~~~l~~kp~IiVlNK~DL~~~~~~~~~~~~   72 (276)
T TIGR03596         3 WFPGHMAKARRE--IKEKLKLVDVVIEVLDARIPLSS----RN----PMIDEIRGNKPRLIVLNKADLADPAVTKQWLKY   72 (276)
T ss_pred             cChHHHHHHHHH--HHHHHhhCCEEEEEEeCCCCCCC----CC----hhHHHHHCCCCEEEEEEccccCCHHHHHHHHHH
Confidence            346665555432  11122356778999999753321    11    11223332 345788899999877655555555


Q ss_pred             HHH
Q 023301          120 IKH  122 (284)
Q Consensus       120 l~~  122 (284)
                      ++.
T Consensus        73 ~~~   75 (276)
T TIGR03596        73 FEE   75 (276)
T ss_pred             HHH
Confidence            543

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.

>PRK12736 elongation factor Tu; Reviewed

Probab=90.22  E-value=1.5  Score=40.52  Aligned_cols=92  Identities=22%  Similarity=0.295  Sum_probs=49.0

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC-EEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~  107 (284)
                      +..+.||.|+|..+   .+...     +...-..+.++.|||+..-....    .+.... +........ +|++||+|+
T Consensus        74 ~~~i~~iDtPGh~~---f~~~~-----~~~~~~~d~~llVvd~~~g~~~~----t~~~~~-~~~~~g~~~~IvviNK~D~  140 (394)
T PRK12736         74 KRHYAHVDCPGHAD---YVKNM-----ITGAAQMDGAILVVAATDGPMPQ----TREHIL-LARQVGVPYLVVFLNKVDL  140 (394)
T ss_pred             CcEEEEEECCCHHH---HHHHH-----HHHHhhCCEEEEEEECCCCCchh----HHHHHH-HHHHcCCCEEEEEEEecCC
Confidence            34679999999432   22221     11223568899999997632110    001111 123334444 467999999


Q ss_pred             CChhHH-H----HHHHHHHHhCC---CCceeeec
Q 023301          108 VTETEL-G----SLTERIKHINA---MAPVKLAK  133 (284)
Q Consensus       108 ~~~~~~-~----~~~~~l~~~np---~a~i~~~~  133 (284)
                      ++.+++ +    ++++.++.+.-   .++++..+
T Consensus       141 ~~~~~~~~~i~~~i~~~l~~~~~~~~~~~ii~vS  174 (394)
T PRK12736        141 VDDEELLELVEMEVRELLSEYDFPGDDIPVIRGS  174 (394)
T ss_pred             cchHHHHHHHHHHHHHHHHHhCCCcCCccEEEee
Confidence            865443 2    34444544432   36777655

>cd04151 Arl1 Arl1 subfamily

Probab=90.12  E-value=1.5  Score=34.32  Aligned_cols=78  Identities=17%  Similarity=0.176  Sum_probs=41.2

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D  106 (284)
                      ....+++++|......+....     +   -..+.++.|+|+...... ... ...+.. +..+.   ...=+||+||+|
T Consensus        43 ~~~~i~Dt~G~~~~~~~~~~~-----~---~~~~~ii~v~d~~~~~~~-~~~-~~~~~~-~~~~~~~~~~piiiv~nK~D  111 (158)
T cd04151          43 LKFQVWDLGGQTSIRPYWRCY-----Y---SNTDAIIYVVDSTDRDRL-GTA-KEELHA-MLEEEELKGAVLLVFANKQD  111 (158)
T ss_pred             EEEEEEECCCCHHHHHHHHHH-----h---cCCCEEEEEEECCCHHHH-HHH-HHHHHH-HHhchhhcCCcEEEEEeCCC
Confidence            456788999986654432221     1   246779999999875321 110 001111 11111   234578889999


Q ss_pred             CCChhHHHHHHH
Q 023301          107 LVTETELGSLTE  118 (284)
Q Consensus       107 ~~~~~~~~~~~~  118 (284)
                      +.+.....++.+
T Consensus       112 l~~~~~~~~i~~  123 (158)
T cd04151         112 MPGALSEAEISE  123 (158)
T ss_pred             CCCCCCHHHHHH
Confidence            865432333433

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.

>cd01885 EF2 EF2 (for archaea and eukarya)

Probab=89.99  E-value=1  Score=38.19  Aligned_cols=81  Identities=19%  Similarity=0.283  Sum_probs=48.3

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKI  105 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~  105 (284)
                      +....|+.|+|..+.......-        .-..++++.|+|+..-...-.        .....+.   ...=++++||+
T Consensus        72 ~~~i~iiDTPG~~~f~~~~~~~--------l~~aD~~ilVvD~~~g~~~~t--------~~~l~~~~~~~~p~ilviNKi  135 (222)
T cd01885          72 EYLINLIDSPGHVDFSSEVTAA--------LRLCDGALVVVDAVEGVCVQT--------ETVLRQALKERVKPVLVINKI  135 (222)
T ss_pred             ceEEEEECCCCccccHHHHHHH--------HHhcCeeEEEEECCCCCCHHH--------HHHHHHHHHcCCCEEEEEECC
Confidence            4556789999998865433221        234677899999976432100        1112222   23558889999


Q ss_pred             CCC------Ch-hHHHHHHHHHHHhCC
Q 023301          106 DLV------TE-TELGSLTERIKHINA  125 (284)
Q Consensus       106 D~~------~~-~~~~~~~~~l~~~np  125 (284)
                      |+.      ++ +...++.+.+.++|.
T Consensus       136 D~~~~e~~~~~~~~~~~~~~ii~~~n~  162 (222)
T cd01885         136 DRLILELKLSPEEAYQRLARIIEQVNA  162 (222)
T ss_pred             CcchhhhcCCHHHHHHHHHHHHHHHhH
Confidence            985      33 334566666666764

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

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

Probab=89.90  E-value=0.88  Score=42.37  Aligned_cols=90  Identities=21%  Similarity=0.317  Sum_probs=47.8

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH--HhhhhcCCccchHHHHHHHhhcC-EEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM--QHLNEVKPRFVVNEAVEQVAYAD-RIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~--~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D  106 (284)
                      ..+.|++++|-.+   +...     .+...-.++.++.|+|+....  .+...    .+ . ....+.... +||+||+|
T Consensus        85 ~~i~liDtPG~~~---f~~~-----~~~~~~~~D~~llVVDa~~~~~~~~t~~----~l-~-~l~~~~i~~iiVVlNK~D  150 (411)
T PRK04000         85 RRVSFVDAPGHET---LMAT-----MLSGAALMDGAILVIAANEPCPQPQTKE----HL-M-ALDIIGIKNIVIVQNKID  150 (411)
T ss_pred             cEEEEEECCCHHH---HHHH-----HHHHHhhCCEEEEEEECCCCCCChhHHH----HH-H-HHHHcCCCcEEEEEEeec
Confidence            4578999999432   2222     222334578899999998632  11000    01 1 122333333 67789999


Q ss_pred             CCChhHHH----HHHHHHHHhC-CCCceeeec
Q 023301          107 LVTETELG----SLTERIKHIN-AMAPVKLAK  133 (284)
Q Consensus       107 ~~~~~~~~----~~~~~l~~~n-p~a~i~~~~  133 (284)
                      +.++++..    .++++++... ...+++.++
T Consensus       151 l~~~~~~~~~~~~i~~~l~~~~~~~~~ii~vS  182 (411)
T PRK04000        151 LVSKERALENYEQIKEFVKGTVAENAPIIPVS  182 (411)
T ss_pred             cccchhHHHHHHHHHHHhccccCCCCeEEEEE
Confidence            98765543    3333333221 246677665

>cd04154 Arl2 Arl2 subfamily

Probab=89.69  E-value=1.6  Score=34.93  Aligned_cols=93  Identities=17%  Similarity=0.165  Sum_probs=45.3

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHH-H-HhhcCEEEEccCCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVE-Q-VAYADRIILNKIDLV  108 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~-Q-i~~Ad~ivlnK~D~~  108 (284)
                      ...+++++|...........     +   -..+.++.|+|+...... .+.. .++...+.. . -...=+||+||+|+.
T Consensus        59 ~l~l~D~~G~~~~~~~~~~~-----~---~~~d~~i~v~d~~~~~s~-~~~~-~~~~~~~~~~~~~~~p~iiv~nK~Dl~  128 (173)
T cd04154          59 KLNIWDVGGQKTLRPYWRNY-----F---ESTDALIWVVDSSDRLRL-DDCK-RELKELLQEERLAGATLLILANKQDLP  128 (173)
T ss_pred             EEEEEECCCCHHHHHHHHHH-----h---CCCCEEEEEEECCCHHHH-HHHH-HHHHHHHhChhhcCCCEEEEEECcccc
Confidence            34678888865433322211     1   145778999999875321 1110 011111111 1 112346777999996


Q ss_pred             ChhHHHHHHHHHHHh---CCCCceeeec
Q 023301          109 TETELGSLTERIKHI---NAMAPVKLAK  133 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~---np~a~i~~~~  133 (284)
                      .....+.+.+.++..   ....++++++
T Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~S  156 (173)
T cd04154         129 GALSEEEIREALELDKISSHHWRIQPCS  156 (173)
T ss_pred             cCCCHHHHHHHhCccccCCCceEEEecc
Confidence            544444455544322   1234566554

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.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=89.63  E-value=3.5  Score=38.28  Aligned_cols=114  Identities=18%  Similarity=0.241  Sum_probs=64.5

Q ss_pred             chHHHHHHHHHHhhcCCCCEEEEecCCCCCc-HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHH
Q 023301           13 GDLVKMLLQLAKKKQGQFDHIVIETTGLAKP-APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAV   91 (284)
Q Consensus        13 ~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p-~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~   91 (284)
                      .++.++|..+.+  ..++|+|||+|.|-..- ...+..+..  .+ ....-+.++.|+|+..-...+.+.     ... .
T Consensus       306 ~~L~~aL~~lk~--~~~~DvVLIDTaGRs~kd~~lm~EL~~--~l-k~~~PdevlLVLsATtk~~d~~~i-----~~~-F  374 (436)
T PRK11889        306 AAMTRALTYFKE--EARVDYILIDTAGKNYRASETVEEMIE--TM-GQVEPDYICLTLSASMKSKDMIEI-----ITN-F  374 (436)
T ss_pred             HHHHHHHHHHHh--ccCCCEEEEeCccccCcCHHHHHHHHH--HH-hhcCCCeEEEEECCccChHHHHHH-----HHH-h
Confidence            345566655543  34699999999999773 233333321  11 122334578889986544332211     011 1


Q ss_pred             HHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCCChhhh
Q 023301           92 EQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFV  142 (284)
Q Consensus        92 ~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v~~~~l  142 (284)
                      .. ..-|-+|++|.|...  ..-.+...+...  +.||...+.|+-=++++
T Consensus       375 ~~-~~idglI~TKLDET~--k~G~iLni~~~~--~lPIsyit~GQ~VPeDI  420 (436)
T PRK11889        375 KD-IHIDGIVFTKFDETA--SSGELLKIPAVS--SAPIVLMTDGQDVKKNI  420 (436)
T ss_pred             cC-CCCCEEEEEcccCCC--CccHHHHHHHHH--CcCEEEEeCCCCCCcch
Confidence            22 456899999999865  344555555544  36777777764333333

>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed

Probab=89.63  E-value=0.52  Score=44.41  Aligned_cols=76  Identities=18%  Similarity=0.236  Sum_probs=43.3

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVT  109 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~  109 (284)
                      ....++.|.|+-++...++.+.....+...-..+.++.|+|+...... .+     . ..+...-...-++|+||+|+.+
T Consensus       263 ~~i~l~DT~G~~~~~~~ie~~gi~~~~~~~~~aD~il~VvD~s~~~s~-~~-----~-~~l~~~~~~piiiV~NK~DL~~  335 (449)
T PRK05291        263 IPLRLIDTAGIRETDDEVEKIGIERSREAIEEADLVLLVLDASEPLTE-ED-----D-EILEELKDKPVIVVLNKADLTG  335 (449)
T ss_pred             eEEEEEeCCCCCCCccHHHHHHHHHHHHHHHhCCEEEEEecCCCCCCh-hH-----H-HHHHhcCCCCcEEEEEhhhccc
Confidence            346789999998877655442111112223457789999999764321 00     0 1112111234588899999976


Q ss_pred             hhH
Q 023301          110 ETE  112 (284)
Q Consensus       110 ~~~  112 (284)
                      ...
T Consensus       336 ~~~  338 (449)
T PRK05291        336 EID  338 (449)
T ss_pred             cch
Confidence            543

>cd01856 YlqF YlqF

Probab=89.56  E-value=0.73  Score=37.14  Aligned_cols=54  Identities=19%  Similarity=0.194  Sum_probs=31.4

Q ss_pred             eeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-hcCEEEEccCCCCChhHHHHHHHHHH
Q 023301           60 VKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-YADRIILNKIDLVTETELGSLTERIK  121 (284)
Q Consensus        60 ~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-~Ad~ivlnK~D~~~~~~~~~~~~~l~  121 (284)
                      -..+.++.|+|+......    .+.    .+...+. ..-++|+||+|+.++++.....+.++
T Consensus        18 ~~aD~il~v~D~~~~~~~----~~~----~i~~~~~~k~~ilVlNK~Dl~~~~~~~~~~~~~~   72 (171)
T cd01856          18 KLVDLVIEVRDARIPLSS----RNP----LLEKILGNKPRIIVLNKADLADPKKTKKWLKYFE   72 (171)
T ss_pred             hhCCEEEEEeeccCccCc----CCh----hhHhHhcCCCEEEEEehhhcCChHHHHHHHHHHH
Confidence            466779999999754321    111    1223332 34688999999987655444434433

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.

>PRK12735 elongation factor Tu; Reviewed

Probab=89.40  E-value=1.5  Score=40.64  Aligned_cols=88  Identities=18%  Similarity=0.282  Sum_probs=47.9

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH-HhhhhcCCccchHHHHHHH---hhcCEE-EEc
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM-QHLNEVKPRFVVNEAVEQV---AYADRI-ILN  103 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~-~~l~~~~~~~~~~~~~~Qi---~~Ad~i-vln  103 (284)
                      +..+.||+|+|..   ..+....     ......+.++.|||+..-. .+.         ......+   ....+| ++|
T Consensus        74 ~~~i~~iDtPGh~---~f~~~~~-----~~~~~aD~~llVvda~~g~~~qt---------~e~l~~~~~~gi~~iivvvN  136 (396)
T PRK12735         74 NRHYAHVDCPGHA---DYVKNMI-----TGAAQMDGAILVVSAADGPMPQT---------REHILLARQVGVPYIVVFLN  136 (396)
T ss_pred             CcEEEEEECCCHH---HHHHHHH-----hhhccCCEEEEEEECCCCCchhH---------HHHHHHHHHcCCCeEEEEEE
Confidence            3467999999973   3333221     2234678899999997622 111         1112222   233354 689


Q ss_pred             cCCCCChhH-HH----HHHHHHHHhC-C--CCceeeec
Q 023301          104 KIDLVTETE-LG----SLTERIKHIN-A--MAPVKLAK  133 (284)
Q Consensus       104 K~D~~~~~~-~~----~~~~~l~~~n-p--~a~i~~~~  133 (284)
                      |+|+++.++ .+    ++++.++.+. +  +.+++..+
T Consensus       137 K~Dl~~~~~~~~~~~~ei~~~l~~~~~~~~~~~ii~~S  174 (396)
T PRK12735        137 KCDMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGS  174 (396)
T ss_pred             ecCCcchHHHHHHHHHHHHHHHHHcCCCcCceeEEecc
Confidence            999986433 22    3444444432 2  35666554

>TIGR00437 feoB ferrous iron transporter FeoB

Probab=89.32  E-value=0.5  Score=46.16  Aligned_cols=100  Identities=16%  Similarity=0.176  Sum_probs=53.3

Q ss_pred             CEEEEecCCCCCcHHHH--HHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccC
Q 023301           31 DHIVIETTGLAKPAPVI--ETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKI  105 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~--~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~  105 (284)
                      ...+++++|..+....-  +.+.. ..+. .-..+.++.|+|+.++...+.          ...|+   ...=++++||+
T Consensus        42 ~i~lvDtPG~~~~~~~s~~e~v~~-~~l~-~~~aDvvI~VvDat~ler~l~----------l~~ql~~~~~PiIIVlNK~  109 (591)
T TIGR00437        42 DIEIVDLPGIYSLTTFSLEEEVAR-DYLL-NEKPDLVVNVVDASNLERNLY----------LTLQLLELGIPMILALNLV  109 (591)
T ss_pred             EEEEEECCCccccCccchHHHHHH-HHHh-hcCCCEEEEEecCCcchhhHH----------HHHHHHhcCCCEEEEEehh
Confidence            46789999987754321  00100 0011 114688999999998654321          12233   34557889999


Q ss_pred             CCCChhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          106 DLVTETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       106 D~~~~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+.+...+..-.+.+.+... .+++.++. .....+.++
T Consensus       110 Dl~~~~~i~~d~~~L~~~lg-~pvv~tSA~tg~Gi~eL~  147 (591)
T TIGR00437       110 DEAEKKGIRIDEEKLEERLG-VPVVPTSATEGRGIERLK  147 (591)
T ss_pred             HHHHhCCChhhHHHHHHHcC-CCEEEEECCCCCCHHHHH
Confidence            98654333222233333322 67776653 233455554

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.

>TIGR00485 EF-Tu translation elongation factor TU

Probab=89.13  E-value=1.2  Score=41.30  Aligned_cols=90  Identities=19%  Similarity=0.280  Sum_probs=48.9

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH-HhhhhcCCccchHHHHHHHhhcCE-EEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM-QHLNEVKPRFVVNEAVEQVAYADR-IILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~-~~l~~~~~~~~~~~~~~Qi~~Ad~-ivlnK~D~  107 (284)
                      ..+.||+|+|..+.   +...     +...-..+.++.|||+..-. .+..     .... ........-+ |++||+|+
T Consensus        75 ~~~~liDtpGh~~f---~~~~-----~~~~~~~D~~ilVvda~~g~~~qt~-----e~l~-~~~~~gi~~iIvvvNK~Dl  140 (394)
T TIGR00485        75 RHYAHVDCPGHADY---VKNM-----ITGAAQMDGAILVVSATDGPMPQTR-----EHIL-LARQVGVPYIVVFLNKCDM  140 (394)
T ss_pred             EEEEEEECCchHHH---HHHH-----HHHHhhCCEEEEEEECCCCCcHHHH-----HHHH-HHHHcCCCEEEEEEEeccc
Confidence            35789999997542   2221     11223578899999997632 1110     0001 1223333445 46899999


Q ss_pred             CChhHH-H----HHHHHHHHhC-C--CCceeeec
Q 023301          108 VTETEL-G----SLTERIKHIN-A--MAPVKLAK  133 (284)
Q Consensus       108 ~~~~~~-~----~~~~~l~~~n-p--~a~i~~~~  133 (284)
                      ++.+++ +    +++++++... +  .++++.++
T Consensus       141 ~~~~~~~~~~~~~i~~~l~~~~~~~~~~~ii~vS  174 (394)
T TIGR00485       141 VDDEELLELVEMEVRELLSEYDFPGDDTPIIRGS  174 (394)
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCCCccCccEEECc
Confidence            875442 2    3555555443 2  26777655

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.

>CHL00071 tufA elongation factor Tu

Probab=88.99  E-value=1.5  Score=40.73  Aligned_cols=92  Identities=18%  Similarity=0.257  Sum_probs=49.5

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCE-EEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADR-IILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~-ivlnK~D~  107 (284)
                      +..++||.++|..   ..+....     ...-..+.++.|||+..-....    .+... .+........+ +++||+|+
T Consensus        74 ~~~~~~iDtPGh~---~~~~~~~-----~~~~~~D~~ilVvda~~g~~~q----t~~~~-~~~~~~g~~~iIvvvNK~D~  140 (409)
T CHL00071         74 NRHYAHVDCPGHA---DYVKNMI-----TGAAQMDGAILVVSAADGPMPQ----TKEHI-LLAKQVGVPNIVVFLNKEDQ  140 (409)
T ss_pred             CeEEEEEECCChH---HHHHHHH-----HHHHhCCEEEEEEECCCCCcHH----HHHHH-HHHHHcCCCEEEEEEEccCC
Confidence            3467999999943   2233221     1233578899999997632110    00111 11233334434 67999999


Q ss_pred             CChhHH-H----HHHHHHHHhC--C-CCceeeec
Q 023301          108 VTETEL-G----SLTERIKHIN--A-MAPVKLAK  133 (284)
Q Consensus       108 ~~~~~~-~----~~~~~l~~~n--p-~a~i~~~~  133 (284)
                      ++.+++ +    ++.+.++.+.  + .++++..+
T Consensus       141 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~ii~~S  174 (409)
T CHL00071        141 VDDEELLELVELEVRELLSKYDFPGDDIPIVSGS  174 (409)
T ss_pred             CCHHHHHHHHHHHHHHHHHHhCCCCCcceEEEcc
Confidence            875542 2    4455555443  2 25666543

>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed

Probab=88.99  E-value=0.72  Score=46.14  Aligned_cols=106  Identities=16%  Similarity=0.115  Sum_probs=57.0

Q ss_pred             CCEEEEecCCCCCcHHH------HHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEc
Q 023301           30 FDHIVIETTGLAKPAPV------IETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILN  103 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i------~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivln  103 (284)
                      .++.+++|+|+......      +..+..   ....-..+.++.|+|+..-.....    ..+.. .......+-+||+|
T Consensus       498 ~~~~liDTaG~~~~~~~~~~~e~~~~~r~---~~~i~~advvilViDat~~~s~~~----~~i~~-~~~~~~~piIiV~N  569 (712)
T PRK09518        498 EDWLFIDTAGIKRRQHKLTGAEYYSSLRT---QAAIERSELALFLFDASQPISEQD----LKVMS-MAVDAGRALVLVFN  569 (712)
T ss_pred             CEEEEEECCCcccCcccchhHHHHHHHHH---HHHhhcCCEEEEEEECCCCCCHHH----HHHHH-HHHHcCCCEEEEEE
Confidence            35678999998643221      111110   111224677999999976432110    00101 11223456789999


Q ss_pred             cCCCCChhHHHHHHHHHHHhC---CCCceeeecc-CCCChhhhh
Q 023301          104 KIDLVTETELGSLTERIKHIN---AMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       104 K~D~~~~~~~~~~~~~l~~~n---p~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+|+.+.+..+.+++.++...   +.++++.++. .......++
T Consensus       570 K~DL~~~~~~~~~~~~~~~~l~~~~~~~ii~iSAktg~gv~~L~  613 (712)
T PRK09518        570 KWDLMDEFRRQRLERLWKTEFDRVTWARRVNLSAKTGWHTNRLA  613 (712)
T ss_pred             chhcCChhHHHHHHHHHHHhccCCCCCCEEEEECCCCCCHHHHH
Confidence            999988666666666665433   4566665542 233444444

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=88.97  E-value=4.6  Score=37.24  Aligned_cols=107  Identities=20%  Similarity=0.181  Sum_probs=59.9

Q ss_pred             chHHHHHHHHHHhhcCCCCEEEEecCCCCCcH-HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHH-
Q 023301           13 GDLVKMLLQLAKKKQGQFDHIVIETTGLAKPA-PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEA-   90 (284)
Q Consensus        13 ~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~-~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~-   90 (284)
                      .++..+|..+..  ....|+|||+|.|..... ..++.+.   .+......+.++.|+++..-...+.+        .+ 
T Consensus       271 ~dL~~al~~l~~--~~~~D~VLIDTAGr~~~d~~~l~EL~---~l~~~~~p~~~~LVLsag~~~~d~~~--------i~~  337 (407)
T PRK12726        271 AELEEAVQYMTY--VNCVDHILIDTVGRNYLAEESVSEIS---AYTDVVHPDLTCFTFSSGMKSADVMT--------ILP  337 (407)
T ss_pred             HHHHHHHHHHHh--cCCCCEEEEECCCCCccCHHHHHHHH---HHhhccCCceEEEECCCcccHHHHHH--------HHH
Confidence            456666665553  356899999999997632 2333332   12222333445677887443322211        11 


Q ss_pred             HHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCC
Q 023301           91 VEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGS  136 (284)
Q Consensus        91 ~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~  136 (284)
                      .-+...-+-+|+||.|...  ..-.+...+...  ..||...+.|+
T Consensus       338 ~f~~l~i~glI~TKLDET~--~~G~~Lsv~~~t--glPIsylt~GQ  379 (407)
T PRK12726        338 KLAEIPIDGFIITKMDETT--RIGDLYTVMQET--NLPVLYMTDGQ  379 (407)
T ss_pred             hcCcCCCCEEEEEcccCCC--CccHHHHHHHHH--CCCEEEEecCC
Confidence            1123346889999999854  344555554444  36777677764

>PRK12297 obgE GTPase CgtA; Reviewed

Probab=88.62  E-value=0.99  Score=42.18  Aligned_cols=107  Identities=13%  Similarity=0.173  Sum_probs=50.9

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH--HhhhhcCCccchHHHH---HH-HhhcCEEEEc
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM--QHLNEVKPRFVVNEAV---EQ-VAYADRIILN  103 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~--~~l~~~~~~~~~~~~~---~Q-i~~Ad~ivln  103 (284)
                      ...++++++|+..-+.--..|- ...++..-..+.+|.|||+....  ..+.+.  ..+..++.   .+ ....-+||+|
T Consensus       206 ~~~~laD~PGliega~~~~gLg-~~fLrhier~~llI~VID~s~~~~~dp~e~~--~~i~~EL~~y~~~L~~kP~IVV~N  282 (424)
T PRK12297        206 RSFVMADIPGLIEGASEGVGLG-HQFLRHIERTRVIVHVIDMSGSEGRDPIEDY--EKINKELKLYNPRLLERPQIVVAN  282 (424)
T ss_pred             ceEEEEECCCCcccccccchHH-HHHHHHHhhCCEEEEEEeCCccccCChHHHH--HHHHHHHhhhchhccCCcEEEEEe
Confidence            4578899999854221100110 01222334578899999996531  111110  00111111   11 2346689999


Q ss_pred             cCCCCChhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          104 KIDLVTETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       104 K~D~~~~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+|+....  +.+.+..+.+.  .+++.+|. .....+.++
T Consensus       283 K~DL~~~~--e~l~~l~~~l~--~~i~~iSA~tgeGI~eL~  319 (424)
T PRK12297        283 KMDLPEAE--ENLEEFKEKLG--PKVFPISALTGQGLDELL  319 (424)
T ss_pred             CCCCcCCH--HHHHHHHHHhC--CcEEEEeCCCCCCHHHHH
Confidence            99984322  22333333333  45665543 333454444

>KOG0780 consensus Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.58  E-value=2.1  Score=39.25  Aligned_cols=71  Identities=25%  Similarity=0.380  Sum_probs=48.2

Q ss_pred             cCCCCEEEEecCCCCCcH-HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccC
Q 023301           27 QGQFDHIVIETTGLAKPA-PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKI  105 (284)
Q Consensus        27 ~~~~d~iiIE~sG~a~p~-~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~  105 (284)
                      +.++|.||+.|||=..-. .+.+.+.   .....+.-+.||.|+|+..-......       .....|--.---|+|+|.
T Consensus       181 ke~fdvIIvDTSGRh~qe~sLfeEM~---~v~~ai~Pd~vi~VmDasiGQaae~Q-------a~aFk~~vdvg~vIlTKl  250 (483)
T KOG0780|consen  181 KENFDVIIVDTSGRHKQEASLFEEMK---QVSKAIKPDEIIFVMDASIGQAAEAQ-------ARAFKETVDVGAVILTKL  250 (483)
T ss_pred             hcCCcEEEEeCCCchhhhHHHHHHHH---HHHhhcCCCeEEEEEeccccHhHHHH-------HHHHHHhhccceEEEEec
Confidence            479999999999998844 3333332   23456778899999999875543221       122445555566889999


Q ss_pred             CC
Q 023301          106 DL  107 (284)
Q Consensus       106 D~  107 (284)
                      |-
T Consensus       251 DG  252 (483)
T KOG0780|consen  251 DG  252 (483)
T ss_pred             cc
Confidence            96

>TIGR00157 ribosome small subunit-dependent GTPase A

Probab=88.49  E-value=1.1  Score=38.58  Aligned_cols=106  Identities=18%  Similarity=0.258  Sum_probs=49.6

Q ss_pred             CCEEEEecCCC--CCcHHHHHHhcccccccc--eeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccC
Q 023301           30 FDHIVIETTGL--AKPAPVIETFCTDELVSQ--YVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKI  105 (284)
Q Consensus        30 ~d~iiIE~sG~--a~p~~i~~~l~~~~~l~~--~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~  105 (284)
                      -|+|.++..+-  +-...|++..   ..+.+  .-.++.++.|.|+......+... ++++. . ...-...=+||+||+
T Consensus         4 GD~V~~~~~~~~~~~i~~i~eR~---~~L~r~~~~n~D~viiV~d~~~p~~s~~~l-~r~l~-~-~~~~~i~~vIV~NK~   77 (245)
T TIGR00157         4 GDRVVWEPGNVVKVYGGAIAERK---NELTRPIVANIDQIVIVSSAVLPELSLNQL-DRFLV-V-AEAQNIEPIIVLNKI   77 (245)
T ss_pred             CcEEEEEecCCCceEEEEEeccc---ceEECcccccCCEEEEEEECCCCCCCHHHH-HHHHH-H-HHHCCCCEEEEEECc
Confidence            38888886532  2222222221   11211  23678889999887532111110 11211 1 111122336888999


Q ss_pred             CCCChhHHH-HHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          106 DLVTETELG-SLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       106 D~~~~~~~~-~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+.+..+.. ...+..++  ...+++.++. ..-..+.++
T Consensus        78 DL~~~~~~~~~~~~~~~~--~g~~v~~~SAktg~gi~eLf  115 (245)
T TIGR00157        78 DLLDDEDMEKEQLDIYRN--IGYQVLMTSSKNQDGLKELI  115 (245)
T ss_pred             ccCCCHHHHHHHHHHHHH--CCCeEEEEecCCchhHHHHH
Confidence            997654432 22233333  2356776653 233455554

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

>PRK09563 rbgA GTPase YlqF; Reviewed

Probab=88.30  E-value=1.1  Score=39.59  Aligned_cols=71  Identities=17%  Similarity=0.157  Sum_probs=40.6

Q ss_pred             CCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-hhcCEEEEccCCCCChhHHHHHHHH
Q 023301           41 AKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-AYADRIILNKIDLVTETELGSLTER  119 (284)
Q Consensus        41 a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-~~Ad~ivlnK~D~~~~~~~~~~~~~  119 (284)
                      +.|..+.+++..  ..+..-..|.|+.|+|++.....    ..    ..+.+.+ ...-++|+||+|+++.++.+...+.
T Consensus         6 wfpgHm~k~~~~--l~~~l~~aDvIL~VvDar~p~~~----~~----~~l~~~~~~kp~iiVlNK~DL~~~~~~~~~~~~   75 (287)
T PRK09563          6 WFPGHMAKARRE--IKENLKLVDVVIEVLDARIPLSS----EN----PMIDKIIGNKPRLLILNKSDLADPEVTKKWIEY   75 (287)
T ss_pred             CcHHHHHHHHHH--HHHHhhhCCEEEEEEECCCCCCC----CC----hhHHHHhCCCCEEEEEEchhcCCHHHHHHHHHH
Confidence            456666665432  12223467789999999764321    11    1122222 3456899999999876555444444


Q ss_pred             HH
Q 023301          120 IK  121 (284)
Q Consensus       120 l~  121 (284)
                      ++
T Consensus        76 ~~   77 (287)
T PRK09563         76 FE   77 (287)
T ss_pred             HH
Confidence            44

>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=88.17  E-value=0.68  Score=39.76  Aligned_cols=87  Identities=21%  Similarity=0.200  Sum_probs=40.7

Q ss_pred             CCCEEEEecCCCCCcHHH---HHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccC
Q 023301           29 QFDHIVIETTGLAKPAPV---IETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKI  105 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i---~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~  105 (284)
                      +.+++++.|+|=-+.-..   ...+.  ..+.....+ .+|.++|+..+.....-...-...-...-+++..-+.|+||+
T Consensus        90 ~~~y~l~DtPGQiElf~~~~~~~~i~--~~L~~~~~~-~~v~LvD~~~~~~~~~f~s~~L~s~s~~~~~~lP~vnvlsK~  166 (238)
T PF03029_consen   90 EDDYLLFDTPGQIELFTHSDSGRKIV--ERLQKNGRL-VVVFLVDSSFCSDPSKFVSSLLLSLSIMLRLELPHVNVLSKI  166 (238)
T ss_dssp             H-SEEEEE--SSHHHHHHSHHHHHHH--HTSSS-----EEEEEE-GGG-SSHHHHHHHHHHHHHHHHHHTSEEEEEE--G
T ss_pred             CCcEEEEeCCCCEEEEEechhHHHHH--HHHhhhcce-EEEEEEecccccChhhHHHHHHHHHHHHhhCCCCEEEeeecc
Confidence            449999999997663221   11111  122222333 478999998765421100000011123566889999999999


Q ss_pred             CCCChhHHHHHHHH
Q 023301          106 DLVTETELGSLTER  119 (284)
Q Consensus       106 D~~~~~~~~~~~~~  119 (284)
                      |+.++. .+...++
T Consensus       167 Dl~~~~-~~~~l~~  179 (238)
T PF03029_consen  167 DLLSKY-LEFILEW  179 (238)
T ss_dssp             GGS-HH-HHHHHHH
T ss_pred             Ccccch-hHHHHHH
Confidence            999855 4444333

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

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

Probab=88.03  E-value=2.6  Score=32.83  Aligned_cols=82  Identities=22%  Similarity=0.283  Sum_probs=44.1

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~ivlnK~D  106 (284)
                      .+..+++++|--.-..+...+     +   -..+.++.|+|+...... .... ..+ ..+..+..   ..=+++.||+|
T Consensus        43 ~~~~i~D~~G~~~~~~~~~~~-----~---~~~~~~i~v~D~~~~~~~-~~~~-~~~-~~~~~~~~~~~~piiiv~nK~D  111 (158)
T cd00878          43 VSFTVWDVGGQDKIRPLWKHY-----Y---ENTNGIIFVVDSSDRERI-EEAK-EEL-HKLLNEEELKGVPLLIFANKQD  111 (158)
T ss_pred             EEEEEEECCCChhhHHHHHHH-----h---ccCCEEEEEEECCCHHHH-HHHH-HHH-HHHHhCcccCCCcEEEEeeccC
Confidence            466788999976544333322     1   134789999999874221 1100 000 11112111   23366789999


Q ss_pred             CCChhHHHHHHHHHHH
Q 023301          107 LVTETELGSLTERIKH  122 (284)
Q Consensus       107 ~~~~~~~~~~~~~l~~  122 (284)
                      +......+++.+.++.
T Consensus       112 ~~~~~~~~~~~~~~~~  127 (158)
T cd00878         112 LPGALSVSELIEKLGL  127 (158)
T ss_pred             CccccCHHHHHHhhCh
Confidence            9775555556555554

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

>COG3276 SelB Selenocysteine-specific translation elongation factor [Translation, ribosomal structure and biogenesis]

Probab=87.76  E-value=1.5  Score=40.73  Aligned_cols=91  Identities=16%  Similarity=0.100  Sum_probs=57.2

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccc-hHHhhhhcCCccchHHHHHHHhhcC-EEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKH-AMQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~-~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~  107 (284)
                      .-.-||+++|-.+.  |..++      ....-++..+.|||+.. +..+..+.      -++.+.+..-. +||+||+|.
T Consensus        50 ~~~~fIDvpgh~~~--i~~mi------ag~~~~d~alLvV~~deGl~~qtgEh------L~iLdllgi~~giivltk~D~  115 (447)
T COG3276          50 GVMGFIDVPGHPDF--ISNLL------AGLGGIDYALLVVAADEGLMAQTGEH------LLILDLLGIKNGIIVLTKADR  115 (447)
T ss_pred             CceEEeeCCCcHHH--HHHHH------hhhcCCceEEEEEeCccCcchhhHHH------HHHHHhcCCCceEEEEecccc
Confidence            35678999996552  22222      12335667899999943 33332221      12467777777 899999999


Q ss_pred             CChhHHHHHHHHHHHh--CCCCceeeecc
Q 023301          108 VTETELGSLTERIKHI--NAMAPVKLAKY  134 (284)
Q Consensus       108 ~~~~~~~~~~~~l~~~--np~a~i~~~~~  134 (284)
                      +++++++...+.|.+-  .+.++++.++.
T Consensus       116 ~d~~r~e~~i~~Il~~l~l~~~~i~~~s~  144 (447)
T COG3276         116 VDEARIEQKIKQILADLSLANAKIFKTSA  144 (447)
T ss_pred             ccHHHHHHHHHHHHhhccccccccccccc
Confidence            9988776665555543  25677776654

>cd01860 Rab5_related Rab5-related subfamily

Probab=87.61  E-value=4.3  Score=31.69  Aligned_cols=64  Identities=13%  Similarity=0.051  Sum_probs=35.0

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhc------CEEEEccCCCCChh--HHHHHHHHHHHhCCCCceeee
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYA------DRIILNKIDLVTET--ELGSLTERIKHINAMAPVKLA  132 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~A------d~ivlnK~D~~~~~--~~~~~~~~l~~~np~a~i~~~  132 (284)
                      ..+.+|.|+|+.+.... ...      .....++...      =+|++||+|+.+..  ..+...+..+..+  .+++++
T Consensus        73 ~~~~~i~v~d~~~~~s~-~~~------~~~~~~~~~~~~~~~~iivv~nK~D~~~~~~~~~~~~~~~~~~~~--~~~~~~  143 (163)
T cd01860          73 GAAAAIVVYDITSEESF-EKA------KSWVKELQRNASPNIIIALVGNKADLESKRQVSTEEAQEYADENG--LLFFET  143 (163)
T ss_pred             cCCEEEEEEECcCHHHH-HHH------HHHHHHHHHhCCCCCeEEEEEECccccccCcCCHHHHHHHHHHcC--CEEEEE
Confidence            35789999999875432 111      1112222222      26677999987422  2344555555444  556665


Q ss_pred             c
Q 023301          133 K  133 (284)
Q Consensus       133 ~  133 (284)
                      +
T Consensus       144 S  144 (163)
T cd01860         144 S  144 (163)
T ss_pred             E
Confidence            4

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

>cd03110 Fer4_NifH_child This protein family's function is unkown

Probab=87.38  E-value=5.8  Score=31.94  Aligned_cols=81  Identities=17%  Similarity=0.237  Sum_probs=45.3

Q ss_pred             cCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCC
Q 023301           27 QGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKID  106 (284)
Q Consensus        27 ~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D  106 (284)
                      ..++|+|||.++|..... ....+         ...+.++.|+.+......  ... + +.. ..++....-.+|+||.|
T Consensus        90 ~~~~d~viiDtpp~~~~~-~~~~l---------~~aD~vliv~~~~~~~~~--~~~-~-~~~-~l~~~~~~~~vV~N~~~  154 (179)
T cd03110          90 AEGAELIIIDGPPGIGCP-VIASL---------TGADAALLVTEPTPSGLH--DLE-R-AVE-LVRHFGIPVGVVINKYD  154 (179)
T ss_pred             hcCCCEEEEECcCCCcHH-HHHHH---------HcCCEEEEEecCCcccHH--HHH-H-HHH-HHHHcCCCEEEEEeCCC
Confidence            368999999999665542 22222         124567888888764221  110 0 101 12222323368999999


Q ss_pred             CCChhHHHHHHHHHHHh
Q 023301          107 LVTETELGSLTERIKHI  123 (284)
Q Consensus       107 ~~~~~~~~~~~~~l~~~  123 (284)
                      ..+. ..+.+++.+++.
T Consensus       155 ~~~~-~~~~~~~~~~~~  170 (179)
T cd03110         155 LNDE-IAEEIEDYCEEE  170 (179)
T ss_pred             CCcc-hHHHHHHHHHHc
Confidence            7543 334566666654

It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.

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

Probab=87.24  E-value=2.5  Score=34.29  Aligned_cols=69  Identities=20%  Similarity=0.251  Sum_probs=37.1

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHH-HH-HhhcCEEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAV-EQ-VAYADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~-~Q-i~~Ad~ivlnK~D~  107 (284)
                      ....+++++|......+....     +   -..+.+|.|+|+...... .... ..+...+. .. -...=+||+||+|+
T Consensus        61 ~~~~~~D~~G~~~~~~~~~~~-----~---~~ad~ii~vvD~~~~~~~-~~~~-~~l~~l~~~~~~~~~piliv~NK~Dl  130 (184)
T smart00178       61 IKFTTFDLGGHQQARRLWKDY-----F---PEVNGIVYLVDAYDKERF-AESK-RELDALLSDEELATVPFLILGNKIDA  130 (184)
T ss_pred             EEEEEEECCCCHHHHHHHHHH-----h---CCCCEEEEEEECCcHHHH-HHHH-HHHHHHHcChhhcCCCEEEEEeCccc
Confidence            455778999976554433321     1   256889999999774321 1110 01101110 11 12345788899998


Q ss_pred             C
Q 023301          108 V  108 (284)
Q Consensus       108 ~  108 (284)
                      .
T Consensus       131 ~  131 (184)
T smart00178      131 P  131 (184)
T ss_pred             c
Confidence            4

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

>COG1161 Predicted GTPases [General function prediction only]

Probab=87.19  E-value=1.5  Score=39.40  Aligned_cols=65  Identities=18%  Similarity=0.247  Sum_probs=42.9

Q ss_pred             eeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceee
Q 023301           60 VKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKL  131 (284)
Q Consensus        60 ~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~  131 (284)
                      -..+.|+-|+|++.+......    .+ .  .-.-....++|+||+|+++........+.....++...+..
T Consensus        33 ~~~d~vvevvDar~P~~s~~~----~l-~--~~v~~k~~i~vlNK~DL~~~~~~~~W~~~~~~~~~~~~~~v   97 (322)
T COG1161          33 KSVDVVVEVVDARDPLGTRNP----EL-E--RIVKEKPKLLVLNKADLAPKEVTKKWKKYFKKEEGIKPIFV   97 (322)
T ss_pred             ccCCEEEEEEeccccccccCc----cH-H--HHHccCCcEEEEehhhcCCHHHHHHHHHHHHhcCCCccEEE
Confidence            357779999999987654221    11 1  11112233889999999999888888777777665444544

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

Probab=87.15  E-value=6.7  Score=30.54  Aligned_cols=99  Identities=14%  Similarity=0.208  Sum_probs=51.1

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCCCC
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKIDLV  108 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D~~  108 (284)
                      ..+++++|.-+...+.....        -..+.++.|+|+.+... +.... .+. ..+..+.   ...=+|++||+|+.
T Consensus        52 ~~i~Dt~G~~~~~~~~~~~~--------~~~~~~ilv~d~~~~~s-~~~~~-~~~-~~~~~~~~~~~~piiiv~NK~Dl~  120 (164)
T cd04145          52 LDILDTAGQEEFSAMREQYM--------RTGEGFLLVFSVTDRGS-FEEVD-KFH-TQILRVKDRDEFPMILVGNKADLE  120 (164)
T ss_pred             EEEEECCCCcchhHHHHHHH--------hhCCEEEEEEECCCHHH-HHHHH-HHH-HHHHHHhCCCCCCEEEEeeCcccc
Confidence            45679999877666544322        13567899999987443 22210 011 1112211   12336788999986


Q ss_pred             ChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          109 TETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       109 ~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +...  .+...+..+..  ..++++++. .......++
T Consensus       121 ~~~~~~~~~~~~~~~~~--~~~~~~~Sa~~~~~i~~l~  156 (164)
T cd04145         121 HQRKVSREEGQELARKL--KIPYIETSAKDRLNVDKAF  156 (164)
T ss_pred             ccceecHHHHHHHHHHc--CCcEEEeeCCCCCCHHHHH
Confidence            5322  23344444433  246666553 233444443

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

>cd04161 Arl2l1_Arl13_like Arl2l1/Arl13 subfamily

Probab=87.03  E-value=2.6  Score=33.54  Aligned_cols=77  Identities=16%  Similarity=0.159  Sum_probs=39.4

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHH-H-HhhcCEEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVE-Q-VAYADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~-Q-i~~Ad~ivlnK~D~  107 (284)
                      ....+++++|-.....+...     .+   -..+.+|.|+|+..... +.+.. ..+...... + -...=+||+||+|+
T Consensus        43 ~~~~i~D~~G~~~~~~~~~~-----~~---~~a~~ii~V~D~s~~~s-~~~~~-~~l~~l~~~~~~~~~piliv~NK~Dl  112 (167)
T cd04161          43 YEVCIFDLGGGANFRGIWVN-----YY---AEAHGLVFVVDSSDDDR-VQEVK-EILRELLQHPRVSGKPILVLANKQDK  112 (167)
T ss_pred             EEEEEEECCCcHHHHHHHHH-----HH---cCCCEEEEEEECCchhH-HHHHH-HHHHHHHcCccccCCcEEEEEeCCCC
Confidence            44568899997554443221     11   24568999999987532 22110 001000000 1 12234788899998


Q ss_pred             CChhHHHHH
Q 023301          108 VTETELGSL  116 (284)
Q Consensus       108 ~~~~~~~~~  116 (284)
                      .+......+
T Consensus       113 ~~~~~~~~i  121 (167)
T cd04161         113 KNALLGADV  121 (167)
T ss_pred             cCCCCHHHH
Confidence            654333333

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.

>cd00550 ArsA_ATPase Oxyanion-translocating ATPase (ArsA)

Probab=86.98  E-value=14  Score=31.93  Aligned_cols=80  Identities=14%  Similarity=0.188  Sum_probs=43.4

Q ss_pred             HHHHHHHhhcCCCCEEEEecCCCCCcHHHHHH---hcc-cccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH
Q 023301           18 MLLQLAKKKQGQFDHIVIETTGLAKPAPVIET---FCT-DELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ   93 (284)
Q Consensus        18 ~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~---l~~-~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q   93 (284)
                      .+.++++  ..++|+|||.|+-.++...++..   +.. ...+. .-....++.|+.+......  +.      ....+.
T Consensus       115 ~~~~~l~--~~~yD~VVvDtpPtg~tlrlL~lp~~l~~~~~~l~-d~~~~~~vlV~~p~~~~~~--e~------~r~~~~  183 (254)
T cd00550         115 EFSRYID--EAEYDVVVFDTAPTGHTLRLLSLPTVLSWAREILS-DPERTSFRLVCIPEKMSLY--ET------ERAIQE  183 (254)
T ss_pred             HHHHHHh--cCCCCEEEECCCCcHHHHHHHHhHHHHHHHHHHhc-CCcceEEEEEeCCChhHHH--HH------HHHHHH
Confidence            3445555  56899999999987665433321   000 00111 1123467888888765432  11      122344


Q ss_pred             Hhhc----CEEEEccCCCC
Q 023301           94 VAYA----DRIILNKIDLV  108 (284)
Q Consensus        94 i~~A----d~ivlnK~D~~  108 (284)
                      +...    .-+|+||....
T Consensus       184 L~~~g~~v~gvV~N~v~~~  202 (254)
T cd00550         184 LAKYGIDVDAVIVNQLLPE  202 (254)
T ss_pred             HHHCCCCCCEEEEecCccc
Confidence            4433    35999998653

This ATPase is involved in transport of arsenite, antimonite or other oxyanions across biological membranes in all three kingdoms of life. ArsA contains a highly conserved AAA motif present in the AAA+ ATPase superfamily associated with a variety of cellular activities. To form a functional ATP-driven pump, ArsA interacts with the permease ArsB, which is a channel-forming integral membrane protein. One of the most interesting features of ArsA is the allosteric activation by its transport substrates. A divalent cation, typically Mg2+, is required for its enzymatic activity.

>cd00154 Rab Rab family

Probab=86.70  E-value=5.3  Score=30.54  Aligned_cols=91  Identities=14%  Similarity=0.153  Sum_probs=46.0

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH--hhcCEEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV--AYADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi--~~Ad~ivlnK~D~  107 (284)
                      .+..+++++|......+...+.        -..+.+|.|+|+..... +.... .++ ..+...-  ...=+|++||+|+
T Consensus        49 ~~~~l~D~~g~~~~~~~~~~~~--------~~~d~ii~v~d~~~~~~-~~~~~-~~~-~~~~~~~~~~~p~ivv~nK~D~  117 (159)
T cd00154          49 VKLQIWDTAGQERFRSITPSYY--------RGAHGAILVYDITNRES-FENLD-KWL-KELKEYAPENIPIILVGNKIDL  117 (159)
T ss_pred             EEEEEEecCChHHHHHHHHHHh--------cCCCEEEEEEECCCHHH-HHHHH-HHH-HHHHHhCCCCCcEEEEEEcccc
Confidence            3455678888754444333221        13688999999987432 22210 111 1111111  1344778899999


Q ss_pred             CCh--hHHHHHHHHHHHhCCCCceeeec
Q 023301          108 VTE--TELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       108 ~~~--~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      .++  ...+.+++..+.  ...+++.++
T Consensus       118 ~~~~~~~~~~~~~~~~~--~~~~~~~~s  143 (159)
T cd00154         118 EDQRQVSTEEAQQFAKE--NGLLFFETS  143 (159)
T ss_pred             cccccccHHHHHHHHHH--cCCeEEEEe
Confidence            622  223444444443  235666554

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

>TIGR02034 CysN sulfate adenylyltransferase, large subunit

Probab=86.32  E-value=2.3  Score=39.51  Aligned_cols=92  Identities=16%  Similarity=0.199  Sum_probs=48.2

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC-EEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~  107 (284)
                      +..+.||+|+|..+.   .....     ...-..+.++.|||+..-...  .  .+.. ..+...+.... +|++||+|+
T Consensus        79 ~~~~~liDtPGh~~f---~~~~~-----~~~~~aD~allVVda~~G~~~--q--t~~~-~~~~~~~~~~~iivviNK~D~  145 (406)
T TIGR02034        79 KRKFIVADTPGHEQY---TRNMA-----TGASTADLAVLLVDARKGVLE--Q--TRRH-SYIASLLGIRHVVLAVNKMDL  145 (406)
T ss_pred             CeEEEEEeCCCHHHH---HHHHH-----HHHhhCCEEEEEEECCCCCcc--c--cHHH-HHHHHHcCCCcEEEEEEeccc
Confidence            346789999995442   22211     122367789999999753221  0  1110 11233434444 458999999


Q ss_pred             CC--hhHHHHHHHHHH----HhC-CCCceeeec
Q 023301          108 VT--ETELGSLTERIK----HIN-AMAPVKLAK  133 (284)
Q Consensus       108 ~~--~~~~~~~~~~l~----~~n-p~a~i~~~~  133 (284)
                      ++  .+.++.+++.++    ... ..++++..+
T Consensus       146 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~iipiS  178 (406)
T TIGR02034       146 VDYDEEVFENIKKDYLAFAEQLGFRDVTFIPLS  178 (406)
T ss_pred             ccchHHHHHHHHHHHHHHHHHcCCCCccEEEee
Confidence            75  333444444443    322 234566554

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).

>PRK00098 GTPase RsgA; Reviewed

Probab=85.89  E-value=1.5  Score=38.87  Aligned_cols=79  Identities=23%  Similarity=0.212  Sum_probs=38.7

Q ss_pred             eeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCC-hhHHHHHHHHHHHhCCCCceeeecc-CCC
Q 023301           60 VKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVT-ETELGSLTERIKHINAMAPVKLAKY-GSV  137 (284)
Q Consensus        60 ~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~-~~~~~~~~~~l~~~np~a~i~~~~~-g~v  137 (284)
                      -.++.++.|+|+...... .+..++++. . ..+-...=+||+||+|+.+ .+......+..+..  ..+++.++. ...
T Consensus        79 aniD~vllV~d~~~p~~~-~~~idr~L~-~-~~~~~ip~iIVlNK~DL~~~~~~~~~~~~~~~~~--g~~v~~vSA~~g~  153 (298)
T PRK00098         79 ANVDQAVLVFAAKEPDFS-TDLLDRFLV-L-AEANGIKPIIVLNKIDLLDDLEEARELLALYRAI--GYDVLELSAKEGE  153 (298)
T ss_pred             ecCCEEEEEEECCCCCCC-HHHHHHHHH-H-HHHCCCCEEEEEEhHHcCCCHHHHHHHHHHHHHC--CCeEEEEeCCCCc
Confidence            478889999999653110 000011111 1 1222234568899999973 33333333444333  346665543 233


Q ss_pred             Chhhhh
Q 023301          138 DMDFVL  143 (284)
Q Consensus       138 ~~~~l~  143 (284)
                      ..+.|+
T Consensus       154 gi~~L~  159 (298)
T PRK00098        154 GLDELK  159 (298)
T ss_pred             cHHHHH
Confidence            444444

>cd04158 ARD1 ARD1 subfamily

Probab=85.89  E-value=3.9  Score=32.52  Aligned_cols=80  Identities=19%  Similarity=0.270  Sum_probs=42.0

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH--Hh-hcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ--VA-YADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q--i~-~Ad~ivlnK~D  106 (284)
                      ....+++++|............        ...+.+|.|+|..+.... .+.. .++ ..+.++  +. ..=+||.||+|
T Consensus        43 ~~i~l~Dt~G~~~~~~~~~~~~--------~~ad~ii~V~D~s~~~s~-~~~~-~~~-~~~~~~~~~~~~piilv~NK~D  111 (169)
T cd04158          43 LKFTIWDVGGKHKLRPLWKHYY--------LNTQAVVFVVDSSHRDRV-SEAH-SEL-AKLLTEKELRDALLLIFANKQD  111 (169)
T ss_pred             EEEEEEECCCChhcchHHHHHh--------ccCCEEEEEEeCCcHHHH-HHHH-HHH-HHHhcChhhCCCCEEEEEeCcC
Confidence            4456789999866544333221        235789999999774322 2210 111 111222  22 23356779999


Q ss_pred             CCChhHHHHHHHHH
Q 023301          107 LVTETELGSLTERI  120 (284)
Q Consensus       107 ~~~~~~~~~~~~~l  120 (284)
                      +...-..+.+++.+
T Consensus       112 l~~~~~~~~~~~~~  125 (169)
T cd04158         112 VAGALSVEEMTELL  125 (169)
T ss_pred             cccCCCHHHHHHHh
Confidence            86433344444444

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

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

Probab=85.83  E-value=3.3  Score=38.73  Aligned_cols=94  Identities=15%  Similarity=0.293  Sum_probs=48.2

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchH-HHHHHHhhcCE-EEEccCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVN-EAVEQVAYADR-IILNKID  106 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~-~~~~Qi~~Ad~-ivlnK~D  106 (284)
                      +....|++++|-.+   .....     +...-..+.++.|+|+..-....   .+..... .+..++....+ |++||+|
T Consensus        84 ~~~i~iiDtpGh~~---f~~~~-----~~~~~~aD~~ilVvDa~~~~~~~---~~~t~~~~~~~~~~~~~~iIVviNK~D  152 (426)
T TIGR00483        84 KYEVTIVDCPGHRD---FIKNM-----ITGASQADAAVLVVAVGDGEFEV---QPQTREHAFLARTLGINQLIVAINKMD  152 (426)
T ss_pred             CeEEEEEECCCHHH---HHHHH-----HhhhhhCCEEEEEEECCCCCccc---CCchHHHHHHHHHcCCCeEEEEEEChh
Confidence            45678999999432   22221     11234578899999998742110   0111101 12233333334 5789999


Q ss_pred             CCC--hhHHH----HHHHHHHHhC---CCCceeeec
Q 023301          107 LVT--ETELG----SLTERIKHIN---AMAPVKLAK  133 (284)
Q Consensus       107 ~~~--~~~~~----~~~~~l~~~n---p~a~i~~~~  133 (284)
                      +.+  ++.++    +++++++...   ...+++.++
T Consensus       153 l~~~~~~~~~~~~~ei~~~~~~~g~~~~~~~~i~iS  188 (426)
T TIGR00483       153 SVNYDEEEFEAIKKEVSNLIKKVGYNPDTVPFIPIS  188 (426)
T ss_pred             ccCccHHHHHHHHHHHHHHHHHcCCCcccceEEEee
Confidence            974  43343    3344444432   135666654

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.

>cd01852 AIG1 AIG1 (avrRpt2-induced gene 1)

Probab=85.39  E-value=1.4  Score=36.26  Aligned_cols=74  Identities=15%  Similarity=0.095  Sum_probs=41.5

Q ss_pred             CCCEEEEecCCCCCcH----HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh--------h
Q 023301           29 QFDHIVIETTGLAKPA----PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA--------Y   96 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~----~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~--------~   96 (284)
                      .....||+|+|+.++.    .+...+.. -.....-.++.++.|+|+.++...-     .    .+.+++.        .
T Consensus        48 ~~~i~viDTPG~~d~~~~~~~~~~~i~~-~~~~~~~g~~~illVi~~~~~t~~d-----~----~~l~~l~~~fg~~~~~  117 (196)
T cd01852          48 GRRVNVIDTPGLFDTSVSPEQLSKEIVR-CLSLSAPGPHAFLLVVPLGRFTEEE-----E----QAVETLQELFGEKVLD  117 (196)
T ss_pred             CeEEEEEECcCCCCccCChHHHHHHHHH-HHHhcCCCCEEEEEEEECCCcCHHH-----H----HHHHHHHHHhChHhHh
Confidence            3467899999999864    23322211 0011122466799999998843221     1    1122232        2


Q ss_pred             cCEEEEccCCCCChhH
Q 023301           97 ADRIILNKIDLVTETE  112 (284)
Q Consensus        97 Ad~ivlnK~D~~~~~~  112 (284)
                      --+||+||.|...++.
T Consensus       118 ~~ivv~T~~d~l~~~~  133 (196)
T cd01852         118 HTIVLFTRGDDLEGGT  133 (196)
T ss_pred             cEEEEEECccccCCCc
Confidence            3367889999876543

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).

>cd01864 Rab19 Rab19 subfamily

Probab=85.37  E-value=7.2  Score=30.61  Aligned_cols=91  Identities=19%  Similarity=0.242  Sum_probs=44.4

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~ivlnK~D  106 (284)
                      ....+++++|......+...+     +   -..+.++.|+|+.+.... ... ..++ ..+ .+..   ..=++|.||+|
T Consensus        52 ~~l~i~D~~G~~~~~~~~~~~-----~---~~~d~~llv~d~~~~~s~-~~~-~~~~-~~i-~~~~~~~~p~ivv~nK~D  119 (165)
T cd01864          52 VKLQIWDTAGQERFRTITQSY-----Y---RSANGAIIAYDITRRSSF-ESV-PHWI-EEV-EKYGASNVVLLLIGNKCD  119 (165)
T ss_pred             EEEEEEECCChHHHHHHHHHH-----h---ccCCEEEEEEECcCHHHH-HhH-HHHH-HHH-HHhCCCCCcEEEEEECcc
Confidence            355777888853322222111     1   135889999999885432 111 0111 111 1211   12367889999


Q ss_pred             CCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          107 LVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       107 ~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +....+  .+...+..+... ...+++++
T Consensus       120 l~~~~~~~~~~~~~~~~~~~-~~~~~e~S  147 (165)
T cd01864         120 LEEQREVLFEEACTLAEKNG-MLAVLETS  147 (165)
T ss_pred             cccccccCHHHHHHHHHHcC-CcEEEEEE
Confidence            965432  233444444322 23455554

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.

>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily

Probab=85.33  E-value=4.3  Score=31.90  Aligned_cols=98  Identities=16%  Similarity=0.273  Sum_probs=48.1

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEEEEccCCCC
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRIILNKIDLV  108 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~ivlnK~D~~  108 (284)
                      .-+++++|.-....+.....        -..+.+|.|+|+.+.... .+.. .++ .. ..+..   ..-++|.||+|+.
T Consensus        53 ~~i~D~~G~~~~~~~~~~~~--------~~~~~ii~v~d~~~~~s~-~~l~-~~~-~~-~~~~~~~~~~~iiv~nK~Dl~  120 (166)
T cd01869          53 LQIWDTAGQERFRTITSSYY--------RGAHGIIIVYDVTDQESF-NNVK-QWL-QE-IDRYASENVNKLLVGNKCDLT  120 (166)
T ss_pred             EEEEECCCcHhHHHHHHHHh--------CcCCEEEEEEECcCHHHH-HhHH-HHH-HH-HHHhCCCCCcEEEEEEChhcc
Confidence            34567888554433332221        145789999999875432 2110 011 11 11211   2447888999986


Q ss_pred             ChhHH--HHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          109 TETEL--GSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       109 ~~~~~--~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      ....+  +......+..  ..++++++. .......++
T Consensus       121 ~~~~~~~~~~~~~~~~~--~~~~~~~Sa~~~~~v~~~~  156 (166)
T cd01869         121 DKRVVDYSEAQEFADEL--GIPFLETSAKNATNVEQAF  156 (166)
T ss_pred             cccCCCHHHHHHHHHHc--CCeEEEEECCCCcCHHHHH
Confidence            54322  3333433332  356776653 223444443

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

>TIGR00484 EF-G translation elongation factor EF-G

Probab=85.33  E-value=3  Score=41.59  Aligned_cols=81  Identities=19%  Similarity=0.212  Sum_probs=47.6

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      +....+|.|+|..+.......     .   .-..+.++.|||+..-...-    ...+.. ...+....-+|++||+|+.
T Consensus        74 ~~~i~liDTPG~~~~~~~~~~-----~---l~~~D~~ilVvda~~g~~~~----~~~~~~-~~~~~~~p~ivviNK~D~~  140 (689)
T TIGR00484        74 GHRINIIDTPGHVDFTVEVER-----S---LRVLDGAVAVLDAVGGVQPQ----SETVWR-QANRYEVPRIAFVNKMDKT  140 (689)
T ss_pred             CeEEEEEECCCCcchhHHHHH-----H---HHHhCEEEEEEeCCCCCChh----HHHHHH-HHHHcCCCEEEEEECCCCC
Confidence            456799999999875432211     1   12457899999997632210    011111 1233345678999999997


Q ss_pred             ChhHHHHHHHHHHHh
Q 023301          109 TETELGSLTERIKHI  123 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~  123 (284)
                      ..+ ...+.+.++..
T Consensus       141 ~~~-~~~~~~~i~~~  154 (689)
T TIGR00484       141 GAN-FLRVVNQIKQR  154 (689)
T ss_pred             CCC-HHHHHHHHHHH
Confidence            643 44555555544

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.

>cd04150 Arf1_5_like Arf1-Arf5-like subfamily

Probab=85.26  E-value=4.5  Score=31.86  Aligned_cols=71  Identities=21%  Similarity=0.296  Sum_probs=35.6

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHH-HHh-hcCEEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVE-QVA-YADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~-Qi~-~Ad~ivlnK~D~  107 (284)
                      ....+.+++|......+....        .-..+.+|.|+|+.+... +.+.. ..+...+.. ... ..=+|+.||+|+
T Consensus        44 ~~~~l~D~~G~~~~~~~~~~~--------~~~ad~~i~v~D~~~~~s-~~~~~-~~~~~~~~~~~~~~~piilv~NK~Dl  113 (159)
T cd04150          44 ISFTVWDVGGQDKIRPLWRHY--------FQNTQGLIFVVDSNDRER-IGEAR-EELQRMLNEDELRDAVLLVFANKQDL  113 (159)
T ss_pred             EEEEEEECCCCHhHHHHHHHH--------hcCCCEEEEEEeCCCHHH-HHHHH-HHHHHHHhcHHhcCCCEEEEEECCCC
Confidence            345667888875443332221        124578999999987432 22210 011111111 111 223677799998


Q ss_pred             CCh
Q 023301          108 VTE  110 (284)
Q Consensus       108 ~~~  110 (284)
                      .+.
T Consensus       114 ~~~  116 (159)
T cd04150         114 PNA  116 (159)
T ss_pred             CCC
Confidence            643

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

>cd04110 Rab35 Rab35 subfamily

Probab=85.21  E-value=9.5  Score=31.31  Aligned_cols=99  Identities=13%  Similarity=0.167  Sum_probs=49.8

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-hcCEEEEccCCCCCh
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-YADRIILNKIDLVTE  110 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-~Ad~ivlnK~D~~~~  110 (284)
                      ..|++++|-.....+....     +.   ..++++.|+|+.+... +.+. ..++ ..+..+.. ..-+||.||+|+.+.
