Psyllid ID: psy5461

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-
Protein Sequence
MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVIPKPTSVVQCSARWTLNLEVGASSPIISKSKRRQNMI
Secondary Structure (PSIPRED)
cccEEEEEccccccHHHHHHHHHHHHHHHHHcHHHHHHHcccHHHHHHHHHHHcccEEEcccccccccccHHHHHHHHHHHccccccccccccccccccccHHHHHHHcccccccEEEEEEEEEcEEccccEEEEccccccHHHHHHHHHHccccccccEEEcccEEEEEcccccccccccccccccccEEEEEcccccccHHcccccccccHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccEEEEcccHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHcHHHHHHHHHHHHHHcccEEEccHHHHcccHHHHHHHHHHHcccccccccccccccccccHHHHEEEEccccccEEEEEEEEEEEEEccccEEEcccccccHHHHHHHHHHcccHHHHHHHHHccHHHHEEcccccccccccccccccccEEEEcccccEEEEEEccccEEEEEEcccccc
Coil and Loop (DISEMBL)
mdaivdilpspterpalAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSgafkknhvpvlcgssyknigvQKLMDAIVDilpspterpalAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEaddykevneiqcgNIAAVtglkrergkdkrtrvipkptsvvqCSARWTLnlevgasspiiskskrrqnmi
Flexible Loop (DISEMBL)
mdaivdilpspteRPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDykevneiqcgniaavtglkrergkdkrtrvipkptsvvqcsarwtlnlevgasspiiskskrrqnmi
Low Complexity Region (SEG)
MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVIPKPTSVVQCSARWTLNLEVGASSPIISKSKRRQNMI
Disordered region (IsUnstruct)
***************ALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK**********VIPKPTSVVQCSARWTLNLEVG****************
Disordered Region (DISOPRED)
MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVIPKPTSVVQCSARWTLNLEVGASSPIISKSKRRQN**
Disordered Region (DISEMBL)
MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVIPKPTSVVQCSARWTLNLEVGASSPIISK********
Disordered Region (DISPRO)
MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVIPKPTSVVQCSARWTLNLEVGASSPIISKSKRR****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVIPKPTSVVQCSARWTLNLEVGASSPIISKSKRRQNMI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	221	2.2.26 [Sep-21-2011]
Q969S9	779	Ribosome-releasing factor	yes	N/A	0.592	0.168	0.462	2e-26
A0JMI9	762	Ribosome-releasing factor	yes	N/A	0.547	0.158	0.483	2e-26
Q5R600	777	Ribosome-releasing factor	yes	N/A	0.592	0.168	0.454	2e-25
A6QNM2	777	Ribosome-releasing factor	yes	N/A	0.592	0.168	0.462	2e-25
Q5BJP6	779	Ribosome-releasing factor	yes	N/A	0.592	0.168	0.439	3e-25
Q8R2Q4	779	Ribosome-releasing factor	yes	N/A	0.547	0.155	0.483	5e-25
B2J5B0	692	Elongation factor G OS=No	yes	N/A	0.660	0.210	0.389	3e-24
B3M011	741	Ribosome-releasing factor	N/A	N/A	0.511	0.152	0.448	6e-24
Q3MDM4	692	Elongation factor G OS=An	yes	N/A	0.552	0.176	0.428	1e-23
Q8YP62	692	Elongation factor G OS=No	yes	N/A	0.552	0.176	0.428	2e-23

>sp|Q969S9|RRF2M_HUMAN Ribosome-releasing factor 2, mitochondrial OS=Homo sapiens GN=GFM2 PE=1 SV=1

 Score =  119 bits (297), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 61/132 (46%), Positives = 79/132 (59%), Gaps = 1/132 (0%)

Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFK 107
           I+     +  VPVLCGS+ KN G+Q L+DA+   LPSP ER      Q + D LCA AFK
Sbjct: 315 IHRVTLAQTAVPVLCGSALKNKGIQPLLDAVTMYLPSPEER-NYEFLQWYKDDLCALAFK 373

Query: 108 VVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167
           V+HDK RG + F RIYSG  K     +NI+ + +E+I+RLLL  AD + E+  +  GNIA
Sbjct: 374 VLHDKQRGPLVFMRIYSGTIKPQLAIHNINGNCTERISRLLLPFADQHVEIPSLTAGNIA 433

Query: 168 AVTGLKRERGKD 179
              GLK     D
Sbjct: 434 LTVGLKHTATGD 445

Mitochondrial GTPase that mediates the disassembly of ribosomes from messenger RNA at the termination of mitochondrial protein biosynthesis. Acts in collaboration with MRRF. GTP hydrolysis follows the ribosome disassembly and probably occurs on the ribosome large subunit. Not involved in the GTP-dependent ribosomal translocation step during translation elongation.
Homo sapiens (taxid: 9606)

>sp|A0JMI9|RRF2M_DANRE Ribosome-releasing factor 2, mitochondrial OS=Danio rerio GN=gfm2 PE=2 SV=2

 Score =  119 bits (297), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 59/122 (48%), Positives = 79/122 (64%), Gaps = 1/122 (0%)

Query: 53  FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDK 112
             +  VPVLCGSS KN GVQ L+DAI   LP+P ER    + + + + LCA AFKVVHDK
Sbjct: 308 LARKGVPVLCGSSLKNKGVQPLLDAITAYLPAPNERNH-DLVRWYKNDLCALAFKVVHDK 366

Query: 113 HRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGL 172
            RG + F RIYSG+ K     +NI+ +++E+++RLLL  AD   E+  +  GNIA   GL
Sbjct: 367 QRGPLVFVRIYSGSMKAQSSVHNINRNETEKMSRLLLPFADQQIEIPSLSAGNIALTVGL 426

Query: 173 KR 174
           K+
Sbjct: 427 KQ 428

Mitochondrial GTPase that mediates the disassembly of ribosomes from messenger RNA at the termination of mitochondrial protein biosynthesis. Acts in collaboration with mrrf. GTP hydrolysis follows the ribosome disassembly and probably occurs on the ribosome large subunit. Not involved in the GTP-dependent ribosomal translocation step during translation elongation.

Danio rerio (taxid: 7955)

>sp|Q5R600|RRF2M_PONAB Ribosome-releasing factor 2, mitochondrial OS=Pongo abelii GN=GFM2 PE=2 SV=1

 Score =  116 bits (290), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 60/132 (45%), Positives = 78/132 (59%), Gaps = 1/132 (0%)

Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFK 107
           I+     +  VPVLCGS+ KN G+Q L+DA+   LPSP E       Q + D LCA AFK
Sbjct: 315 IHRVTLAQTAVPVLCGSALKNKGIQPLLDAVTMYLPSP-EECNCEFLQWYKDDLCALAFK 373

Query: 108 VVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167
           V+HDK RG + F RIYSG  K     +NI+ + +E+I+RLLL  AD + E+  +  GNIA
Sbjct: 374 VLHDKQRGPLVFMRIYSGTIKPQLAIHNINGNCTERISRLLLPFADQHVEIPSLTAGNIA 433

Query: 168 AVTGLKRERGKD 179
              GLK     D
Sbjct: 434 LTVGLKHTATGD 445

Mitochondrial GTPase that mediates the disassembly of ribosomes from messenger RNA at the termination of mitochondrial protein biosynthesis. Acts in collaboration with MRRF. GTP hydrolysis follows the ribosome disassembly and probably occurs on the ribosome large subunit. Not involved in the GTP-dependent ribosomal translocation step during translation elongation.

Pongo abelii (taxid: 9601)

>sp|A6QNM2|RRF2M_BOVIN Ribosome-releasing factor 2, mitochondrial OS=Bos taurus GN=GFM2 PE=2 SV=1

 Score =  115 bits (288), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 61/132 (46%), Positives = 78/132 (59%), Gaps = 1/132 (0%)

Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFK 107
           I+     +  VPVLCGS+ KN GVQ L+DAI   LPSP ER      Q +   LCA AFK
Sbjct: 315 IHRVTLAQTAVPVLCGSALKNKGVQPLLDAITMYLPSPEER-NYEFLQWYKGDLCALAFK 373

Query: 108 VVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167
           V+HDK RG + F RIYSG  K     +NI+ + +E+++RLLL  AD + E+  +  GNIA
Sbjct: 374 VLHDKQRGPLVFMRIYSGMLKPQTAIHNINGNCTERVSRLLLPFADQHIEIPLLTAGNIA 433

Query: 168 AVTGLKRERGKD 179
              GLK     D
Sbjct: 434 LTVGLKHTATGD 445

Mitochondrial GTPase that mediates the disassembly of ribosomes from messenger RNA at the termination of mitochondrial protein biosynthesis. Acts in collaboration with MRRF. GTP hydrolysis follows the ribosome disassembly and probably occurs on the ribosome large subunit. Not involved in the GTP-dependent ribosomal translocation step during translation elongation.

Bos taurus (taxid: 9913)

>sp|Q5BJP6|RRF2M_RAT Ribosome-releasing factor 2, mitochondrial OS=Rattus norvegicus GN=Gfm2 PE=2 SV=2

 Score =  115 bits (287), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 58/132 (43%), Positives = 78/132 (59%), Gaps = 1/132 (0%)

Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFK 107
           I+     +  VPVLCGS+ KN GVQ L+DA+   LPSP ER      Q +   LCA AFK
Sbjct: 315 IHRVTLAQAAVPVLCGSALKNKGVQPLLDAVTTYLPSPEEREH-GFLQWYKGDLCALAFK 373

Query: 108 VVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167
           V+HDK RG + F RIYSG        +N++ + +E+++RLLL  AD + E+  +  GNIA
Sbjct: 374 VLHDKQRGPLVFLRIYSGTLTPQSAVHNVNRNCTERMSRLLLPFADQHVEIPSLTAGNIA 433

Query: 168 AVTGLKRERGKD 179
              GLK+    D
Sbjct: 434 LTVGLKQTATGD 445

Mitochondrial GTPase that mediates the disassembly of ribosomes from messenger RNA at the termination of mitochondrial protein biosynthesis. Acts in collaboration with MRRF. GTP hydrolysis follows the ribosome disassembly and probably occurs on the ribosome large subunit. Not involved in the GTP-dependent ribosomal translocation step during translation elongation.

Rattus norvegicus (taxid: 10116)

>sp|Q8R2Q4|RRF2M_MOUSE Ribosome-releasing factor 2, mitochondrial OS=Mus musculus GN=Gfm2 PE=2 SV=2

 Score =  114 bits (285), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 59/122 (48%), Positives = 77/122 (63%), Gaps = 1/122 (0%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
           VPVLCGS+ KN GVQ L+DA+   LPSP ER    +  + GD LCA AFKV+HDK RG +
Sbjct: 325 VPVLCGSALKNKGVQPLLDAVTTYLPSPEEREDRFLQWYEGD-LCALAFKVLHDKQRGPL 383

Query: 118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERG 177
            F RIYSG        +NI+ + +E+++RLLL  AD + E+  +  GNIA   GLK+   
Sbjct: 384 VFLRIYSGTLTPQLAVHNINRNCTERMSRLLLPFADQHVEIPSLTAGNIALTVGLKQTAT 443

Query: 178 KD 179
            D
Sbjct: 444 GD 445

Mitochondrial GTPase that mediates the disassembly of ribosomes from messenger RNA at the termination of mitochondrial protein biosynthesis. Acts in collaboration with MRRF. GTP hydrolysis follows the ribosome disassembly and probably occurs on the ribosome large subunit. Not involved in the GTP-dependent ribosomal translocation step during translation elongation.

Mus musculus (taxid: 10090)

>sp|B2J5B0|EFG_NOSP7 Elongation factor G OS=Nostoc punctiforme (strain ATCC 29133 / PCC 73102) GN=fusA PE=3 SV=1

 Score =  111 bits (278), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 62/159 (38%), Positives = 93/159 (58%), Gaps = 13/159 (8%)

Query: 25  DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84
           D+L A+ F+      +   T  R   G      VPVLCGS++KN GVQ ++DA+VD LP+
Sbjct: 223 DALMAKYFEGEELTEQEIRTALR--KGTIAGTIVPVLCGSAFKNKGVQLMLDAVVDYLPA 280

Query: 85  PTERPALAMFQHFGDS----------LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFY 134
           P+E P +      GD+          L A AFK++ D + G +TF R+YSG  KKG    
Sbjct: 281 PSEVPPIQGLLPNGDTIERRADDNEPLAALAFKIMADPY-GRLTFVRVYSGVLKKGSYVL 339

Query: 135 NIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173
           N   ++ E+I+RL+L +ADD ++V+E++ G++ A  GLK
Sbjct: 340 NASKNKKERISRLVLMKADDRQDVDELRAGDLGAALGLK 378

Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome.

Nostoc punctiforme (strain ATCC 29133 / PCC 73102) (taxid: 63737)

>sp|B3M011|RRF2M_DROAN Ribosome-releasing factor 2, mitochondrial OS=Drosophila ananassae GN=EF-G2 PE=3 SV=1

 Score =  110 bits (276), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 52/116 (44%), Positives = 75/116 (64%), Gaps = 3/116 (2%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
           VPVL GS+YKN+G+Q+LMDA+   LP+P ER  +  +  FG  +  + FK+VHDK RGA+
Sbjct: 282 VPVLLGSAYKNVGIQRLMDAVNSYLPAPEERNQI--YDCFGSEVAGKVFKIVHDKQRGAL 339

Query: 118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173
           T  RI  G  KKG +  +    Q+E +++L    AD+Y+EVN +Q G++    GLK
Sbjct: 340 TLVRILRGEIKKGMRLISAR-GQAEVVSKLYEPLADEYREVNAVQSGDVVICAGLK 394

Mitochondrial GTPase that mediates the disassembly of ribosomes from messenger RNA at the termination of mitochondrial protein biosynthesis. Not involved in the GTP-dependent ribosomal translocation step during translation elongation.

Drosophila ananassae (taxid: 7217)

>sp|Q3MDM4|EFG_ANAVT Elongation factor G OS=Anabaena variabilis (strain ATCC 29413 / PCC 7937) GN=fusA PE=3 SV=1

 Score =  109 bits (273), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/133 (42%), Positives = 82/133 (61%), Gaps = 11/133 (8%)

Query: 51  GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS---------- 100
           G      VPVLCGS++KN GVQ ++DA+VD LP+PTE P +      GD+          
Sbjct: 247 GTIAGTIVPVLCGSAFKNKGVQLMLDAVVDYLPAPTEVPPIQGTLANGDTVERRADDNEP 306

Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
           L A AFK++ D + G +TF R+YSG  KKG    N   ++ E+I+RL+L +ADD ++V E
Sbjct: 307 LAALAFKIMADPY-GRLTFVRVYSGVLKKGSYVLNATKNKKERISRLVLMKADDRQDVEE 365

Query: 161 IQCGNIAAVTGLK 173
           ++ G++ A  GLK
Sbjct: 366 LRAGDLGAALGLK 378

Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome.

Anabaena variabilis (strain ATCC 29413 / PCC 7937) (taxid: 240292)

>sp|Q8YP62|EFG_NOSS1 Elongation factor G OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=fusA PE=3 SV=1

 Score =  109 bits (272), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 57/133 (42%), Positives = 82/133 (61%), Gaps = 11/133 (8%)

Query: 51  GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS---------- 100
           G      VPVLCGS++KN GVQ ++DA+VD LP+PTE P +      GD+          
Sbjct: 247 GTIAGTIVPVLCGSAFKNKGVQLMLDAVVDYLPAPTEVPPIQGTLPNGDAIERRADDNEP 306

Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
           L A AFK++ D + G +TF R+YSG  KKG    N   ++ E+I+RL+L +ADD ++V E
Sbjct: 307 LAALAFKIMADPY-GRLTFVRVYSGVLKKGSYVLNATKNKKERISRLVLMKADDRQDVEE 365

Query: 161 IQCGNIAAVTGLK 173
           ++ G++ A  GLK
Sbjct: 366 LRAGDLGAALGLK 378

Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

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	221
307205784	747	Elongation factor G 2, mitochondrial [Ha	0.524	0.155	0.637	6e-37
328701929	742	PREDICTED: ribosome-releasing factor 2,	0.520	0.154	0.620	1e-36
307191029	743	Elongation factor G 2, mitochondrial [Ca	0.552	0.164	0.598	1e-35
340713650	832	PREDICTED: ribosome-releasing factor 2,	0.597	0.158	0.515	7e-35
322792141	695	hypothetical protein SINV_02354 [Solenop	0.524	0.166	0.637	1e-34
383859899	824	PREDICTED: LOW QUALITY PROTEIN: ribosome	0.597	0.160	0.515	2e-33
328784337	831	PREDICTED: ribosome-releasing factor 2,	0.597	0.158	0.515	2e-33
332030184	753	Ribosome-releasing factor 2, mitochondri	0.524	0.154	0.594	9e-33
189239328	740	PREDICTED: similar to mitochondrial elon	0.552	0.164	0.564	1e-32
350409609	845	PREDICTED: ribosome-releasing factor 2,	0.597	0.156	0.507	2e-32

>gi|307205784|gb|EFN84014.1| Elongation factor G 2, mitochondrial [Harpegnathos saltator]

 Score =  159 bits (403), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 74/116 (63%), Positives = 89/116 (76%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
           VPV+ GSSYKN+GVQ LMD ++  LPSP     L+ ++HFGDSL AR FK+VHDKH+G V
Sbjct: 290 VPVMLGSSYKNVGVQPLMDNVILYLPSPGNLKKLSSYRHFGDSLAARVFKIVHDKHKGPV 349

Query: 118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173
           TFFRIYSG+ KKGQK YN+   QSEQ T L +A A+DY+EV E+  GNIAAV GLK
Sbjct: 350 TFFRIYSGSMKKGQKLYNVTRQQSEQCTYLYIACANDYEEVTEVSYGNIAAVAGLK 405

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328701929|ref|XP_001944132.2| PREDICTED: ribosome-releasing factor 2, mitochondrial-like [Acyrthosiphon pisum]

 Score =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 72/116 (62%), Positives = 87/116 (75%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
           VP+ CGSSYKNIGVQ LMD I+D LPSP +   L  F+ FG S+ ARAFK+VH+K +G V
Sbjct: 287 VPLFCGSSYKNIGVQTLMDGIIDYLPSPNDCITLDPFKFFGTSMSARAFKIVHEKQKGPV 346

Query: 118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173
           TF RIY+G  +KGQK YN    +SE I R+++A ADDYKEVN +Q GNI AVTGLK
Sbjct: 347 TFLRIYTGTLEKGQKLYNASQSKSENINRVMIAYADDYKEVNNVQSGNIVAVTGLK 402

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307191029|gb|EFN74783.1| Elongation factor G 2, mitochondrial [Camponotus floridanus]

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 73/122 (59%), Positives = 91/122 (74%)

Query: 52  AFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHD 111
              K  VPV+ GSSYKNIGVQ LMD+++  LPSP     L  +++F ++L AR FK+VHD
Sbjct: 285 TISKKGVPVILGSSYKNIGVQPLMDSVILYLPSPANIKHLNPYKYFDNNLAARVFKIVHD 344

Query: 112 KHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTG 171
           K RG +TFFRIYSG+ KKGQK YN+  +QSEQ TRL +A ADDY+EV E++ GNIAAV G
Sbjct: 345 KQRGPITFFRIYSGSMKKGQKLYNMTREQSEQCTRLYIACADDYEEVAEVRLGNIAAVGG 404

Query: 172 LK 173
           LK
Sbjct: 405 LK 406

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340713650|ref|XP_003395353.1| PREDICTED: ribosome-releasing factor 2, mitochondrial-like [Bombus terrestris]

 Score =  152 bits (385), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 68/132 (51%), Positives = 93/132 (70%)

Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFK 107
           ++     +  VPVL GSSYKNIGVQ LMD+++  LPSP +  + A ++ F D +CARAFK
Sbjct: 281 LHRSTISRKGVPVLLGSSYKNIGVQPLMDSVLLYLPSPNKTKSSAYYRCFSDKVCARAFK 340

Query: 108 VVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167
           +VHDK +G +TFFRIYSG+ KKG K YN+  ++ E + +L +A AD+Y+E+  I CGNIA
Sbjct: 341 IVHDKQKGPITFFRIYSGSLKKGMKLYNVRKEEKELVGKLYIAYADEYQEIPNITCGNIA 400

Query: 168 AVTGLKRERGKD 179
           A+TGLK     D
Sbjct: 401 AITGLKSTTAGD 412

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322792141|gb|EFZ16193.1| hypothetical protein SINV_02354 [Solenopsis invicta]

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 74/116 (63%), Positives = 87/116 (75%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
           VPVL GSSYKNIGVQ LMD+++  LPSP     L  ++ F ++L AR FKVVHDK RG +
Sbjct: 243 VPVLLGSSYKNIGVQPLMDSVILYLPSPPNVDRLNPYRCFENNLAARIFKVVHDKQRGPI 302

Query: 118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173
           TFFRIYSG  KKGQK YN+  +QSEQ TRL +A ADDY+EV E+  GNIAAV GLK
Sbjct: 303 TFFRIYSGNMKKGQKLYNVTREQSEQCTRLYIACADDYEEVGEVSYGNIAAVAGLK 358

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383859899|ref|XP_003705429.1| PREDICTED: LOW QUALITY PROTEIN: ribosome-releasing factor 2, mitochondrial-like [Megachile rotundata]

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 68/132 (51%), Positives = 90/132 (68%)

Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFK 107
           +Y     +  VPVL GSSYKNIGVQ LMDA++  LPSP E   L  +  F ++L AR FK
Sbjct: 281 LYRSTISRKAVPVLLGSSYKNIGVQPLMDAVLLYLPSPNENKYLKYYNTFNNNLSARVFK 340

Query: 108 VVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167
           V+HDK RG ++F R+Y+G+ ++  K YNIH +Q EQ+ RL +A ADDY+EV+++  GNIA
Sbjct: 341 VIHDKQRGPISFLRVYTGSIERHNKLYNIHKEQREQVNRLYVACADDYQEVSKVTHGNIA 400

Query: 168 AVTGLKRERGKD 179
           AV GLK     D
Sbjct: 401 AVAGLKTTTTGD 412

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328784337|ref|XP_392362.3| PREDICTED: ribosome-releasing factor 2, mitochondrial-like [Apis mellifera]

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 68/132 (51%), Positives = 90/132 (68%)

Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFK 107
           ++     K  +PVL GSSYKNIGVQ LMD+I+  LPSP        +Q F + LCARAFK
Sbjct: 280 LHRATINKKGIPVLLGSSYKNIGVQPLMDSILLYLPSPNASKHSKYYQCFDNKLCARAFK 339

Query: 108 VVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167
           VVHDK +G +TFFRIYSG+ +KG K YN+  ++ EQ+ +L +A AD+Y+E+ +I  GNIA
Sbjct: 340 VVHDKQKGPITFFRIYSGSIEKGTKLYNLRTEKKEQVGKLYIAYADEYEEIKQISQGNIA 399

Query: 168 AVTGLKRERGKD 179
           A+TGL      D
Sbjct: 400 AITGLTSTSAGD 411

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332030184|gb|EGI69978.1| Ribosome-releasing factor 2, mitochondrial [Acromyrmex echinatior]

 Score =  145 bits (367), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 69/116 (59%), Positives = 86/116 (74%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
           VP++ GSSYKNIGVQ LMD+++  LPSP     L  ++ F ++L AR FK+VHDK RG +
Sbjct: 291 VPIMLGSSYKNIGVQPLMDSVILYLPSPMNVYQLNPYRCFENNLAARVFKIVHDKQRGPI 350

Query: 118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173
           TFFRIYSG  KKGQK YN+   Q EQ TRL +A AD+Y+EV E+  GNIAAV+GLK
Sbjct: 351 TFFRIYSGNMKKGQKLYNVTRGQIEQCTRLYIACADNYEEVTEVSYGNIAAVSGLK 406

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189239328|ref|XP_973240.2| PREDICTED: similar to mitochondrial elongation factor G2 [Tribolium castaneum]

 Score =  145 bits (366), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 70/124 (56%), Positives = 90/124 (72%), Gaps = 2/124 (1%)

Query: 50  SGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVV 109
           S   K+  VPVL GS+YKNIG+Q LMD+I+  LPSP+ER     F  F ++LCARAFKV 
Sbjct: 277 SVTLKQKAVPVLMGSAYKNIGIQPLMDSILLYLPSPSERDT--HFSSFEENLCARAFKVR 334

Query: 110 HDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV 169
           HDK +G +TFFRIY+G F K Q+ Y+I  +Q+EQ  +L +A ADD+KEV+ I  GNIA V
Sbjct: 335 HDKQKGPLTFFRIYNGKFNKNQRIYSIQQEQTEQCGKLYVAYADDFKEVDSIGTGNIAVV 394

Query: 170 TGLK 173
           +GLK
Sbjct: 395 SGLK 398

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350409609|ref|XP_003488792.1| PREDICTED: ribosome-releasing factor 2, mitochondrial-like [Bombus impatiens]

 Score =  145 bits (365), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 67/132 (50%), Positives = 91/132 (68%)

Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFK 107
           ++     +  VPVL GSSYKNIGVQ LMD ++  LPSP +  + A ++ F D LCARAFK
Sbjct: 281 LHRSTISRKGVPVLLGSSYKNIGVQPLMDGVLLYLPSPNKTKSSAYYRCFDDKLCARAFK 340

Query: 108 VVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167
           VVHDK +G +TFFRIYSG+ +KG K YN+  ++ E + +L +A AD+Y+E+ +I  GNIA
Sbjct: 341 VVHDKQKGPITFFRIYSGSVEKGMKLYNVRKEEKELVGKLYIAYADEYQEIPKITRGNIA 400

Query: 168 AVTGLKRERGKD 179
           A+ GLK     D
Sbjct: 401 AIMGLKSTTAGD 412

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	221
ZFIN|ZDB-GENE-060201-3	762	gfm2 "G elongation factor, mit	0.524	0.152	0.504	1.1e-23
UNIPROTKB|Q969S9	779	GFM2 "Ribosome-releasing facto	0.520	0.147	0.508	1.5e-23
UNIPROTKB|E2R4T4	780	GFM2 "Uncharacterized protein"	0.520	0.147	0.525	2.4e-23
UNIPROTKB|E1C430	782	GFM2 "Uncharacterized protein"	0.597	0.168	0.477	3.1e-23
UNIPROTKB|F1S2J6	777	GFM2 "Uncharacterized protein"	0.520	0.148	0.525	6.5e-23
UNIPROTKB|Q5R600	777	GFM2 "Ribosome-releasing facto	0.520	0.148	0.5	8.3e-23
UNIPROTKB|A6QNM2	777	GFM2 "Ribosome-releasing facto	0.615	0.175	0.457	1.1e-22
UNIPROTKB|D4A0Y8	741	Gfm2 "Ribosome-releasing facto	0.524	0.156	0.478	1.2e-22
MGI|MGI:2444783	779	Gfm2 "G elongation factor, mit	0.524	0.148	0.495	1.4e-22
RGD|1309854	779	Gfm2 "G elongation factor, mit	0.524	0.148	0.478	1.4e-22

ZFIN|ZDB-GENE-060201-3 gfm2 "G elongation factor, mitochondrial 2" [Danio rerio (taxid:7955)]

 Score = 282 (104.3 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 59/117 (50%), Positives = 78/117 (66%)

Query:    58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
             VPVLCGSS KN GVQ L+DAI   LP+P ER    + + + + LCA AFKVVHDK RG +
Sbjct:   313 VPVLCGSSLKNKGVQPLLDAITAYLPAPNERNH-DLVRWYKNDLCALAFKVVHDKQRGPL 371

Query:   118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKR 174
              F RIYSG+ K     +NI+ +++E+++RLLL  AD   E+  +  GNIA   GLK+
Sbjct:   372 VFVRIYSGSMKAQSSVHNINRNETEKMSRLLLPFADQQIEIPSLSAGNIALTVGLKQ 428

GO:0005525 "GTP binding" evidence=IEA

GO:0003924 "GTPase activity" evidence=IEA;ISS

GO:0032543 "mitochondrial translation" evidence=ISS

GO:0005739 "mitochondrion" evidence=IEA;ISS

GO:0032790 "ribosome disassembly" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|Q969S9 GFM2 "Ribosome-releasing factor 2, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 281 (104.0 bits), Expect = 1.5e-23, P = 1.5e-23
 Identities = 59/116 (50%), Positives = 75/116 (64%)

Query:    58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
             VPVLCGS+ KN G+Q L+DA+   LPSP ER      Q + D LCA AFKV+HDK RG +
Sbjct:   325 VPVLCGSALKNKGIQPLLDAVTMYLPSPEERN-YEFLQWYKDDLCALAFKVLHDKQRGPL 383

Query:   118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173
              F RIYSG  K     +NI+ + +E+I+RLLL  AD + E+  +  GNIA   GLK
Sbjct:   384 VFMRIYSGTIKPQLAIHNINGNCTERISRLLLPFADQHVEIPSLTAGNIALTVGLK 439

GO:0005525 "GTP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0003746 "translation elongation factor activity" evidence=IDA

GO:0070125 "mitochondrial translational elongation" evidence=IDA

GO:0032790 "ribosome disassembly" evidence=IDA

GO:0032543 "mitochondrial translation" evidence=IDA

GO:0003924 "GTPase activity" evidence=IDA

GO:0006184 "GTP catabolic process" evidence=IDA

UNIPROTKB|E2R4T4 GFM2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 279 (103.3 bits), Expect = 2.4e-23, P = 2.4e-23
 Identities = 61/116 (52%), Positives = 76/116 (65%)

Query:    58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
             VPVLCGS+ KN GVQ L+DAI   LPSP ER    +  + GD LCA +FKV+HDK RG +
Sbjct:   325 VPVLCGSALKNKGVQPLLDAITMYLPSPEERNYEFLQWYKGD-LCALSFKVLHDKQRGPL 383

Query:   118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173
              F RIYSG  K     YNI+ + +E+I+RLLL  AD + E+  +  GNIA   GLK
Sbjct:   384 VFMRIYSGTIKPQSAIYNINGNCTERISRLLLPFADQHIEIPSLTAGNIALTVGLK 439

GO:0005525 "GTP binding" evidence=IEA

GO:0003924 "GTPase activity" evidence=IEA

UNIPROTKB|E1C430 GFM2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 278 (102.9 bits), Expect = 3.1e-23, P = 3.1e-23
 Identities = 64/134 (47%), Positives = 82/134 (61%)

Query:    58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
             VPVLCGS+ KN GVQ L+DAI   LP+P ER    +  +  D LCA AFKV+HDK RG +
Sbjct:   327 VPVLCGSALKNKGVQPLLDAITMYLPAPHERSYEFLQWYKDDDLCALAFKVLHDKSRGPL 386

Query:   118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERG 177
              F RIYSG+ K     YNI+   +E+++RLLL  AD   E+  +  GNIA   GLK+   
Sbjct:   387 VFIRIYSGSLKPQSAVYNINKSCTERMSRLLLPFADQQIEIPSLMPGNIALAVGLKQSAT 446

Query:   178 KDKRTRVIPKPTSV 191
              D  T V  K ++V
Sbjct:   447 GD--TLVSSKASAV 458

GO:0003924 "GTPase activity" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0032543 "mitochondrial translation" evidence=IEA

GO:0032790 "ribosome disassembly" evidence=IEA

UNIPROTKB|F1S2J6 GFM2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 275 (101.9 bits), Expect = 6.5e-23, P = 6.5e-23
 Identities = 61/116 (52%), Positives = 76/116 (65%)

Query:    58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
             VPVLCGS+ KN GVQ L+DAI   LPSP ER    +  + GD LCA AFKV+HDK RG +
Sbjct:   325 VPVLCGSALKNKGVQPLLDAITMYLPSPEERNYEFLQWYKGD-LCALAFKVLHDKQRGPL 383

Query:   118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173
              F RIYSG  K     +NI+ + +E+I+RLLL  AD + E+  +  GNIA   GLK
Sbjct:   384 VFMRIYSGMIKPQLAIHNINGNCTERISRLLLPFADQHVEIPSLTAGNIALTVGLK 439

GO:0032790 "ribosome disassembly" evidence=IEA

GO:0032543 "mitochondrial translation" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

GO:0003924 "GTPase activity" evidence=IEA

UNIPROTKB|Q5R600 GFM2 "Ribosome-releasing factor 2, mitochondrial" [Pongo abelii (taxid:9601)]

 Score = 274 (101.5 bits), Expect = 8.3e-23, P = 8.3e-23
 Identities = 58/116 (50%), Positives = 74/116 (63%)

Query:    58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
             VPVLCGS+ KN G+Q L+DA+   LPSP E       Q + D LCA AFKV+HDK RG +
Sbjct:   325 VPVLCGSALKNKGIQPLLDAVTMYLPSPEECNC-EFLQWYKDDLCALAFKVLHDKQRGPL 383

Query:   118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173
              F RIYSG  K     +NI+ + +E+I+RLLL  AD + E+  +  GNIA   GLK
Sbjct:   384 VFMRIYSGTIKPQLAIHNINGNCTERISRLLLPFADQHVEIPSLTAGNIALTVGLK 439

GO:0003924 "GTPase activity" evidence=ISS

GO:0006184 "GTP catabolic process" evidence=ISS

GO:0032543 "mitochondrial translation" evidence=ISS

GO:0032790 "ribosome disassembly" evidence=ISS

UNIPROTKB|A6QNM2 GFM2 "Ribosome-releasing factor 2, mitochondrial" [Bos taurus (taxid:9913)]

 Score = 273 (101.2 bits), Expect = 1.1e-22, P = 1.1e-22
 Identities = 64/140 (45%), Positives = 84/140 (60%)

Query:    58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
             VPVLCGS+ KN GVQ L+DAI   LPSP ER    +  + GD LCA AFKV+HDK RG +
Sbjct:   325 VPVLCGSALKNKGVQPLLDAITMYLPSPEERNYEFLQWYKGD-LCALAFKVLHDKQRGPL 383

Query:   118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERG 177
              F RIYSG  K     +NI+ + +E+++RLLL  AD + E+  +  GNIA   GLK    
Sbjct:   384 VFMRIYSGMLKPQTAIHNINGNCTERVSRLLLPFADQHIEIPLLTAGNIALTVGLKHTAT 443

Query:   178 KDKRTRVIPKPTSVVQCSAR 197
              D    ++   +S +  S R
Sbjct:   444 GDT---IVSSRSSALAASRR 460

GO:0003924 "GTPase activity" evidence=ISS

GO:0032790 "ribosome disassembly" evidence=ISS

GO:0032543 "mitochondrial translation" evidence=ISS

GO:0005739 "mitochondrion" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

UNIPROTKB|D4A0Y8 Gfm2 "Ribosome-releasing factor 2, mitochondrial" [Rattus norvegicus (taxid:10116)]

 Score = 272 (100.8 bits), Expect = 1.2e-22, P = 1.2e-22
 Identities = 56/117 (47%), Positives = 74/117 (63%)

Query:    58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
             VPVLCGS+ KN GVQ L+DA+   LPSP ER      Q +   LCA AFKV+HDK RG +
Sbjct:   325 VPVLCGSALKNKGVQPLLDAVTTYLPSPEEREH-GFLQWYKGDLCALAFKVLHDKQRGPL 383

Query:   118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKR 174
              F RIYSG        +N++ + +E+++RLLL  AD + E+  +  GNIA   GLK+
Sbjct:   384 VFLRIYSGTLTPQSAVHNVNRNCTERMSRLLLPFADQHVEIPSLTAGNIALTVGLKQ 440

GO:0003924 "GTPase activity" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

MGI|MGI:2444783 Gfm2 "G elongation factor, mitochondrial 2" [Mus musculus (taxid:10090)]

 Score = 272 (100.8 bits), Expect = 1.4e-22, P = 1.4e-22
 Identities = 58/117 (49%), Positives = 76/117 (64%)

Query:    58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
             VPVLCGS+ KN GVQ L+DA+   LPSP ER    +  + GD LCA AFKV+HDK RG +
Sbjct:   325 VPVLCGSALKNKGVQPLLDAVTTYLPSPEEREDRFLQWYEGD-LCALAFKVLHDKQRGPL 383

Query:   118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKR 174
              F RIYSG        +NI+ + +E+++RLLL  AD + E+  +  GNIA   GLK+
Sbjct:   384 VFLRIYSGTLTPQLAVHNINRNCTERMSRLLLPFADQHVEIPSLTAGNIALTVGLKQ 440

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003924 "GTPase activity" evidence=ISO

GO:0005525 "GTP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0006184 "GTP catabolic process" evidence=ISO

GO:0006412 "translation" evidence=IEA

GO:0032543 "mitochondrial translation" evidence=ISO

GO:0032790 "ribosome disassembly" evidence=ISO

RGD|1309854 Gfm2 "G elongation factor, mitochondrial 2" [Rattus norvegicus (taxid:10116)]

 Score = 272 (100.8 bits), Expect = 1.4e-22, P = 1.4e-22
 Identities = 56/117 (47%), Positives = 74/117 (63%)

Query:    58 VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
             VPVLCGS+ KN GVQ L+DA+   LPSP ER      Q +   LCA AFKV+HDK RG +
Sbjct:   325 VPVLCGSALKNKGVQPLLDAVTTYLPSPEEREH-GFLQWYKGDLCALAFKVLHDKQRGPL 383

Query:   118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKR 174
              F RIYSG        +N++ + +E+++RLLL  AD + E+  +  GNIA   GLK+
Sbjct:   384 VFLRIYSGTLTPQSAVHNVNRNCTERMSRLLLPFADQHVEIPSLTAGNIALTVGLKQ 440

GO:0003924 "GTPase activity" evidence=IEA;ISO;ISS

GO:0005525 "GTP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0006184 "GTP catabolic process" evidence=ISO;ISS

GO:0032543 "mitochondrial translation" evidence=ISO;ISS

GO:0032790 "ribosome disassembly" evidence=ISO;ISS

GO:0003746 "translation elongation factor activity" evidence=ISO

GO:0070125 "mitochondrial translational elongation" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	221
COG0480	697	COG0480, FusA, Translation elongation factors (GTP	5e-35
PRK00007	693	PRK00007, PRK00007, elongation factor G; Reviewed	5e-33
PRK12740	668	PRK12740, PRK12740, elongation factor G; Reviewed	2e-32
PRK12739	691	PRK12739, PRK12739, elongation factor G; Reviewed	1e-31
PRK13351	687	PRK13351, PRK13351, elongation factor G; Reviewed	8e-31
cd04092	83	cd04092, mtEFG2_II_like, mtEFG2_C: C-terminus of m	7e-28
TIGR00484	689	TIGR00484, EF-G, translation elongation factor EF-	6e-27
cd04088	83	cd04088, EFG_mtEFG_II, EFG_mtEFG_II: this subfamil	1e-24
cd01886	270	cd01886, EF-G, Elongation factor G (EF-G) family i	3e-12
PRK12740	668	PRK12740, PRK12740, elongation factor G; Reviewed	6e-11
cd04092	83	cd04092, mtEFG2_II_like, mtEFG2_C: C-terminus of m	2e-10
cd04091	81	cd04091, mtEFG1_II_like, mtEFG1_C: C-terminus of m	2e-10
COG0480	697	COG0480, FusA, Translation elongation factors (GTP	4e-10
cd01342	83	cd01342, Translation_Factor_II_like, Translation_F	1e-09
cd04088	83	cd04088, EFG_mtEFG_II, EFG_mtEFG_II: this subfamil	7e-09
PRK00007	693	PRK00007, PRK00007, elongation factor G; Reviewed	9e-09
PRK13351	687	PRK13351, PRK13351, elongation factor G; Reviewed	3e-08
TIGR00490	720	TIGR00490, aEF-2, translation elongation factor aE	9e-08
PRK12739	691	PRK12739, PRK12739, elongation factor G; Reviewed	2e-07
cd03690	85	cd03690, Tet_II, Tet_II: This subfamily represents	2e-07
cd03700	93	cd03700, eEF2_snRNP_like_II, EF2_snRNP_like_II: th	3e-07
COG4108	528	COG4108, PrfC, Peptide chain release factor RF-3 [	3e-07
TIGR00503	527	TIGR00503, prfC, peptide chain release factor 3	7e-07
TIGR01393	595	TIGR01393, lepA, GTP-binding protein LepA	8e-07
PRK07560	731	PRK07560, PRK07560, elongation factor EF-2; Review	9e-07
pfam03144	70	pfam03144, GTP_EFTU_D2, Elongation factor Tu domai	9e-07
TIGR00484	689	TIGR00484, EF-G, translation elongation factor EF-	1e-06
PRK00741	526	PRK00741, prfC, peptide chain release factor 3; Pr	1e-06
COG0481	603	COG0481, LepA, Membrane GTPase LepA [Cell envelope	1e-06
cd04170	268	cd04170, EF-G_bact, Elongation factor G (EF-G) fam	2e-06
PRK05433	600	PRK05433, PRK05433, GTP-binding protein LepA; Prov	3e-06
pfam00009	184	pfam00009, GTP_EFTU, Elongation factor Tu GTP bind	4e-05
cd03691	86	cd03691, BipA_TypA_II, BipA_TypA_II: domain II of	2e-04
cd04090	94	cd04090, eEF2_II_snRNP, Loc2 eEF2_C_snRNP, cd01514	7e-04
TIGR01394	594	TIGR01394, TypA_BipA, GTP-binding protein TypA/Bip	7e-04
COG1217	603	COG1217, TypA, Predicted membrane GTPase involved	0.001
cd04169	268	cd04169, RF3, Release Factor 3 (RF3) protein invol	0.002
cd01342	83	cd01342, Translation_Factor_II_like, Translation_F	0.003

>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]

 Score =  130 bits (329), Expect = 5e-35
 Identities = 53/128 (41%), Positives = 76/128 (59%), Gaps = 12/128 (9%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL----------AMFQHFGDS--LCARA 105
           VPVLCGS++KN GVQ L+DA+VD LPSP + P +          A+ +   D   L A  
Sbjct: 253 VPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPPIKGDLDDEIEKAVLRKASDEGPLSALV 312

Query: 106 FKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN 165
           FK++ D   G +TF R+YSG  K G +  N    + E++ RLLL   ++ +EV+E+  G+
Sbjct: 313 FKIMTDPFVGKLTFVRVYSGTLKSGSEVLNSTKGKKERVGRLLLMHGNEREEVDEVPAGD 372

Query: 166 IAAVTGLK 173
           I A+ GLK
Sbjct: 373 IVALVGLK 380

Length = 697

>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed

 Score =  124 bits (315), Expect = 5e-33
 Identities = 53/128 (41%), Positives = 74/128 (57%), Gaps = 12/128 (9%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS------------LCARA 105
           VPVLCGS++KN GVQ L+DA+VD LPSP + PA+      G+               A A
Sbjct: 255 VPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPAIKGILPDGEEEEVERKASDDEPFSALA 314

Query: 106 FKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN 165
           FK++ D   G +TFFR+YSG  + G    N    + E+I R+L   A+  +E+ E++ G+
Sbjct: 315 FKIMTDPFVGKLTFFRVYSGVLESGSYVLNSTKGKKERIGRILQMHANKREEIKEVRAGD 374

Query: 166 IAAVTGLK 173
           IAA  GLK
Sbjct: 375 IAAAVGLK 382

Length = 693

>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed

 Score =  123 bits (311), Expect = 2e-32
 Identities = 49/126 (38%), Positives = 65/126 (51%), Gaps = 9/126 (7%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS---------LCARAFKV 108
           VPV CGS+ KN GVQ+L+DA+VD LPSP E P +        +         L A  FK 
Sbjct: 237 VPVFCGSALKNKGVQRLLDAVVDYLPSPLEVPPVDGEDGEEGAELAPDPDGPLVALVFKT 296

Query: 109 VHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA 168
           + D   G ++  R+YSG  KKG   YN    + E++ RL        +EV+E   G+I A
Sbjct: 297 MDDPFVGKLSLVRVYSGTLKKGDTLYNSGTGKKERVGRLYRMHGKQREEVDEAVAGDIVA 356

Query: 169 VTGLKR 174
           V  LK 
Sbjct: 357 VAKLKD 362

Length = 668

>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed

 Score =  121 bits (305), Expect = 1e-31
 Identities = 53/129 (41%), Positives = 72/129 (55%), Gaps = 15/129 (11%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS-------------LCAR 104
            PVLCGS++KN GVQ L+DA+VD LPSP + PA  +     D+               A 
Sbjct: 253 FPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPA--IKGINPDTEEEIERPASDDEPFAAL 310

Query: 105 AFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCG 164
           AFK++ D   G +TFFR+YSG  + G    N    + E+I RLL   A+  +E+ E+  G
Sbjct: 311 AFKIMTDPFVGRLTFFRVYSGVLESGSYVLNTTKGKKERIGRLLQMHANKREEIKEVYAG 370

Query: 165 NIAAVTGLK 173
           +IAA  GLK
Sbjct: 371 DIAAAVGLK 379

Length = 691

>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed

 Score =  118 bits (298), Expect = 8e-31
 Identities = 51/139 (36%), Positives = 74/139 (53%), Gaps = 11/139 (7%)

Query: 52  AFKKNH-VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS---------- 100
             +  H VPVL GS+ KNIG++ L+DA+VD LPSP E P     +  G            
Sbjct: 246 GTRSGHLVPVLFGSALKNIGIEPLLDAVVDYLPSPLEVPPPRGSKDNGKPVKVDPDPEKP 305

Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
           L A  FKV +D + G +T+ R+YSG  + G + YN    + E++ RL   + +  +EV+ 
Sbjct: 306 LLALVFKVQYDPYAGKLTYLRVYSGTLRAGSQLYNGTGGKREKVGRLFRLQGNKREEVDR 365

Query: 161 IQCGNIAAVTGLKRERGKD 179
            + G+I AV GLK     D
Sbjct: 366 AKAGDIVAVAGLKELETGD 384

Length = 687

>gnl|CDD|239759 cd04092, mtEFG2_II_like, mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes

 Score =  100 bits (252), Expect = 7e-28
 Identities = 38/73 (52%), Positives = 49/73 (67%)

Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
           LCA AFKVVHD  RG +TF R+YSG  K+G   YN +  + E+I+RLL   AD Y+E+  
Sbjct: 1   LCALAFKVVHDPQRGPLTFVRVYSGTLKRGSALYNTNTGKKERISRLLQPFADQYQEIPS 60

Query: 161 IQCGNIAAVTGLK 173
           +  GNI  +TGLK
Sbjct: 61  LSAGNIGVITGLK 73

Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are not present in this group. Length = 83

>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G

 Score =  107 bits (269), Expect = 6e-27
 Identities = 52/127 (40%), Positives = 74/127 (58%), Gaps = 11/127 (8%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA---------MFQHFGDSL--CARAF 106
            PVLCGS++KN GVQ L+DA+VD LPSPT+ PA+          + +   D     A AF
Sbjct: 254 FPVLCGSAFKNKGVQLLLDAVVDYLPSPTDVPAIKGIDPDTEKEIERKASDDEPFSALAF 313

Query: 107 KVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
           KV  D   G +TF R+YSG  K G    N   ++ E++ RL+   A++ +E+ E++ G+I
Sbjct: 314 KVATDPFVGQLTFVRVYSGVLKSGSYVKNSRKNKKERVGRLVKMHANNREEIKEVRAGDI 373

Query: 167 AAVTGLK 173
            A  GLK
Sbjct: 374 CAAIGLK 380

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 [Protein synthesis, Translation factors]. Length = 689

>gnl|CDD|239755 cd04088, EFG_mtEFG_II, EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes

 Score = 92.2 bits (230), Expect = 1e-24
 Identities = 29/73 (39%), Positives = 38/73 (52%)

Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
             A  FK +HD   G ++F R+YSG  K G   YN    + E++ RLL       +EV E
Sbjct: 1   FVALVFKTIHDPFVGKLSFVRVYSGTLKAGSTLYNSTKGKKERVGRLLRMHGKKQEEVEE 60

Query: 161 IQCGNIAAVTGLK 173
              G+I AV GLK
Sbjct: 61  AGAGDIGAVAGLK 73

During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. mtEFG1 and mtEFG2 show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. Length = 83

>gnl|CDD|206673 cd01886, EF-G, Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis

 Score = 63.7 bits (156), Expect = 3e-12
 Identities = 21/28 (75%), Positives = 25/28 (89%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSP 85
           VPVLCGS++KN GVQ L+DA+VD LPSP
Sbjct: 243 VPVLCGSAFKNKGVQPLLDAVVDYLPSP 270

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 contains both eukaryotic and bacterial members. Length = 270

>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed

 Score = 60.9 bits (149), Expect = 6e-11
 Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 9/66 (13%)

Query: 1   MDAIVDILPSPTERPALAMFQHFGDS---------LCARAFKVVHDKHRGAVTFFRIYSG 51
           +DA+VD LPSP E P +        +         L A  FK + D   G ++  R+YSG
Sbjct: 254 LDAVVDYLPSPLEVPPVDGEDGEEGAELAPDPDGPLVALVFKTMDDPFVGKLSLVRVYSG 313

Query: 52  AFKKNH 57
             KK  
Sbjct: 314 TLKKGD 319

Length = 668

>gnl|CDD|239759 cd04092, mtEFG2_II_like, mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes

 Score = 54.9 bits (133), Expect = 2e-10
 Identities = 19/32 (59%), Positives = 22/32 (68%)

Query: 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHV 58
          LCA AFKVVHD  RG +TF R+YSG  K+   
Sbjct: 1  LCALAFKVVHDPQRGPLTFVRVYSGTLKRGSA 32

Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are not present in this group. Length = 83

>gnl|CDD|239758 cd04091, mtEFG1_II_like, mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes

 Score = 55.4 bits (134), Expect = 2e-10
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
               AFK+   +  G +T+ RIY G  KKG   YN+   +  ++ RL+   +++ +EV E
Sbjct: 1   FVGLAFKLEEGRF-GQLTYMRIYQGKLKKGDTIYNVRTGKKVRVPRLVRMHSNEMEEVEE 59

Query: 161 IQCGNIAAVTGLK 173
              G+I A+ G+ 
Sbjct: 60  AGAGDICAIFGID 72

Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG2s are not present in this group. Length = 81

>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]

 Score = 58.4 bits (142), Expect = 4e-10
 Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 12/67 (17%)

Query: 1   MDAIVDILPSPTERPAL----------AMFQHFGDS--LCARAFKVVHDKHRGAVTFFRI 48
           +DA+VD LPSP + P +          A+ +   D   L A  FK++ D   G +TF R+
Sbjct: 270 LDAVVDYLPSPLDVPPIKGDLDDEIEKAVLRKASDEGPLSALVFKIMTDPFVGKLTFVRV 329

Query: 49  YSGAFKK 55
           YSG  K 
Sbjct: 330 YSGTLKS 336

Length = 697

>gnl|CDD|238652 cd01342, Translation_Factor_II_like, Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins

 Score = 52.7 bits (127), Expect = 1e-09
 Identities = 23/77 (29%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD--QSEQITRLLLAEADDYKEV 158
           L A  FKV  DK RG V   R+ SG  KKG K            ++  L   +     EV
Sbjct: 1   LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFK----GEV 56

Query: 159 NEIQCGNIAAVTGLKRE 175
           +E   G+I  +    ++
Sbjct: 57  DEAVAGDIVGIVLKDKD 73

Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E.coli IF-2 to 30S subunits. Length = 83

>gnl|CDD|239755 cd04088, EFG_mtEFG_II, EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes

 Score = 50.9 bits (123), Expect = 7e-09
 Identities = 12/31 (38%), Positives = 16/31 (51%)

Query: 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNH 57
            A  FK +HD   G ++F R+YSG  K   
Sbjct: 1  FVALVFKTIHDPFVGKLSFVRVYSGTLKAGS 31

During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. mtEFG1 and mtEFG2 show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. Length = 83

>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed

 Score = 54.4 bits (132), Expect = 9e-09
 Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 12/66 (18%)

Query: 2   DAIVDILPSPTERPALAMFQHFGDS------------LCARAFKVVHDKHRGAVTFFRIY 49
           DA+VD LPSP + PA+      G+               A AFK++ D   G +TFFR+Y
Sbjct: 273 DAVVDYLPSPLDVPAIKGILPDGEEEEVERKASDDEPFSALAFKIMTDPFVGKLTFFRVY 332

Query: 50  SGAFKK 55
           SG  + 
Sbjct: 333 SGVLES 338

Length = 693

>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed

 Score = 53.0 bits (128), Expect = 3e-08
 Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 10/65 (15%)

Query: 2   DAIVDILPSPTERPALAMFQHFGDS----------LCARAFKVVHDKHRGAVTFFRIYSG 51
           DA+VD LPSP E P     +  G            L A  FKV +D + G +T+ R+YSG
Sbjct: 271 DAVVDYLPSPLEVPPPRGSKDNGKPVKVDPDPEKPLLALVFKVQYDPYAGKLTYLRVYSG 330

Query: 52  AFKKN 56
             +  
Sbjct: 331 TLRAG 335

Length = 687

>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2

 Score = 51.4 bits (123), Expect = 9e-08
 Identities = 26/67 (38%), Positives = 37/67 (55%)

Query: 107 KVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
           K+V DKH G V   R+YSG  + G + Y +      +I ++ +    +  EV+EI  GNI
Sbjct: 296 KIVVDKHAGEVAVGRLYSGTIRPGMEVYIVDRKAKARIQQVGVYMGPERVEVDEIPAGNI 355

Query: 167 AAVTGLK 173
            AV GLK
Sbjct: 356 VAVIGLK 362

This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD [Protein synthesis, Translation factors]. Length = 720

>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed

 Score = 50.6 bits (122), Expect = 2e-07
 Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 15/68 (22%)

Query: 1   MDAIVDILPSPTERPALAMFQHFGDS-------------LCARAFKVVHDKHRGAVTFFR 47
           +DA+VD LPSP + PA  +     D+               A AFK++ D   G +TFFR
Sbjct: 270 LDAVVDYLPSPLDVPA--IKGINPDTEEEIERPASDDEPFAALAFKIMTDPFVGRLTFFR 327

Query: 48  IYSGAFKK 55
           +YSG  + 
Sbjct: 328 VYSGVLES 335

Length = 691

>gnl|CDD|239661 cd03690, Tet_II, Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O)

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 98  GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKE 157
              L    FK+  D     + + R+YSG  +  +    ++ ++  +IT L +    +   
Sbjct: 1   ESELSGTVFKIERDDKGERLAYLRLYSGTLRL-RDSVRVNREEKIKITELRVFNNGEVVT 59

Query: 158 VNEIQCGNIAAVTGLK 173
            + +  G+IA +TGLK
Sbjct: 60  ADTVTAGDIAILTGLK 75

This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. Length = 85

>gnl|CDD|239671 cd03700, eEF2_snRNP_like_II, EF2_snRNP_like_II: this subfamily represents domain II of elongation factor (EF) EF-2 found eukaryotes and archaea and, the C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 10/77 (12%)

Query: 107 KVVHDK-HRGAVTFFRIYSGAFKKGQKFY----NIHLDQSE-----QITRLLLAEADDYK 156
           K+V      G + F R++SG  +KGQK      N   +  E      I RL L      +
Sbjct: 7   KMVPTPDKGGFIAFGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYRE 66

Query: 157 EVNEIQCGNIAAVTGLK 173
            V+E+  GNI  + GL 
Sbjct: 67  PVDEVPAGNIVLIVGLD 83

During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. Length = 93

>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]

 Score = 49.9 bits (120), Expect = 3e-07
 Identities = 36/112 (32%), Positives = 54/112 (48%), Gaps = 4/112 (3%)

Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSPTERPA-LAMFQHFGDSLCARAFKV---VHDKHR 114
           PV  GS+  N GV   +DA+VD  PSP  R A     +   D      FK+   +  KHR
Sbjct: 252 PVFFGSALGNFGVDHFLDALVDWAPSPRARQADTREVEPTEDKFSGFVFKIQANMDPKHR 311

Query: 115 GAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
             + F R+ SG F++G K  ++   +  +++  L   A D + V E   G+I
Sbjct: 312 DRIAFMRVCSGKFERGMKVTHVRTGKDVKLSDALTFMAQDRETVEEAYAGDI 363

Length = 528

>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3

 Score = 48.7 bits (116), Expect = 7e-07
 Identities = 34/119 (28%), Positives = 50/119 (42%), Gaps = 18/119 (15%)

Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSPTER--------PALAMFQHFGDSLCARAFKV-- 108
           PV  G++  N GV   +D ++   P P  R        P    F  F        FK+  
Sbjct: 251 PVFFGTALGNFGVDHFLDGLLQWAPKPEARQSDTRTVEPTEEKFSGF-------VFKIQA 303

Query: 109 -VHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
            +  KHR  V F R+ SG ++KG K  ++   +   I+  L   A D + V E   G+I
Sbjct: 304 NMDPKHRDRVAFMRVVSGKYEKGMKLKHVRTGKDVVISDALTFMAGDREHVEEAYAGDI 362

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 [Protein synthesis, Translation factors]. Length = 527

>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA

 Score = 48.5 bits (116), Expect = 8e-07
 Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 8/88 (9%)

Query: 60  VLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTF 119
            +  S+   IG++++++AIV  +P P   P           L A  F   +D +RG V  
Sbjct: 157 AILASAKTGIGIEEILEAIVKRVPPPKGDP--------DAPLKALIFDSHYDNYRGVVAL 208

Query: 120 FRIYSGAFKKGQKFYNIHLDQSEQITRL 147
            R++ G  K G K   +   +  ++  +
Sbjct: 209 VRVFEGTIKPGDKIRFMSTGKEYEVDEV 236

LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function is unknown [Unknown function, General]. Length = 595

>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed

 Score = 48.7 bits (117), Expect = 9e-07
 Identities = 26/70 (37%), Positives = 41/70 (58%)

Query: 107 KVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
            ++ D H G V   R++SG  +KGQ+ Y +   +  ++ ++ +    + +EV EI  GNI
Sbjct: 297 DIIVDPHAGEVATGRVFSGTLRKGQEVYLVGAKKKNRVQQVGIYMGPEREEVEEIPAGNI 356

Query: 167 AAVTGLKRER 176
           AAVTGLK  R
Sbjct: 357 AAVTGLKDAR 366

Length = 731

>gnl|CDD|217388 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2

 Score = 44.5 bits (106), Expect = 9e-07
 Identities = 19/61 (31%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 115 GAVTFFRIYSGAFKKGQKFYNIHL--DQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGL 172
           G V   R+ SG  KKG K         +  ++T L +   D  + V     G I A  GL
Sbjct: 1   GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60

Query: 173 K 173
           K
Sbjct: 61  K 61

Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to pfam03143, and in fact has weak sequence matches to this domain. Length = 70

>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G

 Score = 48.3 bits (115), Expect = 1e-06
 Identities = 31/84 (36%), Positives = 39/84 (46%), Gaps = 18/84 (21%)

Query: 1   MDAIVDILPSPTERPALA---------MFQHFGDSL--CARAFKVVHDKHRGAVTFFRIY 49
           +DA+VD LPSPT+ PA+          + +   D     A AFKV  D   G +TF R+Y
Sbjct: 271 LDAVVDYLPSPTDVPAIKGIDPDTEKEIERKASDDEPFSALAFKVATDPFVGQLTFVRVY 330

Query: 50  SGAFKKNHVPVLCGSSYKNIGVQK 73
           SG  K        GS  KN    K
Sbjct: 331 SGVLKS-------GSYVKNSRKNK 347

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 [Protein synthesis, Translation factors]. Length = 689

>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional

 Score = 48.2 bits (116), Expect = 1e-06
 Identities = 27/78 (34%), Positives = 39/78 (50%), Gaps = 4/78 (5%)

Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA-MFQHFGDSLCARAFKV---VHDKHR 114
           PV  GS+  N GVQ+ +DA V+  P+P  R       +   +      FK+   +  KHR
Sbjct: 250 PVFFGSALNNFGVQEFLDAFVEWAPAPQPRQTDEREVEPTEEKFSGFVFKIQANMDPKHR 309

Query: 115 GAVTFFRIYSGAFKKGQK 132
             + F R+ SG F+KG K
Sbjct: 310 DRIAFVRVCSGKFEKGMK 327

Length = 526

>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]

 Score = 47.9 bits (115), Expect = 1e-06
 Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 9/89 (10%)

Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVT 118
            VL  S+   IG++ +++AIV+ +P P   P           L A  F   +D + G V 
Sbjct: 163 AVLV-SAKTGIGIEDVLEAIVEKIPPPKGDP--------DAPLKALIFDSWYDNYLGVVV 213

Query: 119 FFRIYSGAFKKGQKFYNIHLDQSEQITRL 147
             RI+ G  KKG K   +   +  ++  +
Sbjct: 214 LVRIFDGTLKKGDKIRMMSTGKEYEVDEV 242

Length = 603

>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family

 Score = 46.8 bits (112), Expect = 2e-06
 Identities = 15/28 (53%), Positives = 22/28 (78%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSP 85
           VPV  GS+   IGV++L+DA+V++ PSP
Sbjct: 241 VPVFFGSALTGIGVRRLLDALVELAPSP 268

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 contains only bacterial members. Length = 268

>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional

 Score = 47.0 bits (113), Expect = 3e-06
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 16/68 (23%)

Query: 69  IGVQKLMDAIVDILPSPT---ERPALAM-FQHFGDSLCARAFKVVHDKHRGAVTFFRIYS 124
           IG++++++AIV+ +P P    + P  A+ F    DS         +D +RG V   R+  
Sbjct: 170 IGIEEVLEAIVERIPPPKGDPDAPLKALIF----DS--------WYDNYRGVVVLVRVVD 217

Query: 125 GAFKKGQK 132
           G  KKG K
Sbjct: 218 GTLKKGDK 225

Length = 600

>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain

 Score = 42.5 bits (101), Expect = 4e-05
 Identities = 12/33 (36%), Positives = 19/33 (57%)

Query: 52  AFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84
            F    VPV+ GS+    G+ +L++A+   LPS
Sbjct: 152 GFGGETVPVVPGSALTGEGIDELLEALDLYLPS 184

This domain contains a P-loop motif, also found in several other families such as pfam00071, pfam00025 and pfam00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains. Length = 184

>gnl|CDD|239662 cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu

 Score = 38.6 bits (91), Expect = 2e-04
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 121 RIYSGAFKKGQKFYNIHLDQSEQ---ITRLLLAEADDYKEVNEIQCGNIAAVTGL 172
           RI+ G  K GQ+   +  D   +   IT+L   E     EV E + G+I A+ G+
Sbjct: 21  RIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVEVEEAEAGDIVAIAGI 75

BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion. Length = 86

>gnl|CDD|239757 cd04090, eEF2_II_snRNP, Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p

 Score = 37.2 bits (87), Expect = 7e-04
 Identities = 26/65 (40%), Positives = 29/65 (44%), Gaps = 11/65 (16%)

Query: 118 TFFRIYSGAFKKGQKFY----NIHLD-----QSEQITRLLLAEADDYK-EVNEIQCGNIA 167
            F RIYSG  KKGQK      N  LD         I RL +     YK EVNE   GN  
Sbjct: 19  AFGRIYSGTIKKGQKVKVLGENYSLDDEEDMTICTIGRLWILGG-RYKIEVNEAPAGNWV 77

Query: 168 AVTGL 172
            + G+
Sbjct: 78  LIKGI 82

This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Length = 94

>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA

 Score = 40.0 bits (94), Expect = 7e-04
 Identities = 29/102 (28%), Positives = 48/102 (47%), Gaps = 11/102 (10%)

Query: 74  LMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKF 133
           L DAIV  +P+P         Q            + +D++ G +   R++ G  KKGQ+ 
Sbjct: 182 LFDAIVRHVPAPKGDLD-EPLQ-------MLVTNLDYDEYLGRIAIGRVHRGTVKKGQQV 233

Query: 134 YNIHLDQSEQ---ITRLLLAEADDYKEVNEIQCGNIAAVTGL 172
             +  D + +   I++LL  E  +  E++E   G+I AV GL
Sbjct: 234 ALMKRDGTIENGRISKLLGFEGLERVEIDEAGAGDIVAVAGL 275

This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP-binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown [Regulatory functions, Other, Cellular processes, Adaptations to atypical conditions, Protein synthesis, Translation factors]. Length = 594

>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]

 Score = 39.1 bits (92), Expect = 0.001
 Identities = 26/102 (25%), Positives = 43/102 (42%), Gaps = 11/102 (10%)

Query: 74  LMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKF 133
           L + I+D +P+P         Q     L   ++        G +   RI+ G  K  Q+ 
Sbjct: 186 LFETILDHVPAPKGDLD-EPLQMQVTQLDYNSY-------VGRIGIGRIFRGTVKPNQQV 237

Query: 134 YNIHLDQSE---QITRLLLAEADDYKEVNEIQCGNIAAVTGL 172
             I  D +    +IT+LL     +  E+ E + G+I A+ GL
Sbjct: 238 ALIKSDGTTENGRITKLLGFLGLERIEIEEAEAGDIVAIAGL 279

Length = 603

>gnl|CDD|206732 cd04169, RF3, Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 14/27 (51%), Positives = 19/27 (70%)

Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSP 85
           PV  GS+  N GVQ+L+DA V + P+P
Sbjct: 242 PVFFGSALNNFGVQELLDAFVKLAPAP 268

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. Length = 268

>gnl|CDD|238652 cd01342, Translation_Factor_II_like, Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins

 Score = 35.0 bits (81), Expect = 0.003
 Identities = 17/43 (39%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNI 69
          L A  FKV  DK RG V   R+ SG  KK    V  G     +
Sbjct: 1  LRALVFKVFKDKGRGTVATGRVESGTLKKGDK-VRVGPGGGGV 42

Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E.coli IF-2 to 30S subunits. Length = 83

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	221
KOG0465|consensus	721		100.0
PRK00007	693	elongation factor G; Reviewed	100.0
TIGR00503	527	prfC peptide chain release factor 3. This translat	100.0
TIGR00484	689	EF-G translation elongation factor EF-G. After pep	100.0
PRK00741	526	prfC peptide chain release factor 3; Provisional	100.0
PRK12739	691	elongation factor G; Reviewed	100.0
PRK13351	687	elongation factor G; Reviewed	100.0
COG0480	697	FusA Translation elongation factors (GTPases) [Tra	100.0
PRK12740	668	elongation factor G; Reviewed	99.97
PRK10218	607	GTP-binding protein; Provisional	99.95
PRK07560	731	elongation factor EF-2; Reviewed	99.95
TIGR01394	594	TypA_BipA GTP-binding protein TypA/BipA. This bact	99.95
TIGR01393	595	lepA GTP-binding protein LepA. LepA (GUF1 in Sacca	99.94
PRK05433	600	GTP-binding protein LepA; Provisional	99.94
TIGR00490	720	aEF-2 translation elongation factor aEF-2. This mo	99.93
COG4108	528	PrfC Peptide chain release factor RF-3 [Translatio	99.92
PLN00116	843	translation elongation factor EF-2 subunit; Provis	99.92
PTZ00416	836	elongation factor 2; Provisional	99.91
COG0481	603	LepA Membrane GTPase LepA [Cell envelope biogenesi	99.91
COG1217	603	TypA Predicted membrane GTPase involved in stress	99.89
KOG0464|consensus	753		99.88
cd03690	85	Tet_II Tet_II: This subfamily represents domain II	99.88
KOG0462|consensus	650		99.87
cd04092	83	mtEFG2_II_like mtEFG2_C: C-terminus of mitochondri	99.87
cd04088	83	EFG_mtEFG_II EFG_mtEFG_II: this subfamily represen	99.86
cd03689	85	RF3_II RF3_II: this subfamily represents the domai	99.85
cd04091	81	mtEFG1_II_like mtEFG1_C: C-terminus of mitochondri	99.85
cd03691	86	BipA_TypA_II BipA_TypA_II: domain II of BipA (also	99.82
cd03699	86	lepA_II lepA_II: This subfamily represents the dom	99.81
KOG0469|consensus	842		99.76
cd03700	93	eEF2_snRNP_like_II EF2_snRNP_like_II: this subfami	99.76
cd04090	94	eEF2_II_snRNP Loc2 eEF2_C_snRNP, cd01514/C termina	99.73
PRK05306	787	infB translation initiation factor IF-2; Validated	99.69
PRK12736	394	elongation factor Tu; Reviewed	99.6
TIGR00487	587	IF-2 translation initiation factor IF-2. This mode	99.59
CHL00189	742	infB translation initiation factor 2; Provisional	99.57
CHL00071	409	tufA elongation factor Tu	99.57
TIGR00485	394	EF-Tu translation elongation factor TU. This align	99.55
KOG0460|consensus	449		99.55
PRK12735	396	elongation factor Tu; Reviewed	99.51
PRK00049	396	elongation factor Tu; Reviewed	99.47
PTZ00327	460	eukaryotic translation initiation factor 2 gamma s	99.45
TIGR00483	426	EF-1_alpha translation elongation factor EF-1 alph	99.44
PRK12317	425	elongation factor 1-alpha; Reviewed	99.43
PRK04000	411	translation initiation factor IF-2 subunit gamma;	99.42
PRK10512	614	selenocysteinyl-tRNA-specific translation factor;	99.41
PLN00043	447	elongation factor 1-alpha; Provisional	99.4
PLN03127	447	Elongation factor Tu; Provisional	99.39
PTZ00141	446	elongation factor 1- alpha; Provisional	99.38
PF03144	74	GTP_EFTU_D2: Elongation factor Tu domain 2; InterP	99.38
TIGR03680	406	eif2g_arch translation initiation factor 2 subunit	99.36
KOG0468|consensus	971		99.35
PLN03126	478	Elongation factor Tu; Provisional	99.32
COG0050	394	TufB GTPases - translation elongation factors [Tra	99.32
COG5258	527	GTPBP1 GTPase [General function prediction only]	99.28
cd01342	83	Translation_Factor_II_like Translation_Factor_II_l	99.21
TIGR00475	581	selB selenocysteine-specific elongation factor Sel	99.21
PRK05124	474	cysN sulfate adenylyltransferase subunit 1; Provis	99.15
COG5256	428	TEF1 Translation elongation factor EF-1alpha (GTPa	99.14
COG3276	447	SelB Selenocysteine-specific translation elongatio	99.12
TIGR02034	406	CysN sulfate adenylyltransferase, large subunit. H	99.12
KOG1145|consensus	683		99.07
PRK04004	586	translation initiation factor IF-2; Validated	99.07
cd03698	83	eRF3_II_like eRF3_II_like: domain similar to domai	99.05
COG0532	509	InfB Translation initiation factor 2 (IF-2; GTPase	98.98
cd03693	91	EF1_alpha_II EF1_alpha_II: this family represents	98.98
PRK05506	632	bifunctional sulfate adenylyltransferase subunit 1	98.98
PRK14845	1049	translation initiation factor IF-2; Provisional	98.96
TIGR00491	590	aIF-2 translation initiation factor aIF-2/yIF-2. T	98.9
cd04089	82	eRF3_II eRF3_II: domain II of the eukaryotic class	98.84
KOG0467|consensus	887		98.75
cd03695	81	CysN_NodQ_II CysN_NodQ_II: This subfamily represen	98.73
cd03696	83	selB_II selB_II: this subfamily represents the dom	98.69
cd03694	87	GTPBP_II Domain II of the GP-1 family of GTPase. T	98.68
cd04168	237	TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), T	98.63
cd03697	87	EFTU_II EFTU_II: Elongation factor Tu domain II. E	98.61
cd01886	270	EF-G Elongation factor G (EF-G) subfamily. Translo	98.53
cd04169	267	RF3 RF3 subfamily. Peptide chain release factor 3	98.52
cd03702	95	IF2_mtIF2_II This family represents the domain II	98.49
cd03692	84	mtIF2_IVc mtIF2_IVc: this family represents the C2	98.44
COG5257	415	GCD11 Translation initiation factor 2, gamma subun	98.42
KOG0461|consensus	522		98.42
KOG0465|consensus	721		98.41
cd04170	268	EF-G_bact Elongation factor G (EF-G) subfamily. Tr	98.36
KOG0459|consensus	501		98.36
cd03701	95	IF2_IF5B_II IF2_IF5B_II: This family represents th	98.28
KOG0458|consensus	603		98.26
COG2895	431	CysN GTPases - Sulfate adenylate transferase subun	97.97
KOG0464|consensus	753		97.93
cd03703	110	aeIF5B_II aeIF5B_II: This family represents the do	97.87
KOG0463|consensus	641		97.77
TIGR00503	527	prfC peptide chain release factor 3. This translat	97.76
cd03688	113	eIF2_gamma_II eIF2_gamma_II: this subfamily repres	97.63
PRK00741	526	prfC peptide chain release factor 3; Provisional	97.54
COG0480	697	FusA Translation elongation factors (GTPases) [Tra	97.48
PRK00007	693	elongation factor G; Reviewed	97.37
PRK12739	691	elongation factor G; Reviewed	97.37
PF00009	188	GTP_EFTU: Elongation factor Tu GTP binding domain;	97.27
TIGR00484	689	EF-G translation elongation factor EF-G. After pep	97.23
KOG1143|consensus	591		97.23
PF14578	81	GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1	97.13
PF14492	75	EFG_II: Elongation Factor G, domain II; PDB: 1WDT_	97.02
PRK13351	687	elongation factor G; Reviewed	96.99
PRK07560	731	elongation factor EF-2; Reviewed	96.97
PTZ00416	836	elongation factor 2; Provisional	96.9
TIGR00490	720	aEF-2 translation elongation factor aEF-2. This mo	96.83
PLN00116	843	translation elongation factor EF-2 subunit; Provis	96.73
PRK12740	668	elongation factor G; Reviewed	96.56
cd03690	85	Tet_II Tet_II: This subfamily represents domain II	95.89
COG4108	528	PrfC Peptide chain release factor RF-3 [Translatio	95.8
TIGR00487	587	IF-2 translation initiation factor IF-2. This mode	95.55
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	95.4
KOG0466|consensus	466		95.34
cd01889	192	SelB_euk SelB subfamily. SelB is an elongation fac	95.32
CHL00189	742	infB translation initiation factor 2; Provisional	95.3
PRK05306	787	infB translation initiation factor IF-2; Validated	95.19
cd00881	189	GTP_translation_factor GTP translation factor fami	95.12
cd04091	81	mtEFG1_II_like mtEFG1_C: C-terminus of mitochondri	95.1
cd01888	203	eIF2_gamma eIF2-gamma (gamma subunit of initiation	95.08
cd04092	83	mtEFG2_II_like mtEFG2_C: C-terminus of mitochondri	94.84
cd01890	179	LepA LepA subfamily. LepA belongs to the GTPase fa	94.61
COG0532	509	InfB Translation initiation factor 2 (IF-2; GTPase	94.38
cd04088	83	EFG_mtEFG_II EFG_mtEFG_II: this subfamily represen	94.34
cd03699	86	lepA_II lepA_II: This subfamily represents the dom	93.86
PRK10218	607	GTP-binding protein; Provisional	93.61
cd04165	224	GTPBP1_like GTPBP1-like. Mammalian GTP binding pro	93.16
cd01884	195	EF_Tu EF-Tu subfamily. This subfamily includes ort	93.11
cd01891	194	TypA_BipA TypA (tyrosine phosphorylated protein A)	93.04
KOG1144|consensus	1064		92.83
TIGR00436	270	era GTP-binding protein Era. Era is an essential G	92.77
TIGR01393	595	lepA GTP-binding protein LepA. LepA (GUF1 in Sacca	92.56
TIGR01394	594	TypA_BipA GTP-binding protein TypA/BipA. This bact	92.24
PRK15467	158	ethanolamine utilization protein EutP; Provisional	92.12
cd01885	222	EF2 EF2 (for archaea and eukarya). Translocation r	91.9
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	91.88
COG1160	444	Predicted GTPases [General function prediction onl	91.75
PRK05433	600	GTP-binding protein LepA; Provisional	91.69
cd01897	168	NOG NOG1 is a nucleolar GTP-binding protein presen	91.47
cd04145	164	M_R_Ras_like M-Ras/R-Ras-like subfamily. This subf	91.24
cd03689	85	RF3_II RF3_II: this subfamily represents the domai	91.16
cd04136	163	Rap_like Rap-like subfamily. The Rap subfamily con	91.05
cd04147	198	Ras_dva Ras-dva subfamily. Ras-dva (Ras - dorsal-v	90.92
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	90.87
TIGR02528	142	EutP ethanolamine utilization protein, EutP. This	90.76
cd04157	162	Arl6 Arl6 subfamily. Arl6 (Arf-like 6) forms a sub	90.71
cd01860	163	Rab5_related Rab5-related subfamily. This subfamil	90.7
TIGR00491	590	aIF-2 translation initiation factor aIF-2/yIF-2. T	90.63
PF02421	156	FeoB_N: Ferrous iron transport protein B; InterPro	90.59
cd04116	170	Rab9 Rab9 subfamily. Rab9 is found in late endosom	90.47
cd04138	162	H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras,	90.46
cd01865	165	Rab3 Rab3 subfamily. The Rab3 subfamily contains R	90.37
cd04160	167	Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related prote	90.34
cd03691	86	BipA_TypA_II BipA_TypA_II: domain II of BipA (also	89.98
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	89.89
cd04154	173	Arl2 Arl2 subfamily. Arl2 (Arf-like 2) GTPases are	89.88
cd04175	164	Rap1 Rap1 subgroup. The Rap1 subgroup is part of t	89.52
cd01863	161	Rab18 Rab18 subfamily. Mammalian Rab18 is implicat	89.47
cd00880	163	Era_like Era (E. coli Ras-like protein)-like. This	89.41
PRK04004	586	translation initiation factor IF-2; Validated	89.32
cd04151	158	Arl1 Arl1 subfamily. Arl1 (Arf-like 1) localizes t	89.17
cd04106	162	Rab23_lke Rab23-like subfamily. Rab23 is a member	88.88
cd04177	168	RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the	88.8
cd04158	169	ARD1 ARD1 subfamily. ARD1 (ADP-ribosylation factor	88.71
cd04156	160	ARLTS1 ARLTS1 subfamily. ARLTS1 (Arf-like tumor su	88.55
cd01855	190	YqeH YqeH. YqeH is an essential GTP-binding protei	88.54
cd04143	247	Rhes_like Rhes_like subfamily. This subfamily incl	88.47
cd04107	201	Rab32_Rab38 Rab38/Rab32 subfamily. Rab32 and Rab38	88.46
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	88.32
cd01864	165	Rab19 Rab19 subfamily. Rab19 proteins are associat	88.28
cd00876	160	Ras Ras family. The Ras family of the Ras superfam	88.26
cd04090	94	eEF2_II_snRNP Loc2 eEF2_C_snRNP, cd01514/C termina	88.09
cd04150	159	Arf1_5_like Arf1-Arf5-like subfamily. This subfami	88.05
cd01887	168	IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryo	88.01
cd03700	93	eEF2_snRNP_like_II EF2_snRNP_like_II: this subfami	87.95
cd00879	190	Sar1 Sar1 subfamily. Sar1 is an essential componen	87.94
cd04153	174	Arl5_Arl8 Arl5/Arl8 subfamily. Arl5 (Arf-like 5) a	87.81
cd04113	161	Rab4 Rab4 subfamily. Rab4 has been implicated in n	87.76
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	87.74
cd01859	156	MJ1464 MJ1464. This family represents archaeal GTP	87.62
TIGR02729	329	Obg_CgtA Obg family GTPase CgtA. This model descri	87.48
COG0481	603	LepA Membrane GTPase LepA [Cell envelope biogenesi	87.36
COG4917	148	EutP Ethanolamine utilization protein [Amino acid	87.23
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	87.22
PRK00089	292	era GTPase Era; Reviewed	87.16
cd01898	170	Obg Obg subfamily. The Obg nucleotide binding prot	87.15
TIGR03594	429	GTPase_EngA ribosome-associated GTPase EngA. EngA	87.05
cd04152	183	Arl4_Arl7 Arl4/Arl7 subfamily. Arl4 (Arf-like 4) i	87.05
cd04149	168	Arf6 Arf6 subfamily. Arf6 (ADP ribosylation factor	86.95
PRK00093	435	GTP-binding protein Der; Reviewed	86.84
PRK04213	201	GTP-binding protein; Provisional	86.82
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	86.82
cd01861	161	Rab6 Rab6 subfamily. Rab6 is involved in microtubu	86.69
cd00878	158	Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-lik	86.63
cd04142	198	RRP22 RRP22 subfamily. RRP22 (Ras-related protein	86.57
cd01868	165	Rab11_like Rab11-like. Rab11a, Rab11b, and Rab25 a	86.33
PRK12299	335	obgE GTPase CgtA; Reviewed	86.31
cd04134	189	Rho3 Rho3 subfamily. Rho3 is a member of the Rho f	85.97
COG1159	298	Era GTPase [General function prediction only]	85.97
cd04135	174	Tc10 TC10 subfamily. TC10 is a Rho family protein	85.84
cd01894	157	EngA1 EngA1 subfamily. This CD represents the firs	85.74
cd04176	163	Rap2 Rap2 subgroup. The Rap2 subgroup is part of t	85.67
cd01869	166	Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in ev	85.67
cd00154	159	Rab Rab family. Rab GTPases form the largest famil	85.65
cd04114	169	Rab30 Rab30 subfamily. Rab30 appears to be associa	85.57
PRK15494	339	era GTPase Era; Provisional	85.49
cd01870	175	RhoA_like RhoA-like subfamily. The RhoA subfamily	85.45
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	85.44
PRK03003	472	GTP-binding protein Der; Reviewed	85.15
PTZ00369	189	Ras-like protein; Provisional	85.13
TIGR00101	199	ureG urease accessory protein UreG. This model rep	84.92
PRK14845	1049	translation initiation factor IF-2; Provisional	84.82
cd04101	164	RabL4 RabL4 (Rab-like4) subfamily. RabL4s are nove	84.81
cd04164	157	trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein	84.76
cd04124	161	RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily	84.56
cd04127	180	Rab27A Rab27a subfamily. The Rab27a subfamily cons	84.48
PRK09435	332	membrane ATPase/protein kinase; Provisional	84.37
COG1160	444	Predicted GTPases [General function prediction onl	84.32
smart00177	175	ARF ARF-like small GTPases; ARF, ADP-ribosylation	84.09
cd01881	176	Obg_like The Obg-like subfamily consists of five w	84.08
cd04110	199	Rab35 Rab35 subfamily. Rab35 is one of several Rab	84.08
PTZ00133	182	ADP-ribosylation factor; Provisional	83.96
PLN00223	181	ADP-ribosylation factor; Provisional	83.81
smart00174	174	RHO Rho (Ras homology) subfamily of Ras-like small	83.72
cd04123	162	Rab21 Rab21 subfamily. The localization and functi	83.69
cd04171	164	SelB SelB subfamily. SelB is an elongation factor	83.22
PTZ00099	176	rab6; Provisional	82.99
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	82.88
cd00157	171	Rho Rho (Ras homology) family. Members of the Rho	82.86
cd04112	191	Rab26 Rab26 subfamily. First identified in rat pan	82.75
PRK12298	390	obgE GTPase CgtA; Reviewed	82.39
TIGR03594	429	GTPase_EngA ribosome-associated GTPase EngA. EngA	82.33
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	82.31
cd04140	165	ARHI_like ARHI subfamily. ARHI (A Ras homolog memb	81.98
PRK09518	712	bifunctional cytidylate kinase/GTPase Der; Reviewe	81.96
cd04109	215	Rab28 Rab28 subfamily. First identified in maize,	81.85
PLN03110	216	Rab GTPase; Provisional	81.61
cd04132	187	Rho4_like Rho4-like subfamily. Rho4 is a GTPase th	81.6
cd01895	174	EngA2 EngA2 subfamily. This CD represents the seco	81.57
cd04167	213	Snu114p Snu114p subfamily. Snu114p is one of sever	81.32
PRK13768	253	GTPase; Provisional	81.19
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	81.13
cd04125	188	RabA_like RabA-like subfamily. RabA was first iden	80.71
cd04141	172	Rit_Rin_Ric Rit/Rin/Ric subfamily. Rit (Ras-like p	80.49
cd00882	157	Ras_like_GTPase Ras-like GTPase superfamily. The R	80.48
cd04137	180	RheB Rheb (Ras Homolog Enriched in Brain) subfamil	80.38
cd01849	155	YlqF_related_GTPase YlqF-related GTPases. These pr	80.31
cd04130	173	Wrch_1 Wrch-1 subfamily. Wrch-1 (Wnt-1 responsive	80.18

>KOG0465|consensus

Probab=100.00  E-value=6.3e-35  Score=265.52  Aligned_cols=193  Identities=29%  Similarity=0.460  Sum_probs=167.0

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCccccccc-------
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMF-------   94 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~-------   94 (221)
                      +.|+.++..+..  ......+-....||+.++++.++|||+|||++|.||++|||+|++|+|+|.+..++.+.       
T Consensus       249 d~DE~l~e~fLe--e~~ps~~~l~~aIRr~Ti~r~fvPVl~GSAlKNkGVQPlLDAVvdYLPsP~Ev~n~a~~ke~~~~e  326 (721)
T KOG0465|consen  249 DVDETLAEMFLE--EEEPSAQQLKAAIRRATIKRSFVPVLCGSALKNKGVQPLLDAVVDYLPSPSEVENYALNKETNSKE  326 (721)
T ss_pred             hhhHHHHHHHhc--cCCCCHHHHHHHHHHHHhhcceeeEEechhhcccCcchHHHHHHHhCCChhhhcccccccCCCCcc
Confidence            346666555544  11235667788999999999999999999999999999999999999999987765321       


Q ss_pred             -----CCCCC-CcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE
Q psy5461          95 -----QHFGD-SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA  168 (221)
Q Consensus        95 -----~~~~~-~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~  168 (221)
                           ...++ ||+|.+||+..+++ |.++|+|||+|+|++||.+||.++++++|+.+|..|++...++++++.|||||+
T Consensus       327 kv~l~~~~d~~Pfv~LAFKle~g~f-GqLTyvRvYqG~L~kG~~iyN~rtgKKvrv~RL~rmHa~~medV~~v~AG~I~a  405 (721)
T KOG0465|consen  327 KVTLSPSRDKDPFVALAFKLEEGRF-GQLTYVRVYQGTLSKGDTIYNVRTGKKVRVGRLVRMHANDMEDVNEVLAGDICA  405 (721)
T ss_pred             ceEeccCCCCCceeeeEEEeeecCc-cceEEEEEeeeeecCCcEEEecCCCceeEhHHHhHhcccccchhhhhhccceee
Confidence                 22333 99999999999999 999999999999999999999999999999999999999999999999999999


Q ss_pred             EcCCCCCccCcEEecCC---------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461         169 VTGLKRERGKDKRTRVI---------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQ  218 (221)
Q Consensus       169 i~gl~~~~~Gdtl~~~~---------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~  218 (221)
                      +.|+ ++.+||||++..         .-|.|++          |.+++++||.++.+|||++.+..|-.
T Consensus       406 lfGi-dcasGDTftd~~~~~~~m~si~vPePVis~aikP~~k~d~~~fskaL~rf~~EDPtFrv~~d~E  473 (721)
T KOG0465|consen  406 LFGI-DCASGDTFTDKQNLALSMESIHIPEPVISVAIKPVNKKDADNFSKALNRFTKEDPTFRVSLDPE  473 (721)
T ss_pred             eecc-ccccCceeccCccccceeeeeecCCCeeEEEecccccccHHHHHHHHHhhcccCCceEEEeccc
Confidence            9999 899999998861         2355666          78899999999999999999988753

>PRK00007 elongation factor G; Reviewed

Probab=100.00  E-value=4.2e-33  Score=266.45  Aligned_cols=177  Identities=32%  Similarity=0.493  Sum_probs=155.6

Q ss_pred             cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc------------cccCCCCCCcEEEEEEEe
Q psy5461          42 AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL------------AMFQHFGDSLCARAFKVV  109 (221)
Q Consensus        42 ~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~------------~~~~~~~~~~~~~Vfk~~  109 (221)
                      +.....+++++..+..+||++|||.++.||++|||+|++++|+|.+++..            .+.|++++|++|+|||+.
T Consensus       239 ~~l~~~l~~~~~~~~~~Pv~~gSa~~~~Gv~~LLd~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~l~a~VfK~~  318 (693)
T PRK00007        239 EEIKAALRKATIANEIVPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPAIKGILPDGEEEEVERKASDDEPFSALAFKIM  318 (693)
T ss_pred             HHHHHHHHHHHhcCcEEEEEecccccCcCHHHHHHHHHHHCCChhhcccccccCCCccccceeecCCCCCCeEEEEEEee
Confidence            44456667778888999999999999999999999999999999865421            234677899999999999


Q ss_pred             ecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC----
Q psy5461         110 HDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI----  185 (221)
Q Consensus       110 ~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~----  185 (221)
                      +|++.|+++|+|||||+|++||+|++.++++++++++|+.+.|.+..+++++.|||||++.|++++++||||++..    
T Consensus       319 ~d~~~G~ia~~RV~sGtl~~g~~v~~~~~~~~eki~~l~~~~g~~~~~v~~~~aGdI~~i~gl~~~~~GdtL~~~~~~~~  398 (693)
T PRK00007        319 TDPFVGKLTFFRVYSGVLESGSYVLNSTKGKKERIGRILQMHANKREEIKEVRAGDIAAAVGLKDTTTGDTLCDEKNPII  398 (693)
T ss_pred             ecCCCCcEEEEEEeeeEEcCCCEEEeCCCCceeEeceeEEeccCCcccccccCCCcEEEEeCCccCCcCCEeeCCCCccc
Confidence            9999999999999999999999999988888899999999999999999999999999999999999999997641    


Q ss_pred             ----CCCCCce----------ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461         186 ----PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQ  218 (221)
Q Consensus       186 ----~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~  218 (221)
                          ..|.|++          |.++|.+||++|+++||+|++.++..
T Consensus       399 l~~~~~~~Pv~~~aIep~~~~d~~kL~~aL~~L~~eDpsl~v~~~~e  445 (693)
T PRK00007        399 LESMEFPEPVISVAVEPKTKADQEKMGIALQKLAEEDPSFRVSTDEE  445 (693)
T ss_pred             cCCCCCCCceEEEEEEECCcccHHHHHHHHHHHHHhCCeEEEEEcCC
Confidence                1233555          78999999999999999999988753

>TIGR00503 prfC peptide chain release factor 3

Probab=100.00  E-value=6.5e-33  Score=257.20  Aligned_cols=167  Identities=21%  Similarity=0.314  Sum_probs=146.0

Q ss_pred             hccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCccccc--ccCCCCCCcEEEEEEEee--c-CCCceEEEEEEEc
Q psy5461          50 SGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA--MFQHFGDSLCARAFKVVH--D-KHRGAVTFFRIYS  124 (221)
Q Consensus        50 ~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~--~~~~~~~~~~~~Vfk~~~--d-~~~G~i~~~RV~s  124 (221)
                      +++.++..+|||||||.+|.||++|||+|++++|+|.++....  +.+ .+++|+|+|||+.+  | +|+|+++|+||||
T Consensus       242 ~~~~~~~~~PV~~GSA~~n~Gv~~LLd~i~~~~PsP~~~~~~~~~~~~-~~~~~~~~VFK~~~~mdp~~~griaf~RV~s  320 (527)
T TIGR00503       242 AAFHGGEMTPVFFGTALGNFGVDHFLDGLLQWAPKPEARQSDTRTVEP-TEEKFSGFVFKIQANMDPKHRDRVAFMRVVS  320 (527)
T ss_pred             HHHhcCCeeEEEEeecccCccHHHHHHHHHHHCCCCccccCCceecCC-CCCCeeEEEEEEEeccCcccCceEEEEEEee
Confidence            4567889999999999999999999999999999998654221  112 35789999999998  7 5999999999999


Q ss_pred             eEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC-------CCCCCce-----
Q psy5461         125 GAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI-------PKPTSVV-----  192 (221)
Q Consensus       125 G~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~-------~~p~~~v-----  192 (221)
                      |++++|++|++.++++++++++++.++|.+++++++|.||||+++.|++++++||||+...       +.|.|++     
T Consensus       321 G~l~~g~~v~~~~~~k~~ri~~~~~~~g~~~~~v~~a~aGDI~~~~~~~~~~~GDtl~~~~~~~~~~i~~~~P~~~~~v~  400 (527)
T TIGR00503       321 GKYEKGMKLKHVRTGKDVVISDALTFMAGDREHVEEAYAGDIIGLHNHGTIQIGDTFTQGEKIKFTGIPNFAPELFRRIR  400 (527)
T ss_pred             eEEcCCCEEEecCCCCcEEecchhhhhcCCceEcceeCCCCEEEEECCCCcccCCEecCCCceeecCCCCCCcceEEEEE
Confidence            9999999999999999999999999999999999999999999999999999999998751       2233444     


Q ss_pred             -----ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461         193 -----QCSARWTLNLEVGASSPIISKSKRRQ  218 (221)
Q Consensus       193 -----~~~~l~~~L~~L~~~Dp~l~~~~~~~  218 (221)
                           |.++|.+||++|++||| +++.++.+
T Consensus       401 ~~~~~d~~kl~~aL~~L~eED~-l~v~~~~~  430 (527)
T TIGR00503       401 LKDPLKQKQLLKGLVQLSEEGA-VQVFRPLD  430 (527)
T ss_pred             ECChhhHHHHHHHHHHHHhhCC-eEEEEcCC
Confidence                 78999999999999999 88887754

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.

>TIGR00484 EF-G translation elongation factor EF-G

Probab=100.00  E-value=7.8e-33  Score=264.59  Aligned_cols=194  Identities=30%  Similarity=0.457  Sum_probs=162.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc-----------
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL-----------   91 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~-----------   91 (221)
                      .|+++...++.  .+....+.....+++++..+..+|||+|||++|.|+++|||+|++++|+|.+++..           
T Consensus       221 ~dd~lle~yle--~~~~~~~~l~~~l~~~~~~~~~~PV~~gSa~~~~Gv~~LLd~I~~~lPsP~~~~~~~~~~~~~~~~~  298 (689)
T TIGR00484       221 FDEELMEKYLE--GEELTIEEIKNAIRKGVLNCEFFPVLCGSAFKNKGVQLLLDAVVDYLPSPTDVPAIKGIDPDTEKEI  298 (689)
T ss_pred             cCHHHHHHHhC--CCCCCHHHHHHHHHHHHhcCCEEEEEeccccCCccHHHHHHHHHHHCCCchhcccccccCCCCCcee
Confidence            45555545443  12222233455677788889999999999999999999999999999999865321           


Q ss_pred             cccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcC
Q psy5461          92 AMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTG  171 (221)
Q Consensus        92 ~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~g  171 (221)
                      .+.|++++||+|+|||+++|++.|+++|+|||||+|++||+|++.+.++++++++|+.+.|.+..+++++.|||||++.|
T Consensus       299 ~~~~~~~~~l~a~VfK~~~d~~~G~i~~~RV~sGtL~~g~~v~~~~~~~~~~i~~l~~~~g~~~~~v~~~~aGdI~~i~g  378 (689)
T TIGR00484       299 ERKASDDEPFSALAFKVATDPFVGQLTFVRVYSGVLKSGSYVKNSRKNKKERVGRLVKMHANNREEIKEVRAGDICAAIG  378 (689)
T ss_pred             eecCCCCCceEEEEEEeeecCCCCeEEEEEEEEeEEcCCCEEEeCCCCceEEecceEEeecCCcccccccCCCCEEEEcC
Confidence            23466788999999999999999999999999999999999999888888999999999999999999999999999999


Q ss_pred             CCCCccCcEEecCC--------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461         172 LKRERGKDKRTRVI--------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQ  218 (221)
Q Consensus       172 l~~~~~Gdtl~~~~--------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~  218 (221)
                      ++++++||||++..        ..|.|++          |.++|++||++|+++||+|++.++..
T Consensus       379 l~~~~~gdtl~~~~~~~~~~~~~~~~Pvl~~~i~p~~~~d~~kL~~aL~~L~~eDpsl~v~~~~e  443 (689)
T TIGR00484       379 LKDTTTGDTLCDPKIDVILERMEFPEPVISLAVEPKTKADQEKMGIALGKLAEEDPTFRTFTDPE  443 (689)
T ss_pred             CCCCCCCCEEeCCCCccccCCCCCCCceEEEEEEECCcccHHHHHHHHHHHHHhCCEEEEEECCC
Confidence            99999999997641        1234555          88999999999999999999988653

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.

>PRK00741 prfC peptide chain release factor 3; Provisional

Probab=100.00  E-value=1.8e-32  Score=254.28  Aligned_cols=169  Identities=22%  Similarity=0.313  Sum_probs=146.5

Q ss_pred             hhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCC-CCCCcEEEEEEEee---cCCCceEEEEEEEc
Q psy5461          49 YSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQH-FGDSLCARAFKVVH---DKHRGAVTFFRIYS  124 (221)
Q Consensus        49 ~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~-~~~~~~~~Vfk~~~---d~~~G~i~~~RV~s  124 (221)
                      ++++.++..+|||||||++|+||++|||+|++++|+|.++.......+ ..++|+|+|||+.+   ++|+|+++|+||||
T Consensus       240 ~~~~~~~~~~PV~~GSA~~n~Gv~~LLd~i~~~~P~P~~~~~~~~~~~~~~~~~~~~VFK~~~~m~~~~~grlafvRV~s  319 (526)
T PRK00741        240 LEAFLAGELTPVFFGSALNNFGVQEFLDAFVEWAPAPQPRQTDEREVEPTEEKFSGFVFKIQANMDPKHRDRIAFVRVCS  319 (526)
T ss_pred             HHHHhcCCeEEEEEeecccCcCHHHHHHHHHHHCCCCCcccccceeecCCCCceEEEEEEEEecCCCCcCceEEEEEEec
Confidence            667788999999999999999999999999999999986542211112 24579999999994   57999999999999


Q ss_pred             eEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC-------CCCCCce-----
Q psy5461         125 GAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI-------PKPTSVV-----  192 (221)
Q Consensus       125 G~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~-------~~p~~~v-----  192 (221)
                      |++++|++|++.++++++++++++.++|.+++++++|.||||+++.|++++++||||+...       +.|.|++     
T Consensus       320 G~l~~g~~v~~~~~~k~~ri~~~~~~~g~~~~~v~~a~aGDIv~v~~l~~~~~GDTL~~~~~~~~~~i~~~~P~~~~~v~  399 (526)
T PRK00741        320 GKFEKGMKVRHVRTGKDVRISNALTFMAQDREHVEEAYAGDIIGLHNHGTIQIGDTFTQGEKLKFTGIPNFAPELFRRVR  399 (526)
T ss_pred             cEECCCCEEEeccCCceEEecceEEEecCCceECceeCCCCEEEEECCCCCccCCCccCCCccccCCCCCCCccEEEEEE
Confidence            9999999999999999999999999999999999999999999999999999999998652       2233444     


Q ss_pred             -----ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461         193 -----QCSARWTLNLEVGASSPIISKSKRRQ  218 (221)
Q Consensus       193 -----~~~~l~~~L~~L~~~Dp~l~~~~~~~  218 (221)
                           |.++|.+||++|++||| +++.++..
T Consensus       400 p~~~~d~~kl~~aL~~L~eED~-l~~~~~~~  429 (526)
T PRK00741        400 LKNPLKQKQLQKGLVQLSEEGA-VQVFRPLD  429 (526)
T ss_pred             ECCchhHHHHHHHHHHHhhcCC-eEEEECCC
Confidence                 78999999999999996 88887754

>PRK12739 elongation factor G; Reviewed

Probab=100.00  E-value=1.1e-32  Score=263.48  Aligned_cols=177  Identities=32%  Similarity=0.487  Sum_probs=156.4

Q ss_pred             cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc-----------cccCCCCCCcEEEEEEEee
Q psy5461          42 AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL-----------AMFQHFGDSLCARAFKVVH  110 (221)
Q Consensus        42 ~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~-----------~~~~~~~~~~~~~Vfk~~~  110 (221)
                      +.....+++++.++..+||++|||.++.|+++|||+|++++|+|.+++..           .+.|++++||+|+|||+++
T Consensus       237 ~~l~~~l~~~~~~~~~~Pv~~gSa~~~~Gv~~LLd~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~pl~a~VfK~~~  316 (691)
T PRK12739        237 EEIKAAIRKATINMEFFPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPAIKGINPDTEEEIERPASDDEPFAALAFKIMT  316 (691)
T ss_pred             HHHHHHHHHHHHcCCEEEEEeccccCCccHHHHHHHHHHHCCChhhccccccccCCCCcceeeccCCCCCeEEEEEEeee
Confidence            34455677788888999999999999999999999999999999865432           1346778999999999999


Q ss_pred             cCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC-----
Q psy5461         111 DKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI-----  185 (221)
Q Consensus       111 d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~-----  185 (221)
                      |+++|+++|+|||||+|++||.|++.++++++++.+|+.++|++..+++++.|||||+|.|++++++||||++..     
T Consensus       317 d~~~G~i~~~RV~sGtL~~g~~v~~~~~~~~~~v~~l~~~~g~~~~~v~~~~aGdI~~i~gl~~~~~gdtl~~~~~~~~l  396 (691)
T PRK12739        317 DPFVGRLTFFRVYSGVLESGSYVLNTTKGKKERIGRLLQMHANKREEIKEVYAGDIAAAVGLKDTTTGDTLCDEKAPIIL  396 (691)
T ss_pred             CCCCCeEEEEEEeeeEEcCCCEEEeCCCCceEEecceEEEecCCcccccccCCCCEEEEeCCCcccCCCEEeCCCCcccc
Confidence            999999999999999999999999998888899999999999999999999999999999999999999997642     


Q ss_pred             ---CCCCCce----------ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461         186 ---PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQ  218 (221)
Q Consensus       186 ---~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~  218 (221)
                         ..|.|++          |.++|++||++|+++||+|.+.+|..
T Consensus       397 ~~~~~~~Pv~~~aiep~~~~d~~kL~~aL~~L~~eDpsl~v~~~~e  442 (691)
T PRK12739        397 ESMEFPEPVISLAVEPKTKADQDKMGLALQKLAEEDPTFRVETDEE  442 (691)
T ss_pred             CCCCCCCceEEEEEEECCcccHHHHHHHHHHHHHhCCeEEEEEcCC
Confidence               1234555          88999999999999999999998753

>PRK13351 elongation factor G; Reviewed

Probab=100.00  E-value=1.9e-32  Score=262.02  Aligned_cols=193  Identities=30%  Similarity=0.411  Sum_probs=164.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc----------c
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL----------A   92 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~----------~   92 (221)
                      .|+.+...+++  ..+...+.....+++++..+..+|||+|||++|.||++|||+|++++|+|.+++..          .
T Consensus       220 ~d~~lle~~l~--~~~l~~~~l~~~~~~~~~~~~~~PV~~gSA~~~~Gv~~LLd~I~~~lPsP~~~~~~~~~~~~~~~~~  297 (687)
T PRK13351        220 FDDELLELYLE--GEELSAEQLRAPLREGTRSGHLVPVLFGSALKNIGIEPLLDAVVDYLPSPLEVPPPRGSKDNGKPVK  297 (687)
T ss_pred             cCHHHHHHHhC--CCCCCHHHHHHHHHHHHHhCCEEEEEecccCcCccHHHHHHHHHHHCCChhhcccccccCCCCCcee
Confidence            45555555554  22233344567778888888999999999999999999999999999999765322          1


Q ss_pred             ccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCC
Q psy5461          93 MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGL  172 (221)
Q Consensus        93 ~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl  172 (221)
                      +.|++++|++|+|||++++++.|+++|+|||||+|++||+|++.++++.+++++|+.++|.+..+++++.||||+++.|+
T Consensus       298 ~~~~~~~pl~a~VfK~~~d~~~G~i~~~RV~sGtl~~g~~v~~~~~~~~~~i~~i~~~~g~~~~~v~~~~aGdI~~i~gl  377 (687)
T PRK13351        298 VDPDPEKPLLALVFKVQYDPYAGKLTYLRVYSGTLRAGSQLYNGTGGKREKVGRLFRLQGNKREEVDRAKAGDIVAVAGL  377 (687)
T ss_pred             ecCCCCCCeEEEEEEeeecCCCceEEEEEEeEEEEcCCCEEEeCCCCCceEeeeEEEEccCCeeECCccCCCCEEEEECc
Confidence            34577889999999999999999999999999999999999999988889999999999999999999999999999999


Q ss_pred             CCCccCcEEecCC--------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         173 KRERGKDKRTRVI--------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       173 ~~~~~Gdtl~~~~--------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                      +++.+||||++..        ..|.|++          |.++|++||++|+++||++++.++.
T Consensus       378 ~~~~~gdtl~~~~~~~~~~~~~~~~pv~~~~Iep~~~~d~~kL~~aL~~L~~eDpsl~v~~~~  440 (687)
T PRK13351        378 KELETGDTLHDSADPVLLELLTFPEPVVSLAVEPERRGDEQKLAEALEKLVWEDPSLRVEEDE  440 (687)
T ss_pred             ccCccCCEEeCCCCccccCCCCCCCccEEEEEEECCcccHHHHHHHHHHHHHhCCeEEEEECC
Confidence            9999999998641        1244555          7899999999999999999999874

>COG0480 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=5.1e-32  Score=256.31  Aligned_cols=195  Identities=30%  Similarity=0.476  Sum_probs=169.0

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCccccc---------
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA---------   92 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~---------   92 (221)
                      ++|+++...+..  ......+.....++++++++.++|++||||.+|.|++.|||++++++|+|.+.+.+.         
T Consensus       219 e~de~l~e~yl~--g~e~~~~~i~~~i~~~~~~~~~~pvl~gsa~kn~gv~~lLdav~~~lPsP~e~~~~~g~~~~~~~~  296 (697)
T COG0480         219 EFDEELMEKYLE--GEEPTEEEIKKALRKGTIAGKIVPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPPIKGDLDDEIEK  296 (697)
T ss_pred             hcCHHHHHHHhc--CCCccHHHHHHHHHHhhhccceeeEEeeecccCCcHHHHHHHHHHHCCChhhcccccccCCccccc
Confidence            456666666666  222334566788888999999999999999999999999999999999998876431         


Q ss_pred             ---ccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE
Q psy5461          93 ---MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV  169 (221)
Q Consensus        93 ---~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i  169 (221)
                         .+++.++||+|+|||+..|++.|+++|+|||||+|++|+.+++.+.+++++|.+|+.|+|.++++++++.||||+++
T Consensus       297 ~~~~~~~~e~p~~a~vfKi~~d~~~g~l~~~RvysGtl~~G~~v~n~~~~~~erv~~l~~~~~~~~~~v~~~~AG~I~a~  376 (697)
T COG0480         297 AVLRKASDEGPLSALVFKIMTDPFVGKLTFVRVYSGTLKSGSEVLNSTKGKKERVGRLLLMHGNEREEVDEVPAGDIVAL  376 (697)
T ss_pred             hhcccCCCCCceEEEEEEeEecCCCCeEEEEEEeccEEcCCCEEEeCCCCccEEEEEEEEccCCceeecccccCccEEEE
Confidence               12345789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCccCcEEecCC--------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461         170 TGLKRERGKDKRTRVI--------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQ  218 (221)
Q Consensus       170 ~gl~~~~~Gdtl~~~~--------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~  218 (221)
                      .|+++..+|||+|+..        .-|.|++          |+++|+.||.+|+++||++.+..|-.
T Consensus       377 ~Gl~~~~tGdTl~~~~~~v~~~~~~~pePVi~vavepk~~~d~~Kl~~aL~~l~~eDPt~~v~~d~E  443 (697)
T COG0480         377 VGLKDATTGDTLCDENKPVILESMEFPEPVISVAVEPKTKADQEKLSEALNKLAEEDPTFRVETDEE  443 (697)
T ss_pred             EcccccccCCeeecCCCccccccccCCCceEEEEEeECChhhHHHHHHHHHHHHhhCCceEEEEcCC
Confidence            9999999999999654        1134666          88999999999999999999998753

>PRK12740 elongation factor G; Reviewed

Probab=99.97  E-value=7.9e-31  Score=250.18  Aligned_cols=175  Identities=30%  Similarity=0.455  Sum_probs=152.9

Q ss_pred             chHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc---------cccCCCCCCcEEEEEEEeecCC
Q psy5461          43 VTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL---------AMFQHFGDSLCARAFKVVHDKH  113 (221)
Q Consensus        43 l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~---------~~~~~~~~~~~~~Vfk~~~d~~  113 (221)
                      .....+++.+..+..+|||+|||++|.|+++|||+|++++|+|.+++..         ...|++++|++|+|||+.++++
T Consensus       222 ~~~~~~~~~~~~~~~~Pv~~gSA~~~~Gv~~LLd~i~~~lPsp~~~~~~~~~~~~~~~~~~~~~~~~l~a~v~k~~~~~~  301 (668)
T PRK12740        222 EIKAGLRKATLAGEIVPVFCGSALKNKGVQRLLDAVVDYLPSPLEVPPVDGEDGEEGAELAPDPDGPLVALVFKTMDDPF  301 (668)
T ss_pred             HHHHHHHHHHHcCCEEEEEeccccCCccHHHHHHHHHHHCCChhhcccccCCCCccccccccCCCCCeEEEEEEeeecCC
Confidence            3345566777888999999999999999999999999999999764421         1245678899999999999999


Q ss_pred             CceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC--------
Q psy5461         114 RGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI--------  185 (221)
Q Consensus       114 ~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~--------  185 (221)
                      .|+++++|||+|+|++||+|++.++++.+++.+|+.++|.+.++++++.||||+++.|++.+.+||||++..        
T Consensus       302 ~G~i~~~RV~sG~L~~g~~v~~~~~~~~~~i~~l~~l~g~~~~~v~~~~aGdI~~i~gl~~~~~Gdtl~~~~~~~~~~~~  381 (668)
T PRK12740        302 VGKLSLVRVYSGTLKKGDTLYNSGTGKKERVGRLYRMHGKQREEVDEAVAGDIVAVAKLKDAATGDTLCDKGDPILLEPM  381 (668)
T ss_pred             CCcEEEEEEeeeEEcCCCEEEeCCCCCcEEecceeeecCCCccccCccCCCCEEEEeccCccCCCCEEeCCCCccccCCC
Confidence            999999999999999999999998887899999999999999999999999999999999999999997641        


Q ss_pred             CCCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         186 PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       186 ~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                      ..|.|++          |.++|++||++|+++||+|++.++.
T Consensus       382 ~~~~P~~~~~i~p~~~~d~~~L~~aL~~l~~~Dpsl~v~~~~  423 (668)
T PRK12740        382 EFPEPVISLAIEPKDKGDEEKLSEALGKLAEEDPTLRVERDE  423 (668)
T ss_pred             CCCCcceEEEEEECCcchHHHHHHHHHHHHHhCCeEEEEECC
Confidence            1233555          7899999999999999999998863

>PRK10218 GTP-binding protein; Provisional

Probab=99.95  E-value=8.3e-27  Score=219.12  Aligned_cols=187  Identities=17%  Similarity=0.177  Sum_probs=147.9

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhc------cccccCceeEecCCCccc----------cHHHHHHHHHhhCCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG------AFKKNHVPVLCGSSYKNI----------GVQKLMDAIVDILPSPT   86 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~------~~~~~~~Pv~~gSa~~~~----------Gi~~LLd~I~~~~PsP~   86 (221)
                      .+.|.+..+||++......+-....+...      ......+||+++||++|+          |+.+|||+|++++|+|.
T Consensus       119 ~gip~IVviNKiD~~~a~~~~vl~ei~~l~~~l~~~~~~~~~PVi~~SA~~G~~~~~~~~~~~~i~~Lld~Ii~~iP~P~  198 (607)
T PRK10218        119 YGLKPIVVINKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNGIAGLDHEDMAEDMTPLYQAIVDHVPAPD  198 (607)
T ss_pred             cCCCEEEEEECcCCCCCchhHHHHHHHHHHhccCccccccCCCEEEeEhhcCcccCCccccccchHHHHHHHHHhCCCCC
Confidence            45678899999764432222222333322      123356999999999998          69999999999999996


Q ss_pred             CcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC-Cc--eeeeceeEeeecCCeeeeCcccc
Q psy5461          87 ERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL-DQ--SEQITRLLLAEADDYKEVNEIQC  163 (221)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~-~~--~~~v~~i~~~~g~~~~~v~~a~a  163 (221)
                      .        +.++||+++|||++++++.|+++++||++|+|++||.|++... ++  +++|++|+.+.|.++.++++|.|
T Consensus       199 ~--------~~~~Pl~~~V~k~~~d~~~G~i~~gRV~sG~lk~Gd~v~~~~~~~~~~~~rv~~l~~~~g~~~~~v~~a~A  270 (607)
T PRK10218        199 V--------DLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEA  270 (607)
T ss_pred             C--------CCCCCeEEEEEeeEecCCCcEEEEEEEEeCcCcCCCEEEEecCCCcEeeEEEEEEEEEecCCceECCEEcC
Confidence            4        5678999999999999999999999999999999999999876 43  57899999999999999999999


Q ss_pred             CCEEEEcCCCCCccCcEEecCC-CC-------CCCce-------------ehHHHHH---HHHHHhh---cCCceEEEcc
Q psy5461         164 GNIAAVTGLKRERGKDKRTRVI-PK-------PTSVV-------------QCSARWT---LNLEVGA---SSPIISKSKR  216 (221)
Q Consensus       164 GdIv~i~gl~~~~~Gdtl~~~~-~~-------p~~~v-------------~~~~l~~---~L~~L~~---~Dp~l~~~~~  216 (221)
                      ||||++.|++++.+|||||+.. +.       |.|++             +.+++.+   ++++|.+   +||+|.+.++
T Consensus       271 GdIvai~gl~~~~~GdTl~~~~~~~~l~~~~~~~P~~~~~~~~~~sp~~g~e~k~~t~~~~~~rL~~~~~~D~sl~v~~~  350 (607)
T PRK10218        271 GDIVAITGLGELNISDTVCDTQNVEALPALSVDEPTVSMFFCVNTSPFCGKEGKFVTSRQILDRLNKELVHNVALRVEET  350 (607)
T ss_pred             CCEEEEECccccccCcEEecCCCcccCCCCCCCCCeEEEEEEeCCCccccchhhhhhHHHHHHHHHHhhCCCCeEEEEEc
Confidence            9999999999999999998651 11       12332             4466644   5555555   9999999887


Q ss_pred             c
Q psy5461         217 R  217 (221)
Q Consensus       217 ~  217 (221)
                      .
T Consensus       351 ~  351 (607)
T PRK10218        351 E  351 (607)
T ss_pred             C
Confidence            4

>PRK07560 elongation factor EF-2; Reviewed

Probab=99.95  E-value=3.5e-27  Score=226.95  Aligned_cols=159  Identities=26%  Similarity=0.376  Sum_probs=140.4

Q ss_pred             eeEecCCCccccHH----------------------------------HHHHHHHhhCCCCCCcccc-------------
Q psy5461          59 PVLCGSSYKNIGVQ----------------------------------KLMDAIVDILPSPTERPAL-------------   91 (221)
Q Consensus        59 Pv~~gSa~~~~Gi~----------------------------------~LLd~I~~~~PsP~~~~~~-------------   91 (221)
                      .|+++||+.++|+.                                  .|||+|++++|+|.+++..             
T Consensus       198 ~v~~~sa~~~~~~~~~~~~~~~~~~~~l~e~~~~~~~~~l~~~~Pv~~~Lld~I~~~lPsP~~~~~~~~~~~~~~~~~~~  277 (731)
T PRK07560        198 TVAFGSALYNWAISVPMMQKTGIKFKDIIDYYEKGKQKELAEKAPLHEVVLDMVVKHLPNPIEAQKYRIPKIWKGDLNSE  277 (731)
T ss_pred             cEeeeecccccceeHHHHHHhCCCHHHHHHHHhcCCHHHHHhhccchhHHHHHHHHhCCChhhhhhhcccccccCCCCcc
Confidence            47899999999886                                  8999999999999864421             


Q ss_pred             ----cccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEE
Q psy5461          92 ----AMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA  167 (221)
Q Consensus        92 ----~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv  167 (221)
                          ...|++++|++|+|||+.+|+++|+++|+|||||+|++||+|++.+.++++++++|+.++|++..+++++.|||||
T Consensus       278 ~~~~~~~~d~~~p~~a~VfK~~~d~~~G~va~~RV~sGtL~~Gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~AGdIv  357 (731)
T PRK07560        278 VGKAMLNCDPNGPLVMMVTDIIVDPHAGEVATGRVFSGTLRKGQEVYLVGAKKKNRVQQVGIYMGPEREEVEEIPAGNIA  357 (731)
T ss_pred             ccceeeccCCCCCEEEEEEeeEEcCCCCeEEEEEEEEeEEcCCCEEEEcCCCCceEeheehhhhcCCCceeeeECCCCEE
Confidence                1235677899999999999999999999999999999999999999888899999999999999999999999999


Q ss_pred             EEcCCCCCccCcEEecCC---------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         168 AVTGLKRERGKDKRTRVI---------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       168 ~i~gl~~~~~Gdtl~~~~---------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                      ++.|++++.+||||+...         ..|.|++          |.++|.+||++|+++||+|.+.++.
T Consensus       358 ~i~gl~~~~~GdtL~~~~~~~~~~~~~~~p~Pv~~~aI~p~~~~d~~kL~~aL~~L~~eDPsl~v~~~~  426 (731)
T PRK07560        358 AVTGLKDARAGETVVSVEDMTPFESLKHISEPVVTVAIEAKNPKDLPKLIEVLRQLAKEDPTLVVKINE  426 (731)
T ss_pred             EEEcccccccCCEEeCCCccccccccccCCCCeEEEEEEECCHHHHHHHHHHHHHHHhhCCcEEEEEcC
Confidence            999999999999998641         1234555          7899999999999999999998874

>TIGR01394 TypA_BipA GTP-binding protein TypA/BipA

Probab=99.95  E-value=3.8e-26  Score=214.64  Aligned_cols=188  Identities=19%  Similarity=0.205  Sum_probs=150.9

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcc------ccccCceeEecCCCccc----------cHHHHHHHHHhhCCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA------FKKNHVPVLCGSSYKNI----------GVQKLMDAIVDILPSPT   86 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~------~~~~~~Pv~~gSa~~~~----------Gi~~LLd~I~~~~PsP~   86 (221)
                      .+-|++..+||++.......-....+....      .+...+|++++||++|+          |+.+||+.|++++|+|.
T Consensus       115 ~~ip~IVviNKiD~~~a~~~~v~~ei~~l~~~~g~~~e~l~~pvl~~SA~~g~~~~~~~~~~~gi~~Lld~Iv~~lP~P~  194 (594)
T TIGR01394       115 LGLKPIVVINKIDRPSARPDEVVDEVFDLFAELGADDEQLDFPIVYASGRAGWASLDLDDPSDNMAPLFDAIVRHVPAPK  194 (594)
T ss_pred             CCCCEEEEEECCCCCCcCHHHHHHHHHHHHHhhccccccccCcEEechhhcCcccccCcccccCHHHHHHHHHHhCCCCC
Confidence            456889999996643221111222222211      13346899999999997          89999999999999997


Q ss_pred             CcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCc---eeeeceeEeeecCCeeeeCcccc
Q psy5461          87 ERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ---SEQITRLLLAEADDYKEVNEIQC  163 (221)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~---~~~v~~i~~~~g~~~~~v~~a~a  163 (221)
                      .        +.++||+++||+++++++.|+++++||++|+|++||+|++.+.+.   +++|++|+.+.|.++.++++|.|
T Consensus       195 ~--------~~~~pl~~~V~~i~~d~~~Grv~~gRV~sG~lk~G~~V~~~~~~~~~~~~kV~~i~~~~g~~~~~v~~a~a  266 (594)
T TIGR01394       195 G--------DLDEPLQMLVTNLDYDEYLGRIAIGRVHRGTVKKGQQVALMKRDGTIENGRISKLLGFEGLERVEIDEAGA  266 (594)
T ss_pred             C--------CCCCCEEEEEEEEEeeCCCceEEEEEEEeCEEccCCEEEEecCCCceeEEEEEEEEEccCCCceECCEECC
Confidence            5        567999999999999999999999999999999999999987632   47999999999999999999999


Q ss_pred             CCEEEEcCCCCCccCcEEecCC-CC-------CCCce-------------eh-H-----HHHHHHHHHhhcCCceEEEcc
Q psy5461         164 GNIAAVTGLKRERGKDKRTRVI-PK-------PTSVV-------------QC-S-----ARWTLNLEVGASSPIISKSKR  216 (221)
Q Consensus       164 GdIv~i~gl~~~~~Gdtl~~~~-~~-------p~~~v-------------~~-~-----~l~~~L~~L~~~Dp~l~~~~~  216 (221)
                      ||||++.|++++.+|||||+.. +.       |.|++             +. .     +|.++|.+++++||+|.+.++
T Consensus       267 GDiv~i~gl~~i~~Gdtl~~~~~~~~l~~~~~~~P~~~~~~~~~~~p~~~~e~k~~t~~~l~~~L~k~~~~d~sl~v~~~  346 (594)
T TIGR01394       267 GDIVAVAGLEDINIGETIADPEVPEALPTITVDEPTLSMTFSVNDSPLAGKEGKKVTSRHIRDRLMRELETNVALRVEDT  346 (594)
T ss_pred             CCEEEEeCCcccCCCCEEeCCCccccCCCCCCCCCeEEEEEEecCCCcccccchhhhHHHHHHHHHHhhccCCeEEEEEe
Confidence            9999999999999999998752 11       12333             11 2     399999999999999999887


Q ss_pred             cc
Q psy5461         217 RQ  218 (221)
Q Consensus       217 ~~  218 (221)
                      .+
T Consensus       347 ~~  348 (594)
T TIGR01394       347 ES  348 (594)
T ss_pred             cC
Confidence            54

This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP-binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.

>TIGR01393 lepA GTP-binding protein LepA

Probab=99.94  E-value=2.5e-25  Score=209.35  Aligned_cols=185  Identities=17%  Similarity=0.222  Sum_probs=146.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcE
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLC  102 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~  102 (221)
                      .+.+++..+||++......+.....+.+. ......+++++||++|.||++|++.|.+.+|+|..        +.++||+
T Consensus       121 ~~ipiIiViNKiDl~~~~~~~~~~el~~~-lg~~~~~vi~vSAktG~GI~~Lle~I~~~lp~p~~--------~~~~pl~  191 (595)
T TIGR01393       121 NDLEIIPVINKIDLPSADPERVKKEIEEV-IGLDASEAILASAKTGIGIEEILEAIVKRVPPPKG--------DPDAPLK  191 (595)
T ss_pred             cCCCEEEEEECcCCCccCHHHHHHHHHHH-hCCCcceEEEeeccCCCCHHHHHHHHHHhCCCCCC--------CCCCCeE
Confidence            35688999999664321111112233221 11112258999999999999999999999999976        5678999


Q ss_pred             EEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc-C---CCCCccC
Q psy5461         103 ARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT-G---LKRERGK  178 (221)
Q Consensus       103 ~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~-g---l~~~~~G  178 (221)
                      |+||++++|+++|+++++||++|+|++||+|++.++++.+++.+|+.+.+ +..+++++.||||+.+. |   ++++++|
T Consensus       192 ~~V~~~~~d~~~G~v~~~rV~sG~lk~Gd~v~~~~~~~~~~v~~i~~~~~-~~~~v~~~~aGdIg~i~~~~~~~~~~~~G  270 (595)
T TIGR01393       192 ALIFDSHYDNYRGVVALVRVFEGTIKPGDKIRFMSTGKEYEVDEVGVFTP-KLTKTDELSAGEVGYIIAGIKDVSDVRVG  270 (595)
T ss_pred             EEEEEEEEeCCCcEEEEEEEECCEEecCCEEEEecCCCeeEEeEEEEecC-CceECCEEcCCCEEEEeccccccCccCCC
Confidence            99999999999999999999999999999999999888899999996554 55899999999999664 4   4568999


Q ss_pred             cEEecCC-C---------CCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         179 DKRTRVI-P---------KPTSVV----------QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       179 dtl~~~~-~---------~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                      ||++... +         .|.|++          |.++|.+||++|+++||+|++...-
T Consensus       271 dtl~~~~~~~~~~l~~~~~~~P~v~~~i~p~~~~d~~kL~~aL~kL~~eD~sl~~~~e~  329 (595)
T TIGR01393       271 DTITHVKNPAKEPLPGFKEVKPMVFAGLYPIDTEDYEDLRDALEKLKLNDASLTYEPES  329 (595)
T ss_pred             CEEECCCCccccCCCCCcCCCcEEEEEEEECCcccHHHHHHHHHHHhccCCeEEEEecC
Confidence            9998652 1         123666          7789999999999999999998643

LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function is unknown.

>PRK05433 GTP-binding protein LepA; Provisional

Probab=99.94  E-value=3.7e-25  Score=208.39  Aligned_cols=184  Identities=17%  Similarity=0.212  Sum_probs=145.9

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcE
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLC  102 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~  102 (221)
                      .+.+++..+||++......+-....+.+. ......+++++||++|.||++|+++|.+.+|+|..        +.++||.
T Consensus       125 ~~lpiIvViNKiDl~~a~~~~v~~ei~~~-lg~~~~~vi~iSAktG~GI~~Ll~~I~~~lp~P~~--------~~~~pl~  195 (600)
T PRK05433        125 NDLEIIPVLNKIDLPAADPERVKQEIEDV-IGIDASDAVLVSAKTGIGIEEVLEAIVERIPPPKG--------DPDAPLK  195 (600)
T ss_pred             CCCCEEEEEECCCCCcccHHHHHHHHHHH-hCCCcceEEEEecCCCCCHHHHHHHHHHhCccccC--------CCCCCce
Confidence            35688999999654321111112222221 11111248899999999999999999999999975        5678999


Q ss_pred             EEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc-C---CCCCccC
Q psy5461         103 ARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT-G---LKRERGK  178 (221)
Q Consensus       103 ~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~-g---l~~~~~G  178 (221)
                      |+|||+++|+++|+++++||++|+|++||+|++..+++.++|.+|+.+ +++..+++++.||||+.+. |   ++++++|
T Consensus       196 ~~Vfd~~~d~~~G~v~~~rV~sG~Lk~Gd~i~~~~~~~~~~V~~i~~~-~~~~~~v~~~~aGdIg~i~~~ik~~~~~~~G  274 (600)
T PRK05433        196 ALIFDSWYDNYRGVVVLVRVVDGTLKKGDKIKMMSTGKEYEVDEVGVF-TPKMVPVDELSAGEVGYIIAGIKDVRDARVG  274 (600)
T ss_pred             EEEEEEEecCCCceEEEEEEEcCEEecCCEEEEecCCceEEEEEeecc-CCCceECcEEcCCCEEEEecccccccccCCC
Confidence            999999999999999999999999999999999998888999999955 4588999999999999764 4   4578999


Q ss_pred             cEEecCC-C---------CCCCce----------ehHHHHHHHHHHhhcCCceEEEcc
Q psy5461         179 DKRTRVI-P---------KPTSVV----------QCSARWTLNLEVGASSPIISKSKR  216 (221)
Q Consensus       179 dtl~~~~-~---------~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~  216 (221)
                      |||+... +         .|.|++          |.++|.+||++|+++||+|++...
T Consensus       275 dtl~~~~~~~~~~l~~~~~~~P~v~~~i~p~~~~d~~kL~~aL~kL~~eD~sl~~~~e  332 (600)
T PRK05433        275 DTITLAKNPAEEPLPGFKEVKPMVFAGLYPVDSDDYEDLRDALEKLQLNDASLTYEPE  332 (600)
T ss_pred             CEEECCCCccccCCCCCCCCCcEEEEEEEECCccCHHHHHHHHHHHHHhCCeEEEEec
Confidence            9998652 1         233666          678999999999999999999744

>TIGR00490 aEF-2 translation elongation factor aEF-2

Probab=99.93  E-value=2.7e-25  Score=213.48  Aligned_cols=148  Identities=26%  Similarity=0.351  Sum_probs=129.9

Q ss_pred             HHHHHHHHHhhCCCCCCccc-----------------ccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEE
Q psy5461          71 VQKLMDAIVDILPSPTERPA-----------------LAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKF  133 (221)
Q Consensus        71 i~~LLd~I~~~~PsP~~~~~-----------------~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v  133 (221)
                      ++.|||+|++++|+|.+++.                 ..+.|++++|++++|||+.++++.|+++|+|||||+|++||+|
T Consensus       243 ~~~Lld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~pl~a~VfK~~~~~~~G~ia~~RV~sGtL~~G~~l  322 (720)
T TIGR00490       243 HQVVLDMVIRHLPSPIEAQKYRIPVIWKGDLNSEVGKAMLNCDPKGPLALMITKIVVDKHAGEVAVGRLYSGTIRPGMEV  322 (720)
T ss_pred             HHHHHHHHHHhCCChhhhhhhcccccccCCCCccchhhcccCCCCCCeEEEEEEEEecCCCcEEEEEEEEeCEEcCCCEE
Confidence            57999999999999976421                 0134667889999999999999999999999999999999999


Q ss_pred             EeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC------C----CCCCce----------e
Q psy5461         134 YNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI------P----KPTSVV----------Q  193 (221)
Q Consensus       134 ~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~------~----~p~~~v----------~  193 (221)
                      ++.++++.++|++|+.++|++.++++++.|||||++.|++++.+||||++..      +    .|.|++          |
T Consensus       323 ~~~~~~~~~kv~~l~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~GdtL~~~~~~~~~~~~~~~~~~Pv~~~~i~p~~~~d  402 (720)
T TIGR00490       323 YIVDRKAKARIQQVGVYMGPERVEVDEIPAGNIVAVIGLKDAVAGETICTTVENITPFESIKHISEPVVTVAIEAKNTKD  402 (720)
T ss_pred             EEcCCCCeeEeeEEEEeccCCccCccEECCCCEEEEECccccccCceeecCCcccccCcccccCCCceEEEEEEECCHHH
Confidence            9999998899999999999999999999999999999999999999997541      1    134666          7


Q ss_pred             hHHHHHHHHHHhhcCCceEEEcccc
Q psy5461         194 CSARWTLNLEVGASSPIISKSKRRQ  218 (221)
Q Consensus       194 ~~~l~~~L~~L~~~Dp~l~~~~~~~  218 (221)
                      .++|.++|++|+++||+|++.++..
T Consensus       403 ~~kL~~aL~~L~~eDPsl~v~~d~e  427 (720)
T TIGR00490       403 LPKLIEVLRQVAKEDPTVHVEINEE  427 (720)
T ss_pred             HHHHHHHHHHHHhhCCeEEEEECCC
Confidence            8999999999999999999988653

This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD.

>COG4108 PrfC Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]

Probab=99.92  E-value=2.2e-25  Score=197.37  Aligned_cols=166  Identities=24%  Similarity=0.303  Sum_probs=141.5

Q ss_pred             ccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCC-CCCcEEEEEEEeec---CCCceEEEEEEEceE
Q psy5461          51 GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHF-GDSLCARAFKVVHD---KHRGAVTFFRIYSGA  126 (221)
Q Consensus        51 ~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~-~~~~~~~Vfk~~~d---~~~G~i~~~RV~sG~  126 (221)
                      ..+++..+|||||||++|.||+.|||++++|.|+|..+........+ +..|.+||||+...   +|+.++||+||+||.
T Consensus       244 ~fl~G~~TPVFFGSAl~NFGV~~~L~~~~~~AP~P~~~~a~~~~v~p~e~kfsGFVFKIQANMDp~HRDRIAFmRv~SGk  323 (528)
T COG4108         244 AFLAGELTPVFFGSALGNFGVDHFLDALVDWAPSPRARQADTREVEPTEDKFSGFVFKIQANMDPKHRDRIAFMRVCSGK  323 (528)
T ss_pred             HHhcCCccceEehhhhhccCHHHHHHHHHhhCCCCCcccCCcCcccCCCCccceEEEEEEcCCCcccccceeEEEecccc
Confidence            35778899999999999999999999999999999887554322233 34699999999873   689999999999999


Q ss_pred             EcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecC---------CCCCC--Cce---
Q psy5461         127 FKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRV---------IPKPT--SVV---  192 (221)
Q Consensus       127 L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~---------~~~p~--~~v---  192 (221)
                      +.+|+++...++|+..++.+-..+++.+++.+++|.||||++|.+-..+++|||++..         .+.|.  .+|   
T Consensus       324 ferGMkv~h~rtGK~~~ls~~~~f~A~dRe~ve~A~aGDIIGl~nhG~~~IGDT~t~Ge~l~f~giP~FaPE~frrvr~k  403 (528)
T COG4108         324 FERGMKVTHVRTGKDVKLSDALTFMAQDRETVEEAYAGDIIGLHNHGTIQIGDTFTEGEKLKFTGIPNFAPELFRRVRLK  403 (528)
T ss_pred             ccCCceeeeeecCCceEecchHhhhhhhhhhhhhccCCCeEeccCCCceeecceeecCceeeecCCCCCCHHHHHHHhcC
Confidence            9999999999999999999999999999999999999999999998899999999886         12232  333   


Q ss_pred             ---ehHHHHHHHHHHhhcCCceEEEcc
Q psy5461         193 ---QCSARWTLNLEVGASSPIISKSKR  216 (221)
Q Consensus       193 ---~~~~l~~~L~~L~~~Dp~l~~~~~  216 (221)
                         ...+|.+||++|++|....-|+..
T Consensus       404 d~~K~Kql~Kgl~QL~eEGavQ~f~p~  430 (528)
T COG4108         404 DPLKQKQLKKGLEQLAEEGAVQVFKPL  430 (528)
T ss_pred             ChHHHHHHHHHHHHHhhcCeeEEEecC
Confidence               668999999999999877555543

>PLN00116 translation elongation factor EF-2 subunit; Provisional

Probab=99.92  E-value=4.9e-25  Score=214.69  Aligned_cols=161  Identities=19%  Similarity=0.239  Sum_probs=134.2

Q ss_pred             HhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc-----------------cccCCCCCCcEEEEEEEee
Q psy5461          48 IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL-----------------AMFQHFGDSLCARAFKVVH  110 (221)
Q Consensus        48 l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~-----------------~~~~~~~~~~~~~Vfk~~~  110 (221)
                      +++++.+...+|+|++|       +.|||+|++++|+|.+++..                 .+.|++++|++|+|||+.+
T Consensus       313 ~~~~l~~~~~~pv~~~s-------~~Lld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~pl~a~VfK~~~  385 (843)
T PLN00116        313 MGKALMKRVMQTWLPAS-------DALLEMIIFHLPSPAKAQRYRVENLYEGPLDDKYATAIRNCDPNGPLMLYVSKMIP  385 (843)
T ss_pred             hhHHHHHHHHHhhcCCh-------HHHHHHHHHhCCChHHhhhHHhhhccCCCCCccccchhhcCCCCCCeEEEEEeeee
Confidence            57778888899999987       69999999999999754311                 1346778899999999999


Q ss_pred             cCCCce-EEEEEEEceEEcCCCEEEe----ccCCce-----eeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-ccCc
Q psy5461         111 DKHRGA-VTFFRIYSGAFKKGQKFYN----IHLDQS-----EQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-RGKD  179 (221)
Q Consensus       111 d~~~G~-i~~~RV~sG~L~~gd~v~~----~~~~~~-----~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-~~Gd  179 (221)
                      +++.|+ ++|+|||||+|++||+|++    .+.+++     +++.+|+.++|.+.++++++.|||||++.|+++. ..||
T Consensus       386 ~~~~g~~l~~~RVysGtL~~g~~v~v~~~n~~~~~~~~~~~~~v~~l~~~~g~~~~~v~~~~AGdI~ai~gl~~~~~~gd  465 (843)
T PLN00116        386 ASDKGRFFAFGRVFSGTVATGMKVRIMGPNYVPGEKKDLYVKSVQRTVIWMGKKQESVEDVPCGNTVAMVGLDQFITKNA  465 (843)
T ss_pred             cCCCCeEEEEEEEEeeeecCCCEEEEeCCCCCCCCccccceeEhheEEEecCCCceECcEECCCCEEEEEeecccccCCc
Confidence            998888 9999999999999999984    333332     5889999999999999999999999999999876 4499


Q ss_pred             EEecCC--C--------CC-CCce----------ehHHHHHHHHHHhhcCCceEEEc
Q psy5461         180 KRTRVI--P--------KP-TSVV----------QCSARWTLNLEVGASSPIISKSK  215 (221)
Q Consensus       180 tl~~~~--~--------~p-~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~  215 (221)
                      ||++..  .        .| .|++          |.++|++||++|+++||++++..
T Consensus       466 TL~~~~~~~~~~l~~~~~~~~Pv~~~aIeP~~~~d~~kL~~aL~~L~~eDPsl~v~~  522 (843)
T PLN00116        466 TLTNEKEVDAHPIKAMKFSVSPVVRVAVQCKNASDLPKLVEGLKRLAKSDPMVQCTI  522 (843)
T ss_pred             eecCCcccCCccccccccCCCceEEEEEEECChhhHHHHHHHHHHHHHhCCCeEEEE
Confidence            997642  1        12 3555          88999999999999999999854

>PTZ00416 elongation factor 2; Provisional

Probab=99.91  E-value=6.1e-24  Score=206.78  Aligned_cols=157  Identities=22%  Similarity=0.317  Sum_probs=129.5

Q ss_pred             HHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc-----------------cccCCCCCCcEEEEEEEe
Q psy5461          47 RIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL-----------------AMFQHFGDSLCARAFKVV  109 (221)
Q Consensus        47 ~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~-----------------~~~~~~~~~~~~~Vfk~~  109 (221)
                      .+.+++. +..+|+          ++.|||+|++++|+|.+++..                 .+.|++++|++|+|||+.
T Consensus       312 ~l~~~~~-~~~~Pv----------~~~Lld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~plva~VfK~~  380 (836)
T PTZ00416        312 PLLKAVM-QKWLPA----------ADTLLEMIVDHLPSPKEAQKYRVENLYEGPMDDEAANAIRNCDPNGPLMMYISKMV  380 (836)
T ss_pred             HHHHHHH-HHHhch----------HHHHHHHHHHhCCChhHhCchhhhccccCCCCccccceeeccCCCCCeEEEEEeee
Confidence            3455555 567776          789999999999999764321                 134677889999999999


Q ss_pred             ecCCCce-EEEEEEEceEEcCCCEEEecc----CCcee-----eeceeEeeecCCeeeeCccccCCEEEEcCCCC--Ccc
Q psy5461         110 HDKHRGA-VTFFRIYSGAFKKGQKFYNIH----LDQSE-----QITRLLLAEADDYKEVNEIQCGNIAAVTGLKR--ERG  177 (221)
Q Consensus       110 ~d~~~G~-i~~~RV~sG~L~~gd~v~~~~----~~~~~-----~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~--~~~  177 (221)
                      ++++.|+ ++|+|||||+|+.||+|++.+    .++++     ++++|+.++|++..+++++.|||||+|.|+++  .++
T Consensus       381 ~~~~~g~~~s~~RV~SGtL~~g~~v~v~~~~~~~~~~e~~~~~~i~~l~~~~g~~~~~v~~v~AGdI~~i~gl~~~~~~t  460 (836)
T PTZ00416        381 PTSDKGRFYAFGRVFSGTVATGQKVRIQGPNYVPGKKEDLFEKNIQRTVLMMGRYVEQIEDVPCGNTVGLVGVDQYLVKS  460 (836)
T ss_pred             ecCCCCcEEEEEEEEeeeecCCCEEEEeCCCCCCCCcccchheecceeEEecCCCceECcEECCCCEEEEEecccceecc
Confidence            9999999 899999999999999999543    33334     59999999999999999999999999999988  799


Q ss_pred             CcEEecCC---------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEc
Q psy5461         178 KDKRTRVI---------PKPTSVV----------QCSARWTLNLEVGASSPIISKSK  215 (221)
Q Consensus       178 Gdtl~~~~---------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~  215 (221)
                      | ||++..         .+|.|++          |+++|++||++|+++||++.+..
T Consensus       461 g-TL~~~~~~~~l~~i~~~~~Pv~~vaIep~~~~d~~kL~~aL~~L~~eDPsl~~~~  516 (836)
T PTZ00416        461 G-TITTSETAHNIRDMKYSVSPVVRVAVEPKNPKDLPKLVEGLKRLAKSDPLVVCTT  516 (836)
T ss_pred             e-eecCCCCcccccccccCCCCeEEEEEEECCHHHHHHHHHHHHHHHhhCCceEEEE
Confidence            9 997542         1124555          88999999999999999998854

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

Probab=99.91  E-value=2e-23  Score=186.59  Aligned_cols=186  Identities=18%  Similarity=0.239  Sum_probs=150.2

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhh--ccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCC
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYS--GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGD   99 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~--~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~   99 (221)
                      +.+.+++--+||++-+.-..+-....+..  |....   -.+..||++|.||+++|++|++.+|+|..        +++.
T Consensus       126 e~~LeIiPViNKIDLP~Adpervk~eIe~~iGid~~---dav~~SAKtG~gI~~iLe~Iv~~iP~P~g--------~~~~  194 (603)
T COG0481         126 ENNLEIIPVLNKIDLPAADPERVKQEIEDIIGIDAS---DAVLVSAKTGIGIEDVLEAIVEKIPPPKG--------DPDA  194 (603)
T ss_pred             HcCcEEEEeeecccCCCCCHHHHHHHHHHHhCCCcc---hheeEecccCCCHHHHHHHHHhhCCCCCC--------CCCC
Confidence            46788999999986443222222222221  22222   24567999999999999999999999987        7899


Q ss_pred             CcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEE-EEcCCC---CC
Q psy5461         100 SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA-AVTGLK---RE  175 (221)
Q Consensus       100 ~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv-~i~gl~---~~  175 (221)
                      |+.|.+|+.|+|+++|.++++||+.|++++||++....+|++..|.++.++ .++..+.+++.||+++ .++|++   +.
T Consensus       195 pLkALifDS~yD~Y~GVv~~vRi~dG~ik~gdki~~m~tg~~y~V~evGvf-tP~~~~~~~L~aGeVG~~~a~iK~v~d~  273 (603)
T COG0481         195 PLKALIFDSWYDNYLGVVVLVRIFDGTLKKGDKIRMMSTGKEYEVDEVGIF-TPKMVKVDELKAGEVGYIIAGIKDVRDA  273 (603)
T ss_pred             cceEEEEeccccccceEEEEEEEeeceecCCCEEEEEecCCEEEEEEEeec-cCCccccccccCCceeEEEEeeeecccC
Confidence            999999999999999999999999999999999999999999999999966 4688999999999999 455655   67


Q ss_pred             ccCcEEecCC-C---------CCCCce----------ehHHHHHHHHHHhhcCCceEEEccccc
Q psy5461         176 RGKDKRTRVI-P---------KPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQN  219 (221)
Q Consensus       176 ~~Gdtl~~~~-~---------~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~~  219 (221)
                      ++|||++... |         ++.|+|          |-+.|.+||++|.++|.+|+|...-+.
T Consensus       274 ~VGDTiT~~~~p~~e~LpGfk~~~P~Vf~GlyPid~~dye~LrdAleKL~LNDasl~~E~EtS~  337 (603)
T COG0481         274 RVGDTITLASNPATEPLPGFKEVKPMVFAGLYPVDSDDYEDLRDALEKLQLNDASLTYEPETSQ  337 (603)
T ss_pred             cccceEeccCCCccccCCCCCcCCceEEEeecccChhHHHHHHHHHHhcccccceeeeccccch
Confidence            9999998542 1         223777          568999999999999999999876553

>COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]

Probab=99.89  E-value=3.8e-22  Score=178.04  Aligned_cols=185  Identities=17%  Similarity=0.216  Sum_probs=149.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHh------hccccccCceeEecCCCccc----------cHHHHHHHHHhhCCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIY------SGAFKKNHVPVLCGSSYKNI----------GVQKLMDAIVDILPSPT   86 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~------~~~~~~~~~Pv~~gSa~~~~----------Gi~~LLd~I~~~~PsP~   86 (221)
                      .+.+.+.-|||++-+..+..-....+.      .+..++.+||++|+||+.|+          .+.+|+|+|.+++|+|.
T Consensus       119 ~gL~PIVVvNKiDrp~Arp~~Vvd~vfDLf~~L~A~deQLdFPivYAS~~~G~a~~~~~~~~~~m~pLfe~I~~hvp~P~  198 (603)
T COG1217         119 LGLKPIVVINKIDRPDARPDEVVDEVFDLFVELGATDEQLDFPIVYASARNGTASLDPEDEADDMAPLFETILDHVPAPK  198 (603)
T ss_pred             cCCCcEEEEeCCCCCCCCHHHHHHHHHHHHHHhCCChhhCCCcEEEeeccCceeccCccccccchhHHHHHHHHhCCCCC
Confidence            456777899998655333333333333      34567789999999999995          58999999999999998


Q ss_pred             CcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC---ceeeeceeEeeecCCeeeeCcccc
Q psy5461          87 ERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD---QSEQITRLLLAEADDYKEVNEIQC  163 (221)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~---~~~~v~~i~~~~g~~~~~v~~a~a  163 (221)
                      .        +.++||.++|+.+.++++.|++.++||++|++++|+++.....+   +..||++++-+.|-++.++++|.|
T Consensus       199 ~--------~~d~PlQ~qvt~Ldyn~y~GrIgigRi~~G~vk~~q~V~~i~~~g~~~~gri~kllgf~GL~R~ei~eA~A  270 (603)
T COG1217         199 G--------DLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALIKSDGTTENGRITKLLGFLGLERIEIEEAEA  270 (603)
T ss_pred             C--------CCCCCeEEEEEeeccccccceeEEEEEecCcccCCCeEEEEcCCCcEEeeEEEeeeeccceeeeecccccc
Confidence            6        78999999999999999999999999999999999999998765   357999999999999999999999


Q ss_pred             CCEEEEcCCCCCccCcEEecCC-CCCC-------Cce-------------------ehHHHHHHHHHHhhcCCceEEEc
Q psy5461         164 GNIAAVTGLKRERGKDKRTRVI-PKPT-------SVV-------------------QCSARWTLNLEVGASSPIISKSK  215 (221)
Q Consensus       164 GdIv~i~gl~~~~~Gdtl~~~~-~~p~-------~~v-------------------~~~~l~~~L~~L~~~Dp~l~~~~  215 (221)
                      |||++|+|++++.+|||+|+.. +.+.       |.+                   ---++.+.|.+=...+-+|.+..
T Consensus       271 GDIVaiaG~~~~~igdTi~d~~~~~aLp~l~iDePTlsMtf~vN~SPfAG~EGk~vTSR~i~dRL~~El~~NValrVe~  349 (603)
T COG1217         271 GDIVAIAGLEDINIGDTICDPDNPEALPALSVDEPTLSMTFSVNDSPFAGKEGKFVTSRQIRDRLNKELETNVALRVEE  349 (603)
T ss_pred             cCEEEEcCcccccccccccCCCCccCCCCcccCCCceEEEEEecCCCCCCcCCceeeHHHHHHHHHHHhhhceeEEEee
Confidence            9999999999999999999862 2111       111                   11366777777777777776654

>KOG0464|consensus

Probab=99.88  E-value=2e-23  Score=184.18  Aligned_cols=174  Identities=34%  Similarity=0.515  Sum_probs=147.8

Q ss_pred             HHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEc
Q psy5461          45 FFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYS  124 (221)
Q Consensus        45 ~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~s  124 (221)
                      ...+++.+..+...||+||||.++.||++|||++.-|+|+|.++. +++.---...++|..||+.+|+.+|.++|+|||+
T Consensus       280 ksai~~lt~aq~a~~i~cgsaiknkgiqplldavtmylpspeern-yeflqwykddlcalafkvlhdkqrg~l~fmriys  358 (753)
T KOG0464|consen  280 KSAIHELTCAQKAAPILCGSAIKNKGIQPLLDAVTMYLPSPEERN-YEFLQWYKDDLCALAFKVLHDKQRGPLSFMRIYS  358 (753)
T ss_pred             HHHHHHHhhhhhhcceehhhhhcccCccchhhhhhhccCChhhcc-hHHHhhhhhhHHHHhhhhhcccccCceeEEEEec
Confidence            445566677788999999999999999999999999999998863 2110012356899999999999999999999999


Q ss_pred             eEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC-------------------
Q psy5461         125 GAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI-------------------  185 (221)
Q Consensus       125 G~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~-------------------  185 (221)
                      |+++..-.++|.+....+.+.+++...+++...++++.||+|....|++...+|||+....                   
T Consensus       359 gsi~~~~ai~nin~~~se~~~kl~~pfade~~~i~qlsagnialt~glk~tatgdtivaskasa~aa~qk~~~egekk~~  438 (753)
T KOG0464|consen  359 GSIHNNLAIFNINGMCSEGILKLFLPFADEHREIEQLSAGNIALTAGLKHTATGDTIVASKASAEAAAQKAAGEGEKKHL  438 (753)
T ss_pred             ccccCceeeeecccccccchHhhhccchhhhhhhhhcccccEEEEecceeeccCCeEEecchhHHHHHHHhhccchhhcc
Confidence            9999999999998777889999999999999999999999999999999999999996530                   


Q ss_pred             -------------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEccccc
Q psy5461         186 -------------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQN  219 (221)
Q Consensus       186 -------------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~~  219 (221)
                                   ..|.++.          +++++..||+.|..+|||+.++.++.+
T Consensus       439 q~~daerll~agie~pd~vffc~iepps~~k~~d~ehale~lqredpslkir~d~ds  495 (753)
T KOG0464|consen  439 QNKDAERLLFAGIEIPDAVFFCCIEPPSLRKLNDFEHALECLQREDPSLKIRFDPDS  495 (753)
T ss_pred             CCccccceeeecccCCCceEEEeccCcccccchhHHHHHHHHhccCCceeEEecCCC
Confidence                         0132333          678999999999999999999988754

>cd03690 Tet_II Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O)

Probab=99.88  E-value=6.1e-22  Score=141.82  Aligned_cols=85  Identities=24%  Similarity=0.380  Sum_probs=80.2

Q ss_pred             CCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCcc
Q psy5461          98 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERG  177 (221)
Q Consensus        98 ~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~  177 (221)
                      ++||+|+|||+.+|++.|+++|+|||||+|++||.+++.+ ++.+++.+|+.++|.+..+++++.||||+++.|++++.+
T Consensus         1 ~~p~~~~Vfkv~~d~~~G~la~~RV~sG~l~~g~~v~~~~-~~~~~v~~l~~~~g~~~~~v~~~~aGdI~ai~gl~~~~~   79 (85)
T cd03690           1 ESELSGTVFKIERDDKGERLAYLRLYSGTLRLRDSVRVNR-EEKIKITELRVFNNGEVVTADTVTAGDIAILTGLKGLRV   79 (85)
T ss_pred             CCCcEEEEEEeEECCCCCeEEEEEEccCEEcCCCEEEeCC-CcEEEeceeEEEeCCCeEECcEECCCCEEEEECCCCCcC
Confidence            3789999999999999999999999999999999999877 566899999999999999999999999999999999999


Q ss_pred             CcEEec
Q psy5461         178 KDKRTR  183 (221)
Q Consensus       178 Gdtl~~  183 (221)
                      ||||++
T Consensus        80 Gdtl~~   85 (85)
T cd03690          80 GDVLGD   85 (85)
T ss_pred             ccccCC
Confidence            999863

This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.

>KOG0462|consensus

Probab=99.87  E-value=6.6e-22  Score=179.22  Aligned_cols=188  Identities=15%  Similarity=0.171  Sum_probs=149.3

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCc
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSL  101 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~  101 (221)
                      +....++--+||++-.....+-+...+.+..... --++++.||++|+|+.++|++|++.+|+|..        ..++||
T Consensus       175 e~~L~iIpVlNKIDlp~adpe~V~~q~~~lF~~~-~~~~i~vSAK~G~~v~~lL~AII~rVPpP~~--------~~d~pl  245 (650)
T KOG0462|consen  175 EAGLAIIPVLNKIDLPSADPERVENQLFELFDIP-PAEVIYVSAKTGLNVEELLEAIIRRVPPPKG--------IRDAPL  245 (650)
T ss_pred             HcCCeEEEeeeccCCCCCCHHHHHHHHHHHhcCC-ccceEEEEeccCccHHHHHHHHHhhCCCCCC--------CCCcch
Confidence            4577888999998644333333344444433333 3379999999999999999999999999987        678999


Q ss_pred             EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEE-EEcC---CCCCcc
Q psy5461         102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA-AVTG---LKRERG  177 (221)
Q Consensus       102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv-~i~g---l~~~~~  177 (221)
                      .|.+|++++|+|+|.++++||..|.+++||+|....+++.+.+..+.+|. ++..++.++.||+++ .+++   +++.++
T Consensus       246 r~Lifds~yD~y~G~I~~vrv~~G~vrkGdkV~~~~t~~~yev~~vgvm~-p~~~~~~~l~agqvGyIi~~mr~~~ea~I  324 (650)
T KOG0462|consen  246 RMLIFDSEYDEYRGVIALVRVVDGVVRKGDKVQSAATGKSYEVKVVGVMR-PEMTPVVELDAGQVGYIICNMRNVKEAQI  324 (650)
T ss_pred             HHHhhhhhhhhhcceEEEEEEeeeeeecCCEEEEeecCcceEeEEeEEec-cCceeeeeecccccceeEecccccccccc
Confidence            99999999999999999999999999999999999999888888888664 667777777776666 3344   557799


Q ss_pred             CcEEecCC-----------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEccccc
Q psy5461         178 KDKRTRVI-----------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQN  219 (221)
Q Consensus       178 Gdtl~~~~-----------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~~  219 (221)
                      ||||+...           .++.|+|          |-..|-+++++|+++|+++.+...-++
T Consensus       325 GdTi~~~~~~~~v~tl~~~~~~~pMvFvg~fP~dgsd~~~l~~a~erL~lnd~sv~v~~~~s~  387 (650)
T KOG0462|consen  325 GDTIAHKSVTKAVETLPGFEPTKPMVFVGLFPLDGSDYETLRDAIERLVLNDESVTVIKESSG  387 (650)
T ss_pred             cceeeecccCcccCcCCCCCCCcceEEeccccCccchhhhHHHHHHHHhcccccceeeecCCc
Confidence            99998752           1223666          557889999999999999998876654

>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes

Probab=99.87  E-value=1.2e-21  Score=139.61  Aligned_cols=83  Identities=48%  Similarity=0.839  Sum_probs=79.4

Q ss_pred             cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcE
Q psy5461         101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDK  180 (221)
Q Consensus       101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdt  180 (221)
                      |+|+|||+++|++.|+++|+|||+|+|++||.+++.+.++++++.+|+.++|.+..+++++.||||+++.|++++++|||
T Consensus         1 ~~a~VfK~~~d~~~g~i~~~Ri~sGtl~~g~~v~~~~~~~~~~v~~l~~~~g~~~~~v~~~~aGdI~~i~gl~~~~~Gdt   80 (83)
T cd04092           1 LCALAFKVVHDPQRGPLTFVRVYSGTLKRGSALYNTNTGKKERISRLLQPFADQYQEIPSLSAGNIGVITGLKQTRTGDT   80 (83)
T ss_pred             CEEEEEecccCCCCCeEEEEEEecCEECCCCEEEECCCCCEEEeeEEEEEECCCceECCeeCCCCEEEEECCCCcccCCE
Confidence            57999999999999999999999999999999999888878899999999999999999999999999999999999999


Q ss_pred             Eec
Q psy5461         181 RTR  183 (221)
Q Consensus       181 l~~  183 (221)
                      ++.
T Consensus        81 l~~   83 (83)
T cd04092          81 LVT   83 (83)
T ss_pred             EeC
Confidence            974

Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n

>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes

Probab=99.86  E-value=4.7e-21  Score=136.30  Aligned_cols=83  Identities=36%  Similarity=0.597  Sum_probs=79.4

Q ss_pred             cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcE
Q psy5461         101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDK  180 (221)
Q Consensus       101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdt  180 (221)
                      |+|+|||+++|++.|+++++|||+|+|++||++++.+.++.+++.+|+.++|.+..+++++.||||+++.|++++++|||
T Consensus         1 ~~a~Vfk~~~d~~~G~~~~~Rv~sG~l~~g~~v~~~~~~~~~~v~~l~~~~g~~~~~v~~~~aGdI~~i~g~~~~~~Gdt   80 (83)
T cd04088           1 FVALVFKTIHDPFVGKLSFVRVYSGTLKAGSTLYNSTKGKKERVGRLLRMHGKKQEEVEEAGAGDIGAVAGLKDTATGDT   80 (83)
T ss_pred             CEEEEEEcccCCCCceEEEEEEecCEEcCCCEEEECCCCcEEEeeEEEEEcCCCceECCEeCCCCEEEEECCCCCccCCE
Confidence            57999999999999999999999999999999999988888899999999999999999999999999999999999999


Q ss_pred             Eec
Q psy5461         181 RTR  183 (221)
Q Consensus       181 l~~  183 (221)
                      +++
T Consensus        81 l~~   83 (83)
T cd04088          81 LCD   83 (83)
T ss_pred             eeC
Confidence            973

During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl

>cd03689 RF3_II RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3)

Probab=99.85  E-value=9.1e-21  Score=135.71  Aligned_cols=81  Identities=25%  Similarity=0.351  Sum_probs=77.7

Q ss_pred             EEEEEEee---cCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCc
Q psy5461         103 ARAFKVVH---DKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKD  179 (221)
Q Consensus       103 ~~Vfk~~~---d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gd  179 (221)
                      |+|||+.+   +++.|+++|+|||||+|++||.|++...++.+++++|+.++|.+..+++++.||||+++.|++++.+||
T Consensus         1 ~~vfKv~~~~~~~~~Gkla~~Rv~sG~l~~g~~v~~~~~~~~~kv~~l~~~~g~~~~~v~~a~aGdIv~v~gl~~~~~Gd   80 (85)
T cd03689           1 GFVFKIQANMDPAHRDRIAFVRVCSGKFERGMKVKHVRLGKEVRLSNPQQFFAQDRETVDEAYPGDIIGLVNPGNFQIGD   80 (85)
T ss_pred             CEEEEEecccCCCCCcEEEEEEEECCEEcCCCEEEEcCCCCEEEeeEeEEEecCCeeEcCEECCCCEEEEECCCCccccC
Confidence            58999999   999999999999999999999999998777889999999999999999999999999999999999999


Q ss_pred             EEec
Q psy5461         180 KRTR  183 (221)
Q Consensus       180 tl~~  183 (221)
                      |||+
T Consensus        81 tl~~   84 (85)
T cd03689          81 TLTE   84 (85)
T ss_pred             EeeC
Confidence            9985

Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ.

>cd04091 mtEFG1_II_like mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes

Probab=99.85  E-value=1.3e-20  Score=133.68  Aligned_cols=81  Identities=31%  Similarity=0.589  Sum_probs=77.1

Q ss_pred             cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcE
Q psy5461         101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDK  180 (221)
Q Consensus       101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdt  180 (221)
                      |+|+|||+.+|++ |+++|+|||+|+|++||+|++.+.++++++.+|+.++|.+..+++++.||||+++.|++ +++|||
T Consensus         1 ~~a~vfK~~~~~~-G~i~~~Rv~sG~lk~gd~v~~~~~~~~~~v~~i~~~~g~~~~~~~~~~aGdI~~i~g~~-~~~Gdt   78 (81)
T cd04091           1 FVGLAFKLEEGRF-GQLTYMRIYQGKLKKGDTIYNVRTGKKVRVPRLVRMHSNEMEEVEEAGAGDICAIFGID-CASGDT   78 (81)
T ss_pred             CeEEEEEeecCCC-CCEEEEEEecCEEcCCCEEEEcCCCCEEEEeEEEEEeCCCceEccEECCCCEEEEECCC-cccCCE
Confidence            5799999999988 99999999999999999999998888899999999999999999999999999999998 999999


Q ss_pred             Eec
Q psy5461         181 RTR  183 (221)
Q Consensus       181 l~~  183 (221)
                      |++
T Consensus        79 l~~   81 (81)
T cd04091          79 FTD   81 (81)
T ss_pred             ecC
Confidence            963

Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals

>cd03691 BipA_TypA_II BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu

Probab=99.82  E-value=9.4e-20  Score=130.49  Aligned_cols=83  Identities=27%  Similarity=0.320  Sum_probs=77.1

Q ss_pred             cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC---ceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCcc
Q psy5461         101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD---QSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERG  177 (221)
Q Consensus       101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~---~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~  177 (221)
                      |.|+|||+++|++.|+++|+|||+|+|++||+|++...+   +++++++|+.++|++..+++++.||||+++.|++++.+
T Consensus         1 ~~~~vfk~~~d~~~g~i~~~Rv~sG~l~~g~~v~~~~~~~~~~~~~v~~l~~~~g~~~~~v~~~~aG~I~~i~gl~~~~~   80 (86)
T cd03691           1 LQMLVTTLDYDDYVGRIAIGRIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVEVEEAEAGDIVAIAGIEDITI   80 (86)
T ss_pred             CeEEEEEeEecCCCCeEEEEEEEeCEEcCCCEEEEEcCCCCEEEEEEeeEeeeeCCCeeECcEECCCCEEEEECCCCCcc
Confidence            579999999999999999999999999999999988763   25789999999999999999999999999999999999


Q ss_pred             CcEEec
Q psy5461         178 KDKRTR  183 (221)
Q Consensus       178 Gdtl~~  183 (221)
                      |||+++
T Consensus        81 Gdtl~~   86 (86)
T cd03691          81 GDTICD   86 (86)
T ss_pred             cceecC
Confidence            999963

BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion.

>cd03699 lepA_II lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane

Probab=99.81  E-value=2.4e-19  Score=128.52  Aligned_cols=82  Identities=23%  Similarity=0.372  Sum_probs=74.4

Q ss_pred             cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc-C---CCCCc
Q psy5461         101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT-G---LKRER  176 (221)
Q Consensus       101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~-g---l~~~~  176 (221)
                      |+|+|||++++++.|+++|+|||+|+|++||.+++...++++++++|+ +.+.+..+++++.||||+++. |   ++++.
T Consensus         1 ~~~~Vfk~~~d~~~G~i~~~Rv~sG~l~~~~~v~~~~~~~~~~i~~l~-~~~~~~~~~~~~~aGdI~~v~~g~~~l~~~~   79 (86)
T cd03699           1 LRALIFDSWYDPYRGVIALVRVFDGTLKKGDKIRFMSTGKEYEVEEVG-IFRPEMTPTDELSAGQVGYIIAGIKTVKDAR   79 (86)
T ss_pred             CEEEEEEeeccCCCCEEEEEEEEcCEEcCCCEEEEecCCCeEEEEEEE-EECCCccCCceECCCCEEEEEccccccCccc
Confidence            589999999999999999999999999999999998877788999999 558888999999999999885 4   66789


Q ss_pred             cCcEEec
Q psy5461         177 GKDKRTR  183 (221)
Q Consensus       177 ~Gdtl~~  183 (221)
                      +||||+.
T Consensus        80 ~Gdtl~~   86 (86)
T cd03699          80 VGDTITL   86 (86)
T ss_pred             cccEeeC
Confidence            9999974

The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu and IF2 have all been demonstrated to interact at overlapping sites on the ribosome. Chemical protection studies demonstrate that they all include the universally conserved alpha-sarcin loop as part of their binding site. These data indicate that LepA may bind to this location on the ribosome as well. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.

>KOG0469|consensus

Probab=99.76  E-value=9e-19  Score=157.72  Aligned_cols=146  Identities=20%  Similarity=0.203  Sum_probs=121.0

Q ss_pred             HHHHHHHHhhCCCCCCccccc-----------------ccCCCCCCcEEEEEEEeecCCCce-EEEEEEEceEEcCCCEE
Q psy5461          72 QKLMDAIVDILPSPTERPALA-----------------MFQHFGDSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKGQKF  133 (221)
Q Consensus        72 ~~LLd~I~~~~PsP~~~~~~~-----------------~~~~~~~~~~~~Vfk~~~d~~~G~-i~~~RV~sG~L~~gd~v  133 (221)
                      +.||++|..++|||..+++++                 ..|++++|++++|.|.......|+ ++|+|||||++..|.++
T Consensus       332 dallemIalhLPSPvtaQkyR~e~LYEGP~DDe~a~aik~CD~~aplmmYvSKMvPtsDkgRFyAFGRVFsG~v~~G~Kv  411 (842)
T KOG0469|consen  332 DALLEMIALHLPSPVTAQKYRAEYLYEGPADDEAAVAIKNCDPKAPLMMYVSKMVPTSDKGRFYAFGRVFSGKVFTGLKV  411 (842)
T ss_pred             HHHHHHHHhhCCCchHHHHHHHHHhhcCCCchHHhhHhhccCCCCCeEEeeeeccccCCCceEEEEeeeecceeccCcEE
Confidence            689999999999999988874                 258999999999999998777776 99999999999999999


Q ss_pred             EeccCC----cee-----eeceeEeeecCCeeeeCccccCCEEEEcCCCCC--ccCcEEecC-C--------CCCCCce-
Q psy5461         134 YNIHLD----QSE-----QITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE--RGKDKRTRV-I--------PKPTSVV-  192 (221)
Q Consensus       134 ~~~~~~----~~~-----~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~--~~Gdtl~~~-~--------~~p~~~v-  192 (221)
                      ++.+.+    +++     .|.+...|+|+..++++..+||+|+.+.|+++.  ++| ||+.. .        +.-+|+| 
T Consensus       412 RiqgPnY~PGkkedl~~K~iqRtvlMMGr~vepied~PaGNIiGlvGvDqfLvKtG-TiTt~e~AHNmrvMKFSVSPVV~  490 (842)
T KOG0469|consen  412 RIQGPNYVPGKKEDLYIKAIQRTVLMMGRFVEPIEDCPAGNIIGLVGVDQFLVKTG-TITTSEAAHNMRVMKFSVSPVVR  490 (842)
T ss_pred             EEeCCCCCCCcHHHHHHHHHHHHHHHhcccccccccCCCCcEEEEeehhHhhhccC-ceeehhhhccceEEEeeccceEE
Confidence            998764    322     455556699999999999999999999999974  676 66543 1        1223555 


Q ss_pred             ---------ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461         193 ---------QCSARWTLNLEVGASSPIISKSKRRQ  218 (221)
Q Consensus       193 ---------~~~~l~~~L~~L~~~Dp~l~~~~~~~  218 (221)
                               |+++|.++|.+|+++||++..-.+.+
T Consensus       491 VAVe~Knp~DLpKLvEGLkrLakSDP~v~~~~~es  525 (842)
T KOG0469|consen  491 VAVEAKNPADLPKLVEGLKRLAKSDPMVQCIIEES  525 (842)
T ss_pred             EEEecCChhhhHHHHHHHHHHhccCCeEEEEeccC
Confidence                     88999999999999999988766543

>cd03700 eEF2_snRNP_like_II EF2_snRNP_like_II: this subfamily represents domain II of elongation factor (EF) EF-2 found eukaryotes and archaea and, the C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p

Probab=99.76  E-value=5.9e-18  Score=123.04  Aligned_cols=82  Identities=29%  Similarity=0.412  Sum_probs=75.1

Q ss_pred             cEEEEEEEeecC-CCceEEEEEEEceEEcCCCEEEecc---------CCceeeeceeEeeecCCeeeeCccccCCEEEEc
Q psy5461         101 LCARAFKVVHDK-HRGAVTFFRIYSGAFKKGQKFYNIH---------LDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT  170 (221)
Q Consensus       101 ~~~~Vfk~~~d~-~~G~i~~~RV~sG~L~~gd~v~~~~---------~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~  170 (221)
                      ++++|||+.+++ +.|+++|+|||||+|+.|+.+++..         ..+++++++|+.++|.+..+++++.|||||++.
T Consensus         1 ~v~~v~Ki~~~~~~~g~la~~RV~sGtl~~g~~v~~~~~~~~~~~~~~~~~~~v~~l~~~~g~~~~~v~~a~aGdIv~i~   80 (93)
T cd03700           1 LVMYVTKMVPTPDKGGFIAFGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYREPVDEVPAGNIVLIV   80 (93)
T ss_pred             CeEEEEeCeECCCCCEEEEEEEEeeCeEeCCCEEEEECCCCCCCccCcEEEEEEeEEEEEcCCCEEEccccCCCCEEEEE
Confidence            478999999999 8999999999999999999999876         234578999999999999999999999999999


Q ss_pred             CCCCCccCcEEe
Q psy5461         171 GLKRERGKDKRT  182 (221)
Q Consensus       171 gl~~~~~Gdtl~  182 (221)
                      |++++++|||.+
T Consensus        81 g~~~~~~g~~~~   92 (93)
T cd03700          81 GLDQLKSGTTAT   92 (93)
T ss_pred             CCccCceEeEec
Confidence            999999999864

During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p.

>cd04090 eEF2_II_snRNP Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p

Probab=99.73  E-value=4.3e-17  Score=118.77  Aligned_cols=81  Identities=30%  Similarity=0.321  Sum_probs=71.3

Q ss_pred             cEEEEEEEeecCCC-ceEEEEEEEceEEcCCCEEEeccCC---------ceeeeceeEeeecCCeeeeCccccCCEEEEc
Q psy5461         101 LCARAFKVVHDKHR-GAVTFFRIYSGAFKKGQKFYNIHLD---------QSEQITRLLLAEADDYKEVNEIQCGNIAAVT  170 (221)
Q Consensus       101 ~~~~Vfk~~~d~~~-G~i~~~RV~sG~L~~gd~v~~~~~~---------~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~  170 (221)
                      ++|+|||+.++++. |+++|+|||||+|++||.|++.+.+         ..+++.+|+.++|.+..+++++.||||+++.
T Consensus         1 ~~a~VfK~~~~~~~~~~la~~RV~sGtl~~g~~v~~~~~~~~~~~~~~~~~~~i~~l~~~~g~~~~~v~~a~aGdIv~v~   80 (94)
T cd04090           1 LVVHVTKLYSTSDGGSFWAFGRIYSGTIKKGQKVKVLGENYSLDDEEDMTICTIGRLWILGGRYKIEVNEAPAGNWVLIK   80 (94)
T ss_pred             CEEEEEeeeecCCCCEEEEEEEEeeCeEcCCCEEEEECCCCCCccCCcEEEEEEeEEEEecCCCEEEcceeCCCCEEEEE
Confidence            47899999999997 6799999999999999999885432         3579999999999999999999999999999


Q ss_pred             CCCCCccCcEE
Q psy5461         171 GLKRERGKDKR  181 (221)
Q Consensus       171 gl~~~~~Gdtl  181 (221)
                      |+++...+.+.
T Consensus        81 gl~~~~~~~~t   91 (94)
T cd04090          81 GIDSSIVKTAT   91 (94)
T ss_pred             CcchheeceEE
Confidence            99987655544

This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.

>PRK05306 infB translation initiation factor IF-2; Validated

Probab=99.69  E-value=8.3e-16  Score=148.25  Aligned_cols=182  Identities=14%  Similarity=0.076  Sum_probs=135.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhh-ccc---cccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYS-GAF---KKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFG   98 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~-~~~---~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~   98 (221)
                      .+-|++..++|++......+-....+.. +..   .+..+|++++||++|.||++|++.|.......      .+.++++
T Consensus       388 ~~vPiIVviNKiDl~~a~~e~V~~eL~~~~~~~e~~g~~vp~vpvSAktG~GI~eLle~I~~~~e~~------~l~~~~~  461 (787)
T PRK05306        388 AGVPIIVAINKIDKPGANPDRVKQELSEYGLVPEEWGGDTIFVPVSAKTGEGIDELLEAILLQAEVL------ELKANPD  461 (787)
T ss_pred             cCCcEEEEEECccccccCHHHHHHHHHHhcccHHHhCCCceEEEEeCCCCCCchHHHHhhhhhhhhh------hcccCCC
Confidence            4678999999965422111111111111 111   13458999999999999999999998632110      1123567


Q ss_pred             CCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-cc
Q psy5461          99 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-RG  177 (221)
Q Consensus        99 ~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-~~  177 (221)
                      .++.++||++..++++|+++++||++|+|+.||.|++.     .++++|+.+.+.+..++++|.|||+|.|.|++++ .+
T Consensus       462 ~~~~g~V~es~~dkg~G~v~~v~V~sGtLk~Gd~vv~g-----~~~gkVr~m~~~~~~~v~~A~pGd~V~I~gl~~~p~~  536 (787)
T PRK05306        462 RPARGTVIEAKLDKGRGPVATVLVQNGTLKVGDIVVAG-----TTYGRVRAMVDDNGKRVKEAGPSTPVEILGLSGVPQA  536 (787)
T ss_pred             CCcEEEEEEEEEcCCCeEEEEEEEecCeEecCCEEEEC-----CcEEEEEEEECCCCCCCCEEcCCCeEEEeCCCCCCCC
Confidence            89999999999999999999999999999999999985     2567777788878889999999999999999988 99


Q ss_pred             CcEEecCCC---------------------------------C---C----CCce-------ehHHHHHHHHHHhhcCCc
Q psy5461         178 KDKRTRVIP---------------------------------K---P----TSVV-------QCSARWTLNLEVGASSPI  210 (221)
Q Consensus       178 Gdtl~~~~~---------------------------------~---p----~~~v-------~~~~l~~~L~~L~~~Dp~  210 (221)
                      ||+|+....                                 .   +    ..++       ..+.|..+|.+|..+|+.
T Consensus       537 Gd~l~~~~~e~~a~~~~~~r~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~iikad~~Gs~eai~~~l~~l~~~~v~  616 (787)
T PRK05306        537 GDEFVVVEDEKKAREIAEYRQEKAREKKLARQQRVSLENLFEQMKEGEVKELNLIIKADVQGSVEALKDSLEKLSTDEVK  616 (787)
T ss_pred             CCEEEEcCCHHHHHHHHHHHHHHHHHHHhhhccccCHHHhhhhhhcCCceEEEEEEEeCCcchHHHHHHHHHhhcccCCc
Confidence            999983200                                 0   0    0222       568999999999999998


Q ss_pred             eEEEc
Q psy5461         211 ISKSK  215 (221)
Q Consensus       211 l~~~~  215 (221)
                      +.+-+
T Consensus       617 ~~i~~  621 (787)
T PRK05306        617 VNIIH  621 (787)
T ss_pred             eEEEe
Confidence            88754

>PRK12736 elongation factor Tu; Reviewed

Probab=99.60  E-value=4e-14  Score=127.83  Aligned_cols=149  Identities=21%  Similarity=0.274  Sum_probs=113.8

Q ss_pred             CCc-eeeeeeeecc-cc-cCCcchHHHHhhcc----ccccCceeEecCCCccc--------cHHHHHHHHHhhCCCCCCc
Q psy5461          24 GDS-LCARAFKVVH-DK-HRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNI--------GVQKLMDAIVDILPSPTER   88 (221)
Q Consensus        24 ~~~-~~~~vfk~~~-d~-~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~--------Gi~~LLd~I~~~~PsP~~~   88 (221)
                      +.+ ++..++|.+. +. ..-+.....+.+..    .+....|++++||++|.        ++..|+++|.+++|.|.. 
T Consensus       127 g~~~~IvviNK~D~~~~~~~~~~i~~~i~~~l~~~~~~~~~~~ii~vSa~~g~~~~~~~~~~i~~Ll~~l~~~lp~~~~-  205 (394)
T PRK12736        127 GVPYLVVFLNKVDLVDDEELLELVEMEVRELLSEYDFPGDDIPVIRGSALKALEGDPKWEDAIMELMDAVDEYIPTPER-  205 (394)
T ss_pred             CCCEEEEEEEecCCcchHHHHHHHHHHHHHHHHHhCCCcCCccEEEeeccccccCCCcchhhHHHHHHHHHHhCCCCCC-
Confidence            445 6788999652 11 11111122232221    22235799999999983        789999999999998754 


Q ss_pred             ccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC--CceeeeceeEeeecCCeeeeCccccCCE
Q psy5461          89 PALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL--DQSEQITRLLLAEADDYKEVNEIQCGNI  166 (221)
Q Consensus        89 ~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~--~~~~~v~~i~~~~g~~~~~v~~a~aGdI  166 (221)
                             +.++||.+.|++++.+++.|+++++||.+|+|+.||+|++.+.  +...+|++|...    ..+++++.|||+
T Consensus       206 -------~~~~p~r~~I~~~~~~~g~G~Vv~G~v~~G~l~~gd~v~i~p~~~~~~~~V~sI~~~----~~~~~~a~aGd~  274 (394)
T PRK12736        206 -------DTDKPFLMPVEDVFTITGRGTVVTGRVERGTVKVGDEVEIVGIKETQKTVVTGVEMF----RKLLDEGQAGDN  274 (394)
T ss_pred             -------CCCCCeEEEEEEEEecCCcEEEEEEEEeecEEecCCEEEEecCCCCeEEEEEEEEEC----CEEccEECCCCE
Confidence                   4578999999999999999999999999999999999998765  456789998742    457899999999


Q ss_pred             EE--EcCCC--CCccCcEEecC
Q psy5461         167 AA--VTGLK--RERGKDKRTRV  184 (221)
Q Consensus       167 v~--i~gl~--~~~~Gdtl~~~  184 (221)
                      ++  +.|++  +++.||+++..
T Consensus       275 v~l~l~~i~~~~i~~G~vl~~~  296 (394)
T PRK12736        275 VGVLLRGVDRDEVERGQVLAKP  296 (394)
T ss_pred             EEEEECCCcHHhCCcceEEecC
Confidence            95  47874  68999999875

>TIGR00487 IF-2 translation initiation factor IF-2

Probab=99.59  E-value=5.3e-14  Score=132.55  Aligned_cols=176  Identities=13%  Similarity=0.068  Sum_probs=129.1

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccc--------cccCceeEecCCCccccHHHHHHHHHhh--CCCCCCccccc
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAF--------KKNHVPVLCGSSYKNIGVQKLMDAIVDI--LPSPTERPALA   92 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~--------~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~--~PsP~~~~~~~   92 (221)
                      .+-|++..++|++....    ...++.+...        -+...|++.+||++|.||++|++.|...  ++.+.      
T Consensus       186 ~~vPiIVviNKiDl~~~----~~e~v~~~L~~~g~~~~~~~~~~~~v~iSAktGeGI~eLl~~I~~~~~~~~l~------  255 (587)
T TIGR00487       186 ANVPIIVAINKIDKPEA----NPDRVKQELSEYGLVPEDWGGDTIFVPVSALTGDGIDELLDMILLQSEVEELK------  255 (587)
T ss_pred             cCCCEEEEEECcccccC----CHHHHHHHHHHhhhhHHhcCCCceEEEEECCCCCChHHHHHhhhhhhhhcccc------
Confidence            46789999999653221    1122222111        1224689999999999999999999753  12211      


Q ss_pred             ccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCC
Q psy5461          93 MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGL  172 (221)
Q Consensus        93 ~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl  172 (221)
                        .+++.|+.+.|+++..++++|++++++|++|+|++||.+.....  ..+|..|+   .....++++|.||+++.+.|+
T Consensus       256 --~~~~~~~~~~V~ev~~~~g~G~v~~~~V~~GtL~~Gd~iv~~~~--~~kVr~l~---~~~g~~v~~a~~g~~v~i~Gl  328 (587)
T TIGR00487       256 --ANPNGQASGVVIEAQLDKGRGPVATVLVQSGTLRVGDIVVVGAA--YGRVRAMI---DENGKSVKEAGPSKPVEILGL  328 (587)
T ss_pred             --CCCCCCceeEEEEEEEeCCCcEEEEEEEEeCEEeCCCEEEECCC--ccEEEEEE---CCCCCCCCEECCCCEEEEeCC
Confidence              24678999999999999999999999999999999999988653  24555554   444567899999999999999


Q ss_pred             CCC-ccCcEEecCC-----------------------CC----------------CC-Cce-------ehHHHHHHHHHH
Q psy5461         173 KRE-RGKDKRTRVI-----------------------PK----------------PT-SVV-------QCSARWTLNLEV  204 (221)
Q Consensus       173 ~~~-~~Gdtl~~~~-----------------------~~----------------p~-~~v-------~~~~l~~~L~~L  204 (221)
                      +++ .+||++....                       ..                |. .++       ..++|.++|++|
T Consensus       329 ~~~p~aGd~~~~~~~e~~a~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viikad~~Gs~eal~~~l~~~  408 (587)
T TIGR00487       329 SDVPAAGDEFIVFKDEKDARLVAEKRAGKLRQKALSRSVKVTLDNLFEQIKEGELKELNIILKADVQGSLEAIKNSLEKL  408 (587)
T ss_pred             CCCCCCCCEEEEcCCHHHHHHHHHHHHHHHHHHhhhhccccchhHhhhhhhccCCceEEEEEEeCCcchHHHHHHHHHhh
Confidence            886 9999997320                       00                10 222       568999999999


Q ss_pred             hhcCCceEEEc
Q psy5461         205 GASSPIISKSK  215 (221)
Q Consensus       205 ~~~Dp~l~~~~  215 (221)
                      ..+|+.+.+.+
T Consensus       409 ~~~~~~~~v~~  419 (587)
T TIGR00487       409 NNEEVKVKVIH  419 (587)
T ss_pred             cccCCeEEEEE
Confidence            99999887754

This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognized by the pfam model GTP_EFTU.