T Consensus        57 l~l~D~~G~~~~~~~~~~~-----~~---~a~~iilv~D~~~~~s-~~~~-~~~~-~~i~~~~~~~piivVgNK~Dl~~~  125 (199)
T cd04110          57 LQIWDTAGQERFRTITSTY-----YR---GTHGVIVVYDVTNGES-FVNV-KRWL-QEIEQNCDDVCKVLVGNKNDDPER  125 (199)
T ss_pred             EEEEeCCCchhHHHHHHHH-----hC---CCcEEEEEEECCCHHH-HHHH-HHHH-HHHHHhCCCCCEEEEEECcccccc
Confidence            4566888865444333221     11   2457899999977543 2221 0111 11112111 234788899999653


Q ss_pred             hH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          111 TE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       111 ~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      ..  .+...+..+..+  .++++++. .......++
T Consensus       126 ~~~~~~~~~~~~~~~~--~~~~e~Sa~~~~gi~~lf  159 (199)
T cd04110         126 KVVETEDAYKFAGQMG--ISLFETSAKENINVEEMF  159 (199)
T ss_pred             cccCHHHHHHHHHHcC--CEEEEEECCCCcCHHHHH
Confidence            22  233444444443  66777653 334555554

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

>PTZ00141 elongation factor 1- alpha; Provisional

Probab=85.11  E-value=2.8  Score=39.46  Aligned_cols=96  Identities=14%  Similarity=0.190  Sum_probs=50.8

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHH--hhhhcCCccchH-HHHHHHhhcCE-EEEcc
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQ--HLNEVKPRFVVN-EAVEQVAYADR-IILNK  104 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~--~l~~~~~~~~~~-~~~~Qi~~Ad~-ivlnK  104 (284)
                      +..+.||+++|-.+.   +...     .......+.++.|||+..-..  .+.. ....... .+...+....+ |++||
T Consensus        84 ~~~i~lIDtPGh~~f---~~~~-----~~g~~~aD~ailVVda~~G~~e~~~~~-~~qT~eh~~~~~~~gi~~iiv~vNK  154 (446)
T PTZ00141         84 KYYFTIIDAPGHRDF---IKNM-----ITGTSQADVAILVVASTAGEFEAGISK-DGQTREHALLAFTLGVKQMIVCINK  154 (446)
T ss_pred             CeEEEEEECCChHHH---HHHH-----HHhhhhcCEEEEEEEcCCCceecccCC-CccHHHHHHHHHHcCCCeEEEEEEc
Confidence            346789999995442   2221     112346778899999976321  1100 0000001 12333444554 79999


Q ss_pred             CCC--C--ChhHHHHHHHHHHHh------CC-CCceeeec
Q 023301          105 IDL--V--TETELGSLTERIKHI------NA-MAPVKLAK  133 (284)
Q Consensus       105 ~D~--~--~~~~~~~~~~~l~~~------np-~a~i~~~~  133 (284)
                      +|.  +  +++.++.+.+.++.+      ++ ..+++..+
T Consensus       155 mD~~~~~~~~~~~~~i~~~i~~~l~~~g~~~~~~~~ipiS  194 (446)
T PTZ00141        155 MDDKTVNYSQERYDEIKKEVSAYLKKVGYNPEKVPFIPIS  194 (446)
T ss_pred             cccccchhhHHHHHHHHHHHHHHHHhcCCCcccceEEEee
Confidence            994  3  345566666666543      32 36667655

>cd01863 Rab18 Rab18 subfamily

Probab=85.05  E-value=8.5  Score=29.91  Aligned_cols=91  Identities=13%  Similarity=0.106  Sum_probs=46.5

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH---HhhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ---VAYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q---i~~Ad~ivlnK~D  106 (284)
                      .+..+++++|......+....     +   -..+.++.|+|....... .... .++ ..+...   -..+-+||.||+|
T Consensus        49 ~~~~l~D~~g~~~~~~~~~~~-----~---~~~d~~i~v~d~~~~~s~-~~~~-~~~-~~i~~~~~~~~~~~~iv~nK~D  117 (161)
T cd01863          49 VKLAIWDTAGQERFRTLTSSY-----Y---RGAQGVILVYDVTRRDTF-TNLE-TWL-NELETYSTNNDIVKMLVGNKID  117 (161)
T ss_pred             EEEEEEECCCchhhhhhhHHH-----h---CCCCEEEEEEECCCHHHH-HhHH-HHH-HHHHHhCCCCCCcEEEEEECCc
Confidence            345677888865433322221     1   135789999998764432 2110 010 111111   1233588899999


Q ss_pred             CCChh-HHHHHHHHHHHhCCCCceeeec
Q 023301          107 LVTET-ELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       107 ~~~~~-~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +.... ..+...+..+..  .+++++++
T Consensus       118 ~~~~~~~~~~~~~~~~~~--~~~~~~~S  143 (161)
T cd01863         118 KENREVTREEGLKFARKH--NMLFIETS  143 (161)
T ss_pred             ccccccCHHHHHHHHHHc--CCEEEEEe
Confidence            96222 234444555443  45666654

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

>cd04149 Arf6 Arf6 subfamily

Probab=84.95  E-value=4.1  Score=32.51  Aligned_cols=81  Identities=19%  Similarity=0.215  Sum_probs=40.7

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHH-HHHh-hcCEEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAV-EQVA-YADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~-~Qi~-~Ad~ivlnK~D~  107 (284)
                      ....+.+++|......+....     +   -..+.+|.|+|+.+.... .+.. ..+...+. .+.. ..=+||.||+|+
T Consensus        53 ~~~~l~Dt~G~~~~~~~~~~~-----~---~~a~~ii~v~D~t~~~s~-~~~~-~~~~~~~~~~~~~~~piilv~NK~Dl  122 (168)
T cd04149          53 VKFNVWDVGGQDKIRPLWRHY-----Y---TGTQGLIFVVDSADRDRI-DEAR-QELHRIINDREMRDALLLVFANKQDL  122 (168)
T ss_pred             EEEEEEECCCCHHHHHHHHHH-----h---ccCCEEEEEEeCCchhhH-HHHH-HHHHHHhcCHhhcCCcEEEEEECcCC
Confidence            345667888876554432221     1   246789999999884321 2110 01111111 1122 234567799998


Q ss_pred             CChhHHHHHHHHH
Q 023301          108 VTETELGSLTERI  120 (284)
Q Consensus       108 ~~~~~~~~~~~~l  120 (284)
                      .+....+++++.+
T Consensus       123 ~~~~~~~~i~~~~  135 (168)
T cd04149         123 PDAMKPHEIQEKL  135 (168)
T ss_pred             ccCCCHHHHHHHc
Confidence            6432334444443

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

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=84.81  E-value=5.9  Score=30.79  Aligned_cols=101  Identities=10%  Similarity=0.133  Sum_probs=51.0

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH---HhhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ---VAYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q---i~~Ad~ivlnK~D  106 (284)
                      ..+.+++++|......+.....        -..+.++.|+|...-.. +.+.. .+. ..+...   ....=+||+||+|
T Consensus        48 ~~~~i~D~~g~~~~~~~~~~~~--------~~~~~~i~v~d~~~~~s-~~~~~-~~~-~~~~~~~~~~~~piiiv~NK~D  116 (164)
T cd04139          48 VQLNILDTAGQEDYAAIRDNYH--------RSGEGFLLVFSITDMES-FTATA-EFR-EQILRVKDDDNVPLLLVGNKCD  116 (164)
T ss_pred             EEEEEEECCChhhhhHHHHHHh--------hcCCEEEEEEECCCHHH-HHHHH-HHH-HHHHHhcCCCCCCEEEEEEccc
Confidence            3577889999776655444322        12356778888755321 11110 011 111222   2345589999999


Q ss_pred             CCCh--hHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          107 LVTE--TELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       107 ~~~~--~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +.+.  .......+..++.+  .++++++. .....+.++
T Consensus       117 ~~~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  154 (164)
T cd04139         117 LEDKRQVSSEEAANLARQWG--VPYVETSAKTRQNVEKAF  154 (164)
T ss_pred             cccccccCHHHHHHHHHHhC--CeEEEeeCCCCCCHHHHH
Confidence            9762  22333444444433  56666553 233444444

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

>cd04168 TetM_like Tet(M)-like subfamily

Probab=84.65  E-value=3.9  Score=34.95  Aligned_cols=83  Identities=22%  Similarity=0.279  Sum_probs=47.2

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      +....+++|+|..+.......     .   .-..+.++.|+|+..-.....    +.+.. ........-+|++||+|+.
T Consensus        63 ~~~i~liDTPG~~~f~~~~~~-----~---l~~aD~~IlVvd~~~g~~~~~----~~~~~-~~~~~~~P~iivvNK~D~~  129 (237)
T cd04168          63 DTKVNLIDTPGHMDFIAEVER-----S---LSVLDGAILVISAVEGVQAQT----RILWR-LLRKLNIPTIIFVNKIDRA  129 (237)
T ss_pred             CEEEEEEeCCCccchHHHHHH-----H---HHHhCeEEEEEeCCCCCCHHH----HHHHH-HHHHcCCCEEEEEECcccc
Confidence            456788999999875432221     1   124578899999976422100    01111 1122234558999999987


Q ss_pred             ChhHHHHHHHHHHHhCC
Q 023301          109 TETELGSLTERIKHINA  125 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~np  125 (284)
                      .. ...++.+.+++...
T Consensus       130 ~a-~~~~~~~~i~~~~~  145 (237)
T cd04168         130 GA-DLEKVYQEIKEKLS  145 (237)
T ss_pred             CC-CHHHHHHHHHHHHC
Confidence            53 33555555665443

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.

>PRK11058 GTPase HflX; Provisional

Probab=84.61  E-value=1.9  Score=40.42  Aligned_cols=74  Identities=18%  Similarity=0.422  Sum_probs=44.7

Q ss_pred             CEEEEecCCCC-C-cHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEEEEccC
Q 023301           31 DHIVIETTGLA-K-PAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRIILNKI  105 (284)
Q Consensus        31 d~iiIE~sG~a-~-p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~ivlnK~  105 (284)
                      ..++++|.|.- + |..+++.+..  .+...-..+.++.|+|+.+.... .+.  .. ...+..++.   ..-++|+||+
T Consensus       246 ~~~l~DTaG~~r~lp~~lve~f~~--tl~~~~~ADlIL~VvDaS~~~~~-e~l--~~-v~~iL~el~~~~~pvIiV~NKi  319 (426)
T PRK11058        246 ETVLADTVGFIRHLPHDLVAAFKA--TLQETRQATLLLHVVDAADVRVQ-ENI--EA-VNTVLEEIDAHEIPTLLVMNKI  319 (426)
T ss_pred             eEEEEecCcccccCCHHHHHHHHH--HHHHhhcCCEEEEEEeCCCccHH-HHH--HH-HHHHHHHhccCCCCEEEEEEcc
Confidence            56899999983 3 7777766542  23344567889999999764211 110  00 011234443   3348899999


Q ss_pred             CCCCh
Q 023301          106 DLVTE  110 (284)
Q Consensus       106 D~~~~  110 (284)
                      |+.+.
T Consensus       320 DL~~~  324 (426)
T PRK11058        320 DMLDD  324 (426)
T ss_pred             cCCCc
Confidence            99753

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

Probab=84.60  E-value=3  Score=36.20  Aligned_cols=81  Identities=14%  Similarity=0.164  Sum_probs=46.9

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      ..+..+|.|+|..+........        .-..+.++.|+|+........    ..+. ....+....-++++||+|+.
T Consensus        63 ~~~i~liDtPG~~~f~~~~~~~--------l~~aD~~i~Vvd~~~g~~~~~----~~~~-~~~~~~~~p~iivvNK~D~~  129 (268)
T cd04170          63 GHKINLIDTPGYADFVGETRAA--------LRAADAALVVVSAQSGVEVGT----EKLW-EFADEAGIPRIIFINKMDRE  129 (268)
T ss_pred             CEEEEEEECcCHHHHHHHHHHH--------HHHCCEEEEEEeCCCCCCHHH----HHHH-HHHHHcCCCEEEEEECCccC
Confidence            3467899999986543222111        124677999999987432110    0010 11234455678999999987


Q ss_pred             ChhHHHHHHHHHHHh
Q 023301          109 TETELGSLTERIKHI  123 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~  123 (284)
                      .. ......+.+++.
T Consensus       130 ~~-~~~~~~~~l~~~  143 (268)
T cd04170         130 RA-DFDKTLAALQEA  143 (268)
T ss_pred             CC-CHHHHHHHHHHH
Confidence            54 345555666654

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

>PRK00007 elongation factor G; Reviewed

Probab=83.95  E-value=2.4  Score=42.29  Aligned_cols=81  Identities=19%  Similarity=0.219  Sum_probs=47.2

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      +..+.||.|+|..+...  +..      ...-.++.+|.|||+..-...    ..+.+.. ...+....-++++||+|+.
T Consensus        74 ~~~~~liDTPG~~~f~~--ev~------~al~~~D~~vlVvda~~g~~~----qt~~~~~-~~~~~~~p~iv~vNK~D~~  140 (693)
T PRK00007         74 DHRINIIDTPGHVDFTI--EVE------RSLRVLDGAVAVFDAVGGVEP----QSETVWR-QADKYKVPRIAFVNKMDRT  140 (693)
T ss_pred             CeEEEEEeCCCcHHHHH--HHH------HHHHHcCEEEEEEECCCCcch----hhHHHHH-HHHHcCCCEEEEEECCCCC
Confidence            45789999999765321  111      112345789999998764321    1111111 1334445678999999998


Q ss_pred             ChhHHHHHHHHHHHh
Q 023301          109 TETELGSLTERIKHI  123 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~  123 (284)
                      +.+ ...+.+.+++.
T Consensus       141 ~~~-~~~~~~~i~~~  154 (693)
T PRK00007        141 GAD-FYRVVEQIKDR  154 (693)
T ss_pred             CCC-HHHHHHHHHHH
Confidence            644 44555555543

>COG1160 Predicted GTPases [General function prediction only]

Probab=83.86  E-value=1.4  Score=41.07  Aligned_cols=76  Identities=17%  Similarity=0.211  Sum_probs=49.3

Q ss_pred             CCCEEEEecCCCCCc--HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCC
Q 023301           29 QFDHIVIETTGLAKP--APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKID  106 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p--~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D  106 (284)
                      .....+|.|.|+-+-  .++...+.. -.+...-.-+.+++|||+..-....    +..+...+. ...-.=++|+||+|
T Consensus        50 ~~~f~lIDTgGl~~~~~~~l~~~i~~-Qa~~Ai~eADvilfvVD~~~Git~~----D~~ia~~Lr-~~~kpviLvvNK~D  123 (444)
T COG1160          50 GREFILIDTGGLDDGDEDELQELIRE-QALIAIEEADVILFVVDGREGITPA----DEEIAKILR-RSKKPVILVVNKID  123 (444)
T ss_pred             CceEEEEECCCCCcCCchHHHHHHHH-HHHHHHHhCCEEEEEEeCCCCCCHH----HHHHHHHHH-hcCCCEEEEEEccc
Confidence            456899999999953  355554432 2344556788899999998844321    122323333 55566789999999


Q ss_pred             CCCh
Q 023301          107 LVTE  110 (284)
Q Consensus       107 ~~~~  110 (284)
                      ....
T Consensus       124 ~~~~  127 (444)
T COG1160         124 NLKA  127 (444)
T ss_pred             Cchh
Confidence            8643

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=83.80  E-value=5.1  Score=37.63  Aligned_cols=93  Identities=26%  Similarity=0.322  Sum_probs=52.6

Q ss_pred             CCCEEEEecCCCCCc-HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCC
Q 023301           29 QFDHIVIETTGLAKP-APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p-~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~  107 (284)
                      ..|+|||+|.|.... ..+++.|.   .+.....-+.++.|+|+..-...+..      ...+.+.+ ..+-||+||.|.
T Consensus       175 ~~DvVIIDTAGr~~~d~~lm~El~---~l~~~~~pdevlLVvda~~gq~av~~------a~~F~~~l-~i~gvIlTKlD~  244 (437)
T PRK00771        175 KADVIIVDTAGRHALEEDLIEEMK---EIKEAVKPDEVLLVIDATIGQQAKNQ------AKAFHEAV-GIGGIIITKLDG  244 (437)
T ss_pred             cCCEEEEECCCcccchHHHHHHHH---HHHHHhcccceeEEEeccccHHHHHH------HHHHHhcC-CCCEEEEecccC
Confidence            349999999997763 44444442   22233455678999999774322211      01111222 357899999997


Q ss_pred             CChhHHHHHHHHHHHhCCCCceeeeccC
Q 023301          108 VTETELGSLTERIKHINAMAPVKLAKYG  135 (284)
Q Consensus       108 ~~~~~~~~~~~~l~~~np~a~i~~~~~g  135 (284)
                      ..  ..-.+.......  ..||.....|
T Consensus       245 ~a--~~G~~ls~~~~~--~~Pi~fig~G  268 (437)
T PRK00771        245 TA--KGGGALSAVAET--GAPIKFIGTG  268 (437)
T ss_pred             CC--cccHHHHHHHHH--CcCEEEEecC
Confidence            43  233344444333  3566655555

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

Probab=83.75  E-value=4.1  Score=32.01  Aligned_cols=66  Identities=17%  Similarity=0.188  Sum_probs=44.2

Q ss_pred             eeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC-ChhHHHHHHHHHHHhCCCCceeeec
Q 023301           59 YVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV-TETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus        59 ~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~-~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ..+.+.|+.|.|+......+.   |.+     ..-....-+=||||+|+. +++++++.+++++...-. +|+.++
T Consensus        61 a~dad~V~ll~dat~~~~~~p---P~f-----a~~f~~pvIGVITK~Dl~~~~~~i~~a~~~L~~aG~~-~if~vS  127 (143)
T PF10662_consen   61 AQDADVVLLLQDATEPRSVFP---PGF-----ASMFNKPVIGVITKIDLPSDDANIERAKKWLKNAGVK-EIFEVS  127 (143)
T ss_pred             HhhCCEEEEEecCCCCCccCC---chh-----hcccCCCEEEEEECccCccchhhHHHHHHHHHHcCCC-CeEEEE
Confidence            457888999999988543321   111     122333455688999998 678899999999877543 455554

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

>KOG1954 consensus Endocytosis/signaling protein EHD1 [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=83.72  E-value=2.1  Score=38.97  Aligned_cols=81  Identities=17%  Similarity=0.280  Sum_probs=49.8

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccc---e--eeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh---cCEEEE
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQ---Y--VKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY---ADRIIL  102 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~---~--~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~---Ad~ivl  102 (284)
                      .+-|||++|+-.-..-  .+...-.+..   .  -+++-++.+.||..+.-     ++++  ..+.+|++.   --.||+
T Consensus       148 ~vtiVdtPGILsgeKQ--risR~ydF~~v~~WFaeR~D~IiLlfD~hKLDI-----sdEf--~~vi~aLkG~EdkiRVVL  218 (532)
T KOG1954|consen  148 SVTIVDTPGILSGEKQ--RISRGYDFTGVLEWFAERVDRIILLFDAHKLDI-----SDEF--KRVIDALKGHEDKIRVVL  218 (532)
T ss_pred             heeeeccCcccccchh--cccccCChHHHHHHHHHhccEEEEEechhhccc-----cHHH--HHHHHHhhCCcceeEEEe
Confidence            3568999999775431  1111011111   1  15677999999987532     1111  334666654   347999


Q ss_pred             ccCCCCChhHHHHHHHHH
Q 023301          103 NKIDLVTETELGSLTERI  120 (284)
Q Consensus       103 nK~D~~~~~~~~~~~~~l  120 (284)
                      ||+|.++..++-++.-.+
T Consensus       219 NKADqVdtqqLmRVyGAL  236 (532)
T KOG1954|consen  219 NKADQVDTQQLMRVYGAL  236 (532)
T ss_pred             ccccccCHHHHHHHHHHH
Confidence            999999999987776554

>PTZ00099 rab6; Provisional

Probab=83.42  E-value=3.9  Score=33.18  Aligned_cols=102  Identities=12%  Similarity=0.206  Sum_probs=53.6

Q ss_pred             CCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC---EEEEcc
Q 023301           28 GQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD---RIILNK  104 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad---~ivlnK  104 (284)
                      ...+..|.+++|...+..+....     +   -..+.+|.|+|..+... +.+. ..++ ..+. +....+   +||.||
T Consensus        27 ~~v~l~iwDt~G~e~~~~~~~~~-----~---~~ad~~ilv~D~t~~~s-f~~~-~~w~-~~i~-~~~~~~~piilVgNK   94 (176)
T PTZ00099         27 GPVRLQLWDTAGQERFRSLIPSY-----I---RDSAAAIVVYDITNRQS-FENT-TKWI-QDIL-NERGKDVIIALVGNK   94 (176)
T ss_pred             EEEEEEEEECCChHHhhhccHHH-----h---CCCcEEEEEEECCCHHH-HHHH-HHHH-HHHH-HhcCCCCeEEEEEEC
Confidence            35677889999987766543322     2   24678899999887432 1211 1111 1111 111223   578899


Q ss_pred             CCCCChh--HHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTET--ELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~--~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+..  ..+......+..+  ..+++++. .......++
T Consensus        95 ~DL~~~~~v~~~e~~~~~~~~~--~~~~e~SAk~g~nV~~lf  134 (176)
T PTZ00099         95 TDLGDLRKVTYEEGMQKAQEYN--TMFHETSAKAGHNIKVLF  134 (176)
T ss_pred             cccccccCCCHHHHHHHHHHcC--CEEEEEECCCCCCHHHHH
Confidence            9986422  1223334444332  45666553 334555554

>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]

Probab=83.37  E-value=3  Score=37.36  Aligned_cols=79  Identities=22%  Similarity=0.345  Sum_probs=49.4

Q ss_pred             eeeceEEEEEcccchHHhhhhcCCccchHHH-HHHHhhcCEEEE-ccCCCCChhH----HHHHHHHHHHhC-CCCceeee
Q 023301           60 VKLDGVITLVDSKHAMQHLNEVKPRFVVNEA-VEQVAYADRIIL-NKIDLVTETE----LGSLTERIKHIN-AMAPVKLA  132 (284)
Q Consensus        60 ~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~-~~Qi~~Ad~ivl-nK~D~~~~~~----~~~~~~~l~~~n-p~a~i~~~  132 (284)
                      .-.|+.+.||+|....-+     |.....++ .+=+..-++|++ ||+|+++.++    -++++++++.-. .+|+|+..
T Consensus       108 AlMDgAlLvIaANEpcPQ-----PQT~EHl~AleIigik~iiIvQNKIDlV~~E~AlE~y~qIk~FvkGt~Ae~aPIIPi  182 (415)
T COG5257         108 ALMDGALLVIAANEPCPQ-----PQTREHLMALEIIGIKNIIIVQNKIDLVSRERALENYEQIKEFVKGTVAENAPIIPI  182 (415)
T ss_pred             hhhcceEEEEecCCCCCC-----CchHHHHHHHhhhccceEEEEecccceecHHHHHHHHHHHHHHhcccccCCCceeee
Confidence            446777888888664432     22222333 344444555554 9999999766    466777777644 57899976


Q ss_pred             cc-CCCChhhhh
Q 023301          133 KY-GSVDMDFVL  143 (284)
Q Consensus       133 ~~-g~v~~~~l~  143 (284)
                      +. -+++.+.|+
T Consensus       183 SA~~~~NIDal~  194 (415)
T COG5257         183 SAQHKANIDALI  194 (415)
T ss_pred             hhhhccCHHHHH
Confidence            53 466666665

>cd01850 CDC_Septin CDC/Septin

Probab=83.27  E-value=5.5  Score=34.95  Aligned_cols=64  Identities=14%  Similarity=0.139  Sum_probs=37.2

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHHHHH--hhcCEEEEccCCCCChhHHHHHHHHHHHhCC--CCceee
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV--AYADRIILNKIDLVTETELGSLTERIKHINA--MAPVKL  131 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi--~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np--~a~i~~  131 (284)
                      .++.+++++|+..-.  +...   .  -.+..++  ...=++|+||+|+.+.+++...++.+++.-.  ..+++.
T Consensus       114 rvh~~ly~i~~~~~~--l~~~---D--~~~lk~l~~~v~vi~VinK~D~l~~~e~~~~k~~i~~~l~~~~i~~~~  181 (276)
T cd01850         114 RVHACLYFIEPTGHG--LKPL---D--IEFMKRLSKRVNIIPVIAKADTLTPEELKEFKQRIMEDIEEHNIKIYK  181 (276)
T ss_pred             ceEEEEEEEeCCCCC--CCHH---H--HHHHHHHhccCCEEEEEECCCcCCHHHHHHHHHHHHHHHHHcCCceEC
Confidence            577899999987511  1000   0  1122333  2344788899999988777666666654332  355554

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.

>cd04157 Arl6 Arl6 subfamily

Probab=83.24  E-value=5.6  Score=30.91  Aligned_cols=76  Identities=18%  Similarity=0.255  Sum_probs=40.2

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHH--HH---hhcCEEEEccCC
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVE--QV---AYADRIILNKID  106 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~--Qi---~~Ad~ivlnK~D  106 (284)
                      ..+++++|......+....     +   -..+.+|.|+|+...... .... .++ ..+..  .+   ...=+||+||+|
T Consensus        47 ~~l~Dt~G~~~~~~~~~~~-----~---~~~d~ii~v~D~~~~~~~-~~~~-~~~-~~~~~~~~~~~~~~p~iiv~NK~D  115 (162)
T cd04157          47 FTAFDMSGQGKYRGLWEHY-----Y---KNIQGIIFVIDSSDRLRL-VVVK-DEL-ELLLNHPDIKHRRVPILFFANKMD  115 (162)
T ss_pred             EEEEECCCCHhhHHHHHHH-----H---ccCCEEEEEEeCCcHHHH-HHHH-HHH-HHHHcCcccccCCCCEEEEEeCcc
Confidence            4588999976654433321     1   246789999999875422 1000 001 01111  11   234578889999


Q ss_pred             CCChhHHHHHHH
Q 023301          107 LVTETELGSLTE  118 (284)
Q Consensus       107 ~~~~~~~~~~~~  118 (284)
                      +.+......+.+
T Consensus       116 l~~~~~~~~~~~  127 (162)
T cd04157         116 LPDALTAVKITQ  127 (162)
T ss_pred             ccCCCCHHHHHH
Confidence            976433333333

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

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=83.19  E-value=11  Score=29.35  Aligned_cols=100  Identities=12%  Similarity=0.078  Sum_probs=49.9

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-------hhcCEEEEc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-------AYADRIILN  103 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-------~~Ad~ivln  103 (284)
                      ..-+++++|......+.....        -..+.+|.|+|+.+.... ... ..++ ..+....       ...=++|.|
T Consensus        50 ~l~i~Dt~G~~~~~~~~~~~~--------~~~d~~ilv~D~~~~~s~-~~~-~~~~-~~~~~~~~~~~~~~~~piilv~n  118 (168)
T cd04119          50 RVNFFDLSGHPEYLEVRNEFY--------KDTQGVLLVYDVTDRQSF-EAL-DSWL-KEMKQEGGPHGNMENIVVVVCAN  118 (168)
T ss_pred             EEEEEECCccHHHHHHHHHHh--------ccCCEEEEEEECCCHHHH-HhH-HHHH-HHHHHhccccccCCCceEEEEEE
Confidence            345778888755444333221        135678999999874321 111 0111 1122221       123477889


Q ss_pred             cCCCCChh--HHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          104 KIDLVTET--ELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       104 K~D~~~~~--~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+|+.+..  ..+..+++.+..+  .++++++. .......++
T Consensus       119 K~Dl~~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  159 (168)
T cd04119         119 KIDLTKHRAVSEDEGRLWAESKG--FKYFETSACTGEGVNEMF  159 (168)
T ss_pred             chhcccccccCHHHHHHHHHHcC--CeEEEEECCCCCCHHHHH
Confidence            99997322  2333344444433  56666653 333444443

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.

>PRK12739 elongation factor G; Reviewed

Probab=83.15  E-value=1.2  Score=44.44  Aligned_cols=81  Identities=19%  Similarity=0.231  Sum_probs=46.6

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      +..+.||.|+|..+...  +.      ....-..+.++.|||+..-...-    .+.+... ..+....-++++||+|+.
T Consensus        72 ~~~i~liDTPG~~~f~~--e~------~~al~~~D~~ilVvDa~~g~~~q----t~~i~~~-~~~~~~p~iv~iNK~D~~  138 (691)
T PRK12739         72 GHRINIIDTPGHVDFTI--EV------ERSLRVLDGAVAVFDAVSGVEPQ----SETVWRQ-ADKYGVPRIVFVNKMDRI  138 (691)
T ss_pred             CEEEEEEcCCCHHHHHH--HH------HHHHHHhCeEEEEEeCCCCCCHH----HHHHHHH-HHHcCCCEEEEEECCCCC
Confidence            45678999999765221  11      11223457899999997643211    1111111 223334668999999998


Q ss_pred             ChhHHHHHHHHHHHh
Q 023301          109 TETELGSLTERIKHI  123 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~  123 (284)
                      ..+ ...+.+.++..
T Consensus       139 ~~~-~~~~~~~i~~~  152 (691)
T PRK12739        139 GAD-FFRSVEQIKDR  152 (691)
T ss_pred             CCC-HHHHHHHHHHH
Confidence            643 44555555544

>cd01866 Rab2 Rab2 subfamily

Probab=83.15  E-value=9.5  Score=30.14  Aligned_cols=96  Identities=14%  Similarity=0.087  Sum_probs=48.1

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh------cCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY------ADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~------Ad~ivlnK  104 (284)
                      ...+++++|......+....     +   -..+.++.|+|+.+.... .+.      ..+..++..      .=+||.||
T Consensus        54 ~~~i~Dt~G~~~~~~~~~~~-----~---~~~d~il~v~d~~~~~s~-~~~------~~~~~~~~~~~~~~~pvivv~nK  118 (168)
T cd01866          54 KLQIWDTAGQESFRSITRSY-----Y---RGAAGALLVYDITRRETF-NHL------TSWLEDARQHSNSNMTIMLIGNK  118 (168)
T ss_pred             EEEEEECCCcHHHHHHHHHH-----h---ccCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhCCCCCcEEEEEEC
Confidence            44567888854433322211     1   245779999999864322 211      112233321      23777799


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+...  .+..+...+..  .+.+++++. .......++
T Consensus       119 ~Dl~~~~~~~~~~~~~~~~~~--~~~~~e~Sa~~~~~i~~~~  158 (168)
T cd01866         119 CDLESRREVSYEEGEAFAKEH--GLIFMETSAKTASNVEEAF  158 (168)
T ss_pred             cccccccCCCHHHHHHHHHHc--CCEEEEEeCCCCCCHHHHH
Confidence            99874322  23344444433  356666543 233444443

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

>cd01893 Miro1 Miro1 subfamily

Probab=83.10  E-value=12  Score=29.57  Aligned_cols=72  Identities=10%  Similarity=0.174  Sum_probs=36.0

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH--hhcCEEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV--AYADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi--~~Ad~ivlnK~D~  107 (284)
                      .+..++.++|..........     .+   -..+.++.|+|..+... +.+....+. ..+ .+.  ...=+||.||+|+
T Consensus        47 ~~~~i~Dt~G~~~~~~~~~~-----~~---~~ad~~ilv~d~~~~~s-~~~~~~~~~-~~i-~~~~~~~pviiv~nK~Dl  115 (166)
T cd01893          47 VPTTIVDTSSRPQDRANLAA-----EI---RKANVICLVYSVDRPST-LERIRTKWL-PLI-RRLGVKVPIILVGNKSDL  115 (166)
T ss_pred             EEEEEEeCCCchhhhHHHhh-----hc---ccCCEEEEEEECCCHHH-HHHHHHHHH-HHH-HHhCCCCCEEEEEEchhc
Confidence            45568888887654332221     11   23556788889876332 111000010 111 111  2234677799999


Q ss_pred             CChhH
Q 023301          108 VTETE  112 (284)
Q Consensus       108 ~~~~~  112 (284)
                      .+...
T Consensus       116 ~~~~~  120 (166)
T cd01893         116 RDGSS  120 (166)
T ss_pred             ccccc
Confidence            76443

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.

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

Probab=83.05  E-value=3  Score=41.10  Aligned_cols=92  Identities=16%  Similarity=0.201  Sum_probs=48.3

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC-EEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~  107 (284)
                      +..++||.|+|..+.   .....     ...-..+.++.|||+......  .  .+.. ..+..++.... +|++||+|+
T Consensus       103 ~~~~~liDtPG~~~f---~~~~~-----~~~~~aD~~llVvda~~g~~~--~--t~e~-~~~~~~~~~~~iivvvNK~D~  169 (632)
T PRK05506        103 KRKFIVADTPGHEQY---TRNMV-----TGASTADLAIILVDARKGVLT--Q--TRRH-SFIASLLGIRHVVLAVNKMDL  169 (632)
T ss_pred             CceEEEEECCChHHH---HHHHH-----HHHHhCCEEEEEEECCCCccc--c--CHHH-HHHHHHhCCCeEEEEEEeccc
Confidence            346799999996432   22111     122356778999999653211  0  0100 11233344334 458999999


Q ss_pred             CC--hhHHHHHHHHHH----HhC-CCCceeeec
Q 023301          108 VT--ETELGSLTERIK----HIN-AMAPVKLAK  133 (284)
Q Consensus       108 ~~--~~~~~~~~~~l~----~~n-p~a~i~~~~  133 (284)
                      ++  .+.++.+.+.++    .+. +..+++..+
T Consensus       170 ~~~~~~~~~~i~~~i~~~~~~~~~~~~~iipiS  202 (632)
T PRK05506        170 VDYDQEVFDEIVADYRAFAAKLGLHDVTFIPIS  202 (632)
T ss_pred             ccchhHHHHHHHHHHHHHHHHcCCCCccEEEEe
Confidence            84  444454544443    332 335566544

>PLN03118 Rab family protein; Provisional

Probab=82.73  E-value=8  Score=32.05  Aligned_cols=97  Identities=11%  Similarity=0.124  Sum_probs=50.5

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-------hcCEEEEc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-------YADRIILN  103 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-------~Ad~ivln  103 (284)
                      ...|++++|......+....     +   -..+.+|.|+|..+.... .+..     .....++.       ..-+||.|
T Consensus        63 ~l~l~Dt~G~~~~~~~~~~~-----~---~~~d~~vlv~D~~~~~sf-~~~~-----~~~~~~~~~~~~~~~~~~ilv~N  128 (211)
T PLN03118         63 KLTIWDTAGQERFRTLTSSY-----Y---RNAQGIILVYDVTRRETF-TNLS-----DVWGKEVELYSTNQDCVKMLVGN  128 (211)
T ss_pred             EEEEEECCCchhhHHHHHHH-----H---hcCCEEEEEEECCCHHHH-HHHH-----HHHHHHHHHhcCCCCCCEEEEEE
Confidence            45688999976655543332     1   145779999999875432 2110     11111121       23468889


Q ss_pred             cCCCCChhHH--HHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          104 KIDLVTETEL--GSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       104 K~D~~~~~~~--~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+|+.....+  +......+..  ...+++++. .......++
T Consensus       129 K~Dl~~~~~i~~~~~~~~~~~~--~~~~~e~SAk~~~~v~~l~  169 (211)
T PLN03118        129 KVDRESERDVSREEGMALAKEH--GCLFLECSAKTRENVEQCF  169 (211)
T ss_pred             CccccccCccCHHHHHHHHHHc--CCEEEEEeCCCCCCHHHHH
Confidence            9998654332  2333333333  355666543 233444444

>cd04156 ARLTS1 ARLTS1 subfamily

Probab=82.71  E-value=7.7  Score=30.15  Aligned_cols=70  Identities=23%  Similarity=0.292  Sum_probs=35.8

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHH-HH-HhhcCEEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAV-EQ-VAYADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~-~Q-i~~Ad~ivlnK~D~  107 (284)
                      ....+.+++|......+....     +   -..+.+|.|+|+.+... +.... ..+...+. .. -...=+||+||+|+
T Consensus        44 ~~l~i~D~~G~~~~~~~~~~~-----~---~~~~~iv~v~D~~~~~~-~~~~~-~~~~~~~~~~~~~~~piilv~nK~Dl  113 (160)
T cd04156          44 LSLTVWDVGGQEKMRTVWKCY-----L---ENTDGLVYVVDSSDEAR-LDESQ-KELKHILKNEHIKGVPVVLLANKQDL  113 (160)
T ss_pred             eEEEEEECCCCHhHHHHHHHH-----h---ccCCEEEEEEECCcHHH-HHHHH-HHHHHHHhchhhcCCCEEEEEECccc
Confidence            345667788765433322221     1   23577899999987542 11110 01111111 11 12345788899998


Q ss_pred             CC
Q 023301          108 VT  109 (284)
Q Consensus       108 ~~  109 (284)
                      ..
T Consensus       114 ~~  115 (160)
T cd04156         114 PG  115 (160)
T ss_pred             cc
Confidence            54

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

>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=82.71  E-value=3.2  Score=33.48  Aligned_cols=58  Identities=26%  Similarity=0.269  Sum_probs=29.9

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHH-HHHhh-cCEEEEccCCCCChhHHHHHHHHH
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAV-EQVAY-ADRIILNKIDLVTETELGSLTERI  120 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~-~Qi~~-Ad~ivlnK~D~~~~~~~~~~~~~l  120 (284)
                      ..+++|+|||+..... +.+.. ..+...+. .++.. .=+|++||.|+.+....+.+.+.+
T Consensus        81 ~~~~iIfVvDssd~~~-l~e~~-~~L~~ll~~~~~~~~piLIl~NK~D~~~~~~~~~i~~~l  140 (175)
T PF00025_consen   81 NADGIIFVVDSSDPER-LQEAK-EELKELLNDPELKDIPILILANKQDLPDAMSEEEIKEYL  140 (175)
T ss_dssp             TESEEEEEEETTGGGG-HHHHH-HHHHHHHTSGGGTTSEEEEEEESTTSTTSSTHHHHHHHT
T ss_pred             ccceeEEEEeccccee-ecccc-cchhhhcchhhcccceEEEEeccccccCcchhhHHHhhh
Confidence            5688999999987432 22211 01111111 12322 335566999986544445555443

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 ....

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=82.54  E-value=12  Score=34.57  Aligned_cols=110  Identities=22%  Similarity=0.322  Sum_probs=66.0

Q ss_pred             chHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHH-HHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHH
Q 023301           13 GDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVI-ETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAV   91 (284)
Q Consensus        13 ~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~-~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~   91 (284)
                      -+|..++..+-+     .|.|+|.|.|...-.... ..|.  ..+.....+. +..|+++..-...+.         +..
T Consensus       270 ~el~~ai~~l~~-----~d~ILVDTaGrs~~D~~~i~el~--~~~~~~~~i~-~~Lvlsat~K~~dlk---------ei~  332 (407)
T COG1419         270 KELAEAIEALRD-----CDVILVDTAGRSQYDKEKIEELK--ELIDVSHSIE-VYLVLSATTKYEDLK---------EII  332 (407)
T ss_pred             HHHHHHHHHhhc-----CCEEEEeCCCCCccCHHHHHHHH--HHHhccccce-EEEEEecCcchHHHH---------HHH
Confidence            468888876654     599999999999843321 1221  2233334444 556777776554443         345


Q ss_pred             HHHhhc--CEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCCChhhhh
Q 023301           92 EQVAYA--DRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVL  143 (284)
Q Consensus        92 ~Qi~~A--d~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v~~~~l~  143 (284)
                      .|.+..  +-++++|.|..+.  +-.+...+-+-  +-+|...++|+-=+++|.
T Consensus       333 ~~f~~~~i~~~I~TKlDET~s--~G~~~s~~~e~--~~PV~YvT~GQ~VPeDI~  382 (407)
T COG1419         333 KQFSLFPIDGLIFTKLDETTS--LGNLFSLMYET--RLPVSYVTNGQRVPEDIV  382 (407)
T ss_pred             HHhccCCcceeEEEcccccCc--hhHHHHHHHHh--CCCeEEEeCCCCCCchhh
Confidence            666655  4589999998652  44444444433  357777778754444443

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=82.47  E-value=9  Score=32.82  Aligned_cols=87  Identities=23%  Similarity=0.374  Sum_probs=50.3

Q ss_pred             CCCceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecC-CCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhh
Q 023301            2 VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETT-GLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNE   80 (284)
Q Consensus         2 L~~GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~s-G~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~   80 (284)
                      -..||.|= + +.|...+.+-+.  ..+.|+|+|.|= |+-+...        .   -.-.+|.+|.|+||..-.-.+..
T Consensus       110 ~GeGC~Cp-~-~allR~~l~~l~--~~~~e~VivDtEAGiEHfgR--------g---~~~~vD~vivVvDpS~~sl~tae  174 (255)
T COG3640         110 GGEGCACP-M-NALLRRLLRHLI--LNRYEVVIVDTEAGIEHFGR--------G---TIEGVDLVIVVVDPSYKSLRTAE  174 (255)
T ss_pred             CCCcccch-H-HHHHHHHHHHHh--cccCcEEEEecccchhhhcc--------c---cccCCCEEEEEeCCcHHHHHHHH
Confidence            36799954 3 345554443333  356899999873 4444321        0   11257789999999763322221


Q ss_pred             cCCccchHHHHHHHh-hcCEEEEccCCCC
Q 023301           81 VKPRFVVNEAVEQVA-YADRIILNKIDLV  108 (284)
Q Consensus        81 ~~~~~~~~~~~~Qi~-~Ad~ivlnK~D~~  108 (284)
                           ....+.+++. --=.+|+||.|..
T Consensus       175 -----ri~~L~~elg~k~i~~V~NKv~e~  198 (255)
T COG3640         175 -----RIKELAEELGIKRIFVVLNKVDEE  198 (255)
T ss_pred             -----HHHHHHHHhCCceEEEEEeeccch
Confidence                 1133456666 3446788999964

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=82.42  E-value=12  Score=34.32  Aligned_cols=97  Identities=19%  Similarity=0.266  Sum_probs=55.2

Q ss_pred             CCCCEEEEecCCCCCcHHH-HHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH--------hhcC
Q 023301           28 GQFDHIVIETTGLAKPAPV-IETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV--------AYAD   98 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~~i-~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi--------~~Ad   98 (284)
                      .+.|.|+|+|.|....... .+.+.   .+.....-..++.|+++..-...+.+.     ... ....        ..-+
T Consensus       214 ~~~DlVLIDTaG~~~~d~~l~e~La---~L~~~~~~~~~lLVLsAts~~~~l~ev-----i~~-f~~~~~~p~~~~~~~~  284 (374)
T PRK14722        214 RNKHMVLIDTIGMSQRDRTVSDQIA---MLHGADTPVQRLLLLNATSHGDTLNEV-----VQA-YRSAAGQPKAALPDLA  284 (374)
T ss_pred             cCCCEEEEcCCCCCcccHHHHHHHH---HHhccCCCCeEEEEecCccChHHHHHH-----HHH-HHHhhcccccccCCCC
Confidence            3579999999999965432 22221   121111222468899998855444321     011 1222        1347


Q ss_pred             EEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCC
Q 023301           99 RIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSV  137 (284)
Q Consensus        99 ~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v  137 (284)
                      -+|++|.|...  .+-.+...+...  +.+|...+.|+-
T Consensus       285 ~~I~TKlDEt~--~~G~~l~~~~~~--~lPi~yvt~Gq~  319 (374)
T PRK14722        285 GCILTKLDEAS--NLGGVLDTVIRY--KLPVHYVSTGQK  319 (374)
T ss_pred             EEEEeccccCC--CccHHHHHHHHH--CcCeEEEecCCC
Confidence            89999999865  344555555443  467777777743

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=82.41  E-value=14  Score=34.64  Aligned_cols=97  Identities=19%  Similarity=0.193  Sum_probs=56.6

Q ss_pred             cCCCCEEEEecCCCCCc-HHHHHHhccccccccee---eeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEE
Q 023301           27 QGQFDHIVIETTGLAKP-APVIETFCTDELVSQYV---KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIIL  102 (284)
Q Consensus        27 ~~~~d~iiIE~sG~a~p-~~i~~~l~~~~~l~~~~---~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivl  102 (284)
                      ..++|+|||+|+|.... ...++.|..   +...+   .-..++.|+|+..-...+.+.       .-.-+--..+-+|+
T Consensus       297 ~~~~D~VLIDTaGr~~rd~~~l~eL~~---~~~~~~~~~~~e~~LVLsAt~~~~~~~~~-------~~~f~~~~~~glIl  366 (432)
T PRK12724        297 RDGSELILIDTAGYSHRNLEQLERMQS---FYSCFGEKDSVENLLVLSSTSSYHHTLTV-------LKAYESLNYRRILL  366 (432)
T ss_pred             hCCCCEEEEeCCCCCccCHHHHHHHHH---HHHhhcCCCCCeEEEEEeCCCCHHHHHHH-------HHHhcCCCCCEEEE
Confidence            36789999999998742 333444321   11111   112478899998765443321       01123445789999


Q ss_pred             ccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCC
Q 023301          103 NKIDLVTETELGSLTERIKHINAMAPVKLAKYGSV  137 (284)
Q Consensus       103 nK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v  137 (284)
                      +|.|...  ..-.+...+...  +.||...+.|+-
T Consensus       367 TKLDEt~--~~G~il~i~~~~--~lPI~ylt~GQ~  397 (432)
T PRK12724        367 TKLDEAD--FLGSFLELADTY--SKSFTYLSVGQE  397 (432)
T ss_pred             EcccCCC--CccHHHHHHHHH--CCCEEEEecCCC
Confidence            9999854  344455555544  367776667643

>TIGR03680 eif2g_arch translation initiation factor 2 subunit gamma

Probab=82.35  E-value=3.9  Score=37.99  Aligned_cols=90  Identities=21%  Similarity=0.313  Sum_probs=47.1

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH--HhhhhcCCccchHHHHHHHhhcC-EEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM--QHLNEVKPRFVVNEAVEQVAYAD-RIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~--~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D  106 (284)
                      ....+++++|-.+.   ....     +...-..+.++.|||+..-.  .+..+    .+ . ....+.... +|++||+|
T Consensus        80 ~~i~liDtPGh~~f---~~~~-----~~g~~~aD~aIlVVDa~~g~~~~qt~e----~l-~-~l~~~gi~~iIVvvNK~D  145 (406)
T TIGR03680        80 RRVSFVDAPGHETL---MATM-----LSGAALMDGALLVIAANEPCPQPQTKE----HL-M-ALEIIGIKNIVIVQNKID  145 (406)
T ss_pred             cEEEEEECCCHHHH---HHHH-----HHHHHHCCEEEEEEECCCCccccchHH----HH-H-HHHHcCCCeEEEEEEccc
Confidence            45679999995332   2221     11223567899999998632  11100    11 1 112222333 67799999


Q ss_pred             CCChhHH----HHHHHHHHHhC-CCCceeeec
Q 023301          107 LVTETEL----GSLTERIKHIN-AMAPVKLAK  133 (284)
Q Consensus       107 ~~~~~~~----~~~~~~l~~~n-p~a~i~~~~  133 (284)
                      +.+.+..    +++.++++... ...+++.++
T Consensus       146 l~~~~~~~~~~~~i~~~l~~~~~~~~~ii~vS  177 (406)
T TIGR03680       146 LVSKEKALENYEEIKEFVKGTVAENAPIIPVS  177 (406)
T ss_pred             cCCHHHHHHHHHHHHhhhhhcccCCCeEEEEE
Confidence            9876554    33333333322 245676654

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

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

Probab=82.35  E-value=7.8  Score=31.06  Aligned_cols=70  Identities=21%  Similarity=0.278  Sum_probs=36.1

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHH-HHhh-cCEEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVE-QVAY-ADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~-Qi~~-Ad~ivlnK~D~  107 (284)
                      ....+.+++|......+.....        -..+.+|.|+|+.+... +.+.. ..+...+.+ .+.. .=+||.||+|+
T Consensus        57 ~~l~l~D~~G~~~~~~~~~~~~--------~~ad~ii~v~D~t~~~s-~~~~~-~~l~~~~~~~~~~~~piilv~NK~Dl  126 (175)
T smart00177       57 ISFTVWDVGGQDKIRPLWRHYY--------TNTQGLIFVVDSNDRDR-IDEAR-EELHRMLNEDELRDAVILVFANKQDL  126 (175)
T ss_pred             EEEEEEECCCChhhHHHHHHHh--------CCCCEEEEEEECCCHHH-HHHHH-HHHHHHhhCHhhcCCcEEEEEeCcCc
Confidence            4456788888766554433321        23567899999876432 11110 011111111 1222 33577799998


Q ss_pred             CC
Q 023301          108 VT  109 (284)
Q Consensus       108 ~~  109 (284)
                      .+
T Consensus       127 ~~  128 (175)
T smart00177      127 PD  128 (175)
T ss_pred             cc
Confidence            54

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).

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

Probab=82.21  E-value=2.2  Score=33.63  Aligned_cols=95  Identities=22%  Similarity=0.237  Sum_probs=46.3

Q ss_pred             CCEEEEecCCCCCcH-----HHH-HHhcccccccceeeeceEEEEEcccchHHh-hhhcCCccchHHHHHHH-hhcCEEE
Q 023301           30 FDHIVIETTGLAKPA-----PVI-ETFCTDELVSQYVKLDGVITLVDSKHAMQH-LNEVKPRFVVNEAVEQV-AYADRII  101 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~-----~i~-~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~-l~~~~~~~~~~~~~~Qi-~~Ad~iv  101 (284)
                      ....+++|+|..+-.     .+. ..+   ..+.  ..-+.++.|+|+...... +...  ......+.... ...=++|
T Consensus        47 ~~~~i~Dt~G~~~~~~~~~~~~~~~~~---~~~~--~~~d~~l~v~d~~~~~~~~~~~~--~~~~~~l~~~~~~~pvilv  119 (168)
T cd01897          47 LRWQVIDTPGLLDRPLEERNTIEMQAI---TALA--HLRAAVLFLFDPSETCGYSLEEQ--LSLFEEIKPLFKNKPVIVV  119 (168)
T ss_pred             eEEEEEECCCcCCccccCCchHHHHHH---HHHH--hccCcEEEEEeCCcccccchHHH--HHHHHHHHhhcCcCCeEEE
Confidence            466889999985411     000 110   0011  113678999999763221 1100  00111111111 3445778


Q ss_pred             EccCCCCChhHHHHHHHHHHHhCCCCceeeec
Q 023301          102 LNKIDLVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       102 lnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +||+|+.+........+..+ . +..+++.++
T Consensus       120 ~NK~Dl~~~~~~~~~~~~~~-~-~~~~~~~~S  149 (168)
T cd01897         120 LNKIDLLTFEDLSEIEEEEE-L-EGEEVLKIS  149 (168)
T ss_pred             EEccccCchhhHHHHHHhhh-h-ccCceEEEE
Confidence            89999987666554333322 2 345666655

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.

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=81.72  E-value=18  Score=28.07  Aligned_cols=100  Identities=15%  Similarity=0.183  Sum_probs=50.9

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~ivlnK~D~  107 (284)
                      ..-+++++|......+.....        -..++++.|+|+..... +.+.. .+. ..+.+...   ..=++|.||+|+
T Consensus        49 ~l~i~Dt~g~~~~~~~~~~~~--------~~~~~~i~v~d~~~~~s-~~~~~-~~~-~~i~~~~~~~~~pii~v~nK~Dl  117 (164)
T smart00173       49 LLDILDTAGQEEFSAMRDQYM--------RTGEGFLLVYSITDRQS-FEEIK-KFR-EQILRVKDRDDVPIVLVGNKCDL  117 (164)
T ss_pred             EEEEEECCCcccchHHHHHHH--------hhCCEEEEEEECCCHHH-HHHHH-HHH-HHHHHhcCCCCCCEEEEEECccc
Confidence            344689999887665544322        13567889999876432 12110 000 11122211   123678899998


Q ss_pred             CChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          108 VTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       108 ~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      .+...  .+...+..+..+  .++++++. .......++
T Consensus       118 ~~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~~i~~l~  154 (164)
T smart00173      118 ESERVVSTEEGKELARQWG--CPFLETSAKERVNVDEAF  154 (164)
T ss_pred             cccceEcHHHHHHHHHHcC--CEEEEeecCCCCCHHHHH
Confidence            65321  233344444443  56666653 333444444

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

>TIGR01007 eps_fam capsular exopolysaccharide family

Probab=81.61  E-value=7.8  Score=31.96  Aligned_cols=14  Identities=36%  Similarity=0.591  Sum_probs=9.5

Q ss_pred             CCCCEEEEecCCCC
Q 023301           28 GQFDHIVIETTGLA   41 (284)
Q Consensus        28 ~~~d~iiIE~sG~a   41 (284)
                      .++|+|||+++.+.
T Consensus       126 ~~yD~ViiD~pp~~  139 (204)
T TIGR01007       126 KYFDYIIIDTPPIG  139 (204)
T ss_pred             hcCCEEEEeCCCcc
Confidence            46777777777543

This model describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis(EPS). Atleast 13 genes espA to espM in streptococcus species seem to direct the EPS proteins and all of which share high homology. Functional roles were characterized by gene disruption experiments which resulted in exopolysaccharide-deficient phenotypes.

>cd04104 p47_IIGP_like p47 (47-kDa) family

Probab=81.58  E-value=4.9  Score=33.09  Aligned_cols=70  Identities=10%  Similarity=0.091  Sum_probs=34.9

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVT  109 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~  109 (284)
                      ++..+++++|+.+...-.+.....-   .....+.++.|.|. .+...-.     .... ...+....-++|+||+|+..
T Consensus        52 ~~l~l~DtpG~~~~~~~~~~~l~~~---~~~~~d~~l~v~~~-~~~~~d~-----~~~~-~l~~~~~~~ilV~nK~D~~~  121 (197)
T cd04104          52 PNVTLWDLPGIGSTAFPPDDYLEEM---KFSEYDFFIIISST-RFSSNDV-----KLAK-AIQCMGKKFYFVRTKVDRDL  121 (197)
T ss_pred             CCceEEeCCCCCcccCCHHHHHHHh---CccCcCEEEEEeCC-CCCHHHH-----HHHH-HHHHhCCCEEEEEecccchh
Confidence            4778999999987533222211100   11234555665543 4432110     0111 12223334489999999854

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

>cd01855 YqeH YqeH

Probab=81.04  E-value=2  Score=35.08  Aligned_cols=43  Identities=23%  Similarity=0.067  Sum_probs=26.1

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHHHHH-hhcCEEEEccCCCCChh
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-AYADRIILNKIDLVTET  111 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-~~Ad~ivlnK~D~~~~~  111 (284)
                      ..+.++.|+|+..+.....        ..+..+. ...-++|+||+|+.+.+
T Consensus        34 ~ad~il~VvD~~~~~~~~~--------~~l~~~~~~~~~ilV~NK~Dl~~~~   77 (190)
T cd01855          34 KKALVVHVVDIFDFPGSLI--------PRLRLFGGNNPVILVGNKIDLLPKD   77 (190)
T ss_pred             CCcEEEEEEECccCCCccc--------hhHHHhcCCCcEEEEEEchhcCCCC
Confidence            4667999999987542211        1122222 23447899999997543

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.

>cd04124 RabL2 RabL2 subfamily

Probab=80.97  E-value=14  Score=28.98  Aligned_cols=98  Identities=13%  Similarity=0.122  Sum_probs=46.8

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-hhcCEEEEccCCCCCh
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-AYADRIILNKIDLVTE  110 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-~~Ad~ivlnK~D~~~~  110 (284)
                      .-+.+++|-.....+....     +   -..+.++.|+|+...... .+. ..++ ..+.... ...=+||.||+|+...
T Consensus        51 ~~i~Dt~G~~~~~~~~~~~-----~---~~~d~~i~v~d~~~~~s~-~~~-~~~~-~~i~~~~~~~p~ivv~nK~Dl~~~  119 (161)
T cd04124          51 VDFWDTAGQERFQTMHASY-----Y---HKAHACILVFDVTRKITY-KNL-SKWY-EELREYRPEIPCIVVANKIDLDPS  119 (161)
T ss_pred             EEEEeCCCchhhhhhhHHH-----h---CCCCEEEEEEECCCHHHH-HHH-HHHH-HHHHHhCCCCcEEEEEECccCchh
Confidence            4467888866544433322     1   245678999998764332 111 0111 1111111 2344788899998532


Q ss_pred             hHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          111 TELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       111 ~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                       ......+..+..  ..+++.++. .......++
T Consensus       120 -~~~~~~~~~~~~--~~~~~~~Sa~~~~gv~~l~  150 (161)
T cd04124         120 -VTQKKFNFAEKH--NLPLYYVSAADGTNVVKLF  150 (161)
T ss_pred             -HHHHHHHHHHHc--CCeEEEEeCCCCCCHHHHH
Confidence             222223332222  255665542 233444443

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

>PTZ00416 elongation factor 2; Provisional

Probab=80.92  E-value=2.5  Score=43.16  Aligned_cols=63  Identities=17%  Similarity=0.263  Sum_probs=39.0

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh---cCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY---ADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~---Ad~ivlnK~D  106 (284)
                      .-+.||.|+|..+...-.        ....-..+++|.|||+..-...    ..    ..+..|+..   .-++++||+|
T Consensus        92 ~~i~liDtPG~~~f~~~~--------~~al~~~D~ailVvda~~g~~~----~t----~~~~~~~~~~~~p~iv~iNK~D  155 (836)
T PTZ00416         92 FLINLIDSPGHVDFSSEV--------TAALRVTDGALVVVDCVEGVCV----QT----ETVLRQALQERIRPVLFINKVD  155 (836)
T ss_pred             eEEEEEcCCCHHhHHHHH--------HHHHhcCCeEEEEEECCCCcCc----cH----HHHHHHHHHcCCCEEEEEEChh
Confidence            346899999998743211        1112357789999999773321    01    122344433   5689999999


Q ss_pred             CC
Q 023301          107 LV  108 (284)
Q Consensus       107 ~~  108 (284)
                      +.
T Consensus       156 ~~  157 (836)
T PTZ00416        156 RA  157 (836)
T ss_pred             hh
Confidence            96

>cd04169 RF3 RF3 subfamily

Probab=80.78  E-value=9.4  Score=33.28  Aligned_cols=80  Identities=14%  Similarity=0.149  Sum_probs=43.5

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      +..+.+++|+|..+...-...     .+   -..+.+|.|+|+..-.....    ..+. ....+....=+|++||+|+.
T Consensus        70 ~~~i~liDTPG~~df~~~~~~-----~l---~~aD~~IlVvda~~g~~~~~----~~i~-~~~~~~~~P~iivvNK~D~~  136 (267)
T cd04169          70 DCVINLLDTPGHEDFSEDTYR-----TL---TAVDSAVMVIDAAKGVEPQT----RKLF-EVCRLRGIPIITFINKLDRE  136 (267)
T ss_pred             CEEEEEEECCCchHHHHHHHH-----HH---HHCCEEEEEEECCCCccHHH----HHHH-HHHHhcCCCEEEEEECCccC
Confidence            567789999998764431111     11   24678999999976321100    0010 11122234568889999985


Q ss_pred             ChhHHHHHHHHHHH
Q 023301          109 TETELGSLTERIKH  122 (284)
Q Consensus       109 ~~~~~~~~~~~l~~  122 (284)
                      ... ..++.+.+++
T Consensus       137 ~a~-~~~~~~~l~~  149 (267)
T cd04169         137 GRD-PLELLDEIEE  149 (267)
T ss_pred             CCC-HHHHHHHHHH
Confidence            432 2233444444

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.

>cd04106 Rab23_lke Rab23-like subfamily

Probab=80.75  E-value=8.8  Score=29.81  Aligned_cols=87  Identities=13%  Similarity=0.182  Sum_probs=45.0

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-----hhcCEEEEcc
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-----AYADRIILNK  104 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-----~~Ad~ivlnK  104 (284)
                      .+..+.+++|......+....     +   -..+.++.|.|....... ...      .....++     ...=+||.||
T Consensus        51 ~~~~i~D~~G~~~~~~~~~~~-----~---~~~~~~v~v~d~~~~~s~-~~l------~~~~~~~~~~~~~~p~iiv~nK  115 (162)
T cd04106          51 VRLMLWDTAGQEEFDAITKAY-----Y---RGAQACILVFSTTDRESF-EAI------ESWKEKVEAECGDIPMVLVQTK  115 (162)
T ss_pred             EEEEEeeCCchHHHHHhHHHH-----h---cCCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhCCCCCEEEEEEC
Confidence            345677888865444433221     1   145667888888664321 111      1112222     2233788899


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +|+.+...  .++..+..+.++  .++++++
T Consensus       116 ~Dl~~~~~v~~~~~~~~~~~~~--~~~~~~S  144 (162)
T cd04106         116 IDLLDQAVITNEEAEALAKRLQ--LPLFRTS  144 (162)
T ss_pred             hhcccccCCCHHHHHHHHHHcC--CeEEEEE
Confidence            99865433  233444444433  4666655

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

>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA

Probab=80.75  E-value=1.1  Score=32.89  Aligned_cols=72  Identities=17%  Similarity=0.123  Sum_probs=41.9

Q ss_pred             EEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhH---HHHHHHHHHHhC-CCCceeee-ccCCCChh
Q 023301           66 ITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETE---LGSLTERIKHIN-AMAPVKLA-KYGSVDMD  140 (284)
Q Consensus        66 v~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~---~~~~~~~l~~~n-p~a~i~~~-~~g~v~~~  140 (284)
                      .-..|+..+...+...+.     ...+..+.||+||+|=+--...++   +..++++. +.+ |.+.|+.+ -+.+...+
T Consensus        11 ~N~~Dse~i~~~l~~~G~-----~~~~~~e~AD~iiiNTC~V~~~Ae~k~~~~i~~l~-~~~~~~~~ivv~GC~aq~~~~   84 (98)
T PF00919_consen   11 MNQYDSERIASILQAAGY-----EIVDDPEEADVIIINTCTVRESAEQKSRNRIRKLK-KLKKPGAKIVVTGCMAQRYGE   84 (98)
T ss_pred             ccHHHHHHHHHHHHhcCC-----eeecccccCCEEEEEcCCCCcHHHHHHHHHHHHHH-HhcCCCCEEEEEeCccccChH
Confidence            344566666666655432     224556889999999996544433   44444433 344 88887754 34444555


Q ss_pred             hhh
Q 023301          141 FVL  143 (284)
Q Consensus       141 ~l~  143 (284)
                      .+.
T Consensus        85 ~l~   87 (98)
T PF00919_consen   85 ELK   87 (98)
T ss_pred             HHH
Confidence            544

A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification

>smart00175 RAB Rab subfamily of small GTPases

Probab=80.70  E-value=9.6  Score=29.58  Aligned_cols=91  Identities=13%  Similarity=0.126  Sum_probs=47.0

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH--hhcCEEEEccCCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV--AYADRIILNKIDLV  108 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi--~~Ad~ivlnK~D~~  108 (284)
                      +..+++++|...-..+....     +   -..+.+|.|+|+.+.... .... .++ ..+..+.  ...-+++.||+|+.
T Consensus        50 ~~~l~D~~G~~~~~~~~~~~-----~---~~~d~~ilv~d~~~~~s~-~~~~-~~l-~~~~~~~~~~~pivvv~nK~D~~  118 (164)
T smart00175       50 KLQIWDTAGQERFRSITSSY-----Y---RGAVGALLVYDITNRESF-ENLK-NWL-KELREYADPNVVIMLVGNKSDLE  118 (164)
T ss_pred             EEEEEECCChHHHHHHHHHH-----h---CCCCEEEEEEECCCHHHH-HHHH-HHH-HHHHHhCCCCCeEEEEEEchhcc
Confidence            34577888854433322221     1   236789999999875432 2110 011 1111111  24567888999986


Q ss_pred             Chh--HHHHHHHHHHHhCCCCceeeecc
Q 023301          109 TET--ELGSLTERIKHINAMAPVKLAKY  134 (284)
Q Consensus       109 ~~~--~~~~~~~~l~~~np~a~i~~~~~  134 (284)
                      ...  ..+.+++..+..+  .++++++.
T Consensus       119 ~~~~~~~~~~~~~~~~~~--~~~~e~Sa  144 (164)
T smart00175      119 DQRQVSREEAEAFAEEHG--LPFFETSA  144 (164)
T ss_pred             cccCCCHHHHHHHHHHcC--CeEEEEeC
Confidence            532  2344555555433  55666553

Rab GTPases are implicated in vesicle trafficking.

>cd04115 Rab33B_Rab33A Rab33B/Rab33A subfamily

Probab=80.62  E-value=11  Score=29.87  Aligned_cols=65  Identities=12%  Similarity=0.130  Sum_probs=34.1

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-------hcCEEEEccCCCCChhHH--HHHHHHHHHhCCCCceee
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-------YADRIILNKIDLVTETEL--GSLTERIKHINAMAPVKL  131 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-------~Ad~ivlnK~D~~~~~~~--~~~~~~l~~~np~a~i~~  131 (284)
                      ..+.+|.|+|+.+.... .+.      .....++.       ..=+||.||+|+....++  +...+..+..  ..++++
T Consensus        75 ~~d~~i~v~d~~~~~s~-~~~------~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~~~~~~~~~~~~~~~~--~~~~~e  145 (170)
T cd04115          75 NVHAVVFVYDVTNMASF-HSL------PSWIEECEQHSLPNEVPRILVGNKCDLREQIQVPTDLAQRFADAH--SMPLFE  145 (170)
T ss_pred             CCCEEEEEEECCCHHHH-HhH------HHHHHHHHHhcCCCCCCEEEEEECccchhhcCCCHHHHHHHHHHc--CCcEEE
Confidence            45778999999874432 111      11222222       234788899998543321  2222333332  366766


Q ss_pred             ecc
Q 023301          132 AKY  134 (284)
Q Consensus       132 ~~~  134 (284)
                      ++.