>CHL00189 infB translation initiation factor 2; Provisional

Probab=99.57  E-value=3.1e-14  Score=136.42  Aligned_cols=147  Identities=12%  Similarity=0.056  Sum_probs=114.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcc--------ccccCceeEecCCCccccHHHHHHHHHhhCCCCCCccccccc
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA--------FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMF   94 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~--------~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~   94 (221)
                      .+-|++..++|++....    .+.++.+..        ..+..+|++.+||++|.||++|++.|..+...+.      +.
T Consensus       346 ~~iPiIVViNKiDl~~~----~~e~v~~eL~~~~ll~e~~g~~vpvv~VSAktG~GIdeLle~I~~l~e~~~------lk  415 (742)
T CHL00189        346 ANVPIIVAINKIDKANA----NTERIKQQLAKYNLIPEKWGGDTPMIPISASQGTNIDKLLETILLLAEIED------LK  415 (742)
T ss_pred             cCceEEEEEECCCcccc----CHHHHHHHHHHhccchHhhCCCceEEEEECCCCCCHHHHHHhhhhhhhhhc------cc
Confidence            46789999999654321    122222211        1134689999999999999999999988753211      11


Q ss_pred             CCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCC-
Q psy5461          95 QHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK-  173 (221)
Q Consensus        95 ~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~-  173 (221)
                      ++++.|+.++||++..|+++|++++++|++|+|++||.|++..     +.++|+.+.+....++++|.|||+|.|.|++ 
T Consensus       416 ~~~~~~~~g~V~e~~iD~~~G~V~~~~V~sGtLr~GD~vv~g~-----~~gkVr~m~~~~~~~v~~a~pgdiV~I~gl~~  490 (742)
T CHL00189        416 ADPTQLAQGIILEAHLDKTKGPVATILVQNGTLHIGDIIVIGT-----SYAKIRGMINSLGNKINLATPSSVVEIWGLSS  490 (742)
T ss_pred             CCCCCCceEEEEEEEEcCCCceEEEEEEEcCEEecCCEEEECC-----cceEEEEEEcCCCcCccEEcCCCceEecCccc
Confidence            2456889999999999999999999999999999999998864     4567777778888899999999999999994 


Q ss_pred             CCccCcEEecC
Q psy5461         174 RERGKDKRTRV  184 (221)
Q Consensus       174 ~~~~Gdtl~~~  184 (221)
                      ...+||+|...
T Consensus       491 ~~~~Gd~l~v~  501 (742)
T CHL00189        491 VPATGEHFQVF  501 (742)
T ss_pred             CCCCCCEEEEe
Confidence            56899999643

>CHL00071 tufA elongation factor Tu

Probab=99.57  E-value=3.9e-14  Score=128.45  Aligned_cols=150  Identities=19%  Similarity=0.245  Sum_probs=112.7

Q ss_pred             CCCc-eeeeeeeecc-cc-cCCcchHHHHhhcc----ccccCceeEecCCCccc------------------cHHHHHHH
Q psy5461          23 FGDS-LCARAFKVVH-DK-HRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNI------------------GVQKLMDA   77 (221)
Q Consensus        23 ~~~~-~~~~vfk~~~-d~-~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~------------------Gi~~LLd~   77 (221)
                      .+-| ++..++|.+. ++ ..-+.....+....    .+...+|++++||++|+                  |+..||++
T Consensus       126 ~g~~~iIvvvNK~D~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~ii~~Sa~~g~n~~~~~~~~~~~~~~w~~~~~~ll~~  205 (409)
T CHL00071        126 VGVPNIVVFLNKEDQVDDEELLELVELEVRELLSKYDFPGDDIPIVSGSALLALEALTENPKIKRGENKWVDKIYNLMDA  205 (409)
T ss_pred             cCCCEEEEEEEccCCCCHHHHHHHHHHHHHHHHHHhCCCCCcceEEEcchhhcccccccCccccccCCchhhhHHHHHHH
Confidence            3456 7789999652 11 11111122333222    12335899999999986                  47899999


Q ss_pred             HHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC--CceeeeceeEeeecCCe
Q psy5461          78 IVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL--DQSEQITRLLLAEADDY  155 (221)
Q Consensus        78 I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~--~~~~~v~~i~~~~g~~~  155 (221)
                      |.+++|+|..        +.++||++.|.+++.+++.|+++++||++|+++.||+|...+.  +...+|++|...    .
T Consensus       206 l~~~~~~p~~--------~~~~p~r~~I~~v~~~~g~G~Vv~G~V~sG~l~~Gd~v~i~p~~~~~~~~VksI~~~----~  273 (409)
T CHL00071        206 VDSYIPTPER--------DTDKPFLMAIEDVFSITGRGTVATGRIERGTVKVGDTVEIVGLRETKTTTVTGLEMF----Q  273 (409)
T ss_pred             HHhhCCCCCC--------CCCCCEEEEEEEEEEeCCCeEEEEEEEecCEEeeCCEEEEeeCCCCcEEEEEEEEEc----C
Confidence            9999988864        4578999999999999999999999999999999999987643  455789998743    2


Q ss_pred             eeeCccccCCEEE--EcCCC--CCccCcEEecC
Q psy5461         156 KEVNEIQCGNIAA--VTGLK--RERGKDKRTRV  184 (221)
Q Consensus       156 ~~v~~a~aGdIv~--i~gl~--~~~~Gdtl~~~  184 (221)
                      +++++|.|||+++  +.|++  +++.||+|++.
T Consensus       274 ~~v~~a~aGd~v~i~l~~i~~~~i~~G~vl~~~  306 (409)
T CHL00071        274 KTLDEGLAGDNVGILLRGIQKEDIERGMVLAKP  306 (409)
T ss_pred             cCCCEECCCceeEEEEcCCCHHHcCCeEEEecC
Confidence            4789999999995  55765  68999999876

>TIGR00485 EF-Tu translation elongation factor TU

Probab=99.55  E-value=9.4e-14  Score=125.40  Aligned_cols=117  Identities=22%  Similarity=0.337  Sum_probs=99.3

Q ss_pred             cCceeEecCCCccc--------cHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEE
Q psy5461          56 NHVPVLCGSSYKNI--------GVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAF  127 (221)
Q Consensus        56 ~~~Pv~~gSa~~~~--------Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L  127 (221)
                      ..+|++++||++|.        ++..||++|.+++|.|..        +.++||++.|++++.+++.|+++++||.+|++
T Consensus       166 ~~~~ii~vSa~~g~~g~~~~~~~~~~ll~~l~~~~~~~~~--------~~~~p~r~~V~~vf~~~g~G~Vv~G~v~~G~l  237 (394)
T TIGR00485       166 DDTPIIRGSALKALEGDAEWEAKILELMDAVDEYIPTPER--------ETDKPFLMPIEDVFSITGRGTVVTGRVERGIV  237 (394)
T ss_pred             cCccEEECccccccccCCchhHhHHHHHHHHHhcCCCCCC--------CCCCCeEEEEEEEEeeCCceEEEEEEEEeeEE
Confidence            34899999999874        578999999999888764        45789999999999999999999999999999


Q ss_pred             cCCCEEEeccC--CceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC--CCccCcEEecC
Q psy5461         128 KKGQKFYNIHL--DQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK--RERGKDKRTRV  184 (221)
Q Consensus       128 ~~gd~v~~~~~--~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~--~~~~Gdtl~~~  184 (221)
                      ++||+|+....  ++..+|++|...    ..++++|.|||.+++  .|++  +++.||++++.
T Consensus       238 ~~gd~v~i~p~~~~~~~~VksI~~~----~~~~~~a~aGd~v~l~l~~i~~~~i~rG~vl~~~  296 (394)
T TIGR00485       238 KVGEEVEIVGLKDTRKTTVTGVEMF----RKELDEGRAGDNVGLLLRGIKREEIERGMVLAKP  296 (394)
T ss_pred             eCCCEEEEecCCCCcEEEEEEEEEC----CeEEEEECCCCEEEEEeCCccHHHCCccEEEecC
Confidence            99999998763  456789998743    357889999999954  7764  68999999885

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.

>KOG0460|consensus

Probab=99.55  E-value=7.3e-15  Score=127.41  Aligned_cols=148  Identities=22%  Similarity=0.290  Sum_probs=124.7

Q ss_pred             Cceeeeeeeec-c-cccCCcchHHHHhhcc----ccccCceeEecCCCcc-------c---cHHHHHHHHHhhCCCCCCc
Q psy5461          25 DSLCARAFKVV-H-DKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKN-------I---GVQKLMDAIVDILPSPTER   88 (221)
Q Consensus        25 ~~~~~~vfk~~-~-d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~-------~---Gi~~LLd~I~~~~PsP~~~   88 (221)
                      ..++.|+||++ + |++.-++.+..+|+..    +++..+||++|||+--       +   -|..|||++.+|+|.|.. 
T Consensus       171 ~~ivvfiNKvD~V~d~e~leLVEmE~RElLse~gf~Gd~~PvI~GSAL~ALeg~~peig~~aI~kLldavDsyip~P~R-  249 (449)
T KOG0460|consen  171 KHIVVFINKVDLVDDPEMLELVEMEIRELLSEFGFDGDNTPVIRGSALCALEGRQPEIGLEAIEKLLDAVDSYIPTPER-  249 (449)
T ss_pred             ceEEEEEecccccCCHHHHHHHHHHHHHHHHHcCCCCCCCCeeecchhhhhcCCCccccHHHHHHHHHHHhccCCCccc-
Confidence            58999999985 4 6778888888888765    6788999999999754       2   389999999999999976 


Q ss_pred             ccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCc--eeeeceeEeeecCCeeeeCccccCCE
Q psy5461          89 PALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ--SEQITRLLLAEADDYKEVNEIQCGNI  166 (221)
Q Consensus        89 ~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~--~~~v~~i~~~~g~~~~~v~~a~aGdI  166 (221)
                             +.+.||++-|-.++.-+++|+++++|+.+|+|++||++...+.++  +..|+.|..++    ..++++.|||-
T Consensus       250 -------~~~~pFl~pie~vfsI~GRGTVvtGrlERG~lKkG~e~eivG~~~~lkttvtgiemF~----K~ld~a~AGDn  318 (449)
T KOG0460|consen  250 -------DLDKPFLLPIEDVFSIPGRGTVVTGRLERGVLKKGDEVEIVGHNKTLKTTVTGIEMFR----KSLDEAQAGDN  318 (449)
T ss_pred             -------ccCCCceeehhheeeecCCceEEEEEEeecccccCCEEEEeccCcceeeEeehHHHHH----HHHHhcccccc
Confidence                   678999999999999999999999999999999999999887654  46778776442    36899999999


Q ss_pred             EE--EcCCC--CCccCcEEecC
Q psy5461         167 AA--VTGLK--RERGKDKRTRV  184 (221)
Q Consensus       167 v~--i~gl~--~~~~Gdtl~~~  184 (221)
                      +.  ++|++  +++.|..++..
T Consensus       319 ~G~LlRGik~~dvkRGmvl~~p  340 (449)
T KOG0460|consen  319 LGALLRGIKREDVKRGMVLAKP  340 (449)
T ss_pred             eehhhhcCCHHHHhcccEEecC
Confidence            94  57775  78999998753

>PRK12735 elongation factor Tu; Reviewed

Probab=99.51  E-value=4.3e-13  Score=121.20  Aligned_cols=117  Identities=23%  Similarity=0.320  Sum_probs=100.5

Q ss_pred             cCceeEecCCCccc----------cHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEce
Q psy5461          56 NHVPVLCGSSYKNI----------GVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSG  125 (221)
Q Consensus        56 ~~~Pv~~gSa~~~~----------Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG  125 (221)
                      ..+|++++||++|.          |+..|+++|.+.+|.|..        +.++||.+.|..++..++.|.++++||.+|
T Consensus       166 ~~~~ii~~Sa~~g~n~~~~~~w~~~~~~Ll~~l~~~~~~p~~--------~~~~p~r~~I~~~f~v~g~Gtvv~G~v~~G  237 (396)
T PRK12735        166 DDTPIIRGSALKALEGDDDEEWEAKILELMDAVDSYIPEPER--------AIDKPFLMPIEDVFSISGRGTVVTGRVERG  237 (396)
T ss_pred             CceeEEecchhccccCCCCCcccccHHHHHHHHHhcCCCCCc--------cCCCCeEEEEEEEEecCCceEEEEEEEEec
Confidence            35899999999983          789999999999998754        457899999999999999999999999999


Q ss_pred             EEcCCCEEEeccC--CceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC--CCccCcEEecC
Q psy5461         126 AFKKGQKFYNIHL--DQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK--RERGKDKRTRV  184 (221)
Q Consensus       126 ~L~~gd~v~~~~~--~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~--~~~~Gdtl~~~  184 (221)
                      ++++||+|++...  +++.+|++|...    ..++++|.|||.+++  .|++  +++.|++++..
T Consensus       238 ~i~~gd~v~i~p~~~~~~~~VksI~~~----~~~v~~a~aGd~v~l~L~~i~~~~i~rG~vl~~~  298 (396)
T PRK12735        238 IVKVGDEVEIVGIKETQKTTVTGVEMF----RKLLDEGQAGDNVGVLLRGTKREDVERGQVLAKP  298 (396)
T ss_pred             EEeCCCEEEEecCCCCeEEEEEEEEEC----CeEeCEECCCCEEEEEeCCCcHHHCCcceEEEcC
Confidence            9999999998865  356788988742    468899999999965  6774  68999999986

>PRK00049 elongation factor Tu; Reviewed

Probab=99.47  E-value=1.3e-12  Score=118.00  Aligned_cols=150  Identities=19%  Similarity=0.210  Sum_probs=112.8

Q ss_pred             CCCcee-eeeeeeccc--ccCCcchHHHHhhccc----cccCceeEecCCCccc----------cHHHHHHHHHhhCCCC
Q psy5461          23 FGDSLC-ARAFKVVHD--KHRGAVTFFRIYSGAF----KKNHVPVLCGSSYKNI----------GVQKLMDAIVDILPSP   85 (221)
Q Consensus        23 ~~~~~~-~~vfk~~~d--~~~g~l~~~~l~~~~~----~~~~~Pv~~gSa~~~~----------Gi~~LLd~I~~~~PsP   85 (221)
                      .+.|.+ ..++|++.-  +..-+.....+.+...    .....|++++||++|.          |+..||++|.+++|.|
T Consensus       126 ~g~p~iiVvvNK~D~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~iv~iSa~~g~~~~~~~~w~~~~~~ll~~l~~~~~~p  205 (396)
T PRK00049        126 VGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGSALKALEGDDDEEWEKKILELMDAVDSYIPTP  205 (396)
T ss_pred             cCCCEEEEEEeecCCcchHHHHHHHHHHHHHHHHhcCCCccCCcEEEeecccccCCCCcccccccHHHHHHHHHhcCCCC
Confidence            345754 689996421  1111111222322221    2345899999999874          7899999999999987


Q ss_pred             CCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC--CceeeeceeEeeecCCeeeeCcccc
Q psy5461          86 TERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL--DQSEQITRLLLAEADDYKEVNEIQC  163 (221)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~--~~~~~v~~i~~~~g~~~~~v~~a~a  163 (221)
                      ..        ..++||.+.|..++..++.|.++.+||.+|++++||++.+...  ++..+|++|...    .++++++.|
T Consensus       206 ~~--------~~~~p~r~~I~~~f~v~g~G~Vv~G~v~~G~i~~gd~v~i~p~~~~~~~~VksI~~~----~~~~~~a~~  273 (396)
T PRK00049        206 ER--------AIDKPFLMPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIRDTQKTTVTGVEMF----RKLLDEGQA  273 (396)
T ss_pred             CC--------CCCCCeEEEEEEEEeeCCceEEEEEEEeeeEEecCCEEEEeecCCCceEEEEEEEEC----CcEeCEEcC
Confidence            54        4578999999999999999999999999999999999988764  456789998743    357899999


Q ss_pred             CCEEEE--cCCC--CCccCcEEecC
Q psy5461         164 GNIAAV--TGLK--RERGKDKRTRV  184 (221)
Q Consensus       164 GdIv~i--~gl~--~~~~Gdtl~~~  184 (221)
                      ||.+++  .|++  +++.|+++++.
T Consensus       274 Gd~v~l~l~~i~~~~i~~G~vl~~~  298 (396)
T PRK00049        274 GDNVGALLRGIKREDVERGQVLAKP  298 (396)
T ss_pred             CCEEEEEeCCCCHHHCCcceEEecC
Confidence            999865  6764  68999999986

>PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional

Probab=99.45  E-value=2e-12  Score=118.70  Aligned_cols=147  Identities=13%  Similarity=0.102  Sum_probs=107.4

Q ss_pred             ceeeeeeeecc-cccCCcchHHHHhhccc--cccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcE
Q psy5461          26 SLCARAFKVVH-DKHRGAVTFFRIYSGAF--KKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLC  102 (221)
Q Consensus        26 ~~~~~vfk~~~-d~~~g~l~~~~l~~~~~--~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~  102 (221)
                      +++..++|++. ++...+-.+..+++...  .....|++..||++|.|++.|+++|.+.+|.|..        +.+.||.
T Consensus       173 ~iIVvlNKiDlv~~~~~~~~~~ei~~~l~~~~~~~~~iipVSA~~G~nI~~Ll~~L~~~lp~~~r--------~~~~p~r  244 (460)
T PTZ00327        173 HIIILQNKIDLVKEAQAQDQYEEIRNFVKGTIADNAPIIPISAQLKYNIDVVLEYICTQIPIPKR--------DLTSPPR  244 (460)
T ss_pred             cEEEEEecccccCHHHHHHHHHHHHHHHHhhccCCCeEEEeeCCCCCCHHHHHHHHHhhCCCCCC--------CCCCCcE
Confidence            57788999652 22211222333333111  1357899999999999999999999999998854        4568898


Q ss_pred             EEEEEEee--------cCCCceEEEEEEEceEEcCCCEEEeccCC-------------ceeeeceeEeeecCCeeeeCcc
Q psy5461         103 ARAFKVVH--------DKHRGAVTFFRIYSGAFKKGQKFYNIHLD-------------QSEQITRLLLAEADDYKEVNEI  161 (221)
Q Consensus       103 ~~Vfk~~~--------d~~~G~i~~~RV~sG~L~~gd~v~~~~~~-------------~~~~v~~i~~~~g~~~~~v~~a  161 (221)
                      +.|..++.        ++++|.++.++|.+|++++||+|.+...+             ...+|++|..    ...++++|
T Consensus       245 ~~Idr~F~V~~~g~~~~~~~GtVv~G~v~~G~l~~Gd~v~i~P~~~~~~~~g~~~~~~~~~~VksI~~----~~~~v~~a  320 (460)
T PTZ00327        245 MIVIRSFDVNKPGEDIENLKGGVAGGSILQGVLKVGDEIEIRPGIISKDSGGEFTCRPIRTRIVSLFA----ENNELQYA  320 (460)
T ss_pred             EEEEEEEeecccCCcccCCceEEEEEEEeeceEecCCEEEEccCcccccccCccccccceEEEEEEEE----CCeECCEE
Confidence            88876543        34479999999999999999999998643             2357888863    34688999


Q ss_pred             ccCCEEEEc-----CCC--CCccCcEEecC
Q psy5461         162 QCGNIAAVT-----GLK--RERGKDKRTRV  184 (221)
Q Consensus       162 ~aGdIv~i~-----gl~--~~~~Gdtl~~~  184 (221)
                      .|||.+++.     +++  ++..|+.++..
T Consensus       321 ~aG~~vai~l~ld~~v~~~dv~rG~Vl~~~  350 (460)
T PTZ00327        321 VPGGLIGVGTTIDPTLTRADRLVGQVLGYP  350 (460)
T ss_pred             cCCCEEEEEeccCCCcchhhcccccEEEcC
Confidence            999998774     332  56799999875

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

Probab=99.44  E-value=1.2e-12  Score=119.24  Aligned_cols=147  Identities=17%  Similarity=0.168  Sum_probs=110.7

Q ss_pred             CceeeeeeeecccccCC---cchHHHHhhcc----ccccCceeEecCCCccccHHH------------HHHHHHhhCCCC
Q psy5461          25 DSLCARAFKVVHDKHRG---AVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQK------------LMDAIVDILPSP   85 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~~g---~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~------------LLd~I~~~~PsP   85 (221)
                      .+++..++|.+.-....   +.....+.+-.    ......|++..||++|.||.+            |+++|.+ +|+|
T Consensus       142 ~~iIVviNK~Dl~~~~~~~~~~~~~ei~~~~~~~g~~~~~~~~i~iSA~~g~ni~~~~~~~~w~~g~~l~~~l~~-~~~~  220 (426)
T TIGR00483       142 NQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTVPFIPISAWNGDNVIKKSENTPWYKGKTLLEALDA-LEPP  220 (426)
T ss_pred             CeEEEEEEChhccCccHHHHHHHHHHHHHHHHHcCCCcccceEEEeeccccccccccccCCccccchHHHHHHhc-CCCC
Confidence            46888999965311111   11122222211    122347899999999999974            9999965 6666


Q ss_pred             CCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCC
Q psy5461          86 TERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN  165 (221)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGd  165 (221)
                      ..        ..++||.+.|..++..++.|+++.+||.+|+++.||+|.+...+...+|++|...    ..++++|.|||
T Consensus       221 ~~--------~~~~p~r~~i~~v~~~~g~G~vv~G~v~~G~i~~gd~v~i~P~~~~~~VksI~~~----~~~~~~a~aG~  288 (426)
T TIGR00483       221 EK--------PTDKPLRIPIQDVYSITGVGTVPVGRVETGVLKPGDKVVFEPAGVSGEVKSIEMH----HEQIEQAEPGD  288 (426)
T ss_pred             CC--------ccCCCcEEEEEEEEecCCCeEEEEEEEccceeecCCEEEECCCCcEEEEEEEEEC----CcccCEEcCCC
Confidence            43        4568999999999999999999999999999999999999988888899999743    34789999999


Q ss_pred             EEEE--cCCC--CCccCcEEecC
Q psy5461         166 IAAV--TGLK--RERGKDKRTRV  184 (221)
Q Consensus       166 Iv~i--~gl~--~~~~Gdtl~~~  184 (221)
                      .+++  .+++  +++.||++++.
T Consensus       289 ~v~i~l~~i~~~~i~rG~vl~~~  311 (426)
T TIGR00483       289 NIGFNVRGVSKKDIRRGDVCGHP  311 (426)
T ss_pred             EEEEEECCCChhhcccceEEecC
Confidence            9965  6653  68999999875

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.

>PRK12317 elongation factor 1-alpha; Reviewed

Probab=99.43  E-value=1.8e-12  Score=118.05  Aligned_cols=148  Identities=16%  Similarity=0.160  Sum_probs=111.2

Q ss_pred             CceeeeeeeecccccCC---cchHHHHhhcc----ccccCceeEecCCCccccHHH------------HHHHHHhhCCCC
Q psy5461          25 DSLCARAFKVVHDKHRG---AVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQK------------LMDAIVDILPSP   85 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~~g---~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~------------LLd~I~~~~PsP   85 (221)
                      .+++..++|++......   ......+.+-.    ......|++..||++|.||.+            |+++|.. +|.|
T Consensus       140 ~~iivviNK~Dl~~~~~~~~~~~~~~i~~~l~~~g~~~~~~~ii~iSA~~g~gi~~~~~~~~wy~g~~L~~~l~~-~~~~  218 (425)
T PRK12317        140 NQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPDDIPFIPVSAFEGDNVVKKSENMPWYNGPTLLEALDN-LKPP  218 (425)
T ss_pred             CeEEEEEEccccccccHHHHHHHHHHHHHHHHhhCCCcCcceEEEeecccCCCccccccCCCcccHHHHHHHHhc-CCCC
Confidence            36888999965322111   11122222211    122247899999999999975            8898765 6766


Q ss_pred             CCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCC
Q psy5461          86 TERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN  165 (221)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGd  165 (221)
                      ..        ..++||.+.|..++..++.|+++.+||.+|++++||+|++...+...+|++|...    ..++++|.|||
T Consensus       219 ~~--------~~~~p~r~~i~~~~~~~g~G~vv~G~v~~G~v~~Gd~v~i~P~~~~~~VksI~~~----~~~~~~a~aG~  286 (425)
T PRK12317        219 EK--------PTDKPLRIPIQDVYSISGVGTVPVGRVETGVLKVGDKVVFMPAGVVGEVKSIEMH----HEELPQAEPGD  286 (425)
T ss_pred             cc--------ccCCCcEEEEEEEEeeCCCeEEEEEEEeeccEecCCEEEECCCCCeEEEEEEEEC----CcccCEECCCC
Confidence            43        4578999999999999999999999999999999999999988888899998743    35789999999


Q ss_pred             EEEE--cCCC--CCccCcEEecCC
Q psy5461         166 IAAV--TGLK--RERGKDKRTRVI  185 (221)
Q Consensus       166 Iv~i--~gl~--~~~~Gdtl~~~~  185 (221)
                      .+++  .+++  +++.||+++...
T Consensus       287 ~v~i~l~~~~~~~i~rG~vl~~~~  310 (425)
T PRK12317        287 NIGFNVRGVGKKDIKRGDVCGHPD  310 (425)
T ss_pred             eEEEEECCCCHHHccCccEecCCC
Confidence            9854  5664  578999998763

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

Probab=99.42  E-value=6.3e-12  Score=114.14  Aligned_cols=149  Identities=15%  Similarity=0.174  Sum_probs=108.4

Q ss_pred             Cceeeeeeeecccc-cCCcchHHHHhhccc--cccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCc
Q psy5461          25 DSLCARAFKVVHDK-HRGAVTFFRIYSGAF--KKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSL  101 (221)
Q Consensus        25 ~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~--~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~  101 (221)
                      .+++..++|++... ......+..++....  .....|++..||++|.|+++|++.|...+|.|..        ..+.||
T Consensus       140 ~~iiVVlNK~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~ii~vSA~~g~gI~~L~~~L~~~l~~~~~--------~~~~~~  211 (411)
T PRK04000        140 KNIVIVQNKIDLVSKERALENYEQIKEFVKGTVAENAPIIPVSALHKVNIDALIEAIEEEIPTPER--------DLDKPP  211 (411)
T ss_pred             CcEEEEEEeeccccchhHHHHHHHHHHHhccccCCCCeEEEEECCCCcCHHHHHHHHHHhCCCCCC--------CCCCCc
Confidence            35778889965322 111112333333221  1235789999999999999999999999988754        457899


Q ss_pred             EEEEEEEee--------cCCCceEEEEEEEceEEcCCCEEEeccCCc------------eeeeceeEeeecCCeeeeCcc
Q psy5461         102 CARAFKVVH--------DKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ------------SEQITRLLLAEADDYKEVNEI  161 (221)
Q Consensus       102 ~~~Vfk~~~--------d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~------------~~~v~~i~~~~g~~~~~v~~a  161 (221)
                      .+.|..++.        ++++|.++.+||.+|+|++||.|.+...++            ..+|++|...    ..++++|
T Consensus       212 r~~I~~~f~v~~~g~~~~~~~G~Vv~G~v~~G~l~~gd~v~i~P~~~~~~~~~~~~~~~~~~VksI~~~----~~~~~~a  287 (411)
T PRK04000        212 RMYVARSFDVNKPGTPPEKLKGGVIGGSLIQGVLKVGDEIEIRPGIKVEEGGKTKWEPITTKIVSLRAG----GEKVEEA  287 (411)
T ss_pred             eEEEEeeeeecCCCccccCCcceEEEEEEEeCEEecCCEEEEcCCcceecccccccccceEEEeEEEEC----CEECCEE
Confidence            999988763        345788999999999999999999987542            3578888632    3678999


Q ss_pred             ccCCEEEEc-----CCC--CCccCcEEecCC
Q psy5461         162 QCGNIAAVT-----GLK--RERGKDKRTRVI  185 (221)
Q Consensus       162 ~aGdIv~i~-----gl~--~~~~Gdtl~~~~  185 (221)
                      .|||.+++.     +++  +++.|+.++...
T Consensus       288 ~~G~~v~i~l~~~~~i~~~~i~~G~vl~~~~  318 (411)
T PRK04000        288 RPGGLVGVGTKLDPSLTKADALAGSVAGKPG  318 (411)
T ss_pred             cCCCEEEEEeccCCCCCHHHccCccEEEcCC
Confidence            999998764     332  578999999763

>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional

Probab=99.41  E-value=2.7e-12  Score=121.76  Aligned_cols=145  Identities=14%  Similarity=0.108  Sum_probs=109.9

Q ss_pred             eeeeeeeecc-cccCCcchHHHHhhcccc--ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEE
Q psy5461          27 LCARAFKVVH-DKHRGAVTFFRIYSGAFK--KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCA  103 (221)
Q Consensus        27 ~~~~vfk~~~-d~~~g~l~~~~l~~~~~~--~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~  103 (221)
                      ++..++|++. ++..-+.....+.+....  ....|++..||++|.|++.|++.|..+. .|..        ..++||.+
T Consensus       107 iIVVlNKiDlv~~~~~~~v~~ei~~~l~~~~~~~~~ii~VSA~tG~gI~~L~~~L~~~~-~~~~--------~~~~~~rl  177 (614)
T PRK10512        107 LTVALTKADRVDEARIAEVRRQVKAVLREYGFAEAKLFVTAATEGRGIDALREHLLQLP-EREH--------AAQHRFRL  177 (614)
T ss_pred             EEEEEECCccCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEeCCCCCCCHHHHHHHHHhh-cccc--------CcCCCceE
Confidence            5688899653 221111222333332211  1247899999999999999999998764 4432        34689999


Q ss_pred             EEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cC-CC--CCccC
Q psy5461         104 RAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TG-LK--RERGK  178 (221)
Q Consensus       104 ~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~g-l~--~~~~G  178 (221)
                      .|-.++..++.|++++++|.+|++++||++.+.+.+...+|++|.. +   ..+++++.|||.+++  .| ++  +++.|
T Consensus       178 ~Id~vf~v~G~GtVvtGtv~sG~l~~Gd~v~i~p~~~~~~VrsIq~-~---~~~v~~a~aG~rval~l~g~~~~~~i~rG  253 (614)
T PRK10512        178 AIDRAFTVKGAGLVVTGTALSGEVKVGDTLWLTGVNKPMRVRGLHA-Q---NQPTEQAQAGQRIALNIAGDAEKEQINRG  253 (614)
T ss_pred             EEEEEeccCCCeEEEEEEEecceEecCCEEEEcCCCCcEEEEEEec-C---CcCCCEEeCCCeEEEEecCCCChhhCCCc
Confidence            9999998999999999999999999999999988877789999873 2   357899999999965  55 53  68999


Q ss_pred             cEEecC
Q psy5461         179 DKRTRV  184 (221)
Q Consensus       179 dtl~~~  184 (221)
                      |+++..
T Consensus       254 dvl~~~  259 (614)
T PRK10512        254 DWLLAD  259 (614)
T ss_pred             CEEeCC
Confidence            999875

>PLN00043 elongation factor 1-alpha; Provisional

Probab=99.40  E-value=4.6e-12  Score=116.12  Aligned_cols=146  Identities=13%  Similarity=0.137  Sum_probs=109.9

Q ss_pred             ceeeeeeeecccc-cCCcchHHHHhhcc--------ccccCceeEecCCCccccHH------------HHHHHHHhhCCC
Q psy5461          26 SLCARAFKVVHDK-HRGAVTFFRIYSGA--------FKKNHVPVLCGSSYKNIGVQ------------KLMDAIVDILPS   84 (221)
Q Consensus        26 ~~~~~vfk~~~d~-~~g~l~~~~l~~~~--------~~~~~~Pv~~gSa~~~~Gi~------------~LLd~I~~~~Ps   84 (221)
                      +++..++|++... ..-+..+.++.+..        .+...+|++..||++|.||.            .||++|.. ++.
T Consensus       147 ~iIV~vNKmD~~~~~~~~~~~~~i~~ei~~~l~~~g~~~~~~~~ipiSa~~G~ni~~~~~~~~Wy~g~tLl~~l~~-i~~  225 (447)
T PLN00043        147 QMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGYNPDKIPFVPISGFEGDNMIERSTNLDWYKGPTLLEALDQ-INE  225 (447)
T ss_pred             cEEEEEEcccCCchhhhHHHHHHHHHHHHHHHHHcCCCcccceEEEEeccccccccccccCCcccchHHHHHHHhh-cCC
Confidence            5788999965321 10112222222211        11234789999999999974            48998875 565


Q ss_pred             CCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccC
Q psy5461          85 PTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCG  164 (221)
Q Consensus        85 P~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aG  164 (221)
                      |..        ..+.||++.|..++..++.|+++.+||.+|++++||+|.....+...+|++|...    ..++++|.||
T Consensus       226 p~~--------~~~~plr~~I~~v~~~~g~G~vv~G~V~~G~l~~Gd~v~~~P~~~~~~VksI~~~----~~~v~~a~aG  293 (447)
T PLN00043        226 PKR--------PSDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFGPTGLTTEVKSVEMH----HESLQEALPG  293 (447)
T ss_pred             Ccc--------ccCCCcEEEEEEEEEeCCcEEEEEEEEECCEEeeCCEEEEcCCCCEEEEEEEEEC----CeEeCEecCC
Confidence            543        4578999999999999999999999999999999999999988888899998742    4688999999


Q ss_pred             CEEE--EcCC--CCCccCcEEecC
Q psy5461         165 NIAA--VTGL--KRERGKDKRTRV  184 (221)
Q Consensus       165 dIv~--i~gl--~~~~~Gdtl~~~  184 (221)
                      |.+.  +.++  ++++.|+.++..
T Consensus       294 d~v~i~l~~~~~~~i~rG~vl~~~  317 (447)
T PLN00043        294 DNVGFNVKNVAVKDLKRGYVASNS  317 (447)
T ss_pred             CeEEEEECCCCHhhCCCccEEccC
Confidence            9995  5566  368999999875

>PLN03127 Elongation factor Tu; Provisional

Probab=99.39  E-value=7.8e-12  Score=114.59  Aligned_cols=150  Identities=21%  Similarity=0.273  Sum_probs=110.6

Q ss_pred             CCCc-eeeeeeeecc-c-ccCCcchHHHHhhcc----ccccCceeEecCCC---cccc-------HHHHHHHHHhhCCCC
Q psy5461          23 FGDS-LCARAFKVVH-D-KHRGAVTFFRIYSGA----FKKNHVPVLCGSSY---KNIG-------VQKLMDAIVDILPSP   85 (221)
Q Consensus        23 ~~~~-~~~~vfk~~~-d-~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~---~~~G-------i~~LLd~I~~~~PsP   85 (221)
                      .+-+ ++..++|++. + +..-+.....+.+..    .....+|++.+||.   +|.|       +..|+++|.+++|.|
T Consensus       175 ~gip~iIvviNKiDlv~~~~~~~~i~~~i~~~l~~~~~~~~~vpiip~Sa~sa~~g~n~~~~~~~i~~Ll~~l~~~lp~p  254 (447)
T PLN03127        175 VGVPSLVVFLNKVDVVDDEELLELVEMELRELLSFYKFPGDEIPIIRGSALSALQGTNDEIGKNAILKLMDAVDEYIPEP  254 (447)
T ss_pred             cCCCeEEEEEEeeccCCHHHHHHHHHHHHHHHHHHhCCCCCcceEEEeccceeecCCCcccccchHHHHHHHHHHhCCCC
Confidence            3456 5788999752 1 111111111222211    22346899999886   3444       789999999999988


Q ss_pred             CCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC----CceeeeceeEeeecCCeeeeCcc
Q psy5461          86 TERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL----DQSEQITRLLLAEADDYKEVNEI  161 (221)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~----~~~~~v~~i~~~~g~~~~~v~~a  161 (221)
                      ..        ..++||.+.|..++..++.|.++.+||.+|++++||+|++.+.    +...+|++|...    ..+++++
T Consensus       255 ~r--------~~~~pfr~~I~~vf~v~g~GtVvtG~v~~G~i~~Gd~v~i~p~~~~g~~~~~VksI~~~----~~~v~~a  322 (447)
T PLN03127        255 VR--------VLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEIVGLRPGGPLKTTVTGVEMF----KKILDQG  322 (447)
T ss_pred             Cc--------ccccceEeeEEEEEEcCCceEEEEEEEEccEEecCCEEEEcccCCCCcEEEEEEEEEEE----CcEeCEE
Confidence            54        4578999999999999999999999999999999999998854    246789998744    2468999


Q ss_pred             ccCCEEE--EcCCC--CCccCcEEecC
Q psy5461         162 QCGNIAA--VTGLK--RERGKDKRTRV  184 (221)
Q Consensus       162 ~aGdIv~--i~gl~--~~~~Gdtl~~~  184 (221)
                      .|||.++  +.|++  +++.||++++.
T Consensus       323 ~aGd~v~l~L~~i~~~~i~rG~Vl~~~  349 (447)
T PLN03127        323 QAGDNVGLLLRGLKREDVQRGQVICKP  349 (447)
T ss_pred             cCCCEEEEEeCCCCHHHCCCccEEecC
Confidence            9999996  46764  68999999985

>PTZ00141 elongation factor 1- alpha; Provisional

Probab=99.38  E-value=6.1e-12  Score=115.30  Aligned_cols=146  Identities=12%  Similarity=0.104  Sum_probs=110.0

Q ss_pred             ceeeeeeeecccc-----cCCcchHHHHhhcc----ccccCceeEecCCCccccHH------------HHHHHHHhhCCC
Q psy5461          26 SLCARAFKVVHDK-----HRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQ------------KLMDAIVDILPS   84 (221)
Q Consensus        26 ~~~~~vfk~~~d~-----~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~------------~LLd~I~~~~Ps   84 (221)
                      .++..++|.+.+.     ..-+-....+....    .+...+|++..||.+|.|+.            .|+++|.+. +.
T Consensus       147 ~iiv~vNKmD~~~~~~~~~~~~~i~~~i~~~l~~~g~~~~~~~~ipiSa~~g~ni~~~~~~~~Wy~G~tL~~~l~~~-~~  225 (446)
T PTZ00141        147 QMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYNPEKVPFIPISGWQGDNMIEKSDNMPWYKGPTLLEALDTL-EP  225 (446)
T ss_pred             eEEEEEEccccccchhhHHHHHHHHHHHHHHHHhcCCCcccceEEEeecccCCCcccCCCCCcccchHHHHHHHhCC-CC
Confidence            4778999965222     11122222332221    12235899999999999986            499998664 44


Q ss_pred             CCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccC
Q psy5461          85 PTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCG  164 (221)
Q Consensus        85 P~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aG  164 (221)
                      |..        ..++||.+.|..++..++.|+++.+||.+|+|+.||+|.+...+...+|++|...    ..++++|.||
T Consensus       226 ~~~--------~~~~p~r~~I~~v~~v~g~Gtvv~G~V~~G~l~~Gd~v~i~P~~~~~~VksI~~~----~~~~~~a~aG  293 (446)
T PTZ00141        226 PKR--------PVDKPLRLPLQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPSGVTTEVKSVEMH----HEQLAEAVPG  293 (446)
T ss_pred             CCc--------CCCCCeEEEEEEEEecCCceEEEEEEEEcceEecCCEEEEccCCcEEEEEEEEec----CcccCEECCC
Confidence            543        3568999999999999999999999999999999999999988878899998743    3578999999


Q ss_pred             CEEEE--cCCC--CCccCcEEecC
Q psy5461         165 NIAAV--TGLK--RERGKDKRTRV  184 (221)
Q Consensus       165 dIv~i--~gl~--~~~~Gdtl~~~  184 (221)
                      |.+++  .+++  +++.||+|+..
T Consensus       294 ~~v~i~L~~i~~~~v~rG~vl~~~  317 (446)
T PTZ00141        294 DNVGFNVKNVSVKDIKRGYVASDS  317 (446)
T ss_pred             CEEEEEECCCCHHHcCCceEEecC
Confidence            99954  5654  58999999875

>PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]

Probab=99.38  E-value=6.1e-13  Score=92.16  Aligned_cols=68  Identities=31%  Similarity=0.428  Sum_probs=62.5

Q ss_pred             ceEEEEEEEceEEcCCCEEEe--ccCCce---eeeceeEeeecCCeeeeCccccCCEEEEcCCCC-CccCcEEe
Q psy5461         115 GAVTFFRIYSGAFKKGQKFYN--IHLDQS---EQITRLLLAEADDYKEVNEIQCGNIAAVTGLKR-ERGKDKRT  182 (221)
Q Consensus       115 G~i~~~RV~sG~L~~gd~v~~--~~~~~~---~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~-~~~Gdtl~  182 (221)
                      |+++++||+||+|++||++++  .+++++   .+|.+|+.+++...+.+..+.||+++.+.++++ +++|||||
T Consensus         1 G~v~~grV~sG~l~~gd~v~~~~~~~~~~~~~~~I~~i~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~~Gdtl~   74 (74)
T PF03144_consen    1 GRVATGRVYSGTLKKGDKVRVLPNGTGKKGQVVKIKSIFMFNGDVQEAVAGANAGDIVAIIGLNDAIRRGDTLT   74 (74)
T ss_dssp             EEEEEEEEEESEEETTEEEEEESTTTTEECEEEEEEEEEETTEEESEEETTEEEEEEEESSSGCSCSSTTEEEE
T ss_pred             CEEEEEEEEEeEEcCCCEEEECccCCcceeeeeecccccccccCccEeCCceeeEEEEEEcCCCCCcCcCCEEC
Confidence            789999999999999999999  545555   899999999999999999999999999999999 89999996

EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A ....

>TIGR03680 eif2g_arch translation initiation factor 2 subunit gamma

Probab=99.36  E-value=2.1e-11  Score=110.59  Aligned_cols=149  Identities=16%  Similarity=0.160  Sum_probs=108.1

Q ss_pred             Cceeeeeeeecccc-cCCcchHHHHhhcccc--ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCc
Q psy5461          25 DSLCARAFKVVHDK-HRGAVTFFRIYSGAFK--KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSL  101 (221)
Q Consensus        25 ~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~~--~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~  101 (221)
                      .+++..++|++... ......+..+.+....  ....|++..||++|.|+++|++.|...+|.|..        +.+.||
T Consensus       135 ~~iIVvvNK~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~ii~vSA~~g~gi~~L~e~L~~~l~~~~~--------~~~~~~  206 (406)
T TIGR03680       135 KNIVIVQNKIDLVSKEKALENYEEIKEFVKGTVAENAPIIPVSALHNANIDALLEAIEKFIPTPER--------DLDKPP  206 (406)
T ss_pred             CeEEEEEEccccCCHHHHHHHHHHHHhhhhhcccCCCeEEEEECCCCCChHHHHHHHHHhCCCCCC--------CCCCCc
Confidence            35788899965321 1111223344332211  125789999999999999999999999987754        457899


Q ss_pred             EEEEEEEee--------cCCCceEEEEEEEceEEcCCCEEEeccCCc------------eeeeceeEeeecCCeeeeCcc
Q psy5461         102 CARAFKVVH--------DKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ------------SEQITRLLLAEADDYKEVNEI  161 (221)
Q Consensus       102 ~~~Vfk~~~--------d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~------------~~~v~~i~~~~g~~~~~v~~a  161 (221)
                      .+.|..++.        ++++|.++.+||.+|+|++||+|.+...+.            ..+|++|...    ..++++|
T Consensus       207 ~~~I~~~f~v~~~g~~~~~~~G~Vv~G~v~~G~i~~gd~v~i~P~~~~~~~g~~~~~~~~~~V~sI~~~----~~~~~~a  282 (406)
T TIGR03680       207 LMYVARSFDVNKPGTPPEKLKGGVIGGSLIQGKLKVGDEIEIRPGIKVEKGGKTKWEPIYTEITSLRAG----GYKVEEA  282 (406)
T ss_pred             EEEEEEEEeecCCCccccCCceeEEEEEEEeCEEeCCCEEEEccCccccccccccccccceEEeEEEEC----CEECCEE
Confidence            999998774        344788999999999999999999986531            2478887632    4688999


Q ss_pred             ccCCEEEEc-----CCC--CCccCcEEecCC
Q psy5461         162 QCGNIAAVT-----GLK--RERGKDKRTRVI  185 (221)
Q Consensus       162 ~aGdIv~i~-----gl~--~~~~Gdtl~~~~  185 (221)
                      .|||.+++.     +++  ++..||.++...
T Consensus       283 ~~G~~v~i~l~~~~~i~~~dv~~G~vl~~~~  313 (406)
T TIGR03680       283 RPGGLVGVGTKLDPALTKADALAGQVVGKPG  313 (406)
T ss_pred             cCCCEEEEeeccCCCCCHHHcccccEEEcCC
Confidence            999999863     332  567899998763

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

>KOG0468|consensus

Probab=99.35  E-value=5.4e-12  Score=117.29  Aligned_cols=144  Identities=19%  Similarity=0.210  Sum_probs=117.5

Q ss_pred             HHHHHHHhhCCCCCCccccc-----------------ccCCCCCCcEEEEEEEeecCC-CceEEEEEEEceEEcCCCEEE
Q psy5461          73 KLMDAIVDILPSPTERPALA-----------------MFQHFGDSLCARAFKVVHDKH-RGAVTFFRIYSGAFKKGQKFY  134 (221)
Q Consensus        73 ~LLd~I~~~~PsP~~~~~~~-----------------~~~~~~~~~~~~Vfk~~~d~~-~G~i~~~RV~sG~L~~gd~v~  134 (221)
                      .+.|++++++|+|.+.+.+.                 ..|+..+|++.++.|.+.... .-..+|+||+||++++|+.|.
T Consensus       428 gfvd~~v~hi~sP~e~a~~K~~hsy~G~~~~~i~~~m~~c~~~~pLm~h~tklyp~dD~~~f~~f~rv~Sg~~~~~q~V~  507 (971)
T KOG0468|consen  428 GFVDMPVEHIPSPRENAARKAEHSYTGTKDSLIYEGMVECNASGPLMVHVTKLYPRDDTVQFHVFGRVYSGQVVTGQDVR  507 (971)
T ss_pred             hhhHhhHhhcCChhhhhccccceeecCCCcchHHHHHHhhCCCCceeEEeecceecCCceeeeeeeeeeecceeecceee
Confidence            58899999999998865441                 358889999999999997443 456999999999999999999


Q ss_pred             eccCC---------ceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-ccCcEEecC-------CCCC-----CCce
Q psy5461         135 NIHLD---------QSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-RGKDKRTRV-------IPKP-----TSVV  192 (221)
Q Consensus       135 ~~~~~---------~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-~~Gdtl~~~-------~~~p-----~~~v  192 (221)
                      +.+++         ....|+++++..+++..+++++.+|.++.|.|+++. -...|+++.       .++|     .++|
T Consensus       508 vlgeny~leDEeD~~~~~v~el~v~~arY~i~V~~~~~G~~VLI~Gidq~i~KtaTi~~~~~ked~yiFrpl~~~t~~Vv  587 (971)
T KOG0468|consen  508 VLGENYSLEDEEDMVICEVGELWVVRARYRIPVSRAPAGLWVLIEGVDQSIVKTATIKSLEYKEDVYIFRPLKFNTEPVV  587 (971)
T ss_pred             EeeccccCCCcccceeeeeeeeeeeeeeEEEEecccCCCcEEEEeccchHHhhhhheeccccccceeeccchhcCCcceE
Confidence            98764         235788999999999999999999999999999863 444577653       2333     3555


Q ss_pred             ----------ehHHHHHHHHHHhhcCCceEEEcc
Q psy5461         193 ----------QCSARWTLNLEVGASSPIISKSKR  216 (221)
Q Consensus       193 ----------~~~~l~~~L~~L~~~Dp~l~~~~~  216 (221)
                                .+++|++||++.+|+.|++..+..
T Consensus       588 KiaveP~nPsELPKmldgLrKinKsYPl~~tkVE  621 (971)
T KOG0468|consen  588 KVAVEPLNPSELPKMLDGLRKINKSYPLVITKVE  621 (971)
T ss_pred             EEEeccCChhhhhHHHHHHHhhcccCCcEEEehh
Confidence                      779999999999999999876543

>PLN03126 Elongation factor Tu; Provisional

Probab=99.32  E-value=3.3e-11  Score=111.26  Aligned_cols=149  Identities=19%  Similarity=0.237  Sum_probs=110.9

Q ss_pred             CCc-eeeeeeeecc-cc-cCCcchHHHHhhcc----ccccCceeEecCCCccc------------------cHHHHHHHH
Q psy5461          24 GDS-LCARAFKVVH-DK-HRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNI------------------GVQKLMDAI   78 (221)
Q Consensus        24 ~~~-~~~~vfk~~~-d~-~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~------------------Gi~~LLd~I   78 (221)
                      +-+ ++..++|.+. ++ ..-+.....+....    +....+|++.+||.+|.                  ++..||++|
T Consensus       196 gi~~iIvvvNK~Dl~~~~~~~~~i~~~i~~~l~~~g~~~~~~~~vp~Sa~~g~n~~~~~~~~~~g~~~wy~~i~~Ll~~l  275 (478)
T PLN03126        196 GVPNMVVFLNKQDQVDDEELLELVELEVRELLSSYEFPGDDIPIISGSALLALEALMENPNIKRGDNKWVDKIYELMDAV  275 (478)
T ss_pred             CCCeEEEEEecccccCHHHHHHHHHHHHHHHHHhcCCCcCcceEEEEEccccccccccccccccCCCchhhhHHHHHHHH
Confidence            445 7889999652 21 11111112222221    23347899999998873                  367899999


Q ss_pred             HhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC--ceeeeceeEeeecCCee
Q psy5461          79 VDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD--QSEQITRLLLAEADDYK  156 (221)
Q Consensus        79 ~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~--~~~~v~~i~~~~g~~~~  156 (221)
                      .++.|.|..        ..++||.+.|..++..++.|.++.+||.+|++++||+|++...+  ...+|++|...    ..
T Consensus       276 ~~~~~~p~r--------~~~~p~r~~I~~vf~v~g~GtVv~G~V~sG~i~~Gd~v~i~p~~~~~~~~VksI~~~----~~  343 (478)
T PLN03126        276 DSYIPIPQR--------QTDLPFLLAVEDVFSITGRGTVATGRVERGTVKVGETVDIVGLRETRSTTVTGVEMF----QK  343 (478)
T ss_pred             HHhCCCCCC--------ccccceeeEEEEEEEeCCceEEEEEEEEcCeEecCCEEEEecCCCceEEEEEEEEEC----Ce
Confidence            998877754        45689999999999999999999999999999999999998654  35688888743    36


Q ss_pred             eeCccccCCEEEE--cCCC--CCccCcEEecC
Q psy5461         157 EVNEIQCGNIAAV--TGLK--RERGKDKRTRV  184 (221)
Q Consensus       157 ~v~~a~aGdIv~i--~gl~--~~~~Gdtl~~~  184 (221)
                      ++++|.|||.+++  .|++  +++.|++++..
T Consensus       344 ~v~~A~aG~~v~l~L~~i~~~di~rG~VL~~~  375 (478)
T PLN03126        344 ILDEALAGDNVGLLLRGIQKADIQRGMVLAKP  375 (478)
T ss_pred             ECCEEeCCceeeeeccCCcHHHcCCccEEecC
Confidence            7899999999865  6765  58999999876

>COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]

Probab=99.32  E-value=4.5e-12  Score=108.44  Aligned_cols=148  Identities=20%  Similarity=0.264  Sum_probs=118.6

Q ss_pred             Cceeeeeeeec-c-cccCCcchHHHHhhcc----ccccCceeEecCCCccc--------cHHHHHHHHHhhCCCCCCccc
Q psy5461          25 DSLCARAFKVV-H-DKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNI--------GVQKLMDAIVDILPSPTERPA   90 (221)
Q Consensus        25 ~~~~~~vfk~~-~-d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~--------Gi~~LLd~I~~~~PsP~~~~~   90 (221)
                      ..++.|++|++ + |++..++....++..+    ..+.+.||+.|||++-.        -|.+|||++.+|+|.|..   
T Consensus       129 p~ivvflnK~Dmvdd~ellelVemEvreLLs~y~f~gd~~Pii~gSal~ale~~~~~~~~i~eLm~avd~yip~Per---  205 (394)
T COG0050         129 PYIVVFLNKVDMVDDEELLELVEMEVRELLSEYGFPGDDTPIIRGSALKALEGDAKWEAKIEELMDAVDSYIPTPER---  205 (394)
T ss_pred             cEEEEEEecccccCcHHHHHHHHHHHHHHHHHcCCCCCCcceeechhhhhhcCCcchHHHHHHHHHHHHhcCCCCCC---
Confidence            37889999994 4 5777888888887654    45678999999998763        389999999999999986   


Q ss_pred             ccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC--ceeeeceeEeeecCCeeeeCccccCCEE-
Q psy5461          91 LAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD--QSEQITRLLLAEADDYKEVNEIQCGNIA-  167 (221)
Q Consensus        91 ~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~--~~~~v~~i~~~~g~~~~~v~~a~aGdIv-  167 (221)
                           +.+.||++-|-++..-.++|+++++||-+|+|+.|+.+...+-.  ++..++.+..+    ++..++..|||-+ 
T Consensus       206 -----~~dkPflmpvEdvfsIsgrgtvvtGrVeRG~lkvg~eveivG~~~~~kttvtgvemf----rk~ld~~~AGdnvg  276 (394)
T COG0050         206 -----DIDKPFLMPVEDVFSISGRGTVVTGRVERGILKVGEEVEIVGIKETQKTTVTGVEMF----RKLLDEGQAGDNVG  276 (394)
T ss_pred             -----cccccccccceeeEEEcCceeEEEEEEeeeeeccCCEEEEecccccceeEEEhHHHH----HHHHhccccCCCcc
Confidence                 67899999999999999999999999999999999999887644  34456655533    2346788999988 


Q ss_pred             -EEcCCC--CCccCcEEecC
Q psy5461         168 -AVTGLK--RERGKDKRTRV  184 (221)
Q Consensus       168 -~i~gl~--~~~~Gdtl~~~  184 (221)
                       .++|.+  ++..|..|+..
T Consensus       277 ~llRg~~r~~veRGqvLakp  296 (394)
T COG0050         277 VLLRGVKREDVERGQVLAKP  296 (394)
T ss_pred             eEEEeccccceecceEeecC
Confidence             356654  67888888754

>COG5258 GTPBP1 GTPase [General function prediction only]

Probab=99.28  E-value=5.9e-11  Score=104.80  Aligned_cols=120  Identities=17%  Similarity=0.165  Sum_probs=98.4

Q ss_pred             ccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCE
Q psy5461          53 FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQK  132 (221)
Q Consensus        53 ~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~  132 (221)
                      .++...|||..|+.+|.|++ ||+-+..++|.-..       .+..+||.+||-|++...+.|.++.+-|.+|.|+.||+
T Consensus       309 ~~~~vvPi~~tSsVTg~Gld-lL~e~f~~Lp~rr~-------~~d~g~flmYId~iYsVtGVGtVvsGsV~~G~l~~gd~  380 (527)
T COG5258         309 AGRGVVPIFYTSSVTGEGLD-LLDEFFLLLPKRRR-------WDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDT  380 (527)
T ss_pred             cCCceEEEEEEecccCccHH-HHHHHHHhCCcccc-------cCCCCCeEEEEEeeEEEeeeEEEEeeeEEeeeeccCCE
Confidence            34458999999999999987 56666677876421       15678999999999999999999999999999999999


Q ss_pred             EEeccCC----ceeeeceeEeeecCCeeeeCccccCCEE--EEcCCC--CCccCcEEecC
Q psy5461         133 FYNIHLD----QSEQITRLLLAEADDYKEVNEIQCGNIA--AVTGLK--RERGKDKRTRV  184 (221)
Q Consensus       133 v~~~~~~----~~~~v~~i~~~~g~~~~~v~~a~aGdIv--~i~gl~--~~~~Gdtl~~~  184 (221)
                      ++.....    ++.+|++|. |   .+.++++|.||+|+  ++.|++  .+..|+.+...
T Consensus       381 vllGP~~~G~fr~v~vkSIe-m---h~~rvdsa~aG~iig~Al~gv~~e~lerGMVl~~~  436 (527)
T COG5258         381 VLLGPFKDGKFREVVVKSIE-M---HHYRVDSAKAGSIIGIALKGVEKEELERGMVLSAG  436 (527)
T ss_pred             EEEccCCCCcEEEEEEEEEE-E---eeEEeccccCCcEEEEEecccCHHHHhcceEecCC
Confidence            9997643    356888886 3   35689999999999  567876  48999999764

>cd01342 Translation_Factor_II_like Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins

Probab=99.21  E-value=1.6e-10  Score=79.58  Aligned_cols=78  Identities=32%  Similarity=0.321  Sum_probs=66.9

Q ss_pred             cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEecc--CCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCC--Cc
Q psy5461         101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIH--LDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKR--ER  176 (221)
Q Consensus       101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~--~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~--~~  176 (221)
                      +.++|+++..+++.|+++++||++|+|++||.+++..  ...+.++.+|+...    .+++++.|||++.+.+.+.  ++
T Consensus         1 ~~~~v~~~~~~~~~g~v~~~rv~~G~l~~g~~v~~~~~~~~~~~~i~~i~~~~----~~~~~~~aG~~~~~~~~~~~~~~   76 (83)
T cd01342           1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFK----GEVDEAVAGDIVGIVLKDKDDIK   76 (83)
T ss_pred             CeeEEEEEEEeCCceEEEEEEEeeCEEecCCEEEEecCCceeEEEEeEeEecC----ceeceecCCCEEEEEEccccccC
Confidence            4678999999999999999999999999999999987  55567888887654    5678899999998877654  89


Q ss_pred             cCcEEe
Q psy5461         177 GKDKRT  182 (221)
Q Consensus       177 ~Gdtl~  182 (221)
                      +||+++
T Consensus        77 ~g~~l~   82 (83)
T cd01342          77 IGDTLT   82 (83)
T ss_pred             CCCEec
Confidence            999885

Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E.coli IF-2 to 30S subunits.

>TIGR00475 selB selenocysteine-specific elongation factor SelB

Probab=99.21  E-value=1.3e-10  Score=109.84  Aligned_cols=149  Identities=13%  Similarity=0.093  Sum_probs=109.7

Q ss_pred             CCc-eeeeeeeecc-cccCCcchHHHHhhcccc---ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCC
Q psy5461          24 GDS-LCARAFKVVH-DKHRGAVTFFRIYSGAFK---KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFG   98 (221)
Q Consensus        24 ~~~-~~~~vfk~~~-d~~~g~l~~~~l~~~~~~---~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~   98 (221)
                      +-+ ++..++|++. |+..-+.....+.+-...   ....|++..||++|.||++|.+.|..+++.....       ..+
T Consensus       102 gi~~iIVVlNK~Dlv~~~~~~~~~~ei~~~l~~~~~~~~~~ii~vSA~tG~GI~eL~~~L~~l~~~~~~~-------~~~  174 (581)
T TIGR00475       102 GIPHTIVVITKADRVNEEEIKRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKELKNLLESLDIK-------RIQ  174 (581)
T ss_pred             CCCeEEEEEECCCCCCHHHHHHHHHHHHHHHHHhCCCCCCcEEEEeCCCCCCchhHHHHHHHHHHhCCCc-------CcC
Confidence            345 8899999653 222111122223221111   1147899999999999999999988776553221       236


Q ss_pred             CCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC--C
Q psy5461          99 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK--R  174 (221)
Q Consensus        99 ~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~--~  174 (221)
                      +||.+.|-.++..++.|+++.++|.+|+++.||++.+...+...+|++|.. +   ..++++|.|||.+++  .|++  +
T Consensus       175 ~p~r~~Id~~f~v~G~GtVv~G~v~~G~i~~Gd~l~i~P~~~~~~Vr~iq~-~---~~~v~~a~aG~rval~L~~i~~~~  250 (581)
T TIGR00475       175 KPLRMAIDRAFKVKGAGTVVTGTAFSGEVKVGDNLRLLPINHEVRVKAIQA-Q---NQDVEIAYAGQRIALNLMDVEPES  250 (581)
T ss_pred             CCcEEEEEEEEecCCcEEEEEEEEecceEecCCEEEECCCCceEEEeEEEE-C---CccCCEEECCCEEEEEeCCCCHHH
Confidence            899999999998899999999999999999999999998888889999974 3   347899999999964  5664  5


Q ss_pred             CccCcEEec
Q psy5461         175 ERGKDKRTR  183 (221)
Q Consensus       175 ~~~Gdtl~~  183 (221)
                      ++.|..++.
T Consensus       251 i~rG~~~~~  259 (581)
T TIGR00475       251 LKRGLLILT  259 (581)
T ss_pred             cCCceEEcC
Confidence            789966554

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.

>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional

Probab=99.15  E-value=9.5e-10  Score=101.63  Aligned_cols=146  Identities=12%  Similarity=0.034  Sum_probs=100.9

Q ss_pred             CceeeeeeeecccccCCcchHHHHhhcc---cc----ccCceeEecCCCccccHHH------------HHHHHHhhCCCC
Q psy5461          25 DSLCARAFKVVHDKHRGAVTFFRIYSGA---FK----KNHVPVLCGSSYKNIGVQK------------LMDAIVDILPSP   85 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~---~~----~~~~Pv~~gSa~~~~Gi~~------------LLd~I~~~~PsP   85 (221)
                      .+++..++|++..... +-.+..+....   .+    ....|++..||++|.|+..            |+++| +.+|.|
T Consensus       161 ~~iIvvvNKiD~~~~~-~~~~~~i~~~l~~~~~~~~~~~~~~iipvSA~~g~ni~~~~~~~~wy~G~tLl~~L-~~i~~~  238 (474)
T PRK05124        161 KHLVVAVNKMDLVDYS-EEVFERIREDYLTFAEQLPGNLDIRFVPLSALEGDNVVSQSESMPWYSGPTLLEVL-ETVDIQ  238 (474)
T ss_pred             CceEEEEEeeccccch-hHHHHHHHHHHHHHHHhcCCCCCceEEEEEeecCCCcccccccccccchhhHHHHH-hhcCCC
Confidence            4688899996532111 11122222211   11    2357899999999999864            67755 456665


Q ss_pred             CCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCC
Q psy5461          86 TERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN  165 (221)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGd  165 (221)
                      ..        ..+.||.+.|..++...+..+-..+||.+|+|+.||+|++...++..+|++|....    .++++|.|||
T Consensus       239 ~~--------~~~~p~r~~I~~v~~~~~~~~g~~G~V~sG~l~~Gd~v~i~P~~~~~~VksI~~~~----~~v~~A~aG~  306 (474)
T PRK05124        239 RV--------VDAQPFRFPVQYVNRPNLDFRGYAGTLASGVVKVGDRVKVLPSGKESNVARIVTFD----GDLEEAFAGE  306 (474)
T ss_pred             CC--------CCCCCceeeEEEEEecCCcccceEEEEEeEEEecCCEEEEecCCceEEEEEEEEcC----ccccCcCCCC
Confidence            43        35689998887765432211224689999999999999999888888999998442    3688999999


Q ss_pred             EEEEc--CCCCCccCcEEecC
Q psy5461         166 IAAVT--GLKRERGKDKRTRV  184 (221)
Q Consensus       166 Iv~i~--gl~~~~~Gdtl~~~  184 (221)
                      .+++.  +..+++.||+|+..
T Consensus       307 ~V~l~L~~~~~i~rG~VL~~~  327 (474)
T PRK05124        307 AITLVLEDEIDISRGDLLVAA  327 (474)
T ss_pred             EEEEEeCCccccCCccEEECC
Confidence            99764  34468999999976

>COG5256 TEF1 Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]

Probab=99.14  E-value=1.8e-09  Score=96.31  Aligned_cols=145  Identities=21%  Similarity=0.245  Sum_probs=109.6

Q ss_pred             CceeeeeeeecccccC-CcchHHHHhh-------cc-ccccCceeEecCCCccccHH------------HHHHHHHhhCC
Q psy5461          25 DSLCARAFKVVHDKHR-GAVTFFRIYS-------GA-FKKNHVPVLCGSSYKNIGVQ------------KLMDAIVDILP   83 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~~-g~l~~~~l~~-------~~-~~~~~~Pv~~gSa~~~~Gi~------------~LLd~I~~~~P   83 (221)
                      ..++..+||.  |... -+--|+.+.+       .. ++...+|.+..||.+|.++.            .||++|. .+.
T Consensus       146 ~~lIVavNKM--D~v~wde~rf~ei~~~v~~l~k~~G~~~~~v~FIPiSg~~G~Nl~~~s~~~pWY~GpTLleaLd-~~~  222 (428)
T COG5256         146 KQLIVAVNKM--DLVSWDEERFEEIVSEVSKLLKMVGYNPKDVPFIPISGFKGDNLTKKSENMPWYKGPTLLEALD-QLE  222 (428)
T ss_pred             ceEEEEEEcc--cccccCHHHHHHHHHHHHHHHHHcCCCccCCeEEecccccCCcccccCcCCcCccCChHHHHHh-ccC
Confidence            5889999994  3211 0111222221       11 23336789999999997654            6888887 555


Q ss_pred             CCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCcccc
Q psy5461          84 SPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQC  163 (221)
Q Consensus        84 sP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~a  163 (221)
                      .|..        ..+.||++-|-+++.-...|++.++||.+|.|++||.|+....+....|+++.. +   .++++.+.|
T Consensus       223 ~p~~--------~~d~Plr~pI~~v~~i~~~gtv~vGrVEsG~i~~g~~v~~~p~~~~~evksie~-~---~~~~~~a~~  290 (428)
T COG5256         223 PPER--------PLDKPLRLPIQDVYSISGIGTVPVGRVESGVIKPGQKVTFMPAGVVGEVKSIEM-H---HEEISQAEP  290 (428)
T ss_pred             CCCC--------CCCCCeEeEeeeEEEecCCceEEEEEEeeeeeccCCEEEEecCcceEEEeeeee-c---ccccccCCC
Confidence            5544        357999999999998788899999999999999999999998887788888873 2   678999999


Q ss_pred             CCEEE--EcCCC--CCccCcEEecC
Q psy5461         164 GNIAA--VTGLK--RERGKDKRTRV  184 (221)
Q Consensus       164 GdIv~--i~gl~--~~~~Gdtl~~~  184 (221)
                      ||.+.  ++|++  ++++||.+++.
T Consensus       291 GD~i~~~vrgv~~~dI~~Gdv~~~~  315 (428)
T COG5256         291 GDNVGFNVRGVEKNDIRRGDVIGHS  315 (428)
T ss_pred             CCeEEEEecCCchhccCCccEeccC
Confidence            99994  67765  69999999876

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

Probab=99.12  E-value=5.1e-10  Score=100.40  Aligned_cols=145  Identities=17%  Similarity=0.186  Sum_probs=112.2

Q ss_pred             eeeeeeec-ccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEE
Q psy5461          28 CARAFKVV-HDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAF  106 (221)
Q Consensus        28 ~~~vfk~~-~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vf  106 (221)
                      +..+.|.+ .|+..-+.....+...+. -...|+|..|+++|.||++|=+.|.+..- +.++       +.+.||..+|-
T Consensus       107 iivltk~D~~d~~r~e~~i~~Il~~l~-l~~~~i~~~s~~~g~GI~~Lk~~l~~L~~-~~e~-------d~~~~fri~ID  177 (447)
T COG3276         107 IIVLTKADRVDEARIEQKIKQILADLS-LANAKIFKTSAKTGRGIEELKNELIDLLE-EIER-------DEQKPFRIAID  177 (447)
T ss_pred             EEEEeccccccHHHHHHHHHHHHhhcc-cccccccccccccCCCHHHHHHHHHHhhh-hhhh-------ccCCceEEEEe
Confidence            44455532 333333334455555554 45678899999999999999999998764 2222       56899999888


Q ss_pred             EEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--CCccCcEEe
Q psy5461         107 KVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--RERGKDKRT  182 (221)
Q Consensus       107 k~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--~~~~Gdtl~  182 (221)
                      .....++.|+++++.++||+++.||+++..+.+++.+|++|...    -.++++|.||+.|+  +.|.+  ++..||.+.
T Consensus       178 raFtVKGvGTVVtGtv~sG~V~v~D~L~l~p~~k~v~VRsIq~~----d~d~~~a~AG~RVgLaL~~v~~eei~RG~~L~  253 (447)
T COG3276         178 RAFTVKGVGTVVTGTVLSGEVKVGDKLYLSPINKEVRVRSIQAH----DVDVEEAKAGQRVGLALKGVEKEEIERGDWLL  253 (447)
T ss_pred             eEEEeccccEEEEeEEeeeeEEECCEEEEecCCCeEEEEeeeec----CcchhhccccceeeeecCCCCHHHhhcccEec
Confidence            88888999999999999999999999999999999999998732    34689999999996  45653  689999988


Q ss_pred             cCC
Q psy5461         183 RVI  185 (221)
Q Consensus       183 ~~~  185 (221)
                      +..
T Consensus       254 ~~~  256 (447)
T COG3276         254 KPE  256 (447)
T ss_pred             cCC
Confidence            763

>TIGR02034 CysN sulfate adenylyltransferase, large subunit

Probab=99.12  E-value=1.6e-09  Score=98.29  Aligned_cols=148  Identities=13%  Similarity=0.029  Sum_probs=100.0

Q ss_pred             CceeeeeeeecccccCCcchHHHHhhcc------ccccCceeEecCCCccccHHH------------HHHHHHhhCCCCC
Q psy5461          25 DSLCARAFKVVHDKHRGAVTFFRIYSGA------FKKNHVPVLCGSSYKNIGVQK------------LMDAIVDILPSPT   86 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~------~~~~~~Pv~~gSa~~~~Gi~~------------LLd~I~~~~PsP~   86 (221)
                      .+++..++|++..... +-.+..+....      ..-...|++..||++|.|+..            |+++|.. +|.|.
T Consensus       134 ~~iivviNK~D~~~~~-~~~~~~i~~~~~~~~~~~~~~~~~iipiSA~~g~ni~~~~~~~~wy~g~tL~~~L~~-~~~~~  211 (406)
T TIGR02034       134 RHVVLAVNKMDLVDYD-EEVFENIKKDYLAFAEQLGFRDVTFIPLSALKGDNVVSRSESMPWYSGPTLLEILET-VEVER  211 (406)
T ss_pred             CcEEEEEEecccccch-HHHHHHHHHHHHHHHHHcCCCCccEEEeecccCCCCcccccCCCccchhHHHHHHHh-cCCCC
Confidence            3588899996532211 11112222111      111346899999999999874            7787765 45554


Q ss_pred             CcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCE
Q psy5461          87 ERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI  166 (221)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdI  166 (221)
                      .        ..++||.+.|..++.....+.-..++|.+|+|++||+|++...+...+|++|... +   .++++|.|||.
T Consensus       212 ~--------~~~~p~r~~i~~v~~~~~~~~g~~G~v~~G~l~~gd~v~i~P~~~~~~VksI~~~-~---~~~~~a~~G~~  279 (406)
T TIGR02034       212 D--------AQDLPLRFPVQYVNRPNLDFRGYAGTIASGSVHVGDEVVVLPSGRSSRVARIVTF-D---GDLEQARAGQA  279 (406)
T ss_pred             C--------cCCCCcccceEEEeecCCCcEEEEEEEecceeecCCEEEEeCCCcEEEEEEEEEC-C---cccCEeCCCCE
Confidence            3        3467888866655432222222569999999999999999888888899999743 2   36899999999


Q ss_pred             EEEc--CCCCCccCcEEecCCC
Q psy5461         167 AAVT--GLKRERGKDKRTRVIP  186 (221)
Q Consensus       167 v~i~--gl~~~~~Gdtl~~~~~  186 (221)
                      +++.  +.++++.||+++....
T Consensus       280 v~l~l~~~~~i~rG~vl~~~~~  301 (406)
T TIGR02034       280 VTLTLDDEIDISRGDLLAAADS  301 (406)
T ss_pred             EEEEECCccccCCccEEEcCCC
Confidence            9764  3346899999998643

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).

>KOG1145|consensus

Probab=99.07  E-value=8.4e-10  Score=101.18  Aligned_cols=148  Identities=16%  Similarity=0.077  Sum_probs=116.2

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhcc--------ccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccc
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGA--------FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAM   93 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~--------~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~   93 (221)
                      +.+.|++..++|++.+    ....+++++..        .-+++++++..||++|.|++.|.++|....---      .+
T Consensus       251 ~A~VpiVvAinKiDkp----~a~pekv~~eL~~~gi~~E~~GGdVQvipiSAl~g~nl~~L~eaill~Ae~m------dL  320 (683)
T KOG1145|consen  251 SANVPIVVAINKIDKP----GANPEKVKRELLSQGIVVEDLGGDVQVIPISALTGENLDLLEEAILLLAEVM------DL  320 (683)
T ss_pred             hcCCCEEEEEeccCCC----CCCHHHHHHHHHHcCccHHHcCCceeEEEeecccCCChHHHHHHHHHHHHHh------hc
Confidence            4688999999997633    23333444332        335789999999999999999999998654221      23


Q ss_pred             cCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCC
Q psy5461          94 FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK  173 (221)
Q Consensus        94 ~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~  173 (221)
                      +.++.+|+.++|.....|+++|.++++-|-.|||++|+.+.....  -.||+.++=   ..-.++++|.||..+-|.|++
T Consensus       321 kA~p~g~~eg~VIES~vdkg~G~~aT~iVkrGTLkKG~vlV~G~~--w~KVr~l~D---~nGk~i~~A~Ps~pv~V~Gwk  395 (683)
T KOG1145|consen  321 KADPKGPAEGWVIESSVDKGRGPVATVIVKRGTLKKGSVLVAGKS--WCKVRALFD---HNGKPIDEATPSQPVEVLGWK  395 (683)
T ss_pred             ccCCCCCceEEEEEeeecCCccceeEEEEeccccccccEEEEech--hhhhhhhhh---cCCCCccccCCCCceEeeccc
Confidence            447889999999999999999999999999999999999887522  246666553   444589999999999999999


Q ss_pred             CC-ccCcEEecC
Q psy5461         174 RE-RGKDKRTRV  184 (221)
Q Consensus       174 ~~-~~Gdtl~~~  184 (221)
                      ++ ..||-+...
T Consensus       396 dlP~aGD~vleV  407 (683)
T KOG1145|consen  396 DLPIAGDEVLEV  407 (683)
T ss_pred             CCCCCCceEEEE
Confidence            87 899988654

>PRK04004 translation initiation factor IF-2; Validated

Probab=99.07  E-value=1.5e-09  Score=102.71  Aligned_cols=121  Identities=16%  Similarity=0.221  Sum_probs=94.5

Q ss_pred             cCceeEecCCCccccHHHHHHHHHhh----CCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCC
Q psy5461          56 NHVPVLCGSSYKNIGVQKLMDAIVDI----LPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQ  131 (221)
Q Consensus        56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~----~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd  131 (221)
                      ...|++..||++|.|+.+|++.+...    ++.+..       .+.+.|+.+.|+++..+++.|++++++|++|+|++||
T Consensus       191 ~~v~ivpiSA~tGeGi~dLl~~i~~~~~~~l~~~l~-------~~~~~~~~~~V~ev~~~~g~G~v~~~~v~~GtL~~Gd  263 (586)
T PRK04004        191 KTVAIVPVSAKTGEGIPDLLMVLAGLAQRYLEERLK-------IDVEGPGKGTVLEVKEERGLGTTIDVILYDGTLRKGD  263 (586)
T ss_pred             CCceEeeccCCCCCChHHHHHHHHHHHHHHHHHhhc-------cCCCCCeEEEEEEEEEeCCCceEEEEEEEcCEEECCC
Confidence            46889999999999999999988642    343332       2467899999999999999999999999999999999


Q ss_pred             EEEeccCCc--eeeeceeEeee--------cCCeeeeCccccCCEEEE--cCCCCCccCcEEec
Q psy5461         132 KFYNIHLDQ--SEQITRLLLAE--------ADDYKEVNEIQCGNIAAV--TGLKRERGKDKRTR  183 (221)
Q Consensus       132 ~v~~~~~~~--~~~v~~i~~~~--------g~~~~~v~~a~aGdIv~i--~gl~~~~~Gdtl~~  183 (221)
                      .|.....+.  ..+|+.|....        +.....++++.|...+-+  .|++.+..||.+.-
T Consensus       264 ~vv~~~~~~~i~~kVr~l~~~~~~~e~~~~~~~~~~~~~~~~~~~v~i~~~gl~~~~~g~~~~v  327 (586)
T PRK04004        264 TIVVGGKDGPIVTKVRALLKPRPLDEMRDPEDKFKPVDEVVAAAGVKISAPDLEDALAGSPLRV  327 (586)
T ss_pred             EEEECcCCCcceEEEEEEecCcchhhccccccccccccccCCCCceEEEeCCccccCCCCeEEE
Confidence            998877653  34788877542        124466777777776644  48888888988754

>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3)

Probab=99.05  E-value=2.8e-09  Score=75.66  Aligned_cols=79  Identities=16%  Similarity=0.216  Sum_probs=67.8

Q ss_pred             CcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--CC
Q psy5461         100 SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--RE  175 (221)
Q Consensus       100 ~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--~~  175 (221)
                      ||.+.|..++..+ .|++..+||.+|++++||+++....+...+|++|...    ..++++|.|||.+.  +.+++  ++
T Consensus         1 p~r~~V~~v~~~~-~g~vv~G~v~~G~i~~Gd~v~i~P~~~~~~V~si~~~----~~~~~~a~aGd~v~~~l~~~~~~~v   75 (83)
T cd03698           1 PFRLPISDKYKDQ-GGTVVSGKVESGSIQKGDTLLVMPSKESVEVKSIYVD----DEEVDYAVAGENVRLKLKGIDEEDI   75 (83)
T ss_pred             CeEEEEEeEEEcC-CCcEEEEEEeeeEEeCCCEEEEeCCCcEEEEEEEEEC----CeECCEECCCCEEEEEECCCCHHHC
Confidence            5788888888777 8999999999999999999999998888899998743    36789999999996  66765  68


Q ss_pred             ccCcEEec
Q psy5461         176 RGKDKRTR  183 (221)
Q Consensus       176 ~~Gdtl~~  183 (221)
                      +.||+|++
T Consensus        76 ~~G~vl~~   83 (83)
T cd03698          76 SPGDVLCS   83 (83)
T ss_pred             CCCCEEeC
Confidence            99999874

In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM

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

Probab=98.98  E-value=2.6e-09  Score=97.84  Aligned_cols=150  Identities=16%  Similarity=0.129  Sum_probs=113.2

Q ss_pred             CCCCceeeeeeeeccccc-----CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCC
Q psy5461          22 HFGDSLCARAFKVVHDKH-----RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQH   96 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~-----~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~   96 (221)
                      ..+-|++..+||++-.+.     ..++....+....+.+ ++.++.+||++|+||.+||++|....--      ++++..
T Consensus       105 ~a~vP~iVAiNKiDk~~~np~~v~~el~~~gl~~E~~gg-~v~~VpvSA~tg~Gi~eLL~~ill~aev------~elka~  177 (509)
T COG0532         105 AAGVPIVVAINKIDKPEANPDKVKQELQEYGLVPEEWGG-DVIFVPVSAKTGEGIDELLELILLLAEV------LELKAN  177 (509)
T ss_pred             HCCCCEEEEEecccCCCCCHHHHHHHHHHcCCCHhhcCC-ceEEEEeeccCCCCHHHHHHHHHHHHHH------HhhhcC
Confidence            367899999999753321     2233333333333444 5789999999999999999999865322      234456


Q ss_pred             CCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-
Q psy5461          97 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-  175 (221)
Q Consensus        97 ~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-  175 (221)
                      ++++..+.|..+..++++|.++..-++.|+|++||.+.....     .+.+..+......++..+.++--+.+.|++++ 
T Consensus       178 ~~~~a~gtviE~~~dkG~G~vatviv~~GtL~~GD~iv~g~~-----~g~I~t~v~~~~~~i~~a~ps~~v~i~g~~evp  252 (509)
T COG0532         178 PEGPARGTVIEVKLDKGLGPVATVIVQDGTLKKGDIIVAGGE-----YGRVRTMVDDLGKPIKEAGPSKPVEILGLSEVP  252 (509)
T ss_pred             CCCcceEEEEEEEeccCCCceEEEEEecCeEecCCEEEEccC-----CCceEEeehhcCCCccccCCCCCeEEecccccc
Confidence            789999999999999999999999999999999999999743     33444455566678888999988889998876 


Q ss_pred             ccCcEEec
Q psy5461         176 RGKDKRTR  183 (221)
Q Consensus       176 ~~Gdtl~~  183 (221)
                      ..||.+..
T Consensus       253 ~Ag~~~~v  260 (509)
T COG0532         253 AAGDVFIV  260 (509)
T ss_pred             ccCceEEe
Confidence            67877754

>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages

Probab=98.98  E-value=6.7e-09  Score=75.01  Aligned_cols=83  Identities=14%  Similarity=0.105  Sum_probs=70.9

Q ss_pred             CCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--
Q psy5461          98 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--  173 (221)
Q Consensus        98 ~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--  173 (221)
                      ++||++.|.+++..++.|+++.+||.+|+++.||++++...+...+|++|...    ..++++|.|||.+.  +.+++  
T Consensus         2 ~~p~r~~V~~vf~~~g~g~vv~G~v~~G~i~~gd~v~i~P~~~~~~V~sI~~~----~~~~~~a~aG~~v~i~l~~i~~~   77 (91)
T cd03693           2 DKPLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGVTGEVKSVEMH----HEPLEEALPGDNVGFNVKNVSKK   77 (91)
T ss_pred             CCCeEEEEEEEEEeCCceEEEEEEEecceeecCCEEEECCCCcEEEEEEEEEC----CcCcCEECCCCEEEEEECCCCHH
Confidence            46899999999988888999999999999999999999988888899999743    34688999999995  55654  


Q ss_pred             CCccCcEEecC
Q psy5461         174 RERGKDKRTRV  184 (221)
Q Consensus       174 ~~~~Gdtl~~~  184 (221)
                      +++.||.|+..
T Consensus        78 ~v~~G~vl~~~   88 (91)
T cd03693          78 DIKRGDVAGDS   88 (91)
T ss_pred             HcCCcCEEccC
Confidence            57999999864

EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.

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

Probab=98.98  E-value=9.8e-09  Score=98.08  Aligned_cols=148  Identities=11%  Similarity=0.027  Sum_probs=100.0

Q ss_pred             CceeeeeeeecccccCCc-c--hHHHHhhcc--ccccCceeEecCCCccccHH------------HHHHHHHhhCCCCCC
Q psy5461          25 DSLCARAFKVVHDKHRGA-V--TFFRIYSGA--FKKNHVPVLCGSSYKNIGVQ------------KLMDAIVDILPSPTE   87 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~~g~-l--~~~~l~~~~--~~~~~~Pv~~gSa~~~~Gi~------------~LLd~I~~~~PsP~~   87 (221)
                      .+++..++|++.-....+ +  ....+.+-.  ..-...|+++.||++|.|+.            .|+++|... |.|..
T Consensus       158 ~~iivvvNK~D~~~~~~~~~~~i~~~i~~~~~~~~~~~~~iipiSA~~g~ni~~~~~~~~wy~g~tL~~~l~~~-~~~~~  236 (632)
T PRK05506        158 RHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGLHDVTFIPISALKGDNVVTRSARMPWYEGPSLLEHLETV-EIASD  236 (632)
T ss_pred             CeEEEEEEecccccchhHHHHHHHHHHHHHHHHcCCCCccEEEEecccCCCccccccCCCcccHhHHHHHHhcC-CCCCC
Confidence            468889999753111111 1  111221111  11134679999999999987            588877654 44433


Q ss_pred             cccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEE
Q psy5461          88 RPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA  167 (221)
Q Consensus        88 ~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv  167 (221)
                              ..++||.+.|..++...+.++-..++|.+|+|++||+|.+...++..+|++|...    ..+++++.|||.+
T Consensus       237 --------~~~~p~r~~i~~v~~~~~~~~g~~G~v~~G~l~~gd~v~i~P~~~~~~VksI~~~----~~~~~~a~aG~~v  304 (632)
T PRK05506        237 --------RNLKDFRFPVQYVNRPNLDFRGFAGTVASGVVRPGDEVVVLPSGKTSRVKRIVTP----DGDLDEAFAGQAV  304 (632)
T ss_pred             --------cCCCCceeeEEEEEecCCCceEEEEEEecceeecCCEEEEcCCCceEEEEEEEEC----CceeCEEcCCCeE
Confidence                    3468998877766543222222569999999999999999988888899999743    2358999999999


Q ss_pred             EEc--CCCCCccCcEEecCC
Q psy5461         168 AVT--GLKRERGKDKRTRVI  185 (221)
Q Consensus       168 ~i~--gl~~~~~Gdtl~~~~  185 (221)
                      ++.  +-.+++.|++|++..
T Consensus       305 ~i~l~~~~~i~rG~vL~~~~  324 (632)
T PRK05506        305 TLTLADEIDISRGDMLARAD  324 (632)
T ss_pred             EEEecCccccCCccEEecCC
Confidence            764  334688999999863

>PRK14845 translation initiation factor IF-2; Provisional

Probab=98.96  E-value=6.5e-09  Score=103.18  Aligned_cols=127  Identities=17%  Similarity=0.214  Sum_probs=96.6

Q ss_pred             ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEE
Q psy5461          55 KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFY  134 (221)
Q Consensus        55 ~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~  134 (221)
                      +..+|++..||++|.||+.|+++|....+.-.+.   .+..+.++|+.+.|..+..+++.|.++.+.|++|+|++||.|.
T Consensus       645 ~~~v~iVpVSA~tGeGId~Ll~~l~~l~~~~l~~---~L~~~~~~~~~g~VlEv~~~kG~G~vvt~iv~~G~Lk~GD~iv  721 (1049)
T PRK14845        645 TRTVAIVPVSAKTGEGIPELLMMVAGLAQKYLEE---RLKLNVEGYAKGTILEVKEEKGLGTTIDAIIYDGTLRRGDTIV  721 (1049)
T ss_pred             CCCceEEEEEcCCCCCHHHHHHHHHHhhHHhhhh---hhccCCCCceEEEEEEEEEecCceeEEEEEEEcCEEecCCEEE
Confidence            3578999999999999999999987654421110   0112456899999999999999999999999999999999999


Q ss_pred             eccCCc--eeeeceeEee--------ecCCeeeeCccccCCEEEE--cCCCCCccCcEEecC
Q psy5461         135 NIHLDQ--SEQITRLLLA--------EADDYKEVNEIQCGNIAAV--TGLKRERGKDKRTRV  184 (221)
Q Consensus       135 ~~~~~~--~~~v~~i~~~--------~g~~~~~v~~a~aGdIv~i--~gl~~~~~Gdtl~~~  184 (221)
                      ....++  ..+|+.|...        .+.+..+++++.|+.-+-|  .|++.+..||.+...
T Consensus       722 ~g~~~~~i~~kVRaLl~p~pl~e~r~~~~~~~~~~~~~~a~~vki~a~gl~~~~aG~~~~v~  783 (1049)
T PRK14845        722 VGGPDDVIVTKVRALLKPKPLDEIRDPRDKFDPVDEVTAAAGVKIAAPGLEEVLAGSPIRIV  783 (1049)
T ss_pred             EccCCCcceEEEEEecCcccccccccccccccccccccCCCceEEecCCccccCCCCeEEEe
Confidence            987654  3566665421        1224567888888888866  488888999988543

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

Probab=98.90  E-value=2.8e-08  Score=93.97  Aligned_cols=125  Identities=17%  Similarity=0.218  Sum_probs=90.8

Q ss_pred             ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEE
Q psy5461          55 KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFY  134 (221)
Q Consensus        55 ~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~  134 (221)
                      +..+|++..||++|.|+++|++.|..+.-.-..   ..+..+.++|+.+.|..+..+++.|.++.++|++|+|++||.|.
T Consensus       188 ~~~v~iVpVSA~tGeGideLl~~l~~l~~~~l~---~~l~~~~~~~~~~~V~e~~~~~G~G~v~t~~v~~G~l~~GD~iv  264 (590)
T TIGR00491       188 TKTVAIIPISAITGEGIPELLTMLAGLAQQYLE---EQLKLEEEGPARGTILEVKEETGLGMTIDAVIYDGILRKGDTIA  264 (590)
T ss_pred             CCCceEEEeecCCCCChhHHHHHHHHHHHHHhh---hhhccCCCCCeEEEEEEEEEcCCCceEEEEEEEcCEEeCCCEEE
Confidence            346899999999999999999998754211000   00112457899999999999999999999999999999999999


Q ss_pred             eccCCc--eeeeceeEeeec--------CCeeeeCcccc--CCEEEEcCCCCCccCcEEe
Q psy5461         135 NIHLDQ--SEQITRLLLAEA--------DDYKEVNEIQC--GNIAAVTGLKRERGKDKRT  182 (221)
Q Consensus       135 ~~~~~~--~~~v~~i~~~~g--------~~~~~v~~a~a--GdIv~i~gl~~~~~Gdtl~  182 (221)
                      ....+.  ..+|+.|.-..+        .+...+.++.|  |--+.+.|++....|+.+.
T Consensus       265 ~~~~~~~i~~kVr~l~~~~~l~e~r~~~~~~~~~~~~~~~~~~~v~~~~l~~~~aG~~~~  324 (590)
T TIGR00491       265 MAGSDDVIVTRVRALLKPRPLEEMRESRKKFQKVDEVVAAAGVKIAAPGLDDVMAGSPIR  324 (590)
T ss_pred             EccCCCcccEEEEEecCCCccccccccccccCCcceecCCCceeEEecCCCCCCCCCEEE
Confidence            987653  346776654321        12345566444  4445667888888888874

This model describes archaeal and eukaryotic orthologs of bacterial IF-2. Like IF-2, it helps convey the initiator tRNA to the ribosome, although the initiator is N-formyl-Met in bacteria and Met here. This protein is not closely related to the subunits of eIF-2 of eukaryotes, which is also involved in the initiation of translation. The aIF-2 of Methanococcus jannaschii contains a large intein interrupting a region of very strongly conserved sequence very near the amino end; this model does not correctly align the sequences from Methanococcus jannaschii and Pyrococcus horikoshii in this region.

>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3)

Probab=98.84  E-value=4.4e-08  Score=69.31  Aligned_cols=78  Identities=18%  Similarity=0.170  Sum_probs=63.3

Q ss_pred             CcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC--CC
Q psy5461         100 SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK--RE  175 (221)
Q Consensus       100 ~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~--~~  175 (221)
                      ||.+.|..++...  |++..+||.+|++++||+++....+...+|++|...    ..++++|.|||.+++  .+++  ++
T Consensus         1 plr~~I~~v~~~~--g~vv~G~v~~G~i~~G~~v~i~P~~~~~~V~si~~~----~~~~~~a~aGd~v~l~l~~i~~~~v   74 (82)
T cd04089           1 PLRLPIIDKYKDM--GTVVLGKVESGTIKKGDKLLVMPNKTQVEVLSIYNE----DVEVRYARPGENVRLRLKGIEEEDI   74 (82)
T ss_pred             CeEEEEEeEEEcC--CEEEEEEEeeeEEecCCEEEEeCCCcEEEEEEEEEC----CEECCEECCCCEEEEEecCCCHHHC
Confidence            5677777776543  899999999999999999999998888889998743    357899999999964  4554  57


Q ss_pred             ccCcEEec
Q psy5461         176 RGKDKRTR  183 (221)
Q Consensus       176 ~~Gdtl~~  183 (221)
                      +.||.+++
T Consensus        75 ~~G~vl~~   82 (82)
T cd04089          75 SPGFVLCS   82 (82)
T ss_pred             CCCCEEeC
Confidence            89998874

In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li

>KOG0467|consensus

Probab=98.75  E-value=1.7e-08  Score=95.51  Aligned_cols=122  Identities=17%  Similarity=0.221  Sum_probs=96.3

Q ss_pred             CCCCCCcEEEEEEEeec-----CCCceEEEEEEEceEEcCCCEEEeccCC-------ceeeeceeEeeecCCeeeeCccc
Q psy5461          95 QHFGDSLCARAFKVVHD-----KHRGAVTFFRIYSGAFKKGQKFYNIHLD-------QSEQITRLLLAEADDYKEVNEIQ  162 (221)
Q Consensus        95 ~~~~~~~~~~Vfk~~~d-----~~~G~i~~~RV~sG~L~~gd~v~~~~~~-------~~~~v~~i~~~~g~~~~~v~~a~  162 (221)
                      |++.+|...+|.|....     +...-++++|||||+++.|+.+++.+.+       .+.+|.++|+++|.+..+.+++.
T Consensus       354 ~~~~~pviv~Vskm~~~~~k~lp~~~l~~~ari~sgTlr~g~~v~v~~pd~~~~e~i~~~~ie~lyl~mgqelv~~d~v~  433 (887)
T KOG0467|consen  354 CSKESPVLVFVSKMLATPLKYLPQSRLLAFARIFSGTLRVGQVVYVLGPDPLSPEHITECTVESLYLFMGQELVPLDEVP  433 (887)
T ss_pred             CCCCCcEEEEEEeeeccchhhCchhhheeeeeeccCceeeccEeeecCCCCCCcceeeeeeehhhHHhhcccceeeeccC
Confidence            56678999999998763     2323589999999999999999999863       24689999999999999999999


Q ss_pred             cCCEEEEcCCCCCccCcEEecCCCC-----------CCCce--------ehHHHHHHHHHHhhcCCceEEEcc
Q psy5461         163 CGNIAAVTGLKRERGKDKRTRVIPK-----------PTSVV--------QCSARWTLNLEVGASSPIISKSKR  216 (221)
Q Consensus       163 aGdIv~i~gl~~~~~Gdtl~~~~~~-----------p~~~v--------~~~~l~~~L~~L~~~Dp~l~~~~~  216 (221)
                      +|++++|.|-+......|+|+..+.           |.-+|        ++++|-++|+.|+.-||++++..+
T Consensus       434 ~gnv~~I~g~~~vlks~TL~s~~~~~p~~~~~f~~tp~vrvaiep~~p~em~~L~~glkll~~adp~v~i~v~  506 (887)
T KOG0467|consen  434 SGNVVAIGGAGIVLKSATLCSKVPCGPNLVVNFQITPIVRVAIEPDDPDEMDKLVEGLKLLNQADPFVKIRVE  506 (887)
T ss_pred             CCcEEEecccceEeccceecccCCCcceeeeeeeeeeEEEEEeecCChHHhHHHHHHHHhhcccchhhHHHHh
Confidence            9999999983334455588876221           22111        789999999999999999876543

>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu

Probab=98.73  E-value=1.7e-07  Score=66.19  Aligned_cols=79  Identities=11%  Similarity=0.033  Sum_probs=62.7

Q ss_pred             cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccC
Q psy5461         101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGK  178 (221)
Q Consensus       101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~G  178 (221)
                      |++-|.+++.....|+.+.+||.+|++++||+++....+...+|.+|...    ..+++.+.|||.+++  .+-+++++|
T Consensus         1 lr~~V~dv~k~~~~~~~v~Gkv~~G~v~~Gd~v~~~P~~~~~~V~si~~~----~~~~~~a~aGd~v~l~l~~~~~i~~G   76 (81)
T cd03695           1 FRFPVQYVIRPNADFRGYAGTIASGSIRVGDEVVVLPSGKTSRVKSIETF----DGELDEAGAGESVTLTLEDEIDVSRG   76 (81)
T ss_pred             CEeeEEEEEeeCCCcEEEEEEEccceEECCCEEEEcCCCCeEEEEEEEEC----CcEeCEEcCCCEEEEEECCccccCCC
Confidence            34556666655556778999999999999999999998888899998743    357889999999954  455578999


Q ss_pred             cEEec
Q psy5461         179 DKRTR  183 (221)
Q Consensus       179 dtl~~  183 (221)
                      |.|+.
T Consensus        77 ~vl~~   81 (81)
T cd03695          77 DVIVA   81 (81)
T ss_pred             CEEeC
Confidence            99873

Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho

>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu

Probab=98.69  E-value=1.5e-07  Score=66.66  Aligned_cols=79  Identities=23%  Similarity=0.280  Sum_probs=63.4

Q ss_pred             cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--CCc
Q psy5461         101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--RER  176 (221)
Q Consensus       101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--~~~  176 (221)
                      |.+.|.+++..++.|.+..+||.+|++++|+++.+...+...+|++|...    ..+++++.|||-+.  +.+++  +++
T Consensus         1 lr~~i~~~~~~~~~g~vv~G~v~sG~i~~g~~v~~~p~~~~~~V~sI~~~----~~~~~~a~aGd~v~i~l~~~~~~~i~   76 (83)
T cd03696           1 FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILPLGEETRVRSIQVH----GKDVEEAKAGDRVALNLTGVDAKDLE   76 (83)
T ss_pred             CEEEEEEEEEcCCcEEEEEEEEeecEEeCCCEEEECCCCceEEEEEEEEC----CcCcCEEcCCCEEEEEEcCCCHHHcC
Confidence            35566677666788999999999999999999999988777888888632    35688999999995  45553  678


Q ss_pred             cCcEEec
Q psy5461         177 GKDKRTR  183 (221)
Q Consensus       177 ~Gdtl~~  183 (221)
                      .||.+++
T Consensus        77 ~G~vl~~   83 (83)
T cd03696          77 RGDVLSS   83 (83)
T ss_pred             CccEEcC
Confidence            9998864

SelB may function by replacing EF-Tu. 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' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.

>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase

Probab=98.68  E-value=3.1e-07  Score=65.75  Aligned_cols=78  Identities=10%  Similarity=0.017  Sum_probs=61.0

Q ss_pred             EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC--C--ceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--
Q psy5461         102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL--D--QSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--  173 (221)
Q Consensus       102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~--~--~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--  173 (221)
                      .+.|-.++..+..|++..+|+.+|++++||++++...  +  ...+|.+|...    ..++++|.|||.+.  +.+++  
T Consensus         2 ~~~I~~vf~v~g~GtVv~G~v~~G~v~~g~~v~~~P~~~g~~~~~~V~sI~~~----~~~~~~a~aGd~v~l~l~~i~~~   77 (87)
T cd03694           2 EFQIDEIYSVPGVGTVVGGTVSKGVIRLGDTLLLGPDQDGSFRPVTVKSIHRN----RSPVRVVRAGQSASLALKKIDRS   77 (87)
T ss_pred             EEEEEeEEEcCCcceEEEEEEecCEEeCCCEEEECCCCCCCEeEEEEEEEEEC----CeECCEECCCCEEEEEEcCCCHH
Confidence            3455555556788999999999999999999999876  3  46788888632    45788999999995  45654  


Q ss_pred             CCccCcEEec
Q psy5461         174 RERGKDKRTR  183 (221)
Q Consensus       174 ~~~~Gdtl~~  183 (221)
                      +++.|+.+++
T Consensus        78 ~i~~G~vl~~   87 (87)
T cd03694          78 LLRKGMVLVS   87 (87)
T ss_pred             HcCCccEEeC
Confidence            6788998874

This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.

>cd04168 TetM_like Tet(M)-like subfamily

Probab=98.63  E-value=1.4e-08  Score=85.77  Aligned_cols=62  Identities=21%  Similarity=0.333  Sum_probs=51.8

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.|+++...+|.  .+....+-.+.++++++.++.++|||||||.++.|+++|||+|++++|+|
T Consensus       176 e~dd~l~e~yl~--~~~~~~~el~~~l~~~~~~~~~~Pv~~gsa~~~~Gv~~ll~~~~~~~p~~  237 (237)
T cd04168         176 EGDDELLEKYLE--GGPIEELELDNELSARIAKRKVFPVYHGSALKGIGIEELLEGITKLFPTS  237 (237)
T ss_pred             cCCHHHHHHHhC--CCCCCHHHHHHHHHHHHHhCCeEEEEEccccCCcCHHHHHHHHHHhcCCC
Confidence            467788888876  22333445578888889999999999999999999999999999999998

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.

>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II

Probab=98.61  E-value=3.1e-07  Score=65.68  Aligned_cols=78  Identities=19%  Similarity=0.201  Sum_probs=60.8

Q ss_pred             EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC--CceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--CC
Q psy5461         102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL--DQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--RE  175 (221)
Q Consensus       102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~--~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--~~  175 (221)
                      ++.|..++.-++.|++..+||.+|+++.||++.+...  +.+.+|++|...    ..++++|.|||.++  +.+++  ++
T Consensus         2 r~~V~~v~~~~g~G~vv~G~v~~G~v~~gd~v~~~p~~~~~~~~V~si~~~----~~~~~~a~~G~~v~l~l~~~~~~~v   77 (87)
T cd03697           2 LMPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFGETLKTTVTGIEMF----RKTLDEAEAGDNVGVLLRGVKREDV   77 (87)
T ss_pred             EeeEEEEEeCCCcEEEEEEEECCCCCccCCEEEEeCCCCCceEEEEEEEEC----CcCCCEECCCCEEEEEECCCCHHHc
Confidence            4556666666788999999999999999999998764  445688888633    34788999999995  45653  57


Q ss_pred             ccCcEEec
Q psy5461         176 RGKDKRTR  183 (221)
Q Consensus       176 ~~Gdtl~~  183 (221)
                      ..|+.|++
T Consensus        78 ~rG~vl~~   85 (87)
T cd03697          78 ERGMVLAK   85 (87)
T ss_pred             CCccEEec
Confidence            89999875

Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher

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

Probab=98.53  E-value=3.8e-08  Score=84.77  Aligned_cols=62  Identities=42%  Similarity=0.683  Sum_probs=51.0

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.|+.+...+|.  .++...+.....+++++.++.++|||||||.++.||++|||+|+.++|+|
T Consensus       209 e~dd~L~e~yl~--~~~~~~~el~~~l~~~~~~~~~~PV~~gSa~~~~Gi~~lld~i~~~~p~p  270 (270)
T cd01886         209 EFDDELMEKYLE--GEEITEEEIKAAIRKGTIANKIVPVLCGSAFKNKGVQPLLDAVVDYLPSP  270 (270)
T ss_pred             cCCHHHHHHHhC--CCCCCHHHHHHHHHHHHHcCcEEEEEeCcCCCCcCHHHHHHHHHHhcCCC
Confidence            467778777776  22333445567777888889999999999999999999999999999998

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

>cd04169 RF3 RF3 subfamily

Probab=98.52  E-value=4.1e-08  Score=84.42  Aligned_cols=62  Identities=27%  Similarity=0.367  Sum_probs=50.5

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.++.++..++..  |....+-....+++++.++.++|||||||.+|.||++|||+|++++|+|
T Consensus       206 e~~~~l~e~~~e~--~~~~~~~~~~~~~~~~~~~~~~Pv~~gsa~~~~Gv~~Lld~i~~~~P~p  267 (267)
T cd04169         206 ELGGDLAEQLREE--LELLEGAGPEFDQEAFLAGELTPVFFGSALNNFGVQELLDALVDLAPAP  267 (267)
T ss_pred             hcCHHHHHHHhCC--CccchhhhHHHhHHHHHcCCEEEEEecccccCcCHHHHHHHHHHHCCCC
Confidence            4567777777773  3333333556778899999999999999999999999999999999998

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.

>cd03702 IF2_mtIF2_II This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2

Probab=98.49  E-value=1.4e-06  Score=63.38  Aligned_cols=78  Identities=22%  Similarity=0.233  Sum_probs=64.5

Q ss_pred             EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-ccCcE
Q psy5461         102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-RGKDK  180 (221)
Q Consensus       102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-~~Gdt  180 (221)
                      .+.|.....++..|.++.+-|.+|+|++||.+.....  ..||+.|+   .....++++|.||+.+.|.|++++ ..||.
T Consensus         2 ~g~VlE~~~~~g~G~vatviV~~GtL~~Gd~iv~G~~--~gkVr~l~---d~~g~~v~~a~Ps~~V~I~G~~~~P~aGd~   76 (95)
T cd03702           2 EGVVIESKLDKGRGPVATVLVQNGTLKVGDVLVAGTT--YGKVRAMF---DENGKRVKEAGPSTPVEILGLKGVPQAGDK   76 (95)
T ss_pred             eEEEEEEEecCCCCccEEEEEEcCeEeCCCEEEEccc--ccEEEEEE---CCCCCCCCEECCCCcEEEcCCCCCCCCCCE
Confidence            5789999999999999999999999999999998632  23555554   455578999999999999999877 88988


Q ss_pred             EecC
Q psy5461         181 RTRV  184 (221)
Q Consensus       181 l~~~  184 (221)
                      +...
T Consensus        77 ~~~~   80 (95)
T cd03702          77 FLVV   80 (95)
T ss_pred             EEEe
Confidence            8643

IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.

>cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu

Probab=98.44  E-value=3.9e-06  Score=59.64  Aligned_cols=74  Identities=15%  Similarity=0.135  Sum_probs=58.1

Q ss_pred             EEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC---ceeeeceeEeeecCCeeeeCccccCCEEE--EcCCCCCccC
Q psy5461         104 RAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD---QSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLKRERGK  178 (221)
Q Consensus       104 ~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~---~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~~~~~G  178 (221)
                      .|-+++.....|.++.+||-+|++++|+.+.+.+.+   .+.++.+|...    ...++++.+|+-|.  +.++++++.|
T Consensus         4 ~V~~vf~~~~~g~vag~kV~~G~l~~g~~v~vlr~~~~~~~g~i~sl~~~----~~~v~~a~~G~ecgi~l~~~~d~~~G   79 (84)
T cd03692           4 EVRAVFKISKVGNIAGCYVTDGKIKRNAKVRVLRNGEVIYEGKISSLKRF----KDDVKEVKKGYECGITLENFNDIKVG   79 (84)
T ss_pred             EEEEEEECCCCcEEEEEEEEECEEeCCCEEEEEcCCCEEEEEEEEEEEEc----CcccCEECCCCEEEEEEeCcccCCCC
Confidence            344444334568999999999999999999999887   34577777643    45788999999995  4578899999


Q ss_pred             cEE
Q psy5461         179 DKR  181 (221)
Q Consensus       179 dtl  181 (221)
                      |+|
T Consensus        80 dvi   82 (84)
T cd03692          80 DII   82 (84)
T ss_pred             CEE
Confidence            987

The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.

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

Probab=98.42  E-value=3.1e-06  Score=73.85  Aligned_cols=149  Identities=16%  Similarity=0.211  Sum_probs=103.8

Q ss_pred             Cceeeeeeeec-ccccCCcchHHHHh---hccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCC
Q psy5461          25 DSLCARAFKVV-HDKHRGAVTFFRIY---SGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS  100 (221)
Q Consensus        25 ~~~~~~vfk~~-~d~~~g~l~~~~l~---~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~  100 (221)
                      +.++..=||++ ++++...-.|..+.   +|+.. +..||+..||.++.+|+.|+++|.+++|.|..        +.+.|
T Consensus       141 k~iiIvQNKIDlV~~E~AlE~y~qIk~FvkGt~A-e~aPIIPiSA~~~~NIDal~e~i~~~IptP~r--------d~~~~  211 (415)
T COG5257         141 KNIIIVQNKIDLVSRERALENYEQIKEFVKGTVA-ENAPIIPISAQHKANIDALIEAIEKYIPTPER--------DLDKP  211 (415)
T ss_pred             ceEEEEecccceecHHHHHHHHHHHHHHhccccc-CCCceeeehhhhccCHHHHHHHHHHhCCCCcc--------CCCCC
Confidence            45566668874 55555555555554   34443 46799999999999999999999999999976        78889


Q ss_pred             cEEEEEEEeec--------CCCceEEEEEEEceEEcCCCEEEeccC-----Cceee----eceeEeeecCCeeeeCcccc
Q psy5461         101 LCARAFKVVHD--------KHRGAVTFFRIYSGAFKKGQKFYNIHL-----DQSEQ----ITRLLLAEADDYKEVNEIQC  163 (221)
Q Consensus       101 ~~~~Vfk~~~d--------~~~G~i~~~RV~sG~L~~gd~v~~~~~-----~~~~~----v~~i~~~~g~~~~~v~~a~a  163 (221)
                      ..++|......        +-.|=+.=+-+.+|.++.||++.+...     +.+..    .++|..++. ....+++|.|
T Consensus       212 p~m~v~RSFDVNkPGt~~~~L~GGViGGsl~~G~l~vGDEIEIrPGi~v~k~~k~~~~pi~T~i~Sl~a-g~~~~~ea~P  290 (415)
T COG5257         212 PRMYVARSFDVNKPGTPPEELKGGVIGGSLVQGVLRVGDEIEIRPGIVVEKGGKTVWEPITTEIVSLQA-GGEDVEEARP  290 (415)
T ss_pred             ceEEEEeecccCCCCCCHHHccCceecceeeeeeEecCCeEEecCCeEeecCCceEEEEeeEEEEEEEe-CCeeeeeccC
Confidence            99999887653        234556677889999999999988642     11111    223333333 3457899999


Q ss_pred             CCEEEE-cCCC-CCccCcEEec
Q psy5461         164 GNIAAV-TGLK-RERGKDKRTR  183 (221)
Q Consensus       164 GdIv~i-~gl~-~~~~Gdtl~~  183 (221)
                      |-.+++ ++++ .+..+|.+..
T Consensus       291 GGLvgvGT~lDP~ltKaD~L~G  312 (415)
T COG5257         291 GGLVGVGTKLDPTLTKADALVG  312 (415)
T ss_pred             CceEEEecccCcchhhhhhhcc
Confidence            998876 4566 3466666543

>KOG0461|consensus

Probab=98.42  E-value=1.4e-06  Score=76.59  Aligned_cols=136  Identities=13%  Similarity=0.109  Sum_probs=106.9

Q ss_pred             CCCceeeeeeeecccccCC---cch--HHHHhhcccc---ccCceeEecCCCcc----ccHHHHHHHHHhhCCCCCCccc
Q psy5461          23 FGDSLCARAFKVVHDKHRG---AVT--FFRIYSGAFK---KNHVPVLCGSSYKN----IGVQKLMDAIVDILPSPTERPA   90 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g---~l~--~~~l~~~~~~---~~~~Pv~~gSa~~~----~Gi~~LLd~I~~~~PsP~~~~~   90 (221)
                      +-..++.-++|++.=++..   .+.  ..++++...+   ++..||+..||+.|    .+|.+|.++|.+.+--|..   
T Consensus       121 ~c~klvvvinkid~lpE~qr~ski~k~~kk~~KtLe~t~f~g~~PI~~vsa~~G~~~~~~i~eL~e~l~s~if~P~R---  197 (522)
T KOG0461|consen  121 LCKKLVVVINKIDVLPENQRASKIEKSAKKVRKTLESTGFDGNSPIVEVSAADGYFKEEMIQELKEALESRIFEPKR---  197 (522)
T ss_pred             hccceEEEEeccccccchhhhhHHHHHHHHHHHHHHhcCcCCCCceeEEecCCCccchhHHHHHHHHHHHhhcCCCc---
Confidence            3468899999986544422   222  3334433222   34689999999999    8999999999999988876   


Q ss_pred             ccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc
Q psy5461          91 LAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT  170 (221)
Q Consensus        91 ~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~  170 (221)
                           +..+||.+.|-.-..-++-|++.++.+.+|+++.|+.|....-+..-||+.+..++    .++.+|.+||..++.
T Consensus       198 -----d~~gpflm~vDHCF~IKGQGTV~TGTvl~G~~~ln~~iE~PAL~e~rkVKslqmf~----~~vtsa~~GdR~g~c  268 (522)
T KOG0461|consen  198 -----DEEGPFLMAVDHCFAIKGQGTVLTGTVLRGVLRLNTEIEFPALNEKRKVKSLQMFK----QRVTSAAAGDRAGFC  268 (522)
T ss_pred             -----CCCCCeEEEeeeeEEeccCceEEeeeEEEeEEecCcEEeecccchhhhhhhHHHHh----hhhhhhhcccceeee
Confidence                 78899999998888889999999999999999999999998777666788776443    468899999988653

>KOG0465|consensus

Probab=98.41  E-value=1.1e-07  Score=88.26  Aligned_cols=80  Identities=30%  Similarity=0.501  Sum_probs=68.9

Q ss_pred             ChhhhhcCCCCCCCCcccccc------------C-CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCc
Q psy5461           1 MDAIVDILPSPTERPALAMFQ------------H-FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYK   67 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~~------------~-~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~   67 (221)
                      ||+|++|+|||+|..+++...            . ++.||++..||+.++++ |+++|.|+|+|+++.+.+ ||+.-..+
T Consensus       300 LDAVvdYLPsP~Ev~n~a~~ke~~~~ekv~l~~~~d~~Pfv~LAFKle~g~f-GqLTyvRvYqG~L~kG~~-iyN~rtgK  377 (721)
T KOG0465|consen  300 LDAVVDYLPSPSEVENYALNKETNSKEKVTLSPSRDKDPFVALAFKLEEGRF-GQLTYVRVYQGTLSKGDT-IYNVRTGK  377 (721)
T ss_pred             HHHHHHhCCChhhhcccccccCCCCccceEeccCCCCCceeeeEEEeeecCc-cceEEEEEeeeeecCCcE-EEecCCCc
Confidence            799999999999999987651            1 22399999999999999 999999999999999988 99998888


Q ss_pred             cccHHHHHHHHHhhC
Q psy5461          68 NIGVQKLMDAIVDIL   82 (221)
Q Consensus        68 ~~Gi~~LLd~I~~~~   82 (221)
                      ..-+.+|+.+-.+..
T Consensus       378 Kvrv~RL~rmHa~~m  392 (721)
T KOG0465|consen  378 KVRVGRLVRMHANDM  392 (721)
T ss_pred             eeEhHHHhHhccccc
Confidence            888889887755443

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

Probab=98.36  E-value=1.8e-07  Score=80.20  Aligned_cols=62  Identities=34%  Similarity=0.517  Sum_probs=51.6

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.|+.+...+|.  ..+...+.....+++++.++..+|||+|||+++.|+++|||+|.+++|+|
T Consensus       207 ~~dd~l~e~yl~--~~~~~~~~l~~~l~~~~~~~~~~pv~~gSa~~~~G~~~ll~~~~~~~p~p  268 (268)
T cd04170         207 ETDDELMEKYLE--GGELTEEELHAGLRRALRAGLLVPVLCGSALTNIGVRELLDALVHLLPSP  268 (268)
T ss_pred             hCCHHHHHHHhC--CCCCCHHHHHHHHHHHHHhCCEEEEEEeeCCCCcCHHHHHHHHHHhCCCC
Confidence            467788888876  22333455566788899999999999999999999999999999999998

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

>KOG0459|consensus

Probab=98.36  E-value=2e-06  Score=76.80  Aligned_cols=122  Identities=14%  Similarity=0.117  Sum_probs=88.4

Q ss_pred             CceeEecCCCccccHHHHHHHHHhhCCCCCCcccc----cccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCE
Q psy5461          57 HVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL----AMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQK  132 (221)
Q Consensus        57 ~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~----~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~  132 (221)
                      +.-.+.+|+.+|.++.+..+.++-|---|.-...+    .++.+.++||++-|..=+.  ..|++.++++-||++++|++
T Consensus       260 d~~f~p~sg~tG~~~k~~~~s~cpwy~gp~fl~~ld~l~~~~R~~~GP~~~pI~~Kyk--dmGTvv~GKvEsGsi~kg~~  337 (501)
T KOG0459|consen  260 DKHFVPVSGLTGANVKDRTDSVCPWYKGPIFLEYLDELPHLERILNGPIRCPVANKYK--DMGTVVGGKVESGSIKKGQQ  337 (501)
T ss_pred             CceeeecccccccchhhcccccCCcccCCccceehhccCcccccCCCCEEeehhhhcc--ccceEEEEEecccceecCCe
Confidence            33456799999999887776333222111110000    0123678999998886553  46899999999999999999


Q ss_pred             EEeccCCceeeeceeEeeecCCeeeeCccccCCEE--EEcCCC--CCccCcEEecC
Q psy5461         133 FYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA--AVTGLK--RERGKDKRTRV  184 (221)
Q Consensus       133 v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv--~i~gl~--~~~~Gdtl~~~  184 (221)
                      +.+...+....|.+|+    .+-.+++++.|||.+  -+.|++  ++.+|-+||+.
T Consensus       338 lvvMPnk~~veV~~I~----~ddvE~~~~~pGenvk~rlkgieeedi~~GfiL~~~  389 (501)
T KOG0459|consen  338 LVVMPNKTNVEVLGIY----SDDVETDRVAPGENVKLRLKGIEEEDISPGFILCSP  389 (501)
T ss_pred             EEEccCCcceEEEEEe----cccceeeeccCCcceEEEecccchhhccCceEEecC
Confidence            9999887777888876    236789999999999  466875  68999888876

>cd03701 IF2_IF5B_II IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B

Probab=98.28  E-value=7.7e-06  Score=59.56  Aligned_cols=78  Identities=22%  Similarity=0.196  Sum_probs=63.5

Q ss_pred             EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-ccCcE
Q psy5461         102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-RGKDK  180 (221)
Q Consensus       102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-~~Gdt  180 (221)
                      .+.|.....++.+|.++.+-|.+|+|++||.+.....  ..+|..   +.......+.++.||+.+.+.|+++. ..||.
T Consensus         2 ~g~ViE~~~~~g~G~vatviV~~GtL~~Gd~iv~G~~--~GkVr~---~~d~~g~~v~~a~Ps~~v~i~g~~~~p~aGd~   76 (95)
T cd03701           2 EGTVIESKLDKGRGPVATVIVQNGTLKKGDVIVAGGT--YGKIRT---MVDENGKALLEAGPSTPVEILGLKDVPKAGDG   76 (95)
T ss_pred             eEEEEEEEecCCCCeeEEEEEEcCeEecCCEEEECCc--cceEEE---EECCCCCCccccCCCCCEEEeeecCCccCCCE
Confidence            4789999999999999999999999999999998642  235554   44555668999999999999998764 88988


Q ss_pred             EecC
Q psy5461         181 RTRV  184 (221)
Q Consensus       181 l~~~  184 (221)
                      +...
T Consensus        77 ~~~~   80 (95)
T cd03701          77 VLVV   80 (95)
T ss_pred             EEEe
Confidence            7543

IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.

>KOG0458|consensus

Probab=98.26  E-value=8.2e-06  Score=75.78  Aligned_cols=115  Identities=16%  Similarity=0.121  Sum_probs=92.1

Q ss_pred             CceeEecCCCccccHH---------------HHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEE
Q psy5461          57 HVPVLCGSSYKNIGVQ---------------KLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFR  121 (221)
Q Consensus        57 ~~Pv~~gSa~~~~Gi~---------------~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~R  121 (221)
                      .+-.+..|+++|.++.               .||+.|.. +-.|..        ..+.||++-|..++..+.-|..+++|
T Consensus       356 ~v~FIPiSGl~GeNL~k~~~~~~l~~WY~Gp~LL~~id~-~~~p~~--------~~~kPl~ltIsdi~~~~~~~~~i~gk  426 (603)
T KOG0458|consen  356 SVKFIPISGLSGENLIKIEQENELSQWYKGPTLLSQIDS-FKIPER--------PIDKPLRLTISDIYPLPSSGVSISGK  426 (603)
T ss_pred             CcceEecccccCCcccccccchhhhhhhcCChHHHHHhh-ccCCCC--------cccCCeEEEhhheeecCCCeeEEEEE
Confidence            3346668999997643               67888887 555654        34679999999999999989999999


Q ss_pred             EEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--CCccCcEEecC
Q psy5461         122 IYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--RERGKDKRTRV  184 (221)
Q Consensus       122 V~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--~~~~Gdtl~~~  184 (221)
                      |.+|.|.+||+|++........|.+|..  +  ..+...+.|||-|.  +.|++  .+..||+++..
T Consensus       427 iesG~iq~gqkl~i~~s~e~~~vk~l~~--~--~~~~~~a~AGD~Vsl~L~~i~~n~v~~g~i~~~~  489 (603)
T KOG0458|consen  427 IESGYIQPGQKLYIMTSREDATVKGLTS--N--DEPKTWAVAGDNVSLKLPGILPNLVQVGDIADSG  489 (603)
T ss_pred             EeccccccCCEEEEecCcceEEEEeeec--C--CCcceeEeeCCEEEEecCccChhhcccceeeecC
Confidence            9999999999999998877788888752  2  45677899999995  45654  67999999853

>COG2895 CysN GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]

Probab=97.97  E-value=6.5e-05  Score=66.42  Aligned_cols=144  Identities=13%  Similarity=0.097  Sum_probs=92.5

Q ss_pred             Cceeeeeeeec-ccccCCcchHHHHhhc------cccccCceeEecCCCccccHH------------HHHHHHHhhCCCC
Q psy5461          25 DSLCARAFKVV-HDKHRGAVTFFRIYSG------AFKKNHVPVLCGSSYKNIGVQ------------KLMDAIVDILPSP   85 (221)
Q Consensus        25 ~~~~~~vfk~~-~d~~~g~l~~~~l~~~------~~~~~~~Pv~~gSa~~~~Gi~------------~LLd~I~~~~PsP   85 (221)
                      .+++..|||.+ +|-.  +-.|++|+..      .+.....-.+..||+.|.+|.            .||+.+...-.. 
T Consensus       140 rhvvvAVNKmDLvdy~--e~~F~~I~~dy~~fa~~L~~~~~~~IPiSAl~GDNV~~~s~~mpWY~GptLLe~LE~v~i~-  216 (431)
T COG2895         140 RHVVVAVNKMDLVDYS--EEVFEAIVADYLAFAAQLGLKDVRFIPISALLGDNVVSKSENMPWYKGPTLLEILETVEIA-  216 (431)
T ss_pred             cEEEEEEeeecccccC--HHHHHHHHHHHHHHHHHcCCCcceEEechhccCCcccccccCCCcccCccHHHHHhhcccc-
Confidence            58999999974 3321  3334444332      222233346779999996543            344444321111 


Q ss_pred             CCcccccccCCCCCCcEEEEEEEee--cCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCcccc
Q psy5461          86 TERPALAMFQHFGDSLCARAFKVVH--DKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQC  163 (221)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~Vfk~~~--d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~a  163 (221)
                      ..        ...++|+.-|--+..  ..++|.  -++|-||++++||+|.+..+|+..+|.+|..+.|.    .++|.|
T Consensus       217 ~~--------~~~~~~RfPVQ~V~Rp~~dfRGy--aGtiasG~v~~Gd~vvvlPsG~~s~V~~Ivt~dg~----~~~A~a  282 (431)
T COG2895         217 DD--------RSAKAFRFPVQYVNRPNLDFRGY--AGTIASGSVKVGDEVVVLPSGKTSRVKRIVTFDGE----LAQASA  282 (431)
T ss_pred             cc--------ccccceeeceEEecCCCCccccc--ceeeeccceecCCeEEEccCCCeeeEEEEeccCCc----hhhccC
Confidence            11        234556555544433  234443  35778999999999999999999999999988664    688999


Q ss_pred             CCEEEEcCCC--CCccCcEEecCC
Q psy5461         164 GNIAAVTGLK--RERGKDKRTRVI  185 (221)
Q Consensus       164 GdIv~i~gl~--~~~~Gdtl~~~~  185 (221)
                      |+-+.+.=-+  +++.||.|+...
T Consensus       283 G~aVtl~L~deidisRGd~i~~~~  306 (431)
T COG2895         283 GEAVTLVLADEIDISRGDLIVAAD  306 (431)
T ss_pred             CceEEEEEcceeecccCcEEEccC
Confidence            9999765323  569999998763

>KOG0464|consensus

Probab=97.93  E-value=1.4e-06  Score=78.31  Aligned_cols=73  Identities=44%  Similarity=0.729  Sum_probs=64.4

Q ss_pred             ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHH
Q psy5461           1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLM   75 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LL   75 (221)
                      ||++.-|+|||.||+.... +=..+++++..||+.+|+.+|+++|.|+|+|.+++... ||+.+....+|+..|+
T Consensus       310 ldavtmylpspeernyefl-qwykddlcalafkvlhdkqrg~l~fmriysgsi~~~~a-i~nin~~~se~~~kl~  382 (753)
T KOG0464|consen  310 LDAVTMYLPSPEERNYEFL-QWYKDDLCALAFKVLHDKQRGPLSFMRIYSGSIHNNLA-IFNINGMCSEGILKLF  382 (753)
T ss_pred             hhhhhhccCChhhcchHHH-hhhhhhHHHHhhhhhcccccCceeEEEEecccccCcee-eeecccccccchHhhh
Confidence            6899999999999876443 45678999999999999999999999999999998665 9999999999988775

>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B

Probab=97.87  E-value=0.00021  Score=53.31  Aligned_cols=81  Identities=15%  Similarity=0.250  Sum_probs=62.9

Q ss_pred             EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCc--eeeeceeEeeecC-------CeeeeCccc--cCCEEEEc
Q psy5461         102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ--SEQITRLLLAEAD-------DYKEVNEIQ--CGNIAAVT  170 (221)
Q Consensus       102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~--~~~v~~i~~~~g~-------~~~~v~~a~--aGdIv~i~  170 (221)
                      .+.|..+..++++|.++.+-+++|+|++||.|...+...  ..||+.|....+.       ++.+++++.  +|--+...
T Consensus         2 ~gtVlEvk~~~G~G~t~dvIl~~GtL~~GD~Iv~g~~~Gpi~tkVRaLl~~~~~~E~r~~~~~~~vk~v~aa~gvkI~~~   81 (110)
T cd03703           2 QGTVLEVKEEEGLGTTIDVILYDGTLREGDTIVVCGLNGPIVTKVRALLKPQPLKELRVKSRFIHVKEVKAAAGVKILAP   81 (110)
T ss_pred             cEEEEEEEEcCCCceEEEEEEECCeEecCCEEEEccCCCCceEEEeEecCCCCchhhccccccceeeEEecCCCcEEEeC
Confidence            467888999999999999999999999999999976542  2367766655442       335777776  67777778


Q ss_pred             CCCCCccCcEEe
Q psy5461         171 GLKRERGKDKRT  182 (221)
Q Consensus       171 gl~~~~~Gdtl~  182 (221)
                      |++++..|+.|.
T Consensus        82 gL~~v~aG~~~~   93 (110)
T cd03703          82 DLEKAIAGSPLL   93 (110)
T ss_pred             CCccccCCCEEE
Confidence            899888898764

aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.

>KOG0463|consensus

Probab=97.77  E-value=9.5e-05  Score=65.98  Aligned_cols=117  Identities=15%  Similarity=0.127  Sum_probs=92.9

Q ss_pred             cCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEe
Q psy5461          56 NHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYN  135 (221)
Q Consensus        56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~  135 (221)
                      ...|||-.|..+|.++. ||.+..+.++.-..-       ..+.|.--+|-+++..++.|+++-+..++|+++-+|.+..
T Consensus       331 r~CPIFQvSNVtG~NL~-LLkmFLNlls~R~~~-------~E~~PAeFQIDD~Y~VpGVGTvvSGT~L~GtIrLND~LlL  402 (641)
T KOG0463|consen  331 RVCPIFQVSNVTGTNLP-LLKMFLNLLSLRRQL-------NENDPAEFQIDDIYWVPGVGTVVSGTLLSGTIRLNDILLL  402 (641)
T ss_pred             cccceEEeccccCCChH-HHHHHHhhcCccccc-------ccCCCcceeecceEecCCcceEeecceeeeeEEeccEEEe
Confidence            36799999999999975 889888888764331       3456777889999999999999999999999999999988


Q ss_pred             ccCC--c--eeeeceeEeeecCCeeeeCccccCCEE--EEcCCC--CCccCcEEecC
Q psy5461         136 IHLD--Q--SEQITRLLLAEADDYKEVNEIQCGNIA--AVTGLK--RERGKDKRTRV  184 (221)
Q Consensus       136 ~~~~--~--~~~v~~i~~~~g~~~~~v~~a~aGdIv--~i~gl~--~~~~Gdtl~~~  184 (221)
                      ....  .  ...|++|.    +++.++..+.+|+-.  ++.+++  .++.|.++.+.
T Consensus       403 GPd~~G~F~pI~iKSIH----RKRMpV~~VrcGQtASFALKKIkr~~vRKGMVmVsp  455 (641)
T KOG0463|consen  403 GPDSNGDFMPIPIKSIH----RKRMPVGIVRCGQTASFALKKIKRKDVRKGMVMVSP  455 (641)
T ss_pred             cCCCCCCeeeeehhhhh----hccccceEEeccchhhhHhhhcchhhhhcceEEecC
Confidence            6542  1  34566654    577889999999987  455665  67899888765

>TIGR00503 prfC peptide chain release factor 3

Probab=97.76  E-value=1.2e-05  Score=75.41  Aligned_cols=75  Identities=23%  Similarity=0.414  Sum_probs=56.8

Q ss_pred             ChhhhhcCCCCCCCCcccc-ccCCCCceeeeeeeecc--c-ccCCcchHHHHhhccccccCceeEecCCCccccHHHHHH
Q psy5461           1 MDAIVDILPSPTERPALAM-FQHFGDSLCARAFKVVH--D-KHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMD   76 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~-~~~~~~~~~~~vfk~~~--d-~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd   76 (221)
                      ||++++|+|+|.++..... ....+++++++|||+.+  | +|.|++++.|+++|+++.+.. +++....+..-+..+..
T Consensus       267 Ld~i~~~~PsP~~~~~~~~~~~~~~~~~~~~VFK~~~~mdp~~~griaf~RV~sG~l~~g~~-v~~~~~~k~~ri~~~~~  345 (527)
T TIGR00503       267 LDGLLQWAPKPEARQSDTRTVEPTEEKFSGFVFKIQANMDPKHRDRVAFMRVVSGKYEKGMK-LKHVRTGKDVVISDALT  345 (527)
T ss_pred             HHHHHHHCCCCccccCCceecCCCCCCeeEEEEEEEeccCcccCceEEEEEEeeeEEcCCCE-EEecCCCCcEEecchhh
Confidence            6899999999988753211 12356789999999987  8 599999999999999998765 77766655554554443

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.

>cd03688 eIF2_gamma_II eIF2_gamma_II: this subfamily represents the domain II of the gamma subunit of eukaryotic translation initiation factor 2 (eIF2-gamma) found in Eukaryota and Archaea

Probab=97.63  E-value=0.00064  Score=50.67  Aligned_cols=81  Identities=17%  Similarity=0.156  Sum_probs=55.5

Q ss_pred             CCCCcEEEEEEEeecC--------CCceEEEEEEEceEEcCCCEEEeccC------C------ceeeeceeEeeecCCee
Q psy5461          97 FGDSLCARAFKVVHDK--------HRGAVTFFRIYSGAFKKGQKFYNIHL------D------QSEQITRLLLAEADDYK  156 (221)
Q Consensus        97 ~~~~~~~~Vfk~~~d~--------~~G~i~~~RV~sG~L~~gd~v~~~~~------~------~~~~v~~i~~~~g~~~~  156 (221)
                      .+.|+.|+|..+..-.        .+|.++-+++.+|.|+.||+|.+..-      +      ...+|.+|+.    ...
T Consensus         2 ~~~pp~M~V~RsFdinkPG~~~~~l~GgVigGsi~~G~lkvgdeIEIrpg~~~~~~~~~~~~pi~T~I~sl~~----~~~   77 (113)
T cd03688           2 FTSPPRMIVIRSFDVNKPGTEVDDLKGGVAGGSLLQGVLKVGDEIEIRPGIVVKDEGKIKCRPIFTKIVSLKA----ENN   77 (113)
T ss_pred             CCCCceEEEEEEEecCCCCCccccceeeEEEEEEEEEEEeCCCEEEEeeceeeecCCCeeEEEEEEEEEEEEe----cCc
Confidence            3567777777766543        77889999999999999999976521      1      1235556552    345


Q ss_pred             eeCccccCCEEEE-cCCC-CCccCcEE
Q psy5461         157 EVNEIQCGNIAAV-TGLK-RERGKDKR  181 (221)
Q Consensus       157 ~v~~a~aGdIv~i-~gl~-~~~~Gdtl  181 (221)
                      .+++|.||+.+++ ++++ .+..+|.+
T Consensus        78 ~l~~a~pGgliGvgT~Ldpsltk~D~l  104 (113)
T cd03688          78 DLQEAVPGGLIGVGTKLDPTLTKADRL  104 (113)
T ss_pred             cccEEeCCCeEEEccccCcccccccee
Confidence            7899999999987 3454 33444544

eIF2 is a G protein that delivers the methionyl initiator tRNA to the small ribosomal subunit and releases it upon GTP hydrolysis after the recognition of the initiation codon. eIF2 is composed three subunits, alpha, beta and gamma. Subunit gamma shows strongest conservation, and it confers both tRNA binding and GTP/GDP binding.

>PRK00741 prfC peptide chain release factor 3; Provisional

Probab=97.54  E-value=3.5e-05  Score=72.29  Aligned_cols=65  Identities=28%  Similarity=0.428  Sum_probs=50.1

Q ss_pred             ChhhhhcCCCCCCCCcccc-ccCCCCceeeeeeeec---ccccCCcchHHHHhhccccccCceeEecCCC
Q psy5461           1 MDAIVDILPSPTERPALAM-FQHFGDSLCARAFKVV---HDKHRGAVTFFRIYSGAFKKNHVPVLCGSSY   66 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~-~~~~~~~~~~~vfk~~---~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~   66 (221)
                      ||++++|+|+|.++..... ....+++++++|||+.   .|+|.|++++.|+++|.++.+.. +++....
T Consensus       266 Ld~i~~~~P~P~~~~~~~~~~~~~~~~~~~~VFK~~~~m~~~~~grlafvRV~sG~l~~g~~-v~~~~~~  334 (526)
T PRK00741        266 LDAFVEWAPAPQPRQTDEREVEPTEEKFSGFVFKIQANMDPKHRDRIAFVRVCSGKFEKGMK-VRHVRTG  334 (526)
T ss_pred             HHHHHHHCCCCCcccccceeecCCCCceEEEEEEEEecCCCCcCceEEEEEEeccEECCCCE-EEeccCC
Confidence            6899999999988654211 1224567999999997   46799999999999999998665 6655443

>COG0480 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]

Probab=97.48  E-value=4.9e-05  Score=73.29  Aligned_cols=67  Identities=37%  Similarity=0.563  Sum_probs=55.0

Q ss_pred             ChhhhhcCCCCCCCCccccc------------cCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCcc
Q psy5461           1 MDAIVDILPSPTERPALAMF------------QHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKN   68 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~------------~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~   68 (221)
                      ||++++|+|+|.|.+.+...            .+.++|+++++||+..|++.|.+++.|+++|+++.+.. |+.+...+.
T Consensus       270 Ldav~~~lPsP~e~~~~~g~~~~~~~~~~~~~~~~e~p~~a~vfKi~~d~~~g~l~~~RvysGtl~~G~~-v~n~~~~~~  348 (697)
T COG0480         270 LDAVVDYLPSPLDVPPIKGDLDDEIEKAVLRKASDEGPLSALVFKIMTDPFVGKLTFVRVYSGTLKSGSE-VLNSTKGKK  348 (697)
T ss_pred             HHHHHHHCCChhhcccccccCCccccchhcccCCCCCceEEEEEEeEecCCCCeEEEEEEeccEEcCCCE-EEeCCCCcc
Confidence            68999999999998854332            13478999999999999999999999999999998774 666655533

>PRK00007 elongation factor G; Reviewed

Probab=97.37  E-value=6.1e-05  Score=72.95  Aligned_cols=61  Identities=41%  Similarity=0.674  Sum_probs=49.8

Q ss_pred             ChhhhhcCCCCCCCCcccc------------ccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEe
Q psy5461           1 MDAIVDILPSPTERPALAM------------FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLC   62 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~------------~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~   62 (221)
                      ||+|++++|+|.+++....            .-+++.+++++|||+..|++.|.+++.|+++|+++.+.. ++.
T Consensus       272 Ld~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~l~a~VfK~~~d~~~G~ia~~RV~sGtl~~g~~-v~~  344 (693)
T PRK00007        272 LDAVVDYLPSPLDVPAIKGILPDGEEEEVERKASDDEPFSALAFKIMTDPFVGKLTFFRVYSGVLESGSY-VLN  344 (693)
T ss_pred             HHHHHHHCCChhhcccccccCCCccccceeecCCCCCCeEEEEEEeeecCCCCcEEEEEEeeeEEcCCCE-EEe
Confidence            6899999999988654311            124678999999999999999999999999999988664 543

>PRK12739 elongation factor G; Reviewed

Probab=97.37  E-value=6.6e-05  Score=72.68  Aligned_cols=63  Identities=40%  Similarity=0.654  Sum_probs=50.7

Q ss_pred             ChhhhhcCCCCCCCCcccc-----------ccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecC
Q psy5461           1 MDAIVDILPSPTERPALAM-----------FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGS   64 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~-----------~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gS   64 (221)
                      ||+|++++|+|.+++....           ..+++.+++++|||+..|++.|.+++.|+++|+++.+.. ++...
T Consensus       270 Ld~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~pl~a~VfK~~~d~~~G~i~~~RV~sGtL~~g~~-v~~~~  343 (691)
T PRK12739        270 LDAVVDYLPSPLDVPAIKGINPDTEEEIERPASDDEPFAALAFKIMTDPFVGRLTFFRVYSGVLESGSY-VLNTT  343 (691)
T ss_pred             HHHHHHHCCChhhccccccccCCCCcceeeccCCCCCeEEEEEEeeeCCCCCeEEEEEEeeeEEcCCCE-EEeCC
Confidence            6899999999988654321           124678999999999999999999999999999987663 54433

>PF00009 GTP_EFTU: Elongation factor Tu GTP binding domain; InterPro: IPR000795 Elongation factors belong to a family of proteins that promote the GTP-dependent binding of aminoacyl tRNA to the A site of ribosomes during protein biosynthesis, and catalyse the translocation of the synthesised protein chain from the A to the P site

Probab=97.27  E-value=0.00031  Score=56.78  Aligned_cols=62  Identities=23%  Similarity=0.227  Sum_probs=40.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhc----c-ccc-cCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG----A-FKK-NHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~----~-~~~-~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+-|++..++|++.-...-+.....+++.    . .++ ..+||+++||++|+|++.|+++|.+++|+
T Consensus       121 ~~~p~ivvlNK~D~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~vi~~Sa~~g~gi~~Ll~~l~~~~P~  188 (188)
T PF00009_consen  121 LGIPIIVVLNKMDLIEKELEEIIEEIKEKLLKEYGENGEEIVPVIPISALTGDGIDELLEALVELLPS  188 (188)
T ss_dssp             TT-SEEEEEETCTSSHHHHHHHHHHHHHHHHHHTTSTTTSTEEEEEEBTTTTBTHHHHHHHHHHHS--
T ss_pred             cccceEEeeeeccchhhhHHHHHHHHHHHhccccccCccccceEEEEecCCCCCHHHHHHHHHHhCcC
Confidence            56789999999543211111222222211    1 222 37999999999999999999999999996

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 ....

>TIGR00484 EF-G translation elongation factor EF-G

Probab=97.23  E-value=0.00011  Score=71.07  Aligned_cols=61  Identities=43%  Similarity=0.630  Sum_probs=49.6

Q ss_pred             ChhhhhcCCCCCCCCcccc-----------ccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEe
Q psy5461           1 MDAIVDILPSPTERPALAM-----------FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLC   62 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~-----------~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~   62 (221)
                      ||+|++++|+|.+++....           ..+++.+++++|||+..|++.|.+++.|+++|+++.+.. ++.
T Consensus       271 Ld~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~l~a~VfK~~~d~~~G~i~~~RV~sGtL~~g~~-v~~  342 (689)
T TIGR00484       271 LDAVVDYLPSPTDVPAIKGIDPDTEKEIERKASDDEPFSALAFKVATDPFVGQLTFVRVYSGVLKSGSY-VKN  342 (689)
T ss_pred             HHHHHHHCCCchhcccccccCCCCCceeeecCCCCCceEEEEEEeeecCCCCeEEEEEEEEeEEcCCCE-EEe
Confidence            6899999999987654221           124578999999999999999999999999999987665 543

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.

>KOG1143|consensus

Probab=97.23  E-value=0.0018  Score=57.98  Aligned_cols=129  Identities=13%  Similarity=0.127  Sum_probs=90.3

Q ss_pred             ccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCE
Q psy5461          53 FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQK  132 (221)
Q Consensus        53 ~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~  132 (221)
                      ..+.++|||+.|...|.|++ ||..+.+.+|+-..+..+..  -...|.--+|-.++..++.|.++=+-+-+|.++.|+.
T Consensus       358 ~s~nivPif~vSsVsGegl~-ll~~fLn~Lsp~~~~~e~~~--L~q~~~eFqvdEiy~Vp~VG~VVGG~Ls~G~l~Eg~~  434 (591)
T KOG1143|consen  358 CSGNIVPIFAVSSVSGEGLR-LLRTFLNCLSPAGTAEERIQ--LVQLPAEFQVDEIYNVPHVGQVVGGMLSEGQLHEGAD  434 (591)
T ss_pred             ccCCceeEEEEeecCccchh-HHHHHHhhcCCcCChHHHHH--HhcCcceeeHhHeecCCcccccccceeeeceeccCce
Confidence            44578999999999999987 55556555554332211100  0123455578888899999999999999999999999


Q ss_pred             EEeccCC----ceeeeceeEeeecCCeeeeCccccCCEEEEcC--CC--CCccCcEEecCCCCC
Q psy5461         133 FYNIHLD----QSEQITRLLLAEADDYKEVNEIQCGNIAAVTG--LK--RERGKDKRTRVIPKP  188 (221)
Q Consensus       133 v~~~~~~----~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~g--l~--~~~~Gdtl~~~~~~p  188 (221)
                      +.+...+    .+.+|+.|.    +.+..+.-+.||+-..++=  .+  .++.|.++.+....|
T Consensus       435 ~~vGP~~DG~F~~itV~sI~----Rnr~acrvvraGqaAslsl~d~D~~~LR~GMVl~~~~~nP  494 (591)
T KOG1143|consen  435 VLVGPMKDGTFEKITVGSIR----RNRQACRVVRAGQAASLSLNDPDGVSLRRGMVLAEIDHNP  494 (591)
T ss_pred             eEeecCCCCceeEEEeeeee----ccccceeeecCccceeeeccCCCccchhcceEEeecCCCC
Confidence            9997653    245777775    3445677789999886652  12  468999987653333

>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A

Probab=97.13  E-value=0.0078  Score=42.40  Aligned_cols=72  Identities=21%  Similarity=0.235  Sum_probs=47.3

Q ss_pred             EEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccCcE
Q psy5461         103 ARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGKDK  180 (221)
Q Consensus       103 ~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~Gdt  180 (221)
                      ..|.....-..++ +..++|..|+|++|..+    .|.  +++.+..++. +.+++++|.+||-|++  .|.-+++-||+
T Consensus         7 i~Ilp~~vFr~~~-~IvG~V~~G~ik~G~~l----~G~--~iG~I~sIe~-~~k~v~~A~~G~eVai~Ieg~~~i~eGDi   78 (81)
T PF14578_consen    7 IRILPVCVFRQSD-AIVGEVLEGIIKPGYPL----DGR--KIGRIKSIED-NGKNVDEAKKGDEVAISIEGPTQIKEGDI   78 (81)
T ss_dssp             EEEEEEEEECTCC-EEEEEEEEEEEETT-EE----CSS--CEEEEEEEEE-TTEEESEEETT-EEEEEEET--TB-TT-E
T ss_pred             EEECCcCEEecCC-eEEEEEeeeEEeCCCcc----CCE--EEEEEEEeEE-CCcCccccCCCCEEEEEEeCCccCCCCCE
Confidence            3344444445666 77889999999999999    332  3666666654 4579999999999965  46558889998


Q ss_pred             Ee
Q psy5461         181 RT  182 (221)
Q Consensus       181 l~  182 (221)
                      |.
T Consensus        79 Ly   80 (81)
T PF14578_consen   79 LY   80 (81)
T ss_dssp             EE
T ss_pred             Ee
Confidence            74

>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H

Probab=97.02  E-value=0.00058  Score=47.39  Aligned_cols=26  Identities=4%  Similarity=0.028  Sum_probs=23.2

Q ss_pred             ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461         193 QCSARWTLNLEVGASSPIISKSKRRQ  218 (221)
Q Consensus       193 ~~~~l~~~L~~L~~~Dp~l~~~~~~~  218 (221)
                      |.++|++||++|+++||++++.+|.+
T Consensus        17 d~~kl~~aL~~l~~eDP~l~~~~d~e   42 (75)
T PF14492_consen   17 DEPKLSEALQKLSEEDPSLRVERDEE   42 (75)
T ss_dssp             HHHHHHHHHHHHHHH-TTSEEEEETT
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEcch
Confidence            78999999999999999999999864

...

>PRK13351 elongation factor G; Reviewed

Probab=96.99  E-value=0.00025  Score=68.63  Aligned_cols=63  Identities=37%  Similarity=0.547  Sum_probs=50.4

Q ss_pred             ChhhhhcCCCCCCCCcccc----------ccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecC
Q psy5461           1 MDAIVDILPSPTERPALAM----------FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGS   64 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~----------~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gS   64 (221)
                      ||++++++|+|.+++....          .-+++.+++++|||+..|++.|.+++.|+++|+++.+.. ++...
T Consensus       270 Ld~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~pl~a~VfK~~~d~~~G~i~~~RV~sGtl~~g~~-v~~~~  342 (687)
T PRK13351        270 LDAVVDYLPSPLEVPPPRGSKDNGKPVKVDPDPEKPLLALVFKVQYDPYAGKLTYLRVYSGTLRAGSQ-LYNGT  342 (687)
T ss_pred             HHHHHHHCCChhhcccccccCCCCCceeecCCCCCCeEEEEEEeeecCCCceEEEEEEeEEEEcCCCE-EEeCC
Confidence            6899999999987654321          114578999999999999999999999999999987665 54443

>PRK07560 elongation factor EF-2; Reviewed

Probab=96.97  E-value=0.00026  Score=69.05  Aligned_cols=63  Identities=25%  Similarity=0.388  Sum_probs=49.6

Q ss_pred             ChhhhhcCCCCCCCCcccc-----------------ccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEec
Q psy5461           1 MDAIVDILPSPTERPALAM-----------------FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCG   63 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~-----------------~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~g   63 (221)
                      ||+|++|+|||.+++....                 ..+++.|++++|||+..|++.|.+++.|+++|+++.+.. ++..
T Consensus       248 ld~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~p~~a~VfK~~~d~~~G~va~~RV~sGtL~~Gd~-v~~~  326 (731)
T PRK07560        248 LDMVVKHLPNPIEAQKYRIPKIWKGDLNSEVGKAMLNCDPNGPLVMMVTDIIVDPHAGEVATGRVFSGTLRKGQE-VYLV  326 (731)
T ss_pred             HHHHHHhCCChhhhhhhcccccccCCCCccccceeeccCCCCCEEEEEEeeEEcCCCCeEEEEEEEEeEEcCCCE-EEEc
Confidence            6899999999987543110                 014567999999999999999999999999999998765 5443


Q ss_pred             C
Q psy5461          64 S   64 (221)
Q Consensus        64 S   64 (221)
                      .
T Consensus       327 ~  327 (731)
T PRK07560        327 G  327 (731)
T ss_pred             C
Confidence            3

>PTZ00416 elongation factor 2; Provisional

Probab=96.90  E-value=0.00028  Score=69.72  Aligned_cols=58  Identities=28%  Similarity=0.393  Sum_probs=46.8

Q ss_pred             ChhhhhcCCCCCCCCcccc-----------------ccCCCCceeeeeeeecccccCCc-chHHHHhhccccccCc
Q psy5461           1 MDAIVDILPSPTERPALAM-----------------FQHFGDSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKNHV   58 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~-----------------~~~~~~~~~~~vfk~~~d~~~g~-l~~~~l~~~~~~~~~~   58 (221)
                      ||+|++|+|||.+++....                 .-++++|++++|||+..|++.|+ +++.|+++|+++.+..
T Consensus       329 ld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~plva~VfK~~~~~~~g~~~s~~RV~SGtL~~g~~  404 (836)
T PTZ00416        329 LEMIVDHLPSPKEAQKYRVENLYEGPMDDEAANAIRNCDPNGPLMMYISKMVPTSDKGRFYAFGRVFSGTVATGQK  404 (836)
T ss_pred             HHHHHHhCCChhHhCchhhhccccCCCCccccceeeccCCCCCeEEEEEeeeecCCCCcEEEEEEEEeeeecCCCE
Confidence            6899999999987543210                 01457799999999999999999 7999999999987654

>TIGR00490 aEF-2 translation elongation factor aEF-2

Probab=96.83  E-value=0.00031  Score=68.42  Aligned_cols=58  Identities=31%  Similarity=0.441  Sum_probs=47.0

Q ss_pred             ChhhhhcCCCCCCCCccc-----------------cccCCCCceeeeeeeecccccCCcchHHHHhhccccccCc
Q psy5461           1 MDAIVDILPSPTERPALA-----------------MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHV   58 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~-----------------~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~   58 (221)
                      ||+|++|+|||.+++...                 ...+++.+++++|||+..|++.|.+++.|+++|+++.+..
T Consensus       247 ld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~pl~a~VfK~~~~~~~G~ia~~RV~sGtL~~G~~  321 (720)
T TIGR00490       247 LDMVIRHLPSPIEAQKYRIPVIWKGDLNSEVGKAMLNCDPKGPLALMITKIVVDKHAGEVAVGRLYSGTIRPGME  321 (720)
T ss_pred             HHHHHHhCCChhhhhhhcccccccCCCCccchhhcccCCCCCCeEEEEEEEEecCCCcEEEEEEEEeCEEcCCCE
Confidence            689999999998753211                 0124578999999999999999999999999999887654

This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD.

>PLN00116 translation elongation factor EF-2 subunit; Provisional

Probab=96.73  E-value=0.00062  Score=67.43  Aligned_cols=58  Identities=21%  Similarity=0.318  Sum_probs=46.6

Q ss_pred             ChhhhhcCCCCCCCCcccc-----------------ccCCCCceeeeeeeecccccCCc-chHHHHhhccccccCc
Q psy5461           1 MDAIVDILPSPTERPALAM-----------------FQHFGDSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKNHV   58 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~-----------------~~~~~~~~~~~vfk~~~d~~~g~-l~~~~l~~~~~~~~~~   58 (221)
                      ||++++|+|||.+++....                 .-++++|++++|||+..+++.|+ +++.|+++|+++.+..
T Consensus       333 ld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~pl~a~VfK~~~~~~~g~~l~~~RVysGtL~~g~~  408 (843)
T PLN00116        333 LEMIIFHLPSPAKAQRYRVENLYEGPLDDKYATAIRNCDPNGPLMLYVSKMIPASDKGRFFAFGRVFSGTVATGMK  408 (843)
T ss_pred             HHHHHHhCCChHHhhhHHhhhccCCCCCccccchhhcCCCCCCeEEEEEeeeecCCCCeEEEEEEEEeeeecCCCE
Confidence            6899999999987543211                 11457899999999988888888 8999999999988665

>PRK12740 elongation factor G; Reviewed

Probab=96.56  E-value=0.00098  Score=64.33  Aligned_cols=64  Identities=34%  Similarity=0.603  Sum_probs=51.1

Q ss_pred             ChhhhhcCCCCCCCCccc---------cccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCC
Q psy5461           1 MDAIVDILPSPTERPALA---------MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSS   65 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~---------~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa   65 (221)
                      ||++++++|+|.+++.+.         ...+++++++++|||+.+|++.|.+++.|+++|+++.+.. ++....
T Consensus       254 Ld~i~~~lPsp~~~~~~~~~~~~~~~~~~~~~~~~l~a~v~k~~~~~~~G~i~~~RV~sG~L~~g~~-v~~~~~  326 (668)
T PRK12740        254 LDAVVDYLPSPLEVPPVDGEDGEEGAELAPDPDGPLVALVFKTMDDPFVGKLSLVRVYSGTLKKGDT-LYNSGT  326 (668)
T ss_pred             HHHHHHHCCChhhcccccCCCCccccccccCCCCCeEEEEEEeeecCCCCcEEEEEEeeeEEcCCCE-EEeCCC
Confidence            688999999998755321         1124578999999999999999999999999999998765 655543

>cd03690 Tet_II Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O)

Probab=95.89  E-value=0.0027  Score=44.99  Aligned_cols=33  Identities=24%  Similarity=0.587  Sum_probs=30.8

Q ss_pred             CceeeeeeeecccccCCcchHHHHhhccccccC
Q psy5461          25 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNH   57 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~   57 (221)
                      +||+++|||+..|++.|++++.|+++|+++...
T Consensus         2 ~p~~~~Vfkv~~d~~~G~la~~RV~sG~l~~g~   34 (85)
T cd03690           2 SELSGTVFKIERDDKGERLAYLRLYSGTLRLRD   34 (85)
T ss_pred             CCcEEEEEEeEECCCCCeEEEEEEccCEEcCCC
Confidence            689999999999999999999999999998765

This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.

>COG4108 PrfC Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]

Probab=95.80  E-value=0.0044  Score=56.45  Aligned_cols=70  Identities=31%  Similarity=0.489  Sum_probs=51.7

Q ss_pred             ChhhhhcCCCCCCCCcc-ccccCCCCceeeeeeeec---ccccCCcchHHHHhhccccccCceeEecCCCccccH
Q psy5461           1 MDAIVDILPSPTERPAL-AMFQHFGDSLCARAFKVV---HDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGV   71 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~-~~~~~~~~~~~~~vfk~~---~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi   71 (221)
                      ||.+++|.|+|..+..- ......+++|+++|||++   ..+|+-++++.|+++|.++++.. +-.....+...+
T Consensus       268 L~~~~~~AP~P~~~~a~~~~v~p~e~kfsGFVFKIQANMDp~HRDRIAFmRv~SGkferGMk-v~h~rtGK~~~l  341 (528)
T COG4108         268 LDALVDWAPSPRARQADTREVEPTEDKFSGFVFKIQANMDPKHRDRIAFMRVCSGKFERGMK-VTHVRTGKDVKL  341 (528)
T ss_pred             HHHHHhhCCCCCcccCCcCcccCCCCccceEEEEEEcCCCcccccceeEEEeccccccCCce-eeeeecCCceEe
Confidence            57899999999887653 233445778999999995   33799999999999999988644 444444444443

>TIGR00487 IF-2 translation initiation factor IF-2

Probab=95.55  E-value=0.061  Score=51.37  Aligned_cols=80  Identities=14%  Similarity=0.084  Sum_probs=59.7

Q ss_pred             EEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccCcE
Q psy5461         103 ARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGKDK  180 (221)
Q Consensus       103 ~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~Gdt  180 (221)
                      |.|-++......|.++=++|..|++++|..+++.+.++....+.|..++ +....++++..|+-|+|  .+..+++.||.
T Consensus       495 a~v~~vf~~~~~~~iaG~~V~~G~i~~~~~~~v~r~~~~i~~g~i~sl~-~~k~~v~ev~~g~ecgi~~~~~~~~~~gD~  573 (587)
T TIGR00487       495 AEVRQVFNVPKIGNIAGCYVTEGVIKRGNPLRVIRDGVVIFEGEIDSLK-RFKDDVKEVSNGYECGIGIKNYNDIKEGDI  573 (587)
T ss_pred             EEEEEEEecCCCCEEEEEEEecCEEecCCeEEEEeCCEEEEeccchHhh-ccCccccEECCCCEEEEEEeccccCCCCCE
Confidence            4455555555668999999999999999999999877543334444333 34467999999999965  56778999999


Q ss_pred             Eec
Q psy5461         181 RTR  183 (221)
Q Consensus       181 l~~  183 (221)
                      |-.
T Consensus       574 i~~  576 (587)
T TIGR00487       574 IEA  576 (587)
T ss_pred             EEE
Confidence            854

This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognized by the pfam model GTP_EFTU.

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

Probab=95.40  E-value=0.036  Score=43.30  Aligned_cols=57  Identities=12%  Similarity=0.060  Sum_probs=40.3

Q ss_pred             cCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHH
Q psy5461          21 QHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIV   79 (221)
Q Consensus        21 ~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~   79 (221)
                      +-|..|++.-|.|++.++...  ..++.++.....+.-.+|..|+.+|.||++|.+.|.
T Consensus        86 ~~f~~pvIGVITK~Dl~~~~~--~i~~a~~~L~~aG~~~if~vS~~~~eGi~eL~~~L~  142 (143)
T PF10662_consen   86 SMFNKPVIGVITKIDLPSDDA--NIERAKKWLKNAGVKEIFEVSAVTGEGIEELKDYLE  142 (143)
T ss_pred             cccCCCEEEEEECccCccchh--hHHHHHHHHHHcCCCCeEEEECCCCcCHHHHHHHHh
Confidence            347889999999987663212  233333444444455679999999999999999885

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

>KOG0466|consensus

Probab=95.34  E-value=0.038  Score=48.50  Aligned_cols=109  Identities=19%  Similarity=0.260  Sum_probs=78.4

Q ss_pred             HhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEee--------cCCCceEEE
Q psy5461          48 IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVH--------DKHRGAVTF  119 (221)
Q Consensus        48 l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~--------d~~~G~i~~  119 (221)
                      +.+++.. +.-||+..||--+.+|+.+.++|+..+|-|..        +...|..+.|.....        +.-.|-++=
T Consensus       207 Fi~~t~a-e~aPiiPisAQlkyNId~v~eyivkkIPvPvR--------df~s~prlIVIRSFDVNkPG~ev~~lkGgvag  277 (466)
T KOG0466|consen  207 FIQGTVA-EGAPIIPISAQLKYNIDVVCEYIVKKIPVPVR--------DFTSPPRLIVIRSFDVNKPGSEVDDLKGGVAG  277 (466)
T ss_pred             HHhcccc-CCCceeeehhhhccChHHHHHHHHhcCCCCcc--------ccCCCCcEEEEEeeccCCCCchhhcccCcccc
Confidence            3344433 35699999999999999999999999999976        677777777776654        334567888


Q ss_pred             EEEEceEEcCCCEEEeccC----C--cee-------eeceeEeeecCCeeeeCccccCCEEEE
Q psy5461         120 FRIYSGAFKKGQKFYNIHL----D--QSE-------QITRLLLAEADDYKEVNEIQCGNIAAV  169 (221)
Q Consensus       120 ~RV~sG~L~~gd~v~~~~~----~--~~~-------~v~~i~~~~g~~~~~v~~a~aGdIv~i  169 (221)
                      +-+..|.|+.||.+.+...    +  ...       ++..+|    .++.+...|.||-.+.+
T Consensus       278 gsil~Gvlkvg~~IEiRPGiv~kd~~g~~~C~Pi~SrI~sL~----AE~n~L~~AvPGGLIGV  336 (466)
T KOG0466|consen  278 GSILKGVLKVGQEIEIRPGIVTKDENGNIKCRPIFSRIVSLF----AEQNDLQFAVPGGLIGV  336 (466)
T ss_pred             chhhhhhhhcCcEEEecCceeeecCCCcEEEeeHHHHHHHHH----hhhccceeecCCceeee
Confidence            8999999999999988532    1  011       333333    34556777888876655

>cd01889 SelB_euk SelB subfamily

Probab=95.32  E-value=0.015  Score=46.83  Aligned_cols=63  Identities=11%  Similarity=0.073  Sum_probs=42.1

Q ss_pred             CCceeeeeeeeccc-ccCCcchHHHHhhcc---c---cccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461          24 GDSLCARAFKVVHD-KHRGAVTFFRIYSGA---F---KKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT   86 (221)
Q Consensus        24 ~~~~~~~vfk~~~d-~~~g~l~~~~l~~~~---~---~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~   86 (221)
                      ..+++..++|++.- ...-+.....+.+..   .   .....|++..||++|.|+++|++.|.+.+|.|.
T Consensus       120 ~~~~iiv~NK~Dl~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~vi~iSa~~g~gi~~L~~~l~~~~~~~~  189 (192)
T cd01889         120 CKKLIVVLNKIDLIPEEERERKIEKMKKKLQKTLEKTRFKNSPIIPVSAKPGGGEAELGKDLNNLIVLPL  189 (192)
T ss_pred             CCCEEEEEECcccCCHHHHHHHHHHHHHHHHHHHHhcCcCCCCEEEEeccCCCCHHHHHHHHHhcccccc
Confidence            45888999996532 111111222222211   1   123578999999999999999999999999985

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

>CHL00189 infB translation initiation factor 2; Provisional

Probab=95.30  E-value=0.12  Score=50.71  Aligned_cols=77  Identities=17%  Similarity=0.079  Sum_probs=56.8

Q ss_pred             EEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccCcEEe
Q psy5461         105 AFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGKDKRT  182 (221)
Q Consensus       105 Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~Gdtl~  182 (221)
                      |-++..-.. |.+|=|+|.+|+++++..+++.+.++..--+.|..++ +....++++..|.-|+|  .+..+++.||+|-
T Consensus       654 v~~vF~~~k-~~iaGc~V~~G~i~~~~~~rv~R~~~~i~~G~i~slk-~~k~~v~ev~~g~ecgi~i~~~~d~~~gD~ie  731 (742)
T CHL00189        654 VKTVFPLAK-RFVAGCRVTEGKITKNALIKVIRENKLIYEGKITSLK-RVKEDVEEAQEGNECGIFIEEFQLWQSGDKIH  731 (742)
T ss_pred             eeEEEecCC-CEEEEEEEecCEEecCCeEEEEeCCeEEEEeEEhhHh-hcCccccEeCCCCEEEEEeeCCCCCCcCCEEE
Confidence            334433344 8999999999999999999999877543333443333 33467999999999965  4677899999984


Q ss_pred             c
Q psy5461         183 R  183 (221)
Q Consensus       183 ~  183 (221)
                      .
T Consensus       732 ~  732 (742)
T CHL00189        732 A  732 (742)
T ss_pred             E
Confidence            3

>PRK05306 infB translation initiation factor IF-2; Validated

Probab=95.19  E-value=0.12  Score=51.05  Aligned_cols=81  Identities=14%  Similarity=0.077  Sum_probs=60.3

Q ss_pred             EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccCc
Q psy5461         102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGKD  179 (221)
Q Consensus       102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~Gd  179 (221)
                      .|.|-++......|.++=|+|..|+++++..+++.+.++..--++|..++ +....+.++..|+-|+|  .+..+++.||
T Consensus       696 ~a~v~~vF~~~k~~~iaGc~V~~G~i~~~~~~rv~R~~~~i~~g~i~slk-~~k~~v~ev~~g~ecgi~~~~~~d~~~gD  774 (787)
T PRK05306        696 QAEVREVFKVSKVGTIAGCMVTEGKIKRNAKVRVLRDGVVIYEGELESLK-RFKDDVKEVRAGYECGIGLENYNDIKEGD  774 (787)
T ss_pred             eEEEEEEEecCCCCeEEEEEEeeCEEecCCeEEEEeCCEEEEEeEEehhc-ccCcCccEeCCCCEEEEEeeccccCCCCC
Confidence            34455555556679999999999999999999999877533333343333 34567999999999965  5777899999


Q ss_pred             EEec
Q psy5461         180 KRTR  183 (221)
Q Consensus       180 tl~~  183 (221)
                      +|-.
T Consensus       775 ~ie~  778 (787)
T PRK05306        775 IIEA  778 (787)
T ss_pred             EEEE
Confidence            9843

>cd00881 GTP_translation_factor GTP translation factor family

Probab=95.12  E-value=0.045  Score=43.05  Aligned_cols=63  Identities=27%  Similarity=0.286  Sum_probs=42.4

Q ss_pred             CCCceeeeeeeecccc-cCCcchHHHHhhccc-------------cccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          23 FGDSLCARAFKVVHDK-HRGAVTFFRIYSGAF-------------KKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~-------------~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      .+.+++..++|++.-. ..-+.....+.+...             .....|++..||++|.|++++++.|..++|.|
T Consensus       113 ~~~~i~iv~nK~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~Sa~~g~gi~~l~~~l~~~l~~~  189 (189)
T cd00881         113 GGLPIIVAINKIDRVGEEDLEEVLREIKELLGLIGFISTKEEGTRNGLLVPIVPGSALTGIGVEELLEAIVEHLPPP  189 (189)
T ss_pred             CCCCeEEEEECCCCcchhcHHHHHHHHHHHHccccccchhhhhcccCCcceEEEEecccCcCHHHHHHHHHhhCCCC
Confidence            4678899999954221 111111222222221             23478999999999999999999999999865

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.

>cd04091 mtEFG1_II_like mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes

Probab=95.10  E-value=0.0053  Score=42.94  Aligned_cols=35  Identities=31%  Similarity=0.604  Sum_probs=30.1

Q ss_pred             eeeeeeeecccccCCcchHHHHhhccccccCceeEec
Q psy5461          27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCG   63 (221)
Q Consensus        27 ~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~g   63 (221)
                      |+++|||+.+|++ |.+++.|+++|+++..+. +...
T Consensus         1 ~~a~vfK~~~~~~-G~i~~~Rv~sG~lk~gd~-v~~~   35 (81)
T cd04091           1 FVGLAFKLEEGRF-GQLTYMRIYQGKLKKGDT-IYNV   35 (81)
T ss_pred             CeEEEEEeecCCC-CCEEEEEEecCEEcCCCE-EEEc
Confidence            5799999999998 999999999999998664 5543

Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals

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

Probab=95.08  E-value=0.028  Score=46.01  Aligned_cols=62  Identities=16%  Similarity=0.192  Sum_probs=40.5

Q ss_pred             Cceeeeeeeecccc-cCCcchHHHHhhcccc--ccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461          25 DSLCARAFKVVHDK-HRGAVTFFRIYSGAFK--KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT   86 (221)
Q Consensus        25 ~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~~--~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~   86 (221)
                      .+++..++|++... ..-......+.+....  ....|++..||++|.||++|++.|.+.+|.|.
T Consensus       138 ~~iiivvNK~Dl~~~~~~~~~~~~i~~~~~~~~~~~~~i~~vSA~~g~gi~~L~~~l~~~l~~~~  202 (203)
T cd01888         138 KHIIIVQNKIDLVKEEQALENYEQIKKFVKGTIAENAPIIPISAQLKYNIDVLLEYIVKKIPTPP  202 (203)
T ss_pred             CcEEEEEEchhccCHHHHHHHHHHHHHHHhccccCCCcEEEEeCCCCCCHHHHHHHHHHhCCCCC
Confidence            36788999954321 1011112333322211  13568999999999999999999999999874

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

>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes

Probab=94.84  E-value=0.0069  Score=42.49  Aligned_cols=32  Identities=59%  Similarity=1.068  Sum_probs=29.0

Q ss_pred             eeeeeeeecccccCCcchHHHHhhccccccCc
Q psy5461          27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHV   58 (221)
Q Consensus        27 ~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~   58 (221)
                      |+++|||+..|++.|.+++.|+++|+++....
T Consensus         1 ~~a~VfK~~~d~~~g~i~~~Ri~sGtl~~g~~   32 (83)
T cd04092           1 LCALAFKVVHDPQRGPLTFVRVYSGTLKRGSA   32 (83)
T ss_pred             CEEEEEecccCCCCCeEEEEEEecCEECCCCE
Confidence            57999999999999999999999999998654

Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n

>cd01890 LepA LepA subfamily

Probab=94.61  E-value=0.066  Score=42.04  Aligned_cols=61  Identities=18%  Similarity=0.171  Sum_probs=39.2

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +-+++..++|.+............+.+.. .....+++..||++|.||++|++.|...+|.|
T Consensus       119 ~~~iiiv~NK~Dl~~~~~~~~~~~~~~~~-~~~~~~~~~~Sa~~g~gi~~l~~~l~~~~~~~  179 (179)
T cd01890         119 NLEIIPVINKIDLPSADPERVKQQIEDVL-GLDPSEAILVSAKTGLGVEDLLEAIVERIPPP  179 (179)
T ss_pred             CCCEEEEEECCCCCcCCHHHHHHHHHHHh-CCCcccEEEeeccCCCCHHHHHHHHHhhCCCC
Confidence            45788888896542211111112222211 11123488999999999999999999999887

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.

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

Probab=94.38  E-value=0.32  Score=45.40  Aligned_cols=81  Identities=14%  Similarity=0.076  Sum_probs=62.2

Q ss_pred             EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccCc
Q psy5461         102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGKD  179 (221)
Q Consensus       102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~Gd  179 (221)
                      .+.+-++...+..|.++=++|..|+++.|..++..+.+....-++|..++ +....++++.+|.-|+|  .+-.+++.||
T Consensus       415 ~~~~r~v~~~~k~g~IaG~~V~~G~ikr~~~v~~~rd~~vi~~G~i~sLk-~~kddv~ev~~G~ecgI~i~~~~di~~gD  493 (509)
T COG0532         415 LAEVRAVFKLPKVGAIAGCMVTEGVIKRGAPVRVVRDGVVIYEGEVESLK-RFKDDVKEVRKGQECGIAIENYRDIKEGD  493 (509)
T ss_pred             ceEEEEEEEcCCCCeEEEEEEecCEEecCCcEEEEeCCeEEEeeEEEeee-ccCccHhHhccCcEEEEEecCcccCCCCC
Confidence            45566666667789999999999999999999999765432225555554 45678999999999965  5667899999


Q ss_pred             EEec
Q psy5461         180 KRTR  183 (221)
Q Consensus       180 tl~~  183 (221)
                      +|..
T Consensus       494 ~le~  497 (509)
T COG0532         494 ILEV  497 (509)
T ss_pred             EEEE
Confidence            9854

>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes

Probab=94.34  E-value=0.0089  Score=41.77  Aligned_cols=35  Identities=34%  Similarity=0.669  Sum_probs=30.2

Q ss_pred             eeeeeeeecccccCCcchHHHHhhccccccCceeEe
Q psy5461          27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLC   62 (221)
Q Consensus        27 ~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~   62 (221)
                      ++++|||+..|++.|++++.|+++|+++.... +..
T Consensus         1 ~~a~Vfk~~~d~~~G~~~~~Rv~sG~l~~g~~-v~~   35 (83)
T cd04088           1 FVALVFKTIHDPFVGKLSFVRVYSGTLKAGST-LYN   35 (83)
T ss_pred             CEEEEEEcccCCCCceEEEEEEecCEEcCCCE-EEE
Confidence            57899999999999999999999999988654 443

During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl

>cd03699 lepA_II lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane

Probab=93.86  E-value=0.027  Score=39.77  Aligned_cols=36  Identities=28%  Similarity=0.433  Sum_probs=30.7

Q ss_pred             eeeeeeeecccccCCcchHHHHhhccccccCceeEec
Q psy5461          27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCG   63 (221)
Q Consensus        27 ~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~g   63 (221)
                      |.++|||++.|++.|++++.|+++|+++.... ++..
T Consensus         1 ~~~~Vfk~~~d~~~G~i~~~Rv~sG~l~~~~~-v~~~   36 (86)
T cd03699           1 LRALIFDSWYDPYRGVIALVRVFDGTLKKGDK-IRFM   36 (86)
T ss_pred             CEEEEEEeeccCCCCEEEEEEEEcCEEcCCCE-EEEe
Confidence            57899999999999999999999999987553 5443

The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu and IF2 have all been demonstrated to interact at overlapping sites on the ribosome. Chemical protection studies demonstrate that they all include the universally conserved alpha-sarcin loop as part of their binding site. These data indicate that LepA may bind to this location on the ribosome as well. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.

>PRK10218 GTP-binding protein; Provisional

Probab=93.61  E-value=0.028  Score=53.84  Aligned_cols=50  Identities=24%  Similarity=0.325  Sum_probs=43.5

Q ss_pred             ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCc
Q psy5461           1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHV   58 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~   58 (221)
                      ||++.+++|+|..        +.+.||.++|||+..|++.|.+++.|+++|+++.+..
T Consensus       187 ld~Ii~~iP~P~~--------~~~~Pl~~~V~k~~~d~~~G~i~~gRV~sG~lk~Gd~  236 (607)
T PRK10218        187 YQAIVDHVPAPDV--------DLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQ  236 (607)
T ss_pred             HHHHHHhCCCCCC--------CCCCCeEEEEEeeEecCCCcEEEEEEEEeCcCcCCCE
Confidence            4788999999952        4578999999999999999999999999999887654

>cd04165 GTPBP1_like GTPBP1-like

Probab=93.16  E-value=0.11  Score=43.35  Aligned_cols=29  Identities=24%  Similarity=0.319  Sum_probs=24.0

Q ss_pred             cCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          56 NHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      ...|+|..||.+|.|++.|+..|. .+|+|
T Consensus       196 ~~~pi~~vSavtg~Gi~~L~~~L~-~lp~~  224 (224)
T cd04165         196 RIVPIFQVSNVTGEGLDLLHAFLN-LLPLR  224 (224)
T ss_pred             ccCcEEEeeCCCccCHHHHHHHHH-hcCCC
Confidence            466999999999999999988774 56764

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

>cd01884 EF_Tu EF-Tu subfamily

Probab=93.11  E-value=0.098  Score=42.76  Aligned_cols=62  Identities=21%  Similarity=0.350  Sum_probs=39.9

Q ss_pred             CCc-eeeeeeeecc-c-ccCCcchHHHHhhcc----ccccCceeEecCCCcccc----------HHHHHHHHHhhCCCC
Q psy5461          24 GDS-LCARAFKVVH-D-KHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIG----------VQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~-~~~~vfk~~~-d-~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~G----------i~~LLd~I~~~~PsP   85 (221)
                      +.+ ++..++|++. + +..-+.....+++..    .+...+|++++||++|.+          +..|+++|.+..|+|
T Consensus       117 ~~~~iIvviNK~D~~~~~~~~~~~~~~i~~~l~~~g~~~~~v~iipiSa~~g~n~~~~~~w~~~~~~l~~~l~~~~~~~  195 (195)
T cd01884         117 GVPYIVVFLNKADMVDDEELLELVEMEVRELLSKYGFDGDNTPIVRGSALKALEGDDPNKWVKKILELLDALDSYIPTP  195 (195)
T ss_pred             CCCcEEEEEeCCCCCCcHHHHHHHHHHHHHHHHHhcccccCCeEEEeeCccccCCCCCCcchhcHhHHHHHHHhCCCCC
Confidence            444 7788999652 1 111122222343332    233468999999999875          679999999988876

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.