T Consensus       146 ~Sa  148 (170)
T cd04115         146 TSA  148 (170)
T ss_pred             Eec
Confidence            653

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

>TIGR00503 prfC peptide chain release factor 3

Probab=80.62  E-value=6.6  Score=37.86  Aligned_cols=67  Identities=15%  Similarity=0.177  Sum_probs=38.8

Q ss_pred             CCCEEEEecCCCCCcHH-HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAP-VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~-i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~  107 (284)
                      +..+.++.|+|..+... ....         .-..+.+|.|||+........    +.+. .........-++++||+|+
T Consensus        79 ~~~inliDTPG~~df~~~~~~~---------l~~aD~aIlVvDa~~gv~~~t----~~l~-~~~~~~~~PiivviNKiD~  144 (527)
T TIGR00503        79 DCLVNLLDTPGHEDFSEDTYRT---------LTAVDNCLMVIDAAKGVETRT----RKLM-EVTRLRDTPIFTFMNKLDR  144 (527)
T ss_pred             CeEEEEEECCChhhHHHHHHHH---------HHhCCEEEEEEECCCCCCHHH----HHHH-HHHHhcCCCEEEEEECccc
Confidence            56678999999865433 1111         235778999999987321100    0111 1122223456789999998


Q ss_pred             CC
Q 023301          108 VT  109 (284)
Q Consensus       108 ~~  109 (284)
                      ..
T Consensus       145 ~~  146 (527)
T TIGR00503       145 DI  146 (527)
T ss_pred             cC
Confidence            53

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.

>PLN00116 translation elongation factor EF-2 subunit; Provisional

Probab=80.59  E-value=2.4  Score=43.37  Aligned_cols=76  Identities=17%  Similarity=0.237  Sum_probs=44.7

Q ss_pred             EEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh---cCEEEEccCCCC-
Q 023301           33 IVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY---ADRIILNKIDLV-  108 (284)
Q Consensus        33 iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~---Ad~ivlnK~D~~-  108 (284)
                      =||.|+|-.+...-..        ...-..++.|.|||+..-.....        ..+..|+..   +-++++||+|+. 
T Consensus       101 nliDtPGh~dF~~e~~--------~al~~~D~ailVvda~~Gv~~~t--------~~~~~~~~~~~~p~i~~iNK~D~~~  164 (843)
T PLN00116        101 NLIDSPGHVDFSSEVT--------AALRITDGALVVVDCIEGVCVQT--------ETVLRQALGERIRPVLTVNKMDRCF  164 (843)
T ss_pred             EEECCCCHHHHHHHHH--------HHHhhcCEEEEEEECCCCCcccH--------HHHHHHHHHCCCCEEEEEECCcccc
Confidence            3789999866432111        11234678899999986432110        122334433   448999999998 


Q ss_pred             ------ChhHHHHHHHHHHHhC
Q 023301          109 ------TETELGSLTERIKHIN  124 (284)
Q Consensus       109 ------~~~~~~~~~~~l~~~n  124 (284)
                            ..+....+.+.+.++|
T Consensus       165 ~~~~~~~~~~~~~~~~vi~~in  186 (843)
T PLN00116        165 LELQVDGEEAYQTFSRVIENAN  186 (843)
T ss_pred             hhhcCCHHHHHHHHHHHHHHHH
Confidence                  4444455566666665

>COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]

Probab=80.59  E-value=3.8  Score=38.53  Aligned_cols=82  Identities=22%  Similarity=0.348  Sum_probs=50.6

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVT  109 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~  109 (284)
                      .-+=||.|+|=|+..-=.+.++        -.+++|+.+|||..-.+  .+  .+++...+. -...-=+||+||+|..+
T Consensus        68 ~~INIvDTPGHADFGGEVERvl--------~MVDgvlLlVDA~EGpM--PQ--TrFVlkKAl-~~gL~PIVVvNKiDrp~  134 (603)
T COG1217          68 TRINIVDTPGHADFGGEVERVL--------SMVDGVLLLVDASEGPM--PQ--TRFVLKKAL-ALGLKPIVVINKIDRPD  134 (603)
T ss_pred             eEEEEecCCCcCCccchhhhhh--------hhcceEEEEEEcccCCC--Cc--hhhhHHHHH-HcCCCcEEEEeCCCCCC
Confidence            3445789999999775444332        25889999999977543  22  233322222 23446799999999854


Q ss_pred             ---hhHHHHHHHHHHHhC
Q 023301          110 ---ETELGSLTERIKHIN  124 (284)
Q Consensus       110 ---~~~~~~~~~~l~~~n  124 (284)
                         ++.++++....-++.
T Consensus       135 Arp~~Vvd~vfDLf~~L~  152 (603)
T COG1217         135 ARPDEVVDEVFDLFVELG  152 (603)
T ss_pred             CCHHHHHHHHHHHHHHhC
Confidence               334555555555554

>PLN03126 Elongation factor Tu; Provisional

Probab=80.57  E-value=2.7  Score=40.03  Aligned_cols=92  Identities=18%  Similarity=0.258  Sum_probs=47.6

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCE-EEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADR-IILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~-ivlnK~D~  107 (284)
                      +..+.||+++|..+.   +...     ....-..+.++.|||+..-.....    +... .+........+ |++||+|+
T Consensus       143 ~~~i~liDtPGh~~f---~~~~-----~~g~~~aD~ailVVda~~G~~~qt----~e~~-~~~~~~gi~~iIvvvNK~Dl  209 (478)
T PLN03126        143 NRHYAHVDCPGHADY---VKNM-----ITGAAQMDGAILVVSGADGPMPQT----KEHI-LLAKQVGVPNMVVFLNKQDQ  209 (478)
T ss_pred             CcEEEEEECCCHHHH---HHHH-----HHHHhhCCEEEEEEECCCCCcHHH----HHHH-HHHHHcCCCeEEEEEecccc
Confidence            446789999996552   2221     111224677899999886422100    0000 11222233434 57999999


Q ss_pred             CChhH-HH----HHHHHHHHh--CC-CCceeeec
Q 023301          108 VTETE-LG----SLTERIKHI--NA-MAPVKLAK  133 (284)
Q Consensus       108 ~~~~~-~~----~~~~~l~~~--np-~a~i~~~~  133 (284)
                      ++.++ .+    ++++.++.+  ++ +.+++..+
T Consensus       210 ~~~~~~~~~i~~~i~~~l~~~g~~~~~~~~vp~S  243 (478)
T PLN03126        210 VDDEELLELVELEVRELLSSYEFPGDDIPIISGS  243 (478)
T ss_pred             cCHHHHHHHHHHHHHHHHHhcCCCcCcceEEEEE
Confidence            87544 23    344444443  21 45665543

>cd01861 Rab6 Rab6 subfamily

Probab=80.43  E-value=6.8  Score=30.44  Aligned_cols=89  Identities=11%  Similarity=0.159  Sum_probs=45.2

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh--hcCEEEEccCCCCC
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA--YADRIILNKIDLVT  109 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~--~Ad~ivlnK~D~~~  109 (284)
                      ..+++++|-.........+.        -..+.+|.|+|....... .+. ..++ ..+..+..  .+=++++||+|+..
T Consensus        51 l~~~D~~G~~~~~~~~~~~~--------~~~~~ii~v~d~~~~~s~-~~~-~~~~-~~~~~~~~~~~~iilv~nK~D~~~  119 (161)
T cd01861          51 LQLWDTAGQERFRSLIPSYI--------RDSSVAVVVYDITNRQSF-DNT-DKWI-DDVRDERGNDVIIVLVGNKTDLSD  119 (161)
T ss_pred             EEEEECCCcHHHHHHHHHHh--------ccCCEEEEEEECcCHHHH-HHH-HHHH-HHHHHhCCCCCEEEEEEEChhccc
Confidence            46788999655544433322        134578999999764322 111 0111 11222222  45677889999943


Q ss_pred             hhH--HHHHHHHHHHhCCCCceeeec
Q 023301          110 ETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       110 ~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ..+  .+......+..  .++++.++
T Consensus       120 ~~~~~~~~~~~~~~~~--~~~~~~~S  143 (161)
T cd01861         120 KRQVSTEEGEKKAKEL--NAMFIETS  143 (161)
T ss_pred             cCccCHHHHHHHHHHh--CCEEEEEe
Confidence            322  22333333333  25666554

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

>cd04162 Arl9_Arfrp2_like Arl9/Arfrp2-like subfamily

Probab=80.38  E-value=12  Score=29.67  Aligned_cols=37  Identities=19%  Similarity=0.151  Sum_probs=20.7

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM   75 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~   75 (284)
                      ...+.+++|......+...     .   .-..+.+|.|+|+....
T Consensus        45 ~l~i~Dt~G~~~~~~~~~~-----~---~~~ad~ii~V~D~t~~~   81 (164)
T cd04162          45 IMELLEIGGSQNLRKYWKR-----Y---LSGSQGLIFVVDSADSE   81 (164)
T ss_pred             EEEEEECCCCcchhHHHHH-----H---HhhCCEEEEEEECCCHH
Confidence            3455677776554433221     1   12456788888887744

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.

>PTZ00133 ADP-ribosylation factor; Provisional

Probab=80.24  E-value=9.7  Score=30.80  Aligned_cols=38  Identities=24%  Similarity=0.439  Sum_probs=23.1

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM   75 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~   75 (284)
                      ....+++++|......+....        .-..+.+|.|+|+.+..
T Consensus        61 ~~~~l~D~~G~~~~~~~~~~~--------~~~ad~iI~v~D~t~~~   98 (182)
T PTZ00133         61 LKFTMWDVGGQDKLRPLWRHY--------YQNTNGLIFVVDSNDRE   98 (182)
T ss_pred             EEEEEEECCCCHhHHHHHHHH--------hcCCCEEEEEEeCCCHH
Confidence            345677888875544432221        12456789999997643

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

Probab=80.17  E-value=10  Score=30.16  Aligned_cols=69  Identities=16%  Similarity=0.272  Sum_probs=37.6

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D  106 (284)
                      +...+++++|......+....        ....+.++.|+|....... ....  .....+.++.   ..+-++++||+|
T Consensus        49 ~~~~l~D~~g~~~~~~~~~~~--------~~~~~~~i~v~d~~~~~~~-~~~~--~~~~~~~~~~~~~~~p~ilv~NK~D  117 (180)
T cd04137          49 YHLEIVDTAGQDEYSILPQKY--------SIGIHGYILVYSVTSRKSF-EVVK--VIYDKILDMLGKESVPIVLVGNKSD  117 (180)
T ss_pred             EEEEEEECCChHhhHHHHHHH--------HhhCCEEEEEEECCCHHHH-HHHH--HHHHHHHHhcCCCCCCEEEEEEchh
Confidence            345788999976543322221        1245667888888775432 1110  0111222222   235689999999


Q ss_pred             CCC
Q 023301          107 LVT  109 (284)
Q Consensus       107 ~~~  109 (284)
                      +..
T Consensus       118 l~~  120 (180)
T cd04137         118 LHT  120 (180)
T ss_pred             hhh
Confidence            864

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	284
1nij_A	318	Yjia Protein Length = 318		4e-35
4ixn_A	318	Crystal Structure Of Zn(ii)-bound E37a,c66a,c67a Tr		5e-33

>pdb|1NIJ|A Chain A, Yjia Protein Length = 318

Iteration: 1
 Score =  144 bits (364), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 97/283 (34%), Positives = 139/283 (49%), Gaps = 30/283 (10%)
Query: 2   VNNGCLCCTVRGDLVKMLLQLAK---KKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQ 58
           + NGC+CC+   +L   LL L     K   QFD +VIE TG+A P P+I+TF + E++ Q
Sbjct: 60  LTNGCICCSRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQ 119
Query: 59  YVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTE 118
              LDGVI LVD+ HA + +N+    F +  A  QV YADRI+L K D+  E E   L E
Sbjct: 120 RYLLDGVIALVDAVHADEQMNQ----FTI--AQSQVGYADRILLTKTDVAGEAE--KLHE 171
Query: 119 RIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNXXXXXXXXXXXXXXXXX 178
           R+  INA APV    +G +D+  +    G+ LE                           
Sbjct: 172 RLARINARAPVYTVTHGDIDLGLLFNTNGFMLEE------------------NVVSTKPR 213
Query: 179 XXXXXXXDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVF 238
                   + +SS+ +  +  +D+ EV   +E L+ E  + L R KG+L + G   + +F
Sbjct: 214 FHFIADKQNDISSIVVELDYPVDISEVSRVMENLLLESADKLLRYKGMLWIDGEPNRLLF 273
Query: 239 QGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKG 281
           QGV         + WG DEK  + +VFIG  L E  +R  F G
Sbjct: 274 QGVQRLYSADWDRPWG-DEKPHSTMVFIGIQLPEEEIRAAFAG 315

>pdb|4IXN|A Chain A, Crystal Structure Of Zn(ii)-bound E37a,c66a,c67a Triple Mutant Yjia Gtpase Length = 318

Iteration: 1
 Score =  137 bits (346), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 95/283 (33%), Positives = 137/283 (48%), Gaps = 30/283 (10%)
Query: 2   VNNGCLCCTVRGDLVKMLLQLAK---KKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQ 58
           + NGC+  +   +L   LL L     K   QFD +VIE TG+A P P+I+TF + E++ Q
Sbjct: 60  LTNGCIAASRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQ 119
Query: 59  YVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTE 118
              LDGVI LVD+ HA + +N+    F +  A  QV YADRI+L K D+  E E   L E
Sbjct: 120 RYLLDGVIALVDAVHADEQMNQ----FTI--AQSQVGYADRILLTKTDVAGEAE--KLHE 171
Query: 119 RIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNXXXXXXXXXXXXXXXXX 178
           R+  INA APV    +G +D+  +    G+ LE                           
Sbjct: 172 RLARINARAPVYTVTHGDIDLGLLFNTNGFMLEE------------------NVVSTKPR 213
Query: 179 XXXXXXXDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVF 238
                   + +SS+ +  +  +D+ EV   +E L+ E  + L R KG+L + G   + +F
Sbjct: 214 FHFIADKQNDISSIVVELDYPVDISEVSRVMENLLLESADKLLRYKGMLWIDGEPNRLLF 273
Query: 239 QGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKG 281
           QGV         + WG DEK  + +VFIG  L E  +R  F G
Sbjct: 274 QGVQRLYSADWDRPWG-DEKPHSTMVFIGIQLPEEEIRAAFAG 315

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	284
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	1e-116

>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 Length = 318

 Score =  334 bits (860), Expect = e-116
 Identities = 95/283 (33%), Positives = 136/283 (48%), Gaps = 30/283 (10%)

Query: 3   NNGCLCCTVRGDLVKMLLQLAKKKQ---GQFDHIVIETTGLAKPAPVIETFCTDELVSQY 59
            NGC+CC+   +L   LL L         QFD +VIE TG+A P P+I+TF + E++ Q 
Sbjct: 61  TNGCICCSRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQR 120

Query: 60  VKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTER 119
             LDGVI LVD+ HA + +N+         A  QV YADRI+L K D+  E E   L ER
Sbjct: 121 YLLDGVIALVDAVHADEQMNQF------TIAQSQVGYADRILLTKTDVAGEAE--KLHER 172

Query: 120 IKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHESAHGHHEGH 179
           +  INA APV    +G +D+  +    G+ LE                            
Sbjct: 173 LARINARAPVYTVTHGDIDLGLLFNTNGFMLEENVVSTK----------------PRFHF 216

Query: 180 HHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQ 239
             +  +D  +SS+ +  +  +D+ EV   +E L+ E  + L R KG+L + G   + +FQ
Sbjct: 217 IADKQND--ISSIVVELDYPVDISEVSRVMENLLLESADKLLRYKGMLWIDGEPNRLLFQ 274

Query: 240 GVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGC 282
           GV         + W  DEK  + +VFIG  L E  +R  F G 
Sbjct: 275 GVQRLYSADWDRPW-GDEKPHSTMVFIGIQLPEEEIRAAFAGL 316

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	284
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	100.0
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	98.56
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	98.19
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	98.12
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	98.11
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	98.1
2hf9_A	226	Probable hydrogenase nickel incorporation protein	98.01
2qpt_A	550	EH domain-containing protein-2; protein-nucleotide	97.87
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	97.72
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	97.07
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	97.01
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	96.87
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	96.66
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	96.57
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	96.0
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.1
3p26_A	483	Elongation factor 1 alpha-like protein; GTP/GDP bi	94.39
3sjy_A	403	Translation initiation factor 2 subunit gamma; zin	94.19
2fh5_B	214	SR-beta, signal recognition particle receptor beta	94.15
3i8s_A	274	Ferrous iron transport protein B; GTPase, GPCR, ir	94.06
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	93.66
3gee_A	476	MNME, tRNA modification GTPase MNME; G protein, cy	93.26
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	93.14
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	93.07
1wb1_A	482	Translation elongation factor SELB; selenocysteine	93.02
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	92.8
1lnz_A	342	SPO0B-associated GTP-binding protein; GTPase, OBG,	92.79
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	92.64
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	92.63
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	92.62
3geh_A	462	MNME, tRNA modification GTPase MNME; G protein, U3	92.53
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	92.51
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	92.49
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	92.47
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	92.46
1jny_A	435	EF-1-alpha, elongation factor 1-alpha, EF-TU, TUF-	92.42
2ged_A	193	SR-beta, signal recognition particle receptor beta	92.39
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	92.39
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	92.37
2c78_A	405	Elongation factor TU-A; hydrolase, GTPase, transla	92.35
3izq_1	611	HBS1P, elongation factor 1 alpha-like protein; NO-	92.17
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	92.11
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	92.06
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	91.98
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	91.86
1f60_A	458	Elongation factor EEF1A; protein-protein complex,	91.75
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	91.68
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	91.65
2elf_A	370	Protein translation elongation factor 1A; tRNA, py	91.63
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	91.62
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	91.62
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	91.48
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	91.45
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	91.38
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	91.19
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	91.08
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	90.97
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	90.89
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	90.88
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	90.79
1kk1_A	410	EIF2gamma; initiation of translation; HET: GNP; 1.	90.79
1zun_B	434	Sulfate adenylate transferase, subunit 1/adenylyls	90.72
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	90.72
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	90.65
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	90.6
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	90.59
1s0u_A	408	EIF-2-gamma, translation initiation factor 2 gamma	90.55
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	90.52
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	90.5
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	90.4
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	90.39
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	90.37
3j2k_7	439	ERF3, eukaryotic polypeptide chain release factor	90.3
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	90.28
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	90.25
1d2e_A	397	Elongation factor TU (EF-TU); G-protein, beta-barr	90.11
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	90.08
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	89.97
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	89.9
1nrj_B	218	SR-beta, signal recognition particle receptor beta	89.84
4dcu_A	456	GTP-binding protein ENGA; GTPase, GDP, protein bin	89.61
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	89.55
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	89.55
3cnl_A	262	YLQF, putative uncharacterized protein; circular p	89.48
3zvr_A	772	Dynamin-1; hydrolase, DRP1, DRP, endocytosis, mito	89.43
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	89.42
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	89.34
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	89.24
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	89.19
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	89.1
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	89.04
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	88.96
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	88.96
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	88.93
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	88.89
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	88.77
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	88.77
3o47_A	329	ADP-ribosylation factor GTPase-activating protein	88.74
1puj_A	282	YLQF, conserved hypothetical protein YLQF; structu	88.68
3t5d_A	274	Septin-7; GTP-binding protein, cytoskeleton, signa	88.52
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	88.39
2x2e_A	353	Dynamin-1; nitration, hydrolase, membrane fission,	88.35
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	88.33
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	88.32
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	88.26
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	88.12
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	87.84
3tr5_A	528	RF-3, peptide chain release factor 3; protein synt	87.8
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	87.76
4djt_A	218	GTP-binding nuclear protein GSP1; structural genom	87.71
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	87.49
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	87.33
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	87.23
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	87.04
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	86.77
3a1s_A	258	Iron(II) transport protein B; FEOB, iron transport	86.52
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	86.42
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	86.38
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	86.11
2j69_A	695	Bacterial dynamin-like protein; FZO, FZL, GTPase,	85.93
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	85.86
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	85.85
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	85.76
1xzp_A	482	Probable tRNA modification GTPase TRME; GTP-bindin	85.74
2xex_A	693	Elongation factor G; GTPase, translation, biosynth	85.64
1r5b_A	467	Eukaryotic peptide chain release factor GTP-bindi	85.55
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	84.98
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	84.84
3avx_A	1289	Elongation factor TS, elongation factor TU, linke	84.83
2xxa_A	433	Signal recognition particle protein; protein trans	84.66
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	84.6
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	84.58
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	84.13
2rdo_7	704	EF-G, elongation factor G; elongation factor G, EF	83.76
1dar_A	691	EF-G, elongation factor G; ribosomal translocase,	83.67
2h5e_A	529	Peptide chain release factor RF-3; beta barrel, tr	83.57
3qq5_A	423	Small GTP-binding protein; hydrogenase, H-cluster,	83.57
3mca_A	592	HBS1, elongation factor 1 alpha-like protein; prot	83.34
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	83.26
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	83.25
3dpu_A	535	RAB family protein; roccor, G-domain, COR, GTP-bin	83.13
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	83.01
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	82.92
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	82.91
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	82.77
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	82.69
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	82.53
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	82.53
3llu_A	196	RAS-related GTP-binding protein C; structural geno	82.45
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	82.22
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	82.1
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	81.63
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	81.62
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	81.23
3vqt_A	548	RF-3, peptide chain release factor 3; translation,	81.12
3cb4_D	599	GTP-binding protein LEPA; GTPase, OB-fold, membran	80.81
1wxq_A	397	GTP-binding protein; structural genomics, riken st	80.71
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	80.66
3r7w_A	307	Gtpase1, GTP-binding protein GTR1; RAG gtpases, GT	80.65
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	80.46
3lvq_E	497	ARF-GAP with SH3 domain, ANK repeat and PH domain	80.21

>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=100.00  E-value=9.4e-41  Score=297.70  Aligned_cols=257  Identities=37%  Similarity=0.637  Sum_probs=206.2

Q ss_pred             CCCCceeeeeeCchHHHHHHHHHHh-hcC--CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHh
Q 023301            1 MVNNGCLCCTVRGDLVKMLLQLAKK-KQG--QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQH   77 (284)
Q Consensus         1 eL~~GCiCCs~~~dl~~~l~~l~~~-~~~--~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~   77 (284)
                      ||+||||||+.+.+|..+|..++.. +..  .+|++++|++|+++|.++++.++.++.......++.++++||+.++..+
T Consensus        59 el~~gCicc~~~~~~~~~l~~l~~~~q~~~~~~~~~v~E~~~l~~p~~~~~~~~~~~~~~~~~~l~~~l~~vd~~~~~~~  138 (318)
T 1nij_A           59 TLTNGCICCSRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQRYLLDGVIALVDAVHADEQ  138 (318)
T ss_dssp             EETTSCEEECTTSCHHHHHHHHHHHHHHTSCCCSEEEEEEETTCCHHHHHHHHHHSHHHHHHEEEEEEEEEEETTTHHHH
T ss_pred             EECCCceEEcccHHHHHHHHHHHhHHhcCCCCCCEEEEeCCCCCCHHHHHHHHhcCccccCeEEECCEEEEEEHHHHHHH
Confidence            5789999999999999999988621 133  3599999999999999988877444555667889999999999998877


Q ss_pred             hhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCCChhhhhcCCCCCcccccccc
Q 023301           78 LNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEV  157 (284)
Q Consensus        78 l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v~~~~l~~~~~~~~~~~~~~~  157 (284)
                      +.+.      ....+|+..||++++||.|+.+++  +.+.+.++++||.+.|+.++++.++++.+++...++.+......
T Consensus       139 ~~~l------s~g~~Q~~~ad~ill~k~dl~de~--~~l~~~l~~l~~~~~ii~~sh~~~~~~~l~~~~~~~~~~~~~~~  210 (318)
T 1nij_A          139 MNQF------TIAQSQVGYADRILLTKTDVAGEA--EKLHERLARINARAPVYTVTHGDIDLGLLFNTNGFMLEENVVST  210 (318)
T ss_dssp             HHHC------HHHHHHHHTCSEEEEECTTTCSCT--HHHHHHHHHHCSSSCEEECCSSCCCGGGGSCCCTTSCCSCCCSS
T ss_pred             Hhhc------hHHHHHHHhCCEEEEECcccCCHH--HHHHHHHHHhCCCCeEEEecccCCCHHHHhCCCCCChhhhhccc
Confidence            6431      345799999999999999999765  78888999999999999999999999999887655432211000


Q ss_pred             cccCCcccccCCcCCCCCCCCCCCCCCCCCCeEEEEEEeCCCCCHHHHHHHHHHHHHHhCCceEEEEEEEEecCCCeeEE
Q 023301          158 HVDNSHCATHHHESAHGHHEGHHHNHMHDSAVSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYV  237 (284)
Q Consensus       158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~l~~~l~~l~~~~~~~i~R~KG~v~~~~~~~~~~  237 (284)
                      .+              .++    +.+.|++++.|+++..++|+++++|.+||+.++..++++++|+||++|+++.+.++.
T Consensus       211 ~~--------------~~~----~~~~~~~~v~s~~~~~~~~~~~~~l~~~l~~l~~~~~~~v~R~KG~~~~~~~~~~~~  272 (318)
T 1nij_A          211 KP--------------RFH----FIADKQNDISSIVVELDYPVDISEVSRVMENLLLESADKLLRYKGMLWIDGEPNRLL  272 (318)
T ss_dssp             CC--------------CSC----STGGGGCSEEEEEEEESSCBCHHHHHHHHHHHHHHTTTTEEEEEEEECBTTCSEEEE
T ss_pred             Cc--------------ccc----cccCCCCCeEEEEEEeCCCCCHHHHHHHHHHHHHhcCCCEEEeeeEEEeCCCCcEEE
Confidence            00              000    112234589999999999999999999999998777789999999999998888899


Q ss_pred             EEccceeeecCCCCCCCCCCCCccEEEEEecCCCHHHHHHHHhhhhC
Q 023301          238 FQGVHSTLDGCPGKAWGPDEKRINKLVFIGRNLDETALRKGFKGCLA  284 (284)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~lv~IG~~ld~~~l~~~l~~c~~  284 (284)
                      |||++..++......|. .+++.++|||||+++|+++|++.|++|+.
T Consensus       273 ~~gv~~~~~~~~~~~~~-~~~~~~~lv~Ig~~ld~~~l~~~l~~~l~  318 (318)
T 1nij_A          273 FQGVQRLYSADWDRPWG-DEKPHSTMVFIGIQLPEEEIRAAFAGLRK  318 (318)
T ss_dssp             EEEETTEEEEEEEEECT-TSCCCEEEEEEEESCCHHHHHHHHHTTCC
T ss_pred             EECCccEEeccccccCC-CCCCceEEEEEcCCCCHHHHHHHHHHHhC
Confidence            99998887643334575 45678999999999999999999999974

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=98.56  E-value=4.8e-08  Score=81.12  Aligned_cols=116  Identities=18%  Similarity=0.204  Sum_probs=76.5

Q ss_pred             CCCceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecCCC-CCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhh
Q 023301            2 VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGL-AKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNE   80 (284)
Q Consensus         2 L~~GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG~-a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~   80 (284)
                      +.+||+||.....+...+.   .  ...+|+++|||+|. ..|...        .    +.-+.+++|+|+........ 
T Consensus        86 ~~~~~~~~~~~~~~~~~~~---~--~~~~d~iiidt~G~~~~~~~~--------~----~~~~~~i~vvd~~~~~~~~~-  147 (221)
T 2wsm_A           86 ISTGKECHLDAHMIYHRLK---K--FSDCDLLLIENVGNLICPVDF--------D----LGENYRVVMVSVTEGDDVVE-  147 (221)
T ss_dssp             CCCTTCSSCCHHHHHTTGG---G--GTTCSEEEEEEEEBSSGGGGC--------C----CSCSEEEEEEEGGGCTTHHH-
T ss_pred             ecCCceeecccHHHHHHHH---h--cCCCCEEEEeCCCCCCCCchh--------c----cccCcEEEEEeCCCcchhhh-
Confidence            5689998754443443343   3  46799999999995 334321        0    12245799999987532221 


Q ss_pred             cCCccchHHHHHHHhhcCEEEEccCCCCCh--hHHHHHHHHHHHhCCCCceeeeccC-CCChhhhh
Q 023301           81 VKPRFVVNEAVEQVAYADRIILNKIDLVTE--TELGSLTERIKHINAMAPVKLAKYG-SVDMDFVL  143 (284)
Q Consensus        81 ~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~--~~~~~~~~~l~~~np~a~i~~~~~g-~v~~~~l~  143 (284)
                              ....++..+.+||+||+|+.+.  ...+.+.+.++.++|.++++.++.. ......++
T Consensus       148 --------~~~~~~~~~~iiv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~i~~~Sa~~g~gi~~l~  205 (221)
T 2wsm_A          148 --------KHPEIFRVADLIVINKVALAEAVGADVEKMKADAKLINPRAKIIEMDLKTGKGFEEWI  205 (221)
T ss_dssp             --------HCHHHHHTCSEEEEECGGGHHHHTCCHHHHHHHHHHHCTTSEEEECBTTTTBTHHHHH
T ss_pred             --------hhhhhhhcCCEEEEecccCCcchhhHHHHHHHHHHHhCCCCeEEEeecCCCCCHHHHH
Confidence                    1235678899999999999654  2577888888888988898877642 33444443

>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=98.19  E-value=9.8e-07  Score=75.12  Aligned_cols=111  Identities=18%  Similarity=0.128  Sum_probs=60.6

Q ss_pred             CCceeeeeeC--chHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHH---HhcccccccceeeeceEEEEEcccchHHh
Q 023301            3 NNGCLCCTVR--GDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIE---TFCTDELVSQYVKLDGVITLVDSKHAMQH   77 (284)
Q Consensus         3 ~~GCiCCs~~--~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~---~l~~~~~l~~~~~l~~vv~vvD~~~~~~~   77 (284)
                      .|||+||+..  ......+.+.+..-...+|++||+|+|..++..+..   .+.  ..+   -. ..+|+|+|+......
T Consensus        80 ~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~d~iiiDtpG~~~~~~~~~l~~~~~--~~~---~~-~~iv~vvD~~~~~~~  153 (262)
T 1yrb_A           80 PNGAIVESYDRLMEKFNEYLNKILRLEKENDYVLIDTPGQMETFLFHEFGVRLM--ENL---PY-PLVVYISDPEILKKP  153 (262)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHCSEEEEECCSSHHHHHHSHHHHHHH--HTS---SS-CEEEEEECGGGCCSH
T ss_pred             CCCcEEecHHHHhhhHHHHHHHHHHHhhcCCEEEEeCCCccchhhhhhhHHHHH--HHH---hh-ceEEeccchhhhcCH
Confidence            4788888631  112233434433112357999999999987754311   111  112   23 678999998764322


Q ss_pred             hhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHH
Q 023301           78 LNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTER  119 (284)
Q Consensus        78 l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~  119 (284)
                      ...............+...+.++|+||+|+.+..+.+.+++.
T Consensus       154 ~~~~~~~~~~~~~~~~~~~p~~iv~NK~D~~~~~~~~~~~~~  195 (262)
T 1yrb_A          154 NDYCFVRFFALLIDLRLGATTIPALNKVDLLSEEEKERHRKY  195 (262)
T ss_dssp             HHHHHHHHHHHHHHHHHTSCEEEEECCGGGCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcccCCCeEEEEecccccccccHHHHHHH
Confidence            110000000001234567788999999999887655444443

>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=98.12  E-value=4.9e-06  Score=74.46  Aligned_cols=110  Identities=20%  Similarity=0.194  Sum_probs=69.4

Q ss_pred             CCCceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhc
Q 023301            2 VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEV   81 (284)
Q Consensus         2 L~~GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~   81 (284)
                      ++++|.||.......+++ ..+.  ...++++||||+|+..+...+-           -..+.++.|+|+...... .. 
T Consensus       147 ~~~~~~~~~~~~~t~d~i-~~~~--~~~~~~iiiDTpGi~~~~~~~~-----------~~aD~vl~V~d~~~~~~~-~~-  210 (355)
T 3p32_A          147 SPTSGTLGGVTRATRETV-VLLE--AAGFDVILIETVGVGQSEVAVA-----------NMVDTFVLLTLARTGDQL-QG-  210 (355)
T ss_dssp             CC--CCHHHHHHHHHHHH-HHHH--HTTCCEEEEEECSCSSHHHHHH-----------TTCSEEEEEEESSTTCTT-TT-
T ss_pred             CCCCccccchhHHHHHHH-HHHh--hCCCCEEEEeCCCCCcHHHHHH-----------HhCCEEEEEECCCCCccH-HH-
Confidence            467888888777777777 4555  4689999999999988654321           134668999998653221 11 


Q ss_pred             CCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHH----HHHHhCC-----CCceeeecc
Q 023301           82 KPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTE----RIKHINA-----MAPVKLAKY  134 (284)
Q Consensus        82 ~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~----~l~~~np-----~a~i~~~~~  134 (284)
                          +.   ....+.+++||+||+|+.+........+    .++..+|     ..+|+.++.
T Consensus       211 ----l~---~~~~~~p~ivVlNK~Dl~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~iSA  265 (355)
T 3p32_A          211 ----IK---KGVLELADIVVVNKADGEHHKEARLAARELSAAIRLIYPREALWRPPVLTMSA  265 (355)
T ss_dssp             ----CC---TTSGGGCSEEEEECCCGGGHHHHHHHHHHHHHHHHHHSTTCCSCCCCEEEEBG
T ss_pred             ----HH---HhHhhcCCEEEEECCCCcChhHHHHHHHHHHHHHhhccccccCCCCceEEEEc
Confidence                10   1234569999999999976655444333    3333443     356776653

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=98.11  E-value=8.3e-06  Score=72.83  Aligned_cols=87  Identities=17%  Similarity=0.154  Sum_probs=47.5

Q ss_pred             CCceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcC
Q 023301            3 NNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVK   82 (284)
Q Consensus         3 ~~GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~   82 (284)
                      +++|.||+...+...++..+ .  ...+|++||||+|+..+..-+   .        -.++.+++|+|+..... ...  
T Consensus       143 ~~~~~lgg~tr~~~~~~~~~-~--~~~~~~iliDT~Gi~~~~~~l---~--------~~~d~vl~V~d~~~~~~-~~~--  205 (349)
T 2www_A          143 PTRGTLGGVTRTTNEAILLC-E--GAGYDIILIETVGVGQSEFAV---A--------DMVDMFVLLLPPAGGDE-LQG--  205 (349)
T ss_dssp             ---------CTTHHHHHHHH-H--HTTCSEEEEECCCC--CHHHH---H--------TTCSEEEEEECCC----------
T ss_pred             CCccccccchHHHHHHHHhh-c--cCCCCEEEEECCCcchhhhhH---H--------hhCCEEEEEEcCCcchh-HHH--
Confidence            46899987777787777633 3  367899999999998765322   1        13567899999976321 110  


Q ss_pred             CccchHHHHHHHhhcCEEEEccCCCCChhH
Q 023301           83 PRFVVNEAVEQVAYADRIILNKIDLVTETE  112 (284)
Q Consensus        83 ~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~  112 (284)
                         +   ....+..++++|+||+|+.+...
T Consensus       206 ---i---~~~il~~~~ivVlNK~Dl~~~~~  229 (349)
T 2www_A          206 ---I---KRGIIEMADLVAVTKSDGDLIVP  229 (349)
T ss_dssp             -----------CCSCSEEEECCCSGGGHHH
T ss_pred             ---h---HHHHHhcCCEEEEeeecCCCchh
Confidence               1   01234568999999999976443

>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=98.10  E-value=2.2e-05  Score=69.76  Aligned_cols=111  Identities=14%  Similarity=0.141  Sum_probs=63.7

Q ss_pred             CCceeeeeeCchHH-----HHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHh
Q 023301            3 NNGCLCCTVRGDLV-----KMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQH   77 (284)
Q Consensus         3 ~~GCiCCs~~~dl~-----~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~   77 (284)
                      .+||+||+..+.+.     +.+..+.......++++||||+|+.++...+.           -..+.++.|+|+..... 
T Consensus       117 ~~~~i~~~~~~~~l~g~~~~~~~~~~~~~~~~~~i~liDTpG~~~~~~~~~-----------~~aD~vl~Vvd~~~~~~-  184 (341)
T 2p67_A          117 EAAFIRPVPSSGHLGGASQRARELMLLCEAAGYDVVIVETVGVGQSETEVA-----------RMVDCFISLQIAGGGDD-  184 (341)
T ss_dssp             TTEEEEEECC-----CHHHHHHHHHHHHHHTTCSEEEEEEECCTTHHHHHH-----------TTCSEEEEEECC------
T ss_pred             CCceeecCccccccchhHHHHHHHHHHhhccCCCEEEEeCCCccchHHHHH-----------HhCCEEEEEEeCCccHH-
Confidence            68999997653321     22222221013578999999999998775431           24567899999975422 


Q ss_pred             hhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHH----HHHHHHHhCC-----CCceeeec
Q 023301           78 LNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGS----LTERIKHINA-----MAPVKLAK  133 (284)
Q Consensus        78 l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~----~~~~l~~~np-----~a~i~~~~  133 (284)
                      +.     .+.   ..+...+.++|+||+|+.+......    +++.++.+++     ..+++.++
T Consensus       185 ~~-----~l~---~~~~~~p~ivv~NK~Dl~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~iS  241 (341)
T 2p67_A          185 LQ-----GIK---KGLMEVADLIVINKDDGDNHTNVAIARHMYESALHILRRKYDEWQPRVLTCS  241 (341)
T ss_dssp             -C-----CCC---HHHHHHCSEEEECCCCTTCHHHHHHHHHHHHHHHHHSCCSBTTBCCEEEECB
T ss_pred             HH-----HHH---HhhhcccCEEEEECCCCCChHHHHHHHHHHHHHHHhccccccCCCCcEEEee
Confidence            11     111   2455778999999999987655443    3333333454     34566554

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=98.01  E-value=3.8e-06  Score=69.70  Aligned_cols=118  Identities=25%  Similarity=0.305  Sum_probs=73.2

Q ss_pred             CCCceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecCCC-CCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhh
Q 023301            2 VNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGL-AKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNE   80 (284)
Q Consensus         2 L~~GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG~-a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~   80 (284)
                      +.+||+||-...++.+.+..+.   ...+|++++|++|. ..+..    +.    .    .-.-++.|+|+........ 
T Consensus        94 ~~~~~~~~l~~~~~~~~~~~l~---~~~~d~~~id~~g~i~~~~s----~~----~----~~~~~~~v~~~~~~~~~~~-  157 (226)
T 2hf9_A           94 LNTGKECHLDAHLVGHALEDLN---LDEIDLLFIENVGNLICPAD----FD----L----GTHKRIVVISTTEGDDTIE-  157 (226)
T ss_dssp             EECTTCSSCCHHHHHHHHTTSC---GGGCSEEEEECCSCSSGGGG----CC----C----SCSEEEEEEEGGGCTTTTT-
T ss_pred             ecCCceEeccHHHHHHHHHHHh---cCCCCEEEEeCCCCccCcch----hh----h----ccCcEEEEEecCcchhhHh-
Confidence            3469997755455544444332   24689999999995 33221    11    0    1122467888754322111 


Q ss_pred             cCCccchHHHHHHHhhcCEEEEccCCCCChh--HHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301           81 VKPRFVVNEAVEQVAYADRIILNKIDLVTET--ELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus        81 ~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~--~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                              ....++..+++||+||+|+.+..  ..+.+.+.++.+++.++++.++. .......++
T Consensus       158 --------~~~~~~~~~~iiv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~~l~  215 (226)
T 2hf9_A          158 --------KHPGIMKTADLIVINKIDLADAVGADIKKMENDAKRINPDAEVVLLSLKTMEGFDKVL  215 (226)
T ss_dssp             --------TCHHHHTTCSEEEEECGGGHHHHTCCHHHHHHHHHHHCTTSEEEECCTTTCTTHHHHH
T ss_pred             --------hhhhHhhcCCEEEEeccccCchhHHHHHHHHHHHHHhCCCCeEEEEEecCCCCHHHHH
Confidence                    11456889999999999996542  46778888888888889887764 233444443

>2qpt_A EH domain-containing protein-2; protein-nucleotide complex, membrane protein, endocytosis; HET: ANP; 3.10A {Mus musculus}

Probab=97.87  E-value=3.4e-05  Score=73.04  Aligned_cols=99  Identities=22%  Similarity=0.307  Sum_probs=59.0

Q ss_pred             CCceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecCCCCCcHH--HHHHhc-ccccccceeeeceEEEEEcccchHHhhh
Q 023301            3 NNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAP--VIETFC-TDELVSQYVKLDGVITLVDSKHAMQHLN   79 (284)
Q Consensus         3 ~~GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~--i~~~l~-~~~~l~~~~~l~~vv~vvD~~~~~~~l~   79 (284)
                      .+||+||++..++..             ..+||+|+|+.++..  +-+.+. ........-..+.+++|+|+.+.... .
T Consensus       140 ~~~~~~~~~~~~ll~-------------~l~lIDTPG~~~~~~~~~~~~~~f~~~~~~~l~~aD~il~VvDa~~~~~~-~  205 (550)
T 2qpt_A          140 LNRFMCAQLPNQVLE-------------SISIIDTPGILSGAKQRVSRGYDFPAVLRWFAERVDLIILLFDAHKLEIS-D  205 (550)
T ss_dssp             CTTEEEEECCCHHHH-------------HCEEEECCCBCC-------CCSCHHHHHHHHHHHCSEEEEEEETTSCCCC-H
T ss_pred             cccceEEeccccccC-------------CEEEEECcCCCCcchhHHHHHhhHHHHHHHHHHhCCEEEEEEeCCcCCCC-H
Confidence            489999999887542             358999999997432  111000 00000011256889999999763100 0


Q ss_pred             hcCCccchHHHHHHH---hhcCEEEEccCCCCChhHHHHHHHHHH
Q 023301           80 EVKPRFVVNEAVEQV---AYADRIILNKIDLVTETELGSLTERIK  121 (284)
Q Consensus        80 ~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D~~~~~~~~~~~~~l~  121 (284)
                      +      ...+.+++   ....++|+||+|+++.+++.++.+.++
T Consensus       206 ~------~~~~l~~l~~~~~pvilVlNK~Dl~~~~el~~~~~~l~  244 (550)
T 2qpt_A          206 E------FSEAIGALRGHEDKIRVVLNKADMVETQQLMRVYGALM  244 (550)
T ss_dssp             H------HHHHHHHTTTCGGGEEEEEECGGGSCHHHHHHHHHHHH
T ss_pred             H------HHHHHHHHHhcCCCEEEEEECCCccCHHHHHHHHHHhh
Confidence            0      01123333   456799999999999888877766664

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=97.72  E-value=0.00012  Score=64.83  Aligned_cols=106  Identities=20%  Similarity=0.199  Sum_probs=60.4

Q ss_pred             eeeeCchHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccch
Q 023301            8 CCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVV   87 (284)
Q Consensus         8 CCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~   87 (284)
                      ||+++|...+++..+.......+|++||||+|+..+...+.           -.++.++.|+|+..... +....     
T Consensus       126 ~~~l~G~tr~~~e~~~~~~~~~~~~iliDT~Gi~~~~~~v~-----------~~~d~vl~v~d~~~~~~-~~~i~-----  188 (337)
T 2qm8_A          126 SGTLGGVAAKTRETMLLCEAAGFDVILVETVGVGQSETAVA-----------DLTDFFLVLMLPGAGDE-LQGIK-----  188 (337)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHTTCCEEEEEECSSSSCHHHHH-----------TTSSEEEEEECSCC-------CC-----
T ss_pred             cccccchHHHHHHHHHHHhcCCCCEEEEECCCCCcchhhHH-----------hhCCEEEEEEcCCCccc-HHHHH-----
Confidence            57766655555544421114689999999999999864322           13456788999854221 11110     


Q ss_pred             HHHHHHHhhcCEEEEccCCCCChhH-----HHHHHHHHHHhCC-----CCceeeec
Q 023301           88 NEAVEQVAYADRIILNKIDLVTETE-----LGSLTERIKHINA-----MAPVKLAK  133 (284)
Q Consensus        88 ~~~~~Qi~~Ad~ivlnK~D~~~~~~-----~~~~~~~l~~~np-----~a~i~~~~  133 (284)
                         ....+.++++++||+|+.+..+     .+++...+.-++|     ..+++.++
T Consensus       189 ---~~i~~~~~ivvlNK~Dl~~~~~~s~~~~~~l~~a~~l~~~~~~~~~~~vl~~S  241 (337)
T 2qm8_A          189 ---KGIFELADMIAVNKADDGDGERRASAAASEYRAALHILTPPSATWTPPVVTIS  241 (337)
T ss_dssp             ---TTHHHHCSEEEEECCSTTCCHHHHHHHHHHHHHHHTTBCCSBTTBCCCEEEEB
T ss_pred             ---HHHhccccEEEEEchhccCchhHHHHHHHHHHHHHHhccccccCCCCCEEEEe
Confidence               1123568999999999765322     2333333333454     35666655

>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=97.07  E-value=0.0007  Score=59.13  Aligned_cols=108  Identities=13%  Similarity=0.217  Sum_probs=64.4

Q ss_pred             CCCEEEEecCCCCCcH--HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEc
Q 023301           29 QFDHIVIETTGLAKPA--PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILN  103 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~--~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivln  103 (284)
                      ..+.+|++|+|..++.  ..+............-..+.++.|+|+......- +      ......++   ...-++|+|
T Consensus        58 ~~~i~lvDTPG~~~~~~~~~l~~~~~~~~~~~l~~aD~il~VvD~~~~~~~~-~------~~~~~~~l~~~~~pvilV~N  130 (308)
T 3iev_A           58 EAQIIFLDTPGIYEPKKSDVLGHSMVEIAKQSLEEADVILFMIDATEGWRPR-D------EEIYQNFIKPLNKPVIVVIN  130 (308)
T ss_dssp             TEEEEEEECCCCCCCCTTCHHHHHHHHHHHHHHHHCSEEEEEEETTTBSCHH-H------HHHHHHHTGGGCCCEEEEEE
T ss_pred             CCeEEEEECcCCCccccchhHHHHHHHHHHHHhhcCCEEEEEEeCCCCCCch-h------HHHHHHHHHhcCCCEEEEEE
Confidence            5578999999998876  2111111100111122578899999998642210 0      01113333   346789999


Q ss_pred             cCCCC-ChhHHHHHHHHHHHhC-CCCceeeecc-CCCChhhhh
Q 023301          104 KIDLV-TETELGSLTERIKHIN-AMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       104 K~D~~-~~~~~~~~~~~l~~~n-p~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+|+. +.+.+....+.+++.. +.++++.++. .......++
T Consensus       131 K~Dl~~~~~~~~~~~~~l~~~~~~~~~i~~vSA~~g~gv~~L~  173 (308)
T 3iev_A          131 KIDKIGPAKNVLPLIDEIHKKHPELTEIVPISALKGANLDELV  173 (308)
T ss_dssp             CGGGSSSGGGGHHHHHHHHHHCTTCCCEEECBTTTTBSHHHHH
T ss_pred             CccCCCCHHHHHHHHHHHHHhccCCCeEEEEeCCCCCCHHHHH
Confidence            99998 6666677777777666 6788887764 233444444

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=97.01  E-value=0.0025  Score=52.14  Aligned_cols=106  Identities=15%  Similarity=0.180  Sum_probs=59.9

Q ss_pred             CCCEEEEecCCCCCc------HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCE
Q 023301           29 QFDHIVIETTGLAKP------APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADR   99 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p------~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~   99 (284)
                      .....|++|+|+.++      .+-...+.. ..+...-.++.++.|+|+........        ..+..++   ...-+
T Consensus        78 ~~~~~l~DtpG~~~~~~~~~~~~~~~~~~~-~~~~~~~~~d~vi~v~d~~~~~~~~~--------~~~~~~l~~~~~p~i  148 (223)
T 4dhe_A           78 EPVAHLVDLPGYGYAEVPGAAKAHWEQLLS-SYLQTRPQLCGMILMMDARRPLTELD--------RRMIEWFAPTGKPIH  148 (223)
T ss_dssp             SCSEEEEECCCCCSSCCCSTHHHHHHHHHH-HHHHHCTTEEEEEEEEETTSCCCHHH--------HHHHHHHGGGCCCEE
T ss_pred             CCcEEEEcCCCCCcccCChhhHHHHHHHHH-HHHhcCcCcCEEEEEEeCCCCCCHHH--------HHHHHHHHhcCCCEE
Confidence            367889999998876      222222211 12222233677999999976321111        1122333   34568


Q ss_pred             EEEccCCCCChhHHH----HHHHHHHHh-----CCCCceeeecc-CCCChhhhh
Q 023301          100 IILNKIDLVTETELG----SLTERIKHI-----NAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       100 ivlnK~D~~~~~~~~----~~~~~l~~~-----np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+||+|+.+..+..    .+.+.++..     ....+++.++. .......++
T Consensus       149 ~v~nK~Dl~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~SA~~g~gv~~l~  202 (223)
T 4dhe_A          149 SLLTKCDKLTRQESINALRATQKSLDAYRDAGYAGKLTVQLFSALKRTGLDDAH  202 (223)
T ss_dssp             EEEECGGGSCHHHHHHHHHHHHHHHHHHHHHTCCSCEEEEEEBTTTTBSHHHHH
T ss_pred             EEEeccccCChhhHHHHHHHHHHHHHhhhhcccCCCCeEEEeecCCCcCHHHHH
Confidence            899999998876643    334445544     45677877653 233444444

>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=96.87  E-value=0.0012  Score=57.58  Aligned_cols=95  Identities=17%  Similarity=0.247  Sum_probs=56.2

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-----hcCEEEEc
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-----YADRIILN  103 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-----~Ad~ivln  103 (284)
                      ....+|++|+|+.+|...+............-..+.++.|+|+.+......        ..+.+++.     ..-++|+|
T Consensus        54 ~~~l~l~DTpG~~~~~~~l~~~~~~~~~~~l~~ad~il~VvD~~~~~~~~~--------~~i~~~l~~~~~~~p~ilV~N  125 (301)
T 1wf3_A           54 RRQIVFVDTPGLHKPMDALGEFMDQEVYEALADVNAVVWVVDLRHPPTPED--------ELVARALKPLVGKVPILLVGN  125 (301)
T ss_dssp             TEEEEEEECCCCCCCCSHHHHHHHHHHHHHTSSCSEEEEEEETTSCCCHHH--------HHHHHHHGGGTTTSCEEEEEE
T ss_pred             CcEEEEecCccccchhhHHHHHHHHHHHHHHhcCCEEEEEEECCCCCChHH--------HHHHHHHHhhcCCCCEEEEEE
Confidence            346789999999998654443221111112236788999999976322110        12234443     44688999


Q ss_pred             cCCCCChhHHHHHHHHHHHhCCCCceeeec
Q 023301          104 KIDLVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       104 K~D~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      |+|+.+.+..  +.+.++.+.+.++++.++
T Consensus       126 K~Dl~~~~~~--~~~~~~~~~~~~~~~~iS  153 (301)
T 1wf3_A          126 KLDAAKYPEE--AMKAYHELLPEAEPRMLS  153 (301)
T ss_dssp             CGGGCSSHHH--HHHHHHHTSTTSEEEECC
T ss_pred             CcccCCchHH--HHHHHHHhcCcCcEEEEe
Confidence            9999875440  344455555556666665

>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=96.66  E-value=0.0051  Score=48.97  Aligned_cols=97  Identities=13%  Similarity=0.187  Sum_probs=56.3

Q ss_pred             CEEEEecCCCCCc------HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEcc
Q 023301           31 DHIVIETTGLAKP------APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p------~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK  104 (284)
                      ...+++++|+.++      .+-...+.. ..+...-.++.++.|+|+.........    .+ .....+....-++|+||
T Consensus        70 ~~~l~Dt~G~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~i~v~d~~~~~~~~~~----~~-~~~~~~~~~p~i~v~nK  143 (195)
T 1svi_A           70 ELHFVDVPGYGFAKVSKSEREAWGRMIE-TYITTREELKAVVQIVDLRHAPSNDDV----QM-YEFLKYYGIPVIVIATK  143 (195)
T ss_dssp             TEEEEECCCBCCCSSCHHHHHHHHHHHH-HHHHHCTTEEEEEEEEETTSCCCHHHH----HH-HHHHHHTTCCEEEEEEC
T ss_pred             cEEEEECCCCCccccCHHHHHHHHHHHH-HHHhhhhcCCEEEEEEECCCCCCHHHH----HH-HHHHHHcCCCEEEEEEC
Confidence            5789999998875      332332221 122222345789999998763221110    00 01123344567899999


Q ss_pred             CCCCChhHHHHHHHHHHH-hC--CCCceeeec
Q 023301          105 IDLVTETELGSLTERIKH-IN--AMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~~~~~~~~l~~-~n--p~a~i~~~~  133 (284)
                      +|+.+..++....+.+++ +.  +..+++.++
T Consensus       144 ~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~S  175 (195)
T 1svi_A          144 ADKIPKGKWDKHAKVVRQTLNIDPEDELILFS  175 (195)
T ss_dssp             GGGSCGGGHHHHHHHHHHHHTCCTTSEEEECC
T ss_pred             cccCChHHHHHHHHHHHHHHcccCCCceEEEE
Confidence            999988777665555554 42  356676665

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=96.57  E-value=0.0039  Score=49.51  Aligned_cols=98  Identities=15%  Similarity=0.149  Sum_probs=56.6

Q ss_pred             CCEEEEecCCCCCc------HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEc
Q 023301           30 FDHIVIETTGLAKP------APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILN  103 (284)
Q Consensus        30 ~d~iiIE~sG~a~p------~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivln  103 (284)
                      ....+++++|+...      ......+.. ..+...-.++.++.|+|+.........    .+ ..........-++|+|
T Consensus        68 ~~~~i~Dt~G~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~vi~v~d~~~~~~~~~~----~~-~~~~~~~~~p~i~v~n  141 (195)
T 3pqc_A           68 SKYYFVDLPGYGYAKVSKKERMLWKRLVE-DYFKNRWSLQMVFLLVDGRIPPQDSDL----MM-VEWMKSLNIPFTIVLT  141 (195)
T ss_dssp             TTEEEEECCCBSSSCCCHHHHHHHHHHHH-HHHHHCTTEEEEEEEEETTSCCCHHHH----HH-HHHHHHTTCCEEEEEE
T ss_pred             CcEEEEECCCCccccCChhhHHHHHHHHH-HHHhcCcCceEEEEEecCCCCCCHHHH----HH-HHHHHHcCCCEEEEEE
Confidence            35789999997653      222222221 122223345789999998653211100    00 1123344567789999


Q ss_pred             cCCCCChhHHHHHHHHHHHhCC---CCceeeec
Q 023301          104 KIDLVTETELGSLTERIKHINA---MAPVKLAK  133 (284)
Q Consensus       104 K~D~~~~~~~~~~~~~l~~~np---~a~i~~~~  133 (284)
                      |+|+.++++++...+.++....   ..+++.++
T Consensus       142 K~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~S  174 (195)
T 3pqc_A          142 KMDKVKMSERAKKLEEHRKVFSKYGEYTIIPTS  174 (195)
T ss_dssp             CGGGSCGGGHHHHHHHHHHHHHSSCCSCEEECC
T ss_pred             ChhcCChHHHHHHHHHHHHHHhhcCCCceEEEe
Confidence            9999987777766666665432   35677665

>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=96.00  E-value=0.019  Score=49.79  Aligned_cols=95  Identities=15%  Similarity=0.181  Sum_probs=53.8

Q ss_pred             CCEEEEecCCCC-CcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccC
Q 023301           30 FDHIVIETTGLA-KPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKI  105 (284)
Q Consensus        30 ~d~iiIE~sG~a-~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~  105 (284)
                      ...++++|+|.. .+...+............-..+.++.|+|+..+...     +    ..+.+++   ...-++++||+
T Consensus        56 ~~i~~iDTpG~~~~~~~~l~~~~~~~~~~~l~~~D~vl~Vvd~~~~~~~-----~----~~i~~~l~~~~~P~ilvlNK~  126 (301)
T 1ega_A           56 YQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTRWTPD-----D----EMVLNKLREGKAPVILAVNKV  126 (301)
T ss_dssp             EEEEEESSSSCCHHHHHHHHHHHTCCTTSCCCCEEEEEEEEETTCCCHH-----H----HHHHHHHHSSSSCEEEEEEST
T ss_pred             eeEEEEECcCCCccchhhHHHHHHHHHHHHHhcCCEEEEEEeCCCCCHH-----H----HHHHHHHHhcCCCEEEEEECc
Confidence            357889999998 565444322221122223367788999999763221     1    1223344   46779999999


Q ss_pred             CCCC-hhHHHHHHHHHHHhCCCCceeeec
Q 023301          106 DLVT-ETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       106 D~~~-~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      |+.+ .+.+....+.+.+..+...++.++
T Consensus       127 D~~~~~~~~~~~l~~l~~~~~~~~~i~iS  155 (301)
T 1ega_A          127 DNVQEKADLLPHLQFLASQMNFLDIVPIS  155 (301)
T ss_dssp             TTCCCHHHHHHHHHHHHTTSCCSEEEECC
T ss_pred             ccCccHHHHHHHHHHHHHhcCcCceEEEE
Confidence            9987 444434434344333334565554

>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=95.10  E-value=0.17  Score=46.26  Aligned_cols=94  Identities=24%  Similarity=0.330  Sum_probs=53.4

Q ss_pred             CCCCEEEEecCCCCCcH-HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCC
Q 023301           28 GQFDHIVIETTGLAKPA-PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKID  106 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~-~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D  106 (284)
                      ..+|+|||+|.|..... .+...+.   .+.....-+.++.|+|+..-.....      ... ...+....+.||+||.|
T Consensus       181 ~~~DvVIIDTaGrl~~d~~lm~el~---~i~~~~~pd~vlLVvDA~~gq~a~~------~a~-~f~~~~~i~gVIlTKlD  250 (443)
T 3dm5_A          181 KGVDIIIVDTAGRHKEDKALIEEMK---QISNVIHPHEVILVIDGTIGQQAYN------QAL-AFKEATPIGSIIVTKLD  250 (443)
T ss_dssp             TTCSEEEEECCCCSSCCHHHHHHHH---HHHHHHCCSEEEEEEEGGGGGGHHH------HHH-HHHHSCTTEEEEEECCS
T ss_pred             CCCCEEEEECCCcccchHHHHHHHH---HHHHhhcCceEEEEEeCCCchhHHH------HHH-HHHhhCCCeEEEEECCC
Confidence            57999999999977633 3444332   1222334567999999987432211      111 12223345679999999


Q ss_pred             CCChhHHHHHHHHHHHhCCCCceeeeccC
Q 023301          107 LVTETELGSLTERIKHINAMAPVKLAKYG  135 (284)
Q Consensus       107 ~~~~~~~~~~~~~l~~~np~a~i~~~~~g  135 (284)
                      .....  ..+...+..  ...||.....|
T Consensus       251 ~~~~g--G~~ls~~~~--~g~PI~fig~G  275 (443)
T 3dm5_A          251 GSAKG--GGALSAVAA--TGAPIKFIGTG  275 (443)
T ss_dssp             SCSSH--HHHHHHHHT--TCCCEEEEECS
T ss_pred             Ccccc--cHHHHHHHH--HCCCEEEEEcC
Confidence            86532  223333332  34677655544

>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=94.39  E-value=0.066  Score=49.51  Aligned_cols=96  Identities=11%  Similarity=0.053  Sum_probs=50.4

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhc--CCccch-HHHHHHHhhc-CEEEEcc
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEV--KPRFVV-NEAVEQVAYA-DRIILNK  104 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~--~~~~~~-~~~~~Qi~~A-d~ivlnK  104 (284)
                      ...+.|++|+|..+........        .-..+.+|.|+|+..-... ...  .+.... ......+... =+||+||
T Consensus       110 ~~~~~iiDTPG~~~f~~~~~~~--------~~~aD~~llVvDa~~g~~~-~~~~~~~qt~e~~~~~~~~~~~~iIvviNK  180 (483)
T 3p26_A          110 RANFTIVDAPGHRDFVPNAIMG--------ISQADMAILCVDCSTNAFE-SGFDLDGQTKEHMLLASSLGIHNLIIAMNK  180 (483)
T ss_dssp             SCEEEEECCCCCGGGHHHHHHH--------HTTCSEEEEEEECCC-------CCCCHHHHHHHHHHHHTTCCCEEEEEEC
T ss_pred             CceEEEEECCCcHHHHHHHHHh--------hhhCCEEEEEEECCCCccc-cccchhhhHHHHHHHHHHcCCCcEEEEEEC
Confidence            3567899999997654322221        1246789999999873210 000  000000 0112333333 3567899


Q ss_pred             CCCCC--hhHHHHHHHHHHHh----C--C-CCceeeec
Q 023301          105 IDLVT--ETELGSLTERIKHI----N--A-MAPVKLAK  133 (284)
Q Consensus       105 ~D~~~--~~~~~~~~~~l~~~----n--p-~a~i~~~~  133 (284)
                      +|+.+  ++..+.+.+.++.+    .  + .++++.++
T Consensus       181 ~Dl~~~~~~~~~~i~~~~~~~l~~~g~~~~~~~~i~iS  218 (483)
T 3p26_A          181 MDNVDWSQQRFEEIKSKLLPYLVDIGFFEDNINWVPIS  218 (483)
T ss_dssp             GGGGTTCHHHHHHHHHHHHHHHHHHTCCGGGEEEEECC
T ss_pred             cCcccchHHHHHHHHHHHHHHHHHcCCCcccceEEEEe
Confidence            99986  44455555555443    2  1 45667654

>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=94.19  E-value=0.16  Score=45.70  Aligned_cols=100  Identities=19%  Similarity=0.221  Sum_probs=56.7

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH--HhhhhcCCccchHHHHHHHhh-cCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM--QHLNEVKPRFVVNEAVEQVAY-ADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~--~~l~~~~~~~~~~~~~~Qi~~-Ad~ivlnK~D  106 (284)
                      ..+.|++++|-.+.......        ..-..+.++.|+|+....  .+..+    .  -....++.. .=++++||+|
T Consensus        75 ~~~~iiDtPGh~~~~~~~~~--------~~~~~D~~ilVvda~~~~~~~qt~~----~--~~~~~~~~~~~iivviNK~D  140 (403)
T 3sjy_A           75 RRISFIDAPGHEVLMATMLS--------GAALMDGAILVVAANEPFPQPQTRE----H--FVALGIIGVKNLIIVQNKVD  140 (403)
T ss_dssp             EEEEEEECCCCGGGHHHHHH--------HHTTCSEEEEEEETTSCSSCHHHHH----H--HHHHHHHTCCCEEEEEECGG
T ss_pred             ceEEEEECCCcHHHHHHHHH--------HHhhCCEEEEEEECCCCCCcHHHHH----H--HHHHHHcCCCCEEEEEECcc
Confidence            45789999996554332211        122467899999998742  11111    0  012333443 2367889999


Q ss_pred             CCChhHHHHHHHHHHHh----C-CCCceeeecc-CCCChhhhh
Q 023301          107 LVTETELGSLTERIKHI----N-AMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       107 ~~~~~~~~~~~~~l~~~----n-p~a~i~~~~~-g~v~~~~l~  143 (284)
                      +++.++.....+.+++.    + ..++++.++. .......|+
T Consensus       141 l~~~~~~~~~~~~i~~~l~~~~~~~~~ii~vSA~~g~gi~~L~  183 (403)
T 3sjy_A          141 VVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLI  183 (403)
T ss_dssp             GSCHHHHHHHHHHHHHHHTTSTTTTCCEEECBTTTTBSHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHHhhCCCCCEEEEEECCCCcChHHHH
Confidence            99887665555555443    2 2567887653 233444444

>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=94.15  E-value=0.073  Score=42.87  Aligned_cols=85  Identities=15%  Similarity=0.219  Sum_probs=47.2

Q ss_pred             CCCEEEEecCCCCCcHH-HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHH-HH---hhcCEEEEc
Q 023301           29 QFDHIVIETTGLAKPAP-VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVE-QV---AYADRIILN  103 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~-i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~-Qi---~~Ad~ivln  103 (284)
                      .....+++++|...... +...+        .-..+.+|.|+|+.++...+.... ......+.. +.   ...=+||.|
T Consensus        53 ~~~~~i~Dt~G~~~~~~~~~~~~--------~~~~~~~i~v~d~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~piilv~n  123 (214)
T 2fh5_B           53 GNSLTLIDLPGHESLRFQLLDRF--------KSSARAVVFVVDSAAFQREVKDVA-EFLYQVLIDSMALKNSPSLLIACN  123 (214)
T ss_dssp             CCEEEEEECCCCHHHHHHHHHHH--------GGGEEEEEEEEETTTHHHHHHHHH-HHHHHHHHHHHTSTTCCEEEEEEE
T ss_pred             ccEEEEEECCCChhHHHHHHHHH--------HhhCCEEEEEEECCCcCHHHHHHH-HHHHHHHhhhhhcccCCCEEEEEE
Confidence            34578889999865444 33221        124567999999988644322210 001111111 11   123478889


Q ss_pred             cCCCCChhHHHHHHHHHHH
Q 023301          104 KIDLVTETELGSLTERIKH  122 (284)
Q Consensus       104 K~D~~~~~~~~~~~~~l~~  122 (284)
                      |+|+.+....+.+.+.+++
T Consensus       124 K~Dl~~~~~~~~~~~~l~~  142 (214)
T 2fh5_B          124 KQDIAMAKSAKLIQQQLEK  142 (214)
T ss_dssp             CTTSTTCCCHHHHHHHHHH
T ss_pred             CCCCCCcccHHHHHHHHHH
Confidence            9999876555555555554

>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=94.06  E-value=0.01  Score=50.70  Aligned_cols=75  Identities=16%  Similarity=0.246  Sum_probs=42.2

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccc-e---eeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEcc
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQ-Y---VKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNK  104 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~-~---~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK  104 (284)
                      .....+++++|..+...+...-..+..+.. .   -..+.+|.|+|+.++...+.      . ..........-++|+||
T Consensus        49 ~~~~~liDtpG~~~~~~~~~~~~~~e~i~~~~~~~~~~d~ii~VvD~~~~~~~~~------~-~~~l~~~~~p~ivv~NK  121 (274)
T 3i8s_A           49 DHQVTLVDLPGTYSLTTISSQTSLDEQIACHYILSGDADLLINVVDASNLERNLY------L-TLQLLELGIPCIVALNM  121 (274)
T ss_dssp             SCEEEEEECCCCSCSCC----CCHHHHHHHHHHHHTCCSEEEEEEEGGGHHHHHH------H-HHHHHHHTCCEEEEEEC
T ss_pred             CCceEEEECcCCCccccccccCCHHHHHHHHHHhhcCCCEEEEEecCCChHHHHH------H-HHHHHhcCCCEEEEEEC
Confidence            446789999999886532110000000100 1   15678999999998654321      0 01123345567899999


Q ss_pred             CCCCCh
Q 023301          105 IDLVTE  110 (284)
Q Consensus       105 ~D~~~~  110 (284)
                      +|+.+.