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

Probab=93.04  E-value=0.16  Score=40.92  Aligned_cols=62  Identities=19%  Similarity=0.255  Sum_probs=39.9

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhcc------ccccCceeEecCCCccc----------cHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGA------FKKNHVPVLCGSSYKNI----------GVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~------~~~~~~Pv~~gSa~~~~----------Gi~~LLd~I~~~~PsP   85 (221)
                      +-|++..++|++............+.+..      .+...+|++++||++|.          ++.+|++.|..++|.|
T Consensus       117 ~~p~iiv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iv~~Sa~~g~~~~~~~~~~~~~~~l~~~~~~~~~~~  194 (194)
T cd01891         117 GLKPIVVINKIDRPDARPEEVVDEVFDLFIELGATEEQLDFPVLYASAKNGWASLNLEDPSEDLEPLFDTIIEHVPAP  194 (194)
T ss_pred             CCCEEEEEECCCCCCCCHHHHHHHHHHHHHHhCCccccCccCEEEeehhccccccccccchhhHHHHHHHHHhcCCCC
Confidence            45788889996543221221222222211      12235689999999995          4679999999999987

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

>KOG1144|consensus

Probab=92.83  E-value=0.18  Score=49.01  Aligned_cols=79  Identities=14%  Similarity=0.207  Sum_probs=61.9

Q ss_pred             cCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEe
Q psy5461          56 NHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYN  135 (221)
Q Consensus        56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~  135 (221)
                      ..+-++..||..|.||..||-.|+++.-.-... .    ..--..+.+.|..+-.-++.|+..=+-+..|.|+.||+|.+
T Consensus       660 ~~vsiVPTSA~sGeGipdLl~llv~ltQk~m~~-k----l~y~~ev~cTVlEVKvieG~GtTIDViLvNG~L~eGD~Ivv  734 (1064)
T KOG1144|consen  660 ETVSIVPTSAISGEGIPDLLLLLVQLTQKTMVE-K----LAYVDEVQCTVLEVKVIEGHGTTIDVILVNGELHEGDQIVV  734 (1064)
T ss_pred             ceEEeeecccccCCCcHHHHHHHHHHHHHHHHH-H----HhhhhheeeEEEEEEeecCCCceEEEEEEcceeccCCEEEE
Confidence            455678899999999999999999886442110 0    01235678889999888999987777788999999999999


Q ss_pred             ccCC
Q psy5461         136 IHLD  139 (221)
Q Consensus       136 ~~~~  139 (221)
                      ++.+
T Consensus       735 cG~~  738 (1064)
T KOG1144|consen  735 CGLQ  738 (1064)
T ss_pred             cCCC
Confidence            8865

>TIGR00436 era GTP-binding protein Era

Probab=92.77  E-value=0.19  Score=42.97  Aligned_cols=62  Identities=13%  Similarity=-0.041  Sum_probs=39.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT   86 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~   86 (221)
                      .+.|++..++|++.-.  -+.....+..........+++..||++|.|+++|++.|.+++|...
T Consensus       106 ~~~p~ilV~NK~Dl~~--~~~~~~~~~~~~~~~~~~~v~~iSA~~g~gi~~L~~~l~~~l~~~~  167 (270)
T TIGR00436       106 LKRPVVLTRNKLDNKF--KDKLLPLIDKYAILEDFKDIVPISALTGDNTSFLAAFIEVHLPEGP  167 (270)
T ss_pred             cCCCEEEEEECeeCCC--HHHHHHHHHHHHhhcCCCceEEEecCCCCCHHHHHHHHHHhCCCCC
Confidence            4568888999965321  1111111111111112237999999999999999999999998643

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

>TIGR01393 lepA GTP-binding protein LepA

Probab=92.56  E-value=0.067  Score=51.19  Aligned_cols=55  Identities=29%  Similarity=0.440  Sum_probs=45.6

Q ss_pred             ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecC
Q psy5461           1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGS   64 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gS   64 (221)
                      |+.+++++|+|.+        +.+.|+.++|||+..|++.|.+++.++++|+++.++. +++.+
T Consensus       172 le~I~~~lp~p~~--------~~~~pl~~~V~~~~~d~~~G~v~~~rV~sG~lk~Gd~-v~~~~  226 (595)
T TIGR01393       172 LEAIVKRVPPPKG--------DPDAPLKALIFDSHYDNYRGVVALVRVFEGTIKPGDK-IRFMS  226 (595)
T ss_pred             HHHHHHhCCCCCC--------CCCCCeEEEEEEEEEeCCCcEEEEEEEECCEEecCCE-EEEec
Confidence            4677888998854        4578999999999999999999999999999988765 54443

LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function is unknown.

>TIGR01394 TypA_BipA GTP-binding protein TypA/BipA

Probab=92.24  E-value=0.074  Score=50.88  Aligned_cols=54  Identities=26%  Similarity=0.335  Sum_probs=45.1

Q ss_pred             ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEec
Q psy5461           1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCG   63 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~g   63 (221)
                      |+.+++++|+|..        +.+.||.++||++..|++.|.+++.++++|+++.+.. |+..
T Consensus       183 ld~Iv~~lP~P~~--------~~~~pl~~~V~~i~~d~~~Grv~~gRV~sG~lk~G~~-V~~~  236 (594)
T TIGR01394       183 FDAIVRHVPAPKG--------DLDEPLQMLVTNLDYDEYLGRIAIGRVHRGTVKKGQQ-VALM  236 (594)
T ss_pred             HHHHHHhCCCCCC--------CCCCCEEEEEEEEEeeCCCceEEEEEEEeCEEccCCE-EEEe
Confidence            4678899999943        4578999999999999999999999999999987654 5443

This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP-binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.

>PRK15467 ethanolamine utilization protein EutP; Provisional

Probab=92.12  E-value=0.26  Score=38.55  Aligned_cols=58  Identities=14%  Similarity=0.050  Sum_probs=39.4

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhcccccc-CceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKN-HVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~-~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      ..|++..++|.+....    ....+.+...+.. ..|++..||++|.||++|++.|.+.++.-
T Consensus        91 ~~~ii~v~nK~Dl~~~----~~~~~~~~~~~~~~~~p~~~~Sa~~g~gi~~l~~~l~~~~~~~  149 (158)
T PRK15467         91 SKRQIAVISKTDMPDA----DVAATRKLLLETGFEEPIFELNSHDPQSVQQLVDYLASLTKQE  149 (158)
T ss_pred             CCCeEEEEEccccCcc----cHHHHHHHHHHcCCCCCEEEEECCCccCHHHHHHHHHHhchhh
Confidence            4578889999653221    2233333222222 25999999999999999999999887654

>cd01885 EF2 EF2 (for archaea and eukarya)

Probab=91.90  E-value=0.19  Score=42.06  Aligned_cols=26  Identities=35%  Similarity=0.653  Sum_probs=24.1

Q ss_pred             eEecCCCcccc--------HHHHHHHHHhhCCCC
Q psy5461          60 VLCGSSYKNIG--------VQKLMDAIVDILPSP   85 (221)
Q Consensus        60 v~~gSa~~~~G--------i~~LLd~I~~~~PsP   85 (221)
                      |.|+||+.||+        +-.|+++|++++|+|
T Consensus       189 v~f~S~~~gw~f~~~~f~~~~~~~~~~~~~~~~p  222 (222)
T cd01885         189 VAFGSALHGWGFTIIKFARIYAVLEMVVKHLPSP  222 (222)
T ss_pred             EEEEecccCEEeccccccchHHHHHHHHhhCCCC
Confidence            99999999985        779999999999998

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

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=91.88  E-value=0.22  Score=38.13  Aligned_cols=58  Identities=16%  Similarity=0.017  Sum_probs=37.8

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+-|++..++|++.... .+........ ..+....|++..||++|.|+++|++.+.+.+
T Consensus       104 ~~~piiiv~NK~D~~~~-~~~~~~~~~~-~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~  161 (164)
T cd04139         104 DNVPLLLVGNKCDLEDK-RQVSSEEAAN-LARQWGVPYVETSAKTRQNVEKAFYDLVREI  161 (164)
T ss_pred             CCCCEEEEEEccccccc-cccCHHHHHH-HHHHhCCeEEEeeCCCCCCHHHHHHHHHHHH
Confidence            46788999999653221 1122222221 1222236899999999999999999988654

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

>COG1160 Predicted GTPases [General function prediction only]

Probab=91.75  E-value=0.27  Score=45.18  Aligned_cols=58  Identities=22%  Similarity=0.271  Sum_probs=41.8

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTE   87 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~   87 (221)
                      .+.|++.-+||++..+  .+......++.    +.-..+..||.+|.|+..|+|.|.+.+| +.+
T Consensus       111 ~~kpviLvvNK~D~~~--~e~~~~efysl----G~g~~~~ISA~Hg~Gi~dLld~v~~~l~-~~e  168 (444)
T COG1160         111 SKKPVILVVNKIDNLK--AEELAYEFYSL----GFGEPVPISAEHGRGIGDLLDAVLELLP-PDE  168 (444)
T ss_pred             cCCCEEEEEEcccCch--hhhhHHHHHhc----CCCCceEeehhhccCHHHHHHHHHhhcC-Ccc
Confidence            4589999999965542  23333333332    3334677999999999999999999998 544

>PRK05433 GTP-binding protein LepA; Provisional

Probab=91.69  E-value=0.09  Score=50.38  Aligned_cols=56  Identities=30%  Similarity=0.446  Sum_probs=46.2

Q ss_pred             ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCC
Q psy5461           1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSS   65 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa   65 (221)
                      |+.+++++|+|.+        +.+.|+.++|||+..|++.|.+++.++.+|.++.+.. +++.+.
T Consensus       176 l~~I~~~lp~P~~--------~~~~pl~~~Vfd~~~d~~~G~v~~~rV~sG~Lk~Gd~-i~~~~~  231 (600)
T PRK05433        176 LEAIVERIPPPKG--------DPDAPLKALIFDSWYDNYRGVVVLVRVVDGTLKKGDK-IKMMST  231 (600)
T ss_pred             HHHHHHhCccccC--------CCCCCceEEEEEEEecCCCceEEEEEEEcCEEecCCE-EEEecC
Confidence            4677888998853        4578999999999999999999999999999988765 555444

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

Probab=91.47  E-value=0.26  Score=38.12  Aligned_cols=55  Identities=15%  Similarity=0.077  Sum_probs=36.5

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++..++|.+.-.. .++..  . +...+....|++..||++|.|++++++.|.+.+
T Consensus       113 ~~pvilv~NK~Dl~~~-~~~~~--~-~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~  167 (168)
T cd01897         113 NKPVIVVLNKIDLLTF-EDLSE--I-EEEEELEGEEVLKISTLTEEGVDEVKNKACELL  167 (168)
T ss_pred             cCCeEEEEEccccCch-hhHHH--H-HHhhhhccCceEEEEecccCCHHHHHHHHHHHh
Confidence            6788888999543211 12221  1 112233457899999999999999999988653

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.

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

Probab=91.24  E-value=0.33  Score=37.25  Aligned_cols=58  Identities=16%  Similarity=0.089  Sum_probs=39.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+-|++...+|.+.... ..+......+-. +...+|++..||++|.||+++++.|...+
T Consensus       106 ~~~piiiv~NK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~~i~~l~~~l~~~~  163 (164)
T cd04145         106 DEFPMILVGNKADLEHQ-RKVSREEGQELA-RKLKIPYIETSAKDRLNVDKAFHDLVRVI  163 (164)
T ss_pred             CCCCEEEEeeCcccccc-ceecHHHHHHHH-HHcCCcEEEeeCCCCCCHHHHHHHHHHhh
Confidence            35689999999654332 233333333322 22235899999999999999999998653

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

>cd03689 RF3_II RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3)

Probab=91.16  E-value=0.056  Score=38.24  Aligned_cols=30  Identities=30%  Similarity=0.582  Sum_probs=26.9

Q ss_pred             eeeeeecc---cccCCcchHHHHhhccccccCc
Q psy5461          29 ARAFKVVH---DKHRGAVTFFRIYSGAFKKNHV   58 (221)
Q Consensus        29 ~~vfk~~~---d~~~g~l~~~~l~~~~~~~~~~   58 (221)
                      +++||+.+   |++.|++++.|+++|+++....
T Consensus         1 ~~vfKv~~~~~~~~~Gkla~~Rv~sG~l~~g~~   33 (85)
T cd03689           1 GFVFKIQANMDPAHRDRIAFVRVCSGKFERGMK   33 (85)
T ss_pred             CEEEEEecccCCCCCcEEEEEEEECCEEcCCCE
Confidence            57999999   9999999999999999997554

Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ.

>cd04136 Rap_like Rap-like subfamily

Probab=91.05  E-value=0.49  Score=36.21  Aligned_cols=57  Identities=14%  Similarity=0.031  Sum_probs=37.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+-|++...+|.+.... .++.......-. +....|++..||++|.||.++++.|...
T Consensus       105 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~~v~~l~~~l~~~  161 (163)
T cd04136         105 ENVPMVLVGNKCDLEDE-RVVSREEGQALA-RQWGCPFYETSAKSKINVDEVFADLVRQ  161 (163)
T ss_pred             CCCCEEEEEECcccccc-ceecHHHHHHHH-HHcCCeEEEecCCCCCCHHHHHHHHHHh
Confidence            35688888999653221 223332222211 1222789999999999999999999864

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

>cd04147 Ras_dva Ras-dva subfamily

Probab=90.92  E-value=0.43  Score=38.53  Aligned_cols=62  Identities=11%  Similarity=-0.052  Sum_probs=40.9

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +-|++...+|.+..+....+......+........+++..||++|.||.++++.|.+.+..+
T Consensus       104 ~~piilv~NK~Dl~~~~~~v~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~~l~~~l~~~~~~~  165 (198)
T cd04147         104 FVPIVVVGNKADSLEEERQVPAKDALSTVELDWNCGFVETSAKDNENVLEVFKELLRQANLP  165 (198)
T ss_pred             CCcEEEEEEccccccccccccHHHHHHHHHhhcCCcEEEecCCCCCCHHHHHHHHHHHhhcc
Confidence            56888999996532222333333333222212235789999999999999999999887643

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

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=90.87  E-value=0.34  Score=37.29  Aligned_cols=58  Identities=14%  Similarity=0.043  Sum_probs=39.1

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+.... ..+..+....-. +....|++..||++|.|++++++.|.+.+.
T Consensus       105 ~~pii~v~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~~i~~l~~~l~~~~~  162 (164)
T smart00173      105 DVPIVLVGNKCDLESE-RVVSTEEGKELA-RQWGCPFLETSAKERVNVDEAFYDLVREIR  162 (164)
T ss_pred             CCCEEEEEECcccccc-ceEcHHHHHHHH-HHcCCEEEEeecCCCCCHHHHHHHHHHHHh
Confidence            5688888999664332 223333322222 222378999999999999999999987654

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

>TIGR02528 EutP ethanolamine utilization protein, EutP

Probab=90.76  E-value=0.42  Score=36.00  Aligned_cols=54  Identities=17%  Similarity=0.080  Sum_probs=34.1

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHH
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIV   79 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~   79 (221)
                      ..|++..++|++..+.  ....+.+.+........|++..||++|.|+++|++.|.
T Consensus        88 ~~p~ilv~NK~Dl~~~--~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~  141 (142)
T TIGR02528        88 VKPVIGLVTKIDLAEA--DVDIERAKELLETAGAEPIFEISSVDEQGLEALVDYLN  141 (142)
T ss_pred             cCCeEEEEEeeccCCc--ccCHHHHHHHHHHcCCCcEEEEecCCCCCHHHHHHHHh
Confidence            3488888899764321  12222222222222234789999999999999998874

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.

>cd04157 Arl6 Arl6 subfamily

Probab=90.71  E-value=0.54  Score=35.91  Aligned_cols=55  Identities=11%  Similarity=-0.019  Sum_probs=35.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcc--c--cccCceeEecCCCccccHHHHHHHHHh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA--F--KKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~--~--~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      .+-|++...+|.+....   .....+....  .  ....++++..||++|.|++++++.|.+
T Consensus       103 ~~~p~iiv~NK~Dl~~~---~~~~~~~~~l~~~~~~~~~~~~~~~Sa~~g~gv~~~~~~l~~  161 (162)
T cd04157         103 RRVPILFFANKMDLPDA---LTAVKITQLLGLENIKDKPWHIFASNALTGEGLDEGVQWLQA  161 (162)
T ss_pred             CCCCEEEEEeCccccCC---CCHHHHHHHhCCccccCceEEEEEeeCCCCCchHHHHHHHhc
Confidence            35789999999653221   1122222211  1  223456899999999999999998864

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

>cd01860 Rab5_related Rab5-related subfamily

Probab=90.70  E-value=0.5  Score=36.21  Aligned_cols=59  Identities=15%  Similarity=0.017  Sum_probs=38.8

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+-+++...+|.+.... .......+.+-.... ..+++..||++|.|+.++++.|...+|
T Consensus       105 ~~~~iivv~nK~D~~~~-~~~~~~~~~~~~~~~-~~~~~~~Sa~~~~~v~~l~~~l~~~l~  163 (163)
T cd01860         105 PNIIIALVGNKADLESK-RQVSTEEAQEYADEN-GLLFFETSAKTGENVNELFTEIAKKLP  163 (163)
T ss_pred             CCCeEEEEEECcccccc-CcCCHHHHHHHHHHc-CCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            34578888899653221 222333333222222 367999999999999999999998775

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

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

Probab=90.63  E-value=1.6  Score=41.88  Aligned_cols=71  Identities=13%  Similarity=0.203  Sum_probs=52.8

Q ss_pred             ceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCC---CCCccCcEEecCCCCCC
Q psy5461         115 GAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGL---KRERGKDKRTRVIPKPT  189 (221)
Q Consensus       115 G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl---~~~~~Gdtl~~~~~~p~  189 (221)
                      +.++=+||..|+|++|..|.. +.+  ..++.|..++. ...+++++.+|+-|+|  .|.   .+++.||+|.+..+.++
T Consensus       480 ~~i~G~~V~~G~i~~~~~v~r-~~~--~~iG~i~slk~-~k~~V~ev~~G~Ecgi~i~~~~~g~~~~~gD~l~~~i~~~~  555 (590)
T TIGR00491       480 PAIVGVEVLTGVIRQGYPLMK-DDG--ETVGTVRSMQD-KGENVKSASAGQEVAIAIKDVVYGRTIHEGDTLYVDVPENH  555 (590)
T ss_pred             CeEEEEEEecCEEecCCeEEe-cCC--EEEEEEchhcc-cCccccEECCCCEEEEEEeCccccCCCCCCCEEEEeCCHHH
Confidence            689999999999999998743 222  23455555543 4568999999999975  354   47899999998866554

This model describes archaeal and eukaryotic orthologs of bacterial IF-2. Like IF-2, it helps convey the initiator tRNA to the ribosome, although the initiator is N-formyl-Met in bacteria and Met here. This protein is not closely related to the subunits of eIF-2 of eukaryotes, which is also involved in the initiation of translation. The aIF-2 of Methanococcus jannaschii contains a large intein interrupting a region of very strongly conserved sequence very near the amino end; this model does not correctly align the sequences from Methanococcus jannaschii and Pyrococcus horikoshii in this region.

>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=90.59  E-value=0.26  Score=39.06  Aligned_cols=53  Identities=21%  Similarity=0.225  Sum_probs=38.0

Q ss_pred             CCCCceeeeeeeec-ccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHH
Q psy5461          22 HFGDSLCARAFKVV-HDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAI   78 (221)
Q Consensus        22 ~~~~~~~~~vfk~~-~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I   78 (221)
                      +.+.|++.-++|++ ..+....+...++.+..    .+||+..||.++.|+++|+++|
T Consensus       103 e~g~P~vvvlN~~D~a~~~g~~id~~~Ls~~L----g~pvi~~sa~~~~g~~~L~~~I  156 (156)
T PF02421_consen  103 ELGIPVVVVLNKMDEAERKGIEIDAEKLSERL----GVPVIPVSARTGEGIDELKDAI  156 (156)
T ss_dssp             HTTSSEEEEEETHHHHHHTTEEE-HHHHHHHH----TS-EEEEBTTTTBTHHHHHHHH
T ss_pred             HcCCCEEEEEeCHHHHHHcCCEECHHHHHHHh----CCCEEEEEeCCCcCHHHHHhhC
Confidence            46789999999964 22333355566665543    4799999999999999999986

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 ....

>cd04116 Rab9 Rab9 subfamily

Probab=90.47  E-value=0.5  Score=36.67  Aligned_cols=56  Identities=11%  Similarity=-0.044  Sum_probs=38.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +-|++...+|.+..  ..+++...+.+-..+....|++..||++|.|+.++++.+...
T Consensus       114 ~~piilv~nK~Dl~--~~~~~~~~~~~~~~~~~~~~~~e~Sa~~~~~v~~~~~~~~~~  169 (170)
T cd04116         114 SFPFVVLGNKNDIP--ERQVSTEEAQAWCRENGDYPYFETSAKDATNVAAAFEEAVRR  169 (170)
T ss_pred             CCcEEEEEECcccc--ccccCHHHHHHHHHHCCCCeEEEEECCCCCCHHHHHHHHHhh
Confidence            35788888995432  234444444443333344689999999999999999998754

Rab9 is found in late endosomes, together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kD (TIP47). Rab9 is a key mediator of vesicular transport from late endosomes to the trans-Golgi network (TGN) by redirecting the MPRs. Rab9 has been identified as a key component for the replication of several viruses, including HIV1, Ebola, Marburg, and measles, making it a potential target for inhibiting a variety of viruses. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CX

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

Probab=90.46  E-value=0.55  Score=35.66  Aligned_cols=55  Identities=15%  Similarity=0.019  Sum_probs=36.3

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +.|++...+|.+...  .......+.+- .+....|++..||++|.||+++++.+...
T Consensus       106 ~~piivv~nK~Dl~~--~~~~~~~~~~~-~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~  160 (162)
T cd04138         106 DVPMVLVGNKCDLAA--RTVSSRQGQDL-AKSYGIPYIETSAKTRQGVEEAFYTLVRE  160 (162)
T ss_pred             CCCEEEEEECccccc--ceecHHHHHHH-HHHhCCeEEEecCCCCCCHHHHHHHHHHH
Confidence            568888889954322  22333332221 12234589999999999999999998764

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

>cd01865 Rab3 Rab3 subfamily

Probab=90.37  E-value=0.36  Score=37.51  Aligned_cols=58  Identities=17%  Similarity=0.141  Sum_probs=38.4

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+..+. ..+..+...+ ..+....|++..||++|.|+.+|++.+...++
T Consensus       106 ~~piivv~nK~Dl~~~-~~~~~~~~~~-~~~~~~~~~~~~Sa~~~~gv~~l~~~l~~~~~  163 (165)
T cd01865         106 NAQVILVGNKCDMEDE-RVVSSERGRQ-LADQLGFEFFEASAKENINVKQVFERLVDIIC  163 (165)
T ss_pred             CCCEEEEEECcccCcc-cccCHHHHHH-HHHHcCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4578899999664332 1222222222 22223458999999999999999999987654

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

>cd04160 Arfrp1 Arfrp1 subfamily

Probab=90.34  E-value=0.62  Score=35.92  Aligned_cols=54  Identities=22%  Similarity=0.147  Sum_probs=35.9

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhcc------ccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGA------FKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~------~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      +-|++..++|.+...   ......+....      ......|++..||++|.|++++++.|.+
T Consensus       107 ~~p~ilv~NK~D~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~e~~~~l~~  166 (167)
T cd04160         107 GVPLLILANKQDLPD---ALSVEEIKEVFQDKAEEIGRRDCLVLPVSALEGTGVREGIEWLVE  166 (167)
T ss_pred             CCCEEEEEEcccccc---CCCHHHHHHHhccccccccCCceEEEEeeCCCCcCHHHHHHHHhc
Confidence            568999999965322   22222222211      1223568999999999999999998864

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.

>cd03691 BipA_TypA_II BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu

Probab=89.98  E-value=0.091  Score=36.87  Aligned_cols=35  Identities=23%  Similarity=0.236  Sum_probs=29.9

Q ss_pred             eeeeeeeecccccCCcchHHHHhhccccccCceeEe
Q psy5461          27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLC   62 (221)
Q Consensus        27 ~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~   62 (221)
                      |.++|||++.|++.|++++.|+++|+++.... +..
T Consensus         1 ~~~~vfk~~~d~~~g~i~~~Rv~sG~l~~g~~-v~~   35 (86)
T cd03691           1 LQMLVTTLDYDDYVGRIAIGRIFRGTVKVGQQ-VAV   35 (86)
T ss_pred             CeEEEEEeEecCCCCeEEEEEEEeCEEcCCCE-EEE
Confidence            45899999999999999999999999998654 443

BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion.

>cd01862 Rab7 Rab7 subfamily

Probab=89.89  E-value=0.51  Score=36.45  Aligned_cols=58  Identities=12%  Similarity=0.114  Sum_probs=39.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +-|++...+|++.... ..+..+.+..........+++..||++|.|++++++.|.+.+
T Consensus       109 ~~p~ilv~nK~Dl~~~-~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~l~~~i~~~~  166 (172)
T cd01862         109 NFPFVVLGNKIDLEEK-RQVSTKKAQQWCQSNGNIPYFETSAKEAINVEQAFETIARKA  166 (172)
T ss_pred             CceEEEEEECcccccc-cccCHHHHHHHHHHcCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            5688888899754321 223333333333333457899999999999999999998754

Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-

>cd04154 Arl2 Arl2 subfamily

Probab=89.88  E-value=0.79  Score=35.87  Aligned_cols=55  Identities=20%  Similarity=0.074  Sum_probs=36.9

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcc----ccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      .+.|++...+|++.....   ....+....    .+....|++..||++|.||+++++.+.+
T Consensus       114 ~~~p~iiv~nK~Dl~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~  172 (173)
T cd04154         114 AGATLLILANKQDLPGAL---SEEEIREALELDKISSHHWRIQPCSAVTGEGLLQGIDWLVD  172 (173)
T ss_pred             cCCCEEEEEECcccccCC---CHHHHHHHhCccccCCCceEEEeccCCCCcCHHHHHHHHhc
Confidence            456888999996543221   222332221    1234678999999999999999998864

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.

>cd04175 Rap1 Rap1 subgroup

Probab=89.52  E-value=0.52  Score=36.36  Aligned_cols=58  Identities=12%  Similarity=-0.012  Sum_probs=38.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+-|++...+|.+.... ..+....... ..+....|++..||++|.|++++++.|.+.+
T Consensus       105 ~~~piilv~nK~Dl~~~-~~~~~~~~~~-~~~~~~~~~~~~Sa~~~~~v~~~~~~l~~~l  162 (164)
T cd04175         105 EDVPMILVGNKCDLEDE-RVVGKEQGQN-LARQWGCAFLETSAKAKINVNEIFYDLVRQI  162 (164)
T ss_pred             CCCCEEEEEECCcchhc-cEEcHHHHHH-HHHHhCCEEEEeeCCCCCCHHHHHHHHHHHh
Confidence            45689999999654322 1233322221 2222336899999999999999999998643

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

>cd01863 Rab18 Rab18 subfamily

Probab=89.47  E-value=0.79  Score=35.07  Aligned_cols=55  Identities=18%  Similarity=0.044  Sum_probs=36.2

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +.+++...+|.+..  ..........+-.. ...+|++..||++|.|++++++.+.+.
T Consensus       106 ~~~~~iv~nK~D~~--~~~~~~~~~~~~~~-~~~~~~~~~Sa~~~~gi~~~~~~~~~~  160 (161)
T cd01863         106 DIVKMLVGNKIDKE--NREVTREEGLKFAR-KHNMLFIETSAKTRDGVQQAFEELVEK  160 (161)
T ss_pred             CCcEEEEEECCccc--ccccCHHHHHHHHH-HcCCEEEEEecCCCCCHHHHHHHHHHh
Confidence            45677778885432  12223333333222 235789999999999999999998764

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

>cd00880 Era_like Era (E

Probab=89.41  E-value=0.77  Score=34.05  Aligned_cols=59  Identities=14%  Similarity=0.103  Sum_probs=37.6

Q ss_pred             CCCceeeeeeeecccccCCcchHH-HHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFF-RIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~-~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      ...|++..++|.+.-......... ............|++..||+++.|+.++++.+.+.
T Consensus       103 ~~~~~ivv~nK~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sa~~~~~v~~l~~~l~~~  162 (163)
T cd00880         103 RGKPVLLVLNKIDLLPEEEEEELLELRLLILLLLLGLPVIAVSALTGEGIDELREALIEA  162 (163)
T ss_pred             cCCeEEEEEEccccCChhhHHHHHHHHHhhcccccCCceEEEeeeccCCHHHHHHHHHhh
Confidence            467888889995422211111111 01122334457789999999999999999999865

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

>PRK04004 translation initiation factor IF-2; Validated

Probab=89.32  E-value=2.4  Score=40.59  Aligned_cols=66  Identities=17%  Similarity=0.195  Sum_probs=49.2

Q ss_pred             ceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCC---CCCccCcEEecC
Q psy5461         115 GAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGL---KRERGKDKRTRV  184 (221)
Q Consensus       115 G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl---~~~~~Gdtl~~~  184 (221)
                      +.++=+||..|+|++|..|.-. .+  ..++.|..++ ....+++++.+|+-|+|  .+.   .+++.||+|-..
T Consensus       482 ~~IaGc~V~~G~i~~~~~v~r~-~g--~~iG~i~Slk-~~k~~V~ev~~G~Ecgi~i~~~~~g~~~~~gD~i~~~  552 (586)
T PRK04004        482 PAIVGVEVLGGTIKPGVPLIKE-DG--KRVGTIKQIQ-DQGENVKEAKAGMEVAISIDGPTVGRQIKEGDILYVD  552 (586)
T ss_pred             CeEEEEEEEeCEEecCCEEEEE-CC--EEEEEEehhh-ccCCcccEeCCCCEEEEEEecccccCCCCCCCEEEEE
Confidence            6899999999999999986431 33  2345555554 34568999999999965  455   578999998765

>cd04151 Arl1 Arl1 subfamily

Probab=89.17  E-value=0.68  Score=35.53  Aligned_cols=55  Identities=22%  Similarity=0.114  Sum_probs=35.9

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhc----cccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG----AFKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      .+.|++...+|.+.....   ...++.+.    .......+++..||++|.||+++++.|.+
T Consensus        99 ~~~piiiv~nK~Dl~~~~---~~~~i~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~  157 (158)
T cd04151          99 KGAVLLVFANKQDMPGAL---SEAEISEKLGLSELKDRTWSIFKTSAIKGEGLDEGMDWLVN  157 (158)
T ss_pred             cCCcEEEEEeCCCCCCCC---CHHHHHHHhCccccCCCcEEEEEeeccCCCCHHHHHHHHhc
Confidence            357999999996432211   12222221    11223358999999999999999998864

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.

>cd04106 Rab23_lke Rab23-like subfamily

Probab=88.88  E-value=0.55  Score=35.94  Aligned_cols=56  Identities=13%  Similarity=0.111  Sum_probs=36.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +-|++...+|.+.... .++..+.... ..+....|++..||++|.|++++++.|...
T Consensus       106 ~~p~iiv~nK~Dl~~~-~~v~~~~~~~-~~~~~~~~~~~~Sa~~~~~v~~l~~~l~~~  161 (162)
T cd04106         106 DIPMVLVQTKIDLLDQ-AVITNEEAEA-LAKRLQLPLFRTSVKDDFNVTELFEYLAEK  161 (162)
T ss_pred             CCCEEEEEEChhcccc-cCCCHHHHHH-HHHHcCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            5688888999654332 2233333222 122234589999999999999999998753

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

>cd04177 RSR1 RSR1 subgroup

Probab=88.80  E-value=0.86  Score=35.42  Aligned_cols=60  Identities=15%  Similarity=0.002  Sum_probs=39.1

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+-|++...+|.+.... -+++.+....-..+....|++..||++|.||.++++.|+..+.
T Consensus       105 ~~~piiiv~nK~D~~~~-~~~~~~~~~~~~~~~~~~~~~~~SA~~~~~i~~~f~~i~~~~~  164 (168)
T cd04177         105 DNVPMVLVGNKADLEDD-RQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQII  164 (168)
T ss_pred             CCCCEEEEEEChhcccc-CccCHHHHHHHHHHcCCceEEEeeCCCCCCHHHHHHHHHHHHh
Confidence            35688888899643222 1233333222222223478999999999999999999987654

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

>cd04158 ARD1 ARD1 subfamily

Probab=88.71  E-value=0.99  Score=35.25  Aligned_cols=58  Identities=12%  Similarity=-0.074  Sum_probs=37.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccc-----cccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAF-----KKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~-----~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.|++...+|.+...   .+....+.+...     .+...+++.+||++|.||+++++.|.+.++.
T Consensus       100 ~~piilv~NK~Dl~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~~~f~~l~~~~~~  162 (169)
T cd04158         100 DALLLIFANKQDVAG---ALSVEEMTELLSLHKLCCGRSWYIQGCDARSGMGLYEGLDWLSRQLVA  162 (169)
T ss_pred             CCCEEEEEeCcCccc---CCCHHHHHHHhCCccccCCCcEEEEeCcCCCCCCHHHHHHHHHHHHhh
Confidence            358889999955322   233333332211     1123467889999999999999999877653

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

>cd04156 ARLTS1 ARLTS1 subfamily

Probab=88.55  E-value=0.99  Score=34.46  Aligned_cols=55  Identities=15%  Similarity=-0.034  Sum_probs=35.4

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhc-----cccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG-----AFKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~-----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      .+.|++...+|.+....   .....+...     .......+++..||++|.||+++++.|..
T Consensus       100 ~~~piilv~nK~Dl~~~---~~~~~i~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~~~~~i~~  159 (160)
T cd04156         100 KGVPVVLLANKQDLPGA---LTAEEITRRFKLKKYCSDRDWYVQPCSAVTGEGLAEAFRKLAS  159 (160)
T ss_pred             cCCCEEEEEECcccccC---cCHHHHHHHcCCcccCCCCcEEEEecccccCCChHHHHHHHhc
Confidence            35689999999654221   112222211     11113457899999999999999998864

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

>cd01855 YqeH YqeH

Probab=88.54  E-value=0.88  Score=36.46  Aligned_cols=62  Identities=18%  Similarity=0.128  Sum_probs=37.9

Q ss_pred             CCCceeeeeeeeccc-ccCCcchHHHHh--h--ccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHD-KHRGAVTFFRIY--S--GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d-~~~g~l~~~~l~--~--~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.+++..++|++.- +...........  .  ........+++..||++|.|+++|++.|.+++|.
T Consensus        60 ~~~~~ilV~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vSA~~~~gi~eL~~~l~~~l~~  126 (190)
T cd01855          60 GNNPVILVGNKIDLLPKDKNLVRIKNWLRAKAAAGLGLKPKDVILISAKKGWGVEELINAIKKLAKK  126 (190)
T ss_pred             CCCcEEEEEEchhcCCCCCCHHHHHHHHHHHHHhhcCCCcccEEEEECCCCCCHHHHHHHHHHHhhc
Confidence            356888999997532 211111111111  0  0111112368899999999999999999999874

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.

>cd04143 Rhes_like Rhes_like subfamily

Probab=88.47  E-value=0.95  Score=38.33  Aligned_cols=63  Identities=14%  Similarity=0.044  Sum_probs=44.2

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTE   87 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~   87 (221)
                      +-|++...+|.+.... -++....+.+........+++..||++|.||++|++.|....-.|.+
T Consensus       113 ~~piIivgNK~Dl~~~-~~v~~~ei~~~~~~~~~~~~~evSAktg~gI~elf~~L~~~~~~p~e  175 (247)
T cd04143         113 KIPMVICGNKADRDFP-REVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMFRALFSLAKLPNE  175 (247)
T ss_pred             CCcEEEEEECccchhc-cccCHHHHHHHHHhcCCCEEEEEeCCCCCCHHHHHHHHHHHhccccc
Confidence            5688899999654332 23444555443322234678999999999999999999998766655

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

>cd04107 Rab32_Rab38 Rab38/Rab32 subfamily

Probab=88.46  E-value=0.66  Score=37.46  Aligned_cols=61  Identities=15%  Similarity=-0.037  Sum_probs=42.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +-|++...+|.+... ...+..+.+.+........+++..||++|.||+++++.|.+.+...
T Consensus       110 ~~piilv~NK~Dl~~-~~~~~~~~~~~~~~~~~~~~~~e~Sak~~~~v~e~f~~l~~~l~~~  170 (201)
T cd04107         110 PIPCLLLANKCDLKK-RLAKDGEQMDQFCKENGFIGWFETSAKEGINIEEAMRFLVKNILAN  170 (201)
T ss_pred             CCcEEEEEECCCccc-ccccCHHHHHHHHHHcCCceEEEEeCCCCCCHHHHHHHHHHHHHHh
Confidence            458888899965432 1334455554444444446899999999999999999999877543

Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=88.32  E-value=0.84  Score=34.86  Aligned_cols=57  Identities=19%  Similarity=0.065  Sum_probs=37.9

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..|++.-.+|.+..+. ..+..........+. ..|++..||++|.||+++++.|.+.+
T Consensus       110 ~~piilv~nK~Dl~~~-~~~~~~~~~~~~~~~-~~~~~~~Sa~~~~gi~~l~~~l~~~l  166 (168)
T cd04119         110 NIVVVVCANKIDLTKH-RAVSEDEGRLWAESK-GFKYFETSACTGEGVNEMFQTLFSSI  166 (168)
T ss_pred             CceEEEEEEchhcccc-cccCHHHHHHHHHHc-CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4678888899654321 233333333322222 36899999999999999999988653

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.

>cd01864 Rab19 Rab19 subfamily

Probab=88.28  E-value=1.1  Score=34.63  Aligned_cols=58  Identities=17%  Similarity=0.026  Sum_probs=38.4

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+-|++...+|.+.... .+.......+........+++..||++|.|++++++.+...
T Consensus       107 ~~~p~ivv~nK~Dl~~~-~~~~~~~~~~~~~~~~~~~~~e~Sa~~~~~v~~~~~~l~~~  164 (165)
T cd01864         107 SNVVLLLIGNKCDLEEQ-REVLFEEACTLAEKNGMLAVLETSAKESQNVEEAFLLMATE  164 (165)
T ss_pred             CCCcEEEEEECcccccc-cccCHHHHHHHHHHcCCcEEEEEECCCCCCHHHHHHHHHHh
Confidence            35678888999653221 23333333333333344568899999999999999998764

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.

>cd00876 Ras Ras family

Probab=88.26  E-value=0.88  Score=34.45  Aligned_cols=57  Identities=14%  Similarity=0.052  Sum_probs=39.5

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..|++...+|.+..+. .++....+.+...+ ...|++..|++++.|++++++.|.+.+
T Consensus       104 ~~p~ivv~nK~D~~~~-~~~~~~~~~~~~~~-~~~~~~~~S~~~~~~i~~l~~~l~~~i  160 (160)
T cd00876         104 DIPIVLVGNKCDLENE-RQVSKEEGKALAKE-WGCPFIETSAKDNINIDEVFKLLVREI  160 (160)
T ss_pred             CCcEEEEEECCccccc-ceecHHHHHHHHHH-cCCcEEEeccCCCCCHHHHHHHHHhhC
Confidence            5788899999654332 33444444333222 237899999999999999999998653

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

>cd04090 eEF2_II_snRNP Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p

Probab=88.09  E-value=0.13  Score=36.85  Aligned_cols=32  Identities=31%  Similarity=0.386  Sum_probs=27.7

Q ss_pred             eeeeeeeecccccC-CcchHHHHhhccccccCc
Q psy5461          27 LCARAFKVVHDKHR-GAVTFFRIYSGAFKKNHV   58 (221)
Q Consensus        27 ~~~~vfk~~~d~~~-g~l~~~~l~~~~~~~~~~   58 (221)
                      ++++|||+..|++. +.+++.|+++|+++....
T Consensus         1 ~~a~VfK~~~~~~~~~~la~~RV~sGtl~~g~~   33 (94)
T cd04090           1 LVVHVTKLYSTSDGGSFWAFGRIYSGTIKKGQK   33 (94)
T ss_pred             CEEEEEeeeecCCCCEEEEEEEEeeCeEcCCCE
Confidence            57899999999997 568999999999998654

This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.

>cd04150 Arf1_5_like Arf1-Arf5-like subfamily

Probab=88.05  E-value=1.1  Score=34.80  Aligned_cols=57  Identities=11%  Similarity=-0.027  Sum_probs=34.3

Q ss_pred             CCceeeeeeeecccccCCc-chHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          24 GDSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~-l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      +.|++...+|.+....... -....+..........+++..||++|.||+++++.|.+
T Consensus       101 ~~piilv~NK~Dl~~~~~~~~i~~~~~~~~~~~~~~~~~~~Sak~g~gv~~~~~~l~~  158 (159)
T cd04150         101 DAVLLVFANKQDLPNAMSAAEVTDKLGLHSLRNRNWYIQATCATSGDGLYEGLDWLSN  158 (159)
T ss_pred             CCCEEEEEECCCCCCCCCHHHHHHHhCccccCCCCEEEEEeeCCCCCCHHHHHHHHhc
Confidence            4688899999654322111 11111111111223456788999999999999998864

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

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

Probab=88.01  E-value=1  Score=34.60  Aligned_cols=59  Identities=12%  Similarity=0.035  Sum_probs=37.1

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcc-----ccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA-----FKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~-----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+.|++..++|++......+-....+....     ..+...|++..||++|.|+.+|++.|.++
T Consensus       101 ~~~p~ivv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~  164 (168)
T cd01887         101 ANVPFIVALNKIDKPNANPERVKNELSELGLQGEDEWGGDVQIVPTSAKTGEGIDDLLEAILLL  164 (168)
T ss_pred             cCCCEEEEEEceecccccHHHHHHHHHHhhccccccccCcCcEEEeecccCCCHHHHHHHHHHh
Confidence            466888899996532211111112221111     11235789999999999999999999865

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.

>cd03700 eEF2_snRNP_like_II EF2_snRNP_like_II: this subfamily represents domain II of elongation factor (EF) EF-2 found eukaryotes and archaea and, the C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p

Probab=87.95  E-value=0.13  Score=36.77  Aligned_cols=32  Identities=28%  Similarity=0.463  Sum_probs=28.3

Q ss_pred             eeeeeeeecccc-cCCcchHHHHhhccccccCc
Q psy5461          27 LCARAFKVVHDK-HRGAVTFFRIYSGAFKKNHV   58 (221)
Q Consensus        27 ~~~~vfk~~~d~-~~g~l~~~~l~~~~~~~~~~   58 (221)
                      +++++||+..|+ +.+.+++.|+++|+++....
T Consensus         1 ~v~~v~Ki~~~~~~~g~la~~RV~sGtl~~g~~   33 (93)
T cd03700           1 LVMYVTKMVPTPDKGGFIAFGRVFSGTIRKGQK   33 (93)
T ss_pred             CeEEEEeCeECCCCCEEEEEEEEeeCeEeCCCE
Confidence            478999999999 88999999999999987643

During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p.

>cd00879 Sar1 Sar1 subfamily

Probab=87.94  E-value=1.1  Score=35.55  Aligned_cols=57  Identities=16%  Similarity=0.026  Sum_probs=38.4

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccc---------------cccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAF---------------KKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~---------------~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+..   ..+....+.....               .....+++..||++|.||+++++.|..++
T Consensus       119 ~~~pvivv~NK~Dl~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~e~~~~l~~~~  190 (190)
T cd00879         119 ANVPFLILGNKIDLP---GAVSEEELRQALGLYGTTTGKGVSLKVSGIRPIEVFMCSVVKRQGYGEAFRWLSQYL  190 (190)
T ss_pred             cCCCEEEEEeCCCCC---CCcCHHHHHHHhCcccccccccccccccCceeEEEEEeEecCCCChHHHHHHHHhhC
Confidence            357899999995432   1333444443321               11335789999999999999999987653

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

>cd04153 Arl5_Arl8 Arl5/Arl8 subfamily

Probab=87.81  E-value=1.3  Score=34.77  Aligned_cols=54  Identities=17%  Similarity=0.048  Sum_probs=35.4

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhcc----ccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      +.|++..++|.+...   ......+.+..    .+...+|++..||++|.||+++++.|..
T Consensus       116 ~~p~viv~NK~Dl~~---~~~~~~i~~~l~~~~~~~~~~~~~~~SA~~g~gi~e~~~~l~~  173 (174)
T cd04153         116 KAVLLVLANKQDLKG---AMTPAEISESLGLTSIRDHTWHIQGCCALTGEGLPEGLDWIAS  173 (174)
T ss_pred             CCCEEEEEECCCCCC---CCCHHHHHHHhCcccccCCceEEEecccCCCCCHHHHHHHHhc
Confidence            568899999965322   22222322221    1223468999999999999999998864

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.

>cd04113 Rab4 Rab4 subfamily

Probab=87.76  E-value=1.1  Score=34.34  Aligned_cols=57  Identities=14%  Similarity=-0.041  Sum_probs=39.1

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      ++-|++...+|.+... ..++....+..-..+. ..+++..||+++.|+.++++.++..
T Consensus       104 ~~~~iivv~nK~D~~~-~~~~~~~~~~~~~~~~-~~~~~~~Sa~~~~~i~~~~~~~~~~  160 (161)
T cd04113         104 PNIVVILVGNKSDLAD-QREVTFLEASRFAQEN-GLLFLETSALTGENVEEAFLKCARS  160 (161)
T ss_pred             CCCeEEEEEEchhcch-hccCCHHHHHHHHHHc-CCEEEEEECCCCCCHHHHHHHHHHh
Confidence            4668888889965332 2344444443333333 3789999999999999999998764

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

>cd04155 Arl3 Arl3 subfamily

Probab=87.74  E-value=0.86  Score=35.36  Aligned_cols=57  Identities=12%  Similarity=0.000  Sum_probs=33.6

Q ss_pred             CCceeeeeeeecccccC-CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          24 GDSLCARAFKVVHDKHR-GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~-g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      +-|++..++|.+..... .+.....+.-........+++..||++|.|++++++.|++
T Consensus       115 ~~p~ivv~nK~D~~~~~~~~~i~~~l~~~~~~~~~~~~~~~Sa~~~~gi~~~~~~l~~  172 (173)
T cd04155         115 GVPVLVFANKQDLATAAPAEEIAEALNLHDLRDRTWHIQACSAKTGEGLQEGMNWVCK  172 (173)
T ss_pred             CCCEEEEEECCCCccCCCHHHHHHHcCCcccCCCeEEEEEeECCCCCCHHHHHHHHhc
Confidence            46788888896432211 1111111111111222456888999999999999998864

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

>cd01859 MJ1464 MJ1464

Probab=87.62  E-value=0.63  Score=35.99  Aligned_cols=58  Identities=16%  Similarity=0.138  Sum_probs=38.9

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|++..++|++.-+. ...  .... ...+....|+++.||+++.|+++|++.|.+.+|.
T Consensus        40 ~~~p~iiv~NK~Dl~~~-~~~--~~~~-~~~~~~~~~~~~iSa~~~~gi~~L~~~l~~~~~~   97 (156)
T cd01859          40 LGKKLLIVLNKADLVPK-EVL--EKWK-SIKESEGIPVVYVSAKERLGTKILRRTIKELAKI   97 (156)
T ss_pred             CCCcEEEEEEhHHhCCH-HHH--HHHH-HHHHhCCCcEEEEEccccccHHHHHHHHHHHHhh
Confidence            46788999999653111 011  1111 1112234689999999999999999999999875

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.

>TIGR02729 Obg_CgtA Obg family GTPase CgtA

Probab=87.48  E-value=0.82  Score=40.51  Aligned_cols=56  Identities=16%  Similarity=0.105  Sum_probs=37.7

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..|++..++|++....   .....+.+...+....+++..||+++.||++|++.|.+.+
T Consensus       273 ~kp~IIV~NK~DL~~~---~~~~~~~~~l~~~~~~~vi~iSAktg~GI~eL~~~I~~~l  328 (329)
T TIGR02729       273 EKPRIVVLNKIDLLDE---EELAELLKELKKALGKPVFPISALTGEGLDELLYALAELL  328 (329)
T ss_pred             cCCEEEEEeCccCCCh---HHHHHHHHHHHHHcCCcEEEEEccCCcCHHHHHHHHHHHh
Confidence            5688888999653221   1123333333222235799999999999999999998765

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.

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

Probab=87.36  E-value=0.16  Score=47.08  Aligned_cols=64  Identities=30%  Similarity=0.413  Sum_probs=53.6

Q ss_pred             ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHH
Q psy5461           1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQK   73 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~   73 (221)
                      |+.|++..|.|.        ++.+.|+-+.+|+.+.|+..|-+.+.|+..|..+.++. |.+.|..+...|.+
T Consensus       178 Le~Iv~~iP~P~--------g~~~~pLkALifDS~yD~Y~GVv~~vRi~dG~ik~gdk-i~~m~tg~~y~V~e  241 (603)
T COG0481         178 LEAIVEKIPPPK--------GDPDAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKGDK-IRMMSTGKEYEVDE  241 (603)
T ss_pred             HHHHHhhCCCCC--------CCCCCcceEEEEeccccccceEEEEEEEeeceecCCCE-EEEEecCCEEEEEE
Confidence            467888899984        46789999999999999999999999999999998776 77777776665543

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

Probab=87.23  E-value=1.7  Score=33.42  Aligned_cols=56  Identities=14%  Similarity=0.134  Sum_probs=39.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +..++++.|-|++.-+ ..+++  +.++-..+.+-.|||..|+..+.||++|+|.+...
T Consensus        89 ~~k~vIgvVTK~DLae-d~dI~--~~~~~L~eaGa~~IF~~s~~d~~gv~~l~~~L~~~  144 (148)
T COG4917          89 GVKKVIGVVTKADLAE-DADIS--LVKRWLREAGAEPIFETSAVDNQGVEELVDYLASL  144 (148)
T ss_pred             cccceEEEEecccccc-hHhHH--HHHHHHHHcCCcceEEEeccCcccHHHHHHHHHhh
Confidence            3456899999964322 22333  33344444457789999999999999999998754

>smart00175 RAB Rab subfamily of small GTPases

Probab=87.22  E-value=0.7  Score=35.31  Aligned_cols=59  Identities=12%  Similarity=0.040  Sum_probs=39.8

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+-|++..++|.+..+. -++..+...+-. +...++++..||.+|.|+.++++.|.+.++
T Consensus       104 ~~~pivvv~nK~D~~~~-~~~~~~~~~~~~-~~~~~~~~e~Sa~~~~~i~~l~~~i~~~~~  162 (164)
T smart00175      104 PNVVIMLVGNKSDLEDQ-RQVSREEAEAFA-EEHGLPFFETSAKTNTNVEEAFEELAREIL  162 (164)
T ss_pred             CCCeEEEEEEchhcccc-cCCCHHHHHHHH-HHcCCeEEEEeCCCCCCHHHHHHHHHHHHh
Confidence            45799999999654331 122222222222 233468999999999999999999988653

Rab GTPases are implicated in vesicle trafficking.

>PRK00089 era GTPase Era; Reviewed

Probab=87.16  E-value=1.3  Score=38.13  Aligned_cols=59  Identities=17%  Similarity=0.164  Sum_probs=38.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhcc-ccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGA-FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~-~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.|++..++|++.-....+  .....+.. ......+++..||+++.|+++|++.|..++|.
T Consensus       113 ~~pvilVlNKiDl~~~~~~--l~~~~~~l~~~~~~~~i~~iSA~~~~gv~~L~~~L~~~l~~  172 (292)
T PRK00089        113 KTPVILVLNKIDLVKDKEE--LLPLLEELSELMDFAEIVPISALKGDNVDELLDVIAKYLPE  172 (292)
T ss_pred             CCCEEEEEECCcCCCCHHH--HHHHHHHHHhhCCCCeEEEecCCCCCCHHHHHHHHHHhCCC
Confidence            4688888899643211111  11111211 11235678999999999999999999999975

>cd01898 Obg Obg subfamily

Probab=87.15  E-value=1.2  Score=34.34  Aligned_cols=55  Identities=15%  Similarity=0.134  Sum_probs=34.9

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccc-cCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKK-NHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~-~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      ..|++...+|++..+. ... ...+.. .... ...|++..||+++.|++++++.|.+.
T Consensus       114 ~~p~ivv~NK~Dl~~~-~~~-~~~~~~-~~~~~~~~~~~~~Sa~~~~gi~~l~~~i~~~  169 (170)
T cd01898         114 EKPRIVVLNKIDLLDE-EEL-FELLKE-LLKELWGKPVFPISALTGEGLDELLRKLAEL  169 (170)
T ss_pred             ccccEEEEEchhcCCc-hhh-HHHHHH-HHhhCCCCCEEEEecCCCCCHHHHHHHHHhh
Confidence            4678888899653221 111 111111 1122 24678999999999999999998764

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.

>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA

Probab=87.05  E-value=0.71  Score=41.90  Aligned_cols=59  Identities=24%  Similarity=0.158  Sum_probs=39.1

Q ss_pred             CCCceeeeeeeecccccCCcchHHHH----hhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRI----YSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l----~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.+++..+||.+...  .+.....+    .+....-...|+++.||++|.|+.++++.+....-
T Consensus       282 ~~~~iiiv~NK~Dl~~--~~~~~~~~~~~~~~~~~~~~~~~vi~~SA~~g~~v~~l~~~i~~~~~  344 (429)
T TIGR03594       282 AGKALVIVVNKWDLVK--DEKTREEFKKELRRKLPFLDFAPIVFISALTGQGVDKLLDAIDEVYE  344 (429)
T ss_pred             cCCcEEEEEECcccCC--CHHHHHHHHHHHHHhcccCCCCceEEEeCCCCCCHHHHHHHHHHHHH
Confidence            4678999999965321  12222222    22222223579999999999999999999887653

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.

>cd04152 Arl4_Arl7 Arl4/Arl7 subfamily

Probab=87.05  E-value=1.2  Score=35.40  Aligned_cols=58  Identities=12%  Similarity=0.017  Sum_probs=37.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhc-----cccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG-----AFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~-----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++..++|.+...   ......+...     .......|++..||++|.|+++|++.|.+.+-
T Consensus       108 ~~~p~iiv~NK~D~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~~~gi~~l~~~l~~~l~  170 (183)
T cd04152         108 QGVPVLVLANKQDLPN---ALSVSEVEKLLALHELSASTPWHVQPACAIIGEGLQEGLEKLYEMIL  170 (183)
T ss_pred             CCCcEEEEEECcCccc---cCCHHHHHHHhCccccCCCCceEEEEeecccCCCHHHHHHHHHHHHH
Confidence            3568899999964322   1222222211     11112357889999999999999999887663

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

>cd04149 Arf6 Arf6 subfamily

Probab=86.95  E-value=1.1  Score=35.24  Aligned_cols=54  Identities=13%  Similarity=-0.034  Sum_probs=35.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhcc----ccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      +.|++...+|.+...   ......+.+..    .++...+++..||++|.||+++++.|.+
T Consensus       110 ~~piilv~NK~Dl~~---~~~~~~i~~~~~~~~~~~~~~~~~~~SAk~g~gv~~~~~~l~~  167 (168)
T cd04149         110 DALLLVFANKQDLPD---AMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLSS  167 (168)
T ss_pred             CCcEEEEEECcCCcc---CCCHHHHHHHcCCCccCCCcEEEEEeeCCCCCChHHHHHHHhc
Confidence            568999999955322   22333333322    1223457888999999999999998864

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

>PRK00093 GTP-binding protein Der; Reviewed

Probab=86.84  E-value=0.74  Score=41.96  Aligned_cols=60  Identities=18%  Similarity=0.067  Sum_probs=39.5

Q ss_pred             CCCceeeeeeeeccc-ccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHD-KHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d-~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.+++..++|.+.. +...+.....+..........|+++.||++|.||.+|++.+....
T Consensus       283 ~~~~~ivv~NK~Dl~~~~~~~~~~~~~~~~l~~~~~~~i~~~SA~~~~gv~~l~~~i~~~~  343 (435)
T PRK00093        283 AGRALVIVVNKWDLVDEKTMEEFKKELRRRLPFLDYAPIVFISALTGQGVDKLLEAIDEAY  343 (435)
T ss_pred             cCCcEEEEEECccCCCHHHHHHHHHHHHHhcccccCCCEEEEeCCCCCCHHHHHHHHHHHH
Confidence            467899999996532 211122223333333233457999999999999999999987643

>PRK04213 GTP-binding protein; Provisional

Probab=86.82  E-value=1.2  Score=35.76  Aligned_cols=60  Identities=20%  Similarity=0.061  Sum_probs=38.6

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcccc-----ccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFK-----KNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~-----~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|++..++|++..... +-....+.+...-     .-..|++..||++| ||+++++.|.+.++.
T Consensus       129 ~~~p~iiv~NK~Dl~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~g-gi~~l~~~l~~~~~~  193 (201)
T PRK04213        129 LGIPPIVAVNKMDKIKNR-DEVLDEIAERLGLYPPWRQWQDIIAPISAKKG-GIEELKEAIRKRLHE  193 (201)
T ss_pred             cCCCeEEEEECccccCcH-HHHHHHHHHHhcCCccccccCCcEEEEecccC-CHHHHHHHHHHhhcC
Confidence            467899999996542211 1122333322110     11237899999999 999999999998754

>cd04159 Arl10_like Arl10-like subfamily

Probab=86.82  E-value=1.1  Score=33.47  Aligned_cols=56  Identities=13%  Similarity=0.062  Sum_probs=34.2

Q ss_pred             CCceeeeeeeecccccCCcch--HHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVT--FFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~--~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      +-|++...+|.+.... ....  ...+..........+++..|+++|.|+.++++.|..
T Consensus       101 ~~p~iiv~nK~D~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~  158 (159)
T cd04159         101 GIPLLVLGNKNDLPGA-LSVDELIEQMNLKSITDREVSCYSISCKEKTNIDIVLDWLIK  158 (159)
T ss_pred             CCCEEEEEeCccccCC-cCHHHHHHHhCcccccCCceEEEEEEeccCCChHHHHHHHhh
Confidence            4578888888542221 1111  111111112233468999999999999999998864

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

>cd01861 Rab6 Rab6 subfamily

Probab=86.69  E-value=1.1  Score=34.23  Aligned_cols=56  Identities=13%  Similarity=-0.048  Sum_probs=38.0

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +.|++...+|++.... .+............ ...+++..||+++.|++++++.|.+.
T Consensus       105 ~~~iilv~nK~D~~~~-~~~~~~~~~~~~~~-~~~~~~~~Sa~~~~~v~~l~~~i~~~  160 (161)
T cd01861         105 DVIIVLVGNKTDLSDK-RQVSTEEGEKKAKE-LNAMFIETSAKAGHNVKELFRKIASA  160 (161)
T ss_pred             CCEEEEEEEChhcccc-CccCHHHHHHHHHH-hCCEEEEEeCCCCCCHHHHHHHHHHh
Confidence            4789999999665322 23333332222222 23778999999999999999999865

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

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

Probab=86.63  E-value=1.5  Score=33.35  Aligned_cols=55  Identities=13%  Similarity=-0.023  Sum_probs=37.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcc----ccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      .+.|++...+|.+.....   ..+.+.+..    ......|++..||++|.|++++++.|..
T Consensus        99 ~~~piiiv~nK~D~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~~~~~l~~  157 (158)
T cd00878          99 KGVPLLIFANKQDLPGAL---SVSELIEKLGLEKILGRRWHIQPCSAVTGDGLDEGLDWLLQ  157 (158)
T ss_pred             CCCcEEEEeeccCCcccc---CHHHHHHhhChhhccCCcEEEEEeeCCCCCCHHHHHHHHhh
Confidence            467888889996543321   222333322    1234678999999999999999998864

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

>cd04142 RRP22 RRP22 subfamily

Probab=86.57  E-value=1.3  Score=35.98  Aligned_cols=61  Identities=11%  Similarity=-0.049  Sum_probs=39.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +-|++...+|.+.... .......+.....+....|++..||++|.||++|++.+...+-..
T Consensus       116 ~~piiivgNK~Dl~~~-~~~~~~~~~~~~~~~~~~~~~e~Sak~g~~v~~lf~~i~~~~~~~  176 (198)
T cd04142         116 EPPIVVVGNKRDQQRH-RFAPRHVLSVLVRKSWKCGYLECSAKYNWHILLLFKELLISATTR  176 (198)
T ss_pred             CCCEEEEEECcccccc-ccccHHHHHHHHHHhcCCcEEEecCCCCCCHHHHHHHHHHHhhcc
Confidence            4688899999765332 122222222211122346899999999999999999998766443

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.

>cd01868 Rab11_like Rab11-like

Probab=86.33  E-value=1.1  Score=34.52  Aligned_cols=57  Identities=14%  Similarity=0.005  Sum_probs=38.0

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++...+|.+.... -++......+.... ...+++..||++|.|++++++.|.+.+
T Consensus       108 ~~pi~vv~nK~Dl~~~-~~~~~~~~~~~~~~-~~~~~~~~Sa~~~~~v~~l~~~l~~~i  164 (165)
T cd01868         108 NIVIMLVGNKSDLRHL-RAVPTEEAKAFAEK-NGLSFIETSALDGTNVEEAFKQLLTEI  164 (165)
T ss_pred             CCeEEEEEECcccccc-ccCCHHHHHHHHHH-cCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            4688888999654332 22333333332222 246799999999999999999998754

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

>PRK12299 obgE GTPase CgtA; Reviewed

Probab=86.31  E-value=0.9  Score=40.39  Aligned_cols=59  Identities=15%  Similarity=0.044  Sum_probs=38.5

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.|++..++|++.... .+.....+.. ..+....|++..||+++.||++|++.|.+.++.
T Consensus       271 ~kp~IIV~NKiDL~~~-~~~~~~~~~~-~~~~~~~~i~~iSAktg~GI~eL~~~L~~~l~~  329 (335)
T PRK12299        271 DKPRILVLNKIDLLDE-EEEREKRAAL-ELAALGGPVFLISAVTGEGLDELLRALWELLEE  329 (335)
T ss_pred             cCCeEEEEECcccCCc-hhHHHHHHHH-HHHhcCCCEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            5688999999754221 1122111111 112223679999999999999999999988754

>cd04134 Rho3 Rho3 subfamily

Probab=85.97  E-value=1.3  Score=35.34  Aligned_cols=64  Identities=19%  Similarity=0.127  Sum_probs=41.4

Q ss_pred             CCceeeeeeeecccccCC-----------cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRG-----------AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTE   87 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g-----------~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~   87 (221)
                      +-|++...+|.+......           .+..+...+...+....+++..||++|.||+++++.|...+-.|..
T Consensus       104 ~~piilvgNK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~e~SAk~~~~v~e~f~~l~~~~~~~~~  178 (189)
T cd04134         104 GVKLVLVALKCDLREARNERDDLQRYGKHTISYEEGLAVAKRINALRYLECSAKLNRGVNEAFTEAARVALNVRP  178 (189)
T ss_pred             CCCEEEEEEChhhccChhhHHHHhhccCCCCCHHHHHHHHHHcCCCEEEEccCCcCCCHHHHHHHHHHHHhcccc
Confidence            567888888865332211           1222222222222234678999999999999999999988876653

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

>COG1159 Era GTPase [General function prediction only]

Probab=85.97  E-value=1.4  Score=38.42  Aligned_cols=59  Identities=15%  Similarity=0.129  Sum_probs=39.2

Q ss_pred             CceeeeeeeecccccCCc-chHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          25 DSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~~g~-l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      -|++..+||++.-...-. +.....+  ........++..||++|.|++.|++.+..++|.-
T Consensus       115 ~pvil~iNKID~~~~~~~l~~~~~~~--~~~~~f~~ivpiSA~~g~n~~~L~~~i~~~Lpeg  174 (298)
T COG1159         115 TPVILVVNKIDKVKPKTVLLKLIAFL--KKLLPFKEIVPISALKGDNVDTLLEIIKEYLPEG  174 (298)
T ss_pred             CCeEEEEEccccCCcHHHHHHHHHHH--HhhCCcceEEEeeccccCCHHHHHHHHHHhCCCC
Confidence            488899999652211111 2222222  2223344688899999999999999999999863

>cd04135 Tc10 TC10 subfamily

Probab=85.84  E-value=1.4  Score=34.17  Aligned_cols=59  Identities=10%  Similarity=-0.079  Sum_probs=36.0

Q ss_pred             CCCceeeeeeeecccccC-----------CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHR-----------GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~-----------g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      ++.|++...+|.+.....           -+++.+....-..+-...+++..||++|.||+++++.+...
T Consensus       103 ~~~piivv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~e~Sa~~~~gi~~~f~~~~~~  172 (174)
T cd04135         103 PNVPYLLVGTQIDLRDDPKTLARLNDMKEKPVTVEQGQKLAKEIGAHCYVECSALTQKGLKTVFDEAILA  172 (174)
T ss_pred             CCCCEEEEeEchhhhcChhhHHHHhhccCCCCCHHHHHHHHHHcCCCEEEEecCCcCCCHHHHHHHHHHH
Confidence            456788888886421110           12332222222222233478899999999999999998764

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

>cd01894 EngA1 EngA1 subfamily

Probab=85.74  E-value=0.91  Score=34.22  Aligned_cols=54  Identities=20%  Similarity=0.146  Sum_probs=35.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ...|++..++|++....  ......+.    +....+++..|+++|.|++++++.|.+.+
T Consensus       104 ~~~piiiv~nK~D~~~~--~~~~~~~~----~~~~~~~~~~Sa~~~~gv~~l~~~l~~~~  157 (157)
T cd01894         104 SKKPVILVVNKVDNIKE--EDEAAEFY----SLGFGEPIPISAEHGRGIGDLLDAILELL  157 (157)
T ss_pred             cCCCEEEEEECcccCCh--HHHHHHHH----hcCCCCeEEEecccCCCHHHHHHHHHhhC
Confidence            35788888999643322  11111211    12233688999999999999999998653

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.

>cd04176 Rap2 Rap2 subgroup

Probab=85.67  E-value=1.3  Score=33.88  Aligned_cols=58  Identities=16%  Similarity=0.024  Sum_probs=36.4

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++.-.+|.+.... ..+...... ...+....|++..||++|.|+.++++.+...+
T Consensus       105 ~~~piviv~nK~Dl~~~-~~~~~~~~~-~~~~~~~~~~~~~Sa~~~~~v~~l~~~l~~~l  162 (163)
T cd04176         105 EKVPIILVGNKVDLESE-REVSSAEGR-ALAEEWGCPFMETSAKSKTMVNELFAEIVRQM  162 (163)
T ss_pred             CCCCEEEEEECccchhc-CccCHHHHH-HHHHHhCCEEEEecCCCCCCHHHHHHHHHHhc
Confidence            45688888899653222 122221111 11122235889999999999999999988653

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

>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily

Probab=85.67  E-value=1  Score=34.70  Aligned_cols=57  Identities=12%  Similarity=0.032  Sum_probs=37.7

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++...+|.+.... -++.......-. +....|++..||++|.||.++++.|.+.+
T Consensus       107 ~~~~iiv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~~v~~~~~~i~~~~  163 (166)
T cd01869         107 NVNKLLVGNKCDLTDK-RVVDYSEAQEFA-DELGIPFLETSAKNATNVEQAFMTMAREI  163 (166)
T ss_pred             CCcEEEEEEChhcccc-cCCCHHHHHHHH-HHcCCeEEEEECCCCcCHHHHHHHHHHHH
Confidence            4578888888553222 233333333322 22346899999999999999999988643

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

>cd00154 Rab Rab family

Probab=85.65  E-value=1.6  Score=32.61  Aligned_cols=55  Identities=13%  Similarity=0.015  Sum_probs=38.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHH
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIV   79 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~   79 (221)
                      .+.|++..++|.+... ..+...+.+.+-.. ....|++..||+++.|+.++++.|.
T Consensus       104 ~~~p~ivv~nK~D~~~-~~~~~~~~~~~~~~-~~~~~~~~~sa~~~~~i~~~~~~i~  158 (159)
T cd00154         104 ENIPIILVGNKIDLED-QRQVSTEEAQQFAK-ENGLLFFETSAKTGENVEELFQSLA  158 (159)
T ss_pred             CCCcEEEEEEcccccc-cccccHHHHHHHHH-HcCCeEEEEecCCCCCHHHHHHHHh
Confidence            3578999999965421 12333444443222 2467899999999999999999875

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

>cd04114 Rab30 Rab30 subfamily

Probab=85.57  E-value=1.3  Score=34.17  Aligned_cols=56  Identities=13%  Similarity=-0.100  Sum_probs=36.0

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +.+.+...+|++.... -++... +.+...+....+++..||++|.|++++++.|...
T Consensus       112 ~~~~i~v~NK~D~~~~-~~i~~~-~~~~~~~~~~~~~~~~Sa~~~~gv~~l~~~i~~~  167 (169)
T cd04114         112 KVITILVGNKIDLAER-REVSQQ-RAEEFSDAQDMYYLETSAKESDNVEKLFLDLACR  167 (169)
T ss_pred             CCeEEEEEECcccccc-cccCHH-HHHHHHHHcCCeEEEeeCCCCCCHHHHHHHHHHH
Confidence            4567788888664322 122222 1122222233678999999999999999999864

Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.

>PRK15494 era GTPase Era; Provisional

Probab=85.49  E-value=1.7  Score=38.57  Aligned_cols=57  Identities=9%  Similarity=-0.090  Sum_probs=38.2

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhcccc-ccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFK-KNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~-~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.+.+..++|++....  .  ...+.+.... ....+++..||++|.|+++|++.|..++|.
T Consensus       160 ~~p~IlViNKiDl~~~--~--~~~~~~~l~~~~~~~~i~~iSAktg~gv~eL~~~L~~~l~~  217 (339)
T PRK15494        160 NIVPIFLLNKIDIESK--Y--LNDIKAFLTENHPDSLLFPISALSGKNIDGLLEYITSKAKI  217 (339)
T ss_pred             CCCEEEEEEhhcCccc--c--HHHHHHHHHhcCCCcEEEEEeccCccCHHHHHHHHHHhCCC
Confidence            4566778899653221  1  2222222222 223578999999999999999999999975

>cd01870 RhoA_like RhoA-like subfamily

Probab=85.45  E-value=1.8  Score=33.55  Aligned_cols=26  Identities=12%  Similarity=0.115  Sum_probs=22.6

Q ss_pred             CceeEecCCCccccHHHHHHHHHhhC
Q psy5461          57 HVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        57 ~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..+++..||++|.||+++++.|...+
T Consensus       149 ~~~~~~~Sa~~~~~v~~lf~~l~~~~  174 (175)
T cd01870         149 AFGYMECSAKTKEGVREVFEMATRAA  174 (175)
T ss_pred             CcEEEEeccccCcCHHHHHHHHHHHh
Confidence            45789999999999999999998643

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

>cd01878 HflX HflX subfamily

Probab=85.44  E-value=1.3  Score=35.61  Aligned_cols=51  Identities=12%  Similarity=0.053  Sum_probs=35.0

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +.+++..++|++..+.  ....     ........|++..||++|.|+.++++.|...
T Consensus       153 ~~~viiV~NK~Dl~~~--~~~~-----~~~~~~~~~~~~~Sa~~~~gi~~l~~~L~~~  203 (204)
T cd01878         153 DIPMILVLNKIDLLDD--EELE-----ERLEAGRPDAVFISAKTGEGLDELLEAIEEL  203 (204)
T ss_pred             CCCEEEEEEccccCCh--HHHH-----HHhhcCCCceEEEEcCCCCCHHHHHHHHHhh
Confidence            4578888888543221  1111     1223446689999999999999999998765

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.

>PRK03003 GTP-binding protein Der; Reviewed

Probab=85.15  E-value=1  Score=41.83  Aligned_cols=62  Identities=21%  Similarity=0.027  Sum_probs=41.2

Q ss_pred             CCCceeeeeeeecccc-cCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDK-HRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.+++..++|.+... .........+.+........|+++.||++|.||++|++.|...+..
T Consensus       321 ~~~piIiV~NK~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~~~SAk~g~gv~~lf~~i~~~~~~  383 (472)
T PRK03003        321 AGRALVLAFNKWDLVDEDRRYYLEREIDRELAQVPWAPRVNISAKTGRAVDKLVPALETALES  383 (472)
T ss_pred             cCCCEEEEEECcccCChhHHHHHHHHHHHhcccCCCCCEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4678999999965322 1111122333333333345799999999999999999999886653

>PTZ00369 Ras-like protein; Provisional

Probab=85.13  E-value=1.2  Score=35.58  Aligned_cols=59  Identities=15%  Similarity=0.045  Sum_probs=37.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +-|++...+|.+.... -++....... ..+....|++..||++|.||.++++.|.+.+..
T Consensus       110 ~~piiiv~nK~Dl~~~-~~i~~~~~~~-~~~~~~~~~~e~Sak~~~gi~~~~~~l~~~l~~  168 (189)
T PTZ00369        110 RVPMILVGNKCDLDSE-RQVSTGEGQE-LAKSFGIPFLETSAKQRVNVDEAFYELVREIRK  168 (189)
T ss_pred             CCCEEEEEECcccccc-cccCHHHHHH-HHHHhCCEEEEeeCCCCCCHHHHHHHHHHHHHH
Confidence            5588888899654221 1222222111 112223689999999999999999999877643

>TIGR00101 ureG urease accessory protein UreG

Probab=84.92  E-value=1.4  Score=36.00  Aligned_cols=27  Identities=15%  Similarity=0.224  Sum_probs=23.8

Q ss_pred             cCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          56 NHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ...|++..||++|.|++++++.|.++.
T Consensus       169 ~~~~i~~~Sa~~g~gi~el~~~i~~~~  195 (199)
T TIGR00101       169 GEKPFIFTNLKTKEGLDTVIDWIEHYA  195 (199)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            357899999999999999999998754

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.

>PRK14845 translation initiation factor IF-2; Provisional

Probab=84.82  E-value=6.4  Score=40.35  Aligned_cols=71  Identities=14%  Similarity=0.224  Sum_probs=51.5

Q ss_pred             ceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc--CC---CCCccCcEEecCCCCCC
Q psy5461         115 GAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT--GL---KRERGKDKRTRVIPKPT  189 (221)
Q Consensus       115 G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~--gl---~~~~~Gdtl~~~~~~p~  189 (221)
                      +.++=++|..|++++|..|.-. .+  ..++.|..++ .....++++.+|+-|+|.  |.   .++..||++....+...
T Consensus       938 ~~IaG~~V~~G~i~~~~~l~r~-~~--~~iG~i~Slk-~~k~~V~ev~~G~ecgI~i~~~~~gr~~~~gD~l~~~i~~~~ 1013 (1049)
T PRK14845        938 PAIVGVEVLEGTLRVGVTLIKE-DG--MKVGTVRSIK-DRGENVKEAKAGKAVAIAIEGAILGRHVDEGETLYVDVPESH 1013 (1049)
T ss_pred             CeEEEEEEeeCEEecCcEEEec-CC--EEEEEEchHh-ccCccccEeCCCCEEEEEEecccccCCCCCCCEEEEecCHHH
Confidence            7899999999999999877531 22  3345555554 344689999999999763  43   27889999988755543

>cd04101 RabL4 RabL4 (Rab-like4) subfamily

Probab=84.81  E-value=1.6  Score=33.43  Aligned_cols=56  Identities=11%  Similarity=0.045  Sum_probs=36.0

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +.|++...+|.+..+. .++.......- ......|++..||++|.|++++++.+.+.
T Consensus       107 ~~p~ilv~nK~Dl~~~-~~~~~~~~~~~-~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~  162 (164)
T cd04101         107 HMPGVLVGNKMDLADK-AEVTDAQAQAF-AQANQLKFFKTSALRGVGYEEPFESLARA  162 (164)
T ss_pred             CCCEEEEEECcccccc-cCCCHHHHHHH-HHHcCCeEEEEeCCCCCChHHHHHHHHHH
Confidence            4678888889654222 23333222111 12223678999999999999999998764

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.

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

Probab=84.76  E-value=1.6  Score=32.80  Aligned_cols=51  Identities=12%  Similarity=0.063  Sum_probs=36.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.+++..++|++.-.....         .......|++..||+++.|+++|++.|..++
T Consensus       106 ~~~~vi~v~nK~D~~~~~~~---------~~~~~~~~~~~~Sa~~~~~v~~l~~~l~~~~  156 (157)
T cd04164         106 ADKPIIVVLNKSDLLPDSEL---------LSLLAGKPIIAISAKTGEGLDELKEALLELA  156 (157)
T ss_pred             cCCCEEEEEEchhcCCcccc---------ccccCCCceEEEECCCCCCHHHHHHHHHHhh
Confidence            46788888888642221111         2344467899999999999999999988653

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.

>cd04124 RabL2 RabL2 subfamily

Probab=84.56  E-value=1.3  Score=34.21  Aligned_cols=55  Identities=20%  Similarity=0.155  Sum_probs=36.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+.++.   ...+ ... ..+....|++..||++|.|++++++.+...+.
T Consensus       104 ~~p~ivv~nK~Dl~~~---~~~~-~~~-~~~~~~~~~~~~Sa~~~~gv~~l~~~l~~~~~  158 (161)
T cd04124         104 EIPCIVVANKIDLDPS---VTQK-KFN-FAEKHNLPLYYVSAADGTNVVKLFQDAIKLAV  158 (161)
T ss_pred             CCcEEEEEECccCchh---HHHH-HHH-HHHHcCCeEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            5688889999654321   1111 111 11222468999999999999999999987654

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

>cd04127 Rab27A Rab27a subfamily

Probab=84.48  E-value=1.1  Score=35.10  Aligned_cols=57  Identities=14%  Similarity=0.157  Sum_probs=36.5

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++.-.+|.+.... -++....... ..+...+|++..||++|.|++++++.|.+.+
T Consensus       120 ~~piiiv~nK~Dl~~~-~~v~~~~~~~-~~~~~~~~~~e~Sak~~~~v~~l~~~l~~~~  176 (180)
T cd04127         120 NPDIVLCGNKADLEDQ-RQVSEEQAKA-LADKYGIPYFETSAATGTNVEKAVERLLDLV  176 (180)
T ss_pred             CCcEEEEEeCccchhc-CccCHHHHHH-HHHHcCCeEEEEeCCCCCCHHHHHHHHHHHH
Confidence            4467777888553222 2333333322 2222246899999999999999999987643

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

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=84.37  E-value=0.78  Score=40.79  Aligned_cols=27  Identities=30%  Similarity=0.416  Sum_probs=25.1

Q ss_pred             ceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          58 VPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        58 ~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .||+..||+++.||++|++.|.+++|.
T Consensus       235 ~pVi~vSA~~g~GIdeL~~~I~~~~~~  261 (332)
T PRK09435        235 PPVLTCSALEGEGIDEIWQAIEDHRAA  261 (332)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            689999999999999999999998764

>COG1160 Predicted GTPases [General function prediction only]

Probab=84.32  E-value=1.1  Score=41.19  Aligned_cols=61  Identities=16%  Similarity=0.121  Sum_probs=43.2

Q ss_pred             CCCCceeeeeeeec-ccc--cCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          22 HFGDSLCARAFKVV-HDK--HRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        22 ~~~~~~~~~vfk~~-~d~--~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +...+++..++|-+ .++  .........+++....-...|+++.||++|.|+..|++++..-.
T Consensus       287 ~~g~~~vIvvNKWDl~~~~~~~~~~~k~~i~~~l~~l~~a~i~~iSA~~~~~i~~l~~~i~~~~  350 (444)
T COG1160         287 EAGRGIVIVVNKWDLVEEDEATMEEFKKKLRRKLPFLDFAPIVFISALTGQGLDKLFEAIKEIY  350 (444)
T ss_pred             HcCCCeEEEEEccccCCchhhHHHHHHHHHHHHhccccCCeEEEEEecCCCChHHHHHHHHHHH
Confidence            35778999999965 333  22233344555544444677999999999999999999987644

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

Probab=84.09  E-value=1.9  Score=33.98  Aligned_cols=56  Identities=11%  Similarity=-0.006  Sum_probs=34.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhh--cc--ccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYS--GA--FKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~--~~--~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +-|++...+|.+....   .....+.+  +.  .....+.++..||++|.||.++++.|.+.+
T Consensus       114 ~~piilv~NK~Dl~~~---~~~~~i~~~~~~~~~~~~~~~~~~~Sa~~g~gv~e~~~~l~~~~  173 (175)
T smart00177      114 DAVILVFANKQDLPDA---MKAAEITEKLGLHSIRDRNWYIQPTCATSGDGLYEGLTWLSNNL  173 (175)
T ss_pred             CCcEEEEEeCcCcccC---CCHHHHHHHhCccccCCCcEEEEEeeCCCCCCHHHHHHHHHHHh
Confidence            4578888899653221   11222222  11  112234466799999999999999987653

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).

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

Probab=84.08  E-value=1.5  Score=33.76  Aligned_cols=56  Identities=14%  Similarity=0.076  Sum_probs=35.7

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      ..|++..++|++..... ......... .......+++..||+++.|+++|++.+...
T Consensus       120 ~~p~ivv~NK~Dl~~~~-~~~~~~~~~-~~~~~~~~~~~~Sa~~~~gl~~l~~~l~~~  175 (176)
T cd01881         120 AKPVIYVLNKIDLDDAE-ELEEELVRE-LALEEGAEVVPISAKTEEGLDELIRAIYEL  175 (176)
T ss_pred             hCCeEEEEEchhcCchh-HHHHHHHHH-HhcCCCCCEEEEehhhhcCHHHHHHHHHhh
Confidence            56888888996543221 111111111 122234678999999999999999998764

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

>cd04110 Rab35 Rab35 subfamily

Probab=84.08  E-value=1.3  Score=35.83  Aligned_cols=57  Identities=16%  Similarity=0.145  Sum_probs=37.3

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +-|++...+|.+..+. ..+......+-. +....+++..||++|.||.++++.|...+
T Consensus       110 ~~piivVgNK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~e~Sa~~~~gi~~lf~~l~~~~  166 (199)
T cd04110         110 DVCKVLVGNKNDDPER-KVVETEDAYKFA-GQMGISLFETSAKENINVEEMFNCITELV  166 (199)
T ss_pred             CCCEEEEEECcccccc-cccCHHHHHHHH-HHcCCEEEEEECCCCcCHHHHHHHHHHHH
Confidence            4577788888553322 223333322222 22337899999999999999999998876

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

>PTZ00133 ADP-ribosylation factor; Provisional

Probab=83.96  E-value=1.7  Score=34.63  Aligned_cols=56  Identities=11%  Similarity=0.022  Sum_probs=35.1

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhh--cc--ccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYS--GA--FKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~--~~--~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++...+|.+....   .....+..  +.  .+...++++..||++|.||+++++.|.+.+
T Consensus       118 ~~piilv~NK~Dl~~~---~~~~~i~~~l~~~~~~~~~~~~~~~Sa~tg~gv~e~~~~l~~~i  177 (182)
T PTZ00133        118 DAVLLVFANKQDLPNA---MSTTEVTEKLGLHSVRQRNWYIQGCCATTAQGLYEGLDWLSANI  177 (182)
T ss_pred             CCCEEEEEeCCCCCCC---CCHHHHHHHhCCCcccCCcEEEEeeeCCCCCCHHHHHHHHHHHH
Confidence            4688888899654221   11122211  11  222235677899999999999999998653

>PLN00223 ADP-ribosylation factor; Provisional

Probab=83.81  E-value=2  Score=34.25  Aligned_cols=56  Identities=13%  Similarity=0.036  Sum_probs=35.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhc--cc--cccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSG--AF--KKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~--~~--~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +-|++...+|.+....   .....+.+.  ..  +.....++.+||++|.||.++++.|.+.+
T Consensus       118 ~~piilv~NK~Dl~~~---~~~~~~~~~l~l~~~~~~~~~~~~~Sa~~g~gv~e~~~~l~~~~  177 (181)
T PLN00223        118 DAVLLVFANKQDLPNA---MNAAEITDKLGLHSLRQRHWYIQSTCATSGEGLYEGLDWLSNNI  177 (181)
T ss_pred             CCCEEEEEECCCCCCC---CCHHHHHHHhCccccCCCceEEEeccCCCCCCHHHHHHHHHHHH
Confidence            4688899999654322   222333321  11  12234566799999999999999997654

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

Probab=83.72  E-value=1.9  Score=33.37  Aligned_cols=60  Identities=15%  Similarity=0.097  Sum_probs=38.2

Q ss_pred             CCCceeeeeeeecccccCC-----------cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRG-----------AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g-----------~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+......           .++.....+...+....+.+..||++|.||+++++.+...+
T Consensus       101 ~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~e~Sa~~~~~v~~lf~~l~~~~  171 (174)
T smart00174      101 PNTPIILVGTKLDLREDKSTLRELSKQKQEPVTYEQGEALAKRIGAVKYLECSALTQEGVREVFEEAIRAA  171 (174)
T ss_pred             CCCCEEEEecChhhhhChhhhhhhhcccCCCccHHHHHHHHHHcCCcEEEEecCCCCCCHHHHHHHHHHHh
Confidence            3678888889965332111           13333322222233345788899999999999999988654

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

>cd04123 Rab21 Rab21 subfamily

Probab=83.69  E-value=1.7  Score=32.87  Aligned_cols=56  Identities=16%  Similarity=0.061  Sum_probs=37.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +.|++...+|.+.... -++....+.+-. +....+++..|+++|.|++++++.+.+.
T Consensus       105 ~~piiiv~nK~D~~~~-~~~~~~~~~~~~-~~~~~~~~~~s~~~~~gi~~~~~~l~~~  160 (162)
T cd04123         105 NISLVIVGNKIDLERQ-RVVSKSEAEEYA-KSVGAKHFETSAKTGKGIEELFLSLAKR  160 (162)
T ss_pred             CCeEEEEEECcccccc-cCCCHHHHHHHH-HHcCCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            5688888999654321 233333333322 2234678999999999999999998764

The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site

>cd04171 SelB SelB subfamily

Probab=83.22  E-value=1.3  Score=33.77  Aligned_cols=55  Identities=11%  Similarity=-0.039  Sum_probs=34.6

Q ss_pred             ceeeeeeeecccccC-CcchHHHHhhccccc--cCceeEecCCCccccHHHHHHHHHh
Q psy5461          26 SLCARAFKVVHDKHR-GAVTFFRIYSGAFKK--NHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        26 ~~~~~vfk~~~d~~~-g~l~~~~l~~~~~~~--~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      +++..++|++..... -+.....+.+.....  ...|++..||++|.|+++|++.+..
T Consensus       106 ~~ilv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~~v~~l~~~l~~  163 (164)
T cd04171         106 RGLVVLTKADLVDEDWLELVEEEIRELLAGTFLADAPIFPVSAVTGEGIEELKEYLDE  163 (164)
T ss_pred             cEEEEEECccccCHHHHHHHHHHHHHHHHhcCcCCCcEEEEeCCCCcCHHHHHHHHhh
Confidence            788999996432210 011222333322221  3478999999999999999998864

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

>PTZ00099 rab6; Provisional

Probab=82.99  E-value=1.4  Score=35.12  Aligned_cols=61  Identities=15%  Similarity=0.018  Sum_probs=38.3

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT   86 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~   86 (221)
                      +-+++...+|++.... -++........... ...+++-.||++|.||.++++.|...+|...
T Consensus        85 ~~piilVgNK~DL~~~-~~v~~~e~~~~~~~-~~~~~~e~SAk~g~nV~~lf~~l~~~l~~~~  145 (176)
T PTZ00099         85 DVIIALVGNKTDLGDL-RKVTYEEGMQKAQE-YNTMFHETSAKAGHNIKVLFKKIAAKLPNLD  145 (176)
T ss_pred             CCeEEEEEECcccccc-cCCCHHHHHHHHHH-cCCEEEEEECCCCCCHHHHHHHHHHHHHhcc
Confidence            3466778888653221 12333222221111 2235778999999999999999999987643

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=82.88  E-value=1.7  Score=35.57  Aligned_cols=55  Identities=7%  Similarity=-0.044  Sum_probs=34.0

Q ss_pred             ceeeeeeeecccccCCcchHHHHhhccc-cccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          26 SLCARAFKVVHDKHRGAVTFFRIYSGAF-KKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        26 ~~~~~vfk~~~d~~~g~l~~~~l~~~~~-~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +.+..++|++..... ......+.+... .....|++..||++|.|++++++.+.++
T Consensus       150 a~iiv~NK~Dl~~~~-~~~~~~~~~~l~~~~~~~~i~~~Sa~~g~gv~~l~~~i~~~  205 (207)
T TIGR00073       150 ADLIVINKADLAEAV-GFDVEKMKADAKKINPEAEIILMSLKTGEGLDEWLEFLEGQ  205 (207)
T ss_pred             CCEEEEEHHHccccc-hhhHHHHHHHHHHhCCCCCEEEEECCCCCCHHHHHHHHHHh
Confidence            557888996532211 111112221111 1134789999999999999999999865

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

>cd00157 Rho Rho (Ras homology) family

Probab=82.86  E-value=2  Score=33.04  Aligned_cols=57  Identities=11%  Similarity=0.019  Sum_probs=36.9

Q ss_pred             CCceeeeeeeecccccCC----------cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          24 GDSLCARAFKVVHDKHRG----------AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g----------~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      ..|++...+|.+.-....          .+......+-.......+++..||++|.|+.++++.|..
T Consensus       104 ~~p~ivv~nK~Dl~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~i~~  170 (171)
T cd00157         104 NVPIILVGTKIDLRDDENTLKKLEKGKEPITPEEGEKLAKEIGAIGYMECSALTQEGVKEVFEEAIR  170 (171)
T ss_pred             CCCEEEEEccHHhhhchhhhhhcccCCCccCHHHHHHHHHHhCCeEEEEeecCCCCCHHHHHHHHhh
Confidence            578888889965322211          222333333222333448999999999999999999875

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

>cd04112 Rab26 Rab26 subfamily

Probab=82.75  E-value=1.4  Score=35.30  Aligned_cols=60  Identities=15%  Similarity=-0.011  Sum_probs=39.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +-|++...+|.+.... .++.......- .+....|++..||++|.|+++|++.|...++..
T Consensus       106 ~~piiiv~NK~Dl~~~-~~~~~~~~~~l-~~~~~~~~~e~Sa~~~~~v~~l~~~l~~~~~~~  165 (191)
T cd04112         106 DVVIMLLGNKADMSGE-RVVKREDGERL-AKEYGVPFMETSAKTGLNVELAFTAVAKELKHR  165 (191)
T ss_pred             CCcEEEEEEcccchhc-cccCHHHHHHH-HHHcCCeEEEEeCCCCCCHHHHHHHHHHHHHHh
Confidence            4588888899654322 12222222221 222346899999999999999999999887653

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

>PRK12298 obgE GTPase CgtA; Reviewed

Probab=82.39  E-value=1.8  Score=39.31  Aligned_cols=59  Identities=14%  Similarity=-0.050  Sum_probs=37.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhcccc-ccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFK-KNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~-~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.|.+..++|++...  .+.....+.+-... +...+++..||+++.||++|++.|.+++|.
T Consensus       275 ~kP~IlVlNKiDl~~--~~el~~~l~~l~~~~~~~~~Vi~ISA~tg~GIdeLl~~I~~~L~~  334 (390)
T PRK12298        275 EKPRWLVFNKIDLLD--EEEAEERAKAIVEALGWEGPVYLISAASGLGVKELCWDLMTFIEE  334 (390)
T ss_pred             CCCEEEEEeCCccCC--hHHHHHHHHHHHHHhCCCCCEEEEECCCCcCHHHHHHHHHHHhhh
Confidence            578888999965321  11111222111111 112368899999999999999999999875

>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA

Probab=82.33  E-value=4.3  Score=36.82  Aligned_cols=58  Identities=24%  Similarity=0.280  Sum_probs=40.6

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT   86 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~   86 (221)
                      .+.|++..++|++...... . ...++    +-+.-+++..||.+|.|+.+|++.+...+|...
T Consensus       106 ~~~piilVvNK~D~~~~~~-~-~~~~~----~lg~~~~~~vSa~~g~gv~~ll~~i~~~l~~~~  163 (429)
T TIGR03594       106 SGKPVILVANKIDGKKEDA-V-AAEFY----SLGFGEPIPISAEHGRGIGDLLDAILELLPEEE  163 (429)
T ss_pred             hCCCEEEEEECccCCcccc-c-HHHHH----hcCCCCeEEEeCCcCCChHHHHHHHHHhcCccc
Confidence            4678999999976433211 1 11222    223446889999999999999999999997743

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.

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

Probab=82.31  E-value=1.3  Score=38.80  Aligned_cols=53  Identities=23%  Similarity=0.176  Sum_probs=37.3

Q ss_pred             eeeeeecccccCCcchHHHHhhcc--------ccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          29 ARAFKVVHDKHRGAVTFFRIYSGA--------FKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        29 ~~vfk~~~d~~~g~l~~~~l~~~~--------~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      -.|||  .|..-.+.++..++.+.        .++-..||+-.||.+|.||++|+++|.++.-
T Consensus       194 ~vINK--aD~~~A~~a~r~l~~al~~~~~~~~~~~W~ppv~~t~A~~g~Gi~~L~~ai~~h~~  254 (323)
T COG1703         194 IVINK--ADRKGAEKAARELRSALDLLREVWRENGWRPPVVTTSALEGEGIDELWDAIEDHRK  254 (323)
T ss_pred             eeEec--cChhhHHHHHHHHHHHHHhhcccccccCCCCceeEeeeccCCCHHHHHHHHHHHHH
Confidence            45777  56544455554444433        2234679999999999999999999998753

>cd04140 ARHI_like ARHI subfamily

Probab=81.98  E-value=2.3  Score=32.82  Aligned_cols=57  Identities=14%  Similarity=0.036  Sum_probs=35.9

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+-|++...+|.+..+. -++.......-..+ ...+++..||++|.||+++++.|.++
T Consensus       107 ~~~piilv~nK~Dl~~~-~~v~~~~~~~~~~~-~~~~~~e~SA~~g~~v~~~f~~l~~~  163 (165)
T cd04140         107 EKIPIMLVGNKCDESHK-REVSSNEGAACATE-WNCAFMETSAKTNHNVQELFQELLNL  163 (165)
T ss_pred             CCCCEEEEEECcccccc-CeecHHHHHHHHHH-hCCcEEEeecCCCCCHHHHHHHHHhc
Confidence            34688888889654321 22333222211111 23578899999999999999998764

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

>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed

Probab=81.96  E-value=1.2  Score=43.54  Aligned_cols=62  Identities=16%  Similarity=-0.040  Sum_probs=40.6

Q ss_pred             CCCceeeeeeeecc-cccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVH-DKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~-d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|++..++|.+. ++...+.....+..........|+++.||++|.||.+|++.+.+..+.
T Consensus       560 ~~~piIiV~NK~DL~~~~~~~~~~~~~~~~l~~~~~~~ii~iSAktg~gv~~L~~~i~~~~~~  622 (712)
T PRK09518        560 AGRALVLVFNKWDLMDEFRRQRLERLWKTEFDRVTWARRVNLSAKTGWHTNRLAPAMQEALES  622 (712)
T ss_pred             cCCCEEEEEEchhcCChhHHHHHHHHHHHhccCCCCCCEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            46789999999653 221111112222222222235688999999999999999999988775

>cd04109 Rab28 Rab28 subfamily

Probab=81.85  E-value=1.7  Score=35.58  Aligned_cols=57  Identities=14%  Similarity=-0.063  Sum_probs=37.0

Q ss_pred             CceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          25 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+++...+|.+... .-+++.+....-. +....|.+..||++|.||+++++.|...+-
T Consensus       110 ~piilVgNK~DL~~-~~~v~~~~~~~~~-~~~~~~~~~iSAktg~gv~~lf~~l~~~l~  166 (215)
T cd04109         110 PLVVLVGNKTDLEH-NRTVKDDKHARFA-QANGMESCLVSAKTGDRVNLLFQQLAAELL  166 (215)
T ss_pred             ceEEEEEECccccc-ccccCHHHHHHHH-HHcCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            35777888965322 1233333333222 222357888999999999999999998764

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

>PLN03110 Rab GTPase; Provisional

Probab=81.61  E-value=1.9  Score=35.45  Aligned_cols=60  Identities=15%  Similarity=0.005  Sum_probs=40.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+-|++...+|++..... ++..+... ........|++..||++|.||+++++.|.+.+..
T Consensus       116 ~~~piiiv~nK~Dl~~~~-~~~~~~~~-~l~~~~~~~~~e~SA~~g~~v~~lf~~l~~~i~~  175 (216)
T PLN03110        116 SNIVIMMAGNKSDLNHLR-SVAEEDGQ-ALAEKEGLSFLETSALEATNVEKAFQTILLEIYH  175 (216)
T ss_pred             CCCeEEEEEEChhccccc-CCCHHHHH-HHHHHcCCEEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence            356788888997643321 23322222 2223345789999999999999999999887754

>cd04132 Rho4_like Rho4-like subfamily

Probab=81.60  E-value=2.7  Score=33.13  Aligned_cols=60  Identities=20%  Similarity=0.098  Sum_probs=39.3

Q ss_pred             CCceeeeeeeeccccc---CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKH---RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~---~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+..+.   ...+......+-.......|++..||++|.||.++++.+...+.
T Consensus       105 ~~piilv~nK~Dl~~~~~~~~~v~~~~~~~~~~~~~~~~~~e~Sa~~~~~v~~~f~~l~~~~~  167 (187)
T cd04132         105 GTPIMLVGLKTDLRKDKNLDRKVTPAQAESVAKKQGAFAYLECSAKTMENVEEVFDTAIEEAL  167 (187)
T ss_pred             CCCEEEEEeChhhhhCccccCCcCHHHHHHHHHHcCCcEEEEccCCCCCCHHHHHHHHHHHHH
Confidence            5688888899653221   11233433333222333448899999999999999999887664

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

>cd01895 EngA2 EngA2 subfamily

Probab=81.57  E-value=2.5  Score=32.15  Aligned_cols=58  Identities=22%  Similarity=0.077  Sum_probs=36.1

Q ss_pred             CCCceeeeeeeecccccC---CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          23 FGDSLCARAFKVVHDKHR---GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~---g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      .+.+++..++|.+.....   .+.....+.+........|++..||+++.|+.++++.+..
T Consensus       112 ~~~~~iiv~nK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~~i~~~~~~l~~  172 (174)
T cd01895         112 EGKALVIVVNKWDLVEKDSKTMKEFKKEIRRKLPFLDYAPIVFISALTGQGVDKLFDAIDE  172 (174)
T ss_pred             cCCCEEEEEeccccCCccHHHHHHHHHHHHhhcccccCCceEEEeccCCCCHHHHHHHHHH
Confidence            357888888996422211   1111223322222223478999999999999999998865

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.

>cd04167 Snu114p Snu114p subfamily

Probab=81.32  E-value=0.89  Score=37.23  Aligned_cols=26  Identities=38%  Similarity=0.459  Sum_probs=24.4

Q ss_pred             eEecCCCccccHH--------HHHHHHHhhCCCC
Q psy5461          60 VLCGSSYKNIGVQ--------KLMDAIVDILPSP   85 (221)
Q Consensus        60 v~~gSa~~~~Gi~--------~LLd~I~~~~PsP   85 (221)
                      |+++||+.+|+..        +|||+|.+.+|+|
T Consensus       180 v~~~s~~~~w~~~~~~~~~~~~~~~~~~~~~~~~  213 (213)
T cd04167         180 VCFASSKFGFCFTLESFAKKYGLVDSIVSNIPSP  213 (213)
T ss_pred             EEEEecCCCeEEecHHHHhhhhHHHHHHhhCCCC
Confidence            8899999999887        9999999999997

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.

>PRK13768 GTPase; Provisional

Probab=81.19  E-value=2.9  Score=35.49  Aligned_cols=29  Identities=24%  Similarity=0.242  Sum_probs=26.4

Q ss_pred             CceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          57 HVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        57 ~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      ..+++..|++++.|+++|++.|.+++|+=
T Consensus       221 ~~~vi~iSa~~~~gl~~L~~~I~~~l~~~  249 (253)
T PRK13768        221 PVRVIPVSAKTGEGFDELYAAIQEVFCGG  249 (253)
T ss_pred             CCcEEEEECCCCcCHHHHHHHHHHHcCCC
Confidence            46899999999999999999999999874

>cd04163 Era Era subfamily

Probab=81.13  E-value=2.8  Score=31.45  Aligned_cols=57  Identities=16%  Similarity=0.140  Sum_probs=36.1

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhcccc-ccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFK-KNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~-~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..+++..++|++......++  ......... ....|++..|++++.|+++|++.|.+++
T Consensus       111 ~~~~iiv~nK~Dl~~~~~~~--~~~~~~~~~~~~~~~~~~~s~~~~~~~~~l~~~l~~~~  168 (168)
T cd04163         111 KTPVILVLNKIDLVKDKEDL--LPLLEKLKELGPFAEIFPISALKGENVDELLEEIVKYL  168 (168)
T ss_pred             CCCEEEEEEchhccccHHHH--HHHHHHHHhccCCCceEEEEeccCCChHHHHHHHHhhC
Confidence            46788888886432111111  222222222 2256899999999999999999997653

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.

>cd04125 RabA_like RabA-like subfamily

Probab=80.71  E-value=2  Score=34.09  Aligned_cols=59  Identities=15%  Similarity=0.008  Sum_probs=37.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.+++...+|.+..+. ..+.......- .+...+|++..||++|.||+++++.+.+.+..
T Consensus       105 ~~~~ivv~nK~Dl~~~-~~v~~~~~~~~-~~~~~~~~~evSa~~~~~i~~~f~~l~~~~~~  163 (188)
T cd04125         105 NVIKVIVANKSDLVNN-KVVDSNIAKSF-CDSLNIPFFETSAKQSINVEEAFILLVKLIIK  163 (188)
T ss_pred             CCeEEEEEECCCCccc-ccCCHHHHHHH-HHHcCCeEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence            4578888888653221 22222222221 12223489999999999999999998887754

RabA was first identified in D. discoideum, where its expression levels were compared to other Rabs in growing and developing cells. The RabA mRNA levels were below the level of detection by Northern blot analysis, suggesting a very low level of expression. The function of RabA remains unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.

>cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily

Probab=80.49  E-value=2  Score=33.76  Aligned_cols=58  Identities=16%  Similarity=0.008  Sum_probs=39.4

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+-|++...+|.+.... .+++.+....-. +....|++..||++|.||+++++.+...+
T Consensus       106 ~~~piilvgNK~Dl~~~-~~v~~~~~~~~a-~~~~~~~~e~Sa~~~~~v~~~f~~l~~~~  163 (172)
T cd04141         106 EDIPLVLVGNKVDLESQ-RQVTTEEGRNLA-REFNCPFFETSAALRHYIDDAFHGLVREI  163 (172)
T ss_pred             CCCCEEEEEEChhhhhc-CccCHHHHHHHH-HHhCCEEEEEecCCCCCHHHHHHHHHHHH
Confidence            35688899999654322 234443333222 22346899999999999999999988654

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

>cd00882 Ras_like_GTPase Ras-like GTPase superfamily

Probab=80.48  E-value=3.5  Score=29.84  Aligned_cols=56  Identities=14%  Similarity=0.035  Sum_probs=36.1

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHH
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIV   79 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~   79 (221)
                      ...+++..++|++........ ..............|++..|+.++.|+.++++.|.
T Consensus       101 ~~~~~ivv~nk~D~~~~~~~~-~~~~~~~~~~~~~~~~~~~s~~~~~~i~~~~~~l~  156 (157)
T cd00882         101 ENIPIILVGNKIDLPEERVVS-EEELAEQLAKELGVPYFETSAKTGENVEELFEELA  156 (157)
T ss_pred             CCCcEEEEEeccccccccchH-HHHHHHHHHhhcCCcEEEEecCCCCChHHHHHHHh
Confidence            467888889996533221111 11112222333467899999999999999999875

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

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

Probab=80.38  E-value=2.2  Score=33.41  Aligned_cols=58  Identities=12%  Similarity=0.016  Sum_probs=37.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++..++|.+.... ..+....+.... +....|++..||++|.|+.++++.+.+.+.
T Consensus       106 ~~p~ilv~NK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gv~~l~~~l~~~~~  163 (180)
T cd04137         106 SVPIVLVGNKSDLHTQ-RQVSTEEGKELA-ESWGAAFLESSARENENVEEAFELLIEEIE  163 (180)
T ss_pred             CCCEEEEEEchhhhhc-CccCHHHHHHHH-HHcCCeEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            5688999999664321 222222222111 112257899999999999999999987653

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

>cd01849 YlqF_related_GTPase YlqF-related GTPases

Probab=80.31  E-value=2.8  Score=32.42  Aligned_cols=59  Identities=12%  Similarity=-0.072  Sum_probs=37.5

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      ....|++..++|++.-+. .++  ........+....++++.||+++.|+++|++.|.+..+
T Consensus        27 ~~~~p~IiVlNK~Dl~~~-~~~--~~~~~~~~~~~~~~ii~vSa~~~~gi~~L~~~i~~~~~   85 (155)
T cd01849          27 EKGKKLILVLNKADLVPK-EVL--RKWLAYLRHSYPTIPFKISATNGQGIEKKESAFTKQTN   85 (155)
T ss_pred             cCCCCEEEEEechhcCCH-HHH--HHHHHHHHhhCCceEEEEeccCCcChhhHHHHHHHHhH
Confidence            346799999999653111 111  11111111112467899999999999999999987643

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.

>cd04130 Wrch_1 Wrch-1 subfamily

Probab=80.18  E-value=2.9  Score=32.60  Aligned_cols=57  Identities=11%  Similarity=-0.013  Sum_probs=35.8

Q ss_pred             CCceeeeeeeecccccC-----------CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          24 GDSLCARAFKVVHDKHR-----------GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~-----------g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      +-|++.-.+|.+..+..           -++..+....-..+....+++..||++|.||+++++.+..
T Consensus       104 ~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~a~~~~~~~~~e~Sa~~~~~v~~lf~~~~~  171 (173)
T cd04130         104 KAPIILVGTQADLRTDVNVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEVFDTAIL  171 (173)
T ss_pred             CCCEEEEeeChhhccChhHHHHHhhcCCCCcCHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHHHHHHh
Confidence            56788888886532211           1233333332222223447999999999999999998763

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	221
2bv3_A	691	Crystal Structure Of A Mutant Elongation Factor G T		3e-20
3izp_E	688	Conformation Of Ef-G During Translocation Length =		3e-20
1zn0_B	655	Coordinates Of Rrf And Ef-G Fitted Into Cryo-Em Map		3e-20
1fnm_A	691	Structure Of Thermus Thermophilus Ef-G H573a Length		3e-20
1ktv_A	691	Crystal Structure Of Elongation Factor G Dimer With		3e-20
1efg_A	691	The Crystal Structure Of Elongation Factor G Comple		3e-20
2j7k_A	691	Crystal Structure Of The T84a Mutant Ef-G:gdpcp Com		3e-20
2bm0_A	691	Ribosomal Elongation Factor G (Ef-G) Fusidic Acid R		3e-20
2bm1_A	691	Ribosomal Elongation Factor G (Ef-G) Fusidic Acid R		3e-20
3zzu_A	693	Crystal Structure Of Staphylococcus Aureus Elongati		6e-19
3zzt_A	693	Crystal Structure Of Staphylococcus Aureus Elongati		6e-19
3zz0_A	693	Crystal Structure Of Ribosomal Elongation Factor (E		6e-19
2xex_A	693	Crystal Structure Of Staphylococcus Aureus Elongati		6e-19
4fn5_A	709	Elongation Factor G 1 (Pseudomonas Aeruginosa) In C		2e-18
3j0e_H	702	Models For The T. Thermophilus Ribosome Recycling F		1e-17
2rdo_7	704	50s Subunit With Ef-G(Gdpnp) And Rrf Bound Length =		1e-17
3tr5_A	528	Structure Of A Peptide Chain Release Factor 3 (Prfc		2e-08
1wdt_A	665	Crystal Structure Of Ttk003000868 From Thermus Ther		3e-08
3vqt_A	548	Crystal Structure Analysis Of The Translation Facto		2e-07
2h5e_A	529	Crystal Structure Of E.Coli Polypeptide Release Fac		3e-07
3uoq_W	534	Crystal Structure Of Release Factor Rf3 Trapped In		3e-07
2ywe_A	600	Crystal Structure Of Lepa From Aquifex Aeolicus Len		7e-06
2ywg_A	600	Crystal Structure Of Gtp-Bound Lepa From Aquifex Ae		2e-05
3j25_A	638	Structural Basis For Tetm-Mediated Tetracycline Res		8e-04

>pdb|2BV3|A Chain A, Crystal Structure Of A Mutant Elongation Factor G Trapped With A Gtp Analogue Length = 691

Iteration: 1
 Score = 94.7 bits (234), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 72/137 (52%), Gaps = 10/137 (7%)
Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGD-------- 99
           I  G       PV  GS+ KN GVQ L+DA+VD LPSP + P +      G+        
Sbjct: 246 IRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDP 305
Query: 100 --SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKE 157
              L A AFK++ D + G +TF R+YSG    G   YN    + E++ RLL   A+  +E
Sbjct: 306 NGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREE 365
Query: 158 VNEIQCGNIAAVTGLKR 174
           V E++ G++ AV GLK 
Sbjct: 366 VEELKAGDLGAVVGLKE 382

>pdb|3IZP|E Chain E, Conformation Of Ef-G During Translocation Length = 688

Iteration: 1
 Score = 94.7 bits (234), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 72/137 (52%), Gaps = 10/137 (7%)
Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGD-------- 99
           I  G       PV  GS+ KN GVQ L+DA+VD LPSP + P +      G+        
Sbjct: 246 IRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDP 305
Query: 100 --SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKE 157
              L A AFK++ D + G +TF R+YSG    G   YN    + E++ RLL   A+  +E
Sbjct: 306 NGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREE 365
Query: 158 VNEIQCGNIAAVTGLKR 174
           V E++ G++ AV GLK 
Sbjct: 366 VEELKAGDLGAVVGLKE 382

>pdb|1ZN0|B Chain B, Coordinates Of Rrf And Ef-G Fitted Into Cryo-Em Map Of The 50s Subunit Bound With Both Ef-G (Gdpnp) And Rrf Length = 655

Iteration: 1
 Score = 94.7 bits (234), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 72/137 (52%), Gaps = 10/137 (7%)
Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGD-------- 99
           I  G       PV  GS+ KN GVQ L+DA+VD LPSP + P +      G+        
Sbjct: 213 IRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDP 272
Query: 100 --SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKE 157
              L A AFK++ D + G +TF R+YSG    G   YN    + E++ RLL   A+  +E
Sbjct: 273 NGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREE 332
Query: 158 VNEIQCGNIAAVTGLKR 174
           V E++ G++ AV GLK 
Sbjct: 333 VEELKAGDLGAVVGLKE 349

>pdb|1FNM|A Chain A, Structure Of Thermus Thermophilus Ef-G H573a Length = 691

Iteration: 1
 Score = 94.7 bits (234), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 72/137 (52%), Gaps = 10/137 (7%)
Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGD-------- 99
           I  G       PV  GS+ KN GVQ L+DA+VD LPSP + P +      G+        
Sbjct: 246 IRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDP 305
Query: 100 --SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKE 157
              L A AFK++ D + G +TF R+YSG    G   YN    + E++ RLL   A+  +E
Sbjct: 306 NGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREE 365
Query: 158 VNEIQCGNIAAVTGLKR 174
           V E++ G++ AV GLK 
Sbjct: 366 VEELKAGDLGAVVGLKE 382

>pdb|1KTV|A Chain A, Crystal Structure Of Elongation Factor G Dimer Without Nucleotide Length = 691

Iteration: 1
 Score = 94.7 bits (234), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 72/137 (52%), Gaps = 10/137 (7%)
Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGD-------- 99
           I  G       PV  GS+ KN GVQ L+DA+VD LPSP + P +      G+        
Sbjct: 246 IRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDP 305
Query: 100 --SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKE 157
              L A AFK++ D + G +TF R+YSG    G   YN    + E++ RLL   A+  +E
Sbjct: 306 NGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREE 365
Query: 158 VNEIQCGNIAAVTGLKR 174
           V E++ G++ AV GLK 
Sbjct: 366 VEELKAGDLGAVVGLKE 382

>pdb|1EFG|A Chain A, The Crystal Structure Of Elongation Factor G Complexed With Gdp, At 2.7 Angstroms Resolution Length = 691

Iteration: 1
 Score = 94.7 bits (234), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 72/137 (52%), Gaps = 10/137 (7%)
Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGD-------- 99
           I  G       PV  GS+ KN GVQ L+DA+VD LPSP + P +      G+        
Sbjct: 246 IRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDP 305
Query: 100 --SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKE 157
              L A AFK++ D + G +TF R+YSG    G   YN    + E++ RLL   A+  +E
Sbjct: 306 NGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREE 365
Query: 158 VNEIQCGNIAAVTGLKR 174
           V E++ G++ AV GLK 
Sbjct: 366 VEELKAGDLGAVVGLKE 382

>pdb|2J7K|A Chain A, Crystal Structure Of The T84a Mutant Ef-G:gdpcp Complex Length = 691

Iteration: 1
 Score = 94.7 bits (234), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 72/137 (52%), Gaps = 10/137 (7%)
Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGD-------- 99
           I  G       PV  GS+ KN GVQ L+DA+VD LPSP + P +      G+        
Sbjct: 246 IRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDP 305
Query: 100 --SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKE 157
              L A AFK++ D + G +TF R+YSG    G   YN    + E++ RLL   A+  +E
Sbjct: 306 NGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREE 365
Query: 158 VNEIQCGNIAAVTGLKR 174
           V E++ G++ AV GLK 
Sbjct: 366 VEELKAGDLGAVVGLKE 382

>pdb|2BM0|A Chain A, Ribosomal Elongation Factor G (Ef-G) Fusidic Acid Resistant Mutant T84a Length = 691

Iteration: 1
 Score = 94.7 bits (234), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 72/137 (52%), Gaps = 10/137 (7%)
Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGD-------- 99
           I  G       PV  GS+ KN GVQ L+DA+VD LPSP + P +      G+        
Sbjct: 246 IRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDP 305
Query: 100 --SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKE 157
              L A AFK++ D + G +TF R+YSG    G   YN    + E++ RLL   A+  +E
Sbjct: 306 NGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREE 365
Query: 158 VNEIQCGNIAAVTGLKR 174
           V E++ G++ AV GLK 
Sbjct: 366 VEELKAGDLGAVVGLKE 382

>pdb|2BM1|A Chain A, Ribosomal Elongation Factor G (Ef-G) Fusidic Acid Resistant Mutant G16v Length = 691

Iteration: 1
 Score = 94.7 bits (234), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 72/137 (52%), Gaps = 10/137 (7%)
Query: 48  IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGD-------- 99
           I  G       PV  GS+ KN GVQ L+DA+VD LPSP + P +      G+        
Sbjct: 246 IRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDP 305
Query: 100 --SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKE 157
              L A AFK++ D + G +TF R+YSG    G   YN    + E++ RLL   A+  +E
Sbjct: 306 NGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREE 365
Query: 158 VNEIQCGNIAAVTGLKR 174
           V E++ G++ AV GLK 
Sbjct: 366 VEELKAGDLGAVVGLKE 382

>pdb|3ZZU|A Chain A, Crystal Structure Of Staphylococcus Aureus Elongation Factor G With Mutations M16i And F88l Length = 693

Iteration: 1
 Score = 90.9 bits (224), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 49/127 (38%), Positives = 71/127 (55%), Gaps = 12/127 (9%)
Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSPTE----------RPALAMFQHFGDS--LCARAF 106
           PVLCG+++KN GVQ ++DA++D LPSP +           P   +     DS    A AF
Sbjct: 255 PVLCGTAFKNKGVQLMLDAVIDYLPSPLDVKPIIGHRASNPEEEVIAKADDSAEFAALAF 314
Query: 107 KVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
           KV+ D + G +TFFR+YSG    G    N    + E++ RLL   A+  +E++ +  G+I
Sbjct: 315 KVMTDPYVGKLTFFRVYSGTMTSGSYVKNSTKGKRERVGRLLQMHANSRQEIDTVYSGDI 374
Query: 167 AAVTGLK 173
           AA  GLK
Sbjct: 375 AAAVGLK 381

>pdb|3ZZT|A Chain A, Crystal Structure Of Staphylococcus Aureus Elongation Factor G With A Fusidic-Acid-Resistant Mutation F88l Length = 693

Iteration: 1
 Score = 90.5 bits (223), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 49/127 (38%), Positives = 71/127 (55%), Gaps = 12/127 (9%)
Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSPTE----------RPALAMFQHFGDS--LCARAF 106
           PVLCG+++KN GVQ ++DA++D LPSP +           P   +     DS    A AF
Sbjct: 255 PVLCGTAFKNKGVQLMLDAVIDYLPSPLDVKPIIGHRASNPEEEVIAKADDSAEFAALAF 314
Query: 107 KVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
           KV+ D + G +TFFR+YSG    G    N    + E++ RLL   A+  +E++ +  G+I
Sbjct: 315 KVMTDPYVGKLTFFRVYSGTMTSGSYVKNSTKGKRERVGRLLQMHANSRQEIDTVYSGDI 374
Query: 167 AAVTGLK 173
           AA  GLK
Sbjct: 375 AAAVGLK 381

>pdb|3ZZ0|A Chain A, Crystal Structure Of Ribosomal Elongation Factor (Ef)-G From Staphylococcus Aureus With A Fusidic Acid Hyper-Sensitivity Mutation M16i Length = 693

Iteration: 1
 Score = 90.5 bits (223), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 49/127 (38%), Positives = 71/127 (55%), Gaps = 12/127 (9%)
Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSPTE----------RPALAMFQHFGDS--LCARAF 106
           PVLCG+++KN GVQ ++DA++D LPSP +           P   +     DS    A AF
Sbjct: 255 PVLCGTAFKNKGVQLMLDAVIDYLPSPLDVKPIIGHRASNPEEEVIAKADDSAEFAALAF 314
Query: 107 KVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
           KV+ D + G +TFFR+YSG    G    N    + E++ RLL   A+  +E++ +  G+I
Sbjct: 315 KVMTDPYVGKLTFFRVYSGTMTSGSYVKNSTKGKRERVGRLLQMHANSRQEIDTVYSGDI 374
Query: 167 AAVTGLK 173
           AA  GLK
Sbjct: 375 AAAVGLK 381

>pdb|2XEX|A Chain A, Crystal Structure Of Staphylococcus Aureus Elongation Factor G Length = 693

Iteration: 1
 Score = 90.5 bits (223), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 49/127 (38%), Positives = 71/127 (55%), Gaps = 12/127 (9%)
Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSPTE----------RPALAMFQHFGDS--LCARAF 106
           PVLCG+++KN GVQ ++DA++D LPSP +           P   +     DS    A AF
Sbjct: 255 PVLCGTAFKNKGVQLMLDAVIDYLPSPLDVKPIIGHRASNPEEEVIAKADDSAEFAALAF 314
Query: 107 KVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166
           KV+ D + G +TFFR+YSG    G    N    + E++ RLL   A+  +E++ +  G+I
Sbjct: 315 KVMTDPYVGKLTFFRVYSGTMTSGSYVKNSTKGKRERVGRLLQMHANSRQEIDTVYSGDI 374
Query: 167 AAVTGLK 173
           AA  GLK
Sbjct: 375 AAAVGLK 381

>pdb|4FN5|A Chain A, Elongation Factor G 1 (Pseudomonas Aeruginosa) In Complex With Argyrin B Length = 709

Iteration: 1
 Score = 88.6 bits (218), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/128 (35%), Positives = 73/128 (57%), Gaps = 12/128 (9%)
Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMF----------QHFGDS--LCARA 105
           VP +CGSS+KN GV  ++DA++D LP+PTE PA+             +H  D+    + A
Sbjct: 265 VPAVCGSSFKNKGVPLVLDAVIDYLPAPTEIPAIKGVSPDDETVEDERHADDNEPFSSLA 324
Query: 106 FKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN 165
           FK+  D   G +TF R+YSG    G    N    + E++ R++   A+  +E+ E++ G+
Sbjct: 325 FKIATDPFVGTLTFARVYSGVLSSGDSVLNSVKGKKERVGRMVQMHANQREEIKEVRAGD 384
Query: 166 IAAVTGLK 173
           IAA+ G+K
Sbjct: 385 IAALIGMK 392

>pdb|3J0E|H Chain H, Models For The T. Thermophilus Ribosome Recycling Factor And The E. Coli Elongation Factor G Bound To The E. Coli Post-Termination Complex Length = 702

Iteration: 1
 Score = 86.7 bits (213), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 47/126 (37%), Positives = 68/126 (53%), Gaps = 12/126 (9%)
Query: 60  VLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMF----------QHFGDS--LCARAFK 107
           V CGS++KN GVQ ++DA++D LPSP + PA+             +H  D     A AFK
Sbjct: 263 VTCGSAFKNKGVQAMLDAVIDYLPSPVDVPAINGILDDGKDTPAERHASDDEPFSALAFK 322
Query: 108 VVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167
           +  D   G +TFFR+YSG    G    N      E+  R++   A+  +E+ E++ G+IA
Sbjct: 323 IATDPFVGNLTFFRVYSGVVNSGDTVLNSVKAARERFGRIVQMHANKREEIKEVRAGDIA 382
Query: 168 AVTGLK 173
           A  GLK
Sbjct: 383 AAIGLK 388

>pdb|2RDO|7 Chain 7, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound Length = 704

Iteration: 1
 Score = 86.7 bits (213), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 47/126 (37%), Positives = 68/126 (53%), Gaps = 12/126 (9%)
Query: 60  VLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMF----------QHFGDS--LCARAFK 107
           V CGS++KN GVQ ++DA++D LPSP + PA+             +H  D     A AFK
Sbjct: 264 VTCGSAFKNKGVQAMLDAVIDYLPSPVDVPAINGILDDGKDTPAERHASDDEPFSALAFK 323
Query: 108 VVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167
           +  D   G +TFFR+YSG    G    N      E+  R++   A+  +E+ E++ G+IA
Sbjct: 324 IATDPFVGNLTFFRVYSGVVNSGDTVLNSVKAARERFGRIVQMHANKREEIKEVRAGDIA 383
Query: 168 AVTGLK 173
           A  GLK
Sbjct: 384 AAIGLK 389

>pdb|3TR5|A Chain A, Structure Of A Peptide Chain Release Factor 3 (Prfc) From Coxiella Burnetii Length = 528

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 36/124 (29%), Positives = 55/124 (44%), Gaps = 4/124 (3%)
Query: 50  SGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA-MFQHFGDSLCARAFKV 108
            G  K    P+  GS+  N GV +L+DA V   P P  R   + + +   +      FK+
Sbjct: 243 EGYLKGELTPIFFGSAINNFGVGELLDAFVKEAPPPQGRETNSRLVKPEEEKFSGFVFKI 302
Query: 109 VHDK---HRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN 165
             +    HR  + F RI SG ++KG K Y++ L +  QI   L   A   +   E   G+
Sbjct: 303 QANXDPGHRDRIAFLRIASGQYQKGXKAYHVRLKKEIQINNALTFXAGKRENAEEAWPGD 362
Query: 166 IAAV 169
           I  +
Sbjct: 363 IIGL 366

>pdb|1WDT|A Chain A, Crystal Structure Of Ttk003000868 From Thermus Thermophilus Hb8 Length = 665

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 43/124 (34%), Positives = 56/124 (45%), Gaps = 22/124 (17%)
Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS-LCARAFKVVHDKHRGAV 117
           PV   S  + IGV  L++ I++ LPSPTER        FGD    A+ FKV  D   G V
Sbjct: 249 PVALASGEREIGVLPLLELILEALPSPTER--------FGDGPPLAKVFKVQVDPFMGQV 300
Query: 118 TFFRIYSGAFKKGQKFYNIHLDQSE----QITRLLLAEADDYKEVNEIQCGNIAAV---T 170
            + R+Y G  K G         QSE    ++  L +    D  EV E + G +  V    
Sbjct: 301 AYLRLYRGRLKPGDSL------QSEAGQVRLPHLYVPMGKDLLEVEEAEAGFVLGVPKAE 354
Query: 171 GLKR 174
           GL R
Sbjct: 355 GLHR 358

>pdb|3VQT|A Chain A, Crystal Structure Analysis Of The Translation Factor Rf3 Length = 548

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/121 (27%), Positives = 52/121 (42%), Gaps = 4/121 (3%)
Query: 53  FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFG-DSLCARAFKV--- 108
            K    PV  GS+  N GV++++D  V+  P P  RPA       G ++     FK+   
Sbjct: 264 LKGELTPVFFGSAINNFGVREMLDMFVEFAPGPQPRPAATRVVEPGEEAFTGVVFKIQAN 323
Query: 109 VHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA 168
           +   HR  + F RI SG F +G +  +    +   +    +  A D   V E   G+I  
Sbjct: 324 MDKAHRDRMAFLRICSGTFTRGMRLKHHRTGKDVTVANATIFMAQDRTGVEEAFPGDIIG 383
Query: 169 V 169
           +
Sbjct: 384 I 384

>pdb|2H5E|A Chain A, Crystal Structure Of E.Coli Polypeptide Release Factor Rf3 Length = 529

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/116 (28%), Positives = 51/116 (43%), Gaps = 4/116 (3%)
Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPA-LAMFQHFGDSLCARAFKV---VHDKH 113
            PV  G++  N GV  ++D +V+  P+P  R       +   D      FK+   +  KH
Sbjct: 252 TPVFFGTALGNFGVDHMLDGLVEWAPAPMPRQTDTRTVEASEDKFTGFVFKIQANMDPKH 311
Query: 114 RGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV 169
           R  V F R+ SG ++KG K   +   +   I+  L   A D   V E   G+I  +
Sbjct: 312 RDRVAFMRVVSGKYEKGMKLRQVRTAKDVVISDALTFMAGDRSHVEEAYPGDILGL 367

>pdb|3UOQ|W Chain W, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp State On A Rotated Conformation Of The Ribosome (Without Viomycin) Length = 534

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/116 (28%), Positives = 51/116 (43%), Gaps = 4/116 (3%)
Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPA-LAMFQHFGDSLCARAFKV---VHDKH 113
            PV  G++  N GV  ++D +V+  P+P  R       +   D      FK+   +  KH
Sbjct: 252 TPVFFGTALGNFGVDHMLDGLVEWAPAPMPRQTDTRTVEASEDKFTGFVFKIQANMDPKH 311
Query: 114 RGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV 169
           R  V F R+ SG ++KG K   +   +   I+  L   A D   V E   G+I  +
Sbjct: 312 RDRVAFMRVVSGKYEKGMKLRQVRTAKDVVISDALTFMAGDRSHVEEAYPGDILGL 367

>pdb|2YWE|A Chain A, Crystal Structure Of Lepa From Aquifex Aeolicus Length = 600

Iteration: 1
 Score = 47.4 bits (111), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 8/87 (9%)
Query: 61  LCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFF 120
           +  S+ + IG++++++AIV+ +P P   P           L A  F   +D +RGAV F 
Sbjct: 161 ILASAKEGIGIEEILEAIVNRIPPPKGDPQ--------KPLKALIFDSYYDPYRGAVAFV 212
Query: 121 RIYSGAFKKGQKFYNIHLDQSEQITRL 147
           RI+ G  K G K   +   +  ++T +
Sbjct: 213 RIFDGEVKPGDKIMLMSTGKEYEVTEV 239

>pdb|2YWG|A Chain A, Crystal Structure Of Gtp-Bound Lepa From Aquifex Aeolicus Length = 600

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 8/87 (9%)
Query: 61  LCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFF 120
           +  S+ + IG++++++AIV+ +P P   P           L A  F   +D +RGAV F 
Sbjct: 161 ILASAKEGIGIEEILEAIVNRIPPPKGDPQ--------KPLKALIFDSYYDPYRGAVAFV 212
Query: 121 RIYSGAFKKGQKFYNIHLDQSEQITRL 147
           RI+ G  K G K       +  ++T +
Sbjct: 213 RIFDGEVKPGDKIXLXSTGKEYEVTEV 239

>pdb|3J25|A Chain A, Structural Basis For Tetm-Mediated Tetracycline Resistance Length = 638

Iteration: 1
 Score = 40.4 bits (93), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 8/69 (11%)
Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVT 118
           P+  GS+  NIG+  L++ I +   S T R            LC   FK+ + K R  + 
Sbjct: 214 PLYHGSAKSNIGIDNLIEVITNKFYSSTHRGP--------SELCGNVFKIEYTKKRQRLA 265
Query: 119 FFRIYSGAF 127
           + R+YSG  
Sbjct: 266 YIRLYSGVL 274

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	221
2dy1_A	665	Elongation factor G; translocation, GTP complex, s	8e-36
2dy1_A	665	Elongation factor G; translocation, GTP complex, s	7e-11
2xex_A	693	Elongation factor G; GTPase, translation, biosynth	1e-34
2xex_A	693	Elongation factor G; GTPase, translation, biosynth	1e-09
1dar_A	691	EF-G, elongation factor G; ribosomal translocase,	1e-34
1dar_A	691	EF-G, elongation factor G; ribosomal translocase,	1e-09
2rdo_7	704	EF-G, elongation factor G; elongation factor G, EF	2e-34
2rdo_7	704	EF-G, elongation factor G; elongation factor G, EF	1e-09
1n0u_A	842	EF-2, elongation factor 2; G-protein, CIS-proline,	1e-13
3tr5_A	528	RF-3, peptide chain release factor 3; protein synt	7e-09
2h5e_A	529	Peptide chain release factor RF-3; beta barrel, tr	9e-09
2ywe_A	600	GTP-binding protein LEPA; G domain, beta-barrel, f	1e-06
3cb4_D	599	GTP-binding protein LEPA; GTPase, OB-fold, membran	2e-06
1wb1_A	482	Translation elongation factor SELB; selenocysteine	2e-04

>2dy1_A Elongation factor G; translocation, GTP complex, structural genomics, NPPSFA; HET: GTP; 1.60A {Thermus thermophilus} SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB: 1wdt_A* Length = 665

 Score =  132 bits (334), Expect = 8e-36
 Identities = 34/116 (29%), Positives = 49/116 (42%), Gaps = 9/116 (7%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAV 117
            PV   S  + IGV  L++ I++ LPSPTER              A+ FKV  D   G V
Sbjct: 248 YPVALASGEREIGVLPLLELILEALPSPTERFGDGPP-------LAKVFKVQVDPFMGQV 300

Query: 118 TFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173
            + R+Y G  K G    +       ++  L +    D  EV E + G +  V   +
Sbjct: 301 AYLRLYRGRLKPGDSLQS--EAGQVRLPHLYVPMGKDLLEVEEAEAGFVLGVPKAE 354

>2dy1_A Elongation factor G; translocation, GTP complex, structural genomics, NPPSFA; HET: GTP; 1.60A {Thermus thermophilus} SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB: 1wdt_A* Length = 665

 Score = 60.2 bits (147), Expect = 7e-11
 Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 7/55 (12%)

Query: 1   MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKK 55
           ++ I++ LPSPTER              A+ FKV  D   G V + R+Y G  K 
Sbjct: 265 LELILEALPSPTERFGDGPP-------LAKVFKVQVDPFMGQVAYLRLYRGRLKP 312

>2xex_A Elongation factor G; GTPase, translation, biosynthetic protein; 1.90A {Staphylococcus aureus} Length = 693

 Score =  128 bits (325), Expect = 1e-34
 Identities = 48/128 (37%), Positives = 71/128 (55%), Gaps = 12/128 (9%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL----------AMFQHFGDS--LCARA 105
            PVLCG+++KN GVQ ++DA++D LPSP +   +           +     DS    A A
Sbjct: 254 YPVLCGTAFKNKGVQLMLDAVIDYLPSPLDVKPIIGHRASNPEEEVIAKADDSAEFAALA 313

Query: 106 FKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN 165
           FKV+ D + G +TFFR+YSG    G    N    + E++ RLL   A+  +E++ +  G+
Sbjct: 314 FKVMTDPYVGKLTFFRVYSGTMTSGSYVKNSTKGKRERVGRLLQMHANSRQEIDTVYSGD 373

Query: 166 IAAVTGLK 173
           IAA  GLK
Sbjct: 374 IAAAVGLK 381

>2xex_A Elongation factor G; GTPase, translation, biosynthetic protein; 1.90A {Staphylococcus aureus} Length = 693

 Score = 56.3 bits (137), Expect = 1e-09
 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 12/67 (17%)

Query: 1   MDAIVDILPSPTERPAL----------AMFQHFGDS--LCARAFKVVHDKHRGAVTFFRI 48
           +DA++D LPSP +   +           +     DS    A AFKV+ D + G +TFFR+
Sbjct: 271 LDAVIDYLPSPLDVKPIIGHRASNPEEEVIAKADDSAEFAALAFKVMTDPYVGKLTFFRV 330

Query: 49  YSGAFKK 55
           YSG    
Sbjct: 331 YSGTMTS 337

>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 ... Length = 691

 Score =  128 bits (325), Expect = 1e-34
 Identities = 50/126 (39%), Positives = 71/126 (56%), Gaps = 10/126 (7%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA--------MFQHFGDS--LCARAFK 107
            PV  GS+ KN GVQ L+DA+VD LPSP + P +         +  H   +  L A AFK
Sbjct: 256 TPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFK 315

Query: 108 VVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167
           ++ D + G +TF R+YSG    G   YN    + E++ RLL   A+  +EV E++ G++ 
Sbjct: 316 IMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLG 375

Query: 168 AVTGLK 173
           AV GLK
Sbjct: 376 AVVGLK 381

>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 ... Length = 691

 Score = 56.3 bits (137), Expect = 1e-09
 Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 10/65 (15%)

Query: 1   MDAIVDILPSPTERPALA--------MFQHFGDS--LCARAFKVVHDKHRGAVTFFRIYS 50
           +DA+VD LPSP + P +         +  H   +  L A AFK++ D + G +TF R+YS
Sbjct: 273 LDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYS 332

Query: 51  GAFKK 55
           G    
Sbjct: 333 GTLTS 337

>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 Length = 704

 Score =  128 bits (324), Expect = 2e-34
 Identities = 47/128 (36%), Positives = 69/128 (53%), Gaps = 12/128 (9%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL----------AMFQHFGDS--LCARA 105
           + V CGS++KN GVQ ++DA++D LPSP + PA+             +H  D     A A
Sbjct: 262 ILVTCGSAFKNKGVQAMLDAVIDYLPSPVDVPAINGILDDGKDTPAERHASDDEPFSALA 321

Query: 106 FKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN 165
           FK+  D   G +TFFR+YSG    G    N      E+  R++   A+  +E+ E++ G+
Sbjct: 322 FKIATDPFVGNLTFFRVYSGVVNSGDTVLNSVKAARERFGRIVQMHANKREEIKEVRAGD 381

Query: 166 IAAVTGLK 173
           IAA  GLK
Sbjct: 382 IAAAIGLK 389

>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 Length = 704

 Score = 56.4 bits (137), Expect = 1e-09
 Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 12/67 (17%)

Query: 1   MDAIVDILPSPTERPAL----------AMFQHFGDS--LCARAFKVVHDKHRGAVTFFRI 48
           +DA++D LPSP + PA+             +H  D     A AFK+  D   G +TFFR+
Sbjct: 279 LDAVIDYLPSPVDVPAINGILDDGKDTPAERHASDDEPFSALAFKIATDPFVGNLTFFRV 338

Query: 49  YSGAFKK 55
           YSG    
Sbjct: 339 YSGVVNS 345

>1n0u_A EF-2, elongation factor 2; G-protein, CIS-proline, translation; HET: SO1; 2.12A {Saccharomyces cerevisiae} SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB: 1n0v_C 1s1h_T 2e1r_A* 2npf_A* 2p8w_T* 3dny_T 3b82_A* 1zm2_A* 1zm3_A* 1zm4_A* 1zm9_A* 2p8x_T* 2p8y_T* 2p8z_T* 2zit_A* 1u2r_A* 3b78_A* 3b8h_A* Length = 842

 Score = 68.5 bits (167), Expect = 1e-13
 Identities = 30/155 (19%), Positives = 51/155 (32%), Gaps = 28/155 (18%)

Query: 53  FKKNHVPVLCGSSYKNIGV-QKLMDAIVDILPSPTERPALAMFQHFGDS----------- 100
                  +L     K +     L++ IV  LPSP    A    Q +              
Sbjct: 312 KDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKN 371

Query: 101 ------LCARAFKVVHDKHRG-AVTFFRIYSGAFKKGQKFYNIHLDQS---------EQI 144
                 L     K+V    +G    F R+++G  K GQK      +           + I
Sbjct: 372 CDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAI 431

Query: 145 TRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKD 179
            R++L      + +++   GNI  + G+ +   K 
Sbjct: 432 QRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKT 466

>3tr5_A RF-3, peptide chain release factor 3; protein synthesis, translation; HET: GDP; 2.11A {Coxiella burnetii} Length = 528

 Score = 54.3 bits (131), Expect = 7e-09
 Identities = 32/106 (30%), Positives = 49/106 (46%), Gaps = 4/106 (3%)

Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA-MFQHFGDSLCARAFKVVHD---KHR 114
           P+  GS+  N GV +L+DA V   P P  R   + + +   +      FK+  +    HR
Sbjct: 252 PIFFGSAINNFGVGELLDAFVKEAPPPQGRETNSRLVKPEEEKFSGFVFKIQANMDPGHR 311

Query: 115 GAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
             + F RI SG ++KG K Y++ L +  QI   L   A   +   E
Sbjct: 312 DRIAFLRIASGQYQKGMKAYHVRLKKEIQINNALTFMAGKRENAEE 357

>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* Length = 529

 Score = 53.6 bits (129), Expect = 9e-09
 Identities = 31/106 (29%), Positives = 47/106 (44%), Gaps = 4/106 (3%)

Query: 59  PVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA-MFQHFGDSLCARAFKVVHD---KHR 114
           PV  G++  N GV  ++D +V+  P+P  R       +   D      FK+  +   KHR
Sbjct: 253 PVFFGTALGNFGVDHMLDGLVEWAPAPMPRQTDTRTVEASEDKFTGFVFKIQANMDPKHR 312

Query: 115 GAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
             V F R+ SG ++KG K   +   +   I+  L   A D   V E
Sbjct: 313 DRVAFMRVVSGKYEKGMKLRQVRTAKDVVISDALTFMAGDRSHVEE 358

>2ywe_A GTP-binding protein LEPA; G domain, beta-barrel, ferredoxin-like domain, structural GE NPPSFA; 2.05A {Aquifex aeolicus} PDB: 2ywf_A* 2ywg_A* 2ywh_A* Length = 600

 Score = 47.5 bits (114), Expect = 1e-06
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 16/68 (23%)

Query: 69  IGVQKLMDAIVDILPSPT---ERPALAM-FQHFGDSLCARAFKVVHDKHRGAVTFFRIYS 124
           IG++++++AIV+ +P P    ++P  A+ F    DS         +D +RGAV F RI+ 
Sbjct: 169 IGIEEILEAIVNRIPPPKGDPQKPLKALIF----DS--------YYDPYRGAVAFVRIFD 216

Query: 125 GAFKKGQK 132
           G  K G K
Sbjct: 217 GEVKPGDK 224

>3cb4_D GTP-binding protein LEPA; GTPase, OB-fold, membrane, nucleotide-binding, translation; 2.80A {Escherichia coli} PDB: 3deg_C* Length = 599

 Score = 47.1 bits (113), Expect = 2e-06
 Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 16/69 (23%)

Query: 69  IGVQKLMDAIVDILPSPT---ERPALAM-FQHFGDSLCARAFKVVHDKHRGAVTFFRIYS 124
           +GVQ +++ +V  +P P    E P  A+      DS          D + G V+  RI +
Sbjct: 167 VGVQDVLERLVRDIPPPEGDPEGPLQALII----DS--------WFDNYLGVVSLIRIKN 214

Query: 125 GAFKKGQKF 133
           G  +KG K 
Sbjct: 215 GTLRKGDKV 223

>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* Length = 482

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 26/161 (16%), Positives = 58/161 (36%), Gaps = 22/161 (13%)

Query: 50  SGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT-ERPALAMFQHFGDSLCARAFKV 108
                  +  ++  S+    GV +L + I+  L +    R   + F+   D     AF +
Sbjct: 155 QSTHNLKNSSIIPISAKTGFGVDELKNLIITTLNNAEIIRNTESYFKMPLD----HAFPI 210

Query: 109 VHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCG-NIA 167
              K  G V    I  G  K G +   + ++ S ++  +   +    + V E + G  + 
Sbjct: 211 ---KGAGTVVTGTINKGIVKVGDELKVLPINMSTKVRSIQYFK----ESVMEAKAGDRVG 263

Query: 168 A-VTGLKR---ERGKDKRTRVIPKPTSVVQCSARWTLNLEV 204
             + G+      RG      ++    + +Q   +    +++
Sbjct: 264 MAIQGVDAKQIYRG-----XILTSKDTKLQTVDKIVAKIKI 299

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	221
2xex_A	693	Elongation factor G; GTPase, translation, biosynth	100.0
2rdo_7	704	EF-G, elongation factor G; elongation factor G, EF	100.0
1dar_A	691	EF-G, elongation factor G; ribosomal translocase,	100.0
4fn5_A	709	EF-G 1, elongation factor G 1; translation, transl	99.98
3vqt_A	548	RF-3, peptide chain release factor 3; translation,	99.98
3tr5_A	528	RF-3, peptide chain release factor 3; protein synt	99.97
2h5e_A	529	Peptide chain release factor RF-3; beta barrel, tr	99.97
2dy1_A	665	Elongation factor G; translocation, GTP complex, s	99.96
3j25_A	638	Tetracycline resistance protein TETM; antibiotic r	99.95
1n0u_A	842	EF-2, elongation factor 2; G-protein, CIS-proline,	99.93
2ywe_A	600	GTP-binding protein LEPA; G domain, beta-barrel, f	99.93
3cb4_D	599	GTP-binding protein LEPA; GTPase, OB-fold, membran	99.91
1g7s_A	594	Translation initiation factor IF2/EIF5B; translati	99.73
2c78_A	405	Elongation factor TU-A; hydrolase, GTPase, transla	99.66
1d2e_A	397	Elongation factor TU (EF-TU); G-protein, beta-barr	99.63
1jny_A	435	EF-1-alpha, elongation factor 1-alpha, EF-TU, TUF-	99.55
2elf_A	370	Protein translation elongation factor 1A; tRNA, py	99.54
1kk1_A	410	EIF2gamma; initiation of translation; HET: GNP; 1.	99.53
3sjy_A	403	Translation initiation factor 2 subunit gamma; zin	99.52
3j2k_7	439	ERF3, eukaryotic polypeptide chain release factor	99.51
3p26_A	483	Elongation factor 1 alpha-like protein; GTP/GDP bi	99.51
1s0u_A	408	EIF-2-gamma, translation initiation factor 2 gamma	99.51
3avx_A	1289	Elongation factor TS, elongation factor TU, linke	99.5
3mca_A	592	HBS1, elongation factor 1 alpha-like protein; prot	99.49
3izy_P	537	Translation initiation factor IF-2, mitochondrial;	99.45
3izq_1	611	HBS1P, elongation factor 1 alpha-like protein; NO-	99.45
1r5b_A	467	Eukaryotic peptide chain release factor GTP-bindi	99.36
1f60_A	458	Elongation factor EEF1A; protein-protein complex,	99.35
1zo1_I	501	IF2, translation initiation factor 2; E. coli, rib	99.35
1zun_B	434	Sulfate adenylate transferase, subunit 1/adenylyls	99.34
1wb1_A	482	Translation elongation factor SELB; selenocysteine	99.23
3e1y_E	204	Eukaryotic peptide chain release factor GTP-bindi	98.87
1xe1_A	116	Hypothetical protein PF0907; structural genomics,	97.69
3vqt_A	548	RF-3, peptide chain release factor 3; translation,	97.5
4fn5_A	709	EF-G 1, elongation factor G 1; translation, transl	97.31
2rdo_7	704	EF-G, elongation factor G; elongation factor G, EF	97.17
1dar_A	691	EF-G, elongation factor G; ribosomal translocase,	97.15
2xex_A	693	Elongation factor G; GTPase, translation, biosynth	97.08
3tr5_A	528	RF-3, peptide chain release factor 3; protein synt	96.98
1d1n_A	99	Initiation factor 2; beta-barrel, gene regulation;	96.83
1n0u_A	842	EF-2, elongation factor 2; G-protein, CIS-proline,	96.76
3qq5_A	423	Small GTP-binding protein; hydrogenase, H-cluster,	96.76
2crv_A	120	IF-2MT, translation initiation factor IF-2; riboso	96.5
2h5e_A	529	Peptide chain release factor RF-3; beta barrel, tr	96.27
3j25_A	638	Tetracycline resistance protein TETM; antibiotic r	96.21
1zo1_I	501	IF2, translation initiation factor 2; E. coli, rib	95.2
3izy_P	537	Translation initiation factor IF-2, mitochondrial;	94.7
2dy1_A	665	Elongation factor G; translocation, GTP complex, s	94.38
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	94.17
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	93.94
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	93.38
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.34
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	93.24
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	93.23
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	93.09
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	93.04
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	93.04
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	92.91
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	92.79
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	92.72
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	92.7
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	92.69
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	92.66
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	92.63
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	92.61
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	92.6
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	92.57
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	92.55
1g7s_A	594	Translation initiation factor IF2/EIF5B; translati	92.5
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	92.29
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	91.9
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	91.89
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	91.81
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	91.81
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	91.75
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	91.7
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	91.63
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	91.59
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	91.5
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	91.27
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	91.21
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	91.07
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	91.03
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	91.02
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	90.99
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	90.95
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	90.88
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	90.87
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	90.87
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	90.84
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	90.69
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	90.68
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	90.67
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	90.65
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	90.63
3o47_A	329	ADP-ribosylation factor GTPase-activating protein	90.63
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	90.51
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	90.49
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	90.48
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	90.39
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	90.34
4djt_A	218	GTP-binding nuclear protein GSP1; structural genom	89.99
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	89.96
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	89.94
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	89.9
3lvq_E	497	ARF-GAP with SH3 domain, ANK repeat and PH domain	89.83
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	89.82
4he6_A	89	Peptidase family U32; ultra-tight crystal packing,	89.8
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	89.79
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	89.79
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	89.68
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	89.68
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	89.66
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	89.58
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	89.53
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	89.53
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	89.45
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	89.37
3i8s_A	274	Ferrous iron transport protein B; GTPase, GPCR, ir	89.33
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	89.22
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	89.11
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	88.99
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	88.83
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	88.74
3l0i_B	199	RAS-related protein RAB-1A; GEF-GDF-RAB complex, G	88.51
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	88.37
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	88.33
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	88.31
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	88.3
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	88.3
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	88.09
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	88.08
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	87.9
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	87.74
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	87.67
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	87.66
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	87.62
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	87.28
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	87.16
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	87.11
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	86.95
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	86.76
3a1s_A	258	Iron(II) transport protein B; FEOB, iron transport	86.65
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	86.35
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	86.25
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	86.23
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	86.22
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	86.14
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	85.78
3th5_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	85.87
3cb4_D	599	GTP-binding protein LEPA; GTPase, OB-fold, membran	85.61
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	85.48
4dcu_A	456	GTP-binding protein ENGA; GTPase, GDP, protein bin	85.4
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	85.26
1lnz_A	342	SPO0B-associated GTP-binding protein; GTPase, OBG,	85.01
2ywe_A	600	GTP-binding protein LEPA; G domain, beta-barrel, f	84.98
2hjg_A	436	GTP-binding protein ENGA; GTPase ENGA KH-domain, h	84.76
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	84.73
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	84.71
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	84.45
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	84.33
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	84.28
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	84.25
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	83.65
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	82.99
2hf9_A	226	Probable hydrogenase nickel incorporation protein	82.77
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	82.66
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	82.31
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	82.11
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	81.99
3e3x_A	332	BIPA; MCSG,PSI2, structural genomics, protein stru	81.97
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	81.53
2hjg_A	436	GTP-binding protein ENGA; GTPase ENGA KH-domain, h	80.27
3gee_A	476	MNME, tRNA modification GTPase MNME; G protein, cy	80.2
3c5h_A	255	Glucocorticoid receptor DNA-binding factor 1; RAS,	80.12

>2xex_A Elongation factor G; GTPase, translation, biosynthetic protein; 1.90A {Staphylococcus aureus}

Probab=100.00  E-value=4e-34  Score=272.35  Aligned_cols=193  Identities=27%  Similarity=0.406  Sum_probs=162.6

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc-----------
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL-----------   91 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~-----------   91 (221)
                      .|+.+...++.  .+....+.....+++++.++..+|||+|||++|.|+++|||+|++++|+|.+++..           
T Consensus       221 ~dd~l~e~~l~--~~~~~~~~~~~~l~~~~~~~~~~Pv~~gSA~~~~Gv~~LLd~i~~~lPsP~~~~~~~~~~~~~~~~~  298 (693)
T 2xex_A          221 TSDELMEKYLG--DEEISVSELKEAIRQATTNVEFYPVLCGTAFKNKGVQLMLDAVIDYLPSPLDVKPIIGHRASNPEEE  298 (693)
T ss_dssp             TCHHHHHHHHT--TCCCCHHHHHHHHHHHHHTTSCEEEEECBTTTTBSHHHHHHHHHHHSCCGGGSCCEEEEETTEEEEE
T ss_pred             CCHHHHHHHhc--CCCCCHHHHHHHHHHHHHhCCeeeEEEeecccCcCHHHHHHHHHHHCCCchhcccccccCCCccccc
Confidence            34455555444  12222333455677788888999999999999999999999999999999875331           


Q ss_pred             -cccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc
Q psy5461          92 -AMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT  170 (221)
Q Consensus        92 -~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~  170 (221)
                       .+.|++++||+|+|||+.+|+++|+++|+|||||+|++||+|++.+++++++|++|+.++|+++++++++.||||+++.
T Consensus       299 ~~~~~~~~~p~~a~VfK~~~d~~~g~~~~~RV~sG~l~~g~~v~~~~~~~~~~v~~l~~~~g~~~~~v~~~~aGdI~~i~  378 (693)
T 2xex_A          299 VIAKADDSAEFAALAFKVMTDPYVGKLTFFRVYSGTMTSGSYVKNSTKGKRERVGRLLQMHANSRQEIDTVYSGDIAAAV  378 (693)
T ss_dssp             EEECSCTTSCCEEEEEEEEEETTTEEEEEEEEEESEEETTEEEEETTTTEEEEECCEEEECSSCEEECSEEETTCEEEEE
T ss_pred             eeecCCCCCceEEEEEEeeecCCCceEEEEEEEeeeEecCCEEEecCCCceEEeceEEEEeCCCceEccccCcCCEEEEe
Confidence             2356778999999999999999999999999999999999999999898999999999999999999999999999999


Q ss_pred             CCCCCccCcEEecCC--------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         171 GLKRERGKDKRTRVI--------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       171 gl~~~~~Gdtl~~~~--------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                      |++++++||||++..        ..|.|++          |.++|.+||++|+++||++++.+|.
T Consensus       379 gl~~~~~GdTl~~~~~~~~~~~~~~~~Pv~~~av~p~~~~d~~kl~~~L~~l~~eDp~l~~~~~~  443 (693)
T 2xex_A          379 GLKDTGTGDTLCGEKNDIILESMEFPEPVIHLSVEPKSKADQDKMTQALVKLQEEDPTFHAHTDE  443 (693)
T ss_dssp             SCSSCCTTCEEEETTCCEECCCCSSCSCSEEEEEEESSHHHHHHHHHHHHHHHHHCTTCEEEC--
T ss_pred             CcccCccCCEEecCCCccccCCcCCCCceEEEEEEeCCchhHHHHHHHHHHHHhhCCeEEEEEcC
Confidence            999999999999752        1233666          7899999999999999999999864

>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=100.00  E-value=1.5e-33  Score=268.73  Aligned_cols=174  Identities=28%  Similarity=0.427  Sum_probs=155.0

Q ss_pred             hHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc------------cccCCCCCCcEEEEEEEeec
Q psy5461          44 TFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL------------AMFQHFGDSLCARAFKVVHD  111 (221)
Q Consensus        44 ~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~------------~~~~~~~~~~~~~Vfk~~~d  111 (221)
                      ....+++++.++..+|||+|||++|.||++|||+|++++|+|.+++..            .+.|++++||+|+|||+.+|
T Consensus       248 l~~~l~~~~~~~~~~Pv~~gSa~~~~Gv~~LLd~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~VfK~~~d  327 (704)
T 2rdo_7          248 IKGALRQRVLNNEIILVTCGSAFKNKGVQAMLDAVIDYLPSPVDVPAINGILDDGKDTPAERHASDDEPFSALAFKIATD  327 (704)
T ss_pred             HHHHHHHHHHhCCeeEEEEeecccCccHHHHHHHHHHHCCChhhcccccccCCcccccccccccCCCCceEEEEEEEEEc
Confidence            345667778888999999999999999999999999999999875321            23456789999999999999


Q ss_pred             CCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC------
Q psy5461         112 KHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI------  185 (221)
Q Consensus       112 ~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~------  185 (221)
                      +++|+++|+|||||+|++||+|++.+.+++++|++|+.++|+++++++++.||||+++.|++++++||||++..      
T Consensus       328 ~~~G~~~~~RV~sG~l~~g~~v~~~~~~~~~~v~~l~~~~g~~~~~v~~~~aGdIv~i~gl~~~~~GdTl~~~~~~~~l~  407 (704)
T 2rdo_7          328 PFVGNLTFFRVYSGVVNSGDTVLNSVKAARERFGRIVQMHANKREEIKEVRAGDIAAAIGLKDVTTGDTLCDPDAPIILE  407 (704)
T ss_pred             CCCceEEEEEEEeeeecCCCEEEeCCCCcEEEeceEEEEeCCCceEcceeCCCCEEEEeCcccCccCCEEeCCCcccccC
Confidence            99999999999999999999999999888999999999999999999999999999999999999999999752      


Q ss_pred             --CCCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         186 --PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       186 --~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                        +.|.|++          |.++|.+||++|+++||++++.+|.
T Consensus       408 ~~~~~~Pv~~~ai~p~~~~d~~kl~~~L~~L~~eDp~l~v~~~~  451 (704)
T 2rdo_7          408 RMEFPEPVISIAVEPKTKADQEKMGLALGRLAKEDPSFRVWTDE  451 (704)
T ss_pred             CCCCCCceEEEEEEECChHHHHHHHHHHHHHHhhCCEEEEEEcC
Confidence              1133555          7899999999999999999999865

>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=100.00  E-value=1.8e-33  Score=267.84  Aligned_cols=175  Identities=32%  Similarity=0.480  Sum_probs=140.2

Q ss_pred             chHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc----------cccCCCCCCcEEEEEEEeecC
Q psy5461          43 VTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL----------AMFQHFGDSLCARAFKVVHDK  112 (221)
Q Consensus        43 l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~----------~~~~~~~~~~~~~Vfk~~~d~  112 (221)
                      .....+++++.++..+|||+|||++|.|+++|||+|++++|+|.+++..          .+.|++++||+|+|||+.+|+
T Consensus       241 ~~~~~~~~~~~~~~~~Pv~~gSA~~~~Gv~~LLd~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~p~~~~Vfk~~~d~  320 (691)
T 1dar_A          241 ELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADP  320 (691)
T ss_dssp             HHHHHHHHHHHTTSCEEEEECBGGGTBSHHHHHHHHHHHSCCTTTSCCEEEECSSSCEEEECCCTTSCCEEEEEEEEEET
T ss_pred             HHHHHHHHHHHhCcEeEEEEeecccCcCHHHHHHHHHHhCCChhhcccccccCCCccccccccCCCCCcEEEEEEEEEcC
Confidence            3455677778888999999999999999999999999999999886432          245677899999999999999


Q ss_pred             CCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCCCC-----
Q psy5461         113 HRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVIPK-----  187 (221)
Q Consensus       113 ~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~~~-----  187 (221)
                      ++|+++|+|||||+|++||+|++.+++++++|++|+.++|+++++++++.||||+++.|++++++||||++...+     
T Consensus       321 ~~G~~~~~RV~sG~l~~g~~v~~~~~~~~~~v~~l~~~~g~~~~~v~~~~aGdI~~i~gl~~~~~Gdtl~~~~~~~~~l~  400 (691)
T 1dar_A          321 YVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILE  400 (691)
T ss_dssp             TTEEEEEEEEEESEEESSCEEEETTTTEEEECCEEEEECSSCEEEESEEETTCEEEEECCSSCCTTCEEEETTCCCCBCC
T ss_pred             CCCcEEEEEEeeeeEecCCEEEecCCCcEEEEceEEEEeCCCceEcceecCCCEEEEeCcccCccCCEEecCCCcccccC
Confidence            999999999999999999999999988899999999999999999999999999999999999999999974211     


Q ss_pred             ----CCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         188 ----PTSVV----------QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       188 ----p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                          |.|++          |.++|.+||++|+++||++++.+|.
T Consensus       401 ~~~~~~P~~~~ai~p~~~~d~~kl~~~L~~l~~eDp~l~v~~~~  444 (691)
T 1dar_A          401 SIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHP  444 (691)
T ss_dssp             --------------------------------CCCCSCEEEC--
T ss_pred             CCCCCCceEEEEEEECCchhHHHHHHHHHHHHhhCCeEEEEEcC
Confidence                22444          7899999999999999999999864

>4fn5_A EF-G 1, elongation factor G 1; translation, translation-antibiotic compl; HET: 0UO; 2.90A {Pseudomonas aeruginosa}

Probab=99.98  E-value=8.6e-33  Score=263.83  Aligned_cols=176  Identities=28%  Similarity=0.442  Sum_probs=157.1

Q ss_pred             cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCccccc------------ccCCCCCCcEEEEEEEe
Q psy5461          42 AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA------------MFQHFGDSLCARAFKVV  109 (221)
Q Consensus        42 ~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~------------~~~~~~~~~~~~Vfk~~  109 (221)
                      ......++..+..+..+|++++||.++.|+..|||+|++++|+|.+++...            ..|++++||+++|||+.
T Consensus       249 ~~~~~~l~~~~~~~~~~pv~~gsa~~~~gv~~lLd~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~d~~~pl~~~VfK~~  328 (709)
T 4fn5_A          249 AEIKEGLRLRTLACEIVPAVCGSSFKNKGVPLVLDAVIDYLPAPTEIPAIKGVSPDDETVEDERHADDNEPFSSLAFKIA  328 (709)
T ss_dssp             HHHHHHHHHHHHTTSCEEEEECBTTTTBTHHHHHHHHHHHSCCTTSSCCEECBCCC-CCSCCEECSCTTSCCEEEEEECC
T ss_pred             HHHHHHHHHhhhhceeeeeeeeecccCCchHHHHHHHHhhCCCCcccccccccCCccccccccccCCccCcceEEEEEee
Confidence            334566677788889999999999999999999999999999998876431            34788899999999999


Q ss_pred             ecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCCC---
Q psy5461         110 HDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVIP---  186 (221)
Q Consensus       110 ~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~~---  186 (221)
                      +|+++|+++|+|||||+|++||+|++.++++++++++++.++|+++++++++.|||||+|.|++++.+||||++...   
T Consensus       329 ~d~~~G~la~~RV~sGtl~~G~~v~~~~~~~~~~v~~l~~~~g~~~~~v~~~~aGdIv~i~Gl~~~~~gdTl~~~~~~~~  408 (709)
T 4fn5_A          329 TDPFVGTLTFARVYSGVLSSGDSVLNSVKGKKERVGRMVQMHANQREEIKEVRAGDIAALIGMKDVTTGDTLCSIEKPII  408 (709)
T ss_dssp             CBTTTBCCCEEEEEESCEETTCBCBCTTTCCCCBCCCEECCCSSCCCEESEECTTCEEEECSCSSCCTTCEEECSSSCCB
T ss_pred             cccCCCceEEEeccCCCCCCCCEEEEecCCcEEeecceeEeecceeeEeeeecCCCeeeecCCCcCccCCEecCCCcccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999997511   


Q ss_pred             -----CCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         187 -----KPTSVV----------QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       187 -----~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                           -|.|++          |.++|.+||++|+++||++++.++.
T Consensus       409 ~~~~~~~~Pvv~vavep~~~~d~~kL~~~L~kL~~eDPsl~v~~~e  454 (709)
T 4fn5_A          409 LERMDFPEPVISVAVEPKTKADQEKMGIALGKLAQEDPSFRVKTDE  454 (709)
T ss_dssp             CC----CCCSEEEEECBSSTTTHHHHHHHHHHHHHHCTTCEEEEET
T ss_pred             CCCCCCCCcceEEEEecCCHHHhhhhHHHHHHHHHhCCeEEEEEec
Confidence                 133555          8899999999999999999998754

>3vqt_A RF-3, peptide chain release factor 3; translation, GTPase; HET: GDP; 1.80A {Desulfovibrio vulgaris} PDB: 3vr1_A*

Probab=99.98  E-value=6.7e-32  Score=250.96  Aligned_cols=164  Identities=21%  Similarity=0.298  Sum_probs=139.5

Q ss_pred             ccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccc-cCCCCCCcEEEEEEEeec---CCCceEEEEEEEceE
Q psy5461          51 GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAM-FQHFGDSLCARAFKVVHD---KHRGAVTFFRIYSGA  126 (221)
Q Consensus        51 ~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~-~~~~~~~~~~~Vfk~~~d---~~~G~i~~~RV~sG~  126 (221)
                      .++++..+|||||||++|.||++|||+|++++|+|.+++.... ....++||.|+|||+..+   +++|+++|+|||||+
T Consensus       262 ~~~~g~~~PV~~gSA~~~~Gv~~LLd~iv~~~PsP~~~~~~~~~~~~~~~p~~a~vfKi~~~~~~~~~Grla~~RV~sG~  341 (548)
T 3vqt_A          262 RYLKGELTPVFFGSAINNFGVREMLDMFVEFAPGPQPRPAATRVVEPGEEAFTGVVFKIQANMDKAHRDRMAFLRICSGT  341 (548)
T ss_dssp             HHHTTSEEEEEECBGGGTBSHHHHHHHHHHHSCCSCCEEBSSSEECTTCSSCEEEEEEEECC-------CEEEEEEEESC
T ss_pred             HHHhCCcceeeecccccCcCHHHHHHHHHHhCCCCCCccccccccCCCCcCceEEEEEEEccCCcCCCCeEEEEEEecce
Confidence            4567789999999999999999999999999999987654321 223467999999999887   899999999999999


Q ss_pred             EcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC-C-------CCCCce------
Q psy5461         127 FKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI-P-------KPTSVV------  192 (221)
Q Consensus       127 L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~-~-------~p~~~v------  192 (221)
                      |++|++|++.+++++++++++++++|.++++++++.|||||+|.|++++++|||||+.. +       .|.|++      
T Consensus       342 l~~g~~v~~~~~~~~~rv~~l~~~~g~~~~~v~~a~AGdIvai~gl~~~~~GDTl~~~~~~~~~~~i~~~~P~~~~av~p  421 (548)
T 3vqt_A          342 FTRGMRLKHHRTGKDVTVANATIFMAQDRTGVEEAFPGDIIGIPNHGTIKIGDTFTESKEVLKFVGIPNFAPEHFRRVRL  421 (548)
T ss_dssp             EETTCEEEETTTTEEEECTTCEECCCSSCCSSCEECTTCEEEEECSSCCCTTCEEESSSSCCCBCCCEEECCSEEEEEEE
T ss_pred             ecCCCEEEeeccccccccchhhhhccccccccCEEecCCEEEecCCccCccCCEecCCCCccccCCCCCCCCcceeeeee
Confidence            99999999999999999999999999999999999999999999999999999999752 1       122444      


Q ss_pred             ----ehHHHHHHHHHHhhcCCceEEE
Q psy5461         193 ----QCSARWTLNLEVGASSPIISKS  214 (221)
Q Consensus       193 ----~~~~l~~~L~~L~~~Dp~l~~~  214 (221)
                          |.++|.++|++|+++||+..++
T Consensus       422 ~~~~d~~kl~~~L~~L~eed~~~v~~  447 (548)
T 3vqt_A          422 KNPLKAKQLQKGLEQLAEEGAVQLFR  447 (548)
T ss_dssp             SCGGGHHHHHHHHHHHHHTTSSEEEE
T ss_pred             CCchhHHHHHHHHHHhhhcCceeEEE
Confidence                7799999999999999975543

>3tr5_A RF-3, peptide chain release factor 3; protein synthesis, translation; HET: GDP; 2.11A {Coxiella burnetii}

Probab=99.97  E-value=2.6e-31  Score=245.91  Aligned_cols=168  Identities=24%  Similarity=0.311  Sum_probs=143.4

Q ss_pred             hhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCC-CCCCcEEEEEEEee--cC-CCceEEEEEEEc
Q psy5461          49 YSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQH-FGDSLCARAFKVVH--DK-HRGAVTFFRIYS  124 (221)
Q Consensus        49 ~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~-~~~~~~~~Vfk~~~--d~-~~G~i~~~RV~s  124 (221)
                      ++++.++..+|||+|||++|.||++|||+|++++|+|.+......... .++||+|+|||+.+  |+ ++|+++|+||||
T Consensus       242 ~~~~~~~~~~PV~~gSA~~~~GV~~Lld~i~~~~p~p~~~~~~~~~~~~~~~~~~~~VFKi~~~~dp~~~g~l~~~RV~s  321 (528)
T 3tr5_A          242 REGYLKGELTPIFFGSAINNFGVGELLDAFVKEAPPPQGRETNSRLVKPEEEKFSGFVFKIQANMDPGHRDRIAFLRIAS  321 (528)
T ss_dssp             HHHHHTTSEEEEEECBGGGTBSHHHHHHHHHHHSCCCCCBCBSSSCBCTTSSSCEEEEEEEEECCC-CCCCEEEEEEEEE
T ss_pred             HHHHhcCceeEEEeccccCCccHHHHHHHHHHhCCCCCcccccceeeCCCcccceeEEEEEecccCccCCceEEEEEEec
Confidence            445566778899999999999999999999999999987644322222 25899999999986  88 999999999999


Q ss_pred             eEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCCC-------CCCCce-----
Q psy5461         125 GAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVIP-------KPTSVV-----  192 (221)
Q Consensus       125 G~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~~-------~p~~~v-----  192 (221)
                      |+|++||.|++.+.++++++++++.++|.+++++++|.||||+++.|++++++|||||+..+       .|.|++     
T Consensus       322 G~l~~g~~v~~~~~~~~~rv~~~~~~~~~~~~~v~~a~aGdI~~~~~l~~~~~GDtl~~~~~~~~~~~~~~~P~~~~~i~  401 (528)
T 3tr5_A          322 GQYQKGMKAYHVRLKKEIQINNALTFMAGKRENAEEAWPGDIIGLHNHGTIQIGDTFTQGERFKFTGIPNFASELFRLVR  401 (528)
T ss_dssp             SCEETTEEEEETTTTEEEEESSCBCCBTTCSSCCSEECTTCEEEEEESSSCCTTCEEESSCCCCBCCCEEECCSEEEEEE
T ss_pred             CeEcCCCEEEecCCCceEEEeeeEEEeCCCeeECCEECCCCEEEEcCCCCCccCCEEcCCCCcccCCCCCCCCCEEEEEE
Confidence            99999999999999999999999999999999999999999999999999999999997521       112333     


Q ss_pred             -----ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         193 -----QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       193 -----~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                           |.++|.+||++|++|||+ ++.++.
T Consensus       402 ~~~~~d~~kl~~aL~~L~~ED~~-~~~~~~  430 (528)
T 3tr5_A          402 LKDPLKQKALLKGLTQLSEEGAT-QLFRPL  430 (528)
T ss_dssp             ESCGGGHHHHHHHHHHHHHTTSC-EEEEET
T ss_pred             ECChhHHHHHHHHHHHHHhcCCe-EEEEcC
Confidence                 789999999999999997 555553

>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=99.97  E-value=6.8e-31  Score=243.28  Aligned_cols=167  Identities=21%  Similarity=0.267  Sum_probs=136.8

Q ss_pred             hccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCC-CCCcEEEEEEEee---cCCCceEEEEEEEce
Q psy5461          50 SGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHF-GDSLCARAFKVVH---DKHRGAVTFFRIYSG  125 (221)
Q Consensus        50 ~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~-~~~~~~~Vfk~~~---d~~~G~i~~~RV~sG  125 (221)
                      +++.++..+|||+|||++|.||++|||+|++++|+|.++......+.+ ++||+|+|||+..   ++++|+++|+||+||
T Consensus       244 ~~~~~~~~~Pv~~gSA~~~~Gv~~LLd~i~~~~P~P~~~~~~~~~~~~~~~~~~~~vfKi~~~~d~~~~G~i~~~RV~sG  323 (529)
T 2h5e_A          244 ELFLAGEITPVFFGTALGNFGVDHMLDGLVEWAPAPMPRQTDTRTVEASEDKFTGFVFKIQANMDPKHRDRVAFMRVVSG  323 (529)
T ss_dssp             HHHHTTSEEEEEECBTTTTBSHHHHHHHHHHHSCSSCCEEBSSCEECTTCCSCEEEEEEECSSCCSSSSCCCEEEEEEES
T ss_pred             HHHHhCceeEEEeeecccCCCHHHHHHHHHHhCCCCCcccccccccCCCCCCeEEEEEEEeeccCcCCCceEEEEEEecC
Confidence            445677899999999999999999999999999999875321111122 5799999999987   467999999999999


Q ss_pred             EEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCCC-------CCCCce------
Q psy5461         126 AFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVIP-------KPTSVV------  192 (221)
Q Consensus       126 ~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~~-------~p~~~v------  192 (221)
                      +|++||+|++.+.++.++|++++.++|.+++++++|.||||+++.|++++++||||++..+       .|.|++      
T Consensus       324 ~l~~g~~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdiv~i~~l~~~~~Gdtl~~~~~~~~~~~~~~~P~~~~~v~~  403 (529)
T 2h5e_A          324 KYEKGMKLRQVRTAKDVVISDALTFMAGDRSHVEEAYPGDILGLHNHGTIQIGDTFTQGEMMKFTGIPNFAPELFRRIRL  403 (529)
T ss_dssp             CEETTCEEEETTTTEEEECSCEECCCC-----CCEECTTCEEEECCSSCCCTTCEEESSCCCCBCCCEEECCSEEEEEEE
T ss_pred             eEcCCCEEEEeeCCCEEEeceeeEEeCCCceEcceECCCCEEEEeccCCCccCCEeecCCccccCCCCCCCccEEEEEEE
Confidence            9999999999999999999999999999999999999999999999999999999998522       122444      


Q ss_pred             ----ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         193 ----QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       193 ----~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                          |.++|.+||++|++||| +++.++.
T Consensus       404 ~~~~d~~kl~~~L~~L~~ed~-~~~~~~~  431 (529)
T 2h5e_A          404 KDPLKQKQLLKGLVQLSEEGA-VQVFRPI  431 (529)
T ss_dssp             SCC---CTHHHHHHHHHHTTS-CEEEEET
T ss_pred             CChHHHHHHHHHHHHHHhhCC-EEEEEeC
Confidence                77899999999999998 6777654

>2dy1_A Elongation factor G; translocation, GTP complex, structural genomics, NPPSFA; HET: GTP; 1.60A {Thermus thermophilus} SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB: 1wdt_A*

Probab=99.96  E-value=6e-30  Score=242.65  Aligned_cols=164  Identities=23%  Similarity=0.262  Sum_probs=146.5

Q ss_pred             HHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEc
Q psy5461          45 FFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYS  124 (221)
Q Consensus        45 ~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~s  124 (221)
                      ...+++++.++..+|++++||++|.||++|||+|++++|+|.++       ..++||+++|||+..|+++|+++++||||
T Consensus       235 ~~~~~~~~~~~~~~pv~~~SA~~~~Gv~~Ll~~i~~~lp~p~~~-------~~~~p~~~~V~k~~~d~~~G~~~~~rV~s  307 (665)
T 2dy1_A          235 EKAFHEAVRRGLLYPVALASGEREIGVLPLLELILEALPSPTER-------FGDGPPLAKVFKVQVDPFMGQVAYLRLYR  307 (665)
T ss_dssp             HHHHHHHHHTTSCEEEEECBTTTTBSHHHHHHHHHHHSCCHHHH-------HCSCSCEEEEEEEEEETTTEEEEEEEEEE
T ss_pred             HHHHHHHHHhCCeeEEEEeecccCcCHHHHHHHHHHhCCCcccc-------CCCCCeEEEEEEEEEcCCCCeEEEEEEcc
Confidence            44566777788899999999999999999999999999999742       15789999999999999999999999999


Q ss_pred             eEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCCC----------CCCCce--
Q psy5461         125 GAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVIP----------KPTSVV--  192 (221)
Q Consensus       125 G~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~~----------~p~~~v--  192 (221)
                      |+|++||+|++.+  +.++|++|+.++|.+.++++++.||||+++.|++++++||||++...          .|.|++  
T Consensus       308 G~l~~g~~v~~~~--~~~~v~~l~~~~g~~~~~v~~a~aG~iv~i~gl~~~~~Gdtl~~~~~~~~~~l~~~~~~~P~~~~  385 (665)
T 2dy1_A          308 GRLKPGDSLQSEA--GQVRLPHLYVPMGKDLLEVEEAEAGFVLGVPKAEGLHRGMVLWQGEKPESEEVPFARLPDPNVPV  385 (665)
T ss_dssp             SEECTTEEEBCTT--SCEEESSEEEEETTEEEEESCEETTCEEEESSCTTCCTTCEEESSSCCCGGGSCCCCCCCCCEEE
T ss_pred             cEEecCCEEEcCC--CeEEEeEEEEEeCCCeeECCEECCCCEEEEeCCccCccCCEEecCCCccccccCCCCCCCceEEE
Confidence            9999999999876  66899999999999999999999999999999999999999997421          122555  


Q ss_pred             --------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         193 --------QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       193 --------~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                              |.++|.++|++|+++||++++.+|.
T Consensus       386 ~i~p~~~~d~~kl~~~L~~l~~edp~l~v~~~~  418 (665)
T 2dy1_A          386 ALHPKGRTDEARLGEALRKLLEEDPSLKLERQE  418 (665)
T ss_dssp             EEEESSHHHHHHHHHHHHHHHHHCTTSEEEECT
T ss_pred             EEEECChhhHHHHHHHHHHHHHhCCeEEEEEcC
Confidence                    7899999999999999999999864

>3j25_A Tetracycline resistance protein TETM; antibiotic resistance, translation; HET: GCP; 7.20A {Enterococcus faecalis}

Probab=99.95  E-value=3.3e-29  Score=236.64  Aligned_cols=162  Identities=18%  Similarity=0.265  Sum_probs=141.8

Q ss_pred             HHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceE
Q psy5461          47 RIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGA  126 (221)
Q Consensus        47 ~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~  126 (221)
                      .++.+..++..+|||+|||++|.||++|||+|++++|+|.+        ...+||+|+|||+.+|+++|+++|+|||||+
T Consensus       202 ~~~~~~~~~~~~Pv~~gSa~~~~Gv~~LLd~i~~~~p~p~~--------~~~~~~~~~Vfk~~~d~~~G~la~~RV~sG~  273 (638)
T 3j25_A          202 EESIRFQNCSLFPLYHGSAKSNIGIDNLIEVITNKFYSSTH--------RGPSELCGNVFKIEYTKKRQRLAYIRLYSGV  273 (638)
T ss_dssp             HHHHHHHHTSCCCCCCCCSTTCCSHHHHHHHHHHSCCCSGG--------GSCCCCCBEEBCCCCCSTTCCCCBCCBSSBC
T ss_pred             HHhhhhcccccccccccccccCCCchhHhhhhhccccCccc--------chhhhhcceeeeeeeeccCceEEEEEEEcCc
Confidence            34445667789999999999999999999999999999987        4578999999999999999999999999999


Q ss_pred             EcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC--------CCCCCce------
Q psy5461         127 FKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI--------PKPTSVV------  192 (221)
Q Consensus       127 L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~--------~~p~~~v------  192 (221)
                      |++||+|++.+.+ ++++.+++.++|+++++++++.||||+++.| ..+++|||+++..        +.|.|++      
T Consensus       274 l~~g~~v~~~~~~-~~~v~~l~~~~g~~~~~v~~a~aGdIv~i~g-~~~~~~~tl~d~~~~~~~~~i~~p~Pv~~~aiep  351 (638)
T 3j25_A          274 LHLRDSVRVSEKE-KIKVTEMYTSINGELCKIDRAYSGEIVILQN-EFLKLNSVLGDTKLLPQRKKIENPHPLLQTTVEP  351 (638)
T ss_dssp             CCSCCCSSSCCCC-CSSBCCCCSSCCCCBSCCCTTBCCCCSCCCS-SSCSSEECSSSSSSGGGCSCCCCCCCCCCCEEEC
T ss_pred             ccCCCccccccCc-ceeEEeeecccccccccccccccceEEEEec-cccccCceecCCCCcccccCccCCCccceeeecc
Confidence            9999999887654 5799999999999999999999999999988 5778888887651        2244444      