T Consensus       122 ~Dl~~~  127 (274)
T 3i8s_A          122 LDIAEK  127 (274)
T ss_dssp             HHHHHH
T ss_pred             ccchhh
Confidence            998654

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=93.66  E-value=0.12  Score=40.84  Aligned_cols=104  Identities=17%  Similarity=0.175  Sum_probs=54.6

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH--H--------hhcC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ--V--------AYAD   98 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q--i--------~~Ad   98 (284)
                      .....|++++|......+....     +   -..+.+|.|+|+...... .+.. .++ ..+...  +        ...-
T Consensus        62 ~~~~~i~Dt~G~~~~~~~~~~~-----~---~~~d~ii~v~D~~~~~s~-~~~~-~~~-~~~~~~~~~~~~~~~~~~~pi  130 (199)
T 4bas_A           62 RVAFTVFDMGGAKKFRGLWETY-----Y---DNIDAVIFVVDSSDHLRL-CVVK-SEI-QAMLKHEDIRRELPGGGRVPF  130 (199)
T ss_dssp             TEEEEEEEECCSGGGGGGGGGG-----C---TTCSEEEEEEETTCGGGH-HHHH-HHH-HHHHTSHHHHSBCTTSCBCCE
T ss_pred             CEEEEEEECCCCHhHHHHHHHH-----H---hcCCEEEEEEECCcHHHH-HHHH-HHH-HHHHhChhhhhcccccCCCCE
Confidence            3456789999986554332221     1   246789999999875321 1110 011 111111  1        3456


Q ss_pred             EEEEccCCCCChhHHHHHHHHHHH--h--CCCCceeeecc-CCCChhhhh
Q 023301           99 RIILNKIDLVTETELGSLTERIKH--I--NAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus        99 ~ivlnK~D~~~~~~~~~~~~~l~~--~--np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +||+||+|+.+....+++.+.+..  +  ....++++++. .......++
T Consensus       131 ilv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~~l~  180 (199)
T 4bas_A          131 LFFANKMDAAGAKTAAELVEILDLTTLMGDHPFVIFASNGLKGTGVHEGF  180 (199)
T ss_dssp             EEEEECTTSTTCCCHHHHHHHHTHHHHHTTSCEEEEECBTTTTBTHHHHH
T ss_pred             EEEEECcCCCCCCCHHHHHHHhcchhhccCCeeEEEEeeCCCccCHHHHH
Confidence            788899999877444444444331  1  13456666653 233444443

>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=93.26  E-value=0.11  Score=47.87  Aligned_cols=108  Identities=15%  Similarity=0.033  Sum_probs=47.6

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-hcCEEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-YADRIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-~Ad~ivlnK~D~  107 (284)
                      .....|++|+|..++....+.+.....+...-..+.++.|+|+....... +.  ... ..+..++. ..-++|+||+|+
T Consensus       280 g~~l~liDT~G~~~~~~~ve~~gi~~~~~~~~~aD~vl~VvD~s~~~s~~-~~--~~~-~~~l~~l~~~piIvV~NK~Dl  355 (476)
T 3gee_A          280 KTMFRLTDTAGLREAGEEIEHEGIRRSRMKMAEADLILYLLDLGTERLDD-EL--TEI-RELKAAHPAAKFLTVANKLDR  355 (476)
T ss_dssp             TEEEEEEC--------------------CCCSSCSEEEEEEETTTCSSGG-GH--HHH-HHHHHHCTTSEEEEEEECTTS
T ss_pred             CeEEEEEECCCCCcchhHHHHHHHHHHHhhcccCCEEEEEEECCCCcchh-hh--HHH-HHHHHhcCCCCEEEEEECcCC
Confidence            34678999999988776555431111122234678899999998743210 00  000 11233333 456788899999


Q ss_pred             CChhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          108 VTETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       108 ~~~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      .+......  +.+.+.+ ..+++.++. .....+.++
T Consensus       356 ~~~~~~~~--~~l~~~~-~~~~i~vSAktg~GI~eL~  389 (476)
T 3gee_A          356 AANADALI--RAIADGT-GTEVIGISALNGDGIDTLK  389 (476)
T ss_dssp             CTTTHHHH--HHHHHHH-TSCEEECBTTTTBSHHHHH
T ss_pred             CCccchhH--HHHHhcC-CCceEEEEECCCCCHHHHH
Confidence            87665432  2333331 145666553 233444444

>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=93.14  E-value=0.22  Score=38.27  Aligned_cols=86  Identities=14%  Similarity=0.114  Sum_probs=48.1

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh------cCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY------ADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~------Ad~ivlnK  104 (284)
                      ...+++++|......+.....        -..+.++.|+|+.+.... .+.      ..+..++..      .=+||+||
T Consensus        65 ~~~l~Dt~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~------~~~~~~~~~~~~~~~piilv~nK  129 (179)
T 1z0f_A           65 KLQIWDTAGQERFRAVTRSYY--------RGAAGALMVYDITRRSTY-NHL------SSWLTDARNLTNPNTVIILIGNK  129 (179)
T ss_dssp             EEEEEECTTGGGTCHHHHHHH--------HTCSEEEEEEETTCHHHH-HTH------HHHHHHHHHHSCTTCEEEEEEEC
T ss_pred             EEEEEECCCChHhhhhHHHHh--------ccCCEEEEEEeCcCHHHH-HHH------HHHHHHHHHhcCCCCcEEEEEEC
Confidence            457789999665444333221        135779999999875432 211      112222222      23788899


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +|+.+..+  .+.++++.+..+  .+++.++
T Consensus       130 ~Dl~~~~~~~~~~~~~~~~~~~--~~~~~~S  158 (179)
T 1z0f_A          130 ADLEAQRDVTYEEAKQFAEENG--LLFLEAS  158 (179)
T ss_dssp             TTCGGGCCSCHHHHHHHHHHTT--CEEEECC
T ss_pred             cccccccccCHHHHHHHHHHcC--CEEEEEe
Confidence            99964322  345555555443  5666654

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=93.07  E-value=0.12  Score=39.48  Aligned_cols=96  Identities=13%  Similarity=0.054  Sum_probs=52.6

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh--------hcCEEEE
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA--------YADRIIL  102 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~--------~Ad~ivl  102 (284)
                      ...+++++|......+.....        -..+.++.|+|+.+.... .+.      .....++.        ..=+||+
T Consensus        52 ~~~~~Dt~G~~~~~~~~~~~~--------~~~~~~i~v~d~~~~~~~-~~~------~~~~~~i~~~~~~~~~~pii~v~  116 (172)
T 2erx_A           52 TLQITDTTGSHQFPAMQRLSI--------SKGHAFILVYSITSRQSL-EEL------KPIYEQICEIKGDVESIPIMLVG  116 (172)
T ss_dssp             EEEEEECCSCSSCHHHHHHHH--------HHCSEEEEEEETTCHHHH-HTT------HHHHHHHHHHHC---CCCEEEEE
T ss_pred             EEEEEECCCchhhHHHHHHhc--------ccCCEEEEEEECcCHHHH-HHH------HHHHHHHHHHhCCCCCCCEEEEE
Confidence            467899999887766544321        125678999999874432 211      11122222        2347888


Q ss_pred             ccCCCCChhHH--HHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          103 NKIDLVTETEL--GSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       103 nK~D~~~~~~~--~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      ||+|+.+..++  ....+..+..+  .+++.++. .......++
T Consensus       117 nK~Dl~~~~~v~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  158 (172)
T 2erx_A          117 NKCDESPSREVQSSEAEALARTWK--CAFMETSAKLNHNVKELF  158 (172)
T ss_dssp             ECGGGGGGCCSCHHHHHHHHHHHT--CEEEECBTTTTBSHHHHH
T ss_pred             EccccccccccCHHHHHHHHHHhC--CeEEEecCCCCcCHHHHH
Confidence            99998654332  23334444333  56666553 233444444

>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=93.02  E-value=0.17  Score=46.86  Aligned_cols=91  Identities=15%  Similarity=0.166  Sum_probs=52.7

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH-HhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM-QHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~-~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      ..+.|++++|..+..   ...     ....-..+.++.|+|+..-. .+..+    .+  .+..++...-+|++||+|+.
T Consensus        73 ~~i~iiDtPGh~~~~---~~~-----~~~~~~aD~~ilVvda~~g~~~qt~e----~l--~~~~~~~ip~IvviNK~Dl~  138 (482)
T 1wb1_A           73 YRITLVDAPGHADLI---RAV-----VSAADIIDLALIVVDAKEGPKTQTGE----HM--LILDHFNIPIIVVITKSDNA  138 (482)
T ss_dssp             EEEEECCCSSHHHHH---HHH-----HHHTTSCCEEEEEEETTTCSCHHHHH----HH--HHHHHTTCCBCEEEECTTSS
T ss_pred             EEEEEEECCChHHHH---HHH-----HHHHhhCCEEEEEEecCCCccHHHHH----HH--HHHHHcCCCEEEEEECCCcc
Confidence            356888999964422   111     11123467899999997621 11010    01  12344555669999999999


Q ss_pred             ChhHHHHHHHHHHHh------CCCCceeeecc
Q 023301          109 TETELGSLTERIKHI------NAMAPVKLAKY  134 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~------np~a~i~~~~~  134 (284)
                      +++.++.+.+.++++      .+..+++.++.
T Consensus       139 ~~~~~~~~~~~l~~~l~~~~~~~~~~ii~vSA  170 (482)
T 1wb1_A          139 GTEEIKRTEMIMKSILQSTHNLKNSSIIPISA  170 (482)
T ss_dssp             CHHHHHHHHHHHHHHHHHSSSGGGCCEEECCT
T ss_pred             cchhHHHHHHHHHHHHhhhcccccceEEEEEC
Confidence            876666555544442      12467776653

>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=92.80  E-value=0.42  Score=35.96  Aligned_cols=101  Identities=10%  Similarity=0.135  Sum_probs=53.6

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D  106 (284)
                      .+..+++++|......+.....        -..+.++.|+|+...... .+.. .+ ...+....   ...=++|+||+|
T Consensus        51 ~~~~~~D~~G~~~~~~~~~~~~--------~~~~~~i~v~d~~~~~~~-~~~~-~~-~~~i~~~~~~~~~p~iiv~nK~D  119 (166)
T 2ce2_X           51 CLLDILDTAGQEEYSAMRDQYM--------RTGEGFLCVFAINNTKSF-EDIH-QY-REQIKRVKDSDDVPMVLVGNKSD  119 (166)
T ss_dssp             EEEEEEECCCCSSCCHHHHHHH--------HHCSEEEEEEETTCHHHH-HHHH-HH-HHHHHHHHTCSCCCEEEEEECTT
T ss_pred             EEEEEEECCCchhhhHHHHHhh--------ccCCEEEEEEECCCHHHH-HHHH-HH-HHHHHHhcCCCCCcEEEEEEchh
Confidence            3457899999887666544322        135678999998765432 1110 00 01111111   233488899999


Q ss_pred             CCChh-HHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          107 LVTET-ELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       107 ~~~~~-~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +.+.+ ..+.+.+..+..+  .+++.++. .......++
T Consensus       120 l~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  156 (166)
T 2ce2_X          120 LAARTVESRQAQDLARSYG--IPYIETSAKTRQGVEDAF  156 (166)
T ss_dssp             CSCCCSCHHHHHHHHHHHT--CCEEEECTTTCTTHHHHH
T ss_pred             hhhcccCHHHHHHHHHHcC--CeEEEecCCCCCCHHHHH
Confidence            87532 2344445555444  46776653 233344443

>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=92.79  E-value=0.019  Score=50.72  Aligned_cols=101  Identities=13%  Similarity=0.165  Sum_probs=50.3

Q ss_pred             CCEEEEecCCCCCcHH----HHHHhcccccccceeeeceEEEEEcccchH--HhhhhcCCccchHHHHHHHh--------
Q 023301           30 FDHIVIETTGLAKPAP----VIETFCTDELVSQYVKLDGVITLVDSKHAM--QHLNEVKPRFVVNEAVEQVA--------   95 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~----i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~--~~l~~~~~~~~~~~~~~Qi~--------   95 (284)
                      ...+|++++|+.+...    +...     .++..-..+.+|.|+|+..+.  ..+.+.      ..+..++.        
T Consensus       206 ~~~~l~DtPG~i~~a~~~~~l~~~-----fl~~i~~~d~ll~VvD~s~~~~~~~~~~~------~~~~~eL~~~~~~l~~  274 (342)
T 1lnz_A          206 RSFVMADLPGLIEGAHQGVGLGHQ-----FLRHIERTRVIVHVIDMSGLEGRDPYDDY------LTINQELSEYNLRLTE  274 (342)
T ss_dssp             CEEEEEEHHHHHHHTTCTTTTHHH-----HHHHHHHCCEEEEEEESSCSSCCCHHHHH------HHHHHHHHHSCSSTTT
T ss_pred             ceEEEecCCCCcccccccchhHHH-----HHHHHHhccEEEEEEECCcccccChHHHH------HHHHHHHHHhhhhhcC
Confidence            4577888888633111    1111     122223467899999996531  111110      11223333        


Q ss_pred             hcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301           96 YADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus        96 ~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      ..-+||+||+|+.+..+  .+.+..+.++...+++.+|. ....++.++
T Consensus       275 ~p~ilV~NK~Dl~~~~e--~~~~l~~~l~~~~~v~~iSA~tg~gi~eL~  321 (342)
T 1lnz_A          275 RPQIIVANKMDMPEAAE--NLEAFKEKLTDDYPVFPISAVTREGLRELL  321 (342)
T ss_dssp             SCBCBEEECTTSTTHHH--HHHHHHHHCCSCCCBCCCSSCCSSTTHHHH
T ss_pred             CCEEEEEECccCCCCHH--HHHHHHHHhhcCCCEEEEECCCCcCHHHHH
Confidence            34589999999986532  33333444443355665543 233344443

>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=92.64  E-value=0.39  Score=36.25  Aligned_cols=90  Identities=12%  Similarity=0.150  Sum_probs=48.9

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D~  107 (284)
                      ...+++++|......+.....        -..+.++.|+|+...... .... .++ ..+....   ...=++|+||+|+
T Consensus        53 ~~~l~D~~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~~-~~~-~~i~~~~~~~~~piilv~nK~Dl  121 (168)
T 1u8z_A           53 QIDILDTAGQEDYAAIRDNYF--------RSGEGFLCVFSITEMESF-AATA-DFR-EQILRVKEDENVPFLLVGNKSDL  121 (168)
T ss_dssp             EEEEEECCC---CHHHHHHHH--------HHCSEEEEEEETTCHHHH-HHHH-HHH-HHHHHHHCCTTSCEEEEEECGGG
T ss_pred             EEEEEECCCcchhHHHHHHHh--------hcCCEEEEEEECCCHHHH-HHHH-HHH-HHHHHhcCCCCCcEEEEEECccc
Confidence            567889999877666544322        135678999999875432 1110 011 1122222   2234788999998


Q ss_pred             CChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          108 VTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       108 ~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      .+..+  .+.+++..+..+  .+++.++
T Consensus       122 ~~~~~~~~~~~~~~~~~~~--~~~~~~S  147 (168)
T 1u8z_A          122 EDKRQVSVEEAKNRADQWN--VNYVETS  147 (168)
T ss_dssp             GGGCCSCHHHHHHHHHHHT--CEEEECC
T ss_pred             cccCccCHHHHHHHHHHcC--CeEEEeC
Confidence            65322  345555565554  4666654

>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=92.63  E-value=0.37  Score=37.75  Aligned_cols=93  Identities=13%  Similarity=0.140  Sum_probs=50.3

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH-----HhhcCEEEEcc
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ-----VAYADRIILNK  104 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q-----i~~Ad~ivlnK  104 (284)
                      ....+++++|......+...     .+   -..+.++.|+|+.+.... .+.. .++ ..+...     -...=+||+||
T Consensus        67 ~~~~l~Dt~G~~~~~~~~~~-----~~---~~~d~ii~v~d~~~~~s~-~~~~-~~~-~~~~~~~~~~~~~~piilv~nK  135 (190)
T 2h57_A           67 LSFTVFDMSGQGRYRNLWEH-----YY---KEGQAIIFVIDSSDRLRM-VVAK-EEL-DTLLNHPDIKHRRIPILFFANK  135 (190)
T ss_dssp             CEEEEEEECCSTTTGGGGGG-----GG---GGCSEEEEEEETTCHHHH-HHHH-HHH-HHHHHSTTTTTSCCCEEEEEEC
T ss_pred             EEEEEEECCCCHHHHHHHHH-----HH---hcCCEEEEEEECCCHHHH-HHHH-HHH-HHHHhChhhccCCCeEEEEEeC
Confidence            46788999997765443221     11   245789999999874321 1110 011 111111     12234788899


Q ss_pred             CCCCChhHHHHHHHHHH--HhC-CCCceeeec
Q 023301          105 IDLVTETELGSLTERIK--HIN-AMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~~~~~~~~l~--~~n-p~a~i~~~~  133 (284)
                      +|+.+....+.+.+.++  .+. ...+++.++
T Consensus       136 ~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~S  167 (190)
T 2h57_A          136 MDLRDAVTSVKVSQLLCLENIKDKPWHICASD  167 (190)
T ss_dssp             TTSTTCCCHHHHHHHHTGGGCCSSCEEEEECB
T ss_pred             cCcccCCCHHHHHHHhChhhccCCceEEEEcc
Confidence            99977555556666553  222 234555554

>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=92.62  E-value=0.54  Score=37.14  Aligned_cols=100  Identities=13%  Similarity=0.164  Sum_probs=56.1

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D~  107 (284)
                      ...|++++|......+.....        -..+.++.|+|+.+.... ... ..++ ..+....   ...=+||+||+|+
T Consensus        63 ~~~l~Dt~G~~~~~~~~~~~~--------~~~~~~i~v~d~~~~~s~-~~~-~~~~-~~i~~~~~~~~~piilv~nK~Dl  131 (206)
T 2bov_A           63 QIDILDTAGQEDYAAIRDNYF--------RSGEGFLCVFSITEMESF-AAT-ADFR-EQILRVKEDENVPFLLVGNKSDL  131 (206)
T ss_dssp             EEEEEECCCTTCCHHHHHHHH--------HHCSEEEEEEETTCHHHH-HHH-HHHH-HHHHHHTTCSCCCEEEEEECTTC
T ss_pred             EEEEEcCCChhhhHHHHHHHH--------hhCCEEEEEEECCCHHHH-HHH-HHHH-HHHHHhcCCCCCCEEEEEeccCc
Confidence            567889999887766554322        135678999999875432 111 0010 1111211   1233788999999


Q ss_pred             CChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          108 VTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       108 ~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      .+..+  .+.+.++.+..+  .+++.++. .......++
T Consensus       132 ~~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~g~gi~~l~  168 (206)
T 2bov_A          132 EDKRQVSVEEAKNRAEQWN--VNYVETSAKTRANVDKVF  168 (206)
T ss_dssp             GGGCCSCHHHHHHHHHHHT--CEEEEECTTTCTTHHHHH
T ss_pred             cccccccHHHHHHHHHHhC--CeEEEEeCCCCCCHHHHH
Confidence            65322  455666666554  46776653 233455544

>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=92.53  E-value=0.054  Score=49.89  Aligned_cols=103  Identities=17%  Similarity=0.201  Sum_probs=45.9

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-hcCEEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-YADRIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-~Ad~ivlnK~D~  107 (284)
                      .....+++|+|+.++....+.+.........-..+.++.|+|+........        ..+..++. ..-++|+||+|+
T Consensus       271 g~~v~liDT~G~~~~~~~ve~~gi~~~~~~~~~aD~vl~VvD~s~~~~~~~--------~~i~~~l~~~piivV~NK~Dl  342 (462)
T 3geh_A          271 GIPVQVLDTAGIRETSDQVEKIGVERSRQAANTADLVLLTIDAATGWTTGD--------QEIYEQVKHRPLILVMNKIDL  342 (462)
T ss_dssp             TEEEEECC--------------------CCCCSCSEEEEEEETTTCSCHHH--------HHHHHHHTTSCEEEEEECTTS
T ss_pred             CEEEEEEECCccccchhHHHHHHHHHHhhhhhcCCEEEEEeccCCCCCHHH--------HHHHHhccCCcEEEEEECCCC
Confidence            446789999999887665554321112222335688999999986322111        12233433 356788899999


Q ss_pred             CChhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          108 VTETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       108 ~~~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      .+.....    .++.+....+++.++. ....++.++
T Consensus       343 ~~~~~~~----~~~~~~~~~~~i~iSAktg~Gi~eL~  375 (462)
T 3geh_A          343 VEKQLIT----SLEYPENITQIVHTAAAQKQGIDSLE  375 (462)
T ss_dssp             SCGGGST----TCCCCTTCCCEEEEBTTTTBSHHHHH
T ss_pred             CcchhhH----HHHHhccCCcEEEEECCCCCCHHHHH
Confidence            8765433    1222223455665543 233344443

>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=92.51  E-value=0.17  Score=40.17  Aligned_cols=101  Identities=12%  Similarity=0.117  Sum_probs=51.0

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH------hhcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV------AYADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi------~~Ad~ivlnK  104 (284)
                      ...|++++|......    +.. ..+   -..+.+|.|+|+...... .+. ..++ ..+....      ...=+||+||
T Consensus        58 ~~~l~Dt~G~~~~~~----~~~-~~~---~~~d~~i~v~d~~~~~s~-~~~-~~~~-~~~~~~~~~~~~~~~piilv~nK  126 (207)
T 1vg8_A           58 TMQIWDTAGQERFQS----LGV-AFY---RGADCCVLVFDVTAPNTF-KTL-DSWR-DEFLIQASPRDPENFPFVVLGNK  126 (207)
T ss_dssp             EEEEEEECSSGGGSC----SCC-GGG---TTCSEEEEEEETTCHHHH-HTH-HHHH-HHHHHHHCCSSGGGSCEEEEEEC
T ss_pred             EEEEEeCCCcHHHHH----hHH-HHH---hCCcEEEEEEECCCHHHH-HHH-HHHH-HHHHHhcccccCCCCcEEEEEEC
Confidence            567889999543322    111 111   246789999999875432 111 0011 1112221      2234788899


Q ss_pred             CCCCChh-HHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTET-ELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~-~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+.. ..+.+.++.+ .....+++.++. .......++
T Consensus       127 ~Dl~~~~~~~~~~~~~~~-~~~~~~~~~~Sa~~g~gi~~l~  166 (207)
T 1vg8_A          127 IDLENRQVATKRAQAWCY-SKNNIPYFETSAKEAINVEQAF  166 (207)
T ss_dssp             TTSSCCCSCHHHHHHHHH-HTTSCCEEECBTTTTBSHHHHH
T ss_pred             CCCcccccCHHHHHHHHH-hcCCceEEEEeCCCCCCHHHHH
Confidence            9997432 2233444333 244567777653 233444444

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=92.49  E-value=0.27  Score=45.71  Aligned_cols=73  Identities=16%  Similarity=0.305  Sum_probs=43.8

Q ss_pred             CCCCEEEEecCCCCCcH-HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCC
Q 023301           28 GQFDHIVIETTGLAKPA-PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKID  106 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~-~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D  106 (284)
                      ..+|+|||+|+|..... .+...+..   ....+..+.++.|||+..-...+.      ....+.+. ...+.||+||+|
T Consensus       182 ~~~DvvIIDTpG~~~~~~~l~~el~~---~~~~i~pd~vllVvDa~~g~~~~~------~a~~~~~~-~~i~gvVlNK~D  251 (504)
T 2j37_W          182 ENFEIIIVDTSGRHKQEDSLFEEMLQ---VANAIQPDNIVYVMDASIGQACEA------QAKAFKDK-VDVASVIVTKLD  251 (504)
T ss_dssp             TTCCEEEEEECCCCTTCHHHHHHHHH---HHHHHCCSEEEEEEETTCCTTHHH------HHHHHHHH-HCCCCEEEECTT
T ss_pred             CCCcEEEEeCCCCcccchhHHHHHHH---HHhhhcCceEEEEEeccccccHHH------HHHHHHhh-cCceEEEEeCCc
Confidence            57899999999998753 33333321   111235677899999987432111      11111221 223789999999


Q ss_pred             CCCh
Q 023301          107 LVTE  110 (284)
Q Consensus       107 ~~~~  110 (284)
                      ....
T Consensus       252 ~~~~  255 (504)
T 2j37_W          252 GHAK  255 (504)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            8653

>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=92.47  E-value=0.4  Score=37.05  Aligned_cols=100  Identities=13%  Similarity=0.156  Sum_probs=54.9

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D~  107 (284)
                      ...|++++|......+.....        -..+.++.|+|+...... .... .+ ...+....   ...=+||+||+|+
T Consensus        67 ~~~l~Dt~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~~-~~-~~~i~~~~~~~~~piilv~nK~Dl  135 (187)
T 2a9k_A           67 QIDILDTAGQEDYAAIRDNYF--------RSGEGFLCVFSITEMESF-AATA-DF-REQILRVKEDENVPFLLVGNKSDL  135 (187)
T ss_dssp             EEEEEECCCTTCCHHHHHHHH--------HHCSEEEEEEETTCHHHH-HHHH-HH-HHHHHHHHCCTTCCEEEEEECGGG
T ss_pred             EEEEEECCCCcccHHHHHHHh--------ccCCEEEEEEECcCHHHH-HHHH-HH-HHHHHHhcCCCCCCEEEEEECccc
Confidence            567899999887766554322        135678999999875432 1110 01 11122222   1233788899998


Q ss_pred             CChh--HHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          108 VTET--ELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       108 ~~~~--~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      .+..  ..+.++++.+..+  .+++.++. .......++
T Consensus       136 ~~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  172 (187)
T 2a9k_A          136 EDKRQVSVEEAKNRAEQWN--VNYVETSAKTRANVDKVF  172 (187)
T ss_dssp             GGGCCSCHHHHHHHHHHTT--CEEEECCTTTCTTHHHHH
T ss_pred             cccCccCHHHHHHHHHHcC--CeEEEeCCCCCCCHHHHH
Confidence            6532  2345555555544  46666553 233444443

>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=92.46  E-value=0.62  Score=36.17  Aligned_cols=87  Identities=17%  Similarity=0.139  Sum_probs=49.8

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-------hhcCEEEE
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-------AYADRIIL  102 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-------~~Ad~ivl  102 (284)
                      ....+++++|......+.....        -..+.+|.|+|+.+.... .+.      .....++       ...-+||+
T Consensus        70 ~~~~l~Dt~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~------~~~~~~i~~~~~~~~~piilv~  134 (195)
T 3bc1_A           70 IHLQLWDTAGLERFRSLTTAFF--------RDAMGFLLLFDLTNEQSF-LNV------RNWISQLQMHAYSENPDIVLCG  134 (195)
T ss_dssp             EEEEEEEECCSGGGHHHHHHTT--------TTCSEEEEEEETTCHHHH-HTH------HHHHHHHHHHSSSSSCCEEEEE
T ss_pred             EEEEEEeCCCcHHHHHHHHHHH--------cCCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhcCCCCCCEEEEE
Confidence            3567889999876655443321        145789999999875432 111      1122222       22347888


Q ss_pred             ccCCCCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          103 NKIDLVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       103 nK~D~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ||+|+.+..+  .+.+++..+..+  .+++.++
T Consensus       135 nK~Dl~~~~~~~~~~~~~~~~~~~--~~~~~~S  165 (195)
T 3bc1_A          135 NKSDLEDQRAVKEEEARELAEKYG--IPYFETS  165 (195)
T ss_dssp             ECTTCGGGCCSCHHHHHHHHHHHT--CCEEECC
T ss_pred             ECcccccccccCHHHHHHHHHHcC--CCEEEEE
Confidence            9999965322  344555555544  4666665

>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=92.42  E-value=0.25  Score=44.91  Aligned_cols=97  Identities=13%  Similarity=0.149  Sum_probs=52.5

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH-HhhhhcCCccchH-HHHHHHhhcC-EEEEccC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM-QHLNEVKPRFVVN-EAVEQVAYAD-RIILNKI  105 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~-~~l~~~~~~~~~~-~~~~Qi~~Ad-~ivlnK~  105 (284)
                      ...+.|++|+|..+.......        ..-..+.+|.|+|+..-. +......+..... ....++.... +|++||+
T Consensus        83 ~~~~~iiDtpG~~~f~~~~~~--------~~~~aD~~ilVvDa~~gsfe~~~~~~~qt~~~~~~~~~~~~~~iivviNK~  154 (435)
T 1jny_A           83 KYFFTIIDAPGHRDFVKNMIT--------GASQADAAILVVSAKKGEYEAGMSVEGQTREHIILAKTMGLDQLIVAVNKM  154 (435)
T ss_dssp             SCEEEECCCSSSTTHHHHHHH--------TSSCCSEEEEEEECSTTHHHHHHSTTCHHHHHHHHHHHTTCTTCEEEEECG
T ss_pred             CeEEEEEECCCcHHHHHHHHh--------hhhhcCEEEEEEECCCCccccccccchHHHHHHHHHHHcCCCeEEEEEEcc
Confidence            467899999999886543221        123568899999998621 0000000000000 1123444443 5779999


Q ss_pred             CCCC----hhHH----HHHHHHHHHhC--C-CCceeeec
Q 023301          106 DLVT----ETEL----GSLTERIKHIN--A-MAPVKLAK  133 (284)
Q Consensus       106 D~~~----~~~~----~~~~~~l~~~n--p-~a~i~~~~  133 (284)
                      |+.+    ++.+    ++++++++.++  + .++++.++
T Consensus       155 Dl~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~i~iS  193 (435)
T 1jny_A          155 DLTEPPYDEKRYKEIVDQVSKFMRSYGFNTNKVRFVPVV  193 (435)
T ss_dssp             GGSSSTTCHHHHHHHHHHHHHHHHHTTCCCTTCEEEECB
T ss_pred             cCCCccccHHHHHHHHHHHHHHHHHcCCCcCCceEEEee
Confidence            9987    3333    34445554443  2 36677665

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=92.39  E-value=0.14  Score=40.32  Aligned_cols=86  Identities=16%  Similarity=0.220  Sum_probs=46.3

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEccc-chHHhhhhcCCccchHHHHHHH------hhcCEEE
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSK-HAMQHLNEVKPRFVVNEAVEQV------AYADRII  101 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~-~~~~~l~~~~~~~~~~~~~~Qi------~~Ad~iv  101 (284)
                      .....+++++|..............    ..-..+.+|.|+|+. .... +.... .++ ..+....      ...-+||
T Consensus        90 ~~~~~l~Dt~G~~~~~~~~~~~~~~----~~~~~~~~i~v~d~~~~~~~-~~~~~-~~~-~~~~~~~~~~~~~~~p~ilv  162 (193)
T 2ged_A           90 GSGVTLVDFPGHVKLRYKLSDYLKT----RAKFVKGLIFMVDSTVDPKK-LTTTA-EFL-VDILSITESSCENGIDILIA  162 (193)
T ss_dssp             CTTCSEEEETTCCBSSCCHHHHHHH----HGGGEEEEEEEEETTCCHHH-HHHHH-HHH-HHHHHHHHHHSTTCCCEEEE
T ss_pred             CCeEEEEECCCCchHHHHHHHHHHh----hcccCCEEEEEEECCCCchh-HHHHH-HHH-HHHHhhhhhccccCCCEEEE
Confidence            3466788999987654333222110    011257899999998 3222 11110 011 1111111      2334788


Q ss_pred             EccCCCCChhHHHHHHHHHH
Q 023301          102 LNKIDLVTETELGSLTERIK  121 (284)
Q Consensus       102 lnK~D~~~~~~~~~~~~~l~  121 (284)
                      +||+|+.+....+.+.+.++
T Consensus       163 ~nK~Dl~~~~~~~~~~~~l~  182 (193)
T 2ged_A          163 CNKSELFTARPPSKIKDALE  182 (193)
T ss_dssp             EECTTSTTCCCHHHHHHHHH
T ss_pred             EEchHhcCCCCHHHHHHHHH
Confidence            89999987766666666554

>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=92.39  E-value=0.017  Score=48.78  Aligned_cols=101  Identities=16%  Similarity=0.168  Sum_probs=54.5

Q ss_pred             CCEEEEecCCCCCcHHH------HHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEE
Q 023301           30 FDHIVIETTGLAKPAPV------IETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRI  100 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i------~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~i  100 (284)
                      ....|++++|.....+.      -+.+.. ..+ ..-..+.+|.|+|+.+....+          .+..|+.   ..-++
T Consensus        48 ~~~~lvDtpG~~~~~~~~~~~~~~e~i~~-~~~-~~~~~d~vi~VvDas~~~~~~----------~l~~~l~~~~~pvil  115 (256)
T 3iby_A           48 HLIEITDLPGVYSLVANAEGISQDEQIAA-QSV-IDLEYDCIINVIDACHLERHL----------YLTSQLFELGKPVVV  115 (256)
T ss_dssp             EEEEEEECCCCSSCC------CHHHHHHH-HHH-HHSCCSEEEEEEEGGGHHHHH----------HHHHHHTTSCSCEEE
T ss_pred             eEEEEEeCCCcccccccccCCCHHHHHHH-HHH-hhCCCCEEEEEeeCCCchhHH----------HHHHHHHHcCCCEEE
Confidence            35789999999876531      111111 011 012478899999999954331          1234444   45689


Q ss_pred             EEccCCCCChhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          101 ILNKIDLVTETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       101 vlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+||+|+.+...+....+.+.+.. ..+++.++. .....+.++
T Consensus       116 v~NK~Dl~~~~~~~~~~~~l~~~l-g~~vi~~SA~~g~gi~el~  158 (256)
T 3iby_A          116 ALNMMDIAEHRGISIDTEKLESLL-GCSVIPIQAHKNIGIPALQ  158 (256)
T ss_dssp             EEECHHHHHHTTCEECHHHHHHHH-CSCEEECBGGGTBSHHHHH
T ss_pred             EEEChhcCCcCCcHHHHHHHHHHc-CCCEEEEECCCCCCHHHHH
Confidence            999999865432211122233222 267776653 233444444

>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=92.37  E-value=0.57  Score=35.90  Aligned_cols=91  Identities=13%  Similarity=0.134  Sum_probs=48.4

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH------hhcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV------AYADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi------~~Ad~ivlnK  104 (284)
                      ...+++++|......+....     +   -..+.++.|+|+...... ... ..+. ..+....      ...=++|+||
T Consensus        57 ~~~i~Dt~G~~~~~~~~~~~-----~---~~~~~~i~v~d~~~~~s~-~~~-~~~~-~~~~~~~~~~~~~~~p~i~v~nK  125 (177)
T 1wms_A           57 TMQIWDTAGQERFRSLRTPF-----Y---RGSDCCLLTFSVDDSQSF-QNL-SNWK-KEFIYYADVKEPESFPFVILGNK  125 (177)
T ss_dssp             EEEEEECCCCGGGHHHHGGG-----G---TTCSEEEEEEETTCHHHH-HTH-HHHH-HHHHHHHTCSCTTTSCEEEEEEC
T ss_pred             EEEEEeCCCchhhhhhHHHH-----H---hcCCEEEEEEECcCHHHH-HHH-HHHH-HHHHHHccccccCCCcEEEEEEC
Confidence            56788999976665543322     1   135678999999875432 111 0011 1111111      1133788899


Q ss_pred             CCCCChh-HHHHHHHHHHHhCCCCceeeec
Q 023301          105 IDLVTET-ELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~-~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +|+.+.+ ..+.+.++.+. ....+++.++
T Consensus       126 ~Dl~~~~~~~~~~~~~~~~-~~~~~~~~~S  154 (177)
T 1wms_A          126 IDISERQVSTEEAQAWCRD-NGDYPYFETS  154 (177)
T ss_dssp             TTCSSCSSCHHHHHHHHHH-TTCCCEEECC
T ss_pred             CcccccccCHHHHHHHHHh-cCCceEEEEe
Confidence            9986322 23444444442 3456777665

>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=92.35  E-value=0.36  Score=43.39  Aligned_cols=92  Identities=18%  Similarity=0.217  Sum_probs=51.7

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC-EEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~  107 (284)
                      ...+.|++|+|..+.......        ..-..+.+|.|+|+......  +.  +... ....+..... ++++||+|+
T Consensus        74 ~~~~~iiDtpG~~~f~~~~~~--------~~~~aD~~ilVvda~~g~~~--qt--~~~l-~~~~~~~ip~iivviNK~Dl  140 (405)
T 2c78_A           74 KRHYSHVDCPGHADYIKNMIT--------GAAQMDGAILVVSAADGPMP--QT--REHI-LLARQVGVPYIVVFMNKVDM  140 (405)
T ss_dssp             SCEEEEEECCCSGGGHHHHHH--------HHTTCSSEEEEEETTTCCCH--HH--HHHH-HHHHHTTCCCEEEEEECGGG
T ss_pred             CeEEEEEECCChHHHHHHHHH--------HHHHCCEEEEEEECCCCCcH--HH--HHHH-HHHHHcCCCEEEEEEECccc
Confidence            357899999998774332211        11246789999999763211  10  0000 1123444454 478999999


Q ss_pred             CC-hhHHH----HHHHHHHHhCC---CCceeeec
Q 023301          108 VT-ETELG----SLTERIKHINA---MAPVKLAK  133 (284)
Q Consensus       108 ~~-~~~~~----~~~~~l~~~np---~a~i~~~~  133 (284)
                      .+ .+.++    +++++++.++.   ..+++.++
T Consensus       141 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~i~~S  174 (405)
T 2c78_A          141 VDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGS  174 (405)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHTTSCTTTSCEEECC
T ss_pred             cCcHHHHHHHHHHHHHHHHHhcccccCCCEEEcc
Confidence            84 33333    34555555542   46777654

>3izq_1 HBS1P, elongation factor 1 alpha-like protein; NO-GO mRNA decay, ribosomal protein,hydrolase; 9.50A {Saccharomyces cerevisiae}

Probab=92.17  E-value=0.28  Score=46.70  Aligned_cols=95  Identities=13%  Similarity=0.107  Sum_probs=49.6

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH--HhhhhcCCccchH-HHHHHHhhc-CEEEEccC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM--QHLNEVKPRFVVN-EAVEQVAYA-DRIILNKI  105 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~--~~l~~~~~~~~~~-~~~~Qi~~A-d~ivlnK~  105 (284)
                      ..+.|++|+|........   .     ...-..+.+|.|||+..-.  ..+.- .+..... ....++... =+||+||+
T Consensus       245 ~~~~iiDTPG~e~f~~~~---~-----~~~~~aD~~llVVDa~~g~~e~~~~~-~~qt~e~l~~~~~lgi~~iIVVvNKi  315 (611)
T 3izq_1          245 ANFTIVDAPGHRDFVPNA---I-----MGISQADMAILCVDCSTNAFESGFDL-DGQTKEHMLLASSLGIHNLIIAMNKM  315 (611)
T ss_dssp             CEEEEEECCSSSCHHHHH---T-----TTSSCCSEEEEEEECSHHHHHTTCCT-TSHHHHHHHHHHTTTCCEEEEEEECT
T ss_pred             ceEEEEECCCCcccHHHH---H-----HHHhhcCceEEEEECCCCcccccchh-hhHHHHHHHHHHHcCCCeEEEEEecc
Confidence            378999999987643211   1     1123478899999998732  10000 0000001 112233333 35668999


Q ss_pred             CCCC--hhHHHHHHHHHH----HhC--C-CCceeeec
Q 023301          106 DLVT--ETELGSLTERIK----HIN--A-MAPVKLAK  133 (284)
Q Consensus       106 D~~~--~~~~~~~~~~l~----~~n--p-~a~i~~~~  133 (284)
                      |+++  ....+.+.+.++    .+.  + .++++.++
T Consensus       316 Dl~~~~~~~~~ei~~~l~~~l~~~g~~~~~~~~i~vS  352 (611)
T 3izq_1          316 DNVDWSQQRFEEIKSKLLPYLVDIGFFEDNINWVPIS  352 (611)
T ss_dssp             TTTTTCHHHHHHHHHHHHHHHHHHTCCGGGCEEEECC
T ss_pred             cccchhHHHHHHHHHHHHHHHHhhcccccCccEEeee
Confidence            9987  333444444443    332  1 46777665

>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=92.11  E-value=0.42  Score=41.14  Aligned_cols=81  Identities=20%  Similarity=0.285  Sum_probs=44.9

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeecc-CCCCh
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKY-GSVDM  139 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~  139 (284)
                      ..+.+|.|+|+.+........ ++++. . ..+-...-+||+||+|+.+..+.+++.++++..+...++++++. .....
T Consensus        84 ~ad~vilV~D~~~~~~s~~~l-~~~l~-~-~~~~~~piilv~NK~DL~~~~~v~~~~~~~~~~~~~~~~~~~SAktg~gv  160 (301)
T 1u0l_A           84 NVDQVILVVTVKMPETSTYII-DKFLV-L-AEKNELETVMVINKMDLYDEDDLRKVRELEEIYSGLYPIVKTSAKTGMGI  160 (301)
T ss_dssp             SCCEEEEEECSSTTCCCHHHH-HHHHH-H-HHHTTCEEEEEECCGGGCCHHHHHHHHHHHHHHTTTSCEEECCTTTCTTH
T ss_pred             cCCEEEEEEeCCCCCCCHHHH-HHHHH-H-HHHCCCCEEEEEeHHHcCCchhHHHHHHHHHHHhhhCcEEEEECCCCcCH
Confidence            688999999998632111110 11111 1 11122344788899999887655455566655543266777664 33455


Q ss_pred             hhhhc
Q 023301          140 DFVLG  144 (284)
Q Consensus       140 ~~l~~  144 (284)
                      +.++.
T Consensus       161 ~~lf~  165 (301)
T 1u0l_A          161 EELKE  165 (301)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55553

>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=92.06  E-value=0.77  Score=35.21  Aligned_cols=101  Identities=18%  Similarity=0.177  Sum_probs=46.9

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH------hhcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV------AYADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi------~~Ad~ivlnK  104 (284)
                      ...+++++|......+...     .+   -..+.+|.|+|+...... .+. ..++ ..+....      ...-+||+||
T Consensus        59 ~~~l~Dt~G~~~~~~~~~~-----~~---~~~d~~i~v~d~~~~~s~-~~~-~~~~-~~~~~~~~~~~~~~~p~ilv~nK  127 (182)
T 1ky3_A           59 TMQVWDTAGQERFQSLGVA-----FY---RGADCCVLVYDVTNASSF-ENI-KSWR-DEFLVHANVNSPETFPFVILGNK  127 (182)
T ss_dssp             EEEEECCC----------C-----CS---TTCCEEEEEEETTCHHHH-HTH-HHHH-HHHHHHHCCSCTTTCCEEEEEEC
T ss_pred             EEEEEECCCChHhhhhhHH-----Hh---hcCCEEEEEEECCChHHH-HHH-HHHH-HHHHHHhcccCcCCCcEEEEEEC
Confidence            4578889985544332211     11   245789999999875432 111 0011 1111111      1234788999


Q ss_pred             CCCCChhH---HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTETE---LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~~---~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+...   .+.+.++.+ .....+++.++. .......++
T Consensus       128 ~Dl~~~~~~v~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~  169 (182)
T 1ky3_A          128 IDAEESKKIVSEKSAQELAK-SLGDIPLFLTSAKNAINVDTAF  169 (182)
T ss_dssp             TTSCGGGCCSCHHHHHHHHH-HTTSCCEEEEBTTTTBSHHHHH
T ss_pred             CccccccccCCHHHHHHHHH-hcCCCeEEEEecCCCCCHHHHH
Confidence            99964321   333444433 234567777653 233444443

>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=91.98  E-value=0.23  Score=37.87  Aligned_cols=90  Identities=19%  Similarity=0.182  Sum_probs=43.9

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH--hhcCEEEEccCCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV--AYADRIILNKIDLV  108 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi--~~Ad~ivlnK~D~~  108 (284)
                      ...+++++|......+..     ..+   -..+.++.|+|+.+.... .... .++ ..+....  ...=++|+||+|+.
T Consensus        56 ~l~i~Dt~G~~~~~~~~~-----~~~---~~~d~~i~v~d~~~~~s~-~~~~-~~~-~~~~~~~~~~~piilv~nK~Dl~  124 (170)
T 1z08_A           56 NLAIWDTAGQERFHALGP-----IYY---RDSNGAILVYDITDEDSF-QKVK-NWV-KELRKMLGNEICLCIVGNKIDLE  124 (170)
T ss_dssp             EEEEEECCCC-------C-----CSS---TTCSEEEEEEETTCHHHH-HHHH-HHH-HHHHHHHGGGSEEEEEEECGGGG
T ss_pred             EEEEEECCCcHhhhhhHH-----HHh---ccCCEEEEEEECcCHHHH-HHHH-HHH-HHHHHhcCCCCeEEEEEECcccc
Confidence            456779999654433211     111   245789999999875432 1110 011 1111111  11237889999996


Q ss_pred             ChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          109 TETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       109 ~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ++.+  .+..+++.+..+  ++++.++
T Consensus       125 ~~~~~~~~~~~~~~~~~~--~~~~~~S  149 (170)
T 1z08_A          125 KERHVSIQEAESYAESVG--AKHYHTS  149 (170)
T ss_dssp             GGCCSCHHHHHHHHHHTT--CEEEEEB
T ss_pred             cccccCHHHHHHHHHHcC--CeEEEec
Confidence            5322  344555555443  5666655

>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=91.86  E-value=0.37  Score=36.96  Aligned_cols=96  Identities=11%  Similarity=0.157  Sum_probs=51.6

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh------hcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA------YADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~------~Ad~ivlnK  104 (284)
                      ...+++++|......+....     +   -..+.++.|+|+.+.... ...      .....++.      ..=++|+||
T Consensus        64 ~~~~~Dt~G~~~~~~~~~~~-----~---~~~d~~i~v~d~~~~~s~-~~~------~~~~~~i~~~~~~~~piilv~nK  128 (179)
T 2y8e_A           64 RLQLWDTAGQERFRSLIPSY-----I---RDSTVAVVVYDITNTNSF-HQT------SKWIDDVRTERGSDVIIMLVGNK  128 (179)
T ss_dssp             EEEEEEECCSGGGGGGSHHH-----H---HTCSEEEEEEETTCHHHH-HTH------HHHHHHHHHHHTTSSEEEEEEEC
T ss_pred             EEEEEECCCcHHHHHHHHHH-----h---cCCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhcCCCCcEEEEEEC
Confidence            45788999976554433221     1   135779999999774321 111      11122221      122788999


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.++.+  .+..++..+..+  .+++.++. .......++
T Consensus       129 ~Dl~~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~~i~~l~  168 (179)
T 2y8e_A          129 TDLSDKRQVSTEEGERKAKELN--VMFIETSAKAGYNVKQLF  168 (179)
T ss_dssp             GGGGGGCCSCHHHHHHHHHHHT--CEEEEEBTTTTBSHHHHH
T ss_pred             CcccccCcCCHHHHHHHHHHcC--CeEEEEeCCCCCCHHHHH
Confidence            99965433  344455555554  56666653 233444443

>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=91.75  E-value=0.51  Score=43.21  Aligned_cols=96  Identities=15%  Similarity=0.127  Sum_probs=51.2

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHh--hhhcCCccchH-HHHHHHhhc-CEEEEcc
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQH--LNEVKPRFVVN-EAVEQVAYA-DRIILNK  104 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~--l~~~~~~~~~~-~~~~Qi~~A-d~ivlnK  104 (284)
                      ...+.|++|+|-.+.......        ..-..+.+|.|||+..-...  +.... ..... ....++... =+|++||
T Consensus        84 ~~~~~iiDtPGh~~f~~~~~~--------~~~~aD~~ilVvda~~g~~~~sf~~~~-qt~~~~~~~~~~~v~~iivviNK  154 (458)
T 1f60_A           84 KYQVTVIDAPGHRDFIKNMIT--------GTSQADCAILIIAGGVGEFEAGISKDG-QTREHALLAFTLGVRQLIVAVNK  154 (458)
T ss_dssp             SEEEEEEECCCCTTHHHHHHH--------SSSCCSEEEEEEECSHHHHHHHTCTTS-HHHHHHHHHHHTTCCEEEEEEEC
T ss_pred             CceEEEEECCCcHHHHHHHHh--------hhhhCCEEEEEEeCCcCccccccCcch-hHHHHHHHHHHcCCCeEEEEEEc
Confidence            346899999997654332211        12367889999999864311  10000 00001 122334444 3567999


Q ss_pred             CCCCC--hhHHHH----HHHHHHHhCC---CCceeeec
Q 023301          105 IDLVT--ETELGS----LTERIKHINA---MAPVKLAK  133 (284)
Q Consensus       105 ~D~~~--~~~~~~----~~~~l~~~np---~a~i~~~~  133 (284)
                      +|+.+  ++.++.    ++++++.+.-   .++++.++
T Consensus       155 ~Dl~~~~~~~~~~i~~~~~~~l~~~g~~~~~~~~i~vS  192 (458)
T 1f60_A          155 MDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPIS  192 (458)
T ss_dssp             GGGGTTCHHHHHHHHHHHHHHHHHHTCCGGGCCEEECC
T ss_pred             cccccCCHHHHHHHHHHHHHHHHHcCCCccCceEEEee
Confidence            99973  444444    4444444431   36777664

>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=91.68  E-value=0.46  Score=37.07  Aligned_cols=103  Identities=13%  Similarity=0.074  Sum_probs=49.6

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH---HhhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ---VAYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q---i~~Ad~ivlnK~D  106 (284)
                      ....+++++|......+....     +   -..+.++.|+|+.+.... .+.. .++ ..+...   -...=++|+||+|
T Consensus        60 ~~~~i~Dt~G~~~~~~~~~~~-----~---~~~d~ii~v~d~~~~~s~-~~~~-~~~-~~~~~~~~~~~~piilv~NK~D  128 (187)
T 1zj6_A           60 TRFLMWDIGGQESLRSSWNTY-----Y---TNTEFVIVVVDSTDRERI-SVTR-EEL-YKMLAHEDLRKAGLLIFANKQD  128 (187)
T ss_dssp             EEEEEEECCC----CGGGHHH-----H---TTCCEEEEEEETTCTTTH-HHHH-HHH-HHHHTSGGGTTCEEEEEEECTT
T ss_pred             EEEEEEECCCCHhHHHHHHHH-----h---cCCCEEEEEEeCCCHHHH-HHHH-HHH-HHHHhchhhCCCeEEEEEECCC
Confidence            456788999986543332221     1   246789999999874211 1100 001 111111   1223478889999


Q ss_pred             CCChhHHHHHHHHHHHh---CCCCceeeecc-CCCChhhhh
Q 023301          107 LVTETELGSLTERIKHI---NAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       107 ~~~~~~~~~~~~~l~~~---np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +.+....+++.+.++..   ....++++++. .....+.++
T Consensus       129 l~~~~~~~~i~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~  169 (187)
T 1zj6_A          129 VKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGL  169 (187)
T ss_dssp             STTCCCHHHHHHHHTGGGCCSSCEEEEECBTTTTBTHHHHH
T ss_pred             CcCCCCHHHHHHHhChhhhcCCCcEEEEccCCCCcCHHHHH
Confidence            97654445555555432   12345665553 233444443

>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=91.65  E-value=0.095  Score=44.34  Aligned_cols=64  Identities=22%  Similarity=0.316  Sum_probs=39.7

Q ss_pred             CCEEEEecCCCCCcHH------HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh----hcCE
Q 023301           30 FDHIVIETTGLAKPAP------VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA----YADR   99 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~------i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~----~Ad~   99 (284)
                      ....+++++|......      +...+.      ..-..+.++.|+|+.++...+.          +..|+.    ..-+
T Consensus        50 ~~~~l~DtpG~~~~~~~~~~~~~~~~~~------~~~~~d~vi~v~D~~~~~~~~~----------~~~~~~~~~~~p~i  113 (271)
T 3k53_A           50 KEFLVVDLPGIYSLTAHSIDELIARNFI------LDGNADVIVDIVDSTCLMRNLF----------LTLELFEMEVKNII  113 (271)
T ss_dssp             EEEEEEECCCCSCCCSSCHHHHHHHHHH------HTTCCSEEEEEEEGGGHHHHHH----------HHHHHHHTTCCSEE
T ss_pred             ceEEEEeCCCccccccCCHHHHHHHHhh------hccCCcEEEEEecCCcchhhHH----------HHHHHHhcCCCCEE
Confidence            3568999999887443      221111      0124678999999999754321          123333    4558


Q ss_pred             EEEccCCCCC
Q 023301          100 IILNKIDLVT  109 (284)
Q Consensus       100 ivlnK~D~~~  109 (284)
                      +|+||+|+.+
T Consensus       114 lv~NK~Dl~~  123 (271)
T 3k53_A          114 LVLNKFDLLK  123 (271)
T ss_dssp             EEEECHHHHH
T ss_pred             EEEEChhcCc
Confidence            8899999754

>2elf_A Protein translation elongation factor 1A; tRNA, pyrrolysine, structural genomics, NPPSFA; HET: CIT; 1.70A {Methanosarcina mazei}

Probab=91.63  E-value=0.69  Score=41.10  Aligned_cols=89  Identities=12%  Similarity=0.095  Sum_probs=51.5

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccc-hHHhhhhcCCccchHHHHHHHhhcC-EEEEc-cC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKH-AMQHLNEVKPRFVVNEAVEQVAYAD-RIILN-KI  105 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~-~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivln-K~  105 (284)
                      ...+.|++|+|-.+...-...        ..-..+.+|.||| .. ...+..+     . -.+..++.... +|++| |+
T Consensus        59 ~~~i~iiDtPGh~~f~~~~~~--------~~~~aD~ailVvd-~~g~~~qt~e-----~-~~~~~~~~i~~~ivvvNNK~  123 (370)
T 2elf_A           59 GRNMVFVDAHSYPKTLKSLIT--------ALNISDIAVLCIP-PQGLDAHTGE-----C-IIALDLLGFKHGIIALTRSD  123 (370)
T ss_dssp             SSEEEEEECTTTTTCHHHHHH--------HHHTCSEEEEEEC-TTCCCHHHHH-----H-HHHHHHTTCCEEEEEECCGG
T ss_pred             CeEEEEEECCChHHHHHHHHH--------HHHHCCEEEEEEc-CCCCcHHHHH-----H-HHHHHHcCCCeEEEEEEecc
Confidence            456899999998875322111        1134678999999 43 1111111     0 01234445556 88999 99


Q ss_pred             CCCChhHHHHHHHHHHHhC-----CCCceee--ec
Q 023301          106 DLVTETELGSLTERIKHIN-----AMAPVKL--AK  133 (284)
Q Consensus       106 D~~~~~~~~~~~~~l~~~n-----p~a~i~~--~~  133 (284)
                      |+ +++.++.+.+.++++.     ...+++.  ++
T Consensus       124 Dl-~~~~~~~~~~~i~~~l~~~~~~~~~ii~~~~S  157 (370)
T 2elf_A          124 ST-HMHAIDELKAKLKVITSGTVLQDWECISLNTN  157 (370)
T ss_dssp             GS-CHHHHHHHHHHHHHHTTTSTTTTCEEEECCCC
T ss_pred             CC-CHHHHHHHHHHHHHHHHhcCCCceEEEecccc
Confidence            99 7665555555555443     2367777  54

>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=91.62  E-value=0.27  Score=40.50  Aligned_cols=90  Identities=10%  Similarity=0.151  Sum_probs=43.3

Q ss_pred             CCEEEEecCCCCCcH----HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHH----HHHhhcCEEE
Q 023301           30 FDHIVIETTGLAKPA----PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAV----EQVAYADRII  101 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~----~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~----~Qi~~Ad~iv  101 (284)
                      ....|++|+|+.+..    .+.+.+.. ......-..+.++.|+|+.++.....    ..+ ..+.    ......-+||
T Consensus        78 ~~i~liDTpG~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~v~d~~~~~~~~~----~~l-~~~~~~~~~~~~~~~iiv  151 (239)
T 3lxx_A           78 TELVVVDTPGIFDTEVPNAETSKEIIR-CILLTSPGPHALLLVVPLGRYTEEEH----KAT-EKILKMFGERARSFMILI  151 (239)
T ss_dssp             EEEEEEECCSCC-----CHHHHHHHHH-HHHHTTTCCSEEEEEEETTCCSSHHH----HHH-HHHHHHHHHHHGGGEEEE
T ss_pred             ceEEEEECCCccCCCCCHHHHHHHHHH-HHHhcCCCCcEEEEEeeCCCCCHHHH----HHH-HHHHHHhhhhccceEEEE
Confidence            356899999998753    11222211 00001124578999999876432110    011 1111    1222357888


Q ss_pred             EccCCCCChhHHH--------HHHHHHHHhCC
Q 023301          102 LNKIDLVTETELG--------SLTERIKHINA  125 (284)
Q Consensus       102 lnK~D~~~~~~~~--------~~~~~l~~~np  125 (284)
                      +||+|+.+...++        .+++.++....