Q ss_pred             ----ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461         193 ----QCSARWTLNLEVGASSPIISKSKRRQ  218 (221)
Q Consensus       193 ----~~~~l~~~L~~L~~~Dp~l~~~~~~~  218 (221)
                          |.++|.++|++|+++||++++.++.+
T Consensus       352 ~~~~d~~kL~~aL~kL~~eDPsl~v~~~~e  381 (638)
T 3j25_A          352 SKPEQREMLLDALLEISDSDPLLRYYVDST  381 (638)
T ss_dssp             CSHHHHHHHHHHHHHHHHTCTTCCCCCCSS
T ss_pred             CChHHHHHHHHHHHHHhhcCCeeEEEecCC
Confidence                78999999999999999999987754

>1n0u_A EF-2, elongation factor 2; G-protein, CIS-proline, translation; HET: SO1; 2.12A {Saccharomyces cerevisiae} SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB: 1n0v_C 1s1h_T 2e1r_A* 2npf_A* 2p8w_T* 3dny_T 3b82_A* 1zm2_A* 1zm3_A* 1zm4_A* 1zm9_A* 2p8x_T* 2p8y_T* 2p8z_T* 2zit_A* 1u2r_A* 3b78_A* 3b8h_A*

Probab=99.93  E-value=6.8e-26  Score=219.71  Aligned_cols=160  Identities=21%  Similarity=0.217  Sum_probs=133.3

Q ss_pred             HHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc-----------------cccCCCCCCcEEEEEEE
Q psy5461          46 FRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL-----------------AMFQHFGDSLCARAFKV  108 (221)
Q Consensus        46 ~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~-----------------~~~~~~~~~~~~~Vfk~  108 (221)
                      ..+++++ .+..+|+          +++|||+|++++|+|.+++..                 ...|++++||+|+|||+
T Consensus       317 ~~l~~~~-~~~~~pv----------~~~LLd~i~~~lPsP~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~p~~a~VfK~  385 (842)
T 1n0u_A          317 KALLKVV-MRKFLPA----------ADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKM  385 (842)
T ss_dssp             HHHHHHH-HHHHSBH----------HHHHHHHHHHHSCCHHHHHHHHHHHHBSSCTTSHHHHHHHTTCTTSSCEEEEEEE
T ss_pred             HHHHHHH-Hhhccch----------HHHHHHHHHHhCCChhHhcccccccccCCcccccccceeeccCCCCCeEEEEEee
Confidence            5666666 4456776          789999999999999865321                 12467889999999999


Q ss_pred             eecCCCce-EEEEEEEceEEcCCCEEEecc------CCc---eeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccC
Q psy5461         109 VHDKHRGA-VTFFRIYSGAFKKGQKFYNIH------LDQ---SEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGK  178 (221)
Q Consensus       109 ~~d~~~G~-i~~~RV~sG~L~~gd~v~~~~------~~~---~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~G  178 (221)
                      ..+++.|+ ++|+|||||+|++||+|++.+      .++   .+||++|++++|+++++++++.|||||+|.|++++.+|
T Consensus       386 ~~~~~~G~~l~~~RV~sG~l~~g~~v~v~~~~~n~~~~~~~~~~rv~~l~~~~g~~~~~v~~~~aGdI~ai~gl~~~~~~  465 (842)
T 1n0u_A          386 VPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLK  465 (842)
T ss_dssp             EEBSSTTCEEEEEEEEESEEETTCEEEEECTTCCSSSCTTEEEEECCEEEEEETTEEEEESEEETTCEEEEESCTTTCCS
T ss_pred             eecCCCCceEEEEEEEeeeecCCCEEEeccccccCCCCcccceEEeeeeEeeccCcccccceeCCCCEEEEEccccceec
Confidence            99999996 999999999999999996543      334   58999999999999999999999999999999988554


Q ss_pred             -cEEecCC--------CCC-CCce----------ehHHHHHHHHHHhhcCCceEEEcc
Q psy5461         179 -DKRTRVI--------PKP-TSVV----------QCSARWTLNLEVGASSPIISKSKR  216 (221)
Q Consensus       179 -dtl~~~~--------~~p-~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~  216 (221)
                       +||++..        .-| .|++          |.++|.+||++|+++||++++.++
T Consensus       466 t~Tl~~~~~~~~l~~~~~~~~Pv~~~avep~~~~d~~kl~~~L~kL~~eDp~l~v~~~  523 (842)
T 1n0u_A          466 TGTLTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMS  523 (842)
T ss_dssp             SEEEESCTTCCCBCCCCCCCSCCEEEEEEESSGGGHHHHHHHHHHHHHHCTTCEEEEC
T ss_pred             ceeecCCCCccccccCCCCCCceEEEEEEECCHHHHHHHHHHHHHHHHhCCcEEEEEc
Confidence             5998741        112 2555          889999999999999999999998

>2ywe_A GTP-binding protein LEPA; G domain, beta-barrel, ferredoxin-like domain, structural GE NPPSFA; 2.05A {Aquifex aeolicus} PDB: 2ywf_A* 2ywg_A* 2ywh_A*

Probab=99.93  E-value=2.3e-24  Score=201.79  Aligned_cols=185  Identities=18%  Similarity=0.219  Sum_probs=148.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcE
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLC  102 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~  102 (221)
                      .+-|++..+||++......+-....+.+.. .-...+++++||++|.||++|+++|.+++|+|..        +.++||.
T Consensus       124 ~~ipiIvviNKiDl~~a~~~~v~~el~~~l-g~~~~~vi~vSAktg~GI~~Lle~I~~~lp~p~~--------~~~~pl~  194 (600)
T 2ywe_A          124 QDLVIIPVINKIDLPSADVDRVKKQIEEVL-GLDPEEAILASAKEGIGIEEILEAIVNRIPPPKG--------DPQKPLK  194 (600)
T ss_dssp             TTCEEEEEEECTTSTTCCHHHHHHHHHHTS-CCCGGGCEECBTTTTBSHHHHHHHHHHHSCCCCC--------CTTSCCE
T ss_pred             CCCCEEEEEeccCccccCHHHHHHHHHHhh-CCCcccEEEEEeecCCCchHHHHHHHHhcccccc--------cccCCcc
Confidence            466899999996543221111122232221 1122358999999999999999999999999975        5678999


Q ss_pred             EEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE-cC---CCCCccC
Q psy5461         103 ARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV-TG---LKRERGK  178 (221)
Q Consensus       103 ~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i-~g---l~~~~~G  178 (221)
                      ++||++++|++.|+++++||++|++++||.|++..+++.+++.+++.+.+ +.++++++.||||+++ .|   ++++++|
T Consensus       195 ~lV~~~~~d~~~G~v~~~rV~sG~l~~Gd~I~~~~~~~~~~v~~i~~~~~-~~~~v~~~~aGdi~~v~~gi~~~~~~~~G  273 (600)
T 2ywe_A          195 ALIFDSYYDPYRGAVAFVRIFDGEVKPGDKIMLMSTGKEYEVTEVGAQTP-KMTKFDKLSAGDVGYIAASIKDVRDIRIG  273 (600)
T ss_dssp             EEEEEEEEETTTEEEEEEEEEESEECTTCEEEETTTTEEEECCEEEEESS-SEEEESCEETTCEEEEESSCCCTTSSCTT
T ss_pred             eeEEEEeecccceEEEEEEEEeCEEecCCEEEeccccceEeeecccccCC-CceECCEEecCceeeeeccccchhhccCC
Confidence            99999999999999999999999999999999999998899999997764 6889999999999976 45   4578999


Q ss_pred             cEEecCC-C---------CCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         179 DKRTRVI-P---------KPTSVV----------QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       179 dtl~~~~-~---------~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                      |||+... +         .|.|++          |.++|.++|++|.++||++.+.+.-
T Consensus       274 Dtl~~~~~~~~~~l~~~~~~~P~v~~~i~p~~~~d~~~l~~aL~kL~~eD~sl~~~~et  332 (600)
T 2ywe_A          274 DTITHAKNPTKEPVPGFQPAKPMVYAGIYPAEDTTYEELRDALEKYAINDAAIVYEPES  332 (600)
T ss_dssp             CEEEESSSCCSSCCSCCCCCCCCEEEEEEECTTCCHHHHHHHHHHHHTTCSSCEEEEEE
T ss_pred             CEEEeCCCccccccCCCCCCCcEEEEEeeccccccHHHHHHHHHHHhhhCCEEEEEECC
Confidence            9998742 1         123555          7789999999999999999998653

>3cb4_D GTP-binding protein LEPA; GTPase, OB-fold, membrane, nucleotide-binding, translation; 2.80A {Escherichia coli} PDB: 3deg_C*

Probab=99.91  E-value=1.9e-23  Score=195.67  Aligned_cols=185  Identities=17%  Similarity=0.170  Sum_probs=147.4

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcE
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLC  102 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~  102 (221)
                      .+.|++..+||++......+-....+.+.. .....+++++||++|.||++|++.|.+++|+|..        +.++|+.
T Consensus       122 ~~ipiIvViNKiDl~~a~~~~v~~ei~~~l-g~~~~~vi~vSAktg~GI~~Ll~~I~~~lp~p~~--------~~~~p~~  192 (599)
T 3cb4_D          122 MDLEVVPVLNKIDLPAADPERVAEEIEDIV-GIDATDAVRCSAKTGVGVQDVLERLVRDIPPPEG--------DPEGPLQ  192 (599)
T ss_dssp             TTCEEEEEEECTTSTTCCHHHHHHHHHHHT-CCCCTTCEEECTTTCTTHHHHHHHHHHHSCCCCC--------CTTSCCE
T ss_pred             CCCCEEEeeeccCcccccHHHHHHHHHHHh-CCCcceEEEeecccCCCchhHHHHHhhcCCCccc--------cccCCce
Confidence            466899999996543221122223333221 2222358999999999999999999999999976        5789999


Q ss_pred             EEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE-cCC---CCCccC
Q psy5461         103 ARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV-TGL---KRERGK  178 (221)
Q Consensus       103 ~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i-~gl---~~~~~G  178 (221)
                      ++||++++|++.|+++++||++|+|++||.+++..+++.+++.+++.+.+ +.++++++.||||+++ .|+   +++++|
T Consensus       193 alI~d~~~d~~~G~v~~~rV~sG~l~~Gd~v~~~~~~~~~~v~~i~~~~~-~~~~~~~~~aGdi~~~~~gi~~~~~~~~G  271 (599)
T 3cb4_D          193 ALIIDSWFDNYLGVVSLIRIKNGTLRKGDKVKVMSTGQTYNADRLGIFTP-KQVDRTELKCGEVGWLVCAIKDIHGAPVG  271 (599)
T ss_dssp             EEEEEEEEETTTEEEEEEEEEESCEESSCEEEETTTCCEEECCEEEEESS-SEEECSEECTTCEEEEECCCSSGGGSCTT
T ss_pred             eeeeeccccccccEEEEEEEEeCEEecCCEEEeccccceeEEeeeeeccC-CceECCEEcCCCeeEeeccccccccCccC
Confidence            99999999999999999999999999999999999998899999997765 5889999999999976 454   478999


Q ss_pred             cEEecCC-C---------CCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461         179 DKRTRVI-P---------KPTSVV----------QCSARWTLNLEVGASSPIISKSKRR  217 (221)
Q Consensus       179 dtl~~~~-~---------~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~  217 (221)
                      |||+... +         .|.|++          |.++|.++|++|+++||++.+....
T Consensus       272 Dtl~~~~~~~~~~l~~~~~~~P~v~~~i~p~~~~d~~~l~~aL~kL~~eD~sl~~~~et  330 (599)
T 3cb4_D          272 DTLTLARNPAEKALPGFKKVKPQVYAGLFPVSSDDYEAFRDALGKLSLNDASLFYEPES  330 (599)
T ss_dssp             CEEEESSSCCSSCCTTCCCCCCCEEEEEEESSGGGHHHHHHHHHHHHTTCSSCEEEEEE
T ss_pred             CEeeecCCccccccccccCCCcceEEEEEecCccCHHHHHHHHHHHHhhCcEEEEEecc
Confidence            9998741 1         122555          5679999999999999999987543

>1g7s_A Translation initiation factor IF2/EIF5B; translational GTPase; HET: GDP; 2.00A {Methanothermobacterthermautotrophicus} SCOP: b.43.3.1 b.43.3.1 c.20.1.1 c.37.1.8 PDB: 1g7r_A* 1g7t_A*

Probab=99.73  E-value=2.4e-17  Score=154.38  Aligned_cols=127  Identities=14%  Similarity=0.195  Sum_probs=109.8

Q ss_pred             ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEE
Q psy5461          55 KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFY  134 (221)
Q Consensus        55 ~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~  134 (221)
                      +..+|++++||++|.||++||++|..++|+|.+.   .+..++++|+.++||++..+++.|+++++||++|+|++||.|+
T Consensus       189 ~~~vpvv~vSA~tG~GI~eLl~~I~~~~~~~~~~---~l~~~~~~p~~~~V~~~~~d~g~G~v~~~rV~~G~Lk~Gd~v~  265 (594)
T 1g7s_A          189 ASQVSIIPISAITGEGIPELLTMLMGLAQQYLRE---QLKIEEDSPARGTILEVKEETGLGMTIDAVIYDGILRKDDTIA  265 (594)
T ss_dssp             TTEEEEEECCTTTCTTHHHHHHHHHHHHHHHCSG---GGEECTTSBCEEEEEEEEEETTEEEEEEEEEEESEEETTCEEE
T ss_pred             cCcceEEEEeccCCCCchhHHHHHHhhccccchh---hhccccCCCceeEEEEEEEeCCcEEEEEEEEeeCEEeeCCEEE
Confidence            3467999999999999999999999998865531   1123567899999999999999999999999999999999999


Q ss_pred             eccCCcee--eeceeEeee--------cCCeeeeCccc--cCCEEEEcCCCCCccCcEEecC
Q psy5461         135 NIHLDQSE--QITRLLLAE--------ADDYKEVNEIQ--CGNIAAVTGLKRERGKDKRTRV  184 (221)
Q Consensus       135 ~~~~~~~~--~v~~i~~~~--------g~~~~~v~~a~--aGdIv~i~gl~~~~~Gdtl~~~  184 (221)
                      +.+.+..+  +|++|+.+.        +.+..+++++.  +|+++++.|++++.+||||+..
T Consensus       266 ~~~~~~~~~~rV~~i~~~~~~~elr~~~~~~~~v~ea~~~aG~~v~~~~l~~~~~Gd~l~~~  327 (594)
T 1g7s_A          266 MMTSKDVISTRIRSLLKPRPLEEMRESRKKFQKVDEVVAAAGIKIVAPGIDDVMAGSPLRVV  327 (594)
T ss_dssp             EEBSSSEEEEECCEEEEECCCC----CCCSEEECSEEESSEEEEEECSSCTTBCTTCEEEEC
T ss_pred             ECCCCCceeEEEeEEEeccccchhhhccCCceEccEEcCCCCcEEEEcccCCCCCCCEEEec
Confidence            98877544  999998763        66788999988  9999999999999999999875

>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=99.66  E-value=3.9e-16  Score=139.66  Aligned_cols=149  Identities=21%  Similarity=0.242  Sum_probs=115.2

Q ss_pred             CCc-eeeeeeeecccc--cCCcchHHHHhhcc----ccccCceeEecCCCcccc------------------HHHHHHHH
Q psy5461          24 GDS-LCARAFKVVHDK--HRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIG------------------VQKLMDAI   78 (221)
Q Consensus        24 ~~~-~~~~vfk~~~d~--~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~G------------------i~~LLd~I   78 (221)
                      +-| ++..++|++...  ..-+.....+.+..    ......|++.+||++|.|                  +.+|+++|
T Consensus       127 ~ip~iivviNK~Dl~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~i~~SA~~g~~v~~~~~~~~~~~~~~~~~i~~Ll~~l  206 (405)
T 2c78_A          127 GVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAI  206 (405)
T ss_dssp             TCCCEEEEEECGGGCCCHHHHHHHHHHHHHHHHHTTSCTTTSCEEECCHHHHHHHHHHCTTCCTTSCHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECccccCcHHHHHHHHHHHHHHHHHhcccccCCCEEEccHHHhhhhhccccccccCCCcccccHHHHHHHH
Confidence            446 788999965321  10111112222211    122357999999999987                  89999999


Q ss_pred             HhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC---ceeeeceeEeeecCCe
Q psy5461          79 VDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD---QSEQITRLLLAEADDY  155 (221)
Q Consensus        79 ~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~---~~~~v~~i~~~~g~~~  155 (221)
                      .+++|.|..        ..++||.+.|.+++.++++|+++++||++|+|++||+|.+.+.+   ...+|.+|...    .
T Consensus       207 ~~~lp~p~~--------~~~~p~~~~v~~v~~~~~~G~v~~g~v~~G~l~~gd~v~~~~~~~~~~~~~V~~i~~~----~  274 (405)
T 2c78_A          207 DEYIPTPVR--------DVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMH----R  274 (405)
T ss_dssp             HHHSCCCCC--------CCSSCCEEECCEEEEETTTEEEEEEECCBSEEETTCEEEEESSSSSCEEEEEEEEEET----T
T ss_pred             HhhcCCCCC--------CCCCCcEEEEEEEEEcCCCceEEEEEEecccccCCCEEEEeCCCCCeeeEEEEEEEEC----C
Confidence            999998865        46789999999999999999999999999999999999998876   47899998643    3


Q ss_pred             eeeCccccCCEEEEc--CC--CCCccCcEEecC
Q psy5461         156 KEVNEIQCGNIAAVT--GL--KRERGKDKRTRV  184 (221)
Q Consensus       156 ~~v~~a~aGdIv~i~--gl--~~~~~Gdtl~~~  184 (221)
                      .++++|.|||++++.  |+  +++++||+++..
T Consensus       275 ~~~~~a~aG~~v~~~l~g~~~~~i~~G~~l~~~  307 (405)
T 2c78_A          275 KTLQEGIAGDNVGVLLRGVSREEVERGQVLAKP  307 (405)
T ss_dssp             EEESEEETTCEEEEEESSCCTTTCCTTCEEEST
T ss_pred             cccCEEcCCCEEEEEECCCcHhhcCceEEEEcC
Confidence            688999999999654  65  578999999975

>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=99.63  E-value=9.4e-16  Score=136.94  Aligned_cols=149  Identities=20%  Similarity=0.226  Sum_probs=114.3

Q ss_pred             CCc-eeeeeeeecccc--cCCcchHHHHhhcc----ccccCceeEecCCCccc---------c-HHHHHHHHHhhCCCCC
Q psy5461          24 GDS-LCARAFKVVHDK--HRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNI---------G-VQKLMDAIVDILPSPT   86 (221)
Q Consensus        24 ~~~-~~~~vfk~~~d~--~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~---------G-i~~LLd~I~~~~PsP~   86 (221)
                      +-| ++..++|++...  ..-+.....+++..    .....+|++.+||++|.         | |.+|+++|.+++|.|.
T Consensus       118 ~vp~iivviNK~Dl~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~i~~SA~~g~n~~~~~~~~g~i~~Ll~~l~~~~p~p~  197 (397)
T 1d2e_A          118 GVEHVVVYVNKADAVQDSEMVELVELEIRELLTEFGYKGEETPIIVGSALCALEQRDPELGLKSVQKLLDAVDTYIPVPT  197 (397)
T ss_dssp             TCCCEEEEEECGGGCSCHHHHHHHHHHHHHHHHHTTSCTTTSCEEECCHHHHHTTCCTTTTHHHHHHHHHHHHHHSCCCC
T ss_pred             CCCeEEEEEECcccCCCHHHHHHHHHHHHHHHHHcCCCcccCcEEEeehhhcccccCCCccCCcHHHHHHHHHHhCCCCC
Confidence            446 678999965321  11111222232222    12235799999999976         4 9999999999999886


Q ss_pred             CcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC--ceeeeceeEeeecCCeeeeCccccC
Q psy5461          87 ERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD--QSEQITRLLLAEADDYKEVNEIQCG  164 (221)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~--~~~~v~~i~~~~g~~~~~v~~a~aG  164 (221)
                      .        +.++||.+.|++++.++++|+++++||++|+|++||+|++.+.+  +..+|++|...    ..++++|.||
T Consensus       198 ~--------~~~~p~~~~v~~v~~~~~~G~v~~g~v~~G~l~~gd~v~~~~~~~~~~~~V~~i~~~----~~~~~~a~aG  265 (397)
T 1d2e_A          198 R--------DLEKPFLLPVESVYSIPGRGTVVTGTLERGILKKGDECEFLGHSKNIRTVVTGIEMF----HKSLDRAEAG  265 (397)
T ss_dssp             C--------CTTSCCEEECCEEEEETTTEEEEEEECCBSEEETTCEEEEEETTEEEEEEEEEEEET----TEEESEEETT
T ss_pred             C--------CCCCcEEEEEEEEEEeCCceEEEEEEEeeceEeCCCEEEEeCCCCCeEEEEEEEEEC----CcccCEecCC
Confidence            5        46789999999999999999999999999999999999987764  56789998643    2678999999


Q ss_pred             CEEEEc--CC--CCCccCcEEecC
Q psy5461         165 NIAAVT--GL--KRERGKDKRTRV  184 (221)
Q Consensus       165 dIv~i~--gl--~~~~~Gdtl~~~  184 (221)
                      |++++.  |+  ++++.||+++..
T Consensus       266 ~~v~~~l~~i~~~~i~~G~~l~~~  289 (397)
T 1d2e_A          266 DNLGALVRGLKREDLRRGLVMAKP  289 (397)
T ss_dssp             CEEEEEESSCCGGGCCTTCEEEST
T ss_pred             CceEEEecccchhccCceeEEeCC
Confidence            999654  66  478999999975

>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=99.55  E-value=1.9e-14  Score=129.99  Aligned_cols=146  Identities=14%  Similarity=0.082  Sum_probs=110.0

Q ss_pred             ceeeeeeeecccc--cC---CcchHHHHhhcccc----ccCceeEecCCCccccHH------------HHHHHHHhhCCC
Q psy5461          26 SLCARAFKVVHDK--HR---GAVTFFRIYSGAFK----KNHVPVLCGSSYKNIGVQ------------KLMDAIVDILPS   84 (221)
Q Consensus        26 ~~~~~vfk~~~d~--~~---g~l~~~~l~~~~~~----~~~~Pv~~gSa~~~~Gi~------------~LLd~I~~~~Ps   84 (221)
                      +++..++|++...  ..   -+.....+.+....    ....|++..||++|.||.            .|+++|.. +|+
T Consensus       146 ~iivviNK~Dl~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~i~iSA~~g~~v~e~~~~~~~~~g~~Ll~~l~~-~~~  224 (435)
T 1jny_A          146 QLIVAVNKMDLTEPPYDEKRYKEIVDQVSKFMRSYGFNTNKVRFVPVVAPSGDNITHKSENMKWYNGPTLEEYLDQ-LEL  224 (435)
T ss_dssp             TCEEEEECGGGSSSTTCHHHHHHHHHHHHHHHHHTTCCCTTCEEEECBTTTTBTTTBCCSSCTTCCSCCHHHHHTT-CCC
T ss_pred             eEEEEEEcccCCCccccHHHHHHHHHHHHHHHHHcCCCcCCceEEEeecccCccccccccccccccchhHHHHHhc-cCC
Confidence            5888999965322  10   11222333332211    224789999999999996            79999766 455


Q ss_pred             CCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccC
Q psy5461          85 PTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCG  164 (221)
Q Consensus        85 P~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aG  164 (221)
                      |..        ..++|+.+.|..++..++.|+++++||++|+|++||.|++.+.+...+|++|+..    ..++++|.||
T Consensus       225 p~~--------~~~~~~~~~v~~v~~~~~~G~v~~g~v~~G~l~~gd~v~~~p~~~~~~V~~i~~~----~~~~~~a~aG  292 (435)
T 1jny_A          225 PPK--------PVDKPLRIPIQDVYSISGVGTVPVGRVESGVLKVGDKIVFMPAGKVGEVRSIETH----HTKMDKAEPG  292 (435)
T ss_dssp             CCC--------GGGSCCBEEEEEEEEETTTEEEEEEECCBSCEETTCEEEEETTTEEEEEEEEEET----TEEESEECTT
T ss_pred             CCC--------CCCCCeEEEEEEEEEeCCCcEEEEEEEecCeEEcCCEEEECCceeEEEEEEEEEC----CcEEeEEcCC
Confidence            653        2357888888888888899999999999999999999999988888999999642    4689999999


Q ss_pred             CEEEE--cCC--CCCccCcEEecC
Q psy5461         165 NIAAV--TGL--KRERGKDKRTRV  184 (221)
Q Consensus       165 dIv~i--~gl--~~~~~Gdtl~~~  184 (221)
                      |++++  .|+  +++++||+++..
T Consensus       293 ~~v~~~l~g~~~~~i~~Gd~l~~~  316 (435)
T 1jny_A          293 DNIGFNVRGVEKKDIKRGDVVGHP  316 (435)
T ss_dssp             CEEEEEEESSCGGGCCTTCEEECT
T ss_pred             CEEEEEEecCCHHHcCCccEecCC
Confidence            99976  454  578999999975

>2elf_A Protein translation elongation factor 1A; tRNA, pyrrolysine, structural genomics, NPPSFA; HET: CIT; 1.70A {Methanosarcina mazei}

Probab=99.54  E-value=8.4e-15  Score=129.89  Aligned_cols=152  Identities=11%  Similarity=-0.021  Sum_probs=106.9

Q ss_pred             CCce-eeeee-eecccccCCcchHHHHhhcccc--ccCceeEe--cCCCc---cccHHHHHHHHHhhCCCCCCccccccc
Q psy5461          24 GDSL-CARAF-KVVHDKHRGAVTFFRIYSGAFK--KNHVPVLC--GSSYK---NIGVQKLMDAIVDILPSPTERPALAMF   94 (221)
Q Consensus        24 ~~~~-~~~vf-k~~~d~~~g~l~~~~l~~~~~~--~~~~Pv~~--gSa~~---~~Gi~~LLd~I~~~~PsP~~~~~~~~~   94 (221)
                      +.+. +..++ |++.++..-+.....+.+....  ...+|+++  +||++   |.||++|++.|.+++|+|... ...  
T Consensus       111 ~i~~~ivvvNNK~Dl~~~~~~~~~~~i~~~l~~~~~~~~~ii~~~~SA~~~~~g~gi~~L~~~l~~~~~~~~~~-~~~--  187 (370)
T 2elf_A          111 GFKHGIIALTRSDSTHMHAIDELKAKLKVITSGTVLQDWECISLNTNKSAKNPFEGVDELKARINEVAEKIEAE-NAE--  187 (370)
T ss_dssp             TCCEEEEEECCGGGSCHHHHHHHHHHHHHHTTTSTTTTCEEEECCCCTTSSSTTTTHHHHHHHHHHHHHHHHHH-HHH--
T ss_pred             CCCeEEEEEEeccCCCHHHHHHHHHHHHHHHHhcCCCceEEEecccccccCcCCCCHHHHHHHHHhhccccccC-Ccc--
Confidence            3455 78888 9654211001112333332211  23579999  99999   999999999999999876210 000  


Q ss_pred             CCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc--CC
Q psy5461          95 QHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT--GL  172 (221)
Q Consensus        95 ~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~--gl  172 (221)
                       ....|+..+|..++..++.|+++++||++|++++||+|++...++..+|++|.. ++   +++++|.|||++++.  |+
T Consensus       188 -~~~~p~r~~v~~vf~~~~~G~v~~g~v~~G~l~~gd~v~~~p~~~~~~V~~i~~-~~---~~v~~a~aGd~v~i~l~gv  262 (370)
T 2elf_A          188 -LNSLPARIFIDHAFNVTGKGCVVLGVVKQGISKDKDKTKIFPLDRDIEIRSIQS-HD---VDIDSAPAGTRVGMRLKNV  262 (370)
T ss_dssp             -GGGSCCEEEEEEEECCC---CEEEEEEEESEEETTCEEEEETTTEEEEEEEEEE-TT---EEESEEETTCEEEEEEESC
T ss_pred             -cccccccccceeEEEcCCCceEEEEEEECCEEeeCCEEEECCCCcEEEEeEEEE-CC---CCccEEcCCCcceEEEecc
Confidence             023455556666666688999999999999999999999998888899999964 32   689999999999765  54


Q ss_pred             --CCCccCcEEec
Q psy5461         173 --KRERGKDKRTR  183 (221)
Q Consensus       173 --~~~~~Gdtl~~  183 (221)
                        +++++||+++.
T Consensus       263 ~~~~i~~Gdvl~~  275 (370)
T 2elf_A          263 QAKDIERGFIISD  275 (370)
T ss_dssp             CGGGCCTTCEEES
T ss_pred             CHHHcCCceEEEC
Confidence              47899999997

>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=99.53  E-value=9.6e-14  Score=124.29  Aligned_cols=149  Identities=17%  Similarity=0.125  Sum_probs=107.1

Q ss_pred             Cceeeeeeeeccccc-CCcchHHHHhhcccc--ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCc
Q psy5461          25 DSLCARAFKVVHDKH-RGAVTFFRIYSGAFK--KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSL  101 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~-~g~l~~~~l~~~~~~--~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~  101 (221)
                      .+++..++|++.... .....++.+.+-...  ...+|++.+||++|.||++|+++|.+++|.|..        +.+.|+
T Consensus       138 ~~iivviNK~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~~i~vSA~~g~gi~~L~~~l~~~~~~p~~--------~~~~~~  209 (410)
T 1kk1_A          138 KNIIIAQNKIELVDKEKALENYRQIKEFIEGTVAENAPIIPISALHGANIDVLVKAIEDFIPTPKR--------DPNKPP  209 (410)
T ss_dssp             CCEEEEEECGGGSCHHHHHHHHHHHHHHHTTSTTTTCCEEECBTTTTBSHHHHHHHHHHHSCCCCC--------CTTSCC
T ss_pred             CcEEEEEECccCCCHHHHHHHHHHHHHHHHhcCcCCCeEEEeeCCCCCCHHHHHHHHHHhCCCCcc--------ccCCCc
Confidence            468888999653221 111233344332221  246799999999999999999999999998865        456788


Q ss_pred             EEEEEEEe--------ecCCCceEEEEEEEceEEcCCCEEEeccCCc------------eeeeceeEeeecCCeeeeCcc
Q psy5461         102 CARAFKVV--------HDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ------------SEQITRLLLAEADDYKEVNEI  161 (221)
Q Consensus       102 ~~~Vfk~~--------~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~------------~~~v~~i~~~~g~~~~~v~~a  161 (221)
                      .+.|..++        .++++|+++++||++|+|++||+|.+...++            ..+|.+|+   . ...++++|
T Consensus       210 ~~~v~~~f~v~~~g~~~~~~~G~v~~g~v~~G~l~~gd~v~~~p~~~~~~~g~~~~~~~~~~v~~i~---~-~~~~v~~a  285 (410)
T 1kk1_A          210 KMLVLRSFDVNKPGTPPEKLVGGVLDGSIVQGKLKVGDEIEIRPGVPYEEHGRIKYEPITTEIVSLQ---A-GGQFVEEA  285 (410)
T ss_dssp             EEEEEEEECCSCCC----CCCCCEEEEEEEESCEETTCEEEEEEEEEEEETTEEEEEEEEEEEEEEE---E-TTEEESEE
T ss_pred             EEEEEEEEeccCCCccccCCceEEEEEEEEeCeEeeCCEEEECCCCccccccccccccceeEEEEEE---E-CCeEecEE
Confidence            88888765        3566899999999999999999999875432            34566655   2 35689999


Q ss_pred             ccCCEEEEc-C----C--CCCccCcEEecCC
Q psy5461         162 QCGNIAAVT-G----L--KRERGKDKRTRVI  185 (221)
Q Consensus       162 ~aGdIv~i~-g----l--~~~~~Gdtl~~~~  185 (221)
                      .|||++++. +    +  +++..||+++...
T Consensus       286 ~aG~~v~~~~~~~~~~~~~d~~~G~vl~~~~  316 (410)
T 1kk1_A          286 YPGGLVGVGTKLDPYLTKGDLMAGNVVGKPG  316 (410)
T ss_dssp             CSSSCEEEEESSCGGGTGGGTTTTCEEECTT
T ss_pred             cCCCEEEEEEecCcccchhhccceeEEecCC
Confidence            999988664 2    2  3567899998753

>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=99.52  E-value=8.9e-14  Score=124.30  Aligned_cols=149  Identities=17%  Similarity=0.170  Sum_probs=111.2

Q ss_pred             Cceeeeeeeeccc-ccCCcchHHHHhhccc--cccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCc
Q psy5461          25 DSLCARAFKVVHD-KHRGAVTFFRIYSGAF--KKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSL  101 (221)
Q Consensus        25 ~~~~~~vfk~~~d-~~~g~l~~~~l~~~~~--~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~  101 (221)
                      .+++..++|++.. ....+..+..+.+...  .....|++..||++|.||++|+++|.+++|.|..        ..+.|+
T Consensus       130 ~~iivviNK~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~ii~vSA~~g~gi~~L~~~l~~~l~~~~~--------~~~~~~  201 (403)
T 3sjy_A          130 KNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYR--------DLSQKP  201 (403)
T ss_dssp             CCEEEEEECGGGSCHHHHHHHHHHHHHHHTTSTTTTCCEEECBTTTTBSHHHHHHHHHHHSCCCCC--------CTTSCC
T ss_pred             CCEEEEEECccccchHHHHHHHHHHHHHHHhhCCCCCEEEEEECCCCcChHHHHHHHHHhCCCCCC--------CCCCCc
Confidence            4788999996532 2111222333333221  2236799999999999999999999999998865        457899


Q ss_pred             EEEEEEEee--------cCCCceEEEEEEEceEEcCCCEEEeccCCc------------eeeeceeEeeecCCeeeeCcc
Q psy5461         102 CARAFKVVH--------DKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ------------SEQITRLLLAEADDYKEVNEI  161 (221)
Q Consensus       102 ~~~Vfk~~~--------d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~------------~~~v~~i~~~~g~~~~~v~~a  161 (221)
                      .+.|..++.        ++++|.++++||.+|++++||+|.+...++            ..+|++|+.    ...++++|
T Consensus       202 ~~~v~~~~~v~~~~~~~~~~~G~v~~g~v~~G~~~~gd~v~~~p~~~~~~~~~~~~~~~~~~v~~i~~----~~~~~~~a  277 (403)
T 3sjy_A          202 VMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIRF----GDEEFKEA  277 (403)
T ss_dssp             EEEEEEEECCCCTTCCSSSCCCCEEEEEEEESCEETTCEEEEEEEEEEEETTEEEEEEEEEEEEEEEE----TTEEESEE
T ss_pred             EEEEEEEEeecCCCcccccCcCcEEEEEEEeCEEecCCEEEEeCCcccccccccccccccEEEEEEEE----CCEEcCEE
Confidence            999988764        455899999999999999999999975443            357888864    34689999


Q ss_pred             ccCCEEEEc-----CC--CCCccCcEEecCC
Q psy5461         162 QCGNIAAVT-----GL--KRERGKDKRTRVI  185 (221)
Q Consensus       162 ~aGdIv~i~-----gl--~~~~~Gdtl~~~~  185 (221)
                      .|||++++.     ++  +++..||+++...
T Consensus       278 ~~G~~v~~~l~~~~~~~~~d~~~G~vl~~~~  308 (403)
T 3sjy_A          278 KPGGLVAIGTYLDPSLTKADNLLGSIITLAD  308 (403)
T ss_dssp             CSSSCEEEEESSCHHHHGGGTTTTCEEEETT
T ss_pred             eCCCEEEEEeccccccchhhhccccEEeCCC
Confidence            999999873     22  3678999998753

>3j2k_7 ERF3, eukaryotic polypeptide chain release factor 3; rabbit 80S ribosome, ribosome-translation complex; 17.00A {Oryctolagus cuniculus}

Probab=99.51  E-value=7.2e-14  Score=126.43  Aligned_cols=113  Identities=14%  Similarity=0.167  Sum_probs=95.2

Q ss_pred             CceeEecCCCccccHHH------------HHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEc
Q psy5461          57 HVPVLCGSSYKNIGVQK------------LMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYS  124 (221)
Q Consensus        57 ~~Pv~~gSa~~~~Gi~~------------LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~s  124 (221)
                      .+|++..||++|.|+.+            |++.+ +.+|+|..        ..++||.+.|..++.  +.|+++.+||.+
T Consensus       198 ~~~~i~iSA~~G~ni~~l~~~~~w~~g~~L~~~l-~~i~~~~~--------~~~~p~r~~v~~~~~--~~G~v~~G~v~~  266 (439)
T 3j2k_7          198 DIHFMPCSGLTGANLKEQSDFCPWYIGLPFIPYL-DNLPNFNR--------SVDGPIRLPIVDKYK--DMGTVVLGKLES  266 (439)
T ss_pred             CeeEEEeeccCCcccccccccccccCchHHHHHH-HhCCCCcc--------CCCCCeEEEEEEEEc--CCCeEEEEEEEe
Confidence            57899999999999998            55544 45777654        457899999998875  569999999999


Q ss_pred             eEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--CCccCcEEecC
Q psy5461         125 GAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--RERGKDKRTRV  184 (221)
Q Consensus       125 G~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--~~~~Gdtl~~~  184 (221)
                      |+|++||+|.+...+.+.+|++|+.    ...++++|.|||.|+  +.|++  +++.||++++.
T Consensus       267 G~l~~Gd~v~~~p~~~~~~V~~i~~----~~~~~~~a~aG~~v~~~l~gi~~~~i~rG~vl~~~  326 (439)
T 3j2k_7          267 GSIFKGQQLVMMPNKHNVEVLGILS----DDTETDFVAPGENLKIRLKGIEEEEILPGFILCDP  326 (439)
T ss_pred             eEEecCCEEEEccCCceEEEEEEEE----CCeEcCEecCCCcceEEEeccchhhcCCcEEecCC
Confidence            9999999999999888889999874    346899999999997  77776  67999999875

>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=99.51  E-value=9.6e-14  Score=126.89  Aligned_cols=152  Identities=14%  Similarity=0.134  Sum_probs=109.4

Q ss_pred             CceeeeeeeecccccCCcchHHHHhhcc--------ccccCceeEecCCCccccHH------------------HHHHHH
Q psy5461          25 DSLCARAFKVVHDKHRGAVTFFRIYSGA--------FKKNHVPVLCGSSYKNIGVQ------------------KLMDAI   78 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~--------~~~~~~Pv~~gSa~~~~Gi~------------------~LLd~I   78 (221)
                      .+++..++|++.... -+..++.+.+..        ......|++..||++|.||.                  ++|+.+
T Consensus       172 ~~iIvviNK~Dl~~~-~~~~~~~i~~~~~~~l~~~g~~~~~~~~i~iSA~~g~gi~el~~~~~~~~wy~g~~L~~~L~~i  250 (483)
T 3p26_A          172 HNLIIAMNKMDNVDW-SQQRFEEIKSKLLPYLVDIGFFEDNINWVPISGFSGEGVYKIEYTDEVRQWYNGPNLMSTLENA  250 (483)
T ss_dssp             CCEEEEEECGGGGTT-CHHHHHHHHHHHHHHHHHHTCCGGGEEEEECCSSSCTTSSSSCCCHHHHHHCCSCCHHHHHHHH
T ss_pred             CcEEEEEECcCcccc-hHHHHHHHHHHHHHHHHHcCCCcccceEEEEeeecCCCccccCcccccccccCCCCHHHHHHHH
Confidence            458889999653221 122222222221        12225789999999999986                  356666


Q ss_pred             HhhCCC--CCCcccccccCCCCCCcEEEEEEEeecC---CCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeee--
Q psy5461          79 VDILPS--PTERPALAMFQHFGDSLCARAFKVVHDK---HRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAE--  151 (221)
Q Consensus        79 ~~~~Ps--P~~~~~~~~~~~~~~~~~~~Vfk~~~d~---~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~--  151 (221)
                      ...+|.  |..        ..+.|+.+.|..++..+   +.|+++.+||.+|+|++||+|.+...+...+|++|....  
T Consensus       251 ~~~~~~~~p~~--------~~~~p~r~~v~~v~~~~~~~g~g~v~~G~v~~G~l~~gd~v~~~p~~~~~~V~~i~~~~~~  322 (483)
T 3p26_A          251 AFKISKENEGI--------NKDDPFLFSVLEIIPSKKTSNDLALVSGKLESGSIQPGESLTIYPSEQSCIVDKIQVGSQQ  322 (483)
T ss_dssp             HHHHHHHHTTC--------CSSSCCEEEEEEEEC---CCSCCEEEEEEEEESEECTTCEEEEETTTEEEEEEEEEETTTC
T ss_pred             Hhhcccccccc--------cCCCceEEEEEEEEccCCcCCCceEEEEEEecceEccCCEEEEeCCCCeEEEEEEEEcCcc
Confidence            655655  433        45789999999988876   479999999999999999999999988888999998552  


Q ss_pred             --cCCeeeeCccccCCEEEE--cCC--CCCccCcEEecCC
Q psy5461         152 --ADDYKEVNEIQCGNIAAV--TGL--KRERGKDKRTRVI  185 (221)
Q Consensus       152 --g~~~~~v~~a~aGdIv~i--~gl--~~~~~Gdtl~~~~  185 (221)
                        |.++.++++|.|||+|++  .+.  ++++.||+++...
T Consensus       323 ~~~~~~~~~~~a~aG~~v~~~l~~~~~~di~rG~vl~~~~  362 (483)
T 3p26_A          323 GQSTNHEETDVAIKGDFVTLKLRKAYPEDIQNGDLAASVD  362 (483)
T ss_dssp             -----CCEESCEETTCEEEEEEESCCGGGCCTTCEEECTT
T ss_pred             ccccccccccEECCCCEEEEEEEecccccCCceEEEEcCC
Confidence              455689999999999976  444  6889999999753

>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=99.51  E-value=3e-13  Score=121.04  Aligned_cols=149  Identities=15%  Similarity=0.118  Sum_probs=104.6

Q ss_pred             Cceeeeeeeecccc-cCCcchHHHHhhcccc--ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCc
Q psy5461          25 DSLCARAFKVVHDK-HRGAVTFFRIYSGAFK--KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSL  101 (221)
Q Consensus        25 ~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~~--~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~  101 (221)
                      .+++..++|++... ......++.+.+....  ....|++..||++|.||++|+++|.+.+|.|..        +.+.|+
T Consensus       136 ~~iivv~NK~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~~i~vSA~~g~gi~~L~~~l~~~i~~~~~--------~~~~~~  207 (408)
T 1s0u_A          136 DKIIIVQNKIDLVDEKQAEENYEQIKEFVKGTIAENAPIIPISAHHEANIDVLLKAIQDFIPTPKR--------DPDATP  207 (408)
T ss_dssp             CCEEEEEECTTSSCTTTTTTHHHHHHHHHTTSTTTTCCEEEC------CHHHHHHHHHHHSCCCCC--------CTTSCC
T ss_pred             CeEEEEEEccCCCCHHHHHHHHHHHHHHHhhcCCCCCeEEEeeCCCCCCHHHHHHHHHHhCCCCcc--------cCCCCe
Confidence            37889999975322 2122344444443221  246799999999999999999999999998864        457889


Q ss_pred             EEEEEEEee--------cCCCceEEEEEEEceEEcCCCEEEeccCCc------------eeeeceeEeeecCCeeeeCcc
Q psy5461         102 CARAFKVVH--------DKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ------------SEQITRLLLAEADDYKEVNEI  161 (221)
Q Consensus       102 ~~~Vfk~~~--------d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~------------~~~v~~i~~~~g~~~~~v~~a  161 (221)
                      .+.|..++.        ++++|.++.+||.+|+|++||.|.+...++            ..+|.+|+.    ...++++|
T Consensus       208 ~~~v~~~f~v~~~g~~~~~~~G~v~~g~v~~G~l~~gd~v~~~p~~~~~~~~~~~~~~~~~~v~~i~~----~~~~~~~a  283 (408)
T 1s0u_A          208 RMYVARSFDINKPGTEIKDLKGGVLGGAIIQGVFKVGDEIEIRPGIKVTEGNKTFWKPLTTKIVSLAA----GNTILRKA  283 (408)
T ss_dssp             EEEEEEEECCCCSSCCGGGCCCCEEEEEEEESCEETTCEEEEEEEEEECCTTCCEEEEEEEECCEEEE----TTEEESEE
T ss_pred             EEEEEEEEeecCCCcccccCceeEEEEEEEECeEecCCEEEEcCCcccccccccccccceeEEEEEEE----CCEEcCEE
Confidence            998887653        445789999999999999999999865321            467888864    23679999


Q ss_pred             ccCCEEEEcC-----C--CCCccCcEEecCC
Q psy5461         162 QCGNIAAVTG-----L--KRERGKDKRTRVI  185 (221)
Q Consensus       162 ~aGdIv~i~g-----l--~~~~~Gdtl~~~~  185 (221)
                      .|||.+++..     +  ++++.||+++...
T Consensus       284 ~~G~~v~~~~~~~~~~~~~~~~~G~vl~~~~  314 (408)
T 1s0u_A          284 HPGGLIGVGTTLDPYLTKSDALTGSVVGLPG  314 (408)
T ss_dssp             CSSSCEEEECSSCGGGTGGGTTTTCEEESTT
T ss_pred             eCCCeEEEEeccCcccchhhccceeEEECCC
Confidence            9999998742     2  2578999998753

>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=99.50  E-value=8.3e-14  Score=137.54  Aligned_cols=149  Identities=17%  Similarity=0.180  Sum_probs=114.2

Q ss_pred             CCc-eeeeeeeecccc--cCCcchHHHHhhcc----ccccCceeEecCCCcc--------ccHHHHHHHHHhhCCCCCCc
Q psy5461          24 GDS-LCARAFKVVHDK--HRGAVTFFRIYSGA----FKKNHVPVLCGSSYKN--------IGVQKLMDAIVDILPSPTER   88 (221)
Q Consensus        24 ~~~-~~~~vfk~~~d~--~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~--------~Gi~~LLd~I~~~~PsP~~~   88 (221)
                      +-| ++..++|++...  ..-+.....+.+..    .....+|++.+||++|        .||.+|+++|.+++|.|.. 
T Consensus       411 gIP~IIVVINKiDLv~d~e~le~i~eEi~elLk~~G~~~~~vp~IpvSAktG~ng~~~w~eGI~eLleaL~~~Ip~P~r-  489 (1289)
T 3avx_A          411 GVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPER-  489 (1289)
T ss_dssp             TCSCEEEEEECCTTCCCHHHHHHHHHHHHHHHHHTTSCTTTCCEEECCSTTTTTCCHHHHHHHHHHHHHHHHTSCCCCC-
T ss_pred             CCCeEEEEEeecccccchhhHHHHHHHHHHHHHhccccccceeEEEEEeccCCCCCccccccchhhHhHHhhhcCCCcc-
Confidence            345 688899965322  11111122222211    1223589999999999        6899999999999998865 


Q ss_pred             ccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC--ceeeeceeEeeecCCeeeeCccccCCE
Q psy5461          89 PALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD--QSEQITRLLLAEADDYKEVNEIQCGNI  166 (221)
Q Consensus        89 ~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~--~~~~v~~i~~~~g~~~~~v~~a~aGdI  166 (221)
                             ..++||.+.|..++.++++|+++++||++|+|++||+|.+.+.+  ...+|++|...    ..++++|.|||+
T Consensus       490 -------~~d~Pfr~pId~Vf~i~G~GtVvtGrV~sGtLkvGD~V~I~ps~~~~~~kVksI~~~----~~~v~eA~AGd~  558 (1289)
T 3avx_A          490 -------AIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMF----RKLLDEGRAGEN  558 (1289)
T ss_dssp             -------GGGSCCEEECCEEEEETTTEEEEEEECCBSEEETTCEEEEESSSSCEEEEEEEEECS----SCEESEEETTCE
T ss_pred             -------ccccceeeeccccccccCCcEEEEEEEeccEEecCCEEEEecCCCceeEEEEEEeec----CceeeEEecCCc
Confidence                   45689999999999899999999999999999999999988776  56899998643    357899999999


Q ss_pred             EEE--cCC--CCCccCcEEecC
Q psy5461         167 AAV--TGL--KRERGKDKRTRV  184 (221)
Q Consensus       167 v~i--~gl--~~~~~Gdtl~~~  184 (221)
                      +++  .|+  ++++.||+|+..
T Consensus       559 Vgl~L~GI~~~dI~RGdVL~~~  580 (1289)
T 3avx_A          559 VGVLLRGIKREEIERGQVLAKP  580 (1289)
T ss_dssp             EEEEESSCCGGGCCTTCEEEST
T ss_pred             ceeEeeecchhcCCcccEEecC
Confidence            865  476  478999999975

>3mca_A HBS1, elongation factor 1 alpha-like protein; protein protein complex, translation regulation; 2.74A {Schizosaccharomyces pombe}

Probab=99.49  E-value=1.9e-13  Score=128.02  Aligned_cols=145  Identities=14%  Similarity=0.155  Sum_probs=112.0

Q ss_pred             ceeeeeeeecccc---cCCcchHHHHhhcc-----ccccCceeEecCCCccccHH--------------HHHHHHHhhCC
Q psy5461          26 SLCARAFKVVHDK---HRGAVTFFRIYSGA-----FKKNHVPVLCGSSYKNIGVQ--------------KLMDAIVDILP   83 (221)
Q Consensus        26 ~~~~~vfk~~~d~---~~g~l~~~~l~~~~-----~~~~~~Pv~~gSa~~~~Gi~--------------~LLd~I~~~~P   83 (221)
                      +++..+||++...   ..-+.....+....     .....+|++.+||++|.||.              .|+++|...+|
T Consensus       317 ~iIvviNKiDl~~~~~~~~~~i~~el~~~l~~~~g~~~~~~~ii~iSA~~G~gI~e~~~~~~~~w~~g~~Lle~l~~~~p  396 (592)
T 3mca_A          317 EIVVSVNKLDLMSWSEDRFQEIKNIVSDFLIKMVGFKTSNVHFVPISAISGTNLIQKDSSDLYKWYKGPTLLSALDQLVP  396 (592)
T ss_dssp             CEEEEEECGGGGTTCHHHHHHHHHHHHHHHTTTSCCCGGGEEEEEECSSSCSSSCSCCCCGGGGTCCSCCHHHHHHTSCC
T ss_pred             eEEEEEeccccccccHHHHHHHHHHHHHHHHHhhCCCccceEEEEEecccCcccccccccccccccchHHHHHHHHhhcc
Confidence            3888999965321   11111222222221     12234689999999999998              89999999887


Q ss_pred             CCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeC-ccc
Q psy5461          84 SPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVN-EIQ  162 (221)
Q Consensus        84 sP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~-~a~  162 (221)
                       |..        ..++||.+.|..++.. +.|+++++||.+|+|++||.|.+...+...+|++|...    ..+++ +|.
T Consensus       397 -p~~--------~~~~p~r~~v~~v~~~-~~g~v~~G~v~~G~l~~Gd~v~i~p~~~~~~V~~i~~~----~~~~~~~a~  462 (592)
T 3mca_A          397 -PEK--------PYRKPLRLSIDDVYRS-PRSVTVTGRVEAGNVQVNQVLYDVSSQEDAYVKNVIRN----SDPSSTWAV  462 (592)
T ss_dssp             -CSC--------TTTSCCEEEEEEEEEE-TTEEEEEEEEEESEEETTCEEEETTTTEEEEEEEEECS----SSCSCCEEE
T ss_pred             -ccc--------cccccchheeeEEEec-CCeEEEEEEEeeeeEccCCEEEEccCCceEEEEEEEEc----CccCcceec
Confidence             332        4578999999999999 89999999999999999999999988888899999842    35788 999


Q ss_pred             cCCEEE--EcCCC--CCccCcEEecC
Q psy5461         163 CGNIAA--VTGLK--RERGKDKRTRV  184 (221)
Q Consensus       163 aGdIv~--i~gl~--~~~~Gdtl~~~  184 (221)
                      |||+|+  +.|++  +++.||+++..
T Consensus       463 aG~~v~~~l~~i~~~~i~rG~vl~~~  488 (592)
T 3mca_A          463 AGDTVTLQLADIEVNQLRPGDILSNY  488 (592)
T ss_dssp             TTCEEEEEESSSCGGGCCTTCEEECS
T ss_pred             CCCEEEEEEccccccccceEEEeccC
Confidence            999996  56765  68999999976

>3izy_P Translation initiation factor IF-2, mitochondrial; E coli, RNA, ribosomal; 10.80A {Bos taurus}

Probab=99.45  E-value=4.7e-14  Score=130.54  Aligned_cols=151  Identities=14%  Similarity=0.072  Sum_probs=112.7

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhc----cccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG----AFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFG   98 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~   98 (221)
                      .+-|++..++|++............+...    ...+..+|++.+||++|.||++|++.|...++.+...      .+++
T Consensus       103 ~~vPiIVViNKiDl~~~~~~~v~~~l~~~~~~~e~~~~~~~iv~vSAktG~GI~eLle~I~~l~~~~~~~------~~~~  176 (537)
T 3izy_P          103 AHVPIVLAINKCDKAEADPEKVKKELLAYDVVCEDYGGDVQAVHVSALTGENMMALAEATIALAEMLELK------ADPT  176 (537)
T ss_dssp             TTCCEEECCBSGGGTTTSCCSSSSHHHHTTSCCCCSSSSEEECCCCSSSSCSSHHHHHHHHHHHTTCCCC------CCSS
T ss_pred             cCCcEEEEEecccccccchHHHHHHHHhhhhhHHhcCCCceEEEEECCCCCCchhHHHHHHHhhhccccc------CCCC
Confidence            45689999999764321111111112111    1112367999999999999999999999887654321      1467


Q ss_pred             CCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-cc
Q psy5461          99 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-RG  177 (221)
Q Consensus        99 ~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-~~  177 (221)
                      .|+.+.|+++..++++|++++++|.+|+|++||.+...  ....+|+.|+...   ..++++|.||++|.|.|+++. ..
T Consensus       177 ~~~~~~V~e~~~~~g~G~V~~g~V~~G~l~~Gd~v~~g--~~~~kVr~i~~~~---g~~v~~A~~G~~V~i~g~~~~~~~  251 (537)
T 3izy_P          177 GAVEGTVIESFTDKGRGPVTTAIIQRGTLRKGSILVAG--KSWAKVRLMFDEN---GRAVNEAYPSMPVGIIGWRDLPSA  251 (537)
T ss_dssp             SSEEEEEEEECCCTTCCCCEEEEEEEECCSSEEEECCS--SCCEEEEEEEECC---CCCSCCSCCSTTCCCCSSEEEEEE
T ss_pred             CCcceeEEEEEEeCCCceEEEEEEecCEEEcCCEEEeC--CceEEEEEEEcCC---CCCCcEEcCCCEEEEECCCCCCCC
Confidence            89999999999999999999999999999999998542  2335777765443   357999999999999999875 89


Q ss_pred             CcEEecC
Q psy5461         178 KDKRTRV  184 (221)
Q Consensus       178 Gdtl~~~  184 (221)
                      ||+|+..
T Consensus       252 Gd~l~~~  258 (537)
T 3izy_P          252 GDEILEV  258 (537)
T ss_dssp             ESSCCSC
T ss_pred             CCEEEec
Confidence            9999875

>3izq_1 HBS1P, elongation factor 1 alpha-like protein; NO-GO mRNA decay, ribosomal protein,hydrolase; 9.50A {Saccharomyces cerevisiae}

Probab=99.45  E-value=3.3e-13  Score=126.76  Aligned_cols=151  Identities=16%  Similarity=0.184  Sum_probs=109.4

Q ss_pred             CceeeeeeeecccccCCcchHHHHhhcc--------ccccCceeEecCCCccccHHH---------------HHHHHHhh
Q psy5461          25 DSLCARAFKVVHDKHRGAVTFFRIYSGA--------FKKNHVPVLCGSSYKNIGVQK---------------LMDAIVDI   81 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~--------~~~~~~Pv~~gSa~~~~Gi~~---------------LLd~I~~~   81 (221)
                      .+++..++|++.... .+..+..+....        ......|++..||++|.||.+               |++.|...
T Consensus       306 ~~iIVVvNKiDl~~~-~~~~~~ei~~~l~~~l~~~g~~~~~~~~i~vSA~tG~gI~el~~~~~~~~Wy~g~~L~~~L~~l  384 (611)
T 3izq_1          306 HNLIIAMNKMDNVDW-SQQRFEEIKSKLLPYLVDIGFFEDNINWVPISGFSGEGVYKIEYTDEVRQWYNGPNLMSTLENA  384 (611)
T ss_dssp             CEEEEEEECTTTTTT-CHHHHHHHHHHHHHHHHHHTCCGGGCEEEECCTTTCTTTSSCTTSCTTCCSCCSCCHHHHHTTS
T ss_pred             CeEEEEEecccccch-hHHHHHHHHHHHHHHHHhhcccccCccEEeeecccCCCccccCccccccccccCCcHHHHHHHH
Confidence            358888999653221 112222222211        112257899999999999874               45555443


Q ss_pred             ---CCC--CCCcccccccCCCCCCcEEEEEEEeecC---CCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeee--
Q psy5461          82 ---LPS--PTERPALAMFQHFGDSLCARAFKVVHDK---HRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAE--  151 (221)
Q Consensus        82 ---~Ps--P~~~~~~~~~~~~~~~~~~~Vfk~~~d~---~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~--  151 (221)
                         +|.  |..        ..+.||.+.|..++..+   +.|+++.+||.+|+|++||.|.+...+...+|++|....  
T Consensus       385 ~~~~p~~~p~~--------~~~~p~r~~V~~v~~~~~~~g~g~v~~G~V~~G~lk~Gd~v~~~p~~~~~~VksI~~~~~~  456 (611)
T 3izq_1          385 AFKISKENEGI--------NKDDPFLFSVLEIIPSKKTSNDLALVSGKLESGSIQPGESLTIYPSEQSCIVDKIQVGSQQ  456 (611)
T ss_dssp             CCCCCCSSSCC--------SCCSCCEEECCEEECCSSSCSSSSEEEEEEEESEECTTCEEEETTTTEEEEEEEEECSSCC
T ss_pred             hhcccccCccc--------ccccchhhheeeeeccCccCCCeeEEEEEEEeceeccCCEEEEecCCceEEEEEEEEcccc
Confidence               232  221        35689999999998876   579999999999999999999999988888999998552  


Q ss_pred             --cCCeeeeCccccCCEEEE--cCC--CCCccCcEEecC
Q psy5461         152 --ADDYKEVNEIQCGNIAAV--TGL--KRERGKDKRTRV  184 (221)
Q Consensus       152 --g~~~~~v~~a~aGdIv~i--~gl--~~~~~Gdtl~~~  184 (221)
                        |..+.++++|.|||+|++  .|+  ++++.||+++..
T Consensus       457 ~~~~~~~~v~~A~aGd~v~l~l~~~~~~di~rGdvl~~~  495 (611)
T 3izq_1          457 GQSTNHEETDVAIKGDFVTLKLRKAYPEDIQNGDLAASV  495 (611)
T ss_dssp             SCSSSCCCCCCEETTCEEEEEESSCCTTSCCTTCEEBCS
T ss_pred             cccccccccceecCCCcceEEeeeccHhhCcceEEccCC
Confidence              556788999999999976  454  688999999975

>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=99.36  E-value=1.1e-12  Score=119.59  Aligned_cols=114  Identities=16%  Similarity=0.200  Sum_probs=93.9

Q ss_pred             CceeEecCCCccccHHH--------------HHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEE
Q psy5461          57 HVPVLCGSSYKNIGVQK--------------LMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRI  122 (221)
Q Consensus        57 ~~Pv~~gSa~~~~Gi~~--------------LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV  122 (221)
                      .+|++..||++|.||.+              |++.|. .+|.|..        ..++||.+.|..++.+  .|+++++||
T Consensus       225 ~~~~i~vSA~~g~~i~~l~~~~~~~w~~g~~L~~~l~-~i~~~~~--------~~~~p~~~~v~~~~~~--~G~v~~G~v  293 (467)
T 1r5b_A          225 DVKYMPVSAYTGQNVKDRVDSSVCPWYQGPSLLEYLD-SMTHLER--------KVNAPFIMPIASKYKD--LGTILEGKI  293 (467)
T ss_dssp             HEEEEECBTTTTBTTSSCCCTTTCSSCCSCCHHHHHH-HCCCCHH--------HHTSCCEEECCEEEES--SSEEEEEEC
T ss_pred             CceEEecccccccccccccccccCccccchhHHHHHH-hCCCCcC--------CCCCCcEEEEEEEEeC--CCeEEEEEE
Confidence            57899999999999875              566654 5777643        3468999999888754  689999999


Q ss_pred             EceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cC-CCCCccCcEEecC
Q psy5461         123 YSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TG-LKRERGKDKRTRV  184 (221)
Q Consensus       123 ~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~g-l~~~~~Gdtl~~~  184 (221)
                      .+|+|++||.|.+...++..+|++|+..   ...++++|.|||++++  .| .++++.||+++..
T Consensus       294 ~~G~l~~gd~v~~~p~~~~~~V~~i~~~---~~~~~~~a~aG~~v~i~l~g~~~~i~rG~vl~~~  355 (467)
T 1r5b_A          294 EAGSIKKNSNVLVMPINQTLEVTAIYDE---ADEEISSSICGDQVRLRVRGDDSDVQTGYVLTST  355 (467)
T ss_dssp             CBSEEETTEEEEEETTTEEEEEEEEECT---TCCEESEEETTCEEEEEEESCCTTCCTTCEEECS
T ss_pred             eeeEEeeCCEEEEccCCeeEEEEEEecc---CCcEeeEEcCCCEEEEEEeccHhhCCceEEEeCC
Confidence            9999999999999888878899988632   2568999999999976  66 5688999999975

>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=99.35  E-value=5.3e-12  Score=114.74  Aligned_cols=146  Identities=15%  Similarity=0.088  Sum_probs=110.1

Q ss_pred             ceeeeeeeecccc---cCCcchHHHHhhccc----cccCceeEecCCCccccHH------------------------HH
Q psy5461          26 SLCARAFKVVHDK---HRGAVTFFRIYSGAF----KKNHVPVLCGSSYKNIGVQ------------------------KL   74 (221)
Q Consensus        26 ~~~~~vfk~~~d~---~~g~l~~~~l~~~~~----~~~~~Pv~~gSa~~~~Gi~------------------------~L   74 (221)
                      +++..+||++...   ..-+.....+.+...    +....|++..||++|.||.                        .|
T Consensus       147 ~iivviNK~Dl~~~~~~~~~~i~~~~~~~l~~~g~~~~~~~~i~vSA~~g~nv~~~~~~~~~~~~~~~~~~tg~~~~~~L  226 (458)
T 1f60_A          147 QLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTL  226 (458)
T ss_dssp             EEEEEEECGGGGTTCHHHHHHHHHHHHHHHHHHTCCGGGCCEEECCTTTCBTTTBCCSSCTTCCCEEEECSSSEEEESSH
T ss_pred             eEEEEEEccccccCCHHHHHHHHHHHHHHHHHcCCCccCceEEEeecccCcCcccccccCchhhcccccccccccchHHH
Confidence            4888999975321   111112222222111    1124789999999999985                        58


Q ss_pred             HHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCC
Q psy5461          75 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADD  154 (221)
Q Consensus        75 Ld~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~  154 (221)
                      +++|.. +|+|..        ..+.|+.+.|..++..++.|+++++||.+|+++.||+|.+...+...+|.+|...    
T Consensus       227 l~~l~~-~~~p~~--------~~~~p~r~~i~~v~~~~g~G~v~~G~v~~G~l~~gd~v~~~p~~~~~~V~~i~~~----  293 (458)
T 1f60_A          227 LEAIDA-IEQPSR--------PTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMH----  293 (458)
T ss_dssp             HHHHHT-SCCCCC--------CTTSCCEEEEEEEEEETTTEEEEEEECCBSCBCTTCEEEEETTTEEEEEEEEEET----
T ss_pred             HHHhhc-cCCCcc--------cCCCCcEEEEEEEEEeCCCcEEEEEEEeCCeEcCCCEEEECCCCceEEEeEEEEC----
Confidence            888765 566654        4578999999999999999999999999999999999999988888899998742    


Q ss_pred             eeeeCccccCCEEEE--cCC--CCCccCcEEecC
Q psy5461         155 YKEVNEIQCGNIAAV--TGL--KRERGKDKRTRV  184 (221)
Q Consensus       155 ~~~v~~a~aGdIv~i--~gl--~~~~~Gdtl~~~  184 (221)
                      ..++++|.|||++++  .|+  ++++.||+|+..
T Consensus       294 ~~~~~~a~aG~~v~i~l~gi~~~~i~rG~vl~~~  327 (458)
T 1f60_A          294 HEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDA  327 (458)
T ss_dssp             TEECSCBCTTCEEEEEESSCCTTTSCTTCEEEET
T ss_pred             CeEEEEEcCCCEEEEEEcCCcccccCceeEEecC
Confidence            357899999999865  576  478999999875

>1zo1_I IF2, translation initiation factor 2; E. coli, ribosome, initiation of protein synthesis, cryo-eletron microscopy, translation/RNA complex; 13.80A {Escherichia coli}

Probab=99.35  E-value=1.5e-12  Score=119.63  Aligned_cols=149  Identities=15%  Similarity=0.117  Sum_probs=106.4

Q ss_pred             CCCceeeeeeeecccccCC-----cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRG-----AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHF   97 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g-----~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~   97 (221)
                      .+-|++..+||++......     ++....+..... +..+|++.+||++|.||++|++.|......+..      ...+
T Consensus       102 ~~vPiIVviNKiDl~~~~~~~v~~~l~~~~~~~~~~-~~~~~~v~vSAktG~gI~eLle~I~~~~~~~~~------~~~~  174 (501)
T 1zo1_I          102 AQVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEW-GGESQFVHVSAKAGTGIDELLDAILLQAEVLEL------KAVR  174 (501)
T ss_dssp             TTCCEEEEEECSSSSTTCCCCTTCCCCCCCCCTTCC-SSSCEEEECCTTTCTTCTTHHHHTTTTCCCSTT------TSCC
T ss_pred             cCceEEEEEEeccccccCHHHHHHHHHHhhhhHHHh-CCCccEEEEeeeeccCcchhhhhhhhhhhhhcc------cccc
Confidence            4568999999975322111     111111111111 235799999999999999999999865322211      1145


Q ss_pred             CCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-c
Q psy5461          98 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-R  176 (221)
Q Consensus        98 ~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-~  176 (221)
                      +.|+.+.|+++..++++|+++++||++|+|++||.+.+..  ...+|+.|   .+.+..+++++.||+.+.+.|+++. .
T Consensus       175 ~~~~~~~V~e~~~d~g~G~v~~~~V~~Gtlk~Gd~v~~g~--~~~kVr~i---~~~~g~~v~~a~~g~~V~i~gl~~~~~  249 (501)
T 1zo1_I          175 KGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGF--EYGRVRAM---RNELGQEVLEAGPSIPVEILGLSGVPA  249 (501)
T ss_dssp             CSBCEEEEEEEEECSSSSEEEEEEEEESBCCTTCEEEEEB--SSCEEEEE---CCTTTTSEEEECCSSCSSSEEECSCCC
T ss_pred             ccccccceEEEEEeCCcEEEEEEEEEeeEEecCCEEEEcc--ceeEEEEE---EecCCCcCcEeccCCcEEEeCCCCCCC
Confidence            6789999999999999999999999999999999998753  22355554   4444457889999999988898874 8


Q ss_pred             cCcEEec
Q psy5461         177 GKDKRTR  183 (221)
Q Consensus       177 ~Gdtl~~  183 (221)
                      .||+++.
T Consensus       250 ~Gd~~~~  256 (501)
T 1zo1_I          250 AGDEVTV  256 (501)
T ss_dssp             TTEEEEE
T ss_pred             CCCEEEe
Confidence            9999964

>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=99.34  E-value=3.8e-12  Score=114.77  Aligned_cols=116  Identities=15%  Similarity=0.068  Sum_probs=95.1

Q ss_pred             CceeEecCCCccccHHH------------HHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEc
Q psy5461          57 HVPVLCGSSYKNIGVQK------------LMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYS  124 (221)
Q Consensus        57 ~~Pv~~gSa~~~~Gi~~------------LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~s  124 (221)
                      ..|++..||++|.||.+            |++.| +.+|.|..        ..++|+.+.|..+....+.|+...+||.+
T Consensus       197 ~~~~i~vSA~~g~gi~~~~~~~~w~~g~~L~~~l-~~i~~~~~--------~~~~~~~~~v~~v~~~~~~~~g~~G~v~~  267 (434)
T 1zun_B          197 TMAFVPMSALKGDNVVNKSERSPWYAGQSLMEIL-ETVEIASD--------RNYTDLRFPVQYVNRPNLNFRGFAGTLAS  267 (434)
T ss_dssp             EEEEEECCTTTCTTTSSCCTTCTTCCSCCTTHHH-HHSCCTTC--------CCSSSCEEECCEEECSSSSCCEEEEECCB
T ss_pred             CceEEEEeccCCCCcccccccCccccCchHHHHH-hcCCCccc--------CCCCCcEEEEEEEeccCCCceEEEEEEec
Confidence            47899999999999987            66644 45777654        45789999888887666667778899999


Q ss_pred             eEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCC--CCccCcEEecCC
Q psy5461         125 GAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK--RERGKDKRTRVI  185 (221)
Q Consensus       125 G~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~--~~~~Gdtl~~~~  185 (221)
                      |+|++||+|.+...++..+|++|....    .++++|.|||++++...+  +++.||+++...
T Consensus       268 G~l~~gd~v~~~p~~~~~~V~~i~~~~----~~~~~a~aG~~v~~~l~~~~~i~~G~~l~~~~  326 (434)
T 1zun_B          268 GIVHKGDEIVVLPSGKSSRVKSIVTFE----GELEQAGPGQAVTLTMEDEIDISRGDLLVHAD  326 (434)
T ss_dssp             SCEETTCEEEETTTCCEEEEEEEEETT----EEESEECTTCEEEEEESSCCCCCTTCEEEETT
T ss_pred             ceEeCCCEEEEecCCeEEEEEEEEEcC----cceeEecCCCEEEEEeCCccccCCccEEECCC
Confidence            999999999999888888999998553    379999999999876543  578999999763

>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=99.23  E-value=1.2e-12  Score=119.72  Aligned_cols=148  Identities=16%  Similarity=0.107  Sum_probs=109.2

Q ss_pred             CCCceeeeeeeeccc-ccCCcchHHHHhhcccc---ccCceeEecCCCccccHHHHHHHHHhhCCCC--CCcccccccCC
Q psy5461          23 FGDSLCARAFKVVHD-KHRGAVTFFRIYSGAFK---KNHVPVLCGSSYKNIGVQKLMDAIVDILPSP--TERPALAMFQH   96 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d-~~~g~l~~~~l~~~~~~---~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP--~~~~~~~~~~~   96 (221)
                      .+-|.+..++|++.. +..-+.....+.+....   -...|++..||++|.||++|++.|.+.+|.|  ..        +
T Consensus       124 ~~ip~IvviNK~Dl~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~vSA~~g~gI~~L~~~L~~~i~~~~~~~--------~  195 (482)
T 1wb1_A          124 FNIPIIVVITKSDNAGTEEIKRTEMIMKSILQSTHNLKNSSIIPISAKTGFGVDELKNLIITTLNNAEIIR--------N  195 (482)
T ss_dssp             TTCCBCEEEECTTSSCHHHHHHHHHHHHHHHHHSSSGGGCCEEECCTTTCTTHHHHHHHHHHHHHHSCCCC--------C
T ss_pred             cCCCEEEEEECCCcccchhHHHHHHHHHHHHhhhcccccceEEEEECcCCCCHHHHHHHHHHhhcCccccc--------c
Confidence            345778889996432 11112222333322111   1257899999999999999999999988755  32        3


Q ss_pred             CCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC-
Q psy5461          97 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK-  173 (221)
Q Consensus        97 ~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~-  173 (221)
                      .++||.+.|..++..++.|+++.+||.+|++++||.+.....+...+|++|...    ..++++|.|||.+++  .|++ 
T Consensus       196 ~~~~~~~~v~~v~~~~g~G~v~~g~v~~G~l~~gd~v~~~p~~~~~~V~~i~~~----~~~v~~a~~G~~v~~~l~~~~~  271 (482)
T 1wb1_A          196 TESYFKMPLDHAFPIKGAGTVVTGTINKGIVKVGDELKVLPINMSTKVRSIQYF----KESVMEAKAGDRVGMAIQGVDA  271 (482)
T ss_dssp             SSSCCBCBCSCEECCSSCCCEECCCCCBSCCCSSEEECCTTTCCCEEECCBCGG----GSCBCCCCSSCCCCEECSSCCS
T ss_pred             ccccccccceeEEEecCCceEEEEEEEEeEEeeCCEEEECCCCcEEEEeEEEEC----CeEeeEecCCCEEEEEecCCCH
Confidence            456887777777777889999999999999999999999887777899998743    346899999999865  4764 


Q ss_pred             -CCccCcEEe
Q psy5461         174 -RERGKDKRT  182 (221)
Q Consensus       174 -~~~~Gdtl~  182 (221)
                       +++.||+++
T Consensus       272 ~~i~~Gdvl~  281 (482)
T 1wb1_A          272 KQIYRGXILT  281 (482)
T ss_dssp             SCCCSSCBCC
T ss_pred             hhccccceEe
Confidence             679999993

>3e1y_E Eukaryotic peptide chain release factor GTP-bindi ERF3A; translation termination, peptide release, PTC, P biosynthesis, GTP-binding; HET: ATP; 3.80A {Homo sapiens}

Probab=98.87  E-value=5.1e-09  Score=85.37  Aligned_cols=82  Identities=15%  Similarity=0.167  Sum_probs=68.0

Q ss_pred             CCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC-
Q psy5461          97 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK-  173 (221)
Q Consensus        97 ~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~-  173 (221)
                      .++||++.|-.++.  +.|++..+||.+|++++||+|.+...+.+.+|++|+..    .+++++|.|||.+++  .|++ 
T Consensus         3 ~~~p~rl~v~~v~~--g~G~v~~G~v~~G~i~~Gd~v~i~P~~~~~~V~~I~~~----~~~~~~A~aGd~V~l~L~gi~~   76 (204)
T 3e1y_E            3 LGSPIRLPIVDKYK--DMGTVVLGKLESGSICKGQQLVMMPNKHNVEVLGILSD----DVETDTVAPGENLKIRLKGIEE   76 (204)
T ss_dssp             ----CBEEEEEEEE--SSSEEEEEECCBSCEESSCCEEETTTTEEEEEEEECSS----SSCBSEECTTSEEEEEEEESSS
T ss_pred             CCCCEEEEEEEEEc--CCCEEEEEEEecCEEECCCEEEECCCCCEEEEEEEEEC----CEEeEEECCCCEEEEEEcCCCH
Confidence            35899999988865  57999999999999999999999988888899999743    257899999999976  7775 


Q ss_pred             -CCccCcEEecC
Q psy5461         174 -RERGKDKRTRV  184 (221)
Q Consensus       174 -~~~~Gdtl~~~  184 (221)
                       +++.||++++.
T Consensus        77 ~di~rG~vl~~~   88 (204)
T 3e1y_E           77 EEILPGFILCDP   88 (204)
T ss_dssp             SCCCTTCEEBCS
T ss_pred             HHCccceEEECC
Confidence             68999999975

>1xe1_A Hypothetical protein PF0907; structural genomics, unknown function, protein structure INI secsg, conserved hypothetical protein; HET: MSE; 2.00A {Pyrococcus furiosus} SCOP: b.43.3.1

Probab=97.69  E-value=0.00048  Score=50.65  Aligned_cols=76  Identities=17%  Similarity=0.059  Sum_probs=53.6

Q ss_pred             CcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC-ceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC-CC
Q psy5461         100 SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD-QSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK-RE  175 (221)
Q Consensus       100 ~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~-~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~-~~  175 (221)
                      |....|..+..-=+ |.+..+||.+|+|++|+.|   ..+ ...+|.+|. +   ..+++++|.+||-|+  |.|.. ++
T Consensus        34 P~k~~ilp~~~~vF-gpvivGrVe~G~LK~G~~V---Pg~~~vg~VkSIE-~---~~e~v~eA~~GdnVai~Ikg~~~~I  105 (116)
T 1xe1_A           34 AGKVVVEEVVNIMG-KDVIIGTVESGMIGVGFKV---KGPSGIGGIVRIE-R---NREKVEFAIAGDRIGISIEGKIGKV  105 (116)
T ss_dssp             SEEEEEEEEEEETT-EEEEEEEEEEEEEETTCEE---ECSSCEEEEEEEE-E---TTEEESEEETTCEEEEEEESCCCCC
T ss_pred             cEEEEEEecCCeEE-CCeeEEEEeEEEEcCCCCc---CCCceEEEEEEEE-E---CCcCcCCcCCCCEEEEEEECCcccc
Confidence            44444444222223 8899999999999999999   233 345666665 2   356899999999996  45644 78


Q ss_pred             ccCcEEec
Q psy5461         176 RGKDKRTR  183 (221)
Q Consensus       176 ~~Gdtl~~  183 (221)
                      +.||++..
T Consensus       106 ~~GdVLyv  113 (116)
T 1xe1_A          106 KKGDVLEI  113 (116)
T ss_dssp             CTTCEEEE
T ss_pred             CCCcEEEE
Confidence            99999864

>3vqt_A RF-3, peptide chain release factor 3; translation, GTPase; HET: GDP; 1.80A {Desulfovibrio vulgaris} PDB: 3vr1_A*

Probab=97.50  E-value=2.2e-05  Score=72.72  Aligned_cols=67  Identities=27%  Similarity=0.489  Sum_probs=49.9

Q ss_pred             ChhhhhcCCCCCCCCccccc-cCCCCceeeeeeeeccc---ccCCcchHHHHhhccccccCceeEecCCCcc
Q psy5461           1 MDAIVDILPSPTERPALAMF-QHFGDSLCARAFKVVHD---KHRGAVTFFRIYSGAFKKNHVPVLCGSSYKN   68 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~-~~~~~~~~~~vfk~~~d---~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~   68 (221)
                      ||++++|+|+|.+++..... .+.++||+++|||+..|   ++.|++++.|+++|+++.+.. |++.+..+.
T Consensus       286 Ld~iv~~~PsP~~~~~~~~~~~~~~~p~~a~vfKi~~~~~~~~~Grla~~RV~sG~l~~g~~-v~~~~~~~~  356 (548)
T 3vqt_A          286 LDMFVEFAPGPQPRPAATRVVEPGEEAFTGVVFKIQANMDKAHRDRMAFLRICSGTFTRGMR-LKHHRTGKD  356 (548)
T ss_dssp             HHHHHHHSCCSCCEEBSSSEECTTCSSCEEEEEEEECC-------CEEEEEEEESCEETTCE-EEETTTTEE
T ss_pred             HHHHHHhCCCCCCccccccccCCCCcCceEEEEEEEccCCcCCCCeEEEEEEecceecCCCE-EEeeccccc
Confidence            68999999999887654332 34578999999999766   899999999999999998665 766555443

>4fn5_A EF-G 1, elongation factor G 1; translation, translation-antibiotic compl; HET: 0UO; 2.90A {Pseudomonas aeruginosa}

Probab=97.31  E-value=6.5e-05  Score=71.53  Aligned_cols=61  Identities=38%  Similarity=0.651  Sum_probs=51.0

Q ss_pred             ChhhhhcCCCCCCCCccccc------------cCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEe
Q psy5461           1 MDAIVDILPSPTERPALAMF------------QHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLC   62 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~------------~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~   62 (221)
                      ||++++++|+|.+++.+...            .++++|++++|||+..|++.|.+++.|+++|+++.+.. |++
T Consensus       282 Ld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~d~~~pl~~~VfK~~~d~~~G~la~~RV~sGtl~~G~~-v~~  354 (709)
T 4fn5_A          282 LDAVIDYLPAPTEIPAIKGVSPDDETVEDERHADDNEPFSSLAFKIATDPFVGTLTFARVYSGVLSSGDS-VLN  354 (709)
T ss_dssp             HHHHHHHSCCTTSSCCEECBCCC-CCSCCEECSCTTSCCEEEEEECCCBTTTBCCCEEEEEESCEETTCB-CBC
T ss_pred             HHHHHhhCCCCcccccccccCCccccccccccCCccCcceEEEEEeecccCCCceEEEeccCCCCCCCCE-EEE
Confidence            68999999999998764321            25689999999999999999999999999999887654 443

>2rdo_7 EF-G, elongation factor G; elongation factor G, EF-G, RRF, GDPNP, 50S subunit, cryo-EM, REAL-space refinement, ribonucleoprotein; 9.10A {Escherichia coli} PDB: 3j0e_H

Probab=97.17  E-value=7.4e-05  Score=71.13  Aligned_cols=63  Identities=38%  Similarity=0.672  Sum_probs=50.6

Q ss_pred             ChhhhhcCCCCCCCCccc------------cccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecC
Q psy5461           1 MDAIVDILPSPTERPALA------------MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGS   64 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~------------~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gS   64 (221)
                      ||++++++|+|.+++.+.            ...+.+.|++++|||+..|++.|.+++.|+++|+++.+.. |+..+
T Consensus       279 Ld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~VfK~~~d~~~G~~~~~RV~sG~l~~g~~-v~~~~  353 (704)
T 2rdo_7          279 LDAVIDYLPSPVDVPAINGILDDGKDTPAERHASDDEPFSALAFKIATDPFVGNLTFFRVYSGVVNSGDT-VLNSV  353 (704)
T ss_pred             HHHHHHHCCChhhcccccccCCcccccccccccCCCCceEEEEEEEEEcCCCceEEEEEEEeeeecCCCE-EEeCC
Confidence            689999999998864321            1124678999999999999999999999999999988665 55544

>1dar_A EF-G, elongation factor G; ribosomal translocase, translational GTPase; HET: GDP; 2.40A {Thermus thermophilus} SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 PDB: 1elo_A 1ktv_A 2om7_L* 2wri_Y* 2wrk_Y* 2xsy_Y* 2xuy_Y* 2j7k_A* 2efg_A* 1jqm_B 1efg_A* 1fnm_A* 1pn6_A 2bm1_A* 2bm0_A* 2bv3_A* 3izp_E 1zn0_B 1jqs_C 2bcw_C ...