T Consensus       152 ~nK~D~~~~~~~~~~i~~~~~~l~~l~~~~~~  183 (239)
T 3lxx_A          152 FTRKDDLGDTNLHDYLREAPEDIQDLMDIFGD  183 (239)
T ss_dssp             EECGGGC------------CHHHHHHHHHHSS
T ss_pred             EeCCccCCcccHHHHHHhchHHHHHHHHHcCC
Confidence            9999998765554        45555555554

>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=91.62  E-value=0.27  Score=37.55  Aligned_cols=77  Identities=19%  Similarity=0.175  Sum_probs=42.2

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH------hhcCEEEEc
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV------AYADRIILN  103 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi------~~Ad~ivln  103 (284)
                      ....+++++|......+...     .+   -..+.++.|+|+.+.... .+.     ...+...+      ...=+||+|
T Consensus        51 ~~~~~~Dt~G~~~~~~~~~~-----~~---~~~d~ii~v~d~~~~~s~-~~~-----~~~~~~~~~~~~~~~~piilv~n  116 (171)
T 1upt_A           51 LKFQVWDLGGLTSIRPYWRC-----YY---SNTDAVIYVVDSCDRDRI-GIS-----KSELVAMLEEEELRKAILVVFAN  116 (171)
T ss_dssp             EEEEEEEECCCGGGGGGGGG-----GC---TTCSEEEEEEETTCCTTH-HHH-----HHHHHHHHTCGGGTTCEEEEEEE
T ss_pred             EEEEEEECCCChhhhHHHHH-----Hh---ccCCEEEEEEECCCHHHH-HHH-----HHHHHHHHhchhhCCCEEEEEEE
Confidence            34578899997654432211     11   256789999999774221 110     01111222      223378889


Q ss_pred             cCCCCChhHHHHHHHHH
Q 023301          104 KIDLVTETELGSLTERI  120 (284)
Q Consensus       104 K~D~~~~~~~~~~~~~l  120 (284)
                      |+|+.+......+.+.+
T Consensus       117 K~Dl~~~~~~~~~~~~~  133 (171)
T 1upt_A          117 KQDMEQAMTSSEMANSL  133 (171)
T ss_dssp             CTTSTTCCCHHHHHHHH
T ss_pred             CCCCcCCCCHHHHHHHh
Confidence            99998764444454444

>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=91.48  E-value=0.85  Score=35.03  Aligned_cols=96  Identities=9%  Similarity=0.080  Sum_probs=50.7

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh------hcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA------YADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~------~Ad~ivlnK  104 (284)
                      ...+++++|......+....     +   -..+.+|.|+|+...... ...      ..+..++.      ..=+||+||
T Consensus        62 ~~~i~Dt~G~~~~~~~~~~~-----~---~~~d~~i~v~d~~~~~s~-~~~------~~~~~~~~~~~~~~~p~i~v~nK  126 (181)
T 2efe_B           62 KFEIWDTAGQERYHSLAPMY-----Y---RGAAAAIIVFDVTNQASF-ERA------KKWVQELQAQGNPNMVMALAGNK  126 (181)
T ss_dssp             EEEEEECCCSGGGGGGTHHH-----H---TTCSEEEEEEETTCHHHH-HHH------HHHHHHHHHHSCTTCEEEEEEEC
T ss_pred             EEEEEeCCCChhhhhhhHHH-----h---ccCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhcCCCCcEEEEEEC
Confidence            45778899965433322211     1   135789999999775432 111      11122222      223678899


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+..+  .+.++++.+..  ..+++.++. .......++
T Consensus       127 ~Dl~~~~~~~~~~~~~~~~~~--~~~~~~~Sa~~g~gi~~l~  166 (181)
T 2efe_B          127 SDLLDARKVTAEDAQTYAQEN--GLFFMETSAKTATNVKEIF  166 (181)
T ss_dssp             TTCTTTCCSCHHHHHHHHHHT--TCEEEECCSSSCTTHHHHH
T ss_pred             CcccccccCCHHHHHHHHHHc--CCEEEEEECCCCCCHHHHH
Confidence            99965432  34455555543  356766653 233444444

>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=91.45  E-value=0.38  Score=37.64  Aligned_cols=86  Identities=15%  Similarity=0.112  Sum_probs=47.2

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh------hcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA------YADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~------~Ad~ivlnK  104 (284)
                      ...+++++|......+...     .   .-..+.+|.|+|+.+.... ...      ..+..++.      ..=+||+||
T Consensus        72 ~~~l~Dt~G~~~~~~~~~~-----~---~~~~d~ii~v~d~~~~~s~-~~~------~~~~~~i~~~~~~~~piilv~nK  136 (189)
T 2gf9_A           72 KLQIWDTAGQERYRTITTA-----Y---YRGAMGFLLMYDIANQESF-AAV------QDWATQIKTYSWDNAQVILVGNK  136 (189)
T ss_dssp             EEEEEECCSCCSSCCSGGG-----G---GTTCSEEEEEEETTCHHHH-HTH------HHHHHHHHHHSCTTCEEEEEEEC
T ss_pred             EEEEEeCCCcHHHhhhHHH-----h---ccCCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhcCCCCCEEEEEEC
Confidence            4567788886554322111     1   1246789999999774432 111      11223332      234788899


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +|+.+..+  .+.++++.+.++  .+++.++
T Consensus       137 ~Dl~~~~~~~~~~~~~~~~~~~--~~~~~~S  165 (189)
T 2gf9_A          137 CDLEDERVVPAEDGRRLADDLG--FEFFEAS  165 (189)
T ss_dssp             TTCGGGCCSCHHHHHHHHHHHT--CEEEECB
T ss_pred             cccccccCCCHHHHHHHHHHcC--CeEEEEE
Confidence            99965322  234555555554  4666665

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=91.38  E-value=0.36  Score=37.16  Aligned_cols=97  Identities=13%  Similarity=0.125  Sum_probs=49.7

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhc-----CEEEEcc
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYA-----DRIILNK  104 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~A-----d~ivlnK  104 (284)
                      ....+++++|......+..     ..   .-..+.++.|+|+...... ...      .....++...     -+||+||
T Consensus        58 ~~~~i~Dt~G~~~~~~~~~-----~~---~~~~d~~i~v~d~~~~~s~-~~~------~~~~~~~~~~~~~~p~ilv~nK  122 (181)
T 3tw8_B           58 VKLQIWDTAGQERFRTITS-----TY---YRGTHGVIVVYDVTSAESF-VNV------KRWLHEINQNCDDVCRILVGNK  122 (181)
T ss_dssp             EEEEEEEETTGGGCSSCCG-----GG---GTTCSEEEEEEETTCHHHH-HHH------HHHHHHHHHHCTTSEEEEEEEC
T ss_pred             EEEEEEcCCCchhhhhhHH-----HH---hccCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhCCCCCEEEEEEC
Confidence            3456778888433222111     11   1245789999999874332 211      1123333322     2888999


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+...  .....+..+..+  ++++.++. .......++
T Consensus       123 ~Dl~~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  162 (181)
T 3tw8_B          123 NDDPERKVVETEDAYKFAGQMG--IQLFETSAKENVNVEEMF  162 (181)
T ss_dssp             TTCGGGCCSCHHHHHHHHHHHT--CCEEECBTTTTBSHHHHH
T ss_pred             CCCchhcccCHHHHHHHHHHcC--CeEEEEECCCCCCHHHHH
Confidence            99865322  233444444443  56776653 233444443

>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=91.19  E-value=0.41  Score=37.12  Aligned_cols=96  Identities=11%  Similarity=0.059  Sum_probs=51.7

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh------hcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA------YADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~------~Ad~ivlnK  104 (284)
                      ...+++++|......+.....        -..+.+|.|+|+.+.... ...      .....++.      ..=+||+||
T Consensus        60 ~~~l~Dt~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~------~~~~~~~~~~~~~~~piilv~nK  124 (186)
T 2bme_A           60 KLQIWDTAGQERFRSVTRSYY--------RGAAGALLVYDITSRETY-NAL------TNWLTDARMLASQNIVIILCGNK  124 (186)
T ss_dssp             EEEEEEECCSGGGHHHHHTTS--------TTCSEEEEEEETTCHHHH-HTH------HHHHHHHHHHSCTTCEEEEEEEC
T ss_pred             EEEEEeCCCcHHHHHHHHHHH--------hcCCEEEEEEECcCHHHH-HHH------HHHHHHHHHhcCCCCcEEEEEEC
Confidence            556889999776655433221        245779999999875432 111      11122222      123788899


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+..+  .....++.+..  ..++++++. .......++
T Consensus       125 ~Dl~~~~~~~~~~~~~~~~~~--~~~~~~~Sa~~~~gi~~l~  164 (186)
T 2bme_A          125 KDLDADREVTFLEASRFAQEN--ELMFLETSALTGENVEEAF  164 (186)
T ss_dssp             GGGGGGCCSCHHHHHHHHHHT--TCEEEECCTTTCTTHHHHH
T ss_pred             cccccccccCHHHHHHHHHHc--CCEEEEecCCCCCCHHHHH
Confidence            99964322  23444444433  356766653 233444443

>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=91.08  E-value=0.86  Score=35.48  Aligned_cols=101  Identities=12%  Similarity=0.139  Sum_probs=47.1

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D  106 (284)
                      .+..|++++|......+....     +   -..+.++.|+|+...... .+.. .+ ...+....   ...=+||+||+|
T Consensus        69 ~~~~l~Dt~G~~~~~~~~~~~-----~---~~~d~~i~v~d~~~~~s~-~~~~-~~-~~~i~~~~~~~~~p~ilv~nK~D  137 (190)
T 3con_A           69 CLLDILDTAGQEEYSAMRDQY-----M---RTGEGFLCVFAINNSKSF-ADIN-LY-REQIKRVKDSDDVPMVLVGNKCD  137 (190)
T ss_dssp             EEEEEEECCC----------------C---TTCSEEEEEEETTCHHHH-HHHH-HH-HHHHHHHHTCSCCCEEEEEECTT
T ss_pred             EEEEEEECCChHHHHHHHHHh-----h---CcCCEEEEEEECcCHHHH-HHHH-HH-HHHHHHHhCCCCCeEEEEEECCc
Confidence            346788999976544433221     1   135678899998775432 1110 00 01111111   123478889999


Q ss_pred             CCChh-HHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          107 LVTET-ELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       107 ~~~~~-~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +.+.. ..+.++++.+..+  .+++.++. .......++
T Consensus       138 l~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  174 (190)
T 3con_A          138 LPTRTVDTKQAHELAKSYG--IPFIETSAKTRQGVEDAF  174 (190)
T ss_dssp             CSCCCSCHHHHHHHHHHHT--CCEEECCTTTCTTHHHHH
T ss_pred             CCcccCCHHHHHHHHHHcC--CeEEEEeCCCCCCHHHHH
Confidence            86521 2344555555554  46666553 233444443

>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=90.97  E-value=0.57  Score=36.80  Aligned_cols=96  Identities=15%  Similarity=0.160  Sum_probs=52.2

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH------hhcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV------AYADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi------~~Ad~ivlnK  104 (284)
                      ...+++++|......+....     +   -..+.+|.|+|+.+.... ...      .....++      ...=+||+||
T Consensus        73 ~~~i~Dt~G~~~~~~~~~~~-----~---~~~d~iilV~d~~~~~s~-~~~------~~~~~~i~~~~~~~~piiiv~NK  137 (192)
T 2fg5_A           73 KFLIWDTAGQERFHSLAPMY-----Y---RGSAAAVIVYDITKQDSF-YTL------KKWVKELKEHGPENIVMAIAGNK  137 (192)
T ss_dssp             EEEEEEECCSGGGGGGTHHH-----H---TTCSEEEEEEETTCTHHH-HHH------HHHHHHHHHHSCTTCEEEEEEEC
T ss_pred             EEEEEcCCCchhhHhhhHHh-----h---ccCCEEEEEEeCCCHHHH-HHH------HHHHHHHHHhCCCCCcEEEEEEC
Confidence            46778999966544432221     1   135789999999775432 111      1122223      2234688899


Q ss_pred             CCCCChh--HHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTET--ELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~--~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+..  ..+.++++.+..+  ++++.++. .......++
T Consensus       138 ~Dl~~~~~v~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  177 (192)
T 2fg5_A          138 CDLSDIREVPLKDAKEYAESIG--AIVVETSAKNAINIEELF  177 (192)
T ss_dssp             GGGGGGCCSCHHHHHHHHHTTT--CEEEECBTTTTBSHHHHH
T ss_pred             cccccccccCHHHHHHHHHHcC--CEEEEEeCCCCcCHHHHH
Confidence            9996422  2345556555443  56776653 233444444

>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=90.89  E-value=0.65  Score=36.83  Aligned_cols=96  Identities=15%  Similarity=0.146  Sum_probs=51.3

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh------hcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA------YADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~------~Ad~ivlnK  104 (284)
                      ...+++++|......+..     ..+   -..+.+|.|+|+...... ...      ......+.      ..=+||+||
T Consensus        58 ~~~l~Dt~G~~~~~~~~~-----~~~---~~~d~vilv~d~~~~~s~-~~~------~~~~~~i~~~~~~~~piilv~nK  122 (206)
T 2bcg_Y           58 KLQIWDTAGQERFRTITS-----SYY---RGSHGIIIVYDVTDQESF-NGV------KMWLQEIDRYATSTVLKLLVGNK  122 (206)
T ss_dssp             EEEEECCTTTTTTTCCCG-----GGG---TTCSEEEEEEETTCHHHH-HHH------HHHHHHHHHHSCTTCEEEEEEEC
T ss_pred             EEEEEeCCChHHHHHHHH-----Hhc---cCCCEEEEEEECcCHHHH-HHH------HHHHHHHHHhcCCCCCEEEEEEC
Confidence            467889999655433211     111   245789999999875432 111      11122222      223788999


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+..+  .+...++.+..+  .+++.++. .......++
T Consensus       123 ~Dl~~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~g~gi~~l~  162 (206)
T 2bcg_Y          123 CDLKDKRVVEYDVAKEFADANK--MPFLETSALDSTNVEDAF  162 (206)
T ss_dssp             TTCTTTCCSCHHHHHHHHHHTT--CCEEECCTTTCTTHHHHH
T ss_pred             CCCccccccCHHHHHHHHHHcC--CeEEEEeCCCCCCHHHHH
Confidence            99976322  234444444433  57776653 233444444

>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=90.88  E-value=1.1  Score=34.42  Aligned_cols=86  Identities=14%  Similarity=0.135  Sum_probs=43.8

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh------hcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA------YADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~------~Ad~ivlnK  104 (284)
                      ...+++++|......+...     .+   -..+.++.|+|+...... .+.      .....++.      ..=+||+||
T Consensus        61 ~~~~~Dt~G~~~~~~~~~~-----~~---~~~d~ii~v~d~~~~~s~-~~~------~~~~~~i~~~~~~~~piilv~nK  125 (180)
T 2g6b_A           61 KLQMWDTAGQERFRSVTHA-----YY---RDAHALLLLYDVTNKASF-DNI------QAWLTEIHEYAQHDVALMLLGNK  125 (180)
T ss_dssp             EEEEEECCCC--------C-----CG---GGCSEEEEEEETTCHHHH-HTH------HHHHHHHHHHSCTTCEEEEEEEC
T ss_pred             EEEEEeCCCcHHHHHHHHH-----Hc---cCCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhCCCCCcEEEEEEC
Confidence            4567789996554332211     11   246789999999875432 111      11122221      233788899


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +|+.++.+  .+..+++.+..+  .+++.++
T Consensus       126 ~Dl~~~~~~~~~~~~~~~~~~~--~~~~~~S  154 (180)
T 2g6b_A          126 VDSAHERVVKREDGEKLAKEYG--LPFMETS  154 (180)
T ss_dssp             CSTTSCCCSCHHHHHHHHHHHT--CCEEECC
T ss_pred             cccCcccccCHHHHHHHHHHcC--CeEEEEe
Confidence            99975322  234444444443  4666655

>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=90.79  E-value=1.4  Score=34.70  Aligned_cols=86  Identities=17%  Similarity=0.154  Sum_probs=49.2

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh------hcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA------YADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~------~Ad~ivlnK  104 (284)
                      ...+++++|......+....     +   -..+.+|.|+|+.+.... ...      ..+..++.      ..=+||+||
T Consensus        58 ~~~l~Dt~G~~~~~~~~~~~-----~---~~~d~ii~v~d~~~~~s~-~~~------~~~~~~i~~~~~~~~piilv~nK  122 (203)
T 1zbd_A           58 KLQIWDTAGLERYRTITTAY-----Y---RGAMGFILMYDITNEESF-NAV------QDWSTQIKTYSWDNAQVLLVGNK  122 (203)
T ss_dssp             EEEEEEECCSGGGHHHHHTT-----G---GGCSEEEEEEETTCHHHH-HHH------HHHHHHHHHHSCSSCEEEEEEEC
T ss_pred             EEEEEECCCchhhcchHHHh-----h---cCCCEEEEEEECcCHHHH-HHH------HHHHHHHHHhcCCCCCEEEEEEC
Confidence            45678999987665543322     1   245779999999875432 111      11223332      234788899


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +|+.+..+  .+..+++.+.++  .+++.++
T Consensus       123 ~Dl~~~~~~~~~~~~~~~~~~~--~~~~~~S  151 (203)
T 1zbd_A          123 CDMEDERVVSSERGRQLADHLG--FEFFEAS  151 (203)
T ss_dssp             TTCTTSCCSCHHHHHHHHHHHT--CEEEECB
T ss_pred             cccCcccccCHHHHHHHHHHCC--CeEEEEE
Confidence            99975322  344455555554  4677665

>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=90.79  E-value=0.63  Score=41.81  Aligned_cols=100  Identities=19%  Similarity=0.247  Sum_probs=53.2

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH--HhhhhcCCccchHHHHHHHhhcCE-EEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM--QHLNEVKPRFVVNEAVEQVAYADR-IILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~--~~l~~~~~~~~~~~~~~Qi~~Ad~-ivlnK~D  106 (284)
                      ..+.||+++|-.+..   ...     +...-..+.+|.|||+....  .+..+    .+  ....++....+ |++||+|
T Consensus        83 ~~i~iiDtPGh~~f~---~~~-----~~~~~~~D~~ilVvda~~g~~~~qt~e----~l--~~~~~~~~~~iivviNK~D  148 (410)
T 1kk1_A           83 RRVSFIDAPGHEALM---TTM-----LAGASLMDGAILVIAANEPCPRPQTRE----HL--MALQIIGQKNIIIAQNKIE  148 (410)
T ss_dssp             EEEEEEECSSHHHHH---HHH-----HHCGGGCSEEEEEEETTSCSSCHHHHH----HH--HHHHHHTCCCEEEEEECGG
T ss_pred             cEEEEEECCChHHHH---HHH-----HhhhhhCCEEEEEEECCCCCCChhHHH----HH--HHHHHcCCCcEEEEEECcc
Confidence            357889999954322   211     11223568899999998531  11111    01  12234444444 6689999


Q ss_pred             CCChhHHH----HHHHHHHHhC-CCCceeeecc-CCCChhhhh
Q 023301          107 LVTETELG----SLTERIKHIN-AMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       107 ~~~~~~~~----~~~~~l~~~n-p~a~i~~~~~-g~v~~~~l~  143 (284)
                      +.+.++..    +++++++... ...+++.++. .......|+
T Consensus       149 l~~~~~~~~~~~~i~~~l~~~~~~~~~~i~vSA~~g~gi~~L~  191 (410)
T 1kk1_A          149 LVDKEKALENYRQIKEFIEGTVAENAPIIPISALHGANIDVLV  191 (410)
T ss_dssp             GSCHHHHHHHHHHHHHHHTTSTTTTCCEEECBTTTTBSHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhcCcCCCeEEEeeCCCCCCHHHHH
Confidence            99876543    3334433321 3567777653 233444443

>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=90.72  E-value=0.7  Score=41.91  Aligned_cols=90  Identities=19%  Similarity=0.168  Sum_probs=49.8

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHH-hhhhcCCccchHHHHHHHhhcC-EEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQ-HLNEVKPRFVVNEAVEQVAYAD-RIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~-~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~  107 (284)
                      ..+.|++|+|..+.......        ..-..+.+|.|+|+..-.. +..+    .+  .+..++.... +||+||+|+
T Consensus       104 ~~~~iiDtpGh~~f~~~~~~--------~~~~aD~~ilVvDa~~g~~~qt~~----~l--~~~~~~~~~~iIvviNK~Dl  169 (434)
T 1zun_B          104 RKFIIADTPGHEQYTRNMAT--------GASTCDLAIILVDARYGVQTQTRR----HS--YIASLLGIKHIVVAINKMDL  169 (434)
T ss_dssp             EEEEEEECCCSGGGHHHHHH--------HHTTCSEEEEEEETTTCSCHHHHH----HH--HHHHHTTCCEEEEEEECTTT
T ss_pred             ceEEEEECCChHHHHHHHHH--------HHhhCCEEEEEEECCCCCcHHHHH----HH--HHHHHcCCCeEEEEEEcCcC
Confidence            35789999997764332211        1235678999999976321 1100    00  1223444333 667999999


Q ss_pred             CC--hhHHHH----HHHHHHHhC---CCCceeeec
Q 023301          108 VT--ETELGS----LTERIKHIN---AMAPVKLAK  133 (284)
Q Consensus       108 ~~--~~~~~~----~~~~l~~~n---p~a~i~~~~  133 (284)
                      .+  ++.++.    ++++++.++   +..+++.++
T Consensus       170 ~~~~~~~~~~i~~~~~~~~~~~g~~~~~~~~i~vS  204 (434)
T 1zun_B          170 NGFDERVFESIKADYLKFAEGIAFKPTTMAFVPMS  204 (434)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHTTTCCCSEEEEEECC
T ss_pred             CcccHHHHHHHHHHHHHHHHHhCCCccCceEEEEe
Confidence            86  333333    344444454   235677655

>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=90.72  E-value=0.26  Score=38.40  Aligned_cols=80  Identities=19%  Similarity=0.243  Sum_probs=41.9

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH---HhhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ---VAYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q---i~~Ad~ivlnK~D  106 (284)
                      ....+++++|......    +.. ..+   -..+.++.|+|+.+.... .+.. .++ ..+...   -...-++|+||+|
T Consensus        62 ~~~~~~Dt~G~~~~~~----~~~-~~~---~~~d~ii~v~d~~~~~s~-~~~~-~~~-~~~~~~~~~~~~piilv~nK~D  130 (186)
T 1ksh_A           62 FKLNIWDVGGQKSLRS----YWR-NYF---ESTDGLIWVVDSADRQRM-QDCQ-REL-QSLLVEERLAGATLLIFANKQD  130 (186)
T ss_dssp             EEEEEEEECCSHHHHT----TGG-GGC---TTCSEEEEEEETTCGGGH-HHHH-HHH-HHHHTCGGGTTCEEEEEEECTT
T ss_pred             EEEEEEECCCCHhHHH----HHH-HHh---cCCCEEEEEEECcCHHHH-HHHH-HHH-HHHHhChhcCCCcEEEEEeCcc
Confidence            3457889999754322    211 111   246789999999774321 1100 000 011111   1223478889999


Q ss_pred             CCChhHHHHHHHHH
Q 023301          107 LVTETELGSLTERI  120 (284)
Q Consensus       107 ~~~~~~~~~~~~~l  120 (284)
                      +.+....+.+.+.+
T Consensus       131 l~~~~~~~~~~~~~  144 (186)
T 1ksh_A          131 LPGALSCNAIQEAL  144 (186)
T ss_dssp             STTCCCHHHHHHHT
T ss_pred             CCCCCCHHHHHHHh
Confidence            97765555554444

>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=90.65  E-value=1  Score=41.00  Aligned_cols=94  Identities=19%  Similarity=0.308  Sum_probs=52.1

Q ss_pred             CCCCEEEEecCCCCC---cHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEcc
Q 023301           28 GQFDHIVIETTGLAK---PAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNK  104 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~---p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK  104 (284)
                      ..+|+|||+|.|...   -..+...+..   +.....-+.++.|+|+..-.....      .... ..+-...+.||+||
T Consensus       178 ~~~DvvIIDTaGr~~~~~d~~lm~el~~---i~~~~~pd~vlLVlDa~~gq~a~~------~a~~-f~~~~~~~gVIlTK  247 (433)
T 3kl4_A          178 NKMDIIIVDTAGRHGYGEETKLLEEMKE---MYDVLKPDDVILVIDASIGQKAYD------LASR-FHQASPIGSVIITK  247 (433)
T ss_dssp             TTCSEEEEEECCCSSSCCTTHHHHHHHH---HHHHHCCSEEEEEEEGGGGGGGHH------HHHH-HHHHCSSEEEEEEC
T ss_pred             cCCCEEEEECCCCccccCCHHHHHHHHH---HHHhhCCcceEEEEeCccchHHHH------HHHH-HhcccCCcEEEEec
Confidence            579999999999744   1223333221   112233467899999987432111      1111 22233568899999


Q ss_pred             CCCCChhHHHHHHHHHHHhCCCCceeeeccC
Q 023301          105 IDLVTETELGSLTERIKHINAMAPVKLAKYG  135 (284)
Q Consensus       105 ~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g  135 (284)
                      .|....  ...+.......  ..||.....|
T Consensus       248 lD~~a~--~G~als~~~~~--g~Pi~fig~G  274 (433)
T 3kl4_A          248 MDGTAK--GGGALSAVVAT--GATIKFIGTG  274 (433)
T ss_dssp             GGGCSC--HHHHHHHHHHH--TCEEEEEECC
T ss_pred             cccccc--chHHHHHHHHH--CCCEEEEECC
Confidence            998542  23333444433  3566555545

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=90.60  E-value=0.58  Score=36.58  Aligned_cols=99  Identities=16%  Similarity=0.281  Sum_probs=52.4

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D~  107 (284)
                      ...|++++|......+.....        -..+.+|.|+|+.+.... .... .++ .. ..+.   ...-+||+||+|+
T Consensus        66 ~~~i~Dt~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~~-~~~-~~-i~~~~~~~~p~ilv~nK~Dl  133 (196)
T 3tkl_A           66 KLQIWDTAGQERFRTITSSYY--------RGAHGIIVVYDVTDQESF-NNVK-QWL-QE-IDRYASENVNKLLVGNKCDL  133 (196)
T ss_dssp             EEEEEEECCSGGGCTTHHHHH--------TTCSEEEEEEETTCHHHH-HTHH-HHH-HH-HHHHSCTTCEEEEEEECTTC
T ss_pred             EEEEEECCCcHhhhhhHHHHH--------hhCCEEEEEEECcCHHHH-HHHH-HHH-HH-HHHhcCCCCCEEEEEECccc
Confidence            466779999655443333221        135779999999885432 2110 011 11 1222   2344788899999


Q ss_pred             CChhHH--HHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          108 VTETEL--GSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       108 ~~~~~~--~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      .+....  ...+++.+.++  +++++++. .......++
T Consensus       134 ~~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~g~gv~~l~  170 (196)
T 3tkl_A          134 TTKKVVDYTTAKEFADSLG--IPFLETSAKNATNVEQSF  170 (196)
T ss_dssp             TTTCCSCHHHHHHHHHHTT--CCEEEECTTTCTTHHHHH
T ss_pred             ccccccCHHHHHHHHHHcC--CcEEEEeCCCCCCHHHHH
Confidence            765332  33444444443  57776653 233455444

>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=90.59  E-value=0.39  Score=36.43  Aligned_cols=90  Identities=11%  Similarity=0.197  Sum_probs=47.2

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-hhcCEEEEccCCCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-AYADRIILNKIDLVT  109 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-~~Ad~ivlnK~D~~~  109 (284)
                      ...+++++|......+....     +   -..+.++.|+|+...... .+.. .++ ..+.... ...-++|+||+|+.+
T Consensus        55 ~~~l~Dt~G~~~~~~~~~~~-----~---~~~d~~i~v~d~~~~~s~-~~~~-~~~-~~i~~~~~~~piilv~nK~Dl~~  123 (168)
T 1z2a_A           55 RLMLWDTAGQEEFDAITKAY-----Y---RGAQACVLVFSTTDRESF-EAIS-SWR-EKVVAEVGDIPTALVQNKIDLLD  123 (168)
T ss_dssp             EEEEECCTTGGGTTCCCHHH-----H---TTCCEEEEEEETTCHHHH-HTHH-HHH-HHHHHHHCSCCEEEEEECGGGGG
T ss_pred             EEEEEcCCCcHhHHHHHHHH-----h---cCCCEEEEEEECcCHHHH-HHHH-HHH-HHHHHhCCCCCEEEEEECcccCc
Confidence            56778899854433221111     1   146789999999875422 2110 011 1111211 345578889999865


Q ss_pred             hhH--HHHHHHHHHHhCCCCceeeec
Q 023301          110 ETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       110 ~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ..+  .+.+++..+..+  .+++.++
T Consensus       124 ~~~~~~~~~~~~~~~~~--~~~~~~S  147 (168)
T 1z2a_A          124 DSCIKNEEAEGLAKRLK--LRFYRTS  147 (168)
T ss_dssp             GCSSCHHHHHHHHHHHT--CEEEECB
T ss_pred             ccccCHHHHHHHHHHcC--CeEEEEe
Confidence            322  344555555443  4666655

>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=90.55  E-value=0.5  Score=42.50  Aligned_cols=100  Identities=23%  Similarity=0.319  Sum_probs=52.4

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH--HhhhhcCCccchHHHHHHHhhcC-EEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM--QHLNEVKPRFVVNEAVEQVAYAD-RIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~--~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D  106 (284)
                      ..+.|++++|-.+.   ....     ....-..+.+|.|+|+..-.  .+..+    .+  ....++.... +|++||+|
T Consensus        81 ~~i~iiDtPGh~~f---~~~~-----~~~~~~~D~~ilVvda~~g~~~~qt~e----~l--~~~~~l~~~~iivv~NK~D  146 (408)
T 1s0u_A           81 RRVSFVDSPGHETL---MATM-----LSGASLMDGAILVIAANEPCPQPQTKE----HL--MALEILGIDKIIIVQNKID  146 (408)
T ss_dssp             EEEEEEECSSHHHH---HHHH-----HTTCSCCSEEEEEEETTSCSSCHHHHH----HH--HHHHHTTCCCEEEEEECTT
T ss_pred             cEEEEEECCCHHHH---HHHH-----HHhHhhCCEEEEEEECCCCCCCchhHH----HH--HHHHHcCCCeEEEEEEccC
Confidence            35788999995332   2221     12233678899999998521  11111    01  1123344333 58889999


Q ss_pred             CCChhH----HHHHHHHHHHhC-CCCceeeecc-CCCChhhhh
Q 023301          107 LVTETE----LGSLTERIKHIN-AMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       107 ~~~~~~----~~~~~~~l~~~n-p~a~i~~~~~-g~v~~~~l~  143 (284)
                      +.+.++    .++++++++... ...+++.++. ....++.|+
T Consensus       147 l~~~~~~~~~~~~i~~~l~~~~~~~~~~i~vSA~~g~gi~~L~  189 (408)
T 1s0u_A          147 LVDEKQAEENYEQIKEFVKGTIAENAPIIPISAHHEANIDVLL  189 (408)
T ss_dssp             SSCTTTTTTHHHHHHHHHTTSTTTTCCEEEC------CHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHhhcCCCCCeEEEeeCCCCCCHHHHH
Confidence            987543    455566555433 3567777653 223444443

>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=90.52  E-value=0.48  Score=37.41  Aligned_cols=77  Identities=19%  Similarity=0.312  Sum_probs=39.2

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-------hhcCEEE
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-------AYADRII  101 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-------~~Ad~iv  101 (284)
                      .....+++++|......+....     +   -..+.++.|+|+.+.... .+.      .....++       ...-+||
T Consensus        72 ~~~~~i~Dt~G~~~~~~~~~~~-----~---~~~d~iilv~D~~~~~s~-~~~------~~~l~~~~~~~~~~~~piilv  136 (192)
T 2b6h_A           72 NICFTVWDVGGQDKIRPLWRHY-----F---QNTQGLIFVVDSNDRERV-QES------ADELQKMLQEDELRDAVLLVF  136 (192)
T ss_dssp             TEEEEEEECC-----CTTHHHH-----H---HTCCEEEEEEETTCGGGH-HHH------HHHHHHHHTCGGGTTCEEEEE
T ss_pred             CEEEEEEECCCCHhHHHHHHHH-----h---ccCCEEEEEEECCCHHHH-HHH------HHHHHHHhcccccCCCeEEEE
Confidence            3456788999975543322221     1   246779999999775321 111      0112222       2234788


Q ss_pred             EccCCCCChhHHHHHHHHH
Q 023301          102 LNKIDLVTETELGSLTERI  120 (284)
Q Consensus       102 lnK~D~~~~~~~~~~~~~l  120 (284)
                      +||+|+.+....+++.+.+
T Consensus       137 ~NK~Dl~~~~~~~~i~~~~  155 (192)
T 2b6h_A          137 ANKQDMPNAMPVSELTDKL  155 (192)
T ss_dssp             EECTTSTTCCCHHHHHHHT
T ss_pred             EECCCCCCCCCHHHHHHHh
Confidence            8999997654444444433

>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=90.50  E-value=0.46  Score=40.91  Aligned_cols=80  Identities=21%  Similarity=0.194  Sum_probs=44.0

Q ss_pred             eeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhH---HHHHHHHHHHhCCCCceeeecc-C
Q 023301           60 VKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETE---LGSLTERIKHINAMAPVKLAKY-G  135 (284)
Q Consensus        60 ~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~---~~~~~~~l~~~np~a~i~~~~~-g  135 (284)
                      -.++.++.|+|+.+........ ++++.  ...+-...-+||+||+|+.++.+   .+.+.+..+.++  .+++.++. .
T Consensus        78 ~naD~vliV~d~~~p~~s~~~l-~~~l~--~~~~~~~~~ilV~NK~DL~~~~~v~~~~~~~~~~~~~g--~~~~~~SA~~  152 (302)
T 2yv5_A           78 ANVDRVIIVETLKMPEFNNYLL-DNMLV--VYEYFKVEPVIVFNKIDLLNEEEKKELERWISIYRDAG--YDVLKVSAKT  152 (302)
T ss_dssp             ESCCEEEEEECSTTTTCCHHHH-HHHHH--HHHHTTCEEEEEECCGGGCCHHHHHHHHHHHHHHHHTT--CEEEECCTTT
T ss_pred             HhcCEEEEEEECCCCCCCHHHH-HHHHH--HHHhCCCCEEEEEEcccCCCccccHHHHHHHHHHHHCC--CeEEEEECCC
Confidence            4788999999998632111100 11111  11122233478899999988753   444555555443  46776653 3


Q ss_pred             CCChhhhhc
Q 023301          136 SVDMDFVLG  144 (284)
Q Consensus       136 ~v~~~~l~~  144 (284)
                      ....+.++.
T Consensus       153 g~gi~~L~~  161 (302)
T 2yv5_A          153 GEGIDELVD  161 (302)
T ss_dssp             CTTHHHHHH
T ss_pred             CCCHHHHHh
Confidence            445566654

>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=90.40  E-value=0.54  Score=36.83  Aligned_cols=79  Identities=14%  Similarity=0.194  Sum_probs=40.2

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH---HhhcCEEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ---VAYADRIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q---i~~Ad~ivlnK~D~  107 (284)
                      ...+++++|......+....     +   -..+.+|.|+|+.+.... .... .++ ..+..+   -...=+||+||+|+
T Consensus        68 ~~~l~Dt~G~~~~~~~~~~~-----~---~~~d~ii~v~D~~~~~s~-~~~~-~~~-~~~~~~~~~~~~piilv~NK~Dl  136 (188)
T 1zd9_A           68 TIKLWDIGGQPRFRSMWERY-----C---RGVSAIVYMVDAADQEKI-EASK-NEL-HNLLDKPQLQGIPVLVLGNKRDL  136 (188)
T ss_dssp             EEEEEEECCSHHHHTTHHHH-----H---TTCSEEEEEEETTCGGGH-HHHH-HHH-HHHHTCGGGTTCCEEEEEECTTS
T ss_pred             EEEEEECCCCHhHHHHHHHH-----H---ccCCEEEEEEECCCHHHH-HHHH-HHH-HHHHhCcccCCCCEEEEEECCCC
Confidence            45688999965433322221     1   245779999999764321 1100 001 011111   12234788899999


Q ss_pred             CChhHHHHHHHHH
Q 023301          108 VTETELGSLTERI  120 (284)
Q Consensus       108 ~~~~~~~~~~~~l  120 (284)
                      .+....+++.+.+
T Consensus       137 ~~~~~~~~~~~~~  149 (188)
T 1zd9_A          137 PGALDEKELIEKM  149 (188)
T ss_dssp             TTCCCHHHHHHHT
T ss_pred             ccCCCHHHHHHHh
Confidence            7653344444433

>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=90.37  E-value=2.4  Score=36.37  Aligned_cols=91  Identities=19%  Similarity=0.275  Sum_probs=50.4

Q ss_pred             CCCCEEEEecCCCCC--cHH-HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh--h-cCEEE
Q 023301           28 GQFDHIVIETTGLAK--PAP-VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA--Y-ADRII  101 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~--p~~-i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~--~-Ad~iv  101 (284)
                      .++|+|||.|+|...  ... +...+.   .+......+.++.|+|+......+         ..+ .++.  . -..||
T Consensus       179 ~~~D~ViIDTpg~~~~~~~~~l~~el~---~i~~~~~~d~vllVvda~~g~~~~---------~~~-~~~~~~~~i~gvV  245 (297)
T 1j8m_F          179 EKMEIIIVDTAGRHGYGEEAALLEEMK---NIYEAIKPDEVTLVIDASIGQKAY---------DLA-SKFNQASKIGTII  245 (297)
T ss_dssp             TTCSEEEEECCCSCCTTCHHHHHHHHH---HHHHHHCCSEEEEEEEGGGGGGHH---------HHH-HHHHHTCTTEEEE
T ss_pred             CCCCEEEEeCCCCcccccHHHHHHHHH---HHHHHhcCCEEEEEeeCCchHHHH---------HHH-HHHHhhCCCCEEE
Confidence            678999999999988  432 332221   111223567789999997532211         111 1221  1 25789


Q ss_pred             EccCCCCChhHHHHHHHHHHHhCCCCceeeeccC
Q 023301          102 LNKIDLVTETELGSLTERIKHINAMAPVKLAKYG  135 (284)
Q Consensus       102 lnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g  135 (284)
                      +||.|....  ...+.......  ..+|.....|
T Consensus       246 lnk~D~~~~--~g~~~~~~~~~--~~pi~~i~~G  275 (297)
T 1j8m_F          246 ITKMDGTAK--GGGALSAVAAT--GATIKFIGTG  275 (297)
T ss_dssp             EECGGGCTT--HHHHHHHHHTT--TCCEEEEECS
T ss_pred             EeCCCCCcc--hHHHHHHHHHH--CcCEEEEeCC
Confidence            999998542  23333433333  3566554444

>3j2k_7 ERF3, eukaryotic polypeptide chain release factor 3; rabbit 80S ribosome, ribosome-translation complex; 17.00A {Oryctolagus cuniculus}

Probab=90.30  E-value=0.65  Score=42.24  Aligned_cols=96  Identities=9%  Similarity=0.108  Sum_probs=49.1

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHh--hhhcCCccchHH-HHHHHhhc-CEEEEcc
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQH--LNEVKPRFVVNE-AVEQVAYA-DRIILNK  104 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~--l~~~~~~~~~~~-~~~Qi~~A-d~ivlnK  104 (284)
                      +..+.|+.|+|-.+......        ...-..+.++.|||+......  +.. .+...... ....+... =+|++||
T Consensus        94 ~~~~~iiDTPGh~~f~~~~~--------~~~~~aD~~ilVVDa~~g~~e~~~~~-~~qt~e~l~~~~~~~v~~iIvviNK  164 (439)
T 3j2k_7           94 KKHFTILDAPGHKSFVPNMI--------GGASQADLAVLVISARKGEFETGFEK-GGQTREHAMLAKTAGVKHLIVLINK  164 (439)
T ss_pred             CeEEEEEECCChHHHHHHHH--------hhHhhCCEEEEEEECCCCccccccCC-CchHHHHHHHHHHcCCCeEEEEeec
Confidence            34678999999755422111        112357889999999874310  000 00000011 12334444 3678899


Q ss_pred             CCCCC----hhHHHHHHH----HHHHhC--C--CCceeeec
Q 023301          105 IDLVT----ETELGSLTE----RIKHIN--A--MAPVKLAK  133 (284)
Q Consensus       105 ~D~~~----~~~~~~~~~----~l~~~n--p--~a~i~~~~  133 (284)
                      +|+.+    .+..+.+.+    +++.+.  |  .++++.++
T Consensus       165 ~Dl~~~~~~~~~~~~i~~~~~~~l~~~g~~~~~~~~~i~iS  205 (439)
T 3j2k_7          165 MDDPTVNWSNERYEECKEKLVPFLKKVGFNPKKDIHFMPCS  205 (439)
T ss_pred             CCCcccchHHHHHHHHHHHHHHHHHHhcccccCCeeEEEee
Confidence            99964    233333333    333332  2  45677654

>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=90.28  E-value=0.72  Score=34.80  Aligned_cols=91  Identities=10%  Similarity=0.068  Sum_probs=49.7

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D~  107 (284)
                      ...+++++|......+.....        -..+.++.|+|+...... .+.. .+. ..+....   ...=++|+||+|+
T Consensus        52 ~~~l~D~~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~~-~~~-~~i~~~~~~~~~piilv~nK~Dl  120 (167)
T 1c1y_A           52 MLEILDTAGTEQFTAMRDLYM--------KNGQGFALVYSITAQSTF-NDLQ-DLR-EQILRVKDTEDVPMILVGNKCDL  120 (167)
T ss_dssp             EEEEEEECSSCSSTTHHHHHH--------HHCSEEEEEEETTCHHHH-HTHH-HHH-HHHHHHHCCSCCCEEEEEECTTC
T ss_pred             EEEEEECCChHHHHHHHHHHh--------ccCCEEEEEEECCCHHHH-HHHH-HHH-HHHHHhhCcCCCcEEEEEECccc
Confidence            357889999877665444322        135678999999875432 1110 011 1112221   1233788899999


Q ss_pred             CChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          108 VTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       108 ~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      .+..+  .+.+.+..+.+ +..+++.++
T Consensus       121 ~~~~~~~~~~~~~~~~~~-~~~~~~~~S  147 (167)
T 1c1y_A          121 EDERVVGKEQGQNLARQW-CNCAFLESS  147 (167)
T ss_dssp             GGGCCSCHHHHHHHHHHT-TSCEEEECB
T ss_pred             cccccCCHHHHHHHHHHc-cCCcEEEec
Confidence            65432  34444444443 456777665

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C

Probab=90.25  E-value=0.69  Score=36.49  Aligned_cols=87  Identities=13%  Similarity=0.068  Sum_probs=45.8

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---------hcCEE
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---------YADRI  100 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---------~Ad~i  100 (284)
                      ....|++++|......+...     .+   -..+.+|.|+|+.+.... ...      ..+..++.         ..=+|
T Consensus        73 ~~~~l~Dt~G~~~~~~~~~~-----~~---~~~d~~i~v~d~~~~~s~-~~~------~~~~~~i~~~~~~~~~~~piil  137 (208)
T 2yc2_C           73 VELFLLDTAGSDLYKEQISQ-----YW---NGVYYAILVFDVSSMESF-ESC------KAWFELLKSARPDRERPLRAVL  137 (208)
T ss_dssp             EEEEEEETTTTHHHHHHHST-----TC---CCCCEEEEEEETTCHHHH-HHH------HHHHHHHHHHCSCTTSCCEEEE
T ss_pred             EEEEEEECCCcHHHHHHHHH-----HH---hhCcEEEEEEECCCHHHH-HHH------HHHHHHHHHhhcccccCCcEEE
Confidence            45788899998554332211     11   246789999999875432 111      11222322         22378


Q ss_pred             EEccCCCCC-hhH--HHHHHHHHHHhCCCCceeeec
Q 023301          101 ILNKIDLVT-ETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       101 vlnK~D~~~-~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      |+||+|+.+ ..+  .+.+.++.+.++  .+++.++
T Consensus       138 v~nK~Dl~~~~~~v~~~~~~~~~~~~~--~~~~~~S  171 (208)
T 2yc2_C          138 VANKTDLPPQRHQVRLDMAQDWATTNT--LDFFDVS  171 (208)
T ss_dssp             EEECC-------CCCHHHHHHHHHHTT--CEEEECC
T ss_pred             EEECcccchhhccCCHHHHHHHHHHcC--CEEEEec
Confidence            889999976 222  345566666554  5666654

>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=90.11  E-value=0.54  Score=42.13  Aligned_cols=92  Identities=16%  Similarity=0.169  Sum_probs=51.1

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC-EEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~  107 (284)
                      ...+.|++|+|..+......        ...-..+.+|.|+|+..-...  +.  +... ....+..... +|++||+|+
T Consensus        65 ~~~~~iiDtpG~~~f~~~~~--------~~~~~aD~~ilVvda~~g~~~--qt--~e~l-~~~~~~~vp~iivviNK~Dl  131 (397)
T 1d2e_A           65 ARHYAHTDCPGHADYVKNMI--------TGTAPLDGCILVVAANDGPMP--QT--REHL-LLARQIGVEHVVVYVNKADA  131 (397)
T ss_dssp             SCEEEEEECSSHHHHHHHHH--------HTSSCCSEEEEEEETTTCSCH--HH--HHHH-HHHHHTTCCCEEEEEECGGG
T ss_pred             CeEEEEEECCChHHHHHHHH--------hhHhhCCEEEEEEECCCCCCH--HH--HHHH-HHHHHcCCCeEEEEEECccc
Confidence            35688999999765322111        112357889999999873211  00  0000 1123344454 578999999


Q ss_pred             CC-hhHH----HHHHHHHHHhCC---CCceeeec
Q 023301          108 VT-ETEL----GSLTERIKHINA---MAPVKLAK  133 (284)
Q Consensus       108 ~~-~~~~----~~~~~~l~~~np---~a~i~~~~  133 (284)
                      .+ ++.+    ++++++++.++-   ..+++.++
T Consensus       132 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~i~~S  165 (397)
T 1d2e_A          132 VQDSEMVELVELEIRELLTEFGYKGEETPIIVGS  165 (397)
T ss_dssp             CSCHHHHHHHHHHHHHHHHHTTSCTTTSCEEECC
T ss_pred             CCCHHHHHHHHHHHHHHHHHcCCCcccCcEEEee
Confidence            85 3333    345555655541   36777664

>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=90.08  E-value=0.56  Score=36.72  Aligned_cols=85  Identities=13%  Similarity=0.078  Sum_probs=47.4

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh------hcCEEEEccC
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA------YADRIILNKI  105 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~------~Ad~ivlnK~  105 (284)
                      ..|++++|......+.....        -..+.+|.|+|+...... ...      .....++.      ..=+||+||+
T Consensus        76 ~~i~Dt~G~~~~~~~~~~~~--------~~~d~vi~v~D~~~~~s~-~~~------~~~l~~i~~~~~~~~piilv~nK~  140 (193)
T 2oil_A           76 AQIWDTAGLERYRAITSAYY--------RGAVGALLVFDLTKHQTY-AVV------ERWLKELYDHAEATIVVMLVGNKS  140 (193)
T ss_dssp             EEEEEESCCCTTCTTHHHHH--------TTCCEEEEEEETTCHHHH-HTH------HHHHHHHHTTSCTTCEEEEEEECG
T ss_pred             EEEEeCCCchhhhhhhHHHh--------ccCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhcCCCCeEEEEEECC
Confidence            35789999876554433321        135678999999875432 111      11223332      2237888999


Q ss_pred             CCCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          106 DLVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       106 D~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      |+.+..+  .+..+++.+..  .++++.++
T Consensus       141 Dl~~~~~~~~~~~~~~~~~~--~~~~~~~S  168 (193)
T 2oil_A          141 DLSQAREVPTEEARMFAENN--GLLFLETS  168 (193)
T ss_dssp             GGGGGCCSCHHHHHHHHHHT--TCEEEEEC
T ss_pred             CcccccccCHHHHHHHHHHc--CCEEEEEe
Confidence            9965322  34444444433  35677665

>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=89.97  E-value=1  Score=33.99  Aligned_cols=86  Identities=16%  Similarity=0.162  Sum_probs=45.3

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcC---EEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YAD---RIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad---~ivlnK  104 (284)
                      ...+++++|......+.....        -..+.++.|+|+.+.... .+.      ..+..++.   ..+   ++|.||
T Consensus        56 ~~~~~Dt~G~~~~~~~~~~~~--------~~~~~~i~v~d~~~~~s~-~~~------~~~~~~l~~~~~~~~~iilv~nK  120 (170)
T 1z0j_A           56 KFLIWDTAGLERFRALAPMYY--------RGSAAAIIVYDITKEETF-STL------KNWVRELRQHGPPSIVVAIAGNK  120 (170)
T ss_dssp             EEEEEEECCSGGGGGGTHHHH--------TTCSEEEEEEETTCHHHH-HHH------HHHHHHHHHHSCTTSEEEEEEEC
T ss_pred             EEEEEcCCCchhhhcccHhhC--------cCCCEEEEEEECcCHHHH-HHH------HHHHHHHHHhCCCCCcEEEEEEC
Confidence            456889999865444332221        134678999999875432 111      11122222   222   355599


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +|+.+..+  .+...+..+..+  .+++.++
T Consensus       121 ~Dl~~~~~v~~~~~~~~~~~~~--~~~~~~S  149 (170)
T 1z0j_A          121 CDLTDVREVMERDAKDYADSIH--AIFVETS  149 (170)
T ss_dssp             TTCGGGCCSCHHHHHHHHHHTT--CEEEECB
T ss_pred             CccccccccCHHHHHHHHHHcC--CEEEEEe
Confidence            99975432  233444444433  5676665

>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=89.90  E-value=1.7  Score=32.47  Aligned_cols=89  Identities=15%  Similarity=0.171  Sum_probs=48.6

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCCCC
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKIDLV  108 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D~~  108 (284)
                      ..+++++|......+.....        -..+.++.|+|+...... .+..  .....+....   ...=++|+||+|+.
T Consensus        53 ~~l~D~~G~~~~~~~~~~~~--------~~~~~~i~v~d~~~~~s~-~~~~--~~~~~i~~~~~~~~~piilv~nK~Dl~  121 (167)
T 1kao_A           53 LEILDTAGTEQFASMRDLYI--------KNGQGFILVYSLVNQQSF-QDIK--PMRDQIIRVKRYEKVPVILVGNKVDLE  121 (167)
T ss_dssp             EEEEECCCTTCCHHHHHHHH--------HHCSEEEEEEETTCHHHH-HHHH--HHHHHHHHHTTTSCCCEEEEEECGGGG
T ss_pred             EEEEECCCchhhHHHHHHHh--------ccCCEEEEEEeCCCHHHH-HHHH--HHHHHHHHhcCCCCCCEEEEEECCccc
Confidence            66889999887766544321        134678999999874432 1110  0001122222   22347888999986


Q ss_pred             ChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          109 TETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       109 ~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +..+  .+..++..+..+  .+++.++
T Consensus       122 ~~~~~~~~~~~~~~~~~~--~~~~~~S  146 (167)
T 1kao_A          122 SEREVSSSEGRALAEEWG--CPFMETS  146 (167)
T ss_dssp             GGCCSCHHHHHHHHHHHT--SCEEEEC
T ss_pred             ccccCCHHHHHHHHHHhC--CCEEEec
Confidence            5332  233444444443  4666654

>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=89.84  E-value=0.4  Score=38.50  Aligned_cols=81  Identities=17%  Similarity=0.201  Sum_probs=41.9

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH------hhcCEEEEc
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV------AYADRIILN  103 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi------~~Ad~ivln  103 (284)
                      ....+++++|..............    ..-..+.+|.|+|+..-...+... ..++ ..+....      ...=+||+|
T Consensus        55 ~~~~l~Dt~G~~~~~~~~~~~~~~----~~~~~~~~i~v~D~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~p~ilv~n  128 (218)
T 1nrj_B           55 SGVTLVDFPGHVKLRYKLSDYLKT----RAKFVKGLIFMVDSTVDPKKLTTT-AEFL-VDILSITESSCENGIDILIACN  128 (218)
T ss_dssp             SSCEEEECCCCGGGTHHHHHHHHH----HGGGEEEEEEEEETTSCTTCCHHH-HHHH-HHHHHHHHHHSTTCCCEEEEEE
T ss_pred             ceEEEEECCCcHHHHHHHHHHHHh----ccccCCEEEEEEECCCChHHHHHH-HHHH-HHHHhcccccccCCCCEEEEEE
Confidence            367789999997765544433211    011256789999998111111110 0011 1111111      123467889


Q ss_pred             cCCCCChhHHHHH
Q 023301          104 KIDLVTETELGSL  116 (284)
Q Consensus       104 K~D~~~~~~~~~~  116 (284)
                      |+|+.+......+
T Consensus       129 K~Dl~~~~~~~~~  141 (218)
T 1nrj_B          129 KSELFTARPPSKI  141 (218)
T ss_dssp             CTTSTTCCCHHHH
T ss_pred             chHhcccCCHHHH
Confidence            9999876554433

>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=89.61  E-value=0.15  Score=46.61  Aligned_cols=105  Identities=15%  Similarity=0.281  Sum_probs=55.8

Q ss_pred             CEEEEecCCCCCcHHH------HHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPV------IETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i------~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK  104 (284)
                      .+.|+.|+|+.....+      ...+.   .+...-..+.++.|+|+..-.....    ..+.. .......+-+||+||
T Consensus       244 ~~~l~DT~G~~~~~~~~~~~e~~~~~~---~~~~~~~ad~~llviD~~~~~~~~~----~~~~~-~~~~~~~~~ilv~NK  315 (456)
T 4dcu_A          244 EFVIVDTAGMRKKGKVYETTEKYSVLR---ALKAIDRSEVVAVVLDGEEGIIEQD----KRIAG-YAHEAGKAVVIVVNK  315 (456)
T ss_dssp             EEEETTGGGTTTBTTBCCCCSHHHHHH---HHHHHHHCSEEEEEEETTTCCCHHH----HHHHH-HHHHTTCEEEEEEEC
T ss_pred             eEEEEECCCCCcCcccchHHHHHHHHH---HHHHHhhCCEEEEEEeCCCCcCHHH----HHHHH-HHHHcCCCEEEEEEC
Confidence            4678899997543211      11111   0111123567899999977321110    01111 112233456889999


Q ss_pred             CCCCCh--hHHHHHHHHHHHhCC---CCceeeecc-CCCChhhhh
Q 023301          105 IDLVTE--TELGSLTERIKHINA---MAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~--~~~~~~~~~l~~~np---~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+.  ...+++.+.+++..+   .++++.++. .......++
T Consensus       316 ~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~g~gv~~l~  360 (456)
T 4dcu_A          316 WDAVDKDESTMKEFEENIRDHFQFLDYAPILFMSALTKKRIHTLM  360 (456)
T ss_dssp             GGGSCCCSSHHHHHHHHHHHHCGGGTTSCEEECCTTTCTTGGGHH
T ss_pred             hhcCCCchHHHHHHHHHHHHhcccCCCCCEEEEcCCCCcCHHHHH
Confidence            999753  345666777776643   578887764 233444443

>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=89.55  E-value=1  Score=34.96  Aligned_cols=96  Identities=11%  Similarity=0.114  Sum_probs=50.9

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh-------cCEEEEc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY-------ADRIILN  103 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~-------Ad~ivln  103 (284)
                      ...|++++|......+.....        -..+.+|.|+|+...... .+.      .....++..       .-+||+|
T Consensus        65 ~~~i~Dt~G~~~~~~~~~~~~--------~~~d~ii~v~d~~~~~s~-~~~------~~~~~~i~~~~~~~~~p~ilv~n  129 (195)
T 1x3s_A           65 KLAIWDTAGQERFRTLTPSYY--------RGAQGVILVYDVTRRDTF-VKL------DNWLNELETYCTRNDIVNMLVGN  129 (195)
T ss_dssp             EEEEEEECSSGGGCCSHHHHH--------TTCCEEEEEEETTCHHHH-HTH------HHHHHHHTTCCSCSCCEEEEEEE
T ss_pred             EEEEEeCCCchhhhhhhHHHh--------ccCCEEEEEEECcCHHHH-HHH------HHHHHHHHHhcCcCCCcEEEEEE
Confidence            456779999654433322211        135789999999875432 111      112233332       2268999


Q ss_pred             cCCCCChh-HHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          104 KIDLVTET-ELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       104 K~D~~~~~-~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+|+.+.+ ..+...++.+..+  .+++.++. .......++
T Consensus       130 K~Dl~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  169 (195)
T 1x3s_A          130 KIDKENREVDRNEGLKFARKHS--MLFIEASAKTCDGVQCAF  169 (195)
T ss_dssp             CTTSSSCCSCHHHHHHHHHHTT--CEEEECCTTTCTTHHHHH
T ss_pred             CCcCcccccCHHHHHHHHHHcC--CEEEEecCCCCCCHHHHH
Confidence            99985422 1234455555443  56776653 233444443

>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=89.55  E-value=0.52  Score=37.45  Aligned_cols=81  Identities=19%  Similarity=0.193  Sum_probs=38.8

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHH--H-HhhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVE--Q-VAYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~--Q-i~~Ad~ivlnK~D  106 (284)
                      .+..+++++|......+..     ..+   -..+.++.|+|+.+.... .+.. .++ ..+..  . -...=++|.||+|
T Consensus        69 ~~l~i~Dt~G~~~~~~~~~-----~~~---~~~d~~i~v~D~~~~~s~-~~~~-~~~-~~~~~~~~~~~~piilv~NK~D  137 (198)
T 1f6b_A           69 MTFTTFDLGGHIQARRVWK-----NYL---PAINGIVFLVDCADHERL-LESK-EEL-DSLMTDETIANVPILILGNKID  137 (198)
T ss_dssp             EEEEEEEECC----CCGGG-----GGG---GGCSEEEEEEETTCGGGH-HHHH-HHH-HHHHTCGGGTTSCEEEEEECTT
T ss_pred             EEEEEEECCCcHhhHHHHH-----HHH---hcCCEEEEEEECCCHHHH-HHHH-HHH-HHHHhCcccCCCcEEEEEECCC
Confidence            4556778888544332111     111   246789999999774321 1100 011 01111  0 1223478889999


Q ss_pred             CCChhHHHHHHHHHH
Q 023301          107 LVTETELGSLTERIK  121 (284)
Q Consensus       107 ~~~~~~~~~~~~~l~  121 (284)
                      +.+....+++++.++
T Consensus       138 l~~~~~~~~~~~~~~  152 (198)
T 1f6b_A          138 RPEAISEERLREMFG  152 (198)
T ss_dssp             STTCCCHHHHHHHHT
T ss_pred             ccccCCHHHHHHHhC
Confidence            975333445555444

>3cnl_A YLQF, putative uncharacterized protein; circular permutation, GNP, signaling protein; HET: GNP; 2.00A {Thermotoga maritima} PDB: 3cnn_A* 3cno_A*

Probab=89.48  E-value=0.46  Score=40.06  Aligned_cols=55  Identities=20%  Similarity=0.171  Sum_probs=36.7

Q ss_pred             eeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHh
Q 023301           60 VKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHI  123 (284)
Q Consensus        60 ~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~  123 (284)
                      -..+.|+.|+|++.......   + .+.  +.   ...-++|+||+|+++.+..+...+.+++.
T Consensus        20 ~~~D~vl~VvDar~P~~~~~---~-~l~--ll---~k~~iivlNK~DL~~~~~~~~~~~~~~~~   74 (262)
T 3cnl_A           20 RLVNTVVEVRDARAPFATSA---Y-GVD--FS---RKETIILLNKVDIADEKTTKKWVEFFKKQ   74 (262)
T ss_dssp             TTCSEEEEEEETTSTTTTSC---T-TSC--CT---TSEEEEEEECGGGSCHHHHHHHHHHHHHT
T ss_pred             hhCCEEEEEeeCCCCCcCcC---h-HHH--hc---CCCcEEEEECccCCCHHHHHHHHHHHHHc
Confidence            36788999999987543211   1 111  11   45668999999999987766666666654

>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=89.43  E-value=0.27  Score=48.04  Aligned_cols=74  Identities=14%  Similarity=0.282  Sum_probs=43.6

Q ss_pred             CCCEEEEecCCCCC------cHHH---HHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---h
Q 023301           29 QFDHIVIETTGLAK------PAPV---IETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---Y   96 (284)
Q Consensus        29 ~~d~iiIE~sG~a~------p~~i---~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~   96 (284)
                      .++.+||.++|+..      |..+   +..+.. ..+.  -..+.+++|+|+......    .+  . ..+..++.   .
T Consensus       149 ~~qL~LVDTPGi~~~~~~~qp~di~~~i~~lv~-~yi~--~~aDlIL~VVDAs~~~~~----~d--~-l~ll~~L~~~g~  218 (772)
T 3zvr_A          149 VLNLTLVDLPGMTKVPVGDQPPDIEFQIRDMLM-QFVT--KENCLILAVSPANSDLAN----SD--A-LKIAKEVDPQGQ  218 (772)
T ss_dssp             CCSEEEEECCCCCCCCSSCCCCHHHHHHHHHHH-HHHT--STTEEEEEEEETTSCSSS----CH--H-HHHHHHHCTTCS
T ss_pred             CCceEEEECCCcccCCCCCCcHHHHHHHHHHHH-HHHh--cCCcEEEEEEcCCCCcch----hH--H-HHHHHHHHhcCC
Confidence            46789999999988      4322   222211 1221  134568999999863211    00  0 12345554   3


Q ss_pred             cCEEEEccCCCCChhH
Q 023301           97 ADRIILNKIDLVTETE  112 (284)
Q Consensus        97 Ad~ivlnK~D~~~~~~  112 (284)
                      .-++|+||+|+++...
T Consensus       219 pvIlVlNKiDlv~~~~  234 (772)
T 3zvr_A          219 RTIGVITKLDLMDEGT  234 (772)
T ss_dssp             SEEEEEECTTSSCTTC
T ss_pred             CEEEEEeCcccCCcch
Confidence            5689999999987544

>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=89.42  E-value=0.078  Score=41.86  Aligned_cols=43  Identities=19%  Similarity=0.244  Sum_probs=28.1

Q ss_pred             CCCceeeeeeCc-hH-HHHHHHHHHhhcCCCCEEEEecCCCCCcHHHH
Q 023301            2 VNNGCLCCTVRG-DL-VKMLLQLAKKKQGQFDHIVIETTGLAKPAPVI   47 (284)
Q Consensus         2 L~~GCiCCs~~~-dl-~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~   47 (284)
                      .++||.||..+. ++ .+.+.+++.. . .+|+||||..|- .|.+.+
T Consensus        69 ~s~~~~~~~~~~~~~~~~~~~~ll~~-~-~~D~vlVEg~~~-~~~pki  113 (169)
T 1xjc_A           69 EGDGLLQLHLRRPLWRLDDVLALYAP-L-RLDLVLVEGYKQ-ERHPKV  113 (169)
T ss_dssp             EETTEEEEEECCSCCCHHHHHHHHGG-G-CCSEEEEECCTT-SCSCEE
T ss_pred             ccCCEEEEEecccccchHHHHHHHHh-c-CCCEEEEeCCCC-CCCCEE
Confidence            468899997731 22 2345566662 3 899999999995 444433

>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=89.34  E-value=0.36  Score=37.09  Aligned_cols=100  Identities=13%  Similarity=0.135  Sum_probs=51.0

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~ivlnK~D~  107 (284)
                      ...+++++|......+.....        -..+.++.|+|+...... .+.. .++ ..+..+..   ..=+||+||+|+
T Consensus        58 ~~~~~Dt~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~~-~~~-~~~~~~~~~~~~piilv~nK~Dl  126 (181)
T 2fn4_A           58 RLDILDTAGQEEFGAMREQYM--------RAGHGFLLVFAINDRQSF-NEVG-KLF-TQILRVKDRDDFPVVLVGNKADL  126 (181)
T ss_dssp             EEEEEECCCTTTTSCCHHHHH--------HHCSEEEEEEETTCHHHH-HHHH-HHH-HHHHHHHTSSCCCEEEEEECGGG
T ss_pred             EEEEEECCCchhhHHHHHHHH--------hhCCEEEEEEeCCCHHHH-HHHH-HHH-HHHHHhcCCCCCCEEEEEECccc
Confidence            456789999766544333221        135678999999875432 1110 011 11112221   233788899998


Q ss_pred             CChhHH--HHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          108 VTETEL--GSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       108 ~~~~~~--~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      .+..++  +...++.+..  ..+++.++. .......++
T Consensus       127 ~~~~~v~~~~~~~~~~~~--~~~~~~~Sa~~~~gv~~l~  163 (181)
T 2fn4_A          127 ESQRQVPRSEASAFGASH--HVAYFEASAKLRLNVDEAF  163 (181)
T ss_dssp             GGGCCSCHHHHHHHHHHT--TCEEEECBTTTTBSHHHHH
T ss_pred             ccccccCHHHHHHHHHHc--CCeEEEecCCCCCCHHHHH
Confidence            654322  3333333332  457776653 233444443

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=89.24  E-value=1.1  Score=35.23  Aligned_cols=101  Identities=15%  Similarity=0.229  Sum_probs=53.1

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~ivlnK~D  106 (284)
                      ....+++++|......+.....        -..+.+|.|+|+.+.... .+. ..++ . ...+..   ..=+||+||+|
T Consensus        75 ~~l~l~Dt~G~~~~~~~~~~~~--------~~~d~iilV~D~~~~~s~-~~~-~~~~-~-~i~~~~~~~~piilV~NK~D  142 (192)
T 2il1_A           75 IRLQIWDTAGQERFNSITSAYY--------RSAKGIILVYDITKKETF-DDL-PKWM-K-MIDKYASEDAELLLVGNKLD  142 (192)
T ss_dssp             EEEEEEEECCSGGGHHHHHHHH--------HHCSEEEEEEETTCHHHH-HTH-HHHH-H-HHHHHSCTTCEEEEEEECGG
T ss_pred             EEEEEEeCCCcHHHHHHHHHHh--------cCCCEEEEEEECcCHHHH-HHH-HHHH-H-HHHHhcCCCCcEEEEEECcc
Confidence            3567889999766555433221        245789999999875432 211 0010 1 122222   22378889999


Q ss_pred             CCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          107 LVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       107 ~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +.+..+  .+..+++.+.+ ...+++.++. .......++
T Consensus       143 l~~~~~v~~~~~~~~~~~~-~~~~~~~~SA~~g~gi~~l~  181 (192)
T 2il1_A          143 CETDREITRQQGEKFAQQI-TGMRFCEASAKDNFNVDEIF  181 (192)
T ss_dssp             GGGGCCSCHHHHHHHHHTS-TTCEEEECBTTTTBSHHHHH
T ss_pred             cccccccCHHHHHHHHHhc-CCCeEEEEeCCCCCCHHHHH
Confidence            965322  23344444432 3466776653 233344443

>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=89.19  E-value=1.1  Score=33.81  Aligned_cols=86  Identities=12%  Similarity=-0.010  Sum_probs=39.5

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-------hcCEEEEc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-------YADRIILN  103 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-------~Ad~ivln  103 (284)
                      ...+++++|......+....        .-..+.++.|+|..+.... .+.      .....++.       ..=++|.|
T Consensus        50 ~~~i~D~~g~~~~~~~~~~~--------~~~~~~~i~v~d~~~~~s~-~~~------~~~~~~~~~~~~~~~~p~ilv~n  114 (166)
T 3q72_A           50 SLMVYDIWEQDGGRWLPGHC--------MAMGDAYVIVYSVTDKGSF-EKA------SELRVQLRRARQTDDVPIILVGN  114 (166)
T ss_dssp             EEEEEECC-----------------------CCEEEEEEETTCHHHH-HHH------HHHHHHHHHCC---CCCEEEEEE
T ss_pred             EEEEEECCCCccchhhhhhh--------hhhCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhcCCCCCCEEEEEe
Confidence            34677888876654332221        1245778999998865432 211      11222332       23478889


Q ss_pred             cCCCCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          104 KIDLVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       104 K~D~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      |+|+.+..+  .+..++..+..+  +++++++
T Consensus       115 K~Dl~~~~~~~~~~~~~~~~~~~--~~~~~~S  144 (166)
T 3q72_A          115 KSDLVRSREVSVDEGRACAVVFD--CKFIETS  144 (166)
T ss_dssp             CTTCCSSCCSCHHHHHHHHHHTT--CEEEECB
T ss_pred             ccccccccccCHHHHHHHHHHhC--CcEEEec
Confidence            999975432  223333333333  5777665

>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=89.10  E-value=1.8  Score=33.58  Aligned_cols=103  Identities=17%  Similarity=0.074  Sum_probs=53.8

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-----hhcCEEEEccC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-----AYADRIILNKI  105 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-----~~Ad~ivlnK~  105 (284)
                      ...+++++|......+.....        -..+.+|.|+|+......-....-..+ .....++     ...=+||.||+
T Consensus        75 ~~~i~Dt~G~~~~~~~~~~~~--------~~~d~~i~v~D~~~~~~~~~~~s~~~l-~~~l~~~~~~~~~~piilv~NK~  145 (198)
T 3t1o_A           75 RFHLYTVPGQVFYNASRKLIL--------RGVDGIVFVADSAPNRLRANAESMRNM-RENLAEYGLTLDDVPIVIQVNKR  145 (198)
T ss_dssp             EEEEEECCSCCSCSHHHHHHT--------TTCCEEEEEEECCGGGHHHHHHHHHHH-HHHHHHTTCCTTSSCEEEEEECT
T ss_pred             EEEEEeCCChHHHHHHHHHHH--------hcCCEEEEEEECCcchhhHhHHHHHHH-HHHHHhhccccCCCCEEEEEEch
Confidence            356889999877655444322        135678999999842111000000000 0112222     23346777999


Q ss_pred             CCCChhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          106 DLVTETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       106 D~~~~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+.+....+.+++.++..+- .++++++. .......++
T Consensus       146 Dl~~~~~~~~~~~~~~~~~~-~~~~~~Sa~~~~gv~~l~  183 (198)
T 3t1o_A          146 DLPDALPVEMVRAVVDPEGK-FPVLEAVATEGKGVFETL  183 (198)
T ss_dssp             TSTTCCCHHHHHHHHCTTCC-SCEEECBGGGTBTHHHHH
T ss_pred             hcccccCHHHHHHHHHhcCC-ceEEEEecCCCcCHHHHH
Confidence            99766555666666654431 26666653 233444444

>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=89.04  E-value=1.3  Score=33.40  Aligned_cols=74  Identities=23%  Similarity=0.312  Sum_probs=42.1

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-------hhcCEEEE
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-------AYADRIIL  102 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-------~~Ad~ivl  102 (284)
                      ....+++++|......+.....        -..+.++.|+|+.+.... .+.      .....++       ...=++|+
T Consensus        44 ~~~~i~Dt~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~------~~~~~~~~~~~~~~~~piilv~  108 (164)
T 1r8s_A           44 ISFTVWDVGGQDKIRPLWRHYF--------QNTQGLIFVVDSNDRERV-NEA------REELMRMLAEDELRDAVLLVFA  108 (164)
T ss_dssp             CEEEEEECCCCGGGHHHHHHHT--------TTCSEEEEEEETTCGGGH-HHH------HHHHHHHHTCGGGTTCEEEEEE
T ss_pred             EEEEEEEcCCChhhHHHHHHHh--------ccCCEEEEEEECCCHHHH-HHH------HHHHHHHHhchhhcCCeEEEEE
Confidence            4567889999876555443321        135678999999774321 110      0111222       22347888


Q ss_pred             ccCCCCChhHHHHHHH
Q 023301          103 NKIDLVTETELGSLTE  118 (284)
Q Consensus       103 nK~D~~~~~~~~~~~~  118 (284)
                      ||+|+.+....+.+.+
T Consensus       109 nK~Dl~~~~~~~~~~~  124 (164)
T 1r8s_A          109 NKQDLPNAMNAAEITD  124 (164)
T ss_dssp             ECTTSTTCCCHHHHHH
T ss_pred             ECcCCcCCCCHHHHHH
Confidence            9999976543344433

>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=88.96  E-value=0.2  Score=41.85  Aligned_cols=74  Identities=8%  Similarity=0.025  Sum_probs=40.2

Q ss_pred             CCEEEEecCCCCCcHH----HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-----hhcCEE
Q 023301           30 FDHIVIETTGLAKPAP----VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-----AYADRI  100 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~----i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-----~~Ad~i  100 (284)
                      .+..||+|+|..++..    +.+.+.. ......-..+.+|.|+|+.++.....     .+.. ...++     ...-++
T Consensus        71 ~~i~iiDTpG~~~~~~~~~~~~~~i~~-~~~~~~~~~d~il~V~d~~~~~~~~~-----~~~~-~l~~~~~~~~~~~~i~  143 (260)
T 2xtp_A           71 REIVIIDTPDMFSWKDHCEALYKEVQR-CYLLSAPGPHVLLLVTQLGRYTSQDQ-----QAAQ-RVKEIFGEDAMGHTIV  143 (260)
T ss_dssp             EEEEEEECCGGGGSSCCCHHHHHHHHH-HHHHHTTCCSEEEEEEETTCCCHHHH-----HHHH-HHHHHHCGGGGGGEEE
T ss_pred             CEEEEEECcCCCCCCCCHHHHHHHHHH-HHHhcCCCCcEEEEEEeCCCCCHHHH-----HHHH-HHHHHhCchhhccEEE
Confidence            3578999999887531    1111110 00001124678999999987432211     1111 12222     456788


Q ss_pred             EEc-cCCCCCh
Q 023301          101 ILN-KIDLVTE  110 (284)
Q Consensus       101 vln-K~D~~~~  110 (284)
                      |+| |+|+.+.
T Consensus       144 vv~nK~Dl~~~  154 (260)
T 2xtp_A          144 LFTHKEDLNGG  154 (260)
T ss_dssp             EEECGGGGTTC
T ss_pred             EEEcccccCCc
Confidence            888 9999753

>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=88.96  E-value=2  Score=33.99  Aligned_cols=97  Identities=16%  Similarity=0.174  Sum_probs=52.6

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh------hcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA------YADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~------~Ad~ivlnK  104 (284)
                      ...|++++|......+.....        -..+.+|.|+|+.+.... .+.      .....++.      ..=+||.||
T Consensus        79 ~l~i~Dt~G~~~~~~~~~~~~--------~~~d~iilv~D~~~~~s~-~~~------~~~~~~i~~~~~~~~piilv~NK  143 (201)
T 2hup_A           79 KLQIWDTAGQERFRTITQSYY--------RSANGAILAYDITKRSSF-LSV------PHWIEDVRKYAGSNIVQLLIGNK  143 (201)
T ss_dssp             EEEEECCTTCGGGHHHHHHHH--------TTCSEEEEEEETTBHHHH-HTH------HHHHHHHHHHSCTTCEEEEEEEC
T ss_pred             EEEEEECCCcHhHHHHHHHHH--------hhCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhcCCCCCEEEEEEC
Confidence            556788899766554433321        135779999999875432 211      11223332      223778899


Q ss_pred             CCCCChh--HHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTET--ELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~--~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+..  ..+.++++.+..+ ..++++++. .......++
T Consensus       144 ~Dl~~~~~v~~~~~~~~~~~~~-~~~~~~~SA~~g~gi~~l~  184 (201)
T 2hup_A          144 SDLSELREVSLAEAQSLAEHYD-ILCAIETSAKDSSNVEEAF  184 (201)
T ss_dssp             TTCGGGCCSCHHHHHHHHHHTT-CSEEEECBTTTTBSHHHHH
T ss_pred             CccccccccCHHHHHHHHHHcC-CCEEEEEeCCCCCCHHHHH
Confidence            9996532  2344555555443 126676653 233444444

>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=88.93  E-value=0.71  Score=36.95  Aligned_cols=97  Identities=15%  Similarity=0.124  Sum_probs=50.9

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-------hcCEEEE
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-------YADRIIL  102 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-------~Ad~ivl  102 (284)
                      ....|++++|......+....     +   -..+.+|.|+|+...... .+.      ..+..++.       ..=+||+
T Consensus        84 ~~l~l~Dt~G~~~~~~~~~~~-----~---~~~d~iilV~D~~~~~s~-~~~------~~~l~~i~~~~~~~~~piilV~  148 (217)
T 2f7s_A           84 VHLQLWDTAGQERFRSLTTAF-----F---RDAMGFLLMFDLTSQQSF-LNV------RNWMSQLQANAYCENPDIVLIG  148 (217)
T ss_dssp             EEEEEEEEESHHHHHHHHHHH-----H---TTCCEEEEEEETTCHHHH-HHH------HHHHHTCCCCCTTTCCEEEEEE
T ss_pred             EEEEEEECCCcHhHHhHHHHH-----h---cCCCEEEEEEECcCHHHH-HHH------HHHHHHHHHhcCcCCCCEEEEE
Confidence            446778888854333322221     1   145789999999774432 110      11223332       2237888


Q ss_pred             ccCCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          103 NKIDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       103 nK~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      ||+|+.+..+  .+.++++.+..+  .+++.++. .......++
T Consensus       149 NK~Dl~~~~~v~~~~~~~~~~~~~--~~~~~~Sa~~g~gi~~l~  190 (217)
T 2f7s_A          149 NKADLPDQREVNERQARELADKYG--IPYFETSAATGQNVEKAV  190 (217)
T ss_dssp             ECTTCGGGCCSCHHHHHHHHHHTT--CCEEEEBTTTTBTHHHHH
T ss_pred             ECCccccccccCHHHHHHHHHHCC--CcEEEEECCCCCCHHHHH
Confidence            9999965322  344455555443  56776653 233444444

>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=88.89  E-value=0.95  Score=34.21  Aligned_cols=86  Identities=15%  Similarity=0.163  Sum_probs=44.4

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH------hhcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV------AYADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi------~~Ad~ivlnK  104 (284)
                      ...+++++|......+...     .   .-..+.++.|+|+.+.... .+.      .....++      ...=++|+||
T Consensus        53 ~~~l~D~~G~~~~~~~~~~-----~---~~~~d~~i~v~d~~~~~s~-~~~------~~~~~~i~~~~~~~~piilv~nK  117 (170)
T 1g16_A           53 KLQIWDTAGQERFRTITTA-----Y---YRGAMGIILVYDITDERTF-TNI------KQWFKTVNEHANDEAQLLLVGNK  117 (170)
T ss_dssp             EEEEECCTTGGGTSCCCHH-----H---HTTEEEEEEEEETTCHHHH-HTH------HHHHHHHHHHSCTTCEEEEEEEC
T ss_pred             EEEEEeCCCChhhhhhHHH-----H---hccCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhcCCCCcEEEEEEC
Confidence            4567788885432221111     1   1245779999999875432 111      1112222      2233788899


Q ss_pred             CCCCChh-HHHHHHHHHHHhCCCCceeeec
Q 023301          105 IDLVTET-ELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~-~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +|+.+.. ..+...++.+..+  .+++.++
T Consensus       118 ~Dl~~~~~~~~~~~~~~~~~~--~~~~~~S  145 (170)
T 1g16_A          118 SDMETRVVTADQGEALAKELG--IPFIESS  145 (170)
T ss_dssp             TTCTTCCSCHHHHHHHHHHHT--CCEEECB
T ss_pred             ccCCcCccCHHHHHHHHHHcC--CeEEEEE
Confidence            9984321 2234444445443  4666665

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=88.77  E-value=1.6  Score=33.92  Aligned_cols=97  Identities=13%  Similarity=0.179  Sum_probs=53.4

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh----hcCEEEEccC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA----YADRIILNKI  105 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~----~Ad~ivlnK~  105 (284)
                      ....|++++|......+.....        -..+.++.|+|+.+.... .+.      ..+..++.    ..=++|+||+
T Consensus        93 ~~~~i~Dt~G~~~~~~~~~~~~--------~~~d~~i~v~D~~~~~s~-~~~------~~~~~~i~~~~~~piilv~NK~  157 (208)
T 3clv_A           93 IKFDIWDTAGQERYASIVPLYY--------RGATCAIVVFDISNSNTL-DRA------KTWVNQLKISSNYIIILVANKI  157 (208)
T ss_dssp             EEEEEEECTTGGGCTTTHHHHH--------TTCSEEEEEEETTCHHHH-HHH------HHHHHHHHHHSCCEEEEEEECT
T ss_pred             eEEEEEECCCcHHHHHHHHHHh--------cCCCEEEEEEECCCHHHH-HHH------HHHHHHHHhhCCCcEEEEEECC
Confidence            6788999999655443332221        134679999999875432 111      11223332    2348899999


Q ss_pred             CCCC-hhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          106 DLVT-ETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       106 D~~~-~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      |... ....+.++++++..+  .+++.++. .......++
T Consensus       158 D~~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~~i~~l~  195 (208)
T 3clv_A          158 DKNKFQVDILEVQKYAQDNN--LLFIQTSAKTGTNIKNIF  195 (208)
T ss_dssp             TCC-CCSCHHHHHHHHHHTT--CEEEEECTTTCTTHHHHH
T ss_pred             CcccccCCHHHHHHHHHHcC--CcEEEEecCCCCCHHHHH
Confidence            9321 223456666666543  46776653 233344443

>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=88.77  E-value=0.54  Score=37.04  Aligned_cols=80  Identities=15%  Similarity=0.220  Sum_probs=40.8

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH---HhhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ---VAYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q---i~~Ad~ivlnK~D  106 (284)
                      ....+++++|......+..     ..+   -..+.++.|+|+.+.... .+.. .++ ..+...   -...=++|.||+|
T Consensus        67 ~~~~i~Dt~G~~~~~~~~~-----~~~---~~~d~~i~v~d~~~~~s~-~~~~-~~~-~~~~~~~~~~~~piilv~NK~D  135 (190)
T 1m2o_B           67 IKFTTFDLGGHIQARRLWK-----DYF---PEVNGIVFLVDAADPERF-DEAR-VEL-DALFNIAELKDVPFVILGNKID  135 (190)
T ss_dssp             EEEEEEECCCSGGGTTSGG-----GGC---TTCCEEEEEEETTCGGGH-HHHH-HHH-HHHHTCGGGTTCCEEEEEECTT
T ss_pred             EEEEEEECCCCHHHHHHHH-----HHH---hcCCEEEEEEECCChHHH-HHHH-HHH-HHHHcchhhcCCCEEEEEECCC
Confidence            3456778888765433211     111   145789999999875321 1100 001 011111   1223477889999


Q ss_pred             CCChhHHHHHHHHH
Q 023301          107 LVTETELGSLTERI  120 (284)
Q Consensus       107 ~~~~~~~~~~~~~l  120 (284)
                      +.+....+++.+.+
T Consensus       136 l~~~~~~~~~~~~~  149 (190)
T 1m2o_B          136 APNAVSEAELRSAL  149 (190)
T ss_dssp             STTCCCHHHHHHHT
T ss_pred             CcCCCCHHHHHHHh
Confidence            97633344444443

>3o47_A ADP-ribosylation factor GTPase-activating protein ribosylation factor 1; structural genomics consortium, GTPase activation; HET: GDP; 2.80A {Homo sapiens}

Probab=88.74  E-value=0.63  Score=40.55  Aligned_cols=101  Identities=19%  Similarity=0.185  Sum_probs=48.9

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh------cCEEEE
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY------ADRIIL  102 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~------Ad~ivl  102 (284)
                      .....|++++|-.....+....     +   -..+.+|.|+|+...... ..     +...+...+..      .=+||+
T Consensus       208 ~~~l~i~Dt~G~~~~~~~~~~~-----~---~~ad~vilV~D~~~~~s~-~~-----~~~~~~~~~~~~~~~~~piilV~  273 (329)
T 3o47_A          208 NISFTVWDVGGQDKIRPLWRHY-----F---QNTQGLIFVVDSNDRERV-NE-----AREELMRMLAEDELRDAVLLVFA  273 (329)
T ss_dssp             TEEEEEEECC-----CCSHHHH-----H---TTEEEEEEEEETTCSSSH-HH-----HHHHHHHHHTCGGGTTCEEEEEE
T ss_pred             cEEEEEEECCCCHhHHHHHHHH-----h---ccCCEEEEEEECCchHHH-HH-----HHHHHHHHHhhhccCCCeEEEEE
Confidence            3456788999944332222111     1   146779999999653221 11     00111222222      237888


Q ss_pred             ccCCCCChhHHHHHHHHHHHhC---CCCceeeecc-CCCChhhhh
Q 023301          103 NKIDLVTETELGSLTERIKHIN---AMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       103 nK~D~~~~~~~~~~~~~l~~~n---p~a~i~~~~~-g~v~~~~l~  143 (284)
                      ||+|+.+....+.+.+.+....   ...+++.++. ....++.++
T Consensus       274 NK~Dl~~~~~~~~i~~~~~~~~~~~~~~~~~~vSAk~g~gi~el~  318 (329)
T 3o47_A          274 NKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGL  318 (329)
T ss_dssp             ECTTSTTCCCHHHHHHHHTCTTCCSSCEEEEECBTTTTBTHHHHH
T ss_pred             ECccCCcccCHHHHHHHhchhhhhcCCCEEEEEECCCCcCHHHHH
Confidence            9999987655556655544222   2334665543 233444443

>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=88.68  E-value=0.63  Score=39.69  Aligned_cols=63  Identities=21%  Similarity=0.212  Sum_probs=38.9

Q ss_pred             eeeceEEEEEcccchHHhhhhcCCccchHHHHHHH--hhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeec
Q 023301           60 VKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV--AYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus        60 ~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi--~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      -..+.|+.|+|++......         +...+++  ...-++|+||+|+++.+..+...++.++.+  .+++..+
T Consensus        22 ~~aDvVl~VvDAr~p~~~~---------~~~l~~~l~~kp~ilVlNK~DL~~~~~~~~~~~~~~~~g--~~~i~iS   86 (282)
T 1puj_A           22 KLIDIVYELVDARIPMSSR---------NPMIEDILKNKPRIMLLNKADKADAAVTQQWKEHFENQG--IRSLSIN   86 (282)
T ss_dssp             GGCSEEEEEEETTSTTTTS---------CHHHHHHCSSSCEEEEEECGGGSCHHHHHHHHHHHHTTT--CCEEECC
T ss_pred             hhCCEEEEEEeCCCCCccC---------CHHHHHHHCCCCEEEEEECcccCCHHHHHHHHHHHHhcC--CcEEEEE
Confidence            4678899999998754321         1112232  234589999999998766666555555332  3555443

>3t5d_A Septin-7; GTP-binding protein, cytoskeleton, signaling protein; HET: GDP; 3.30A {Homo sapiens} PDB: 3tw4_A*

Probab=88.52  E-value=1.6  Score=36.68  Aligned_cols=65  Identities=11%  Similarity=0.115  Sum_probs=37.0

Q ss_pred             eeceEEEEEcccc-hHHhhhhcCCccchHHHHHHHh--hcCEEEEccCCCCChhHHHHHHHHHHHhC--CCCceeeec
Q 023301           61 KLDGVITLVDSKH-AMQHLNEVKPRFVVNEAVEQVA--YADRIILNKIDLVTETELGSLTERIKHIN--AMAPVKLAK  133 (284)
Q Consensus        61 ~l~~vv~vvD~~~-~~~~l~~~~~~~~~~~~~~Qi~--~Ad~ivlnK~D~~~~~~~~~~~~~l~~~n--p~a~i~~~~  133 (284)
                      .++.++.+||+.. ......        ..+..++.  ..=++|+||+|+.+.+++...++.+++..  ...+++..+
T Consensus       115 r~~~~l~~i~~~~~~~~~~d--------~~~l~~l~~~~pvi~V~nK~D~~~~~e~~~~~~~i~~~l~~~~i~v~~~s  184 (274)
T 3t5d_A          115 RVQCCLYFIAPSGHGLKPLD--------IEFMKRLHEKVNIIPLIAKADTLTPEECQQFKKQIMKEIQEHKIKIYEFP  184 (274)
T ss_dssp             CCCEEEEEECSCCSSCCHHH--------HHHHHHHTTTSCEEEEESSGGGSCHHHHHHHHHHHHHHHHHTTCCCCCC-
T ss_pred             ceeEEEEEecCCCCCCCHHH--------HHHHHHHhccCCEEEEEeccCCCCHHHHHHHHHHHHHHHHHcCCeEEcCC
Confidence            3557888887755 111110        12234443  45678889999998888776655555432  234555443

>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=88.39  E-value=1.1  Score=34.52  Aligned_cols=97  Identities=9%  Similarity=0.123  Sum_probs=44.7

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh------hcCEEEEc
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA------YADRIILN  103 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~------~Ad~ivln  103 (284)
                      ....+++++|......    +.. ..+   -..+.++.|+|+.+... +.+.      .....++.      ..=+||+|
T Consensus        57 ~~~~l~Dt~G~~~~~~----~~~-~~~---~~~d~~i~v~d~~~~~s-~~~~------~~~~~~i~~~~~~~~piilv~n  121 (183)
T 2fu5_C           57 IKLQIWDTAGQERFRT----ITT-AYY---RGAMGIMLVYDITNEKS-FDNI------RNWIRNIEEHASADVEKMILGN  121 (183)
T ss_dssp             EEEEEEEC-------------CC-TTT---TTCSEEEEEEETTCHHH-HHHH------HHHHHHHHHHSCTTCEEEEEEE
T ss_pred             EEEEEEcCCCChhhhh----hHH-HHH---hcCCEEEEEEECcCHHH-HHHH------HHHHHHHHHhcCCCCCEEEEEE
Confidence            4567889999654332    111 111   24678999999987543 1211      11122222      23378889


Q ss_pred             cCCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          104 KIDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       104 K~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+|+.+..+  .+.++++.+..+  .++++++. .......++
T Consensus       122 K~Dl~~~~~v~~~~~~~~~~~~~--~~~~~~Sa~~~~~i~~l~  162 (183)
T 2fu5_C          122 KCDVNDKRQVSKERGEKLALDYG--IKFMETSAKANINVENAF  162 (183)
T ss_dssp             C--CCSCCCSCHHHHHHHHHHHT--CEEEECCC---CCHHHHH
T ss_pred             CccCCccCcCCHHHHHHHHHHcC--CeEEEEeCCCCCCHHHHH
Confidence            999965322  344555555554  56776653 233444444

>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=88.35  E-value=0.31  Score=42.93  Aligned_cols=73  Identities=12%  Similarity=0.231  Sum_probs=38.3

Q ss_pred             CCCEEEEecCCCCC------cHHHHH---HhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---h
Q 023301           29 QFDHIVIETTGLAK------PAPVIE---TFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---Y   96 (284)
Q Consensus        29 ~~d~iiIE~sG~a~------p~~i~~---~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~   96 (284)
                      .++.+||+|+|+..      |..+.+   .+.. ..+..  .-+.+++|+|+..-..   +.   .. ..+.+++.   .
T Consensus       129 ~~~l~lvDTPG~~~~~~~~~~~~~~~~~~~~~~-~~~~~--~~~iiL~v~~a~~~~~---~~---~~-~~i~~~~~~~~~  198 (353)
T 2x2e_A          129 VLNLTLVDLPGMTKVPVGDQPPDIEFQIRDMLM-QFVTK--ENCLILAVSPANSDLA---NS---DA-LKVAKEVDPQGQ  198 (353)
T ss_dssp             CCSEEEEECCCBCSSCCTTCCTTHHHHHHHHHH-HHHTS--TTEEEEEEEETTSCGG---GC---HH-HHHHHHHCTTCT
T ss_pred             CCCcEEEECCCCCCCccCCCchhHHHHHHHHHH-HHHcC--CCeEEEEEecCCCccc---hh---HH-HHHHHHhCcCCC
Confidence            47899999999976      544322   2211 11111  1223566777754211   10   00 11233332   2


Q ss_pred             cCEEEEccCCCCChh
Q 023301           97 ADRIILNKIDLVTET  111 (284)
Q Consensus        97 Ad~ivlnK~D~~~~~  111 (284)
                      .-++|+||+|+.+..
T Consensus       199 ~~i~V~NK~Dl~~~~  213 (353)
T 2x2e_A          199 RTIGVITKLDLMDEG  213 (353)
T ss_dssp             TEEEEEECGGGSCTT
T ss_pred             ceEEEeccccccCcc
Confidence            339999999998653

>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=88.33  E-value=1  Score=35.22  Aligned_cols=96  Identities=13%  Similarity=0.105  Sum_probs=48.8

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh------hcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA------YADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~------~Ad~ivlnK  104 (284)
                      ...|++++|......+...     .   .-..+.+|.|+|+.+.... .+.      .....++.      ..=+||+||
T Consensus        71 ~~~i~Dt~G~~~~~~~~~~-----~---~~~~d~ii~v~d~~~~~s~-~~~------~~~l~~i~~~~~~~~piilv~nK  135 (191)
T 2a5j_A           71 KLQIWDTAGQESFRSITRS-----Y---YRGAAGALLVYDITRRETF-NHL------TSWLEDARQHSSSNMVIMLIGNK  135 (191)
T ss_dssp             EEEEECCTTGGGTSCCCHH-----H---HTTCSEEEEEEETTCHHHH-HTH------HHHHHHHHHHSCTTCEEEEEEEC
T ss_pred             EEEEEECCCchhhhhhHHH-----H---hccCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhcCCCCCEEEEEEC
Confidence            4567788885432221111     1   1146789999999875432 211      11222222      223788899


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+..+  .+..+++.+..+  .++++++. .......++
T Consensus       136 ~Dl~~~~~v~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  175 (191)
T 2a5j_A          136 SDLESRRDVKREEGEAFAREHG--LIFMETSAKTACNVEEAF  175 (191)
T ss_dssp             TTCGGGCCSCHHHHHHHHHHHT--CEEEEECTTTCTTHHHHH
T ss_pred             cccCCccccCHHHHHHHHHHcC--CEEEEEeCCCCCCHHHHH
Confidence            99965322  234445555443  56666653 233444443

>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=88.32  E-value=2.9  Score=31.62  Aligned_cols=96  Identities=11%  Similarity=-0.012  Sum_probs=45.8

Q ss_pred             CEEEEecCCCCCc--HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-------hcCEEE
Q 023301           31 DHIVIETTGLAKP--APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-------YADRII  101 (284)
Q Consensus        31 d~iiIE~sG~a~p--~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-------~Ad~iv  101 (284)
                      ...+++++|....  ..+....     +   -..+.++.|+|..+.... .+.      ..+..++.       ..=+||
T Consensus        53 ~~~~~D~~g~~~~~~~~~~~~~-----~---~~~~~~i~v~d~~~~~s~-~~~------~~~~~~l~~~~~~~~~piilv  117 (175)
T 2nzj_A           53 TLVVVDTWEAEKLDKSWSQESC-----L---QGGSAYVIVYSIADRGSF-ESA------SELRIQLRRTHQADHVPIILV  117 (175)
T ss_dssp             EEEEECCC-------CHHHHHT-----T---TSCSEEEEEEETTCHHHH-HHH------HHHHHHHHHCC----CCEEEE
T ss_pred             EEEEEecCCCCccchhhhHHhh-----c---ccCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhhccCCCCEEEE
Confidence            4567888887652  2222111     1   124678999998764432 111      11222222       234788


Q ss_pred             EccCCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          102 LNKIDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       102 lnK~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +||+|+.+..+  .+..+.+.+..+  .++++++. .......++
T Consensus       118 ~NK~Dl~~~~~v~~~~~~~~~~~~~--~~~~~~Sa~~g~gi~~l~  160 (175)
T 2nzj_A          118 GNKADLARCREVSVEEGRACAVVFD--CKFIETSATLQHNVAELF  160 (175)
T ss_dssp             EECTTCTTTCCSCHHHHHHHHHHHT--SEEEECBTTTTBSHHHHH
T ss_pred             EEChhhccccccCHHHHHHHHHHcC--CeEEEEecCCCCCHHHHH
Confidence            89999975422  233344444443  56666653 233444443

>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=88.26  E-value=0.61  Score=36.00  Aligned_cols=76  Identities=17%  Similarity=0.181  Sum_probs=38.5

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-------hcCEEEE
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-------YADRIIL  102 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-------~Ad~ivl  102 (284)
                      ....+++++|......+...     .   .-..+.++.|+|+...... .+.      .....++.       ..-++|+
T Consensus        62 ~~~~i~Dt~G~~~~~~~~~~-----~---~~~~d~ii~v~d~~~~~s~-~~~------~~~~~~~~~~~~~~~~piilv~  126 (183)
T 1moz_A           62 LKLNVWDLGGQTSIRPYWRC-----Y---YADTAAVIFVVDSTDKDRM-STA------SKELHLMLQEEELQDAALLVFA  126 (183)
T ss_dssp             EEEEEEEEC----CCTTGGG-----T---TTTEEEEEEEEETTCTTTH-HHH------HHHHHHHTTSSTTSSCEEEEEE
T ss_pred             EEEEEEECCCCHhHHHHHHH-----H---hccCCEEEEEEECCCHHHH-HHH------HHHHHHHHcChhhCCCeEEEEE
Confidence            45568899998654332111     1   1256789999998764211 110      01112221       2347888


Q ss_pred             ccCCCCChhHHHHHHHHH
Q 023301          103 NKIDLVTETELGSLTERI  120 (284)
Q Consensus       103 nK~D~~~~~~~~~~~~~l  120 (284)
                      ||+|+.+....+.+.+.+
T Consensus       127 nK~Dl~~~~~~~~i~~~~  144 (183)
T 1moz_A          127 NKQDQPGALSASEVSKEL  144 (183)
T ss_dssp             ECTTSTTCCCHHHHHHHT
T ss_pred             ECCCCCCCCCHHHHHHHh
Confidence            999997654444454443

>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=88.12  E-value=0.27  Score=42.62  Aligned_cols=118  Identities=19%  Similarity=0.212  Sum_probs=56.7

Q ss_pred             ceeeeeeCchHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhccccccc--ceeeeceEEEEEcccchHHhhhhcC
Q 023301            5 GCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVS--QYVKLDGVITLVDSKHAMQHLNEVK   82 (284)
Q Consensus         5 GCiCCs~~~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~--~~~~l~~vv~vvD~~~~~~~l~~~~   82 (284)
                      |=+=|.+++.|...     .....--|+|.+++.+-. ...|.+.+-....+.  ..-.+|.++.|+|+....-... .-
T Consensus        34 ~~~~~~~rg~~~~~-----~~~~~vGD~V~~~~~~~~-~~~i~~i~~R~~~l~R~~~anvD~v~~V~~~~~p~~~~~-~i  106 (307)
T 1t9h_A           34 KVIQCRGRGIFRKN-----KITPLVGDYVVYQAENDK-EGYLMEIKERTNELIRPPICNVDQAVLVFSAVQPSFSTA-LL  106 (307)
T ss_dssp             EEEEEESCSSCCSC-----CCCCCBTCEEEEECCTTS-CEEEEEECCCSCEETTTTEECCCEEEEEEESTTTTCCHH-HH
T ss_pred             cEEEEEEccccccc-----CCCCCCCeEEEEEEcCCC-ceEEEEEcchhhhhhHHHHHhCCEEEEEEeCCCCCCCHH-HH
Confidence            34457777755310     000123599999865411 111111111111111  2458899999999985332111 00


Q ss_pred             CccchHHHHHHHhhcCEEEEccCCCCChhH----HHHHHHHHHHhCCCCceeeec
Q 023301           83 PRFVVNEAVEQVAYADRIILNKIDLVTETE----LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus        83 ~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~----~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ++++.  ....-...=+||+||+|++++++    ++.+.+..+.+.  .+++.++
T Consensus       107 ~r~L~--~~~~~~~~~vivlnK~DL~~~~~~~~~~~~~~~~y~~~g--~~v~~~s  157 (307)
T 1t9h_A          107 DRFLV--LVEANDIQPIICITKMDLIEDQDTEDTIQAYAEDYRNIG--YDVYLTS  157 (307)
T ss_dssp             HHHHH--HHHTTTCEEEEEEECGGGCCCHHHHHHHHHHHHHHHHHT--CCEEECC
T ss_pred             HHHHH--HHHHCCCCEEEEEECCccCchhhhHHHHHHHHHHHHhCC--CeEEEEe
Confidence            01100  01111223488999999998754    445555544443  4666543

>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=87.84  E-value=0.78  Score=35.78  Aligned_cols=90  Identities=11%  Similarity=0.181  Sum_probs=45.4

Q ss_pred             CEEEEecCCCCCcH-HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCC
Q 023301           31 DHIVIETTGLAKPA-PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKID  106 (284)
Q Consensus        31 d~iiIE~sG~a~p~-~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D  106 (284)
                      ...+++++|..... .+....     +   -..+.+|.|+|+.+.... .+.. .++ ..+...+   ...=+||+||+|
T Consensus        70 ~~~l~Dt~G~~~~~~~~~~~~-----~---~~~d~iilv~D~~~~~s~-~~~~-~~~-~~i~~~~~~~~~piilv~nK~D  138 (189)
T 1z06_A           70 KIQLWDTAGQERFRKSMVQHY-----Y---RNVHAVVFVYDMTNMASF-HSLP-AWI-EECKQHLLANDIPRILVGNKCD  138 (189)
T ss_dssp             EEEEEECCCSHHHHTTTHHHH-----H---TTCCEEEEEEETTCHHHH-HTHH-HHH-HHHHHHCCCSCCCEEEEEECTT
T ss_pred             EEEEEECCCchhhhhhhhHHH-----h---cCCCEEEEEEECcCHHHH-HHHH-HHH-HHHHHhcCCCCCCEEEEEECcc
Confidence            45778899954322 222111     1   146789999999875432 1110 011 1122222   123478889999


Q ss_pred             CCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          107 LVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       107 ~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +.+..+  .+..+++.+..  ..+++.++
T Consensus       139 l~~~~~v~~~~~~~~~~~~--~~~~~~~S  165 (189)
T 1z06_A          139 LRSAIQVPTDLAQKFADTH--SMPLFETS  165 (189)
T ss_dssp             CGGGCCSCHHHHHHHHHHT--TCCEEECC
T ss_pred             ccccceeCHHHHHHHHHHc--CCEEEEEe
Confidence            965322  23334444433  25666655

>3tr5_A RF-3, peptide chain release factor 3; protein synthesis, translation; HET: GDP; 2.11A {Coxiella burnetii}

Probab=87.80  E-value=1.5  Score=40.98  Aligned_cols=79  Identities=15%  Similarity=0.159  Sum_probs=45.9

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKI  105 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~  105 (284)
                      ...+.||.|+|..+.......     .+   -..+.+|.|+|+........        ..+..++   ...-++|+||+
T Consensus        81 ~~~i~liDTPG~~df~~~~~~-----~l---~~aD~allVvDa~~g~~~~t--------~~~~~~~~~~~iPiivviNK~  144 (528)
T 3tr5_A           81 DYLINLLDTPGHADFTEDTYR-----TL---TAVDSALMVIDAAKGVEPRT--------IKLMEVCRLRHTPIMTFINKM  144 (528)
T ss_dssp             TEEEEEECCCCSTTCCHHHHH-----GG---GGCSEEEEEEETTTCSCHHH--------HHHHHHHHTTTCCEEEEEECT
T ss_pred             CEEEEEEECCCchhHHHHHHH-----HH---HhCCEEEEEEeCCCCCCHHH--------HHHHHHHHHcCCCEEEEEeCC
Confidence            456789999999886543222     12   24688999999987322100        1122333   34558999999


Q ss_pred             CCCChhHHHHHHHHHHHh
Q 023301          106 DLVTETELGSLTERIKHI  123 (284)
Q Consensus       106 D~~~~~~~~~~~~~l~~~  123 (284)
                      |+......+.+.+..+.+
T Consensus       145 Dl~~~~~~~~l~ei~~~l  162 (528)
T 3tr5_A          145 DRDTRPSIELLDEIESIL  162 (528)
T ss_dssp             TSCCSCHHHHHHHHHHHH
T ss_pred             CCccccHHHHHHHHHHhh
Confidence            997544333333333333

>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=87.76  E-value=1.4  Score=34.01  Aligned_cols=92  Identities=14%  Similarity=0.163  Sum_probs=45.1

Q ss_pred             CEEEEecCCCCCcH-------HHHHHhcccccccc-eeeeceEEEEEcccchHHhhhhc---CCccchHHHHHH---Hhh
Q 023301           31 DHIVIETTGLAKPA-------PVIETFCTDELVSQ-YVKLDGVITLVDSKHAMQHLNEV---KPRFVVNEAVEQ---VAY   96 (284)
Q Consensus        31 d~iiIE~sG~a~p~-------~i~~~l~~~~~l~~-~~~l~~vv~vvD~~~~~~~l~~~---~~~~~~~~~~~Q---i~~   96 (284)
                      ...+++++|+....       +-+..+.. ..+.. .-.+..++.|+|+..+.......   +.......+..+   ...
T Consensus        45 ~~~l~Dt~G~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~v~d~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (190)
T 2cxx_A           45 NHKIIDMPGFGFMMGLPKEVQERIKDEIV-HFIEDNAKNIDVAVLVVDGKAAPEIIKRWEKRGEIPIDVEFYQFLRELDI  123 (190)
T ss_dssp             TEEEEECCCBSCCTTSCHHHHHHHHHHHH-HHHHHHGGGCCEEEEEEETTHHHHHHHHHHHTTCCCHHHHHHHHHHHTTC
T ss_pred             CEEEEECCCccccccCCHHHHHHHHHHHH-HHHHhhhccCCEEEEEEcchhhhhHHHhhhccCccHHHHHHHHHHHhcCC
Confidence            46789999975431       11222211 11111 22345688999998875421110   000000011222   234


Q ss_pred             cCEEEEccCCCCChhHHHHHHHHHHHhC
Q 023301           97 ADRIILNKIDLVTETELGSLTERIKHIN  124 (284)
Q Consensus        97 Ad~ivlnK~D~~~~~~~~~~~~~l~~~n  124 (284)
                      .-++|+||+|+.+.. .+...+..+.++
T Consensus       124 piilv~nK~Dl~~~~-~~~~~~~~~~~~  150 (190)
T 2cxx_A          124 PTIVAVNKLDKIKNV-QEVINFLAEKFE  150 (190)
T ss_dssp             CEEEEEECGGGCSCH-HHHHHHHHHHHT
T ss_pred             ceEEEeehHhccCcH-HHHHHHHHHHhh
Confidence            568889999997754 233444444444

>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=87.71  E-value=0.8  Score=36.65  Aligned_cols=92  Identities=21%  Similarity=0.255  Sum_probs=45.0

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH--hhcCEEEEccCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV--AYADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi--~~Ad~ivlnK~D~  107 (284)
                      ....+++++|......+....        .-..+.+|.|+|+...... .+. ..++ ..+....  ...-+||+||+|+
T Consensus        61 ~~~~l~Dt~G~~~~~~~~~~~--------~~~~d~~i~v~d~~~~~s~-~~~-~~~~-~~~~~~~~~~~piilv~nK~Dl  129 (218)
T 4djt_A           61 IKFNVWDTAGQEKKAVLKDVY--------YIGASGAILFFDVTSRITC-QNL-ARWV-KEFQAVVGNEAPIVVCANKIDI  129 (218)
T ss_dssp             EEEEEEEECSGGGTSCCCHHH--------HTTCSEEEEEEETTCHHHH-HTH-HHHH-HHHHHHHCSSSCEEEEEECTTC
T ss_pred             EEEEEEecCCchhhchHHHHH--------hhcCCEEEEEEeCCCHHHH-HHH-HHHH-HHHHHhcCCCCCEEEEEECCCC
Confidence            457788999964432211111        1236779999999875432 111 0111 1111111  2345788899999


Q ss_pred             CChhHH--HHHHHHHHHhCCCCceeeecc
Q 023301          108 VTETEL--GSLTERIKHINAMAPVKLAKY  134 (284)
Q Consensus       108 ~~~~~~--~~~~~~l~~~np~a~i~~~~~  134 (284)
                      .+..++  +...+..+  ....+++.++.
T Consensus       130 ~~~~~~~~~~~~~~~~--~~~~~~~~~Sa  156 (218)
T 4djt_A          130 KNRQKISKKLVMEVLK--GKNYEYFEISA  156 (218)
T ss_dssp             C----CCHHHHHHHTT--TCCCEEEEEBT
T ss_pred             ccccccCHHHHHHHHH--HcCCcEEEEec
Confidence            764332  22222222  23466777653

>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=87.49  E-value=1.6  Score=33.50  Aligned_cols=98  Identities=17%  Similarity=0.224  Sum_probs=50.1

Q ss_pred             EEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEEEEccCCCCC
Q 023301           33 IVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRIILNKIDLVT  109 (284)
Q Consensus        33 iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~ivlnK~D~~~  109 (284)
                      -+++++|......+....        .-..+.++.|+|+.+.... .... .+. ..+.....   ..=++|+||+|+.+
T Consensus        69 ~i~Dt~G~~~~~~~~~~~--------~~~~d~~i~v~d~~~~~s~-~~~~-~~~-~~~~~~~~~~~~p~ilv~nK~Dl~~  137 (183)
T 3kkq_A           69 DVLDTAGQEEFSAMREQY--------MRTGDGFLIVYSVTDKASF-EHVD-RFH-QLILRVKDRESFPMILVANKVDLMH  137 (183)
T ss_dssp             EEEECCSCGGGCSSHHHH--------HHHCSEEEEEEETTCHHHH-HTHH-HHH-HHHHHHHTSSCCCEEEEEECTTCST
T ss_pred             EEEECCCchhhHHHHHHH--------HhcCCEEEEEEECCCHHHH-HHHH-HHH-HHHHHhcCCCCCcEEEEEECCCchh
Confidence            358888865433322221        1136789999999875432 1110 011 11222222   13478889999865


Q ss_pred             hh--HHHHHHHHHHHhCCCCceeeeccC--CCChhhhh
Q 023301          110 ET--ELGSLTERIKHINAMAPVKLAKYG--SVDMDFVL  143 (284)
Q Consensus       110 ~~--~~~~~~~~l~~~np~a~i~~~~~g--~v~~~~l~  143 (284)
                      ..  ..+..+++.+..+  +++++++.-  ......++
T Consensus       138 ~~~v~~~~~~~~~~~~~--~~~~~~Sa~~~~~~v~~l~  173 (183)
T 3kkq_A          138 LRKVTRDQGKEMATKYN--IPYIETSAKDPPLNVDKTF  173 (183)
T ss_dssp             TCCSCHHHHHHHHHHHT--CCEEEEBCSSSCBSHHHHH
T ss_pred             ccCcCHHHHHHHHHHhC--CeEEEeccCCCCCCHHHHH
Confidence            22  2344555566555  667766532  33444443

>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=87.33  E-value=2.4  Score=33.22  Aligned_cols=63  Identities=21%  Similarity=0.263  Sum_probs=37.3

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH------hhcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV------AYADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi------~~Ad~ivlnK  104 (284)
                      ...|++++|......+.....        -..+.+|.|+|+.+.... .+.      ......+      ...=+||+||
T Consensus        78 ~l~i~Dt~G~~~~~~~~~~~~--------~~~d~iilv~d~~~~~s~-~~~------~~~~~~i~~~~~~~~piilv~NK  142 (199)
T 2p5s_A           78 VLQLWDTAGQERFRSIAKSYF--------RKADGVLLLYDVTCEKSF-LNI------REWVDMIEDAAHETVPIMLVGNK  142 (199)
T ss_dssp             EEEEEECTTCTTCHHHHHHHH--------HHCSEEEEEEETTCHHHH-HTH------HHHHHHHHHHC---CCEEEEEEC
T ss_pred             EEEEEECCCCcchhhhHHHHH--------hhCCEEEEEEECCChHHH-HHH------HHHHHHHHHhcCCCCCEEEEEEC
Confidence            356889999877655443321        135779999999875432 111      1112222      2344788899


Q ss_pred             CCCC
Q 023301          105 IDLV  108 (284)
Q Consensus       105 ~D~~  108 (284)
                      +|+.
T Consensus       143 ~Dl~  146 (199)
T 2p5s_A          143 ADIR  146 (199)
T ss_dssp             GGGH
T ss_pred             cccc
Confidence            9985

>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=87.23  E-value=3.5  Score=32.63  Aligned_cols=99  Identities=17%  Similarity=0.174  Sum_probs=50.2

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~ivlnK~D~  107 (284)
                      ...+++++|......+...     .+   -..+.+|.|+|+.+.... ... ..++ .. ..+..   ..=+||.||+|+
T Consensus        76 ~l~l~Dt~G~~~~~~~~~~-----~~---~~~d~~i~v~D~~~~~s~-~~~-~~~~-~~-i~~~~~~~~piilv~NK~Dl  143 (201)
T 2ew1_A           76 KLQIWDTAGQERFRSITQS-----YY---RSANALILTYDITCEESF-RCL-PEWL-RE-IEQYASNKVITVLVGNKIDL  143 (201)
T ss_dssp             EEEEEEECCSGGGHHHHGG-----GS---TTCSEEEEEEETTCHHHH-HTH-HHHH-HH-HHHHSCTTCEEEEEEECGGG
T ss_pred             EEEEEECCCcHHHHHHHHH-----HH---hcCCEEEEEEECCCHHHH-HHH-HHHH-HH-HHHhcCCCCCEEEEEECCCC
Confidence            4567789996554433221     11   246789999999875432 111 0111 11 11221   223678899998


Q ss_pred             CChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          108 VTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       108 ~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      .+..+  .+..+++.+..+  .++++++. .......++
T Consensus       144 ~~~~~v~~~~~~~~~~~~~--~~~~~~Sa~~g~gv~~l~  180 (201)
T 2ew1_A          144 AERREVSQQRAEEFSEAQD--MYYLETSAKESDNVEKLF  180 (201)
T ss_dssp             GGGCSSCHHHHHHHHHHHT--CCEEECCTTTCTTHHHHH
T ss_pred             ccccccCHHHHHHHHHHcC--CEEEEEeCCCCCCHHHHH
Confidence            64322  233444444443  56776653 234455544

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=87.04  E-value=1  Score=39.63  Aligned_cols=104  Identities=17%  Similarity=0.183  Sum_probs=54.1

Q ss_pred             CEEEEecCCCCCcH-----HHH-HHhcccccccceeeeceEEEEEcccchHHh-hhhcCCccchHHHHHHH-hhcCEEEE
Q 023301           31 DHIVIETTGLAKPA-----PVI-ETFCTDELVSQYVKLDGVITLVDSKHAMQH-LNEVKPRFVVNEAVEQV-AYADRIIL  102 (284)
Q Consensus        31 d~iiIE~sG~a~p~-----~i~-~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~-l~~~~~~~~~~~~~~Qi-~~Ad~ivl  102 (284)
                      +..+++|+|..++.     .+. +.+.   .+  ....+.++.|+|+...... +.+.  ......+.... ...-++|+
T Consensus       215 ~~~l~Dt~G~~~~~~~~~~~~~~~~~~---~~--~~~ad~illV~D~s~~~~~~~~~~--~~~~~~i~~~~~~~piilV~  287 (357)
T 2e87_A          215 RYQIIDTPGLLDRPISERNEIEKQAIL---AL--RYLGNLIIYIFDPSEHCGFPLEEQ--IHLFEEVHGEFKDLPFLVVI  287 (357)
T ss_dssp             EEEEEECTTTSSSCSTTSCHHHHHHHH---GG--GGTCSEEEEEECTTCTTSSCHHHH--HHHHHHHHHHTTTSCEEEEE
T ss_pred             eEEEEeCCCccccchhhhhHHHHHHHH---HH--HhcCCEEEEEEeCCccccCCHHHH--HHHHHHHHHhcCCCCEEEEE
Confidence            46789999986642     111 1111   01  1235678999998653210 0000  00111222222 34457888


Q ss_pred             ccCCCCChhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          103 NKIDLVTETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       103 nK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      ||+|+.+..+++.+.+.++..  ..+++.++. .....+.++
T Consensus       288 NK~Dl~~~~~~~~~~~~~~~~--~~~~~~iSA~~g~gi~~l~  327 (357)
T 2e87_A          288 NKIDVADEENIKRLEKFVKEK--GLNPIKISALKGTGIDLVK  327 (357)
T ss_dssp             CCTTTCCHHHHHHHHHHHHHT--TCCCEECBTTTTBTHHHHH
T ss_pred             ECcccCChHHHHHHHHHHHhc--CCCeEEEeCCCCcCHHHHH
Confidence            999998877776666666543  356666552 223444443

>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=86.77  E-value=0.84  Score=35.37  Aligned_cols=80  Identities=14%  Similarity=0.113  Sum_probs=40.4

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHH---HhhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQ---VAYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Q---i~~Ad~ivlnK~D  106 (284)
                      ....+++++|......+...     .+   -..+.++.|+|+.+.... .+.. .++ ..+..+   -...=+||+||+|
T Consensus        65 ~~~~i~Dt~G~~~~~~~~~~-----~~---~~~d~ii~v~D~~~~~s~-~~~~-~~~-~~~~~~~~~~~~piilv~NK~D  133 (181)
T 2h17_A           65 TRFLMWDIGGQESLRSSWNT-----YY---TNTEFVIVVVDSTDRERI-SVTR-EEL-YKMLAHEDLRKAGLLIFANKQD  133 (181)
T ss_dssp             EEEEEEEESSSGGGTCGGGG-----GG---TTCCEEEEEEETTCTTTH-HHHH-HHH-HHHHTCGGGTTCEEEEEEECTT
T ss_pred             EEEEEEECCCCHhHHHHHHH-----Hh---ccCCEEEEEEECCCHHHH-HHHH-HHH-HHHHhChhhCCCeEEEEEECCC
Confidence            45677888887543332211     11   245789999999874211 1100 000 011111   1122378889999


Q ss_pred             CCChhHHHHHHHHH
Q 023301          107 LVTETELGSLTERI  120 (284)
Q Consensus       107 ~~~~~~~~~~~~~l  120 (284)
                      +.+....+.+.+.+
T Consensus       134 l~~~~~~~~i~~~~  147 (181)
T 2h17_A          134 VKECMTVAEISQFL  147 (181)
T ss_dssp             STTCCCHHHHHHHT
T ss_pred             cccCCCHHHHHHHh
Confidence            97643344444443

>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=86.52  E-value=0.2  Score=42.18  Aligned_cols=97  Identities=18%  Similarity=0.166  Sum_probs=54.5

Q ss_pred             CCCEEEEecCCCCCcHH------HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCE
Q 023301           29 QFDHIVIETTGLAKPAP------VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADR   99 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~------i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~   99 (284)
                      .....+++++|.....+      +...+.     . .-..+.++.|+|+.++...+.          +..|+   ...-+
T Consensus        51 ~~~~~l~DtpG~~~~~~~~~~e~v~~~~~-----~-~~~~d~ii~V~D~t~~~~~~~----------~~~~l~~~~~pvi  114 (258)
T 3a1s_A           51 GYTINLIDLPGTYSLGYSSIDEKIARDYL-----L-KGDADLVILVADSVNPEQSLY----------LLLEILEMEKKVI  114 (258)
T ss_dssp             TEEEEEEECCCCSSCCSSSHHHHHHHHHH-----H-HSCCSEEEEEEETTSCHHHHH----------HHHHHHTTTCCEE
T ss_pred             CeEEEEEECCCcCccCCCCHHHHHHHHHH-----h-hcCCCEEEEEeCCCchhhHHH----------HHHHHHhcCCCEE
Confidence            34678999999876542      112111     0 125678999999998654321          23344   34568


Q ss_pred             EEEccCCCCChhHHH-HHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          100 IILNKIDLVTETELG-SLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       100 ivlnK~D~~~~~~~~-~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+||+|+.+...+. ...+..+.++  .+++.++. .......++
T Consensus       115 lv~NK~Dl~~~~~i~~~~~~l~~~lg--~~vi~~SA~~g~gi~el~  158 (258)
T 3a1s_A          115 LAMTAIDEAKKTGMKIDRYELQKHLG--IPVVFTSSVTGEGLEELK  158 (258)
T ss_dssp             EEEECHHHHHHTTCCBCHHHHHHHHC--SCEEECCTTTCTTHHHHH
T ss_pred             EEEECcCCCCccchHHHHHHHHHHcC--CCEEEEEeeCCcCHHHHH
Confidence            899999985432211 1233333343  57777653 233444544

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=86.42  E-value=2.3  Score=32.40  Aligned_cols=101  Identities=9%  Similarity=0.077  Sum_probs=52.0

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH----hhc-CEEEEcc
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV----AYA-DRIILNK  104 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi----~~A-d~ivlnK  104 (284)
                      ....+++++|......+.....        -..+.++.|+|+.+.... .+.. .++ ..+....    ... =+||.||
T Consensus        56 ~~~~~~Dt~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~~-~~~-~~i~~~~~~~~~~~~iilv~nK  124 (178)
T 2hxs_A           56 VTLQIWDIGGQTIGGKMLDKYI--------YGAQGVLLVYDITNYQSF-ENLE-DWY-TVVKKVSEESETQPLVALVGNK  124 (178)
T ss_dssp             EEEEEEECTTCCTTCTTHHHHH--------TTCSEEEEEEETTCHHHH-HTHH-HHH-HHHHHHHHHHTCCCEEEEEEEC
T ss_pred             EEEEEEECCCCccccchhhHHH--------hhCCEEEEEEECCCHHHH-HHHH-HHH-HHHHHHhcccCCCCeEEEEEEc
Confidence            4567889999766544333221        135779999999875432 2110 011 1111111    122 2578899


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+..+  .+...++.+..+  .++++++. .......++
T Consensus       125 ~Dl~~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  164 (178)
T 2hxs_A          125 IDLEHMRTIKPEKHLRFCQENG--FSSHFVSAKTGDSVFLCF  164 (178)
T ss_dssp             GGGGGGCSSCHHHHHHHHHHHT--CEEEEECTTTCTTHHHHH
T ss_pred             cccccccccCHHHHHHHHHHcC--CcEEEEeCCCCCCHHHHH
Confidence            99864321  234444555443  56666653 223344443

>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=86.38  E-value=0.46  Score=42.10  Aligned_cols=37  Identities=24%  Similarity=0.328  Sum_probs=24.0

Q ss_pred             cCEEEEccCCCCChhHHHHHHHHHHHhC-CCCceeeec
Q 023301           97 ADRIILNKIDLVTETELGSLTERIKHIN-AMAPVKLAK  133 (284)
Q Consensus        97 Ad~ivlnK~D~~~~~~~~~~~~~l~~~n-p~a~i~~~~  133 (284)
                      .=+||+||+|++++++.+.+.+++..+. ...+++.++
T Consensus       162 ~~iivlNK~DL~~~~~~~~~~~~~~~y~~~G~~v~~~S  199 (358)
T 2rcn_A          162 EPLIVLNKIDLLDDEGMDFVNEQMDIYRNIGYRVLMVS  199 (358)
T ss_dssp             EEEEEEECGGGCCHHHHHHHHHHHHHHHTTTCCEEECB
T ss_pred             CEEEEEECccCCCchhHHHHHHHHHHHHhCCCcEEEEe
Confidence            3489999999998876444555554432 345676654

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=86.11  E-value=0.53  Score=37.29  Aligned_cols=88  Identities=13%  Similarity=0.139  Sum_probs=47.6

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-------hhcCEEEE
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-------AYADRIIL  102 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-------~~Ad~ivl  102 (284)
                      ....|++++|......+...     .+   -..+.++.|+|+.+.... ...      .....++       ...=+||+
T Consensus        72 ~~~~l~Dt~G~~~~~~~~~~-----~~---~~~d~~i~v~d~~~~~s~-~~~------~~~~~~i~~~~~~~~~piilv~  136 (201)
T 3oes_A           72 FHLHLVDTAGQDEYSILPYS-----FI---IGVHGYVLVYSVTSLHSF-QVI------ESLYQKLHEGHGKTRVPVVLVG  136 (201)
T ss_dssp             EEEEEEEECCCCTTCCCCGG-----GT---TTCCEEEEEEETTCHHHH-HHH------HHHHHHHHC-----CCCEEEEE
T ss_pred             EEEEEEECCCccchHHHHHH-----HH---hcCCEEEEEEeCCCHHHH-HHH------HHHHHHHHHhcCCCCCCEEEEE
Confidence            34578899996554322111     11   246789999999875432 111      1112222       22457888


Q ss_pred             ccCCCCChhH--HHHHHHHHHHhCCCCceeeecc
Q 023301          103 NKIDLVTETE--LGSLTERIKHINAMAPVKLAKY  134 (284)
Q Consensus       103 nK~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~  134 (284)
                      ||+|+.+..+  ....+++.+..+  +++++++.
T Consensus       137 nK~Dl~~~~~v~~~~~~~~~~~~~--~~~~~~Sa  168 (201)
T 3oes_A          137 NKADLSPEREVQAVEGKKLAESWG--ATFMESSA  168 (201)
T ss_dssp             ECTTCGGGCCSCHHHHHHHHHHHT--CEEEECCT
T ss_pred             ECccCccccccCHHHHHHHHHHhC--CeEEEEeC
Confidence            9999865432  233444444443  56776653

>2j69_A Bacterial dynamin-like protein; FZO, FZL, GTPase, hydrolase; 3.0A {Nostoc punctiforme} PDB: 2j68_A 2w6d_A*

Probab=85.93  E-value=0.58  Score=45.29  Aligned_cols=69  Identities=13%  Similarity=0.120  Sum_probs=40.3

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~ivlnK~D  106 (284)
                      .+..||+|+|+.++....... . ..+   -..+.++.|+|+.+.... .+     . ..+...+.   ..-++|+||+|
T Consensus       174 ~~l~LiDTPGl~~~~~~~~~~-~-~~i---~~aD~vL~Vvda~~~~s~-~e-----~-~~l~~~l~~~~~~iiiVlNK~D  241 (695)
T 2j69_A          174 KGIEIVDSPGLNDTEARNELS-L-GYV---NNCHAILFVMRASQPCTL-GE-----R-RYLENYIKGRGLTVFFLVNAWD  241 (695)
T ss_dssp             TTEEEEECCCHHHHHTCHHHH-T-HHH---HSSSEEEEEEETTSTTCH-HH-----H-HHHHHHTTTSCCCEEEEEECGG
T ss_pred             CCeEEEECCCCCchhhHHHHH-H-HHH---HhCCEEEEEEeCCCccch-hH-----H-HHHHHHHHhhCCCEEEEEECcc
Confidence            579999999988754322211 1 112   246789999999764221 00     0 11222332   23578999999


Q ss_pred             CCCh
Q 023301          107 LVTE  110 (284)
Q Consensus       107 ~~~~  110 (284)
                      +.+.
T Consensus       242 l~~~  245 (695)
T 2j69_A          242 QVRE  245 (695)
T ss_dssp             GGGG
T ss_pred             cccc
Confidence            8754

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=85.86  E-value=0.65  Score=39.33  Aligned_cols=72  Identities=17%  Similarity=0.316  Sum_probs=39.0

Q ss_pred             CCCEEEEecCCCCC------cHHH---HHHhcccccccceeeeceEE-EEEcccchHHhhhhcCCccchHHHHHHHh---
Q 023301           29 QFDHIVIETTGLAK------PAPV---IETFCTDELVSQYVKLDGVI-TLVDSKHAMQHLNEVKPRFVVNEAVEQVA---   95 (284)
Q Consensus        29 ~~d~iiIE~sG~a~------p~~i---~~~l~~~~~l~~~~~l~~vv-~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---   95 (284)
                      .++..|++|+|+..      +..+   ...+.. ..+.   .-+.+| +|+|+..-....      .. ..+..++.   
T Consensus       124 ~~~l~lvDtpG~~~~~~~~~~~~~~~~~~~~~~-~~~~---~~~~~il~v~d~~~~~~~~------~~-~~~~~~~~~~~  192 (299)
T 2aka_B          124 VLNLTLVDLPGMTKVPVGDQPPDIEFQIRDMLM-QFVT---KENCLILAVSPANSDLANS------DA-LKIAKEVDPQG  192 (299)
T ss_dssp             CCSEEEEECCCBCSSCCSSSCTTHHHHHHHHHH-HHHT---STTEEEEEEEESSSCGGGC------HH-HHHHHHHCTTC
T ss_pred             CCCceEEeCCCCCCCcCCCCCchHHHHHHHHHH-HHHc---CCCeEEEEEecCCcchhhh------HH-HHHHHHhCCCC
Confidence            37999999999975      4332   222111 1111   223344 789997632110      00 11233433   


Q ss_pred             hcCEEEEccCCCCChh
Q 023301           96 YADRIILNKIDLVTET  111 (284)
Q Consensus        96 ~Ad~ivlnK~D~~~~~  111 (284)
                      ..-++|+||+|+.+..
T Consensus       193 ~~~i~V~NK~Dl~~~~  208 (299)
T 2aka_B          193 QRTIGVITKLDLMDEG  208 (299)
T ss_dssp             SSEEEEEECGGGSCTT
T ss_pred             CeEEEEEEccccCCCC
Confidence            3448999999998654

>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=85.85  E-value=1.8  Score=39.28  Aligned_cols=69  Identities=20%  Similarity=0.273  Sum_probs=42.9

Q ss_pred             CCCCEEEEecCCCCCcH-HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh----hcCEEEE
Q 023301           28 GQFDHIVIETTGLAKPA-PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA----YADRIIL  102 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~-~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~----~Ad~ivl  102 (284)
                      ..+|+|||+|.|..... .+...+.   .+......+.++.|+|+..-....         .. ...+.    ....||+
T Consensus       179 ~~~D~vIIDT~G~~~~~~~l~~~l~---~i~~~~~~d~vllVvda~~g~~~~---------~~-~~~~~~~~~~i~gvVl  245 (432)
T 2v3c_C          179 KKADVLIIDTAGRHKEEKGLLEEMK---QIKEITNPDEIILVIDGTIGQQAG---------IQ-AKAFKEAVGEIGSIIV  245 (432)
T ss_dssp             SSCSEEEEECCCSCSSHHHHHHHHH---HTTSSSCCSEEEEEEEGGGGGGHH---------HH-HHHHHTTSCSCEEEEE
T ss_pred             hCCCEEEEcCCCCccccHHHHHHHH---HHHHHhcCcceeEEeeccccHHHH---------HH-HHHHhhcccCCeEEEE
Confidence            46899999999998753 2333332   122334567789999997643211         11 12222    2268999


Q ss_pred             ccCCCCC
Q 023301          103 NKIDLVT  109 (284)
Q Consensus       103 nK~D~~~  109 (284)
                      ||.|...
T Consensus       246 nK~D~~~  252 (432)
T 2v3c_C          246 TKLDGSA  252 (432)
T ss_dssp             ECSSSCS
T ss_pred             eCCCCcc
Confidence            9999864

>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=85.76  E-value=2.1  Score=32.16  Aligned_cols=86  Identities=10%  Similarity=0.097  Sum_probs=44.4

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh---cC---EEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY---AD---RIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~---Ad---~ivlnK  104 (284)
                      ...+++++|......+.....        -..+.++.|+|+...... ...      .....++..   .+   ++|.||
T Consensus        56 ~~~~~D~~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~------~~~~~~~~~~~~~~~~iilv~nK  120 (170)
T 1r2q_A           56 KFEIWDTAGQERYHSLAPMYY--------RGAQAAIVVYDITNEESF-ARA------KNWVKELQRQASPNIVIALSGNK  120 (170)
T ss_dssp             EEEEEEECCSGGGGGGHHHHH--------TTCSEEEEEEETTCHHHH-HHH------HHHHHHHHHHSCTTCEEEEEEEC
T ss_pred             EEEEEeCCCcHHhhhhhHHhc--------cCCCEEEEEEECCCHHHH-HHH------HHHHHHHHHhcCCCCcEEEEEEC
Confidence            456788999655443332221        135678999999875432 111      111222221   12   345599


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +|+.++.+  .+...++.+..  ..+++.++
T Consensus       121 ~Dl~~~~~~~~~~~~~~~~~~--~~~~~~~S  149 (170)
T 1r2q_A          121 ADLANKRAVDFQEAQSYADDN--SLLFMETS  149 (170)
T ss_dssp             GGGGGGCCSCHHHHHHHHHHT--TCEEEECC
T ss_pred             ccCccccccCHHHHHHHHHHc--CCeEEEEe
Confidence            99865322  23444444433  35666654

>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=85.74  E-value=0.45  Score=43.92  Aligned_cols=103  Identities=12%  Similarity=0.253  Sum_probs=52.4

Q ss_pred             CCEEEEecCCCC-CcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-hcCEEEEccCCC
Q 023301           30 FDHIVIETTGLA-KPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-YADRIILNKIDL  107 (284)
Q Consensus        30 ~d~iiIE~sG~a-~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-~Ad~ivlnK~D~  107 (284)
                      ....|++|.|+- .+...++.+-....+...-..+.++.|+|+...... .+       ..+.+.+. ..-+||+||+|+
T Consensus       291 ~~~~l~DTaG~~~~~~~~ve~~gi~~~~~~~~~aD~vl~VvD~s~~~s~-~~-------~~il~~l~~~piivV~NK~DL  362 (482)
T 1xzp_A          291 ILFRIVDTAGVRSETNDLVERLGIERTLQEIEKADIVLFVLDASSPLDE-ED-------RKILERIKNKRYLVVINKVDV  362 (482)
T ss_dssp             EEEEEEESSCCCSSCCTTCCCCCHHHHHHHHHHCSEEEEEEETTSCCCH-HH-------HHHHHHHTTSSEEEEEEECSS
T ss_pred             eEEEEEECCCccccchhhHHHHHHHHHHHHhhcccEEEEEecCCCCCCH-HH-------HHHHHHhcCCCEEEEEECccc
Confidence            356899999998 654322111000011112356789999998763221 11       11223332 244788899999


Q ss_pred             CChhHHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          108 VTETELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       108 ~~~~~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      .+....+.+.+.+   ....+++.++. ....++.++
T Consensus       363 ~~~~~~~~~~~~~---~~~~~~i~iSAktg~Gi~eL~  396 (482)
T 1xzp_A          363 VEKINEEEIKNKL---GTDRHMVKISALKGEGLEKLE  396 (482)
T ss_dssp             CCCCCHHHHHHHH---TCSTTEEEEEGGGTCCHHHHH
T ss_pred             ccccCHHHHHHHh---cCCCcEEEEECCCCCCHHHHH
Confidence            7542333343332   22356666553 233455544

>2xex_A Elongation factor G; GTPase, translation, biosynthetic protein; 1.90A {Staphylococcus aureus}

Probab=85.64  E-value=0.94  Score=43.77  Aligned_cols=81  Identities=16%  Similarity=0.222  Sum_probs=47.3

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      .....||+|+|..+.......     .+   -..+.++.|+|+........    ..+.. ...+....-++|+||+|+.
T Consensus        74 ~~~i~liDTPG~~df~~~~~~-----~l---~~aD~~llVvDa~~g~~~~~----~~~~~-~~~~~~~p~ilviNK~Dl~  140 (693)
T 2xex_A           74 GHRVNIIDTPGHVDFTVEVER-----SL---RVLDGAVTVLDAQSGVEPQT----ETVWR-QATTYGVPRIVFVNKMDKL  140 (693)
T ss_dssp             TEEEEEECCCCCSSCCHHHHH-----HH---HHCSEEEEEEETTTBSCHHH----HHHHH-HHHHTTCCEEEEEECTTST
T ss_pred             CeeEEEEECcCCcchHHHHHH-----HH---HHCCEEEEEECCCCCCcHHH----HHHHH-HHHHcCCCEEEEEECCCcc
Confidence            346789999999875433221     11   23778999999976322100    00101 1233345668999999997


Q ss_pred             ChhHHHHHHHHHHHh
Q 023301          109 TETELGSLTERIKHI  123 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~  123 (284)
                      +. +...+.+.+++.
T Consensus       141 ~~-~~~~~~~~l~~~  154 (693)
T 2xex_A          141 GA-NFEYSVSTLHDR  154 (693)
T ss_dssp             TC-CHHHHHHHHHHH
T ss_pred             cc-chHHHHHHHHHH
Confidence            64 344455555544

>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=85.55  E-value=1.5  Score=40.26  Aligned_cols=95  Identities=7%  Similarity=0.085  Sum_probs=45.8

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHH--hhhhcCCccchHH-HHHHHhhcC-EEEEccC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQ--HLNEVKPRFVVNE-AVEQVAYAD-RIILNKI  105 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~--~l~~~~~~~~~~~-~~~Qi~~Ad-~ivlnK~  105 (284)
                      ..+.|++|+|-.+.....        ....-..+.+|.|||+..-..  .+.. .+...... ...++.... +|++||+
T Consensus       121 ~~~~iiDtPGh~~f~~~~--------~~~~~~aD~~ilVvDa~~g~~e~sf~~-~~qt~e~l~~~~~~~vp~iivviNK~  191 (467)
T 1r5b_A          121 RRFSLLDAPGHKGYVTNM--------INGASQADIGVLVISARRGEFEAGFER-GGQTREHAVLARTQGINHLVVVINKM  191 (467)
T ss_dssp             EEEEECCCCC-------------------TTSCSEEEEEEECSTTHHHHTTST-TCCHHHHHHHHHHTTCSSEEEEEECT
T ss_pred             eEEEEEECCCcHHHHHHH--------HhhcccCCEEEEEEeCCcCccccccCC-CCcHHHHHHHHHHcCCCEEEEEEECc
Confidence            356789999976543211        112235788999999987531  1110 01111111 123344443 5779999


Q ss_pred             CCCC----hhHHH----HHHHHHHHh-C-C---CCceeeec
Q 023301          106 DLVT----ETELG----SLTERIKHI-N-A---MAPVKLAK  133 (284)
Q Consensus       106 D~~~----~~~~~----~~~~~l~~~-n-p---~a~i~~~~  133 (284)
                      |+.+    .+.++    +++++++.+ . .   .++++.++
T Consensus       192 Dl~~~~~~~~~~~~i~~e~~~~l~~~~g~~~~~~~~~i~vS  232 (467)
T 1r5b_A          192 DEPSVQWSEERYKECVDKLSMFLRRVAGYNSKTDVKYMPVS  232 (467)
T ss_dssp             TSTTCSSCHHHHHHHHHHHHHHHHHHHCCCHHHHEEEEECB
T ss_pred             cCCCccccHHHHHHHHHHHHHHHHHhcCCCccCCceEEecc
Confidence            9954    23333    345555554 2 1   45666654

>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=84.98  E-value=2.8  Score=32.58  Aligned_cols=99  Identities=10%  Similarity=0.033  Sum_probs=52.5

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-----hhcCEEEEccC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-----AYADRIILNKI  105 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-----~~Ad~ivlnK~  105 (284)
                      ...+++++|......+.....        -..+.++.|+|+...... .+.  ...... ..++     ...=+||+||+
T Consensus        57 ~~~l~Dt~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~--~~~~~~-i~~~~~~~~~~piilv~nK~  124 (199)
T 2gf0_A           57 TLQITDTTGSHQFPAMQRLSI--------SKGHAFILVFSVTSKQSL-EEL--GPIYKL-IVQIKGSVEDIPVMLVGNKC  124 (199)
T ss_dssp             EEEEEECCGGGSCHHHHHHHH--------HHCSEEEEEEETTCHHHH-HTT--HHHHHH-HHHHHSCGGGSCEEEEEECT
T ss_pred             EEEEEeCCChHHhHHHHHHhh--------ccCCEEEEEEECcCHHHH-HHH--HHHHHH-HHHHhcCCCCCCEEEEEECc
Confidence            456889999777665443321        135778999999874432 211  001011 1222     12347888999


Q ss_pred             CCCChh-HHHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          106 DLVTET-ELGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       106 D~~~~~-~~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      |+.+.+ ..+...+..+..+  .+++.++. .......++
T Consensus       125 Dl~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  162 (199)
T 2gf0_A          125 DETQREVDTREAQAVAQEWK--CAFMETSAKMNYNVKELF  162 (199)
T ss_dssp             TCSSCSSCHHHHHHHHHHHT--CEEEECBTTTTBSHHHHH
T ss_pred             cCCccccCHHHHHHHHHHhC--CeEEEEecCCCCCHHHHH
Confidence            996532 2334444444443  46666653 233444444

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=84.84  E-value=0.56  Score=36.62  Aligned_cols=76  Identities=21%  Similarity=0.160  Sum_probs=41.1

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH------hhcCEEEEc
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV------AYADRIILN  103 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi------~~Ad~ivln  103 (284)
                      ....+++++|......+    .. ..+   -..+.++.|+|+.+.... .+.     ...+...+      ...=+||+|
T Consensus        66 ~~~~~~Dt~G~~~~~~~----~~-~~~---~~~d~ii~v~d~~~~~s~-~~~-----~~~~~~~~~~~~~~~~piilv~n  131 (189)
T 2x77_A           66 ISFEVWDLGGQTGVRPY----WR-CYF---SDTDAVIYVVDSTDRDRM-GVA-----KHELYALLDEDELRKSLLLIFAN  131 (189)
T ss_dssp             EEEEEEEECCSSSSCCC----CS-SSS---TTCCEEEEEEETTCCTTH-HHH-----HHHHHHHHTCSTTTTCEEEEEEE
T ss_pred             EEEEEEECCCCHhHHHH----HH-HHh---hcCCEEEEEEeCCCHHHH-HHH-----HHHHHHHHhhhhcCCCeEEEEEE
Confidence            45678899997654321    11 111   256789999999764211 110     01111221      223478889


Q ss_pred             cCCCCChhHHHHHHHH
Q 023301          104 KIDLVTETELGSLTER  119 (284)
Q Consensus       104 K~D~~~~~~~~~~~~~  119 (284)
                      |+|+.+....+.+.+.
T Consensus       132 K~Dl~~~~~~~~~~~~  147 (189)
T 2x77_A          132 KQDLPDAASEAEIAEQ  147 (189)
T ss_dssp             CTTSTTCCCHHHHHHH
T ss_pred             CCCCcCCCCHHHHHHH
Confidence            9999775444444443

>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=84.83  E-value=1.6  Score=44.64  Aligned_cols=93  Identities=19%  Similarity=0.206  Sum_probs=52.1

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC-EEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD-RIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~  107 (284)
                      ...+.|++|+|..+......        ...-..+.+|.|||+..-..  .+  .+... ....+..... +|++||+|+
T Consensus       358 ~~kI~IIDTPGHedF~~~mi--------~gas~AD~aILVVDAtdGv~--~Q--TrEhL-~ll~~lgIP~IIVVINKiDL  424 (1289)
T 3avx_A          358 TRHYAHVDCPGHADYVKNMI--------TGAAQMDGAILVVAATDGPM--PQ--TREHI-LLGRQVGVPYIIVFLNKCDM  424 (1289)
T ss_dssp             SCEEEEEECCCHHHHHHHHH--------HTSCCCSEEEEEEETTTCSC--TT--HHHHH-HHHHHHTCSCEEEEEECCTT
T ss_pred             CEEEEEEECCChHHHHHHHH--------HHHhhCCEEEEEEcCCccCc--HH--HHHHH-HHHHHcCCCeEEEEEeeccc
Confidence            35678999999765432111        11235788999999976321  11  00000 1123444454 578999999


Q ss_pred             CChhH-H----HHHHHHHHHhCC---CCceeeecc
Q 023301          108 VTETE-L----GSLTERIKHINA---MAPVKLAKY  134 (284)
Q Consensus       108 ~~~~~-~----~~~~~~l~~~np---~a~i~~~~~  134 (284)
                      .+.++ +    +++++.++..+-   ..+++.++.
T Consensus       425 v~d~e~le~i~eEi~elLk~~G~~~~~vp~IpvSA  459 (1289)
T 3avx_A          425 VDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSA  459 (1289)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHTTSCTTTCCEEECCS
T ss_pred             ccchhhHHHHHHHHHHHHHhccccccceeEEEEEe
Confidence            86332 3    345555655542   467877653

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=84.66  E-value=2.2  Score=38.67  Aligned_cols=72  Identities=15%  Similarity=0.235  Sum_probs=40.9

Q ss_pred             CCCCEEEEecCCCCCcH-HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCC
Q 023301           28 GQFDHIVIETTGLAKPA-PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKID  106 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~-~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D  106 (284)
                      ..+|+|||+|+|..... .+...+..   +.....-+.++.|+|+......+.      ....+...+. -.-||+||.|
T Consensus       182 ~~~D~VIIDTpG~l~~~~~l~~~L~~---~~~~~~p~~vllVvda~~g~~~~~------~~~~f~~~l~-i~gvVlnK~D  251 (433)
T 2xxa_A          182 KFYDVLLVDTAGRLHVDEAMMDEIKQ---VHASINPVETLFVVDAMTGQDAAN------TAKAFNEALP-LTGVVLTKVD  251 (433)
T ss_dssp             TTCSEEEEECCCCCTTCHHHHHHHHH---HHHHSCCSEEEEEEETTBCTTHHH------HHHHHHHHSC-CCCEEEECTT
T ss_pred             CCCCEEEEECCCcccccHHHHHHHHH---HHHhhcCcceeEEeecchhHHHHH------HHHHHhccCC-CeEEEEecCC
Confidence            57999999999987753 34443321   112234567889999976322111      0011111221 1458999999


Q ss_pred             CCC
Q 023301          107 LVT  109 (284)
Q Consensus       107 ~~~  109 (284)
                      ...
T Consensus       252 ~~~  254 (433)
T 2xxa_A          252 GDA  254 (433)
T ss_dssp             SSS
T ss_pred             CCc
Confidence            753

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=84.60  E-value=1.4  Score=35.57  Aligned_cols=96  Identities=14%  Similarity=0.087  Sum_probs=47.9

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh------hcCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA------YADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~------~Ad~ivlnK  104 (284)
                      ...|++++|......+..     ..+   -..+.+|.|+|+...... .+.      ..+..++.      ..=+||+||
T Consensus        63 ~~~i~Dt~G~~~~~~~~~-----~~~---~~~d~vilV~D~~~~~s~-~~~------~~~l~~i~~~~~~~~piilv~nK  127 (223)
T 3cpj_B           63 KAQIWDTAGQERYRAITS-----AYY---RGAVGALIVYDISKSSSY-ENC------NHWLSELRENADDNVAVGLIGNK  127 (223)
T ss_dssp             EEEEECCTTTTTTTCCCG-----GGT---TTCCEEEEEEC-CCHHHH-HHH------HHHHHHHHHHCC--CEEEEEECC
T ss_pred             EEEEEECCCccchhhhHH-----HHh---ccCCEEEEEEeCCCHHHH-HHH------HHHHHHHHHhCCCCCeEEEEEEC
Confidence            456778888554322111     111   245779999999875432 111      11122222      223678899


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+..+  .+...++.+..+  .++++++. .......++
T Consensus       128 ~Dl~~~~~v~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  167 (223)
T 3cpj_B          128 SDLAHLRAVPTEESKTFAQENQ--LLFTETSALNSENVDKAF  167 (223)
T ss_dssp             GGGGGGCCSCHHHHHHHHHHTT--CEEEECCCC-CCCHHHHH
T ss_pred             cccccccccCHHHHHHHHHHcC--CEEEEEeCCCCCCHHHHH
Confidence            99865322  234445554433  56766653 233444444

>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=84.58  E-value=3.4  Score=31.68  Aligned_cols=99  Identities=10%  Similarity=0.144  Sum_probs=49.1

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCCCC
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKIDLV  108 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D~~  108 (284)
                      ..+++++|......+.....        -..+.++.|+|+...... .+.. .+. ..+....   ...=+||+||+|+.
T Consensus        54 ~~i~Dt~G~~~~~~~~~~~~--------~~~~~~i~v~d~~~~~s~-~~~~-~~~-~~~~~~~~~~~~p~i~v~nK~Dl~  122 (189)
T 4dsu_A           54 LDILDTAGQEEYSAMRDQYM--------RTGEGFLCVFAINNTKSF-EDIH-HYR-EQIKRVKDSEDVPMVLVGNKCDLP  122 (189)
T ss_dssp             EEEEECCCC---CTTHHHHH--------HHCSEEEEEEETTCHHHH-HHHH-HHH-HHHHHHTTCSCCCEEEEEECTTSS
T ss_pred             EEEEECCCcHHHHHHHHHHH--------hcCCEEEEEEECCCHHHH-HHHH-HHH-HHHHHhcCCCCCcEEEEEECccCc
Confidence            45689999766544433321        135678999999874332 1110 000 1111111   12347888999996


Q ss_pred             ChhH-HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          109 TETE-LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       109 ~~~~-~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +... .+.+.+..+..+  .+++.++. .......++
T Consensus       123 ~~~~~~~~~~~~~~~~~--~~~~~~Sa~~g~gi~~l~  157 (189)
T 4dsu_A          123 SRTVDTKQAQDLARSYG--IPFIETSAKTRQGVDDAF  157 (189)
T ss_dssp             SCSSCHHHHHHHHHHHT--CCEEECCTTTCTTHHHHH
T ss_pred             ccccCHHHHHHHHHHcC--CeEEEEeCCCCCCHHHHH
Confidence            5322 334444444444  56776653 233455544

>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=84.13  E-value=2.3  Score=37.61  Aligned_cols=99  Identities=19%  Similarity=0.268  Sum_probs=50.1

Q ss_pred             CEEEEecCCC-CC-cHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh---hcCEEEEccC
Q 023301           31 DHIVIETTGL-AK-PAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA---YADRIILNKI  105 (284)
Q Consensus        31 d~iiIE~sG~-a~-p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~---~Ad~ivlnK~  105 (284)
                      ...++.|.|. .+ |..+++.+..  .+...-..+.++.|+|+.+......... .. ...+..++.   ..-++|.||+
T Consensus       227 ~v~l~DT~G~i~~lp~~lve~f~~--tl~~~~~aD~il~VvD~s~~~~~~~~~~-~~-~~~~L~~l~~~~~p~ilV~NK~  302 (364)
T 2qtf_A          227 KIMLVDTVGFIRGIPPQIVDAFFV--TLSEAKYSDALILVIDSTFSENLLIETL-QS-SFEILREIGVSGKPILVTLNKI  302 (364)
T ss_dssp             EEEEEECCCBCSSCCGGGHHHHHH--HHHGGGGSSEEEEEEETTSCHHHHHHHH-HH-HHHHHHHHTCCSCCEEEEEECG
T ss_pred             EEEEEeCCCchhcCCHHHHHHHHH--HHHHHHhCCEEEEEEECCCCcchHHHHH-HH-HHHHHHHhCcCCCCEEEEEECC
Confidence            4567899996 33 5555444321  1222345678899999876431001000 00 012233432   3457888999


Q ss_pred             CCCChhHH---HHHHHHHHHh-CCCCceeeec
Q 023301          106 DLVTETEL---GSLTERIKHI-NAMAPVKLAK  133 (284)
Q Consensus       106 D~~~~~~~---~~~~~~l~~~-np~a~i~~~~  133 (284)
                      |+.+....   ..+.+..+.+ .+..+++.++
T Consensus       303 Dl~~~~~~~~~~~~~~l~~~l~~~~~~~~~~S  334 (364)
T 2qtf_A          303 DKINGDLYKKLDLVEKLSKELYSPIFDVIPIS  334 (364)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCSCEEEEEECB
T ss_pred             CCCCchHHHHHHHHHHHHHHhcCCCCcEEEEE
Confidence            99875422   1222233555 4444555554

>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=83.76  E-value=2  Score=41.61  Aligned_cols=80  Identities=18%  Similarity=0.176  Sum_probs=47.3

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVT  109 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~  109 (284)
                      .++.||+|+|-.+.......     .+   -..+.+|.|+|+........    ..... ...+....-++++||+|+..
T Consensus        82 ~~i~liDTPG~~df~~~~~~-----~l---~~aD~aIlVvDa~~gv~~qt----~~~~~-~~~~~~ip~ilviNKiD~~~  148 (704)
T 2rdo_7           82 HRINIIDTPGHVDFTIEVER-----SM---RVLDGAVMVYCAVGGVQPQS----ETVWR-QANKYKVPRIAFVNKMDRMG  148 (704)
T ss_pred             eeEEEEeCCCccchHHHHHH-----HH---HHCCEEEEEEeCCCCCcHHH----HHHHH-HHHHcCCCEEEEEeCCCccc
Confidence            77899999999885433222     11   24678999999986432100    00000 11223445689999999965


Q ss_pred             hhHHHHHHHHHHHh
Q 023301          110 ETELGSLTERIKHI  123 (284)
Q Consensus       110 ~~~~~~~~~~l~~~  123 (284)
                      . ...++.+.++..
T Consensus       149 ~-~~~~~~~~l~~~  161 (704)
T 2rdo_7          149 A-NFLKVVNQIKTR  161 (704)
T ss_pred             c-cHHHHHHHHHHH
Confidence            4 345555555544

>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=83.67  E-value=1.4  Score=42.46  Aligned_cols=81  Identities=20%  Similarity=0.215  Sum_probs=48.9

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      .....||+|+|..+........     +   -..+.+|.|+|+......-.    ..... ...+....-++|+||+|+.
T Consensus        76 ~~~i~liDTPG~~df~~~~~~~-----l---~~aD~~ilVvDa~~g~~~~t----~~~~~-~~~~~~~p~ivviNKiD~~  142 (691)
T 1dar_A           76 DHRINIIDTPGHVDFTIEVERS-----M---RVLDGAIVVFDSSQGVEPQS----ETVWR-QAEKYKVPRIAFANKMDKT  142 (691)
T ss_dssp             TEEEEEECCCSSTTCHHHHHHH-----H---HHCSEEEEEEETTTCSCHHH----HHHHH-HHHHTTCCEEEEEECTTST
T ss_pred             CeEEEEEECcCccchHHHHHHH-----H---HHCCEEEEEEECCCCcchhh----HHHHH-HHHHcCCCEEEEEECCCcc
Confidence            4567899999998855433221     1   24678999999986332100    00001 1233455678999999997


Q ss_pred             ChhHHHHHHHHHHHh
Q 023301          109 TETELGSLTERIKHI  123 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~  123 (284)
                      .. +...+.+.+++.
T Consensus       143 ~~-~~~~~~~~l~~~  156 (691)
T 1dar_A          143 GA-DLWLVIRTMQER  156 (691)
T ss_dssp             TC-CHHHHHHHHHHT
T ss_pred             cC-CHHHHHHHHHHH
Confidence            54 355555666654

>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=83.57  E-value=2.4  Score=39.48  Aligned_cols=68  Identities=12%  Similarity=0.122  Sum_probs=41.5

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKI  105 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~  105 (284)
                      ...+.||+|+|..+.......     .+   -..+.+|.|+|+.......       . ..+..++   ...-++++||+
T Consensus        81 ~~~i~liDTPG~~df~~~~~~-----~l---~~aD~~IlVvDa~~g~~~~-------t-~~~~~~~~~~~ipiivviNK~  144 (529)
T 2h5e_A           81 DCLVNLLDTPGHEDFSEDTYR-----TL---TAVDCCLMVIDAAKGVEDR-------T-RKLMEVTRLRDTPILTFMNKL  144 (529)
T ss_dssp             TEEEEEECCCCSTTCCHHHHH-----GG---GGCSEEEEEEETTTCSCHH-------H-HHHHHHHTTTTCCEEEEEECT
T ss_pred             CeEEEEEECCCChhHHHHHHH-----HH---HHCCEEEEEEeCCccchHH-------H-HHHHHHHHHcCCCEEEEEcCc
Confidence            456789999999875542222     11   2577899999997632110       0 1122222   33458899999


Q ss_pred             CCCChhH
Q 023301          106 DLVTETE  112 (284)
Q Consensus       106 D~~~~~~  112 (284)
                      |+.+.+.
T Consensus       145 Dl~~~~~  151 (529)
T 2h5e_A          145 DRDIRDP  151 (529)
T ss_dssp             TSCCSCH
T ss_pred             CCccccH
Confidence            9976543

>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation, GTP-binding domain, maturation enzyme, oxidoreductase; 2.99A {Thermotoga neapolitana}

Probab=83.57  E-value=0.19  Score=45.66  Aligned_cols=75  Identities=20%  Similarity=0.253  Sum_probs=40.8

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCCh
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTE  110 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~  110 (284)
                      ...+++|+|..+...+-.. .........-..+.++.|+|+ ........     .... ..+....-++|+||+|+.+.
T Consensus        84 ~l~liDTpG~~d~~~l~~~-~~~~~~~~l~~aD~vllVvD~-~~~~~~~~-----~l~~-l~~~~~piIvV~NK~Dl~~~  155 (423)
T 3qq5_A           84 PVTLVDTPGLDDVGELGRL-RVEKARRVFYRADCGILVTDS-APTPYEDD-----VVNL-FKEMEIPFVVVVNKIDVLGE  155 (423)
T ss_dssp             EEEEEECSSTTCCCTTCCC-CHHHHHHHHTSCSEEEEECSS-SCCHHHHH-----HHHH-HHHTTCCEEEECCCCTTTTC
T ss_pred             eEEEEECcCCCcccchhHH-HHHHHHHHHhcCCEEEEEEeC-CChHHHHH-----HHHH-HHhcCCCEEEEEeCcCCCCc
Confidence            5788999999876432100 000001111246789999999 33322111     1111 22334556888999999776


Q ss_pred             hHH
Q 023301          111 TEL  113 (284)
Q Consensus       111 ~~~  113 (284)
                      ...
T Consensus       156 ~~~  158 (423)
T 3qq5_A          156 KAE  158 (423)
T ss_dssp             CCT
T ss_pred             cHH
Confidence            554

>3mca_A HBS1, elongation factor 1 alpha-like protein; protein protein complex, translation regulation; 2.74A {Schizosaccharomyces pombe}

Probab=83.34  E-value=0.31  Score=46.24  Aligned_cols=86  Identities=13%  Similarity=0.144  Sum_probs=39.3

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH--HhhhhcCCccchH-HHHHHHhhcC-EEEEccC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM--QHLNEVKPRFVVN-EAVEQVAYAD-RIILNKI  105 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~--~~l~~~~~~~~~~-~~~~Qi~~Ad-~ivlnK~  105 (284)
                      ..+.||+|+|..+...        ......-..+.+|.|||+..-.  ..+.. .+..... .+..++.... +||+||+
T Consensus       255 ~~i~iiDTPGh~~f~~--------~~~~~~~~aD~alLVVDa~~g~~e~gi~~-~~qt~e~l~~~~~lgip~iIvviNKi  325 (592)
T 3mca_A          255 KIYEIGDAPGHRDFIS--------GMIAGASSADFAVLVVDSSQNNFERGFLE-NGQTREHAYLLRALGISEIVVSVNKL  325 (592)
T ss_dssp             ----CCEEESSSEEEE--------ECCC-------CCSEEEEEECCSSTTSCS-CSSHHHHHHHHHHSSCCCEEEEEECG
T ss_pred             eEEEEEECCChHHHHH--------HHHHHHhhCCEEEEEEECCCCcccccccc-chHHHHHHHHHHHcCCCeEEEEEecc
Confidence            4667888998765321        1122233577899999998621  00000 0001101 1223344443 4588999


Q ss_pred             CCCC--hhHHHHHHHHHHHhC
Q 023301          106 DLVT--ETELGSLTERIKHIN  124 (284)
Q Consensus       106 D~~~--~~~~~~~~~~l~~~n  124 (284)
                      |+++  .+.++.+.+.++.+.
T Consensus       326 Dl~~~~~~~~~~i~~el~~~l  346 (592)
T 3mca_A          326 DLMSWSEDRFQEIKNIVSDFL  346 (592)
T ss_dssp             GGGTTCHHHHHHHHHHHHHHH
T ss_pred             ccccccHHHHHHHHHHHHHHH
Confidence            9975  555666666666543

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=83.26  E-value=6.3  Score=34.07  Aligned_cols=95  Identities=19%  Similarity=0.283  Sum_probs=50.2

Q ss_pred             CCCCEEEEecCCCCCcH-HHHHHhccc-cccc--ceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh--cCEEE
Q 023301           28 GQFDHIVIETTGLAKPA-PVIETFCTD-ELVS--QYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY--ADRII  101 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~-~i~~~l~~~-~~l~--~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~--Ad~iv  101 (284)
                      ..+|+|||+|+|..... .++..+..- ..+.  ....-+.++.|+|+..-...+..         +....+.  -.-||
T Consensus       190 ~~yD~VIIDTpg~l~~~~~l~~eL~~~~~vi~~~~p~~~d~vllVl~a~~~~~~l~~---------~~~~~~~~~i~GvV  260 (320)
T 1zu4_A          190 QNYDLLLIDTAGRLQNKTNLMAELEKMNKIIQQVEKSAPHEVLLVIDATTGQNGVIQ---------AEEFSKVADVSGII  260 (320)
T ss_dssp             TTCSEEEEECCCCGGGHHHHHHHHHHHHHHHHTTCTTCCSEEEEEEEGGGTHHHHHH---------HHHHTTTSCCCEEE
T ss_pred             cCCCEEEEcCCCcccccHHHHHHHHHHHHHHhcccCCCCceEEEEEECCCcHHHHHH---------HHHHhhcCCCcEEE
Confidence            67999999999988753 233332110 0000  01124578999999864332221         1111112  33489


Q ss_pred             EccCCCCChhHHHHHHHHHHHhCCCCceeeeccC
Q 023301          102 LNKIDLVTETELGSLTERIKHINAMAPVKLAKYG  135 (284)
Q Consensus       102 lnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g  135 (284)
                      +||.|....  ...+...+...+  .+|.....|
T Consensus       261 ltk~d~~~~--~g~~~~~~~~~~--~Pi~~i~~G  290 (320)
T 1zu4_A          261 LTKMDSTSK--GGIGLAIKELLN--IPIKMIGVG  290 (320)
T ss_dssp             EECGGGCSC--TTHHHHHHHHHC--CCEEEEECS
T ss_pred             EeCCCCCCc--hhHHHHHHHHHC--cCEEEEeCC
Confidence            999997442  224445555554  455444444

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=83.25  E-value=1  Score=37.74  Aligned_cols=69  Identities=9%  Similarity=0.116  Sum_probs=37.9

Q ss_pred             CEEEEecCCCCCcH----HHHHHhcccccccceeeeceEEEEEcccc--hHHhhhhcCCccchHHHHHHHh--------h
Q 023301           31 DHIVIETTGLAKPA----PVIETFCTDELVSQYVKLDGVITLVDSKH--AMQHLNEVKPRFVVNEAVEQVA--------Y   96 (284)
Q Consensus        31 d~iiIE~sG~a~p~----~i~~~l~~~~~l~~~~~l~~vv~vvD~~~--~~~~l~~~~~~~~~~~~~~Qi~--------~   96 (284)
                      ...|++|+|..+..    ...+.+..  .+ ..-..+.++.|+|...  +... .        ..+..++.        .
T Consensus        88 ~l~iiDTpG~~~~~~~~~~~~~~i~~--~~-~~~~~d~il~v~~~d~~~~~~~-~--------~~~~~~l~~~~~~~~~~  155 (270)
T 1h65_A           88 TLNIIDTPGLIEGGYINDMALNIIKS--FL-LDKTIDVLLYVDRLDAYRVDNL-D--------KLVAKAITDSFGKGIWN  155 (270)
T ss_dssp             EEEEEECCCSEETTEECHHHHHHHHH--HT-TTCEECEEEEEEESSCCCCCHH-H--------HHHHHHHHHHHCGGGGG
T ss_pred             EEEEEECCCCCCCccchHHHHHHHHH--Hh-hcCCCCEEEEEEeCCCCcCCHH-H--------HHHHHHHHHHhCccccc
Confidence            57899999997653    22222210  01 1125788999966543  2211 0        01122222        2


Q ss_pred             cCEEEEccCCCCChh
Q 023301           97 ADRIILNKIDLVTET  111 (284)
Q Consensus        97 Ad~ivlnK~D~~~~~  111 (284)
                      .-++|+||+|+.+++
T Consensus       156 ~iivV~nK~Dl~~~~  170 (270)
T 1h65_A          156 KAIVALTHAQFSPPD  170 (270)
T ss_dssp             GEEEEEECCSCCCGG
T ss_pred             CEEEEEECcccCCcC
Confidence            457889999998654

>3dpu_A RAB family protein; roccor, G-domain, COR, GTP-binding, nucleotide-binding, SIGN protein; 2.90A {Chlorobaculum tepidum}

Probab=83.13  E-value=2.2  Score=39.69  Aligned_cols=85  Identities=14%  Similarity=0.139  Sum_probs=48.0

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHh-----hcCEEEEc
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVA-----YADRIILN  103 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~-----~Ad~ivln  103 (284)
                      .....+++++|......+...+     +.   ..+.+|.|+|+.++...          ..+..++.     ..-+||.|
T Consensus        97 ~~~~~i~Dt~G~e~~~~~~~~~-----l~---~~d~ii~V~D~s~~~~~----------~~~~~~l~~~~~~~pvilV~N  158 (535)
T 3dpu_A           97 ECLFHFWDFGGQEIMHASHQFF-----MT---RSSVYMLLLDSRTDSNK----------HYWLRHIEKYGGKSPVIVVMN  158 (535)
T ss_dssp             TCEEEEECCCSCCTTTTTCHHH-----HH---SSEEEEEEECGGGGGGH----------HHHHHHHHHHSSSCCEEEEEC
T ss_pred             eEEEEEEECCcHHHHHHHHHHH-----cc---CCcEEEEEEeCCCchhH----------HHHHHHHHHhCCCCCEEEEEE
Confidence            4567888999954433222111     11   35678999999876321          12233333     34578889


Q ss_pred             cCCCCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          104 KIDLVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       104 K~D~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      |+|+.+..+  .+.+++..+.++  .+++.++
T Consensus       159 K~Dl~~~~~v~~~~~~~~~~~~~--~~~~~vS  188 (535)
T 3dpu_A          159 KIDENPSYNIEQKKINERFPAIE--NRFHRIS  188 (535)
T ss_dssp             CTTTCTTCCCCHHHHHHHCGGGT--TCEEECC
T ss_pred             CCCcccccccCHHHHHHHHHhcC--CceEEEe
Confidence            999976433  344444444433  4566654

>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=83.01  E-value=1.8  Score=33.16  Aligned_cols=90  Identities=14%  Similarity=0.113  Sum_probs=46.7

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D~  107 (284)
                      ...+++++|......+...     .+   -..+.++.|+|....... .... .+ ...+....   ...-+||+||+|+
T Consensus        55 ~~~l~Dt~G~~~~~~~~~~-----~~---~~~~~~i~v~d~~~~~s~-~~~~-~~-~~~~~~~~~~~~~p~ilv~nK~Dl  123 (181)
T 3t5g_A           55 HLQLVDTAGQDEYSIFPQT-----YS---IDINGYILVYSVTSIKSF-EVIK-VI-HGKLLDMVGKVQIPIMLVGNKKDL  123 (181)
T ss_dssp             EEEEEECCCCCTTCCCCGG-----GT---TTCSEEEEEEETTCHHHH-HHHH-HH-HHHHHHHC----CCEEEEEECTTC
T ss_pred             EEEEEeCCCchhhhHHHHH-----HH---hcCCEEEEEEECCCHHHH-HHHH-HH-HHHHHHhcCCCCCCEEEEEECccc
Confidence            3468899997654321111     11   146789999999874432 1110 00 01122222   2344788899998


Q ss_pred             CChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          108 VTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       108 ~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      .+..+  .+..+++.+..  .+++++++
T Consensus       124 ~~~~~~~~~~~~~~~~~~--~~~~~~~S  149 (181)
T 3t5g_A          124 HMERVISYEEGKALAESW--NAAFLESS  149 (181)
T ss_dssp             TTTCCSCHHHHHHHHHHT--TCEEEECC
T ss_pred             hhcceecHHHHHHHHHHh--CCcEEEEe
Confidence            54322  24445555544  35677665

>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=82.92  E-value=0.66  Score=39.69  Aligned_cols=77  Identities=14%  Similarity=0.247  Sum_probs=39.3

Q ss_pred             CCCEEEEecCCCCC-c-----HHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCE
Q 023301           29 QFDHIVIETTGLAK-P-----APVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADR   99 (284)
Q Consensus        29 ~~d~iiIE~sG~a~-p-----~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~   99 (284)
                      ..+.+||+|+|+.. +     ..+-..+.. ......-..+.++.|+|+.+..  +... ..   ..+..++   ...-+
T Consensus       130 ~~~~~lvDTpG~~~~~~~~~~~~~~~~~~~-~~~~~~~~~d~iilvvd~~~~~--~~~~-~~---~~i~~~~~~~~~~~i  202 (315)
T 1jwy_B          130 VVNLTLVDLPGITKVPVGDQPTDIEQQIRR-MVMAYIKKQNAIIVAVTPANTD--LANS-DA---LQLAKEVDPEGKRTI  202 (315)
T ss_dssp             SCSEEEEECCCCC---------CSHHHHHH-HHHHHHHSTTEEEEEEEESSSC--STTC-SH---HHHHHHHCSSCSSEE
T ss_pred             CCCcEEEECCCCccCCCCCCchhHHHHHHH-HHHHHHcCCCeEEEEEEecCcc--hhhh-HH---HHHHHHhCCCCCcEE
Confidence            46899999999975 2     111111100 0011112456789999974321  1110 00   1223343   34558


Q ss_pred             EEEccCCCCChhH
Q 023301          100 IILNKIDLVTETE  112 (284)
Q Consensus       100 ivlnK~D~~~~~~  112 (284)
                      +|+||+|+.+...
T Consensus       203 ~v~NK~Dl~~~~~  215 (315)
T 1jwy_B          203 GVITKLDLMDKGT  215 (315)
T ss_dssp             EEEECTTSSCSSC
T ss_pred             EEEcCcccCCcch
Confidence            8999999986543

>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=82.91  E-value=3.8  Score=30.64  Aligned_cols=100  Identities=14%  Similarity=0.125  Sum_probs=48.9

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH--hhcCEEEEccCCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV--AYADRIILNKIDLV  108 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi--~~Ad~ivlnK~D~~  108 (284)
                      ...+++++|......+.....        -..+.++.|+|+.+.... .+.. .++ ..+....  ...=++|+||+|+.
T Consensus        53 ~~~~~D~~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~~~-~~~-~~~~~~~~~~~piilv~nK~Dl~  121 (170)
T 1ek0_A           53 KFEIWDTAGQERFASLAPXYY--------RNAQAALVVYDVTKPQSF-IKAR-HWV-KELHEQASKDIIIALVGNKIDXL  121 (170)
T ss_dssp             EEEEEEECCSGGGGGGHHHHH--------TTCSEEEEEEETTCHHHH-HHHH-HHH-HHHHHHSCTTCEEEEEEECGGGG
T ss_pred             EEEEEECCCChhhhhhhhhhh--------ccCcEEEEEEecCChHHH-HHHH-HHH-HHHHHhcCCCCcEEEEEECCCcc
Confidence            456789999655444332221        135779999999875432 1110 011 1111111  22335788999986


Q ss_pred             Ch---hH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          109 TE---TE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       109 ~~---~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +.   .+  .+..++..+..+  ++++.++. .......++
T Consensus       122 ~~~~~~~v~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  160 (170)
T 1ek0_A          122 QEGGERKVAREEGEKLAEEKG--LLFFETSAKTGENVNDVF  160 (170)
T ss_dssp             GSSCCCCSCHHHHHHHHHHHT--CEEEECCTTTCTTHHHHH
T ss_pred             ccccccCCCHHHHHHHHHHcC--CEEEEEeCCCCCCHHHHH
Confidence            53   11  123333333332  56666553 233344443

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=82.77  E-value=4  Score=36.88  Aligned_cols=95  Identities=18%  Similarity=0.253  Sum_probs=50.1

Q ss_pred             CCCCEEEEecCCCCCcH-HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCC
Q 023301           28 GQFDHIVIETTGLAKPA-PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKID  106 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~-~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D  106 (284)
                      ..+|+|||+|+|..... .+...+.   .+...+.-+.++.|+|+..-...+..      ...+.+.+ .-.-||+||.|
T Consensus       179 ~~~DvVIIDTaG~l~~d~~l~~el~---~i~~~~~pd~vlLVvDa~tgq~av~~------a~~f~~~l-~i~GVIlTKlD  248 (425)
T 2ffh_A          179 EARDLILVDTAGRLQIDEPLMGELA---RLKEVLGPDEVLLVLDAMTGQEALSV------ARAFDEKV-GVTGLVLTKLD  248 (425)
T ss_dssp             TTCSEEEEECCCCSSCCHHHHHHHH---HHHHHHCCSEEEEEEEGGGTTHHHHH------HHHHHHHT-CCCEEEEESGG
T ss_pred             CCCCEEEEcCCCcccccHHHHHHHH---HhhhccCCceEEEEEeccchHHHHHH------HHHHHhcC-CceEEEEeCcC
Confidence            67999999999987642 2333321   11222345678999999764322111      01111222 23678999999


Q ss_pred             CCChhHHHHHHHHHHHhCCCCceeeeccCC
Q 023301          107 LVTETELGSLTERIKHINAMAPVKLAKYGS  136 (284)
Q Consensus       107 ~~~~~~~~~~~~~l~~~np~a~i~~~~~g~  136 (284)
                      .....  ..+........  .+|.....|+
T Consensus       249 ~~~~~--g~alsi~~~~g--~PI~flg~Ge  274 (425)
T 2ffh_A          249 GDARG--GAALSARHVTG--KPIYFAGVSE  274 (425)
T ss_dssp             GCSSC--HHHHHHHHHHC--CCEEEEECSS
T ss_pred             CcccH--HHHHHHHHHHC--CCEEEEeCCC
Confidence            74321  22333333333  4555444443

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=82.69  E-value=7.6  Score=30.36  Aligned_cols=77  Identities=19%  Similarity=0.189  Sum_probs=44.0

Q ss_pred             CCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcC--------E
Q 023301           28 GQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYAD--------R   99 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad--------~   99 (284)
                      ..+|+|||+++|...... ...+.         ..+.+|.++++.... .--        ..+.+.+....        .
T Consensus        74 ~~yD~viiD~~~~~~~~~-~~~l~---------~ad~viiv~~~~~~~-~~~--------~~~~~~l~~~~~~~~~~~~~  134 (206)
T 4dzz_A           74 ADYDFAIVDGAGSLSVIT-SAAVM---------VSDLVIIPVTPSPLD-FSA--------AGSVVTVLEAQAYSRKVEAR  134 (206)
T ss_dssp             TTSSEEEEECCSSSSHHH-HHHHH---------HCSEEEEEECSCTTT-HHH--------HHHHHHHHTTSCGGGCCEEE
T ss_pred             CCCCEEEEECCCCCCHHH-HHHHH---------HCCEEEEEecCCHHH-HHH--------HHHHHHHHHHHHhCCCCcEE
Confidence            469999999998775432 22221         234588888887653 210        12233333221        7


Q ss_pred             EEEccCCCCChhHHHHHHHHHHHhC
Q 023301          100 IILNKIDLVTETELGSLTERIKHIN  124 (284)
Q Consensus       100 ivlnK~D~~~~~~~~~~~~~l~~~n  124 (284)
                      +|+||.+..+. ....+++.+++..
T Consensus       135 vv~N~~~~~~~-~~~~~~~~l~~~~  158 (206)
T 4dzz_A          135 FLITRKIEMAT-MLNVLKESIKDTG  158 (206)
T ss_dssp             EEECSBCTTEE-EEHHHHHHHHHHT
T ss_pred             EEEeccCCCch-HHHHHHHHHHHcC
Confidence            99999986432 2244566666643

>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=82.53  E-value=0.77  Score=38.89  Aligned_cols=97  Identities=19%  Similarity=0.248  Sum_probs=53.5

Q ss_pred             CCCEEEEecCCCCCcH------HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCE
Q 023301           29 QFDHIVIETTGLAKPA------PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADR   99 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~------~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~   99 (284)
                      .....++.++|.....      .+....     +. .-..+.+|.|+|+.+....+          .+..|+   ...-+
T Consensus        48 ~~~l~l~DtpG~~~~~~~~~~e~v~~~~-----~~-~~~~d~vi~V~D~t~~e~~~----------~~~~~l~~~~~p~i  111 (272)
T 3b1v_A           48 NKDLEIQDLPGIYSMSPYSPEAKVARDY-----LL-SQRADSILNVVDATNLERNL----------YLTTQLIETGIPVT  111 (272)
T ss_dssp             CTTEEEEECCCCSCSSCSSHHHHHHHHH-----HH-TTCCSEEEEEEEGGGHHHHH----------HHHHHHHHTCSCEE
T ss_pred             CCeEEEEECCCcCccCCCChHHHHHHHH-----Hh-cCCCCEEEEEecCCchHhHH----------HHHHHHHhcCCCEE
Confidence            3578899999987653      122211     11 01467899999999865321          123343   45668


Q ss_pred             EEEccCCCCChhHH-HHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          100 IILNKIDLVTETEL-GSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       100 ivlnK~D~~~~~~~-~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +++||+|+.....+ ....++.+.++  .+++.++. .......++
T Consensus       112 lv~NK~Dl~~~~~~~~~~~~l~~~lg--~~vi~~SA~~g~gi~el~  155 (272)
T 3b1v_A          112 IALNMIDVLDGQGKKINVDKLSYHLG--VPVVATSALKQTGVDQVV  155 (272)
T ss_dssp             EEEECHHHHHHTTCCCCHHHHHHHHT--SCEEECBTTTTBSHHHHH
T ss_pred             EEEEChhhCCcCCcHHHHHHHHHHcC--CCEEEEEccCCCCHHHHH
Confidence            88999998543211 11222233333  56776654 233455544

>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=82.53  E-value=0.85  Score=35.67  Aligned_cols=96  Identities=14%  Similarity=0.105  Sum_probs=47.8

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh------cCEEEEcc
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY------ADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~------Ad~ivlnK  104 (284)
                      ...|++++|......+....     +   -..+.++.|+|+.+.... ...      ..+..++..      .=+||+||
T Consensus        73 ~~~i~Dt~G~~~~~~~~~~~-----~---~~~d~~i~v~d~~~~~s~-~~~------~~~~~~i~~~~~~~~piilv~nK  137 (191)
T 3dz8_A           73 KLQIWDTAGQERYRTITTAY-----Y---RGAMGFILMYDITNEESF-NAV------QDWATQIKTYSWDNAQVILVGNK  137 (191)
T ss_dssp             EEEEECHHHHHHCHHHHHHH-----H---TTCCEEEEEEETTCHHHH-HTH------HHHHHHHHHHSCTTCEEEEEEEC
T ss_pred             EEEEEeCCChHHHHHHHHHH-----H---ccCCEEEEEEECcCHHHH-HHH------HHHHHHHHHhcCCCCCEEEEEEC
Confidence            45566777743333322221     1   135679999999874332 211      112233322      23677899


Q ss_pred             CCCCChhH--HHHHHHHHHHhCCCCceeeecc-CCCChhhhh
Q 023301          105 IDLVTETE--LGSLTERIKHINAMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       105 ~D~~~~~~--~~~~~~~l~~~np~a~i~~~~~-g~v~~~~l~  143 (284)
                      +|+.+...  .+..+++.+..+  +++++++. .......++
T Consensus       138 ~Dl~~~~~~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~  177 (191)
T 3dz8_A          138 CDMEEERVVPTEKGQLLAEQLG--FDFFEASAKENISVRQAF  177 (191)
T ss_dssp             TTCGGGCCSCHHHHHHHHHHHT--CEEEECBTTTTBSHHHHH
T ss_pred             CCCccccccCHHHHHHHHHHcC--CeEEEEECCCCCCHHHHH
Confidence            99854321  233444444443  46776653 233444443

>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=82.45  E-value=3.9  Score=31.96  Aligned_cols=69  Identities=13%  Similarity=0.236  Sum_probs=37.7

Q ss_pred             CCEEEEecCCCCCcHHHH---HHhcccccccceeeeceEEEEEcccch-HHhhhhcCCccchHHHHHHH-----hhcCEE
Q 023301           30 FDHIVIETTGLAKPAPVI---ETFCTDELVSQYVKLDGVITLVDSKHA-MQHLNEVKPRFVVNEAVEQV-----AYADRI  100 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~---~~l~~~~~l~~~~~l~~vv~vvD~~~~-~~~l~~~~~~~~~~~~~~Qi-----~~Ad~i  100 (284)
                      ....+++++|......+.   ..     .+   -..+.+|.|+|+.+- .+.+..     + .....++     ...=+|
T Consensus        69 ~~l~i~Dt~G~~~~~~~~~~~~~-----~~---~~~~~~i~v~d~~~~~~~~~~~-----~-~~~l~~~~~~~~~~piil  134 (196)
T 3llu_A           69 VNFQIWDFPGQMDFFDPTFDYEM-----IF---RGTGALIYVIDAQDDYMEALTR-----L-HITVSKAYKVNPDMNFEV  134 (196)
T ss_dssp             CCEEEEECCSSCCTTCTTCCHHH-----HH---HTCSEEEEEEETTSCCHHHHHH-----H-HHHHHHHHHHCTTCEEEE
T ss_pred             eEEEEEECCCCHHHHhhhhhccc-----cc---ccCCEEEEEEECCCchHHHHHH-----H-HHHHHHHHhcCCCCcEEE
Confidence            566788888865533221   11     11   136789999999873 111111     1 1112222     233467


Q ss_pred             EEccCCCCChhH
Q 023301          101 ILNKIDLVTETE  112 (284)
Q Consensus       101 vlnK~D~~~~~~  112 (284)
                      |.||+|+.+++.
T Consensus       135 v~nK~Dl~~~~~  146 (196)
T 3llu_A          135 FIHKVDGLSDDH  146 (196)
T ss_dssp             EEECGGGSCHHH
T ss_pred             EEeccccCchhh
Confidence            779999987543

>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=82.22  E-value=5.1  Score=31.83  Aligned_cols=72  Identities=14%  Similarity=0.130  Sum_probs=31.4

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-hhcCEEEEccCCCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-AYADRIILNKIDLVT  109 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-~~Ad~ivlnK~D~~~  109 (284)
                      ...+++++|......+....        .-..+.++.|+|+.+.... .+....++ ..+.... ...=+||+||+|+.+
T Consensus        83 ~l~l~Dt~G~~~~~~~~~~~--------~~~~d~~i~v~d~~~~~s~-~~~~~~~~-~~~~~~~~~~piilv~nK~Dl~~  152 (214)
T 2j1l_A           83 HLHIWDTAGQDDYDRLRPLF--------YPDASVLLLCFDVTSPNSF-DNIFNRWY-PEVNHFCKKVPIIVVGCKTDLRK  152 (214)
T ss_dssp             EEEEEEC-----------------------CEEEEEEEEETTCHHHH-HHHHHTHH-HHHHHHCSSCCEEEEEECGGGGS
T ss_pred             EEEEEECCCchhhhHHHHHH--------hccCCEEEEEEECcCHHHH-HHHHHHHH-HHHHHhCCCCCEEEEEEChhhhc
Confidence            35577888865543322211        1256789999999875432 11100011 1111111 123467889999976


Q ss_pred             hhH
Q 023301          110 ETE  112 (284)
Q Consensus       110 ~~~  112 (284)
                      ...
T Consensus       153 ~~~  155 (214)
T 2j1l_A          153 DKS  155 (214)
T ss_dssp             CHH
T ss_pred             cch
Confidence            543

>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=82.10  E-value=0.74  Score=37.05  Aligned_cols=91  Identities=14%  Similarity=0.109  Sum_probs=46.1

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-hhcCEEEEccCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-AYADRIILNKIDLV  108 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-~~Ad~ivlnK~D~~  108 (284)
                      ....+++++|......+...     .   .-..+.++.|+|+...... .+.. .++ ..+.... ...=+||+||+|+.
T Consensus        64 ~~~~i~Dt~G~~~~~~~~~~-----~---~~~~~~~i~v~d~~~~~s~-~~~~-~~~-~~~~~~~~~~p~ilv~nK~Dl~  132 (221)
T 3gj0_A           64 IKFNVWDTAGQEKFGGLRDG-----Y---YIQAQCAIIMFDVTSRVTY-KNVP-NWH-RDLVRVCENIPIVLCGNKVDIK  132 (221)
T ss_dssp             EEEEEEEECSGGGTSCCCHH-----H---HTTCCEEEEEEETTCHHHH-HTHH-HHH-HHHHHHSTTCCEEEEEECTTSS
T ss_pred             EEEEEEeCCChHHHhHHHHH-----H---HhcCCEEEEEEECCCHHHH-HHHH-HHH-HHHHHhCCCCCEEEEEECCccc
Confidence            34667889985332211111     1   1146789999999885432 2110 111 1112211 22457788999997


Q ss_pred             ChhHHHHHHHHHHHhCCCCceeeec
Q 023301          109 TETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       109 ~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +........++.+..+  .+++.++
T Consensus       133 ~~~~~~~~~~~~~~~~--~~~~~~S  155 (221)
T 3gj0_A          133 DRKVKAKSIVFHRKKN--LQYYDIS  155 (221)
T ss_dssp             SCSSCGGGCCHHHHHT--CEEEECB
T ss_pred             cccccHHHHHHHHHcC--CEEEEEe
Confidence            6433333333444443  5666654

>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=81.63  E-value=3.5  Score=32.15  Aligned_cols=89  Identities=15%  Similarity=0.057  Sum_probs=46.5

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKIDL  107 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D~  107 (284)
                      ...+++++|... ..+....     +   -..+.++.|+|+.+.... .+.. .+. ..+....   ...=+||+||+|+
T Consensus        77 ~~~l~Dt~G~~~-~~~~~~~-----~---~~~d~iilv~D~~~~~s~-~~~~-~~~-~~i~~~~~~~~~piilv~NK~Dl  144 (196)
T 2atv_A           77 SMEILDTAGQED-TIQREGH-----M---RWGEGFVLVYDITDRGSF-EEVL-PLK-NILDEIKKPKNVTLILVGNKADL  144 (196)
T ss_dssp             EEEEEECCCCCC-CHHHHHH-----H---HHCSEEEEEEETTCHHHH-HTHH-HHH-HHHHHHHTTSCCCEEEEEECGGG
T ss_pred             EEEEEECCCCCc-ccchhhh-----h---ccCCEEEEEEECcCHHHH-HHHH-HHH-HHHHHhhCCCCCcEEEEEECccc
Confidence            356789999877 3222221     1   134678999999875432 2110 011 1112211   1123788899998


Q ss_pred             CChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          108 VTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       108 ~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      .+..+  .+..+++.+..+  .++++++
T Consensus       145 ~~~~~v~~~~~~~~~~~~~--~~~~~~S  170 (196)
T 2atv_A          145 DHSRQVSTEEGEKLATELA--CAFYECS  170 (196)
T ss_dssp             GGGCCSCHHHHHHHHHHHT--SEEEECC
T ss_pred             ccccccCHHHHHHHHHHhC--CeEEEEC
Confidence            65322  234445555543  5666665

>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=81.62  E-value=3.8  Score=32.25  Aligned_cols=79  Identities=16%  Similarity=0.251  Sum_probs=39.1

Q ss_pred             CEEEEecCCCCCcH------HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEcc
Q 023301           31 DHIVIETTGLAKPA------PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNK  104 (284)
Q Consensus        31 d~iiIE~sG~a~p~------~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK  104 (284)
                      ...+++++|.....      ....... ...++..-..+.++.|+|+.........    .+ ...........+++.||
T Consensus        73 ~~~l~Dt~G~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~d~~~~~~~~~~----~~-~~~~~~~~~~~~~v~nK  146 (210)
T 1pui_A           73 GKRLVDLPGYGYAEVPEEMKRKWQRAL-GEYLEKRQSLQGLVVLMDIRHPLKDLDQ----QM-IEWAVDSNIAVLVLLTK  146 (210)
T ss_dssp             TEEEEECCCCC------CCHHHHHHHH-HHHHHHCTTEEEEEEEEETTSCCCHHHH----HH-HHHHHHTTCCEEEEEEC
T ss_pred             CEEEEECcCCcccccCHHHHHHHHHHH-HHHHHhhhcccEEEEEEECCCCCchhHH----HH-HHHHHHcCCCeEEEEec
Confidence            46788999986421      1111110 0112222246678899998653211100    01 11123334445677999


Q ss_pred             CCCCChhHHHH
Q 023301          105 IDLVTETELGS  115 (284)
Q Consensus       105 ~D~~~~~~~~~  115 (284)
                      +|+.+..+.++
T Consensus       147 ~D~~s~~~~~~  157 (210)
T 1pui_A          147 ADKLASGARKA  157 (210)
T ss_dssp             GGGSCHHHHHH
T ss_pred             ccCCCchhHHH
Confidence            99988765443

>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=81.23  E-value=2.6  Score=31.68  Aligned_cols=92  Identities=11%  Similarity=0.020  Sum_probs=43.4

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH---hhcCEEEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV---AYADRIILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi---~~Ad~ivlnK~D  106 (284)
                      ....+++++|.......+..    ..+   -..+.++.|+|....... .... .++ ..+....   ...=++|.||+|
T Consensus        51 ~~~~i~D~~g~~~~~~~~~~----~~~---~~~d~~i~v~d~~~~~s~-~~~~-~~~-~~~~~~~~~~~~p~ilv~nK~D  120 (169)
T 3q85_A           51 VTLIVYDIWEQGDAGGWLQD----HCL---QTGDAFLIVFSVTDRRSF-SKVP-ETL-LRLRAGRPHHDLPVILVGNKSD  120 (169)
T ss_dssp             EEEEEECCCCC--------C----HHH---HHCSEEEEEEETTCHHHH-HTHH-HHH-HHHHHHSTTSCCCEEEEEECTT
T ss_pred             EEEEEEECCCccccchhhhh----hhh---ccCCEEEEEEECCChHHH-HHHH-HHH-HHHHhcccCCCCCEEEEeeCcc
Confidence            34567789988765432211    111   125778999999874332 2110 111 1111111   224478889999


Q ss_pred             CCChhH--HHHHHHHHHHhCCCCceeeec
Q 023301          107 LVTETE--LGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       107 ~~~~~~--~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +.+..+  .+...+..+..  .+++++++
T Consensus       121 l~~~~~~~~~~~~~~~~~~--~~~~~~~S  147 (169)
T 3q85_A          121 LARSREVSLEEGRHLAGTL--SCKHIETS  147 (169)
T ss_dssp             CGGGCCSCHHHHHHHHHHT--TCEEEECB
T ss_pred             hhhcccCCHHHHHHHHHHc--CCcEEEec
Confidence            864322  23344444444  35666665

>3vqt_A RF-3, peptide chain release factor 3; translation, GTPase; HET: GDP; 1.80A {Desulfovibrio vulgaris} PDB: 3vr1_A*

Probab=81.12  E-value=2.8  Score=39.30  Aligned_cols=78  Identities=13%  Similarity=0.159  Sum_probs=47.3

Q ss_pred             CCEEEEecCCCCCcH-HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           30 FDHIVIETTGLAKPA-PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~-~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      ..+=||.|+|-.|.. ++...|.         .+|++|.||||..-.+--.    +.+. ....+....-+++|||+|..
T Consensus       100 ~~iNlIDTPGHvDF~~Ev~raL~---------~~DgAvlVvda~~GV~~qT----~~v~-~~a~~~~lp~i~fINK~Dr~  165 (548)
T 3vqt_A          100 RVVNLLDTPGHQDFSEDTYRVLT---------AVDSALVVIDAAKGVEAQT----RKLM-DVCRMRATPVMTFVNKMDRE  165 (548)
T ss_dssp             EEEEEECCCCGGGCSHHHHHHHH---------SCSEEEEEEETTTBSCHHH----HHHH-HHHHHTTCCEEEEEECTTSC
T ss_pred             EEEEEEeCCCcHHHHHHHHHHHH---------hcCceEEEeecCCCccccc----HHHH-HHHHHhCCceEEEEecccch
Confidence            345689999999964 4444432         5788999999987543211    0010 11234455668999999985


Q ss_pred             ChhHHHHHHHHHHH
Q 023301          109 TETELGSLTERIKH  122 (284)
Q Consensus       109 ~~~~~~~~~~~l~~  122 (284)
                      .. +..++.+.++.
T Consensus       166 ~a-d~~~~~~~i~~  178 (548)
T 3vqt_A          166 AL-HPLDVMADIEQ  178 (548)
T ss_dssp             CC-CHHHHHHHHHH
T ss_pred             hc-chhHhhhhhhh
Confidence            43 34444444544

>3cb4_D GTP-binding protein LEPA; GTPase, OB-fold, membrane, nucleotide-binding, translation; 2.80A {Escherichia coli} PDB: 3deg_C*

Probab=80.81  E-value=5.7  Score=37.61  Aligned_cols=100  Identities=18%  Similarity=0.196  Sum_probs=52.3

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVT  109 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~  109 (284)
                      ...-||+|+|-.+.......     .+   -..+.+|.|+|+..-... ..   ...... .......-++++||+|+.+
T Consensus        71 ~~l~liDTPGh~dF~~ev~~-----~l---~~aD~aILVVDa~~gv~~-qt---~~~~~~-~~~~~ipiIvViNKiDl~~  137 (599)
T 3cb4_D           71 YQLNFIDTPGHVDFSYEVSR-----SL---AACEGALLVVDAGQGVEA-QT---LANCYT-AMEMDLEVVPVLNKIDLPA  137 (599)
T ss_dssp             EEEEEEECCCCGGGHHHHHH-----HH---HHCSEEEEEEETTTCCCT-HH---HHHHHH-HHHTTCEEEEEEECTTSTT
T ss_pred             EEEEEEECCCchHHHHHHHH-----HH---HHCCEEEEEEECCCCCCH-HH---HHHHHH-HHHCCCCEEEeeeccCccc
Confidence            34569999999886543322     11   235789999999763211 00   000000 1122334588999999976


Q ss_pred             hhHHHHHHHHHHHhC--CCCceeeecc-CCCChhhhh
Q 023301          110 ETELGSLTERIKHIN--AMAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       110 ~~~~~~~~~~l~~~n--p~a~i~~~~~-g~v~~~~l~  143 (284)
                      .. ..++.+.++...  +..+++.++. .......++
T Consensus       138 a~-~~~v~~ei~~~lg~~~~~vi~vSAktg~GI~~Ll  173 (599)
T 3cb4_D          138 AD-PERVAEEIEDIVGIDATDAVRCSAKTGVGVQDVL  173 (599)
T ss_dssp             CC-HHHHHHHHHHHTCCCCTTCEEECTTTCTTHHHHH
T ss_pred             cc-HHHHHHHHHHHhCCCcceEEEeecccCCCchhHH
Confidence            43 333444444432  1234555543 334444444

>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=80.71  E-value=5  Score=35.86  Aligned_cols=37  Identities=16%  Similarity=0.047  Sum_probs=23.6

Q ss_pred             hhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeec
Q 023301           95 AYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus        95 ~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ...-++|+||+|+...+.+..+.+.....  .++++..+
T Consensus       214 ~kP~i~v~NK~D~~~~~~l~~l~~~~~~~--~~~vv~iS  250 (397)
T 1wxq_A          214 NKPMVIAANKADAASDEQIKRLVREEEKR--GYIVIPTS  250 (397)
T ss_dssp             HSCEEEEEECGGGSCHHHHHHHHHHHHHT--TCEEEEEC
T ss_pred             CCCEEEEEeCccccchHHHHHHHHHHhhc--CCcEEEEe
Confidence            35679999999998655555555544322  35666554

>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=80.66  E-value=8.2  Score=29.77  Aligned_cols=70  Identities=19%  Similarity=0.118  Sum_probs=37.1

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-hhcCEEEEccCCCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-AYADRIILNKIDLVT  109 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-~~Ad~ivlnK~D~~~  109 (284)
                      ...+++++|......+...     .   .-..+.++.|+|+.+.... .+....++ ..+.... ...=+||+||+|+.+
T Consensus        67 ~~~i~D~~G~~~~~~~~~~-----~---~~~~d~~i~v~d~~~~~s~-~~~~~~~~-~~~~~~~~~~piilv~nK~Dl~~  136 (194)
T 2atx_A           67 LLGLYDTAGQEDYDRLRPL-----S---YPMTDVFLICFSVVNPASF-QNVKEEWV-PELKEYAPNVPFLLIGTQIDLRD  136 (194)
T ss_dssp             EEEEECCCCSSSSTTTGGG-----G---CTTCSEEEEEEETTCHHHH-HHHHHTHH-HHHHHHSTTCCEEEEEECTTSTT
T ss_pred             EEEEEECCCCcchhHHHHH-----h---cCCCCEEEEEEECCCHHHH-HHHHHHHH-HHHHHhCCCCCEEEEEEChhhcc
Confidence            3467788887664432211     1   1246789999999875432 11100111 1112111 223478889999976


Q ss_pred             h
Q 023301          110 E  110 (284)
Q Consensus       110 ~  110 (284)
                      .
T Consensus       137 ~  137 (194)
T 2atx_A          137 D  137 (194)
T ss_dssp             C
T ss_pred             c
Confidence            4

>3r7w_A Gtpase1, GTP-binding protein GTR1; RAG gtpases, GTR1P, GTR2P, MTOR, protein transport; HET: GNP; 2.77A {Saccharomyces cerevisiae} PDB: 4arz_A*

Probab=80.65  E-value=3  Score=35.73  Aligned_cols=97  Identities=14%  Similarity=0.114  Sum_probs=49.2

Q ss_pred             CCEEEEecCCCCCcHHHH-HHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-----hhcCEEEEc
Q 023301           30 FDHIVIETTGLAKPAPVI-ETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-----AYADRIILN  103 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~-~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-----~~Ad~ivln  103 (284)
                      ....+++++|.....+-. ..+. ...+   -..+.+|.|+|+.+.... .+.. .+  .....++     ...=+||+|
T Consensus        52 ~~l~i~Dt~G~~~~~~~~~~~~~-~~~~---~~ad~vi~V~D~t~~~s~-~~l~-~~--~~~l~~l~~~~~~~piilv~N  123 (307)
T 3r7w_A           52 MTLNLWDCGGQDVFMENYFTKQK-DHIF---QMVQVLIHVFDVESTEVL-KDIE-IF--AKALKQLRKYSPDAKIFVLLH  123 (307)
T ss_dssp             EEEEEEEECCSHHHHHHHHTTTH-HHHH---TTCSEEEEEEETTCSCHH-HHHH-HH--HHHHHHHHHHCTTCEEEEEEE
T ss_pred             eEEEEEECCCcHHHhhhhhhhHH-HHHh---ccCCEEEEEEECCChhhH-HHHH-HH--HHHHHHHHHhCCCCeEEEEEe
Confidence            356678889965431100 1110 0111   146789999999875321 1100 00  0112222     234567779


Q ss_pred             cCCCCChhHHH--------HHHHHHHHhC-CCCceeeecc
Q 023301          104 KIDLVTETELG--------SLTERIKHIN-AMAPVKLAKY  134 (284)
Q Consensus       104 K~D~~~~~~~~--------~~~~~l~~~n-p~a~i~~~~~  134 (284)
                      |+|+.++++..        .+.++.+.++ |..+++.++.
T Consensus       124 K~Dl~~~~~r~~~~~v~~~~~~~~~~~~g~~~~~~~~tSa  163 (307)
T 3r7w_A          124 KMDLVQLDKREELFQIMMKNLSETSSEFGFPNLIGFPTSI  163 (307)
T ss_dssp             CGGGSCHHHHHHHHHHHHHHHHHHHHTTTCCSCEEEECCT
T ss_pred             cccccchhhhhHHHHHHHHHHHHHHHHcCCCCeEEEEeee
Confidence            99998854443        3344444443 2477887764

>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=80.46  E-value=3.5  Score=31.96  Aligned_cols=89  Identities=8%  Similarity=0.075  Sum_probs=44.4

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHH-----hhcCEEEEccCC
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-----AYADRIILNKID  106 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-----~~Ad~ivlnK~D  106 (284)
                      ..|++++|......+.. .     +   -..+.++.|+|..+.... .+.. .++ ..+....     ...=+||.||+|
T Consensus        71 l~i~Dt~G~~~~~~~~~-~-----~---~~~~~~ilv~d~~~~~s~-~~~~-~~~-~~i~~~~~~~~~~~piilv~nK~D  138 (187)
T 3c5c_A           71 LRVMDTADLDTPRNCER-Y-----L---NWAHAFLVVYSVDSRQSF-DSSS-SYL-ELLALHAKETQRSIPALLLGNKLD  138 (187)
T ss_dssp             EEEEECCC---CCCTHH-H-----H---TTCSEEEEEEETTCHHHH-HHHH-HHH-HHHHHHHHHHCCCCCEEEEEECGG
T ss_pred             EEEEECCCCCcchhHHH-H-----H---hhCCEEEEEEECCCHHHH-HHHH-HHH-HHHHHHhhccCCCCCEEEEEECcc
Confidence            44678888765443211 1     1   135678999999864332 2110 111 1222221     223477889999


Q ss_pred             CCChhH--HHHHHHHHHHhCCCCceeeecc
Q 023301          107 LVTETE--LGSLTERIKHINAMAPVKLAKY  134 (284)
Q Consensus       107 ~~~~~~--~~~~~~~l~~~np~a~i~~~~~  134 (284)
                      +.+..+  .+...++.+.++  +++++++.
T Consensus       139 l~~~~~v~~~~~~~~~~~~~--~~~~e~Sa  166 (187)
T 3c5c_A          139 MAQYRQVTKAEGVALAGRFG--CLFFEVSA  166 (187)
T ss_dssp             GGGGCSSCHHHHHHHHHHHT--CEEEECCS
T ss_pred             hhhcCccCHHHHHHHHHHcC--CcEEEEee
Confidence            854322  244555556554  46766653

---

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	284
d1nija2	95	d.237.1.1 (A:224-318) Hypothetical protein YjiA, C	7e-28
d1nija1	222	c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-t	5e-22
d1yrba1	244	c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB09	0.001

>d1nija2 d.237.1.1 (A:224-318) Hypothetical protein YjiA, C-terminal domain {Escherichia coli [TaxId: 562]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Hypothetical protein YjiA, C-terminal domain
superfamily: Hypothetical protein YjiA, C-terminal domain
family: Hypothetical protein YjiA, C-terminal domain
domain: Hypothetical protein YjiA, C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score =  101 bits (252), Expect = 7e-28
 Identities = 31/94 (32%), Positives = 48/94 (51%), Gaps = 1/94 (1%)

Query: 189 VSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQGVHSTLDGC 248
           +SS+ +  +  +D+ EV   +E L+ E  + L R KG+L + G   + +FQGV       
Sbjct: 1   ISSIVVELDYPVDISEVSRVMENLLLESADKLLRYKGMLWIDGEPNRLLFQGVQRLYSAD 60

Query: 249 PGKAWGPDEKRINKLVFIGRNLDETALRKGFKGC 282
             + W  DEK  + +VFIG  L E  +R  F G 
Sbjct: 61  WDRPW-GDEKPHSTMVFIGIQLPEEEIRAAFAGL 93

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 222

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]

 Score = 89.6 bits (221), Expect = 5e-22
 Identities = 63/172 (36%), Positives = 86/172 (50%), Gaps = 11/172 (6%)

Query: 2   VNNGCLCCTVRGDLVKMLLQLAKK---KQGQFDHIVIETTGLAKPAPVIETFCTDELVSQ 58
           + NGC+CC+   +L   LL L         QFD +VIE TG+A P P+I+TF + E++ Q
Sbjct: 59  LTNGCICCSRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQ 118

Query: 59  YVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTE 118
              LDGVI LVD+ HA +             A  QV YADRI+L K D+  E E   L E
Sbjct: 119 RYLLDGVIALVDAVHADEQ------MNQFTIAQSQVGYADRILLTKTDVAGEAE--KLHE 170

Query: 119 RIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLERIDSEVHVDNSHCATHHHE 170
           R+  INA APV    +G +D+  +    G+ LE             A   ++
Sbjct: 171 RLARINARAPVYTVTHGDIDLGLLFNTNGFMLEENVVSTKPRFHFIADKQND 222

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]} Length = 244

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]

 Score = 37.3 bits (85), Expect = 0.001
 Identities = 18/128 (14%), Positives = 44/128 (34%), Gaps = 3/128 (2%)

Query: 1   MVNNGCLCCTVRGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYV 60
                        +     L    + + + D+++I+T G  +     E       + + +
Sbjct: 66  PNGAIVESYDRLMEKFNEYLNKILRLEKENDYVLIDTPGQMETFLFHEFGVR---LMENL 122

Query: 61  KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERI 120
               V+ + D +   +  +    RF       ++       LNK+DL++E E     +  
Sbjct: 123 PYPLVVYISDPEILKKPNDYCFVRFFALLIDLRLGATTIPALNKVDLLSEEEKERHRKYF 182

Query: 121 KHINAMAP 128
           + I+ +  
Sbjct: 183 EDIDYLTA 190

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	284
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	99.97
d1nija2	95	Hypothetical protein YjiA, C-terminal domain {Esch	99.88
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	98.55
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	97.67
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.64
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	96.2
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	95.15
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	94.49
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	94.33
d1j8yf2	211	GTPase domain of the signal sequence recognition p	93.7
d2qy9a2	211	GTPase domain of the signal recognition particle r	91.58
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	91.29
d2qn6a3	205	Initiation factor eIF2 gamma subunit, N-terminal (	90.89
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	90.71
d1f60a3	239	Elongation factor eEF-1alpha, N-terminal (G) domai	90.65
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	90.23
d1d2ea3	196	Elongation factor Tu (EF-Tu), N-terminal (G) domai	89.97
d1vmaa2	213	GTPase domain of the signal recognition particle r	89.86
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	89.86
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	89.83
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	89.81
d1ls1a2	207	GTPase domain of the signal sequence recognition p	89.43
d1kk1a3	195	Initiation factor eIF2 gamma subunit, N-terminal (	88.39
d2fh5b1	207	Signal recognition particle receptor beta-subunit	88.17
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	87.46
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	87.04
d1okkd2	207	GTPase domain of the signal recognition particle r	86.44
d1jnya3	224	Elongation factor eEF-1alpha, N-terminal (G) domai	84.57
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	83.95
d1zunb3	222	Sulfate adenylate transferase subunit cysN/C, EF-T	83.55
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	81.24
d1r5ba3	245	Eukaryotic peptide chain release factor ERF2, G do	80.3

>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=99.97  E-value=2.5e-31  Score=222.97  Aligned_cols=144  Identities=43%  Similarity=0.730  Sum_probs=127.2

Q ss_pred             CCCCceeeeeeCchHHHHHHHHHHh---hcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHh
Q 023301            1 MVNNGCLCCTVRGDLVKMLLQLAKK---KQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQH   77 (284)
Q Consensus         1 eL~~GCiCCs~~~dl~~~l~~l~~~---~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~   77 (284)
                      |++|||+||+.++++..++..++.+   ...+||+||||+||+++|.+++..+..++.+...+.++++|+|||+.++..+
T Consensus        58 el~~gcicc~~~~~~~~~l~~~~~~~~~~~~~~d~iiIE~sG~~~p~~l~~~~~~~~~~~~~~~l~~vi~vVDa~~~~~~  137 (222)
T d1nija1          58 TLTNGCICCSRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQRYLLDGVIALVDAVHADEQ  137 (222)
T ss_dssp             EETTSCEEECTTSCHHHHHHHHHHHHHHTSCCCSEEEEEEETTCCHHHHHHHHHHSHHHHHHEEEEEEEEEEETTTHHHH
T ss_pred             EecCCcceeccchhHHHHHHHHHHHHhhccCCcceeEEeecccchhhHHHHHHHhhhcccccccccchhhhhhhhhhhhh
Confidence            4799999999999999998877653   2357999999999999999999998777667778999999999999999988


Q ss_pred             hhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCCChhhhhcCCCCCccc
Q 023301           78 LNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFVLGVGGYDLER  152 (284)
Q Consensus        78 l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v~~~~l~~~~~~~~~~  152 (284)
                      +...      ..+.+||++||+||+||+|++++  .+++++.++++||.|+|+.+++|+++++.|++++.|+.++
T Consensus       138 ~~~~------~~~~~Qi~~AD~ivlNK~Dl~~~--~~~~~~~l~~lNP~a~Ii~~~~g~v~~~~ll~~~~~d~e~  204 (222)
T d1nija1         138 MNQF------TIAQSQVGYADRILLTKTDVAGE--AEKLHERLARINARAPVYTVTHGDIDLGLLFNTNGFMLEE  204 (222)
T ss_dssp             HHHC------HHHHHHHHTCSEEEEECTTTCSC--THHHHHHHHHHCSSSCEEECCSSCCCGGGGSCCCTTSCCS
T ss_pred             hhhh------HHHHHHHHhCCcccccccccccH--HHHHHHHHHHHhCCCeEEEeeCCccCHHHhhCCCCCCccc
Confidence            7653      46789999999999999999874  4689999999999999999999999999999998887643

>d1nija2 d.237.1.1 (A:224-318) Hypothetical protein YjiA, C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Hypothetical protein YjiA, C-terminal domain
superfamily: Hypothetical protein YjiA, C-terminal domain
family: Hypothetical protein YjiA, C-terminal domain
domain: Hypothetical protein YjiA, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.88  E-value=8.1e-23  Score=147.67  Aligned_cols=94  Identities=34%  Similarity=0.596  Sum_probs=86.7

Q ss_pred             eEEEEEEeCCCCCHHHHHHHHHHHHHHhCCceEEEEEEEEecCCCeeEEEEccceeeecCCCCCCCCCCCCccEEEEEec
Q 023301          189 VSSVTIVSEGTLDLDEVDDWLERLIEEKGEDLYRMKGILSVSGSEQQYVFQGVHSTLDGCPGKAWGPDEKRINKLVFIGR  268 (284)
Q Consensus       189 ~~s~~~~~~~~~~~~~l~~~l~~l~~~~~~~i~R~KG~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lv~IG~  268 (284)
                      ++|++++.++|||+++|..||+.+++.++.+|||+||++|+++.+.++.+|+++..++..+...|+ .+++.++|||||+
T Consensus         1 IsS~~~~~~~P~d~~~f~~~l~~ll~~~~~~ilR~KG~v~~~~~~~~~~~q~v~~~~~~~~~~~w~-~~~r~~~lVfIG~   79 (95)
T d1nija2           1 ISSIVVELDYPVDISEVSRVMENLLLESADKLLRYKGMLWIDGEPNRLLFQGVQRLYSADWDRPWG-DEKPHSTMVFIGI   79 (95)
T ss_dssp             EEEEEEEESSCBCHHHHHHHHHHHHHHTTTTEEEEEEEECBTTCSEEEEEEEETTEEEEEEEEECT-TSCCCEEEEEEEE
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHhcCCCEEEEEEEEEeccCCcceEEEEeeeEeccCcCCCCC-CCCCCCEEEEEeC
Confidence            579999999999999999999999988899999999999999999999999999988876666786 4667899999999


Q ss_pred             CCCHHHHHHHHhhhh
Q 023301          269 NLDETALRKGFKGCL  283 (284)
Q Consensus       269 ~ld~~~l~~~l~~c~  283 (284)
                      +||+++|++.|++|.
T Consensus        80 ~Ld~~~l~~~l~~c~   94 (95)
T d1nija2          80 QLPEEEIRAAFAGLR   94 (95)
T ss_dssp             SCCHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHHhc
Confidence            999999999999995

>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=98.55  E-value=3.7e-09  Score=87.06  Aligned_cols=120  Identities=16%  Similarity=0.072  Sum_probs=75.8

Q ss_pred             CCceeeeee-CchHHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhc
Q 023301            3 NNGCLCCTV-RGDLVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEV   81 (284)
Q Consensus         3 ~~GCiCCs~-~~dl~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~   81 (284)
                      ++||+||.. ..+....+.+.+......+++++++++|..++.......   +.+.+....+.+++|+|+..........
T Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~g~~~~~~~~~~~---~~~~~~~~~~~~v~vvd~~~~~~~~~~~  143 (244)
T d1yrba1          67 NGAIVESYDRLMEKFNEYLNKILRLEKENDYVLIDTPGQMETFLFHEFG---VRLMENLPYPLVVYISDPEILKKPNDYC  143 (244)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHHHHHCSEEEEECCSSHHHHHHSHHH---HHHHHTSSSCEEEEEECGGGCCSHHHHH
T ss_pred             CCchhhhhHhHHhhHHHHHHHHHhhccccceeeeccccchhHHHHHHHH---HHHHhhccCceEEEEeccccccCchhHh
Confidence            467777752 233333333333222347899999999999886544432   2344556677899999997644321110


Q ss_pred             CCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCC
Q 023301           82 KPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINA  125 (284)
Q Consensus        82 ~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np  125 (284)
                      ...........|+..++++++||+|+.+.++...++.....+++
T Consensus       144 ~~~l~~~~~~~~~~~~~ivvinK~D~~~~~~~~~~~~~~~~~~~  187 (244)
T d1yrba1         144 FVRFFALLIDLRLGATTIPALNKVDLLSEEEKERHRKYFEDIDY  187 (244)
T ss_dssp             HHHHHHHHHHHHHTSCEEEEECCGGGCCHHHHHHHHHHHHCHHH
T ss_pred             hHHHHHHHHHHHhCCCceeeeeccccccHHHHHHHHHHHHHHHH
Confidence            00011223467999999999999999999888877766665543

>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=97.67  E-value=0.00018  Score=61.22  Aligned_cols=81  Identities=20%  Similarity=0.206  Sum_probs=50.7

Q ss_pred             chHHHHHHHHHHh-hcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHH
Q 023301           13 GDLVKMLLQLAKK-KQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAV   91 (284)
Q Consensus        13 ~dl~~~l~~l~~~-~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~   91 (284)
                      +.+...+.+.+.. +...+|+|||||.|++.-..-+..+           .+.+++|+.+..-.+ +.        ..-.
T Consensus       126 gg~~~~~~~~i~~~~~~g~d~iiiETVG~gq~e~~~~~~-----------~D~~v~v~~p~~GD~-iQ--------~~k~  185 (323)
T d2qm8a1         126 GGVAAKTRETMLLCEAAGFDVILVETVGVGQSETAVADL-----------TDFFLVLMLPGAGDE-LQ--------GIKK  185 (323)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEEEEECSSSSCHHHHHTT-----------SSEEEEEECSCC---------------CCT
T ss_pred             cchhHHHHHHHHhhccCCCCeEEEeehhhhhhhhhhhcc-----------cceEEEEeeccchhh-hh--------hhhh
Confidence            3344444443321 1468999999999999866433322           334677777766321 11        1225


Q ss_pred             HHHhhcCEEEEccCCCCChhHH
Q 023301           92 EQVAYADRIILNKIDLVTETEL  113 (284)
Q Consensus        92 ~Qi~~Ad~ivlnK~D~~~~~~~  113 (284)
                      .+++.||++|+||+|+.+.++.
T Consensus       186 gilE~aDi~vvNKaD~~~~~~~  207 (323)
T d2qm8a1         186 GIFELADMIAVNKADDGDGERR  207 (323)
T ss_dssp             THHHHCSEEEEECCSTTCCHHH
T ss_pred             hHhhhhheeeEeccccccchHH
Confidence            7899999999999998765543

>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=96.64  E-value=0.0052  Score=51.97  Aligned_cols=68  Identities=22%  Similarity=0.312  Sum_probs=43.2

Q ss_pred             cCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCC
Q 023301           27 QGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKID  106 (284)
Q Consensus        27 ~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D  106 (284)
                      ...+|+|+|||.|++.-..-+..           ..+.++.|++|.... .+...        -..-++.||++|+||+|
T Consensus       144 ~~g~d~iliEtvG~gq~e~~i~~-----------~aD~~l~v~~P~~Gd-~iq~~--------k~gi~e~aDi~VvNKaD  203 (327)
T d2p67a1         144 AAGYDVVIVETVGVGQSETEVAR-----------MVDCFISLQIAGGGD-DLQGI--------KKGLMEVADLIVINKDD  203 (327)
T ss_dssp             HTTCSEEEEEEECCTTHHHHHHT-----------TCSEEEEEECC-------CCC--------CHHHHHHCSEEEECCCC
T ss_pred             hcCCCeEEEeeccccccchhhhh-----------ccceEEEEecCCCch-hhhhh--------chhhhccccEEEEEeec
Confidence            57899999999999985432211           234567788775532 22211        13557789999999999


Q ss_pred             CCChhHHH
Q 023301          107 LVTETELG  114 (284)
Q Consensus       107 ~~~~~~~~  114 (284)
                      ....+...
T Consensus       204 ~~~~~~~~  211 (327)
T d2p67a1         204 GDNHTNVA  211 (327)
T ss_dssp             TTCHHHHH
T ss_pred             ccchHHHH
Confidence            97755543

>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=96.20  E-value=0.0042  Score=47.29  Aligned_cols=94  Identities=16%  Similarity=0.232  Sum_probs=54.6

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhh-----cCEEEEcc
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAY-----ADRIILNK  104 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~-----Ad~ivlnK  104 (284)
                      ....++.++|....................-..+.++.|+|+........        ..+.+.+..     .-++|+||
T Consensus        53 ~~~~~~DtpG~~~~~~~~~~~~~~~~~~~~~~ad~il~v~D~~~~~~~~~--------~~i~~~l~~~~~~~piilv~NK  124 (178)
T d1wf3a1          53 RQIVFVDTPGLHKPMDALGEFMDQEVYEALADVNAVVWVVDLRHPPTPED--------ELVARALKPLVGKVPILLVGNK  124 (178)
T ss_dssp             EEEEEEECCCCCCCCSHHHHHHHHHHHHHTSSCSEEEEEEETTSCCCHHH--------HHHHHHHGGGTTTSCEEEEEEC
T ss_pred             eeeeecccccccccccccchhcccccccccccccceeeeechhhhhcccc--------cchhhheeccccchhhhhhhcc
Confidence            45788999999876544433211111111224678999999976332111        112233321     23778899


Q ss_pred             CCCCChhHHHHHHHHHHHhCCCCceeeec
Q 023301          105 IDLVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       105 ~D~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      +|+.+..  +...+.+++..+...++.+|
T Consensus       125 ~Dl~~~~--~~~~~~~~~~~~~~~~~~iS  151 (178)
T d1wf3a1         125 LDAAKYP--EEAMKAYHELLPEAEPRMLS  151 (178)
T ss_dssp             GGGCSSH--HHHHHHHHHTSTTSEEEECC
T ss_pred             cccccCH--HHHHHHHHhhcccCceEEEe
Confidence            9997643  34456677777777777654

>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=95.15  E-value=0.01  Score=45.01  Aligned_cols=101  Identities=14%  Similarity=0.178  Sum_probs=55.1

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH-HhhhhcCCccchHHHHHHHhhcCEEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM-QHLNEVKPRFVVNEAVEQVAYADRIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~-~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~  107 (284)
                      .....++.+.|+.....-...+. ...+......+.++.++|..... ..+.... ..+......+....-++|+||+|+
T Consensus        48 ~~~~~~~DtpG~~~~~~~~~~~~-~~~l~~~~~~~~~~~~~d~~~~~~~~~~~~~-~~~~~~~~~~~~~p~iiv~NK~D~  125 (180)
T d1udxa2          48 EERFTLADIPGIIEGASEGKGLG-LEFLRHIARTRVLLYVLDAADEPLKTLETLR-KEVGAYDPALLRRPSLVALNKVDL  125 (180)
T ss_dssp             SCEEEEEECCCCCCCGGGSCCSC-HHHHHHHTSSSEEEEEEETTSCHHHHHHHHH-HHHHHHCHHHHHSCEEEEEECCTT
T ss_pred             CCeEEEcCCCeeecCchHHHHHH-HHHHHHHHhhhhhhhhcccccccccchhhhh-hhhhccccccchhhhhhhhhhhhh
Confidence            34577899999876543211111 01222334556678888875432 2211100 000000012233456789999999


Q ss_pred             CChhHHHHHHHHHHHhCCCCceeeec
Q 023301          108 VTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       108 ~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      .+.++.+.+.+.++.  ...+++.+|
T Consensus       126 ~~~~~~~~~~~~~~~--~~~~~~~iS  149 (180)
T d1udxa2         126 LEEEAVKALADALAR--EGLAVLPVS  149 (180)
T ss_dssp             SCHHHHHHHHHHHHT--TTSCEEECC
T ss_pred             hhHHHHHHHHHHHHh--cCCeEEEEE
Confidence            999888887777764  345676654

>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=94.49  E-value=0.02  Score=44.70  Aligned_cols=81  Identities=17%  Similarity=0.208  Sum_probs=46.9

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEE-EEccCCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRI-ILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~i-vlnK~D~  107 (284)
                      +..+.||+|+|-.+...-  ++      +..-..+.+|.||||..-...  +.  +.. -.+...+....+| ++||+|+
T Consensus        66 ~~~i~iiDtPGh~df~~~--~~------~~~~~aD~avlVvda~~Gv~~--qt--~~~-~~~~~~~gi~~iiv~iNK~D~  132 (204)
T d2c78a3          66 KRHYSHVDCPGHADYIKN--MI------TGAAQMDGAILVVSAADGPMP--QT--REH-ILLARQVGVPYIVVFMNKVDM  132 (204)
T ss_dssp             SCEEEEEECCCSGGGHHH--HH------HHHTTCSSEEEEEETTTCCCH--HH--HHH-HHHHHHTTCCCEEEEEECGGG
T ss_pred             CeEEEEEeCCCchhhHHH--HH------HHHHHCCEEEEEEECCCCCcH--HH--HHH-HHHHHHcCCCeEEEEEEeccc
Confidence            567899999998875532  21      122346789999999764321  00  000 0112334445665 5899999


Q ss_pred             CChh-HHHHHHHHHHH
Q 023301          108 VTET-ELGSLTERIKH  122 (284)
Q Consensus       108 ~~~~-~~~~~~~~l~~  122 (284)
                      ++.+ .++.+.+.++.
T Consensus       133 ~~~~~~~~~~~~~i~~  148 (204)
T d2c78a3         133 VDDPELLDLVEMEVRD  148 (204)
T ss_dssp             CCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            8643 34555555554

>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=94.33  E-value=0.038  Score=42.17  Aligned_cols=70  Identities=16%  Similarity=0.189  Sum_probs=42.3

Q ss_pred             eeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHh---CCCCceeeec
Q 023301           59 YVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHI---NAMAPVKLAK  133 (284)
Q Consensus        59 ~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~---np~a~i~~~~  133 (284)
                      ...++.++.|+|+.........    .+. ....+....-+||+||+|+.++.+++...+.+++.   ++..+++.++
T Consensus       103 ~~~~~~vi~viD~~~~~~~~~~----~~~-~~l~~~~~piivv~NK~D~~~~~~~~~~~~~~~~~l~~~~~~~~~~~S  175 (195)
T d1svia_         103 REELKAVVQIVDLRHAPSNDDV----QMY-EFLKYYGIPVIVIATKADKIPKGKWDKHAKVVRQTLNIDPEDELILFS  175 (195)
T ss_dssp             CTTEEEEEEEEETTSCCCHHHH----HHH-HHHHHTTCCEEEEEECGGGSCGGGHHHHHHHHHHHHTCCTTSEEEECC
T ss_pred             ccchhhhhhhhhcccccccccc----ccc-cccccccCcceechhhccccCHHHHHHHHHHHHHHhcccCCCCEEEEe
Confidence            3456789999999753221100    011 11233344456888999999888777766666543   4666776654

>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=93.70  E-value=0.22  Score=38.76  Aligned_cols=109  Identities=18%  Similarity=0.246  Sum_probs=61.6

Q ss_pred             chHHHHHHHHHHh-hcCCCCEEEEecCCCCCcH---HHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchH
Q 023301           13 GDLVKMLLQLAKK-KQGQFDHIVIETTGLAKPA---PVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVN   88 (284)
Q Consensus        13 ~dl~~~l~~l~~~-~~~~~d~iiIE~sG~a~p~---~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~   88 (284)
                      .++...+.+-+.. +....|+|+|.|.|...-.   ..++.+.   .+...+.-..++.|+|+..-.+.+...       
T Consensus        77 ~~~~~~~~~a~~~~~~~~~d~IlIDTaGr~~~~~~~~~~~el~---~~~~~~~~~~~~LVl~a~~~~~~~~~~-------  146 (211)
T d1j8yf2          77 KDVVGIAKRGVEKFLSEKMEIIIVDTAGRHGYGEEAALLEEMK---NIYEAIKPDEVTLVIDASIGQKAYDLA-------  146 (211)
T ss_dssp             CCHHHHHHHHHHHHHHTTCSEEEEECCCSCCTTCHHHHHHHHH---HHHHHHCCSEEEEEEEGGGGGGHHHHH-------
T ss_pred             hhhhHHHHHHHHHhhccCCceEEEecCCcCccchhhHHHHHHH---HHHhhcCCceEEEEEecccCcchHHHH-------
Confidence            3555544432211 1367899999999985422   1122221   122333445689999998755443221       


Q ss_pred             HHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccC
Q 023301           89 EAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYG  135 (284)
Q Consensus        89 ~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g  135 (284)
                      ....+....+-+|+||.|...  ..-.+...+.+.  ..+|...+.|
T Consensus       147 ~~~~~~~~~~~lI~TKlDet~--~~G~~l~~~~~~--~lPi~~it~G  189 (211)
T d1j8yf2         147 SKFNQASKIGTIIITKMDGTA--KGGGALSAVAAT--GATIKFIGTG  189 (211)
T ss_dssp             HHHHHHCTTEEEEEECTTSCS--CHHHHHHHHHTT--TCCEEEEECS
T ss_pred             hhhhcccCcceEEEecccCCC--cccHHHHHHHHH--CcCEEEEeCC
Confidence            112333445679999999865  345555555443  4677666666

>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=91.58  E-value=0.59  Score=36.19  Aligned_cols=112  Identities=14%  Similarity=0.206  Sum_probs=64.4

Q ss_pred             chHHHHHHHHHHh-hcCCCCEEEEecCCCCCcH-HHHHHhcccccccc---eeeeceEEEEEcccchHHhhhhcCCccch
Q 023301           13 GDLVKMLLQLAKK-KQGQFDHIVIETTGLAKPA-PVIETFCTDELVSQ---YVKLDGVITLVDSKHAMQHLNEVKPRFVV   87 (284)
Q Consensus        13 ~dl~~~l~~l~~~-~~~~~d~iiIE~sG~a~p~-~i~~~l~~~~~l~~---~~~l~~vv~vvD~~~~~~~l~~~~~~~~~   87 (284)
                      .++...+.+.... +....|+|||.|.|...-. ..++.|..-.....   ...-..++.|+|+..-...+...      
T Consensus        74 ~d~~~~l~~~~~~a~~~~~d~ilIDTaGr~~~d~~~~~el~~l~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~------  147 (211)
T d2qy9a2          74 ADSASVIFDAIQAAKARNIDVLIADTAGRLQNKSHLMEELKKIVRVMKKLDVEAPHEVMLTIDASTGQNAVSQA------  147 (211)
T ss_dssp             CCHHHHHHHHHHHHHHTTCSEEEECCCCCGGGHHHHHHHHHHHHHHHTTTCTTCCSEEEEEEEGGGTHHHHHHH------
T ss_pred             CCHHHHHHHHHHHHHHcCCCEEEeccCCCccccHHHHHHHHHHHHHHhhhcccCcceeeeehhcccCcchHHHH------
Confidence            4666666666542 1357899999999976533 33333321000000   01124578999998865544321      


Q ss_pred             HHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccC
Q 023301           88 NEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYG  135 (284)
Q Consensus        88 ~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g  135 (284)
                       ...-+-...+-++++|.|...  ..-.+...+.+.  ..||...+.|
T Consensus       148 -~~~~~~~~~~~lIlTKlDe~~--~~G~~l~~~~~~--~~Pi~~i~~G  190 (211)
T d2qy9a2         148 -KLFHEAVGLTGITLTKLDGTA--KGGVIFSVADQF--GIPIRYIGVG  190 (211)
T ss_dssp             -HHHHHHSCCCEEEEECCTTCT--TTTHHHHHHHHH--CCCEEEEECS
T ss_pred             -hhhhhccCCceEEEeecCCCC--CccHHHHHHHHH--CCCEEEEeCC
Confidence             112344568899999999854  234444444444  3677766666

>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=91.29  E-value=0.1  Score=41.25  Aligned_cols=79  Identities=19%  Similarity=0.291  Sum_probs=48.9

Q ss_pred             eeeeceEEEEEcccch--HHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeecc-C
Q 023301           59 YVKLDGVITLVDSKHA--MQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKY-G  135 (284)
Q Consensus        59 ~~~l~~vv~vvD~~~~--~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~-g  135 (284)
                      ...+|.++.|+.+...  ...+   -+|++  .+...-...=+||+||+|++++++.+.+.+.........+++.++. .
T Consensus         8 vANiD~vliV~s~~~P~~~~~~---ldR~L--v~a~~~~i~pvIvlnK~DL~~~~~~~~~~~~~~~~~~~~~v~~vSa~~   82 (225)
T d1u0la2           8 VANVDQVILVVTVKMPETSTYI---IDKFL--VLAEKNELETVMVINKMDLYDEDDLRKVRELEEIYSGLYPIVKTSAKT   82 (225)
T ss_dssp             EESCCEEEEEECSSTTCCCHHH---HHHHH--HHHHHTTCEEEEEECCGGGCCHHHHHHHHHHHHHHTTTSCEEECCTTT
T ss_pred             cccCCEEEEEEeCCCCCCCHHH---HHHHH--HHHHHcCCCEEEEEeCcccCCHHHHHHHHHhhcccccceeEEEecccc
Confidence            3578888888876542  1111   01222  1123344456788899999999888888887777766677776653 3


Q ss_pred             CCChhhh
Q 023301          136 SVDMDFV  142 (284)
Q Consensus       136 ~v~~~~l  142 (284)
                      ....+.|
T Consensus        83 ~~g~~~L   89 (225)
T d1u0la2          83 GMGIEEL   89 (225)
T ss_dssp             CTTHHHH
T ss_pred             chhHhhH
Confidence            3444444

>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=90.89  E-value=0.28  Score=37.58  Aligned_cols=98  Identities=21%  Similarity=0.256  Sum_probs=50.7

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH-H-hhhhcCCccchHHHHHHHhhcC-EEEEccCCCC
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM-Q-HLNEVKPRFVVNEAVEQVAYAD-RIILNKIDLV  108 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~-~-~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~~  108 (284)
                      +-+|.++|=.+...  .++.      .....+.+|.|||+..-. . +..+     . -.+...+...- +|++||+|++
T Consensus        88 ~~iiD~PGH~df~~--~~~~------~~~~ad~ailvVda~~gi~~~~t~e-----~-~~~~~~~~i~~iIV~vNK~Dl~  153 (205)
T d2qn6a3          88 ISFIDAPGHEVLMA--TMLS------GAALMDGAILVVAANEPFPQPQTRE-----H-FVALGIIGVKNLIIVQNKVDVV  153 (205)
T ss_dssp             EEEEECSCHHHHHH--HHHH------TSSCCSEEEEEEETTSCSSCHHHHH-----H-HHHHHHTTCCCEEEEEECGGGS
T ss_pred             EEEeccchHHHHHh--hhhc------ceeccccccccccccccccchhHHH-----H-HHHHHHcCCceeeeccccCCCc
Confidence            56888888776432  1111      122357789999997732 1 1110     0 01122233334 4558999999


Q ss_pred             ChhHHHHHHHHHH----HhCC-CCceeeecc-CCCChhhhh
Q 023301          109 TETELGSLTERIK----HINA-MAPVKLAKY-GSVDMDFVL  143 (284)
Q Consensus       109 ~~~~~~~~~~~l~----~~np-~a~i~~~~~-g~v~~~~l~  143 (284)
                      +..+.......++    ..++ .++++..|. ...+...|+
T Consensus       154 ~~~~~~~~~~~~~~~l~~~~~~~~p~ipiSA~~g~nI~~L~  194 (205)
T d2qn6a3         154 SKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLI  194 (205)
T ss_dssp             CHHHHHHHHHHHHHHHTTSTTTTCCEEECBTTTTBSHHHHH
T ss_pred             cchHHHHHHHHHHHHhccccCCCCeEEEEeCCCCCChHHHH
Confidence            8766554433333    3333 466665543 233444443

>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=90.71  E-value=0.22  Score=37.23  Aligned_cols=68  Identities=15%  Similarity=0.130  Sum_probs=40.2

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHh-----C-CCCceeeec
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHI-----N-AMAPVKLAK  133 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~-----n-p~a~i~~~~  133 (284)
                      ..+.++.|+|+..-...  +  .+.+ ..........=++|+||+|+++.++.....+..+.+     + +..+++..|
T Consensus        82 ~~d~~ilv~d~~~g~~~--~--~~~~-~~~~~~~~~p~iiv~NKiD~~~~~~~~~~~~~~~~~~~~~~~~~~~~iv~iS  155 (179)
T d1wb1a4          82 IIDLALIVVDAKEGPKT--Q--TGEH-MLILDHFNIPIIVVITKSDNAGTEEIKRTEMIMKSILQSTHNLKNSSIIPIS  155 (179)
T ss_dssp             SCCEEEEEEETTTCSCH--H--HHHH-HHHHHHTTCCBCEEEECTTSSCHHHHHHHHHHHHHHHHHSSSGGGCCEEECC
T ss_pred             hccccccccccccccch--h--hhhh-hhhhhhcCCcceeccccccccCHHHHHHHHHHHHHHHHHhhcCCCCeEEEEE
Confidence            45678899999763211  0  0111 112334455678999999999988766555554443     2 245666554

>d1f60a3 c.37.1.8 (A:2-240) Elongation factor eEF-1alpha, N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor eEF-1alpha, N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.65  E-value=0.32  Score=38.49  Aligned_cols=73  Identities=12%  Similarity=0.122  Sum_probs=41.7

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhh-hcCCccchHH-HHHHHhhcCE-EEEccC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLN-EVKPRFVVNE-AVEQVAYADR-IILNKI  105 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~-~~~~~~~~~~-~~~Qi~~Ad~-ivlnK~  105 (284)
                      +..+.||+|+|=.+...  .++      ...-..+..|.||||..-...-. ...+...... +...+....+ |++||+
T Consensus        83 ~~~i~iiDtPGH~df~~--~~~------~g~~~~D~ailvvda~~G~~e~g~~~~~QT~eh~~~~~~~gv~~iiv~iNKm  154 (239)
T d1f60a3          83 KYQVTVIDAPGHRDFIK--NMI------TGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKM  154 (239)
T ss_dssp             SEEEEEEECCCCTTHHH--HHH------HSSSCCSEEEEEEECSHHHHHHHTCTTSHHHHHHHHHHHTTCCEEEEEEECG
T ss_pred             CEEEEEEECCCcHHHHH--HHH------HHHHHhCEEEEEEECCCCccccccCchHhHHHHHHHHHHcCCCeEEEEEECC
Confidence            34589999999999753  121      12346788999999976421100 0000001011 2344445555 479999


Q ss_pred             CCCC
Q 023301          106 DLVT  109 (284)
Q Consensus       106 D~~~  109 (284)
                      |+++
T Consensus       155 D~~~  158 (239)
T d1f60a3         155 DSVK  158 (239)
T ss_dssp             GGGT
T ss_pred             CCCC
Confidence            9865

>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=90.23  E-value=0.31  Score=36.06  Aligned_cols=81  Identities=17%  Similarity=0.171  Sum_probs=40.5

Q ss_pred             CEEEEecCCCCCc----HHHHHHhcc---cccccceeeeceEEEEEcccchHHhhhhc---CCccchHHHHHHHhhc---
Q 023301           31 DHIVIETTGLAKP----APVIETFCT---DELVSQYVKLDGVITLVDSKHAMQHLNEV---KPRFVVNEAVEQVAYA---   97 (284)
Q Consensus        31 d~iiIE~sG~a~p----~~i~~~l~~---~~~l~~~~~l~~vv~vvD~~~~~~~l~~~---~~~~~~~~~~~Qi~~A---   97 (284)
                      ++.++.++|+...    ....+.+..   .......-.++.++.|||+..........   +.......+.+.+...   
T Consensus        44 ~~~ivDtpG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~vvD~~~~~~~~~~~~~~~~~~~d~~~~~~l~~~~~p  123 (184)
T d2cxxa1          44 NHKIIDMPGFGFMMGLPKEVQERIKDEIVHFIEDNAKNIDVAVLVVDGKAAPEIIKRWEKRGEIPIDVEFYQFLRELDIP  123 (184)
T ss_dssp             TEEEEECCCBSCCTTSCHHHHHHHHHHHHHHHHHHGGGCCEEEEEEETTHHHHHHHHHHHTTCCCHHHHHHHHHHHTTCC
T ss_pred             cceecccCCceeccccccccccccchhhhhhhhhcccccchheeeeeccccchhhhhhhhccccHHHHHHHHHHHHcCCC
Confidence            5678899997542    222222110   00111122467899999997654322110   0011111223344433   


Q ss_pred             CEEEEccCCCCChh
Q 023301           98 DRIILNKIDLVTET  111 (284)
Q Consensus        98 d~ivlnK~D~~~~~  111 (284)
                      -+||+||+|+++..
T Consensus       124 ~iiv~NK~D~~~~~  137 (184)
T d2cxxa1         124 TIVAVNKLDKIKNV  137 (184)
T ss_dssp             EEEEEECGGGCSCH
T ss_pred             EEEEEeeeehhhhH
Confidence            37899999987643

>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=89.97  E-value=0.21  Score=38.34  Aligned_cols=79  Identities=19%  Similarity=0.230  Sum_probs=43.4

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHH-HHHHhhcCEE-EEccCC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEA-VEQVAYADRI-ILNKID  106 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~-~~Qi~~Ad~i-vlnK~D  106 (284)
                      +..+-+|.++|-.+...  .+      .+..-..+.++.||||..-...  +.  +.  ... ...+....+| ++||+|
T Consensus        65 ~~~~~~iDtPGh~~f~~--~~------~~~~~~aD~allVVda~~G~~~--QT--~~--~~~~a~~~~~~~iIv~iNK~D  130 (196)
T d1d2ea3          65 ARHYAHTDCPGHADYVK--NM------ITGTAPLDGCILVVAANDGPMP--QT--RE--HLLLARQIGVEHVVVYVNKAD  130 (196)
T ss_dssp             SCEEEEEECSSHHHHHH--HH------HHTSSCCSEEEEEEETTTCSCH--HH--HH--HHHHHHHTTCCCEEEEEECGG
T ss_pred             eeeEEeecCcchHHHHH--HH------HHHHhhcCeEEEEEEcCCCCch--hH--HH--HHHHHHHhcCCcEEEEEeccc
Confidence            45678889998666432  11      1123456889999999864321  10  00  111 2333445555 589999


Q ss_pred             CCChhH-HHHHHHHHH
Q 023301          107 LVTETE-LGSLTERIK  121 (284)
Q Consensus       107 ~~~~~~-~~~~~~~l~  121 (284)
                      ++++++ .+.+++.++
T Consensus       131 ~~~~~~~~~~i~~~i~  146 (196)
T d1d2ea3         131 AVQDSEMVELVELEIR  146 (196)
T ss_dssp             GCSCHHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHH
Confidence            986433 344443343

>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=89.86  E-value=1.6  Score=33.55  Aligned_cols=110  Identities=17%  Similarity=0.270  Sum_probs=62.8

Q ss_pred             chHHHHHHHHHHh-hcCCCCEEEEecCCCCCcHH-HHHHhccccccccee------eeceEEEEEcccchHHhhhhcCCc
Q 023301           13 GDLVKMLLQLAKK-KQGQFDHIVIETTGLAKPAP-VIETFCTDELVSQYV------KLDGVITLVDSKHAMQHLNEVKPR   84 (284)
Q Consensus        13 ~dl~~~l~~l~~~-~~~~~d~iiIE~sG~a~p~~-i~~~l~~~~~l~~~~------~l~~vv~vvD~~~~~~~l~~~~~~   84 (284)
                      .++...+...... ...+.|+|||+|.|...-.. .++.+..   +....      .-..++.|+|+..-...+...   
T Consensus        76 ~d~~~~~~~~~~~~~~~~~d~ilIDTaGr~~~d~~~~~el~~---~~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~---  149 (213)
T d1vmaa2          76 ADPAAVAFDAVAHALARNKDVVIIDTAGRLHTKKNLMEELRK---VHRVVKKKIPDAPHETLLVIDATTGQNGLVQA---  149 (213)
T ss_dssp             CCHHHHHHHHHHHHHHTTCSEEEEEECCCCSCHHHHHHHHHH---HHHHGGGTCTTCCSEEEEEEEGGGHHHHHHHH---
T ss_pred             CcHHHHHHHHHHHHHHcCCCEEEEeccccccchHHHHHHHHH---HHhhhhhccccccceeEEeeccccCcchhhhh---
Confidence            3455444333221 13578999999999877443 2222211   11111      134578999997755543321   


Q ss_pred             cchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCC
Q 023301           85 FVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGS  136 (284)
Q Consensus        85 ~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~  136 (284)
                          ....+-...+-+|++|.|...  ..-.+...+.+.+  .||...+.|+
T Consensus       150 ----~~~~~~~~~~~lI~TKlDe~~--~~G~~l~~~~~~~--~Pi~~i~~Gq  193 (213)
T d1vmaa2         150 ----KIFKEAVNVTGIILTKLDGTA--KGGITLAIARELG--IPIKFIGVGE  193 (213)
T ss_dssp             ----HHHHHHSCCCEEEEECGGGCS--CTTHHHHHHHHHC--CCEEEEECSS
T ss_pred             ----hhhccccCCceEEEecccCCC--cccHHHHHHHHHC--CCEEEEeCCC
Confidence                123455678999999999854  2334445554444  6676666663

>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=89.86  E-value=0.17  Score=40.95  Aligned_cols=57  Identities=19%  Similarity=0.180  Sum_probs=37.5

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHHHHH-hhcCEEEEccCCCCChhHHHHHHHHHHHhCC
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQV-AYADRIILNKIDLVTETELGSLTERIKHINA  125 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi-~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np  125 (284)
                      .+|-|+.|+||+......    ..    .+.+-+ .-.-++|+||+|+++.+..+.+.+..+..+.
T Consensus        15 ~~DvIl~V~DaR~P~ss~----~~----~l~~~~~~Kp~IlVlNK~DLv~~~~~~~w~~~f~~~~~   72 (273)
T d1puja_          15 LIDIVYELVDARIPMSSR----NP----MIEDILKNKPRIMLLNKADKADAAVTQQWKEHFENQGI   72 (273)
T ss_dssp             GCSEEEEEEETTSTTTTS----CH----HHHHHCSSSCEEEEEECGGGSCHHHHHHHHHHHHTTTC
T ss_pred             hCCEEEEEEECCCCCCCC----CH----HHHHHHcCCCeEEEEECccCCchHHHHHHHHHHHhcCC
Confidence            567799999998754321    11    111222 2356888899999998887777777665443

>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=89.83  E-value=0.18  Score=39.53  Aligned_cols=72  Identities=17%  Similarity=0.051  Sum_probs=43.0

Q ss_pred             CCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCC
Q 023301           28 GQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDL  107 (284)
Q Consensus        28 ~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~  107 (284)
                      ....+.||.|+|..+...        .........+.+|.||||..-.+...    ..... ........=+|++||+|+
T Consensus        68 ~~~~~~~iDtPGh~~f~~--------~~~~~~~~~D~~ilVvda~~g~~~~~----~~~~~-~~~~~~~p~iivlNK~D~  134 (227)
T d1g7sa4          68 TLPGLFFIDTPGHEAFTT--------LRKRGGALADLAILIVDINEGFKPQT----QEALN-ILRMYRTPFVVAANKIDR  134 (227)
T ss_dssp             TCCEEEEECCCTTSCCTT--------SBCSSSBSCSEEEEEEETTTCCCHHH----HHHHH-HHHHTTCCEEEEEECGGG
T ss_pred             cccccccccccceecccc--------cchhcccccceEEEEEecccCcccch----hHHHH-HhhcCCCeEEEEEECccC
Confidence            345789999999655321        11223345789999999976322111    01111 122334567899999999


Q ss_pred             CChhH
Q 023301          108 VTETE  112 (284)
Q Consensus       108 ~~~~~  112 (284)
                      .+.+.
T Consensus       135 ~~~~~  139 (227)
T d1g7sa4         135 IHGWR  139 (227)
T ss_dssp             STTCC
T ss_pred             CCchh
Confidence            87554

>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=89.81  E-value=0.087  Score=38.46  Aligned_cols=94  Identities=13%  Similarity=0.263  Sum_probs=52.4

Q ss_pred             CCCEEEEecCCCCCcHH-HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhc-CEEEEccCC
Q 023301           29 QFDHIVIETTGLAKPAP-VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYA-DRIILNKID  106 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~-i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~A-d~ivlnK~D  106 (284)
                      .....+++++|+..+.. ..+.......+...-..+.++.|+|+........        ..+..++... -++++||+|
T Consensus        47 ~~~~~~~Dt~G~~~~~~~~~~~~~~~~~~~~~~~ad~ii~v~d~~~~~~~~~--------~~~~~~~~~~~~i~~~~k~d  118 (160)
T d1xzpa2          47 GILFRIVDTAGVRSETNDLVERLGIERTLQEIEKADIVLFVLDASSPLDEED--------RKILERIKNKRYLVVINKVD  118 (160)
T ss_dssp             TEEEEEEESSCCCSSCCTTCCCCCHHHHHHHHHHCSEEEEEEETTSCCCHHH--------HHHHHHHTTSSEEEEEEECS
T ss_pred             CeeEEeccccccccCCccHHHHHHHHHHHHHHHhCCEEEEEEeCCCCcchhh--------hhhhhhcccccceeeeeecc
Confidence            34567889999865421 1110000011111234678999999987432211        1233444444 456679999


Q ss_pred             CCChhHHHHHHHHHHHhCCCCceeeec
Q 023301          107 LVTETELGSLTERIKHINAMAPVKLAK  133 (284)
Q Consensus       107 ~~~~~~~~~~~~~l~~~np~a~i~~~~  133 (284)
                      ..+....+.+.+   .+.+..+++.+|
T Consensus       119 ~~~~~~~~~~~~---~~~~~~~~~~vS  142 (160)
T d1xzpa2         119 VVEKINEEEIKN---KLGTDRHMVKIS  142 (160)
T ss_dssp             SCCCCCHHHHHH---HHTCSTTEEEEE
T ss_pred             ccchhhhHHHHH---HhCCCCcEEEEE
Confidence            988766655543   456677887654

>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=89.43  E-value=1.2  Score=34.25  Aligned_cols=97  Identities=15%  Similarity=0.204  Sum_probs=57.7

Q ss_pred             cCCCCEEEEecCCCCCcHH-HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccC
Q 023301           27 QGQFDHIVIETTGLAKPAP-VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKI  105 (284)
Q Consensus        27 ~~~~d~iiIE~sG~a~p~~-i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~  105 (284)
                      ....|.|+|.|.|...-.. .++.+.   .+.....-+.++.|+|+..-.+.+...       ....+.-..+-++++|.
T Consensus        90 ~~~~d~vlIDTaGr~~~d~~~~~el~---~~~~~~~~~~~llv~~a~~~~~~~~~~-------~~f~~~~~~~~~I~TKl  159 (207)
T d1ls1a2          90 LEARDLILVDTAGRLQIDEPLMGELA---RLKEVLGPDEVLLVLDAMTGQEALSVA-------RAFDEKVGVTGLVLTKL  159 (207)
T ss_dssp             HHTCCEEEEECCCCSSCCHHHHHHHH---HHHHHHCCSEEEEEEEGGGTHHHHHHH-------HHHHHHTCCCEEEEECG
T ss_pred             hccCcceeecccccchhhhhhHHHHH---HHHhhcCCceEEEEeccccchhHHHHH-------HHHHhhCCCCeeEEeec
Confidence            3578999999999877432 333332   232334556789999998866544321       11234445788999999


Q ss_pred             CCCChhHHHHHHHHHHHhCCCCceeeeccCCC
Q 023301          106 DLVTETELGSLTERIKHINAMAPVKLAKYGSV  137 (284)
Q Consensus       106 D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v  137 (284)
                      |...  ..-.+.....+.+  .||.....|++
T Consensus       160 De~~--~~G~~l~~~~~~~--~Pi~~i~~Gq~  187 (207)
T d1ls1a2         160 DGDA--RGGAALSARHVTG--KPIYFAGVSEK  187 (207)
T ss_dssp             GGCS--SCHHHHHHHHHHC--CCEEEEC----
T ss_pred             Cccc--cchHHHHHHHHHC--CCEEEEeCCCC
Confidence            9754  3445555555444  57766777765

>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=88.39  E-value=0.66  Score=34.96  Aligned_cols=88  Identities=20%  Similarity=0.209  Sum_probs=47.9

Q ss_pred             EEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchH-H-hhhhcCCccchHHHHHHHhhcC-EEEEccCCCC
Q 023301           32 HIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAM-Q-HLNEVKPRFVVNEAVEQVAYAD-RIILNKIDLV  108 (284)
Q Consensus        32 ~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~-~-~l~~~~~~~~~~~~~~Qi~~Ad-~ivlnK~D~~  108 (284)
                      +.+|+++|-.+......        +.....+.++.|||+.... . +..+    .  -.....+.-.. +|++||+|+.
T Consensus        80 ~~~iDtPGh~~f~~~~~--------~~~~~~d~~ilvvda~~g~~~~~t~e----~--~~~~~~~~~~~iiv~inK~D~~  145 (195)
T d1kk1a3          80 VSFIDAPGHEALMTTML--------AGASLMDGAILVIAANEPCPRPQTRE----H--LMALQIIGQKNIIIAQNKIELV  145 (195)
T ss_dssp             EEEEECSSHHHHHHHHH--------HCGGGCSEEEEEEETTSCSSCHHHHH----H--HHHHHHHTCCCEEEEEECGGGS
T ss_pred             EeeeccchhhhhhHHhh--------cccccccccccccchhhhhhhhhhHH----H--HHHHHHhcCccceeeeecccch
Confidence            67899999554332211        1223467789999987742 1 1111    0  11233334444 4569999999


Q ss_pred             ChhHHHHH----HHHHHHhCC-CCceeeec
Q 023301          109 TETELGSL----TERIKHINA-MAPVKLAK  133 (284)
Q Consensus       109 ~~~~~~~~----~~~l~~~np-~a~i~~~~  133 (284)
                      +..+....    .++++..++ .++++..+
T Consensus       146 d~~~~~~~~~~~~~~~~~~~~~~~~iIpiS  175 (195)
T d1kk1a3         146 DKEKALENYRQIKEFIEGTVAENAPIIPIS  175 (195)
T ss_dssp             CHHHHHHHHHHHHHHHTTSTTTTCCEEECB
T ss_pred             hhHHHHHHHHHHHHHhccccCCCCeEEEEE
Confidence            87654443    444444333 45666554

>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=88.17  E-value=0.25  Score=37.71  Aligned_cols=59  Identities=17%  Similarity=0.216  Sum_probs=30.8

Q ss_pred             eeceEEEEEcccchHHhhhhcCCccchHHHH-HHHhhc---CEEEEccCCCCChhHHHHHHHHH
Q 023301           61 KLDGVITLVDSKHAMQHLNEVKPRFVVNEAV-EQVAYA---DRIILNKIDLVTETELGSLTERI  120 (284)
Q Consensus        61 ~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~-~Qi~~A---d~ivlnK~D~~~~~~~~~~~~~l  120 (284)
                      ..+.++.|+|+......+.+.. ..+...+. .+...-   =+|++||+|+.+....+.+++.+
T Consensus        71 ~~~~~i~v~D~~d~~~~~~~~~-~~l~~~l~~~~~~~~~~pilvv~NK~Dl~~a~~~~~i~~~l  133 (207)
T d2fh5b1          71 SARAVVFVVDSAAFQREVKDVA-EFLYQVLIDSMALKNSPSLLIACNKQDIAMAKSAKLIQQQL  133 (207)
T ss_dssp             GEEEEEEEEETTTHHHHHHHHH-HHHHHHHHHHHTSTTCCEEEEEEECTTSTTCCCHHHHHHHH
T ss_pred             hccccceEEEcccccccHHHHH-HHHHHHHHhHHHhhcCCcEEEEEECcccCCCCCHHHHHHHH
Confidence            4457899999987655433211 11111111 111111   14667999997655555555544

>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=87.46  E-value=0.03  Score=41.71  Aligned_cols=69  Identities=14%  Similarity=0.112  Sum_probs=42.0

Q ss_pred             CCCceeeeeeCch----HHHHHHHHHHhhcCCCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccch
Q 023301            2 VNNGCLCCTVRGD----LVKMLLQLAKKKQGQFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHA   74 (284)
Q Consensus         2 L~~GCiCCs~~~d----l~~~l~~l~~~~~~~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~   74 (284)
                      +.++|.||.....    +...+. ++.  ...+|+|++|..+.+.+.++. .+..+........+..++.|++....
T Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~-~~~--~~~~D~iivEg~~~~~~~ki~-~~~~~~~~~~~~~~~~iiavv~~~~~  137 (165)
T d1xjca_          65 VEGDGLLQLHLRRPLWRLDDVLA-LYA--PLRLDLVLVEGYKQERHPKVV-LVRSEEDWASLQHLANIRAVIAWEPL  137 (165)
T ss_dssp             EEETTEEEEEECCSCCCHHHHHH-HHG--GGCCSEEEEECCTTSCSCEEE-EESSHHHHHHHTTSTTEEEEEESSCC
T ss_pred             ccChHHHHHHhhccccchhhHHH-HHh--hcccCeEeeecccccCcceeE-EEecccCcccccCCCCEEEEEeCccc
Confidence            3567777776542    333333 333  467999999999999876653 22222222233456778888877654

>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=87.04  E-value=0.14  Score=40.42  Aligned_cols=71  Identities=17%  Similarity=0.191  Sum_probs=37.2

Q ss_pred             eeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhC--CCCceeeec
Q 023301           60 VKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLVTETELGSLTERIKHIN--AMAPVKLAK  133 (284)
Q Consensus        60 ~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~n--p~a~i~~~~  133 (284)
                      ..+|.++.|+.+.+..-... .-+|++.  +..+-...=+||+||+|++++++.+...+.+.+..  ...+++.++
T Consensus         9 ANiD~~~iV~s~~~P~~~~~-~idR~Lv--~a~~~~i~pvIvlnK~DL~~~~~~~~~~~~~~~~y~~~g~~v~~~S   81 (231)
T d1t9ha2           9 CNVDQAVLVFSAVQPSFSTA-LLDRFLV--LVEANDIQPIICITKMDLIEDQDTEDTIQAYAEDYRNIGYDVYLTS   81 (231)
T ss_dssp             ECCCEEEEEEESTTTTCCHH-HHHHHHH--HHHTTTCEEEEEEECGGGCCCHHHHHHHHHHHHHHHHHTCCEEECC
T ss_pred             cccCEEEEEEECCCCCCCHH-HHHHHHH--HHHHcCCCEEEEEecccccccHHHHHHHHHHHHHHhhccccceeee
Confidence            57888888887754321000 0012211  12233334578899999998766544333333332  246777654

>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=86.44  E-value=1.6  Score=33.41  Aligned_cols=118  Identities=15%  Similarity=0.239  Sum_probs=65.6

Q ss_pred             chHHHHHHHHHHh-hcCCCCEEEEecCCCCCcHH-HHHHhccccc-c--cceeeeceEEEEEcccchHHhhhhcCCccch
Q 023301           13 GDLVKMLLQLAKK-KQGQFDHIVIETTGLAKPAP-VIETFCTDEL-V--SQYVKLDGVITLVDSKHAMQHLNEVKPRFVV   87 (284)
Q Consensus        13 ~dl~~~l~~l~~~-~~~~~d~iiIE~sG~a~p~~-i~~~l~~~~~-l--~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~   87 (284)
                      .|+...+.+.... +....|+|||.|.|...-.. .++.+..-.. .  .....-..++.|+|+..-.+.+...      
T Consensus        71 ~d~~~~~~~~~~~~~~~~~d~ilIDTaGr~~~d~~l~~el~~~~~~~~~~~~~~p~~~~LVl~a~~~~~~~~~~------  144 (207)
T d1okkd2          71 TDPAALAYDAVQAMKARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQA------  144 (207)
T ss_dssp             CCHHHHHHHHHHHHHHHTCSEEEECCCCCCTTCHHHHHHHHHHHHHHHHHCTTCCSEEEEEEETTBCTHHHHHH------
T ss_pred             ccHHHHHHHHHHHHHHCCCCEEEcCccccchhhHHHHHHHHHHHHHhhhcccCCCceEEEEeecccCchHHHHH------
Confidence            4566555544321 13468999999999876432 2222211000 0  0011224578999998865544321      


Q ss_pred             HHHHHHHhhcCEEEEccCCCCChhHHHHHHHHHHHhCCCCceeeeccCCCChhhh
Q 023301           88 NEAVEQVAYADRIILNKIDLVTETELGSLTERIKHINAMAPVKLAKYGSVDMDFV  142 (284)
Q Consensus        88 ~~~~~Qi~~Ad~ivlnK~D~~~~~~~~~~~~~l~~~np~a~i~~~~~g~v~~~~l  142 (284)
                       ....+....+-++++|.|...  ..-.+...+.+.+  .+|...+.|+. ++.|
T Consensus       145 -~~~~~~~~~~~lI~TKlDet~--~~G~~l~~~~~~~--~Pi~~i~~Gq~-p~Dl  193 (207)
T d1okkd2         145 -KKFHEAVGLTGVIVTKLDGTA--KGGVLIPIVRTLK--VPIKFVGVGEG-PDDL  193 (207)
T ss_dssp             -HHHHHHHCCSEEEEECTTSSC--CCTTHHHHHHHHC--CCEEEEECSSS-TTCE
T ss_pred             -HHhhhccCCceEEEeccCCCC--CccHHHHHHHHHC--CCEEEEeCCCC-hHhC
Confidence             113455668899999999854  2333444444443  67766667765 4544

>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=84.57  E-value=0.78  Score=35.53  Aligned_cols=86  Identities=15%  Similarity=0.214  Sum_probs=45.4

Q ss_pred             CCCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhh-hhcCCccchHH-HHHHHhhcCE-EEEccC
Q 023301           29 QFDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHL-NEVKPRFVVNE-AVEQVAYADR-IILNKI  105 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l-~~~~~~~~~~~-~~~Qi~~Ad~-ivlnK~  105 (284)
                      ...+-||.|+|=.+...-..+        ...-.|+.|.|||+.....-- ....+...... +...+..-.+ |++||+
T Consensus        80 ~~~i~iiDtPGH~df~~~~~~--------g~~~~D~allVVda~~G~~~~t~~~~~qt~e~l~~~~~~~~~~iIv~iNK~  151 (224)
T d1jnya3          80 KYFFTIIDAPGHRDFVKNMIT--------GASQADAAILVVSAKKGEYEAGMSVEGQTREHIILAKTMGLDQLIVAVNKM  151 (224)
T ss_dssp             SCEEEECCCSSSTTHHHHHHH--------TSSCCSEEEEEEECSTTHHHHHHSTTCHHHHHHHHHHHTTCTTCEEEEECG
T ss_pred             CceeEEeeCCCcHHHHHHHHH--------HHHhhceEEEEEecccCcccccccccchhHHHHHHHHHhCCCceEEEEEcc
Confidence            445678999999987642221        223468899999998743210 00000000011 1233333334 459999


Q ss_pred             CCCC----hhHHHHHHHHHHH
Q 023301          106 DLVT----ETELGSLTERIKH  122 (284)
Q Consensus       106 D~~~----~~~~~~~~~~l~~  122 (284)
                      |+..    ...++.+.+.++.
T Consensus       152 D~~~~~~~~~~~~~v~~~i~~  172 (224)
T d1jnya3         152 DLTEPPYDEKRYKEIVDQVSK  172 (224)
T ss_dssp             GGSSSTTCHHHHHHHHHHHHH
T ss_pred             cCCCccccHHHHHHHHHHHHh
Confidence            9864    3334444444443

>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=83.95  E-value=0.39  Score=38.66  Aligned_cols=64  Identities=13%  Similarity=0.177  Sum_probs=41.6

Q ss_pred             CEEEEecCCCCCcHH-HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCCC
Q 023301           31 DHIVIETTGLAKPAP-VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDLV  108 (284)
Q Consensus        31 d~iiIE~sG~a~p~~-i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~~  108 (284)
                      .+-+|.|+|-.+... +...         .-..++.|.||||..-...-..    .. -....+....-+|++||+|..
T Consensus        68 ~~n~iDtPGh~dF~~e~~~a---------l~~~D~avlvvda~~Gv~~~t~----~~-~~~~~~~~~p~~i~iNk~D~~  132 (267)
T d2dy1a2          68 RVFLLDAPGYGDFVGEIRGA---------LEAADAALVAVSAEAGVQVGTE----RA-WTVAERLGLPRMVVVTKLDKG  132 (267)
T ss_dssp             EEEEEECCCSGGGHHHHHHH---------HHHCSEEEEEEETTTCSCHHHH----HH-HHHHHHTTCCEEEEEECGGGC
T ss_pred             ceeEEccCchhhhhhhhhhh---------hcccCceEEEeeccCCccchhH----HH-HHhhhhccccccccccccccc
Confidence            468999999999653 2222         2346789999999864322110    01 123466677889999999984

>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=83.55  E-value=1.3  Score=34.35  Aligned_cols=65  Identities=22%  Similarity=0.250  Sum_probs=38.5

Q ss_pred             CEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHH-HHHHHhhcC-EEEEccCCCC
Q 023301           31 DHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNE-AVEQVAYAD-RIILNKIDLV  108 (284)
Q Consensus        31 d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~-~~~Qi~~Ad-~ivlnK~D~~  108 (284)
                      .+-||+++|=.+...-...        .....+.+|.||||......  +    ..... +...+.... +|++||+|++
T Consensus        90 ~~~iiD~PGH~dfv~~~~~--------g~~~aD~ailVvda~~G~~~--Q----t~e~~~~~~~~gv~~iiv~vNK~D~~  155 (222)
T d1zunb3          90 KFIIADTPGHEQYTRNMAT--------GASTCDLAIILVDARYGVQT--Q----TRRHSYIASLLGIKHIVVAINKMDLN  155 (222)
T ss_dssp             EEEEEECCCSGGGHHHHHH--------HHTTCSEEEEEEETTTCSCH--H----HHHHHHHHHHTTCCEEEEEEECTTTT
T ss_pred             EEEEEeccchhhhhhhhcc--------ccccCceEEEEeccccCccc--c----hHHHHHHHHHcCCCEEEEEEEccccc
Confidence            5789999999886532211        22356788999999764321  1    11111 123333232 5678999997


Q ss_pred             C
Q 023301          109 T  109 (284)
Q Consensus       109 ~  109 (284)
                      +
T Consensus       156 ~  156 (222)
T d1zunb3         156 G  156 (222)
T ss_dssp             T
T ss_pred             c
Confidence            6

>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=81.24  E-value=0.69  Score=37.34  Aligned_cols=81  Identities=20%  Similarity=0.203  Sum_probs=50.0

Q ss_pred             CCCEEEEecCCCCCcHH-HHHHhcccccccceeeeceEEEEEcccchHHhhhhcCCccchHHHHHHHhhcCEEEEccCCC
Q 023301           29 QFDHIVIETTGLAKPAP-VIETFCTDELVSQYVKLDGVITLVDSKHAMQHLNEVKPRFVVNEAVEQVAYADRIILNKIDL  107 (284)
Q Consensus        29 ~~d~iiIE~sG~a~p~~-i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l~~~~~~~~~~~~~~Qi~~Ad~ivlnK~D~  107 (284)
                      +..+-||.|+|-.+... +...         .-..++.|.||||..-.+--..    .+ -...+.-...-+++|||+|.
T Consensus        70 ~~~~n~iDtPG~~dF~~e~~~~---------l~~~D~avlVvda~~Gv~~~T~----~~-w~~a~~~~lP~i~fINKmDr  135 (276)
T d2bv3a2          70 DHRINIIDAPGHVDFTIEVERS---------MRVLDGAIVVFDSSQGVEPQSE----TV-WRQAEKYKVPRIAFANKMDK  135 (276)
T ss_dssp             TEEEEEECCCSSSSCSTTHHHH---------HHHCCEEEEEEETTTSSCHHHH----HH-HHHHHTTTCCEEEEEECTTS
T ss_pred             CeEEEEecCCchhhhHHHHHHH---------HHhhhheEEeccccCCcchhHH----HH-HHHHHHcCCCEEEEEecccc
Confidence            34567899999999643 2222         2346789999999875432110    00 01124445667999999998


Q ss_pred             CChhHHHHHHHHHHHhC
Q 023301          108 VTETELGSLTERIKHIN  124 (284)
Q Consensus       108 ~~~~~~~~~~~~l~~~n  124 (284)
                      .. ....++.+.+++..
T Consensus       136 ~~-ad~~~~l~ei~~~l  151 (276)
T d2bv3a2         136 TG-ADLWLVIRTMQERL  151 (276)
T ss_dssp             TT-CCHHHHHHHHHHTT
T ss_pred             cc-cccchhHHHHHHHh
Confidence            54 34566666677644

>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=80.30  E-value=2.8  Score=32.77  Aligned_cols=72  Identities=8%  Similarity=0.085  Sum_probs=34.4

Q ss_pred             CCEEEEecCCCCCcHHHHHHhcccccccceeeeceEEEEEcccchHHhh-hhcCCccchHH-HHHHHhhcCE-EEEccCC
Q 023301           30 FDHIVIETTGLAKPAPVIETFCTDELVSQYVKLDGVITLVDSKHAMQHL-NEVKPRFVVNE-AVEQVAYADR-IILNKID  106 (284)
Q Consensus        30 ~d~iiIE~sG~a~p~~i~~~l~~~~~l~~~~~l~~vv~vvD~~~~~~~l-~~~~~~~~~~~-~~~Qi~~Ad~-ivlnK~D  106 (284)
                      ..+.+|.++|-.+...   .     ........+.++.|||+..-...- ........... +...+..-.+ +++||+|
T Consensus       102 ~~i~~iDtPGH~df~~---~-----~~~g~~~aD~ailVVda~~G~~~~~~~~~~QT~e~l~l~~~~~i~~iiv~iNKmD  173 (245)
T d1r5ba3         102 RRFSLLDAPGHKGYVT---N-----MINGASQADIGVLVISARRGEFEAGFERGGQTREHAVLARTQGINHLVVVINKMD  173 (245)
T ss_dssp             EEEEECCCCC-------------------TTSCSEEEEEEECSTTHHHHTTSTTCCHHHHHHHHHHTTCSSEEEEEECTT
T ss_pred             ceeeeecccccccchh---h-----hhhhhhhhcceeeEEEcCCCccCCccccccchHHHHHHHHHcCCCeEEEEEEcCC
Confidence            4578899999887543   1     122345677899999997632110 00011111111 1233333344 7889999


Q ss_pred             CCC
Q 023301          107 LVT  109 (284)
Q Consensus       107 ~~~  109 (284)
                      +.+
T Consensus       174 ~~~  176 (245)
T d1r5ba3         174 EPS  176 (245)
T ss_dssp             STT
T ss_pred             CCc
Confidence            864