Probab=97.15  E-value=0.00011  Score=69.92  Aligned_cols=62  Identities=37%  Similarity=0.629  Sum_probs=50.5

Q ss_pred             ChhhhhcCCCCCCCCccc----------cccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEec
Q psy5461           1 MDAIVDILPSPTERPALA----------MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCG   63 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~----------~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~g   63 (221)
                      ||++++++|+|.+++.+.          ...+.+.|++++|||+..|++.|.+++.|+++|+++.+.. |++.
T Consensus       273 Ld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~p~~~~Vfk~~~d~~~G~~~~~RV~sG~l~~g~~-v~~~  344 (691)
T 1dar_A          273 LDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSY-VYNT  344 (691)
T ss_dssp             HHHHHHHSCCTTTSCCEEEECSSSCEEEECCCTTSCCEEEEEEEEEETTTEEEEEEEEEESEEESSCE-EEET
T ss_pred             HHHHHHhCCChhhcccccccCCCccccccccCCCCCcEEEEEEEEEcCCCCcEEEEEEeeeeEecCCE-EEec
Confidence            589999999999875431          1124688999999999999999999999999999988665 5544

>2xex_A Elongation factor G; GTPase, translation, biosynthetic protein; 1.90A {Staphylococcus aureus}

Probab=97.08  E-value=9.3e-05  Score=70.31  Aligned_cols=62  Identities=35%  Similarity=0.564  Sum_probs=50.2

Q ss_pred             ChhhhhcCCCCCCCCccc------------cccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEec
Q psy5461           1 MDAIVDILPSPTERPALA------------MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCG   63 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~------------~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~g   63 (221)
                      ||++++++|+|.+++.+.            ...+.++||+++|||+..|++.|++++.|+++|+++.+.. |++.
T Consensus       271 Ld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~p~~a~VfK~~~d~~~g~~~~~RV~sG~l~~g~~-v~~~  344 (693)
T 2xex_A          271 LDAVIDYLPSPLDVKPIIGHRASNPEEEVIAKADDSAEFAALAFKVMTDPYVGKLTFFRVYSGTMTSGSY-VKNS  344 (693)
T ss_dssp             HHHHHHHSCCGGGSCCEEEEETTEEEEEEEECSCTTSCCEEEEEEEEEETTTEEEEEEEEEESEEETTEE-EEET
T ss_pred             HHHHHHHCCCchhcccccccCCCccccceeecCCCCCceEEEEEEeeecCCCceEEEEEEEeeeEecCCE-EEec
Confidence            689999999999864431            1124678999999999999999999999999999988654 5543

>3tr5_A RF-3, peptide chain release factor 3; protein synthesis, translation; HET: GDP; 2.11A {Coxiella burnetii}

Probab=96.98  E-value=0.00021  Score=65.87  Aligned_cols=67  Identities=27%  Similarity=0.411  Sum_probs=51.5

Q ss_pred             ChhhhhcCCCCCCCCccccc-cCCCCceeeeeeeecc--cc-cCCcchHHHHhhccccccCceeEecCCCcc
Q psy5461           1 MDAIVDILPSPTERPALAMF-QHFGDSLCARAFKVVH--DK-HRGAVTFFRIYSGAFKKNHVPVLCGSSYKN   68 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~-~~~~~~~~~~vfk~~~--d~-~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~   68 (221)
                      ||++++++|+|.++...... ...+++++++|||+.+  |+ +.|++++.|+++|+++.+.. +++....+.
T Consensus       268 ld~i~~~~p~p~~~~~~~~~~~~~~~~~~~~VFKi~~~~dp~~~g~l~~~RV~sG~l~~g~~-v~~~~~~~~  338 (528)
T 3tr5_A          268 LDAFVKEAPPPQGRETNSRLVKPEEEKFSGFVFKIQANMDPGHRDRIAFLRIASGQYQKGMK-AYHVRLKKE  338 (528)
T ss_dssp             HHHHHHHSCCCCCBCBSSSCBCTTSSSCEEEEEEEEECCC-CCCCEEEEEEEEESCEETTEE-EEETTTTEE
T ss_pred             HHHHHHhCCCCCcccccceeeCCCcccceeEEEEEecccCccCCceEEEEEEecCeEcCCCE-EEecCCCce
Confidence            57899999999987653322 2347899999999974  88 99999999999999998665 666554433

>1d1n_A Initiation factor 2; beta-barrel, gene regulation; NMR {Geobacillus stearothermophilus} SCOP: b.43.3.1

Probab=96.83  E-value=0.0029  Score=45.24  Aligned_cols=75  Identities=13%  Similarity=0.128  Sum_probs=58.8

Q ss_pred             EEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCc---eeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccC
Q psy5461         104 RAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ---SEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGK  178 (221)
Q Consensus       104 ~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~---~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~G  178 (221)
                      .|-++...+..|.+|=++|.+|.++.+..+++.+.+.   ..++.+|..+    ...++++.+|.=|.|  .+.++++.|
T Consensus        10 eVr~vF~isk~g~IAGc~V~~G~i~r~~~vRv~Rd~~vI~eG~i~SLkr~----KddV~EV~~G~ECGi~l~~~~dik~G   85 (99)
T 1d1n_A           10 EVRQTFKVSKVGTIAGCYVTDGKITRDSKVRLIRQGIVVYEGEIDSLKRY----KDDVREVAQGYECGLTIKNFNDIKEG   85 (99)
T ss_dssp             EECCCCCCSSSCCCEEEEECSSBCCSSSEEEEECSSSEEEEEECSEEECS----SSCCSCCBTTCEEEEECTTCSSCSSC
T ss_pred             EEEEEEEcCCceEEEEEEEEcCEEEcCCeEEEEECCEEEEEeEEhhhccc----ccccceECCCcEEEEEEcCcCCCCCC
Confidence            3444444467799999999999999999999998874   3467776644    346899999999966  466789999


Q ss_pred             cEEe
Q psy5461         179 DKRT  182 (221)
Q Consensus       179 dtl~  182 (221)
                      |+|-
T Consensus        86 D~Ie   89 (99)
T 1d1n_A           86 DVIE   89 (99)
T ss_dssp             SEEE
T ss_pred             CEEE
Confidence            9984

>1n0u_A EF-2, elongation factor 2; G-protein, CIS-proline, translation; HET: SO1; 2.12A {Saccharomyces cerevisiae} SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB: 1n0v_C 1s1h_T 2e1r_A* 2npf_A* 2p8w_T* 3dny_T 3b82_A* 1zm2_A* 1zm3_A* 1zm4_A* 1zm9_A* 2p8x_T* 2p8y_T* 2p8z_T* 2zit_A* 1u2r_A* 3b78_A* 3b8h_A*

Probab=96.76  E-value=8.2e-05  Score=72.17  Aligned_cols=58  Identities=26%  Similarity=0.331  Sum_probs=47.5

Q ss_pred             ChhhhhcCCCCCCCCcccc-----------------ccCCCCceeeeeeeecccccCCc-chHHHHhhccccccCc
Q psy5461           1 MDAIVDILPSPTERPALAM-----------------FQHFGDSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKNHV   58 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~-----------------~~~~~~~~~~~vfk~~~d~~~g~-l~~~~l~~~~~~~~~~   58 (221)
                      ||+|++++|||.+++.+..                 ..++++|++++|||+..|++.|+ +++.|+++|+++.+..
T Consensus       335 Ld~i~~~lPsP~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~p~~a~VfK~~~~~~~G~~l~~~RV~sG~l~~g~~  410 (842)
T 1n0u_A          335 LEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQK  410 (842)
T ss_dssp             HHHHHHHSCCHHHHHHHHHHHHBSSCTTSHHHHHHHTTCTTSSCEEEEEEEEEBSSTTCEEEEEEEEESEEETTCE
T ss_pred             HHHHHHhCCChhHhcccccccccCCcccccccceeeccCCCCCeEEEEEeeeecCCCCceEEEEEEEeeeecCCCE
Confidence            6899999999987542210                 12568899999999999999996 9999999999887654

>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation, GTP-binding domain, maturation enzyme, oxidoreductase; 2.99A {Thermotoga neapolitana}

Probab=96.76  E-value=8.3e-06  Score=73.25  Aligned_cols=153  Identities=15%  Similarity=0.107  Sum_probs=84.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcE
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLC  102 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~  102 (221)
                      .+.|++..++|++.......    ...+...+...+|++..||++|.|+++|++.|.+.+|.+.+.+... ..-..+.+.
T Consensus       139 ~~~piIvV~NK~Dl~~~~~~----~~~~~l~~~~g~~v~~vSAktg~gI~eL~~~L~~~l~~~~e~~l~~-dLv~~gd~v  213 (423)
T 3qq5_A          139 MEIPFVVVVNKIDVLGEKAE----ELKGLYESRYEAKVLLVSALQKKGFDDIGKTISEILPGDEEIPYLG-DLIDGGDLV  213 (423)
T ss_dssp             TTCCEEEECCCCTTTTCCCT----HHHHHSSCCTTCCCCCCSSCCTTSTTTHHHHHHHHSCCCCCCCSCS-CCCCTTCCE
T ss_pred             cCCCEEEEEeCcCCCCccHH----HHHHHHHHHcCCCEEEEECCCCCCHHHHHHHHHHhhhhhccCcchh-hccccCceE
Confidence            46799999999653332222    2233333444568999999999999999999999997762221000 011234455


Q ss_pred             EEEEEEeecCCCc--------------------eEEEEEEEceEEc---CCCEEEeccCCceeeeceeEeeecCCeeeeC
Q psy5461         103 ARAFKVVHDKHRG--------------------AVTFFRIYSGAFK---KGQKFYNIHLDQSEQITRLLLAEADDYKEVN  159 (221)
Q Consensus       103 ~~Vfk~~~d~~~G--------------------~i~~~RV~sG~L~---~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~  159 (221)
                      +.|..+......|                    .++..|.+.++|+   ....+....++...+|..+    .++..+..
T Consensus       214 ~lv~pid~~~pkgr~ilp~~~~ird~l~~~~~~~~~~~~~l~~~l~~l~~~~~lv~tdsq~~~~v~~~----~p~~~~~t  289 (423)
T 3qq5_A          214 ILVVPIDLGAPKGRLIMPQVHAIREALDREAIALVVKERELRYVMENIGMKPKLVITDSQVAMKVASD----VPEDVELT  289 (423)
T ss_dssp             EEECCCSCCSSTTCCCHHHHHHHHHHHHTTCEEEECCSTTHHHHHHHCSSCCSCCCBCTTHHHHHHHT----CCCSSSCC
T ss_pred             EEEeeccccCcCCccccchHHHHHHHHHhhhHHHHhhHHHHHHHHHhcCCCccEEEeccHHHHHHhcc----CCCCCCcc
Confidence            5555444333223                    3333333344432   2233333333322233322    23334444


Q ss_pred             cccc------CCEE-EEcC---CCCCccCcEEecC
Q psy5461         160 EIQC------GNIA-AVTG---LKRERGKDKRTRV  184 (221)
Q Consensus       160 ~a~a------GdIv-~i~g---l~~~~~Gdtl~~~  184 (221)
                      +...      ||+. .++|   +++++.|||+...
T Consensus       290 ~~s~l~a~~kG~~~~~~~g~~~~~~~~~gd~v~~~  324 (423)
T 3qq5_A          290 TFSIVESRYRGDLAYFVESVRKIEELEDGDTVVIM  324 (423)
T ss_dssp             CBHHHHHHHSSCSHHHHHHHHTTTTCCTTCEEEEE
T ss_pred             cHHHHhhccCCCHHHHHHHHHHHHhCCCCCEEEEe
Confidence            4444      9998 3444   6688999999654

>2crv_A IF-2MT, translation initiation factor IF-2; ribosome, beta barrel, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=96.50  E-value=0.0089  Score=44.15  Aligned_cols=75  Identities=20%  Similarity=0.201  Sum_probs=57.8

Q ss_pred             EEEEEEEeecCCCce---EEEEEEEceEEcCCCEEEeccCCce---eeeceeEeeecCCeeeeCccccCCEEEE--cCCC
Q psy5461         102 CARAFKVVHDKHRGA---VTFFRIYSGAFKKGQKFYNIHLDQS---EQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK  173 (221)
Q Consensus       102 ~~~Vfk~~~d~~~G~---i~~~RV~sG~L~~gd~v~~~~~~~~---~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~  173 (221)
                      +-.||++-   ..|+   +|=++|.+|.++.+..+++.+.+..   .++.+|.++    ...++++.+|.=|.|  .+.+
T Consensus        15 Vr~vF~is---k~g~~~~IAGC~V~~G~i~r~~~vRviRdg~vI~eG~i~SLkrf----KdDVkEV~~G~ECGi~l~~fn   87 (120)
T 2crv_A           15 ILATFTVT---EGKKKIPVADCRVQKGQLERHKKFKLIRNGQVIWKGSLTSLKHH----KDDISVIKTGMDCGLSLDEEK   87 (120)
T ss_dssp             EEEEEEEE---ETTEEEEEEEEEEEESCEETTSCEEEEETTEEEEEECCSEEESS----SSCCSEECTTCEEEEECSCTT
T ss_pred             EeEEEEeC---CCCceeEEeEEEEEcCEEEcCCeEEEEECCEEEEEeEehhhccc----ccccceecCCCEEEEEEccCC
Confidence            44566653   4466   9999999999999999999988742   366666543    346899999999965  4677


Q ss_pred             -CCccCcEEec
Q psy5461         174 -RERGKDKRTR  183 (221)
Q Consensus       174 -~~~~Gdtl~~  183 (221)
                       +++.||+|-.
T Consensus        88 iDik~GDiIE~   98 (120)
T 2crv_A           88 VEFKPGDQVIC   98 (120)
T ss_dssp             SCCCTTEEEEE
T ss_pred             CCCCCCCEEEE
Confidence             8999999843

>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=96.27  E-value=0.0011  Score=60.95  Aligned_cols=64  Identities=27%  Similarity=0.443  Sum_probs=48.6

Q ss_pred             ChhhhhcCCCCCCCCccc-cccCCCCceeeeeeeecc---cccCCcchHHHHhhccccccCceeEecCC
Q psy5461           1 MDAIVDILPSPTERPALA-MFQHFGDSLCARAFKVVH---DKHRGAVTFFRIYSGAFKKNHVPVLCGSS   65 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~-~~~~~~~~~~~~vfk~~~---d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa   65 (221)
                      ||++++++|+|.++.... .....+++|+++|||+..   +++.|++++.|+++|+++.+.. |++...
T Consensus       269 Ld~i~~~~P~P~~~~~~~~~~~~~~~~~~~~vfKi~~~~d~~~~G~i~~~RV~sG~l~~g~~-v~~~~~  336 (529)
T 2h5e_A          269 LDGLVEWAPAPMPRQTDTRTVEASEDKFTGFVFKIQANMDPKHRDRVAFMRVVSGKYEKGMK-LRQVRT  336 (529)
T ss_dssp             HHHHHHHSCSSCCEEBSSCEECTTCCSCEEEEEEECSSCCSSSSCCCEEEEEEESCEETTCE-EEETTT
T ss_pred             HHHHHHhCCCCCcccccccccCCCCCCeEEEEEEEeeccCcCCCceEEEEEEecCeEcCCCE-EEEeeC
Confidence            588999999998764311 111236899999999975   4789999999999999998665 665443

>3j25_A Tetracycline resistance protein TETM; antibiotic resistance, translation; HET: GCP; 7.20A {Enterococcus faecalis}

Probab=96.21  E-value=0.00095  Score=62.77  Aligned_cols=50  Identities=28%  Similarity=0.519  Sum_probs=43.3

Q ss_pred             ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCc
Q psy5461           1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHV   58 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~   58 (221)
                      ||++++++|+|.++        .+.+++++|||+..|++.|.+++.|+++|+++.+..
T Consensus       230 Ld~i~~~~p~p~~~--------~~~~~~~~Vfk~~~d~~~G~la~~RV~sG~l~~g~~  279 (638)
T 3j25_A          230 IEVITNKFYSSTHR--------GPSELCGNVFKIEYTKKRQRLAYIRLYSGVLHLRDS  279 (638)
T ss_dssp             HHHHHHSCCCSGGG--------SCCCCCBEEBCCCCCSTTCCCCBCCBSSBCCCSCCC
T ss_pred             hhhhhccccCcccc--------hhhhhcceeeeeeeeccCceEEEEEEEcCcccCCCc
Confidence            58899999999653        457899999999999999999999999999876543

>1zo1_I IF2, translation initiation factor 2; E. coli, ribosome, initiation of protein synthesis, cryo-eletron microscopy, translation/RNA complex; 13.80A {Escherichia coli}

Probab=95.20  E-value=0.083  Score=48.19  Aligned_cols=76  Identities=16%  Similarity=0.143  Sum_probs=58.2

Q ss_pred             EEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCce---eeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccC
Q psy5461         104 RAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQS---EQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGK  178 (221)
Q Consensus       104 ~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~---~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~G  178 (221)
                      .|-++...+..|.++=++|..|++++|..+++.+.+..   .++.+|..    ....++++..|.-|+|  .+..+++.|
T Consensus       412 ~v~~~f~~~~~~~iaG~~v~~G~~~~~~~~~~~r~~~~i~~g~i~sl~~----~k~~v~e~~~g~ecgi~~~~~~~~~~g  487 (501)
T 1zo1_I          412 EVRDVFKSPKFGAIAGCMVTEGVVKRHNPIRVLRDNVVIYEGELESLRR----FKDDVNEVRNGMECGIGVKNYNDVRTG  487 (501)
T ss_dssp             EEEECSSCCCSSCEEEEEEEEEEEETTCEEECCSSSCCCEEEEBCCEEE----TTEEESEEETTCCEEEEBCCCTTCCTT
T ss_pred             EEEEEEecCCCCEEEEEEEEeCEEecCCeEEEEeCCeEEEEEEEehhcc----cCccccEECCCCEEEEEEcCcCCCCCC
Confidence            34444444566899999999999999999999987753   35555543    4568999999999975  466789999


Q ss_pred             cEEec
Q psy5461         179 DKRTR  183 (221)
Q Consensus       179 dtl~~  183 (221)
                      |.|-.
T Consensus       488 d~~~~  492 (501)
T 1zo1_I          488 DVIEV  492 (501)
T ss_dssp             CEEEE
T ss_pred             CEEEE
Confidence            99854

>3izy_P Translation initiation factor IF-2, mitochondrial; E coli, RNA, ribosomal; 10.80A {Bos taurus}

Probab=94.70  E-value=0.28  Score=45.10  Aligned_cols=80  Identities=14%  Similarity=0.073  Sum_probs=57.8

Q ss_pred             EEEEEEEeecC---CCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc--C-CCCC
Q psy5461         102 CARAFKVVHDK---HRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT--G-LKRE  175 (221)
Q Consensus       102 ~~~Vfk~~~d~---~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~--g-l~~~  175 (221)
                      .|.|-++..-+   ..|.+|=|+|..|+++++..+++.+.+.....+.|..++ +....++++..|.=|+|.  + ..++
T Consensus       449 ~a~v~~~f~~~~~~~~~~iaG~~v~~G~i~~~~~~r~~r~~~~i~~g~i~slk-~~k~~v~ev~~g~ecgi~~~~~~~~~  527 (537)
T 3izy_P          449 EASILATFSITEGKKKVPVAGCRVQKGQIEKQKKFKLIRNGHVIWKGSLISLK-HHKDDTSVVKTGMDCGLSLDEEKIEF  527 (537)
T ss_dssp             EEEEEEEESSCSSSCCSCEEEEEECSSEEESSSEEEEESSSSEEEEEECCCCC-CSSCCCSEEETTCEEEEESSSSCSSC
T ss_pred             EEEEcCcEEECCCCccCcEEEEEEEeCeEeeCCeEEEecCCEEEEEEEEehhc-ccCcccceEcCCCEEEEEEcCcccCC
Confidence            34444444333   257899999999999999999999987543333333332 345679999999999764  5 6689


Q ss_pred             ccCcEEe
Q psy5461         176 RGKDKRT  182 (221)
Q Consensus       176 ~~Gdtl~  182 (221)
                      +.||+|-
T Consensus       528 ~~gd~ie  534 (537)
T 3izy_P          528 KVGDAII  534 (537)
T ss_dssp             SCCCEEE
T ss_pred             CCCCEEE
Confidence            9999984

>2dy1_A Elongation factor G; translocation, GTP complex, structural genomics, NPPSFA; HET: GTP; 1.60A {Thermus thermophilus} SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB: 1wdt_A*

Probab=94.38  E-value=0.0028  Score=59.87  Aligned_cols=51  Identities=37%  Similarity=0.630  Sum_probs=43.8

Q ss_pred             ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCc
Q psy5461           1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHV   58 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~   58 (221)
                      ||++++++|+|.+.       +.+.|++++|||+..|++.|.+++.|+++|+++.+..
T Consensus       265 l~~i~~~lp~p~~~-------~~~~p~~~~V~k~~~d~~~G~~~~~rV~sG~l~~g~~  315 (665)
T 2dy1_A          265 LELILEALPSPTER-------FGDGPPLAKVFKVQVDPFMGQVAYLRLYRGRLKPGDS  315 (665)
T ss_dssp             HHHHHHHSCCHHHH-------HCSCSCEEEEEEEEEETTTEEEEEEEEEESEECTTEE
T ss_pred             HHHHHHhCCCcccc-------CCCCCeEEEEEEEEEcCCCCeEEEEEEcccEEecCCE
Confidence            57889999999653       1567999999999999999999999999999887654

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=94.17  E-value=0.028  Score=44.38  Aligned_cols=65  Identities=12%  Similarity=0.020  Sum_probs=41.9

Q ss_pred             CCCceeeeeeeeccccc-CCcchHHHHhhcccc------ccCceeEecCCCccccHHHHHHHHHhhCCCCCC
Q psy5461          23 FGDSLCARAFKVVHDKH-RGAVTFFRIYSGAFK------KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTE   87 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~-~g~l~~~~l~~~~~~------~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~   87 (221)
                      .+.|++..++|++.... ........+.+....      ....|++..||++|.||++|++.|.+.+|.+..
T Consensus       143 ~~~p~i~v~nK~Dl~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~SA~~g~gv~~l~~~l~~~~~~~~~  214 (223)
T 4dhe_A          143 TGKPIHSLLTKCDKLTRQESINALRATQKSLDAYRDAGYAGKLTVQLFSALKRTGLDDAHALIESWLRPAAA  214 (223)
T ss_dssp             GCCCEEEEEECGGGSCHHHHHHHHHHHHHHHHHHHHHTCCSCEEEEEEBTTTTBSHHHHHHHHHHHHC----
T ss_pred             cCCCEEEEEeccccCChhhHHHHHHHHHHHHHhhhhcccCCCCeEEEeecCCCcCHHHHHHHHHHhcCccCC
Confidence            46788899999653221 111122333333322      356799999999999999999999999987653

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=93.94  E-value=0.057  Score=41.25  Aligned_cols=61  Identities=16%  Similarity=0.073  Sum_probs=42.0

Q ss_pred             CCCceeeeeeeeccc-ccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHD-KHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d-~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|.+.. +..-+.....+.+........|++..||++|.||++|++.|.+.++
T Consensus       132 ~~~p~i~v~nK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~l~~~l~~~l~  193 (195)
T 3pqc_A          132 LNIPFTIVLTKMDKVKMSERAKKLEEHRKVFSKYGEYTIIPTSSVTGEGISELLDLISTLLK  193 (195)
T ss_dssp             TTCCEEEEEECGGGSCGGGHHHHHHHHHHHHHSSCCSCEEECCTTTCTTHHHHHHHHHHHHC
T ss_pred             cCCCEEEEEEChhcCChHHHHHHHHHHHHHHhhcCCCceEEEecCCCCCHHHHHHHHHHHhh
Confidence            467889999996532 2212333344444333334578999999999999999999988765

>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=93.38  E-value=0.14  Score=39.05  Aligned_cols=62  Identities=15%  Similarity=0.033  Sum_probs=41.1

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhc----cccccCceeEecCCCccccHHHHHHHHHhhCCCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG----AFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTE   87 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~   87 (221)
                      .+.|++...+|.+...   +.....+.+.    ..+...++++..||++|.||+++++.|.+.++.+..
T Consensus       116 ~~~piilv~NK~Dl~~---~~~~~~i~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~~~~~~~  181 (187)
T 1zj6_A          116 RKAGLLIFANKQDVKE---CMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRLKIRLE  181 (187)
T ss_dssp             TTCEEEEEEECTTSTT---CCCHHHHHHHHTGGGCCSSCEEEEECBTTTTBTHHHHHHHHHHHHCC---
T ss_pred             CCCeEEEEEECCCCcC---CCCHHHHHHHhChhhhcCCCcEEEEccCCCCcCHHHHHHHHHHHHHHHhh
Confidence            4678899999965332   1222222221    123345689999999999999999999998877644

>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=93.34  E-value=0.084  Score=39.71  Aligned_cols=60  Identities=13%  Similarity=0.055  Sum_probs=40.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+.......+....+..-.......|++..||++|.||+++++.|.+.+
T Consensus       117 ~~~p~ilv~nK~Dl~~~~~~v~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~  176 (182)
T 1ky3_A          117 ETFPFVILGNKIDAEESKKIVSEKSAQELAKSLGDIPLFLTSAKNAINVDTAFEEIARSA  176 (182)
T ss_dssp             TTCCEEEEEECTTSCGGGCCSCHHHHHHHHHHTTSCCEEEEBTTTTBSHHHHHHHHHHHH
T ss_pred             CCCcEEEEEECCccccccccCCHHHHHHHHHhcCCCeEEEEecCCCCCHHHHHHHHHHHH
Confidence            456888999996542222233343333322223456899999999999999999998754

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=93.24  E-value=0.097  Score=39.57  Aligned_cols=64  Identities=14%  Similarity=0.148  Sum_probs=41.9

Q ss_pred             CCceeeeeeeecccccC-----------CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCC
Q psy5461          24 GDSLCARAFKVVHDKHR-----------GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTE   87 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~-----------g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~   87 (221)
                      +.|++...+|.+.....           -.+...............|++..||++|.||++|++.|.+.++.|..
T Consensus       109 ~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~~~~~~~  183 (186)
T 1mh1_A          109 NTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCPPP  183 (186)
T ss_dssp             TSCEEEEEECHHHHTCHHHHHHHHHTTCCCCCHHHHHHHHHHTTCSEEEECCTTTCTTHHHHHHHHHHHHSCCCC
T ss_pred             CCCEEEEeEcccccccchhhhhhcccccccCCHHHHHHHHHhcCCcEEEEecCCCccCHHHHHHHHHHHHhcccc
Confidence            66888889996532210           12222222222222233489999999999999999999998876643

>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=93.23  E-value=0.11  Score=38.90  Aligned_cols=59  Identities=10%  Similarity=-0.039  Sum_probs=41.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|.+..  ..++..+.+.+........|++..||++|.||+++++.|.+.+.
T Consensus       115 ~~~p~i~v~nK~Dl~--~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~~  173 (177)
T 1wms_A          115 ESFPFVILGNKIDIS--ERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRVL  173 (177)
T ss_dssp             TTSCEEEEEECTTCS--SCSSCHHHHHHHHHHTTCCCEEECCTTTCTTHHHHHHHHHHHHH
T ss_pred             CCCcEEEEEECCccc--ccccCHHHHHHHHHhcCCceEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            456888999996533  23344444444333244678999999999999999999987653

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=93.09  E-value=0.051  Score=41.09  Aligned_cols=62  Identities=15%  Similarity=0.071  Sum_probs=39.9

Q ss_pred             CCceeeeeeeecccccCC---------cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRG---------AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g---------~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.|++...+|.+......         .++.....+-.......|++..||++|.||+++++.|.+.+..|
T Consensus       112 ~~piilv~nK~Dl~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i~~~  182 (182)
T 3bwd_D          112 GVPIVLVGTKLDLRDDKQFFIDHPGAVPITTVQGEELKKLIGAPAYIECSSKSQENVKGVFDAAIRVVLQP  182 (182)
T ss_dssp             TCCEEEEEECHHHHTCHHHHHHC--CCCCCHHHHHHHHHHHTCSEEEECCTTTCTTHHHHHHHHHHHHSCC
T ss_pred             CCCEEEEEechhhhcCcccccccccCCCCCHHHHHHHHHHcCCCEEEEEECCCCCCHHHHHHHHHHHHhcC
Confidence            568888889965322211         12333332222222335899999999999999999999876544

>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=93.04  E-value=0.12  Score=38.27  Aligned_cols=59  Identities=14%  Similarity=-0.020  Sum_probs=39.6

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|++.... -++..+.+.+-.......|++..||++|.||++|++.|.+.+
T Consensus       107 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i  165 (167)
T 1c1y_A          107 EDVPMILVGNKCDLEDE-RVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQI  165 (167)
T ss_dssp             SCCCEEEEEECTTCGGG-CCSCHHHHHHHHHHTTSCEEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             CCCcEEEEEECcccccc-ccCCHHHHHHHHHHccCCcEEEecCCCCCCHHHHHHHHHHHH
Confidence            36788899999653322 223333333322222357899999999999999999998754

>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=93.04  E-value=0.14  Score=38.61  Aligned_cols=60  Identities=17%  Similarity=0.009  Sum_probs=40.7

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.|++...+|.+.... .++..+.+.+... ....|++..||++|.||++|++.|.+.++..
T Consensus       117 ~~p~i~v~nK~Dl~~~-~~~~~~~~~~~~~-~~~~~~~~~Sa~~g~gi~~l~~~l~~~~~~~  176 (181)
T 2efe_B          117 NMVMALAGNKSDLLDA-RKVTAEDAQTYAQ-ENGLFFMETSAKTATNVKEIFYEIARRLPRV  176 (181)
T ss_dssp             TCEEEEEEECTTCTTT-CCSCHHHHHHHHH-HTTCEEEECCSSSCTTHHHHHHHHHHTCC--
T ss_pred             CCcEEEEEECCccccc-ccCCHHHHHHHHH-HcCCEEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            5678888899653222 2344444433222 2346899999999999999999999988764

>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=92.91  E-value=0.12  Score=39.56  Aligned_cols=61  Identities=13%  Similarity=-0.037  Sum_probs=40.9

Q ss_pred             CCCceeeeeeeecccccC-CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHR-GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~-g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|.+..... -......+.+........|++..||++|.||++|++.|.+.++
T Consensus       133 ~~~p~i~v~nK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~l~~~l~~~l~  194 (195)
T 1svi_A          133 YGIPVIVIATKADKIPKGKWDKHAKVVRQTLNIDPEDELILFSSETKKGKDEAWGAIKKMIN  194 (195)
T ss_dssp             TTCCEEEEEECGGGSCGGGHHHHHHHHHHHHTCCTTSEEEECCTTTCTTHHHHHHHHHHHHT
T ss_pred             cCCCEEEEEECcccCChHHHHHHHHHHHHHHcccCCCceEEEEccCCCCHHHHHHHHHHHhc
Confidence            467889999996532211 1112234444333334678999999999999999999987653

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=92.79  E-value=0.16  Score=37.36  Aligned_cols=55  Identities=25%  Similarity=0.204  Sum_probs=37.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|.+....  +   ..+.+.. +.+..|++..||++|.|++++++.|.+.+|
T Consensus       107 ~~~p~ilv~nK~Dl~~~--~---~~~~~~~-~~~~~~~~~~Sa~~~~gv~~l~~~l~~~l~  161 (161)
T 2dyk_A          107 KGKPVILVATKVDDPKH--E---LYLGPLY-GLGFGDPIPTSSEHARGLEELLEAIWERLP  161 (161)
T ss_dssp             HTCCEEEEEECCCSGGG--G---GGCGGGG-GGSSCSCEECBTTTTBSHHHHHHHHHHHCC
T ss_pred             cCCCEEEEEECcccccc--h---HhHHHHH-hCCCCCeEEEecccCCChHHHHHHHHHhCc
Confidence            35688888899653322  1   1111111 222337899999999999999999999876

>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=92.72  E-value=0.2  Score=38.39  Aligned_cols=62  Identities=8%  Similarity=-0.057  Sum_probs=39.6

Q ss_pred             CCCceeeeeeeecccccCC-cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRG-AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g-~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|++...+|.+...... +-....+..........+++..||++|.||++|++.|.+.+..
T Consensus       123 ~~~piilv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~g~gv~~l~~~l~~~~~~  185 (188)
T 1zd9_A          123 QGIPVLVLGNKRDLPGALDEKELIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHSKS  185 (188)
T ss_dssp             TTCCEEEEEECTTSTTCCCHHHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHTCC-
T ss_pred             CCCCEEEEEECCCCccCCCHHHHHHHhChhhhccCCeeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            4678899999965332211 1111111111222345789999999999999999999987754

>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=92.70  E-value=0.099  Score=38.79  Aligned_cols=58  Identities=14%  Similarity=-0.036  Sum_probs=38.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+-|++...+|.+.... .++..+...... .....|++..||++|.||+++++.|.+.+
T Consensus       105 ~~~p~ilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~  162 (166)
T 3q72_A          105 DDVPIILVGNKSDLVRS-REVSVDEGRACA-VVFDCKFIETSAALHHNVQALFEGVVRQI  162 (166)
T ss_dssp             -CCCEEEEEECTTCCSS-CCSCHHHHHHHH-HHTTCEEEECBGGGTBSHHHHHHHHHHHH
T ss_pred             CCCCEEEEEeccccccc-cccCHHHHHHHH-HHhCCcEEEeccCCCCCHHHHHHHHHHHH
Confidence            45688999999654322 233333332222 22246899999999999999999998753

>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=92.69  E-value=0.23  Score=36.61  Aligned_cols=57  Identities=12%  Similarity=0.029  Sum_probs=38.4

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhh----ccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYS----GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~----~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+....   .....+.+    ...+...+|++..||++|.||+++++.|.+.++
T Consensus       101 ~~piilv~nK~Dl~~~---~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i~  161 (164)
T 1r8s_A          101 DAVLLVFANKQDLPNA---MNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLR  161 (164)
T ss_dssp             TCEEEEEEECTTSTTC---CCHHHHHHHTTGGGCSSCCEEEEECBTTTTBTHHHHHHHHHHHC-
T ss_pred             CCeEEEEEECcCCcCC---CCHHHHHHHhCcccccCccEEEEEcccCCCcCHHHHHHHHHHHHh
Confidence            6688899999654322   11122222    122234578999999999999999999998764

>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=92.66  E-value=0.13  Score=38.00  Aligned_cols=58  Identities=22%  Similarity=0.194  Sum_probs=38.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +-+++...+|.+.... .++......+.. +....|++..||++|.||++|++.|.+.++
T Consensus       111 ~~~iilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~g~gi~~l~~~i~~~~~  168 (170)
T 1r2q_A          111 NIVIALSGNKADLANK-RAVDFQEAQSYA-DDNSLLFMETSAKTSMNVNEIFMAIAKKLP  168 (170)
T ss_dssp             TCEEEEEEECGGGGGG-CCSCHHHHHHHH-HHTTCEEEECCTTTCTTHHHHHHHHHHTSC
T ss_pred             CCcEEEEEECccCccc-cccCHHHHHHHH-HHcCCeEEEEeCCCCCCHHHHHHHHHHHHh
Confidence            4566777789653322 233333333322 223468999999999999999999998875

>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=92.63  E-value=0.13  Score=39.18  Aligned_cols=57  Identities=12%  Similarity=0.074  Sum_probs=40.8

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|++...   +...+.+.+........|++..||++|.||+++++.|.+.+
T Consensus       134 ~~~piilv~NK~Dl~~---~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~l~~~l~~~i  190 (198)
T 3t1o_A          134 DDVPIVIQVNKRDLPD---ALPVEMVRAVVDPEGKFPVLEAVATEGKGVFETLKEVSRLV  190 (198)
T ss_dssp             TSSCEEEEEECTTSTT---CCCHHHHHHHHCTTCCSCEEECBGGGTBTHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEchhccc---ccCHHHHHHHHHhcCCceEEEEecCCCcCHHHHHHHHHHHH
Confidence            4668889999965332   24555555444444444899999999999999999988754

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=92.61  E-value=0.14  Score=38.02  Aligned_cols=60  Identities=12%  Similarity=0.025  Sum_probs=40.1

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.|++...+|.+.... .++......... +....|++..||++|.||+++++.|.+.+...
T Consensus       109 ~~pii~v~nK~Dl~~~-~~v~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~~~~  168 (172)
T 2erx_A          109 SIPIMLVGNKCDESPS-REVQSSEAEALA-RTWKCAFMETSAKLNHNVKELFQELLNLEKRR  168 (172)
T ss_dssp             CCCEEEEEECGGGGGG-CCSCHHHHHHHH-HHHTCEEEECBTTTTBSHHHHHHHHHHTCCSS
T ss_pred             CCCEEEEEEccccccc-cccCHHHHHHHH-HHhCCeEEEecCCCCcCHHHHHHHHHHHHhhh
Confidence            5688899999653222 122222222211 22236899999999999999999999987653

>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=92.60  E-value=0.13  Score=39.80  Aligned_cols=58  Identities=17%  Similarity=0.166  Sum_probs=40.2

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+..  ..+.....+..-.......|++..||++|.||++|++.|.+.++
T Consensus       117 ~~piilv~nK~Dl~--~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~~~  174 (207)
T 1vg8_A          117 NFPFVVLGNKIDLE--NRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNAL  174 (207)
T ss_dssp             GSCEEEEEECTTSS--CCCSCHHHHHHHHHHTTSCCEEECBTTTTBSHHHHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCc--ccccCHHHHHHHHHhcCCceEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            55888889996433  22333344333332244578999999999999999999988764

>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=92.57  E-value=0.16  Score=37.68  Aligned_cols=59  Identities=15%  Similarity=0.021  Sum_probs=38.4

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .-+++...+|.+.... .++..+.... ..+....|++..||++|.|+++|++.|.+.++.
T Consensus       111 ~~~iilv~nK~Dl~~~-~~v~~~~~~~-~~~~~~~~~~~~Sa~~~~~i~~l~~~i~~~i~~  169 (170)
T 1z0j_A          111 SIVVAIAGNKCDLTDV-REVMERDAKD-YADSIHAIFVETSAKNAININELFIEISRRIPS  169 (170)
T ss_dssp             TSEEEEEEECTTCGGG-CCSCHHHHHH-HHHHTTCEEEECBTTTTBSHHHHHHHHHHHCCC
T ss_pred             CCcEEEEEECCccccc-cccCHHHHHH-HHHHcCCEEEEEeCCCCcCHHHHHHHHHHHHhc
Confidence            4567777788653221 1233333222 222234689999999999999999999988763

>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=92.55  E-value=0.21  Score=38.42  Aligned_cols=60  Identities=15%  Similarity=0.073  Sum_probs=41.1

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.|++...+|.+.... .++..+.+.+.. +....|++..||++|.||++|++.|.+.++..
T Consensus       128 ~~piiiv~NK~Dl~~~-~~v~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i~~~  187 (192)
T 2fg5_A          128 NIVMAIAGNKCDLSDI-REVPLKDAKEYA-ESIGAIVVETSAKNAINIEELFQGISRQIPPL  187 (192)
T ss_dssp             TCEEEEEEECGGGGGG-CCSCHHHHHHHH-HTTTCEEEECBTTTTBSHHHHHHHHHHTCC--
T ss_pred             CCcEEEEEECcccccc-cccCHHHHHHHH-HHcCCEEEEEeCCCCcCHHHHHHHHHHHHHhh
Confidence            5688888999654321 233344443332 22346899999999999999999999988653

>1g7s_A Translation initiation factor IF2/EIF5B; translational GTPase; HET: GDP; 2.00A {Methanothermobacterthermautotrophicus} SCOP: b.43.3.1 b.43.3.1 c.20.1.1 c.37.1.8 PDB: 1g7r_A* 1g7t_A*

Probab=92.50  E-value=0.74  Score=42.76  Aligned_cols=67  Identities=15%  Similarity=0.165  Sum_probs=51.1

Q ss_pred             ceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCC---CCCccCcEEecCC
Q psy5461         115 GAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGL---KRERGKDKRTRVI  185 (221)
Q Consensus       115 G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl---~~~~~Gdtl~~~~  185 (221)
                      |.++=++|..|++++|..+++ +.+.  ..+.|..++ +....++++..|.-|+|  .|.   .+++.||.|....
T Consensus       479 ~~i~g~~v~~G~~~~~~~~~~-~~~~--~~g~i~sl~-~~k~~v~~~~~g~e~gi~~~~~~~~~~~~~~d~~~~~~  550 (594)
T 1g7s_A          479 PAIGGVEVLTGVIRQGYPLMN-DDGE--TVGTVESMQ-DKGENLKSASRGQKVAMAIKDAVYGKTIHEGDTLYVDI  550 (594)
T ss_dssp             SEEEEEEEEEEEEETTCEEEC-TTSC--EEEEEEEEE-ETTEEESEEETTCCEEEEEETCCBTTTBCTTCEEEECC
T ss_pred             CeEEEEEEecCEEecCCeEEe-cCCc--EEEEEehhc-ccCccccccCCCCEEEEEEeCcccCCCCCCCCEEEEEE
Confidence            799999999999999999998 4443  344444343 24568999999999965  454   5899999997653

>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=92.29  E-value=0.25  Score=38.08  Aligned_cols=57  Identities=14%  Similarity=0.008  Sum_probs=39.7

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccc-----------cccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAF-----------KKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~-----------~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|++...   +...+.+.+...           +....+++..||++|.||+++++.|.+.+
T Consensus       123 ~~~piilv~NK~Dl~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~l  190 (190)
T 1m2o_B          123 KDVPFVILGNKIDAPN---AVSEAELRSALGLLNTTGSQRIEGQRPVEVFMCSVVMRNGYLEAFQWLSQYI  190 (190)
T ss_dssp             TTCCEEEEEECTTSTT---CCCHHHHHHHTTCSSCCC---CCSSCCEEEEECBTTTTBSHHHHHHHHHTTC
T ss_pred             cCCCEEEEEECCCCcC---CCCHHHHHHHhCCccccccccccccceEEEEEeECCcCCCHHHHHHHHHhhC
Confidence            4678999999964332   344444443221           12356899999999999999999998653

>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=91.90  E-value=0.18  Score=37.39  Aligned_cols=61  Identities=18%  Similarity=0.091  Sum_probs=39.2

Q ss_pred             CCCceeeeeeeecccccCC-cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRG-AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g-~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|.+...... +-....+.........+|++..||++|.||+++++.|.+.++
T Consensus       107 ~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i~  168 (171)
T 1upt_A          107 RKAILVVFANKQDMEQAMTSSEMANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLK  168 (171)
T ss_dssp             TTCEEEEEEECTTSTTCCCHHHHHHHHTGGGCTTSCEEEEECCTTTCTTHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECCCCcCCCCHHHHHHHhCchhccCCceEEEECcCCCCcCHHHHHHHHHHHHh
Confidence            4678899999965332211 111112212223334568999999999999999999987654

>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=91.89  E-value=0.28  Score=38.09  Aligned_cols=57  Identities=12%  Similarity=-0.010  Sum_probs=39.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcccc----------------ccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFK----------------KNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~----------------~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|++...   ++..+.+.+....                ....+++..||++|.||+++++.|.+.+
T Consensus       125 ~~~piilv~NK~Dl~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~g~gv~~l~~~l~~~l  197 (198)
T 1f6b_A          125 ANVPILILGNKIDRPE---AISEERLREMFGLYGQTTGKGSVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYI  197 (198)
T ss_dssp             TTSCEEEEEECTTSTT---CCCHHHHHHHHTCTTTCCCSSCCCTTTCCSCCEEEEECBTTTTBSHHHHHHHHHTTC
T ss_pred             CCCcEEEEEECCCccc---cCCHHHHHHHhCcccccccccccccccccCceEEEEEEECCCCCCHHHHHHHHHHhc
Confidence            4678999999965432   3344444332110                1346899999999999999999998754

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=91.81  E-value=0.2  Score=38.57  Aligned_cols=59  Identities=15%  Similarity=0.015  Sum_probs=39.6

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+.... .++..+.+.+........+++..||++|.||+++++.|.+.+
T Consensus       130 ~~~piilV~NK~Dl~~~-~~v~~~~~~~~~~~~~~~~~~~~SA~~g~gi~~l~~~l~~~i  188 (192)
T 2il1_A          130 EDAELLLVGNKLDCETD-REITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDI  188 (192)
T ss_dssp             TTCEEEEEEECGGGGGG-CCSCHHHHHHHHHTSTTCEEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             CCCcEEEEEECcccccc-cccCHHHHHHHHHhcCCCeEEEEeCCCCCCHHHHHHHHHHHH
Confidence            35688999999754332 233333333322221356899999999999999999998654

>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=91.81  E-value=0.13  Score=39.57  Aligned_cols=61  Identities=7%  Similarity=-0.042  Sum_probs=39.6

Q ss_pred             CCceeeeeeeecccccC-----------CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHR-----------GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~-----------g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.|++...+|.+.....           -.+..+...+...+....|++..||++|.||+++++.|.+.+..
T Consensus       122 ~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~i~~  193 (194)
T 2atx_A          122 NVPFLLIGTQIDLRDDPKTLARLNDMKEKPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILT  193 (194)
T ss_dssp             TCCEEEEEECTTSTTCHHHHHHHTTTTCCCCCHHHHHHHHHHHTCSCEEECCTTTCTTHHHHHHHHHHHHHC
T ss_pred             CCCEEEEEEChhhcccccchhhcccccCcccCHHHHHHHHHHcCCcEEEEeeCCCCCCHHHHHHHHHHHHhc
Confidence            66888899996532210           12333333332222233489999999999999999999876544

>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=91.75  E-value=0.39  Score=36.60  Aligned_cols=58  Identities=19%  Similarity=0.083  Sum_probs=39.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcc----ccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.+++...+|++...   +.....+.+..    .....++++..||++|.||++|++.|.+.+-
T Consensus       125 ~~~piilv~nK~Dl~~---~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i~  186 (190)
T 2h57_A          125 RRIPILFFANKMDLRD---AVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQIQ  186 (190)
T ss_dssp             SCCCEEEEEECTTSTT---CCCHHHHHHHHTGGGCCSSCEEEEECBTTTTBTHHHHHHHHHHHC-
T ss_pred             CCCeEEEEEeCcCccc---CCCHHHHHHHhChhhccCCceEEEEccCCCCcCHHHHHHHHHHHHH
Confidence            4678889999965332   22223332222    2223578999999999999999999988763

>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=91.70  E-value=0.25  Score=37.51  Aligned_cols=56  Identities=13%  Similarity=0.019  Sum_probs=37.4

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhc----cccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG----AFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+.|++...+|.+...   +.....+.+.    ......++++..||++|.||+++++.|.+.
T Consensus       121 ~~~piilv~NK~Dl~~---~~~~~~i~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~  180 (181)
T 2h17_A          121 RKAGLLIFANKQDVKE---CMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSR  180 (181)
T ss_dssp             TTCEEEEEEECTTSTT---CCCHHHHHHHTTGGGCCSSCEEEEECBTTTTBTHHHHHHHHHTC
T ss_pred             CCCeEEEEEECCCccc---CCCHHHHHHHhCcccccCCceEEEEccCCCCcCHHHHHHHHHhh
Confidence            4678889999965322   1222222221    123345689999999999999999999864

>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=91.63  E-value=0.28  Score=41.46  Aligned_cols=61  Identities=15%  Similarity=0.090  Sum_probs=40.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcccc-ccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFK-KNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~-~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|++..++|++... ..+.....+..-... +...+++..||++|.|+++|++.|..++|.
T Consensus       121 ~~~pvilV~NK~Dl~~-~~~~~~~~~~~l~~~~~~~~~i~~vSA~~g~gv~~L~~~l~~~l~~  182 (308)
T 3iev_A          121 LNKPVIVVINKIDKIG-PAKNVLPLIDEIHKKHPELTEIVPISALKGANLDELVKTILKYLPE  182 (308)
T ss_dssp             GCCCEEEEEECGGGSS-SGGGGHHHHHHHHHHCTTCCCEEECBTTTTBSHHHHHHHHHHHSCB
T ss_pred             cCCCEEEEEECccCCC-CHHHHHHHHHHHHHhccCCCeEEEEeCCCCCCHHHHHHHHHHhCcc
Confidence            4578999999965321 112222111111111 134689999999999999999999999975

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=91.59  E-value=0.17  Score=39.49  Aligned_cols=59  Identities=14%  Similarity=0.133  Sum_probs=39.2

Q ss_pred             CCceeeeeeeecccccC-----------CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHR-----------GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~-----------g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++...+|++.....           -.+...............|++..||++|.||+++++.|.+.+
T Consensus       134 ~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~SA~~g~gi~~l~~~l~~~~  203 (204)
T 4gzl_A          134 NTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAV  203 (204)
T ss_dssp             SCCEEEEEECHHHHTCHHHHHHHHHTTCCCCCHHHHHHHHHHTTCSEEEECCTTTCTTHHHHHHHHHHTT
T ss_pred             CCCEEEEEechhhccchhhhhhhhccccccccHHHHHHHHHhcCCcEEEEeeCCCCCCHHHHHHHHHHHh
Confidence            67888999997532211           013333333333333456899999999999999999998753

>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=91.50  E-value=0.19  Score=37.11  Aligned_cols=60  Identities=10%  Similarity=-0.072  Sum_probs=39.5

Q ss_pred             CCCceeeeeeeeccccc--CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKH--RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~--~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|.+....  ..++........ .+....|++..||++|.||+++++.|.+.++
T Consensus       107 ~~~piilv~nK~Dl~~~~~~~~v~~~~~~~~-~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i~  168 (170)
T 1ek0_A          107 KDIIIALVGNKIDXLQEGGERKVAREEGEKL-AEEKGLLFFETSAKTGENVNDVFLGIGEKIP  168 (170)
T ss_dssp             TTCEEEEEEECGGGGGSSCCCCSCHHHHHHH-HHHHTCEEEECCTTTCTTHHHHHHHHHTTSC
T ss_pred             CCCcEEEEEECCCccccccccCCCHHHHHHH-HHHcCCEEEEEeCCCCCCHHHHHHHHHHHHh
Confidence            35678888899753221  123333332222 2222458999999999999999999998765

>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=91.27  E-value=0.19  Score=37.53  Aligned_cols=60  Identities=15%  Similarity=0.017  Sum_probs=39.7

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|++...+|.+.... .++.......... ....|++..||++|.|++++++.|.+.++.
T Consensus       118 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~~-~~~~~~~~~Sa~~~~~i~~l~~~l~~~~~~  177 (179)
T 2y8e_A          118 SDVIIMLVGNKTDLSDK-RQVSTEEGERKAK-ELNVMFIETSAKAGYNVKQLFRRVAAALPG  177 (179)
T ss_dssp             TSSEEEEEEECGGGGGG-CCSCHHHHHHHHH-HHTCEEEEEBTTTTBSHHHHHHHHHHTCC-
T ss_pred             CCCcEEEEEECCccccc-CcCCHHHHHHHHH-HcCCeEEEEeCCCCCCHHHHHHHHHHHHhh
Confidence            35678888999653322 2233333222222 224689999999999999999999988753

>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=91.21  E-value=0.24  Score=37.38  Aligned_cols=58  Identities=12%  Similarity=0.018  Sum_probs=39.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|.+...  .....+.+..- .+....|++..||++|.||+++++.|.+.+.
T Consensus       108 ~~~p~i~v~nK~Dl~~--~~~~~~~~~~~-~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~~~  165 (189)
T 4dsu_A          108 EDVPMVLVGNKCDLPS--RTVDTKQAQDL-ARSYGIPFIETSAKTRQGVDDAFYTLVREIR  165 (189)
T ss_dssp             SCCCEEEEEECTTSSS--CSSCHHHHHHH-HHHHTCCEEECCTTTCTTHHHHHHHHHHHHH
T ss_pred             CCCcEEEEEECccCcc--cccCHHHHHHH-HHHcCCeEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            3678889999964332  22333332222 2222468999999999999999999988764

>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=91.07  E-value=0.2  Score=37.18  Aligned_cols=57  Identities=11%  Similarity=-0.056  Sum_probs=39.1

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +-|++...+|.+.... .++......+.. +....|++..||++|.||+++++.|.+.+
T Consensus       109 ~~p~ilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~~v~~l~~~l~~~i  165 (169)
T 3q85_A          109 DLPVILVGNKSDLARS-REVSLEEGRHLA-GTLSCKHIETSAALHHNTRELFEGAVRQI  165 (169)
T ss_dssp             CCCEEEEEECTTCGGG-CCSCHHHHHHHH-HHTTCEEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             CCCEEEEeeCcchhhc-ccCCHHHHHHHH-HHcCCcEEEecCccCCCHHHHHHHHHHHH
Confidence            6789999999654322 234444433322 22245899999999999999999998753

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=91.03  E-value=0.15  Score=38.25  Aligned_cols=58  Identities=14%  Similarity=0.114  Sum_probs=38.1

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+.... ..+......... .....|++..||++|.||++|++.|.+.+.
T Consensus       113 ~~p~ilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~~  170 (181)
T 3tw8_B          113 DVCRILVGNKNDDPER-KVVETEDAYKFA-GQMGIQLFETSAKENVNVEEMFNCITELVL  170 (181)
T ss_dssp             TSEEEEEEECTTCGGG-CCSCHHHHHHHH-HHHTCCEEECBTTTTBSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCchh-cccCHHHHHHHH-HHcCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            5688888899653322 122323322222 222358999999999999999999987654

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=91.02  E-value=0.2  Score=38.08  Aligned_cols=56  Identities=13%  Similarity=0.125  Sum_probs=38.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++...+|++  ...-+.....+.+-..+ ...|++..||++|.||+++++.|.+.+
T Consensus       147 ~~piilv~NK~D--~~~~~~~~~~~~~~~~~-~~~~~~~~Sa~~~~~i~~l~~~l~~~~  202 (208)
T 3clv_A          147 NYIIILVANKID--KNKFQVDILEVQKYAQD-NNLLFIQTSAKTGTNIKNIFYMLAEEI  202 (208)
T ss_dssp             CCEEEEEEECTT--CC-CCSCHHHHHHHHHH-TTCEEEEECTTTCTTHHHHHHHHHHHH
T ss_pred             CCcEEEEEECCC--cccccCCHHHHHHHHHH-cCCcEEEEecCCCCCHHHHHHHHHHHH
Confidence            368888889965  22224444444443333 345899999999999999999987654

>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=90.99  E-value=0.43  Score=36.74  Aligned_cols=57  Identities=12%  Similarity=0.030  Sum_probs=38.7

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhh----ccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYS----GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~----~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|++....   .....+.+    ...+...+|++..||++|.||+++++.|.+.+.
T Consensus       130 ~~piilv~NK~Dl~~~---~~~~~i~~~~~~~~~~~~~~~~~~~SA~~g~gi~~l~~~l~~~i~  190 (192)
T 2b6h_A          130 DAVLLVFANKQDMPNA---MPVSELTDKLGLQHLRSRTWYVQATCATQGTGLYDGLDWLSHELS  190 (192)
T ss_dssp             TCEEEEEEECTTSTTC---CCHHHHHHHTTGGGCSSCCEEEEECBTTTTBTHHHHHHHHHHHTT
T ss_pred             CCeEEEEEECCCCCCC---CCHHHHHHHhCcccccCCceEEEECcCCCcCCHHHHHHHHHHHHh
Confidence            6788999999654322   11222222    122234578999999999999999999988763

>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=90.95  E-value=0.25  Score=38.41  Aligned_cols=61  Identities=11%  Similarity=-0.116  Sum_probs=41.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|++...+|.+.... .++..+.+.+........+++..||++|.||+++++.|.+.+..
T Consensus       133 ~~~piilv~NK~Dl~~~-~~v~~~~~~~~~~~~~~~~~~~~SA~~g~gi~~l~~~l~~~i~~  193 (201)
T 2hup_A          133 SNIVQLLIGNKSDLSEL-REVSLAEAQSLAEHYDILCAIETSAKDSSNVEEAFLRVATELIM  193 (201)
T ss_dssp             TTCEEEEEEECTTCGGG-CCSCHHHHHHHHHHTTCSEEEECBTTTTBSHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCccccc-cccCHHHHHHHHHHcCCCEEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence            45688888899654322 23444444433333333389999999999999999999887753

>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=90.88  E-value=0.17  Score=38.22  Aligned_cols=57  Identities=16%  Similarity=0.190  Sum_probs=38.4

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcc----ccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|++....   .....+.+..    ......|++..||++|.||+++++.|.+.+
T Consensus       118 ~~~piilv~nK~Dl~~~---~~~~~i~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~  178 (183)
T 1moz_A          118 QDAALLVFANKQDQPGA---LSASEVSKELNLVELKDRSWSIVASSAIKGEGITEGLDWLIDVI  178 (183)
T ss_dssp             SSCEEEEEEECTTSTTC---CCHHHHHHHTTTTTCCSSCEEEEEEBGGGTBTHHHHHHHHHHHH
T ss_pred             CCCeEEEEEECCCCCCC---CCHHHHHHHhCcccccCCceEEEEccCCCCcCHHHHHHHHHHHH
Confidence            46788999999653221   2222222221    223356899999999999999999998765

>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=90.87  E-value=0.12  Score=37.97  Aligned_cols=58  Identities=17%  Similarity=0.028  Sum_probs=38.4

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+.... .++......+-. +....|++..||++|.||++|++.|.+.+
T Consensus       107 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~  164 (167)
T 1kao_A          107 EKVPVILVGNKVDLESE-REVSSSEGRALA-EEWGCPFMETSAKSKTMVDELFAEIVRQM  164 (167)
T ss_dssp             SCCCEEEEEECGGGGGG-CCSCHHHHHHHH-HHHTSCEEEECTTCHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCccccc-ccCCHHHHHHHH-HHhCCCEEEecCCCCcCHHHHHHHHHHHH
Confidence            36788999999753221 233333322221 22245899999999999999999998754

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=90.87  E-value=0.32  Score=37.13  Aligned_cols=61  Identities=10%  Similarity=0.006  Sum_probs=39.1

Q ss_pred             CCceeeeeeeecccccCC-cchHHHHhhccc-cccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRG-AVTFFRIYSGAF-KKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g-~l~~~~l~~~~~-~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +-|++...+|++...... +-....+..... +...++++..||++|.||+++++.|.+.+..
T Consensus       127 ~~piilv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~~l~~~l~~~~~~  189 (199)
T 4bas_A          127 RVPFLFFANKMDAAGAKTAAELVEILDLTTLMGDHPFVIFASNGLKGTGVHEGFSWLQETASR  189 (199)
T ss_dssp             BCCEEEEEECTTSTTCCCHHHHHHHHTHHHHHTTSCEEEEECBTTTTBTHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECcCCCCCCCHHHHHHHhcchhhccCCeeEEEEeeCCCccCHHHHHHHHHHHHHH
Confidence            668899999965332211 111111111111 3356789999999999999999999887643

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=90.84  E-value=0.26  Score=37.02  Aligned_cols=59  Identities=8%  Similarity=0.001  Sum_probs=39.7

Q ss_pred             CCceeeeeeeeccc-ccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHD-KHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d-~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +-|++...+|.+.. ...-.+..+.+.+-.......|++..||++|.||+++++.|...+
T Consensus       108 ~~piilv~nK~Dl~~~~~~~v~~~~~~~~~~~~~~~~~~~~Sa~~~~~i~~lf~~l~~~~  167 (178)
T 2iwr_A          108 GLALALVGTQDRISASSPRVVGDARARALXADMKRCSYYETXATYGLNVDRVFQEVAQKV  167 (178)
T ss_dssp             CCEEEEEEECTTCBTTBCCCSCHHHHHHHHHHHSSEEEEEEBTTTTBTHHHHHHHHHHHH
T ss_pred             CCCEEEEEECccccccccCcCCHHHHHHHHHhhcCCeEEEEeccccCCHHHHHHHHHHHH
Confidence            56888889996542 112234444443322222356899999999999999999998764

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=90.69  E-value=0.2  Score=38.21  Aligned_cols=58  Identities=10%  Similarity=0.001  Sum_probs=38.2

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+.... .++....... ..+....|++..||++|.||+++++.|.+.+.
T Consensus       121 ~~p~ilv~nK~Dl~~~-~~~~~~~~~~-~~~~~~~~~~~~Sa~~g~gv~~l~~~l~~~i~  178 (196)
T 3tkl_A          121 NVNKLLVGNKCDLTTK-KVVDYTTAKE-FADSLGIPFLETSAKNATNVEQSFMTMAAEIK  178 (196)
T ss_dssp             TCEEEEEEECTTCTTT-CCSCHHHHHH-HHHHTTCCEEEECTTTCTTHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECcccccc-cccCHHHHHH-HHHHcCCcEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            5688888899653322 2233333222 22223468999999999999999998887664

>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=90.68  E-value=0.17  Score=38.79  Aligned_cols=58  Identities=16%  Similarity=0.075  Sum_probs=38.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+.... -.+......... +....|++..||++|.||+++++.|.+.+
T Consensus       127 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i  184 (191)
T 3dz8_A          127 DNAQVILVGNKCDMEEE-RVVPTEKGQLLA-EQLGFDFFEASAKENISVRQAFERLVDAI  184 (191)
T ss_dssp             TTCEEEEEEECTTCGGG-CCSCHHHHHHHH-HHHTCEEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCccc-cccCHHHHHHHH-HHcCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            46688888999654322 123333332222 22245899999999999999999988764

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=90.67  E-value=0.43  Score=36.30  Aligned_cols=59  Identities=15%  Similarity=-0.001  Sum_probs=38.7

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhc----cccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG----AFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|++...+|.+.....   ....+.+.    .......+++..||++|.||+++++.|.+.+..
T Consensus       116 ~~~piilv~NK~Dl~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~~~~  178 (181)
T 1fzq_A          116 SCVPVLIFANKQDLLTAA---PASEIAEGLNLHTIRDRVWQIQSCSALTGEGVQDGMNWVCKNVNA  178 (181)
T ss_dssp             TTCCEEEEEECTTSTTCC---CHHHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHTC--
T ss_pred             cCCCEEEEEECcCcccCC---CHHHHHHHhCchhccCCceEEEEccCCCCCCHHHHHHHHHHHHHh
Confidence            456889999996543321   11222221    122335689999999999999999999987753

>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=90.65  E-value=0.2  Score=37.31  Aligned_cols=57  Identities=14%  Similarity=-0.003  Sum_probs=38.0

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++...+|++.... -++..+...... .....|++..||++|.||++|++.|.+.+
T Consensus       111 ~~piilv~NK~Dl~~~-~~v~~~~~~~~~-~~~~~~~~~~Sa~~g~gi~~l~~~l~~~~  167 (175)
T 2nzj_A          111 HVPIILVGNKADLARC-REVSVEEGRACA-VVFDCKFIETSATLQHNVAELFEGVVRQL  167 (175)
T ss_dssp             -CCEEEEEECTTCTTT-CCSCHHHHHHHH-HHHTSEEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             CCCEEEEEEChhhccc-cccCHHHHHHHH-HHcCCeEEEEecCCCCCHHHHHHHHHHHH
Confidence            6788999999654322 233333322211 12236899999999999999999998765

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=90.63  E-value=0.27  Score=37.73  Aligned_cols=60  Identities=3%  Similarity=-0.045  Sum_probs=40.8

Q ss_pred             CCCceeeeeeeeccc-ccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHD-KHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d-~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+-|++...+|.+.. ...-.+..+.+.+........+++..||++|.||+++++.|.+.+
T Consensus       118 ~~~piilv~nK~Dl~~~~~~~v~~~~~~~~~~~~~~~~~~e~Sa~~~~gv~~lf~~l~~~i  178 (184)
T 3ihw_A          118 SEVPMVLVGTQDAISAANPRVIDDSRARKLSTDLKRCTYYETCATYGLNVERVFQDVAQKV  178 (184)
T ss_dssp             GGSCEEEEEECTTCBTTBCCCSCHHHHHHHHHHTTTCEEEEEBTTTTBTHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECcccccccccccCHHHHHHHHHHcCCCeEEEecCCCCCCHHHHHHHHHHHH
Confidence            356888888996542 122345554444433333346899999999999999999988653

>3o47_A ADP-ribosylation factor GTPase-activating protein ribosylation factor 1; structural genomics consortium, GTPase activation; HET: GDP; 2.80A {Homo sapiens}

Probab=90.63  E-value=0.28  Score=41.87  Aligned_cols=60  Identities=12%  Similarity=-0.012  Sum_probs=39.6

Q ss_pred             CCceeeeeeeeccccc-CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKH-RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~-~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|++.... ..+-....+..........|++..||++|.||++|++.|.+.+.
T Consensus       266 ~~piilV~NK~Dl~~~~~~~~i~~~~~~~~~~~~~~~~~~vSAk~g~gi~el~~~l~~~l~  326 (329)
T 3o47_A          266 DAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLR  326 (329)
T ss_dssp             TCEEEEEEECTTSTTCCCHHHHHHHHTCTTCCSSCEEEEECBTTTTBTHHHHHHHHHHHHT
T ss_pred             CCeEEEEEECccCCcccCHHHHHHHhchhhhhcCCCEEEEEECCCCcCHHHHHHHHHHHHH
Confidence            6688999999653321 11111122222223345678999999999999999999988654

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=90.51  E-value=0.31  Score=37.12  Aligned_cols=60  Identities=18%  Similarity=0.021  Sum_probs=38.7

Q ss_pred             CCceeeeeeeecccccCC-cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRG-AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g-~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+...... +-....+.........+|++..||++|.||+++++.|.+.++
T Consensus       123 ~~piilv~nK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i~  183 (189)
T 2x77_A          123 KSLLLIFANKQDLPDAASEAEIAEQLGVSSIMNRTWTIVKSSSKTGDGLVEGMDWLVERLR  183 (189)
T ss_dssp             TCEEEEEEECTTSTTCCCHHHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHHHH
T ss_pred             CCeEEEEEECCCCcCCCCHHHHHHHhChhhccCCceEEEEccCCCccCHHHHHHHHHHHHH
Confidence            578889999965332211 111111111222333568999999999999999999988764

>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=90.49  E-value=0.22  Score=37.28  Aligned_cols=59  Identities=12%  Similarity=0.006  Sum_probs=39.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|++.... .++........ ......+++..||++|.||+++++.|.+.+.
T Consensus       113 ~~~piilv~nK~Dl~~~-~~v~~~~~~~~-~~~~~~~~~~~Sa~~~~gv~~l~~~l~~~~~  171 (181)
T 2fn4_A          113 DDFPVVLVGNKADLESQ-RQVPRSEASAF-GASHHVAYFEASAKLRLNVDEAFEQLVRAVR  171 (181)
T ss_dssp             SCCCEEEEEECGGGGGG-CCSCHHHHHHH-HHHTTCEEEECBTTTTBSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECcccccc-cccCHHHHHHH-HHHcCCeEEEecCCCCCCHHHHHHHHHHHHH
Confidence            35688899999654322 12333333222 2223468999999999999999999987764

>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=90.48  E-value=0.2  Score=37.15  Aligned_cols=57  Identities=19%  Similarity=0.161  Sum_probs=38.0

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++...+|.+.... .++..+.+.+-. +....|++..||++|.||+++++.|.+.+
T Consensus       111 ~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~  167 (170)
T 1z08_A          111 EICLCIVGNKIDLEKE-RHVSIQEAESYA-ESVGAKHYHTSAKQNKGIEELFLDLCKRM  167 (170)
T ss_dssp             GSEEEEEEECGGGGGG-CCSCHHHHHHHH-HHTTCEEEEEBTTTTBSHHHHHHHHHHHH
T ss_pred             CCeEEEEEECcccccc-cccCHHHHHHHH-HHcCCeEEEecCCCCCCHHHHHHHHHHHH
Confidence            4577888889654322 233333333322 22236899999999999999999998765

>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=90.39  E-value=0.34  Score=36.38  Aligned_cols=57  Identities=12%  Similarity=-0.002  Sum_probs=39.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++...+|.+.... .++....+.+... ....|++..||++|.||+++++.|.+.+
T Consensus       123 ~~piilv~nK~Dl~~~-~~~~~~~~~~~~~-~~~~~~~~~Sa~~~~gi~~l~~~l~~~i  179 (187)
T 2a9k_A          123 NVPFLLVGNKSDLEDK-RQVSVEEAKNRAE-QWNVNYVETSAKTRANVDKVFFDLMREI  179 (187)
T ss_dssp             TCCEEEEEECGGGGGG-CCSCHHHHHHHHH-HTTCEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             CCCEEEEEECcccccc-CccCHHHHHHHHH-HcCCeEEEeCCCCCCCHHHHHHHHHHHH
Confidence            6788999999654322 1334444433322 2346899999999999999999998765

>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=90.34  E-value=0.29  Score=37.11  Aligned_cols=58  Identities=16%  Similarity=0.064  Sum_probs=39.4

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcc----ccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|.+....   .....+.+..    .....+|++..||++|.||+++++.|.+.++
T Consensus       118 ~~~piilv~nK~Dl~~~---~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i~  179 (186)
T 1ksh_A          118 AGATLLIFANKQDLPGA---LSCNAIQEALELDSIRSHHWRIQGCSAVTGEDLLPGIDWLLDDIS  179 (186)
T ss_dssp             TTCEEEEEEECTTSTTC---CCHHHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHHHH
T ss_pred             CCCcEEEEEeCccCCCC---CCHHHHHHHhChhhccCCceEEEEeeCCCCCCHHHHHHHHHHHHH
Confidence            46788999999653322   1222222221    2234568999999999999999999988764

>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=89.99  E-value=0.22  Score=38.93  Aligned_cols=60  Identities=8%  Similarity=-0.015  Sum_probs=40.7

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.+++...+|++.... .++....... ..+....|++..||++|.||+++++.|.+.+..-
T Consensus       117 ~~piilv~nK~Dl~~~-~~~~~~~~~~-~~~~~~~~~~~~Sa~~g~gv~~l~~~l~~~~~~~  176 (218)
T 4djt_A          117 EAPIVVCANKIDIKNR-QKISKKLVME-VLKGKNYEYFEISAKTAHNFGLPFLHLARIFTGR  176 (218)
T ss_dssp             SSCEEEEEECTTCC-----CCHHHHHH-HTTTCCCEEEEEBTTTTBTTTHHHHHHHHHHHCC
T ss_pred             CCCEEEEEECCCCccc-cccCHHHHHH-HHHHcCCcEEEEecCCCCCHHHHHHHHHHHHhcc
Confidence            4688899999653321 2333333333 3333457899999999999999999999887553

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=89.96  E-value=0.23  Score=38.07  Aligned_cols=61  Identities=23%  Similarity=0.121  Sum_probs=40.9

Q ss_pred             CCceeeeeeeeccccc-CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKH-RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~-~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.|++...+|.+.... ..++..+.+.+........+++..||++|.||+++++.|.+.+..
T Consensus       127 ~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i~~  188 (194)
T 3reg_A          127 TAKTVLVGLKVDLRKDGSDDVTKQEGDDLCQKLGCVAYIEASSVAKIGLNEVFEKSVDCIFS  188 (194)
T ss_dssp             TSEEEEEEECGGGCCTTTTCCCHHHHHHHHHHHTCSCEEECBTTTTBSHHHHHHHHHHHHHC
T ss_pred             CCCEEEEEEChhhccCCCCcccHHHHHHHHHhcCCCEEEEeecCCCCCHHHHHHHHHHHHHh
Confidence            5688888999753321 233444444433333333338999999999999999999887644

>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=89.94  E-value=0.18  Score=38.52  Aligned_cols=58  Identities=16%  Similarity=0.099  Sum_probs=38.5

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|++.... .++..+.+.+-. +...+|++..||++|.||++|++.|.+.++
T Consensus       127 ~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~g~gi~~l~~~l~~~i~  184 (189)
T 2gf9_A          127 NAQVILVGNKCDLEDE-RVVPAEDGRRLA-DDLGFEFFEASAKENINVKQVFERLVDVIC  184 (189)
T ss_dssp             TCEEEEEEECTTCGGG-CCSCHHHHHHHH-HHHTCEEEECBTTTTBSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECcccccc-cCCCHHHHHHHH-HHcCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            5688888999653322 123333332222 222358999999999999999999987653

>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=89.90  E-value=0.24  Score=36.36  Aligned_cols=57  Identities=12%  Similarity=-0.005  Sum_probs=38.9

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++...+|.+.... .++....+...... ...|++..||++|.||+++++.|.+.+
T Consensus       109 ~~piilv~nK~Dl~~~-~~~~~~~~~~~~~~-~~~~~~~~Sa~~~~gi~~l~~~l~~~i  165 (168)
T 1u8z_A          109 NVPFLLVGNKSDLEDK-RQVSVEEAKNRADQ-WNVNYVETSAKTRANVDKVFFDLMREI  165 (168)
T ss_dssp             TSCEEEEEECGGGGGG-CCSCHHHHHHHHHH-HTCEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             CCcEEEEEECcccccc-CccCHHHHHHHHHH-cCCeEEEeCCCCCCCHHHHHHHHHHHH
Confidence            6789999999654322 12333343332222 235899999999999999999998654

>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=89.82  E-value=0.49  Score=36.04  Aligned_cols=59  Identities=10%  Similarity=0.018  Sum_probs=39.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.|++...+|.+...  .++........ ......+++..||++|.||++|++.|.+.+...
T Consensus       114 ~~piilv~nK~Dl~~--~~~~~~~~~~~-~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~~~~  172 (199)
T 2gf0_A          114 DIPVMLVGNKCDETQ--REVDTREAQAV-AQEWKCAFMETSAKMNYNVKELFQELLTLETRR  172 (199)
T ss_dssp             GSCEEEEEECTTCSS--CSSCHHHHHHH-HHHHTCEEEECBTTTTBSHHHHHHHHHHHCSSS
T ss_pred             CCCEEEEEECccCCc--cccCHHHHHHH-HHHhCCeEEEEecCCCCCHHHHHHHHHHHHhhh
Confidence            558889999965322  22333222221 122235899999999999999999999988654

>4he6_A Peptidase family U32; ultra-tight crystal packing, unknown function; 1.10A {Geobacillus thermoleovorans} PDB: 4he5_A

Probab=89.80  E-value=1.8  Score=29.57  Aligned_cols=76  Identities=9%  Similarity=0.090  Sum_probs=49.5

Q ss_pred             CCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCc---eeeeceeEeeecCCeeeeCcc-ccCCEEEEcCCCC
Q psy5461          99 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ---SEQITRLLLAEADDYKEVNEI-QCGNIAAVTGLKR  174 (221)
Q Consensus        99 ~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~---~~~v~~i~~~~g~~~~~v~~a-~aGdIv~i~gl~~  174 (221)
                      -.|++.|....  ...| .+.+. ....+..||.|.+..++.   ..++.+|+   ..+-++++.| +||+++.|.--..
T Consensus         6 ~~fvG~V~~~~--~~~g-~~~ie-~rN~f~~GD~iEi~~P~g~~~~~~v~~m~---d~~G~~i~~A~~~~~~v~i~~~~~   78 (89)
T 4he6_A            6 REFAGLVLGYD--PETG-IATVQ-QRNHFRPGDEVEFFGPEIENFTQVIEKIW---DEDGNELDAARHPLQIVKFKVKRP   78 (89)
T ss_dssp             GGCSEEEEEEE--TTTT-EEEEE-ESSCBCTTCEEEEESTTSCCEEEECCCEE---ETTSCEESCBCSTTCEEEEECSSC
T ss_pred             cEEEEEEEEEe--CCCC-EEEEE-EcCCcCCCCEEEEEcCCCCcEEEEeHHeE---cCCCCEeeEcCCCCeEEEEECCCC
Confidence            34667665433  3223 34444 467999999998876653   24566654   3455688888 9999998854345


Q ss_pred             CccCcEE
Q psy5461         175 ERGKDKR  181 (221)
Q Consensus       175 ~~~Gdtl  181 (221)
                      +..||.|
T Consensus        79 ~~~~dil   85 (89)
T 4he6_A           79 LFPYNMM   85 (89)
T ss_dssp             CCTTCEE
T ss_pred             CCCCCEE
Confidence            6778776

>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=89.79  E-value=0.37  Score=35.54  Aligned_cols=58  Identities=16%  Similarity=0.060  Sum_probs=38.8

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|.+...  .....+...+-. +...+|++..||++|.||+++++.|.+.+.
T Consensus       107 ~~~piilv~nK~Dl~~--~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gv~~l~~~l~~~~~  164 (170)
T 1g16_A          107 DEAQLLLVGNKSDMET--RVVTADQGEALA-KELGIPFIESSAKNDDNVNEIFFTLAKLIQ  164 (170)
T ss_dssp             TTCEEEEEEECTTCTT--CCSCHHHHHHHH-HHHTCCEEECBTTTTBSHHHHHHHHHHHHH
T ss_pred             CCCcEEEEEECccCCc--CccCHHHHHHHH-HHcCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3568889999965422  223333322221 222358999999999999999999988764

>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=89.79  E-value=0.43  Score=36.17  Aligned_cols=58  Identities=16%  Similarity=0.031  Sum_probs=39.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.|++...+|++...  .++......+.. +....+++..||++|.||+++++.|.+.++.
T Consensus       121 ~~p~ilv~nK~Dl~~--~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~~~  178 (195)
T 1x3s_A          121 DIVNMLVGNKIDKEN--REVDRNEGLKFA-RKHSMLFIEASAKTCDGVQCAFEELVEKIIQ  178 (195)
T ss_dssp             CCEEEEEEECTTSSS--CCSCHHHHHHHH-HHTTCEEEECCTTTCTTHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEECCcCcc--cccCHHHHHHHH-HHcCCEEEEecCCCCCCHHHHHHHHHHHHHh
Confidence            567888889965422  233333333322 2234689999999999999999999987754

>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=89.68  E-value=0.39  Score=35.04  Aligned_cols=56  Identities=13%  Similarity=0.035  Sum_probs=37.7

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++...+|++...  .+.....+.+. .+....|++..||++|.|++++++.|.+.+
T Consensus       108 ~~p~iiv~nK~Dl~~--~~~~~~~~~~~-~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~  163 (166)
T 2ce2_X          108 DVPMVLVGNKSDLAA--RTVESRQAQDL-ARSYGIPYIETSAKTRQGVEDAFYTLVREI  163 (166)
T ss_dssp             CCCEEEEEECTTCSC--CCSCHHHHHHH-HHHHTCCEEEECTTTCTTHHHHHHHHHHHH
T ss_pred             CCcEEEEEEchhhhh--cccCHHHHHHH-HHHcCCeEEEecCCCCCCHHHHHHHHHHHH
Confidence            678899999965322  22223332222 222245899999999999999999998754

>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=89.68  E-value=0.34  Score=36.54  Aligned_cols=58  Identities=21%  Similarity=0.057  Sum_probs=39.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCC-ccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSY-KNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~-~~~Gi~~LLd~I~~~~   82 (221)
                      .+-|++...+|.+.... -++..+.+.+..... ..|++..||+ +|.||+++++.|.+.+
T Consensus       122 ~~~p~ilv~nK~Dl~~~-~~v~~~~~~~~~~~~-~~~~~~~Sa~~~~~~v~~l~~~l~~~i  180 (183)
T 3kkq_A          122 ESFPMILVANKVDLMHL-RKVTRDQGKEMATKY-NIPYIETSAKDPPLNVDKTFHDLVRVI  180 (183)
T ss_dssp             SCCCEEEEEECTTCSTT-CCSCHHHHHHHHHHH-TCCEEEEBCSSSCBSHHHHHHHHHHHH
T ss_pred             CCCcEEEEEECCCchhc-cCcCHHHHHHHHHHh-CCeEEEeccCCCCCCHHHHHHHHHHHH
Confidence            45688899999653322 234444443322222 3789999999 9999999999998753

>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=89.66  E-value=0.27  Score=36.88  Aligned_cols=59  Identities=20%  Similarity=0.062  Sum_probs=39.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|.+.... .++......+-. +...+|++..||++|.||+++++.|.+.+.
T Consensus       115 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~~  173 (180)
T 2g6b_A          115 HDVALMLLGNKVDSAHE-RVVKREDGEKLA-KEYGLPFMETSAKTGLNVDLAFTAIAKELK  173 (180)
T ss_dssp             TTCEEEEEEECCSTTSC-CCSCHHHHHHHH-HHHTCCEEECCTTTCTTHHHHHHHHHHHHH
T ss_pred             CCCcEEEEEECcccCcc-cccCHHHHHHHH-HHcCCeEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            45688889999653322 123333322222 222358999999999999999999988764

>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=89.58  E-value=0.28  Score=36.98  Aligned_cols=61  Identities=10%  Similarity=-0.092  Sum_probs=40.7

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      .+-|++...+|++.... -++..+...+... ....|++..||++|.||+++++.|.+.+...
T Consensus       110 ~~~p~ilv~nK~Dl~~~-~~~~~~~~~~~~~-~~~~~~~~~Sa~~~~~v~~l~~~l~~~~~~~  170 (181)
T 3t5g_A          110 VQIPIMLVGNKKDLHME-RVISYEEGKALAE-SWNAAFLESSAKENQTAVDVFRRIILEAEKM  170 (181)
T ss_dssp             --CCEEEEEECTTCTTT-CCSCHHHHHHHHH-HTTCEEEECCTTSHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCEEEEEECccchhc-ceecHHHHHHHHH-HhCCcEEEEecCCCCCHHHHHHHHHHHHHHh
Confidence            35688899999654322 2344444333222 2345899999999999999999999877543

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=89.53  E-value=0.4  Score=36.86  Aligned_cols=62  Identities=8%  Similarity=-0.110  Sum_probs=40.3

Q ss_pred             CCceeeeeeeeccccc-----------CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKH-----------RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~-----------~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.|++...+|.+....           ...+.......-.......|++..||++|.||+++++.|.+.+..+
T Consensus       124 ~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~~~~~  196 (201)
T 2q3h_A          124 KAPIILVGTQSDLREDVKVLIELDKCKEKPVPEEAAKLLAEEIKAASYIECSALTQKNLKEVFDAAIVAGIQY  196 (201)
T ss_dssp             SSCEEEEEECGGGGGCHHHHHHHHTTTCCCCCHHHHHHHHHHHTCSEEEECCTTTCTTHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECHhhhhchhhhhhhcccccccCCHHHHHHHHHhcCCcEEEEEecCCCCCHHHHHHHHHHHHhcc
Confidence            5688888899753321           1223333333222222344899999999999999999998876543

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=89.53  E-value=0.34  Score=37.70  Aligned_cols=62  Identities=13%  Similarity=-0.040  Sum_probs=39.0

Q ss_pred             CCceeeeeeeecccccC-----------CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHR-----------GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~-----------g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.|++...+|++.....           ..+...............+++..||++|.||++|++.|.+.+..+
T Consensus       129 ~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~SA~~g~gi~el~~~l~~~i~~~  201 (207)
T 2fv8_A          129 NVPIILVANKKDLRSDEHVRTELARMKQEPVRTDDGRAMAVRIQAYDYLECSAKTKEGVREVFETATRAALQK  201 (207)
T ss_dssp             TCCEEEEEECGGGGGCHHHHHHHHHTTCCCCCHHHHHHHHHHTTCSEEEECCTTTCTTHHHHHHHHHHHHHSC
T ss_pred             CCCEEEEEEchhhhccccchhhhhhcccCCCCHHHHHHHHHhcCCCEEEEeeCCCCCCHHHHHHHHHHHHHHH
Confidence            67888899996532210           112222222211122234889999999999999999999877544

>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=89.45  E-value=0.42  Score=36.28  Aligned_cols=57  Identities=16%  Similarity=0.071  Sum_probs=38.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|++...  .+.....+.+.. +...+|++..||++|.|++++++.|.+.+.
T Consensus       126 ~~p~ilv~nK~Dl~~--~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~~  182 (190)
T 3con_A          126 DVPMVLVGNKCDLPT--RTVDTKQAHELA-KSYGIPFIETSAKTRQGVEDAFYTLVREIR  182 (190)
T ss_dssp             CCCEEEEEECTTCSC--CCSCHHHHHHHH-HHHTCCEEECCTTTCTTHHHHHHHHHHHHH
T ss_pred             CCeEEEEEECCcCCc--ccCCHHHHHHHH-HHcCCeEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            568889999965322  223333333322 222358999999999999999999987653

>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=89.37  E-value=0.31  Score=36.35  Aligned_cols=58  Identities=14%  Similarity=-0.017  Sum_probs=39.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+.... .++..+.+.+-... ...|++..||++|.||+++++.|.+.+
T Consensus       119 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~~~-~~~~~~~~Sa~~~~gi~~l~~~l~~~i  176 (179)
T 1z0f_A          119 PNTVIILIGNKADLEAQ-RDVTYEEAKQFAEE-NGLLFLEASAKTGENVEDAFLEAAKKI  176 (179)
T ss_dssp             TTCEEEEEEECTTCGGG-CCSCHHHHHHHHHH-TTCEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             CCCcEEEEEECcccccc-cccCHHHHHHHHHH-cCCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence            45678888999654322 23344444332222 346899999999999999999998754

>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=89.33  E-value=0.29  Score=40.56  Aligned_cols=59  Identities=14%  Similarity=0.015  Sum_probs=41.2

Q ss_pred             CCCceeeeeeeeccccc-CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          23 FGDSLCARAFKVVHDKH-RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~-~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      .+.|++..++|++.... ........+.+.    ..+|++..||++|.||++|++.|.+.++..
T Consensus       111 ~~~p~ivv~NK~Dl~~~~~~~~~~~~l~~~----lg~~~i~~SA~~g~gi~el~~~i~~~~~~~  170 (274)
T 3i8s_A          111 LGIPCIVALNMLDIAEKQNIRIEIDALSAR----LGCPVIPLVSTRGRGIEALKLAIDRYKANE  170 (274)
T ss_dssp             HTCCEEEEEECHHHHHHTTEEECHHHHHHH----HTSCEEECCCGGGHHHHHHHHHHHTCCCCC
T ss_pred             cCCCEEEEEECccchhhhhHHHHHHHHHHh----cCCCEEEEEcCCCCCHHHHHHHHHHHHhcC
Confidence            46789999999653221 112223333332    236899999999999999999999988764

>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=89.22  E-value=0.38  Score=36.94  Aligned_cols=58  Identities=12%  Similarity=-0.007  Sum_probs=40.1

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+.... -++....+.....+ ...|++..||++|.||++|++.|.+.+.
T Consensus       119 ~~piilv~nK~Dl~~~-~~~~~~~~~~~~~~-~~~~~~~~Sa~~g~gi~~l~~~l~~~i~  176 (206)
T 2bov_A          119 NVPFLLVGNKSDLEDK-RQVSVEEAKNRAEQ-WNVNYVETSAKTRANVDKVFFDLMREIR  176 (206)
T ss_dssp             CCCEEEEEECTTCGGG-CCSCHHHHHHHHHH-HTCEEEEECTTTCTTHHHHHHHHHHHHH
T ss_pred             CCCEEEEEeccCcccc-ccccHHHHHHHHHH-hCCeEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            6788999999654322 23444444333222 2358999999999999999999988764

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=89.11  E-value=0.25  Score=36.96  Aligned_cols=60  Identities=7%  Similarity=-0.077  Sum_probs=39.2

Q ss_pred             CCc-eeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDS-LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~-~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      ..+ ++...+|.+.... .++..+...+-. +...+|++..||++|.||+++++.|.+.++.-
T Consensus       114 ~~~~iilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~~~~  174 (178)
T 2hxs_A          114 TQPLVALVGNKIDLEHM-RTIKPEKHLRFC-QENGFSSHFVSAKTGDSVFLCFQKVAAEILGI  174 (178)
T ss_dssp             CCCEEEEEEECGGGGGG-CSSCHHHHHHHH-HHHTCEEEEECTTTCTTHHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEEEccccccc-cccCHHHHHHHH-HHcCCcEEEEeCCCCCCHHHHHHHHHHHHHhh
Confidence            344 6778899654322 123333332222 22236899999999999999999999887653

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=88.99  E-value=0.42  Score=36.98  Aligned_cols=58  Identities=12%  Similarity=-0.046  Sum_probs=37.0

Q ss_pred             CCceeeeeeeecccccC-----------CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHR-----------GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~-----------g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +.|++...+|++.....           ..+..+...+........+++..||++|.||++|++.|.+.
T Consensus       129 ~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~SA~~g~gi~~l~~~i~~~  197 (201)
T 2gco_A          129 NVPIILVGNKKDLRQDEHTRRELAKMKQEPVRSEEGRDMANRISAFGYLECSAKTKEGVREVFEMATRA  197 (201)
T ss_dssp             TCCEEEEEECGGGTTCHHHHHHHHTTTCCCCCHHHHHHHHHHTTCSEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             CCCEEEEEecHHhhcCccchhhhcccccCcCCHHHHHHHHHhCCCcEEEEeeCCCCCCHHHHHHHHHHH
Confidence            66888889996532210           11223332222222233489999999999999999998764

>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=88.83  E-value=0.37  Score=37.30  Aligned_cols=60  Identities=13%  Similarity=0.007  Sum_probs=39.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|++...+|.+.... .++.......-. +....|++..||++|.||+++++.|.+.+..
T Consensus       112 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~g~gi~~l~~~l~~~i~~  171 (206)
T 2bcg_Y          112 STVLKLLVGNKCDLKDK-RVVEYDVAKEFA-DANKMPFLETSALDSTNVEDAFLTMARQIKE  171 (206)
T ss_dssp             TTCEEEEEEECTTCTTT-CCSCHHHHHHHH-HHTTCCEEECCTTTCTTHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCccc-cccCHHHHHHHH-HHcCCeEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence            34678888899653322 123333332222 2234689999999999999999999887753

>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=88.74  E-value=0.31  Score=36.78  Aligned_cols=58  Identities=14%  Similarity=0.125  Sum_probs=38.8

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+.... .++..+.+.+-. +...+|++..||++|.||+++++.|.+.+
T Consensus       126 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~~v~~l~~~l~~~~  183 (195)
T 3bc1_A          126 ENPDIVLCGNKSDLEDQ-RAVKEEEARELA-EKYGIPYFETSAANGTNISHAIEMLLDLI  183 (195)
T ss_dssp             SSCCEEEEEECTTCGGG-CCSCHHHHHHHH-HHHTCCEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECcccccc-cccCHHHHHHHH-HHcCCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            46688899999654322 123333333322 22235899999999999999999998765

>3l0i_B RAS-related protein RAB-1A; GEF-GDF-RAB complex, GTP-binding, guanine-nucleotide exchang GDI-displacement factor; 2.85A {Homo sapiens}

Probab=88.51  E-value=0.14  Score=39.66  Aligned_cols=58  Identities=10%  Similarity=-0.004  Sum_probs=32.7

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+.... -.+...... ...+....|++..||++|.||++|++.|.+.+.
T Consensus       138 ~~p~ilv~nK~Dl~~~-~~v~~~~~~-~~~~~~~~~~~~vSA~~g~gv~~l~~~l~~~l~  195 (199)
T 3l0i_B          138 NVNKLLVGNKCDLTTK-KVVDYTTAK-EFADSLGIPFLETSAKNATNVEQSFMTMAAEIK  195 (199)
T ss_dssp             CSEEEEC-CCSSCC---CCCCSCC-C-HHHHTTTCCBCCCCC---HHHHHHHHHHTTTTT
T ss_pred             CCCEEEEEECccCCcc-ccCCHHHHH-HHHHHcCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            5688888899653321 111111111 111222468899999999999999999988764

>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=88.37  E-value=0.36  Score=36.86  Aligned_cols=58  Identities=12%  Similarity=-0.020  Sum_probs=38.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+.... .++......... +....+++..||++|.||+++++.|.+.+
T Consensus       129 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i  186 (193)
T 2oil_A          129 ATIVVMLVGNKSDLSQA-REVPTEEARMFA-ENNGLLFLETSALDSTNVELAFETVLKEI  186 (193)
T ss_dssp             TTCEEEEEEECGGGGGG-CCSCHHHHHHHH-HHTTCEEEEECTTTCTTHHHHHHHHHHHH
T ss_pred             CCCeEEEEEECCCcccc-cccCHHHHHHHH-HHcCCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence            35678888999653322 123333333322 22345899999999999999999988654

>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=88.33  E-value=0.47  Score=37.22  Aligned_cols=60  Identities=17%  Similarity=0.069  Sum_probs=39.3

Q ss_pred             CCceeeeeeeecccccC-----------CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHR-----------GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~-----------g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+.....           ..++.....+........|++..||++|.||+++++.|.+.+.
T Consensus       138 ~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~SA~~g~gi~el~~~l~~~~~  208 (214)
T 2j1l_A          138 KVPIIVVGCKTDLRKDKSLVNKLRRNGLEPVTYHRGQEMARSVGAVAYLECSARLHDNVHAVFQEAAEVAL  208 (214)
T ss_dssp             SCCEEEEEECGGGGSCHHHHHHHHHTTCCCCCHHHHHHHHHHTTCSEEEECBTTTTBSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEChhhhccchhhhhhcccccCcccHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHHHHHH
Confidence            56888888996533211           1233333333222223458999999999999999999987654

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=88.31  E-value=0.3  Score=37.81  Aligned_cols=60  Identities=10%  Similarity=-0.073  Sum_probs=40.2

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +-|++...+|.+.... .++........... ...|++..||++|.||+++++.|.+.+...
T Consensus       129 ~~piilv~nK~Dl~~~-~~v~~~~~~~~~~~-~~~~~~~~Sa~~~~~v~~l~~~l~~~i~~~  188 (201)
T 3oes_A          129 RVPVVLVGNKADLSPE-REVQAVEGKKLAES-WGATFMESSARENQLTQGIFTKVIQEIARV  188 (201)
T ss_dssp             CCCEEEEEECTTCGGG-CCSCHHHHHHHHHH-HTCEEEECCTTCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCEEEEEECccCccc-cccCHHHHHHHHHH-hCCeEEEEeCCCCCCHHHHHHHHHHHHHhh
Confidence            5688999999653322 23333333222222 235899999999999999999998877443

>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=88.30  E-value=0.34  Score=37.36  Aligned_cols=58  Identities=17%  Similarity=0.107  Sum_probs=38.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+.... .++..+.+..-. +...+|++..||++|.||+++++.|.+.+
T Consensus       112 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i  169 (203)
T 1zbd_A          112 DNAQVLLVGNKCDMEDE-RVVSSERGRQLA-DHLGFEFFEASAKDNINVKQTFERLVDVI  169 (203)
T ss_dssp             SSCEEEEEEECTTCTTS-CCSCHHHHHHHH-HHHTCEEEECBTTTTBSSHHHHHHHHHHH
T ss_pred             CCCCEEEEEECcccCcc-cccCHHHHHHHH-HHCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35688889999654322 123333332222 22235899999999999999999887665

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=88.30  E-value=0.53  Score=37.26  Aligned_cols=59  Identities=10%  Similarity=0.095  Sum_probs=38.1

Q ss_pred             CCceeeeeeeecccccCCcchHH--HHhhcccccc--CceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFF--RIYSGAFKKN--HVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~--~l~~~~~~~~--~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|++.... .++...  ...+...+..  ..+++..||++|.||++|++.|.+.+.
T Consensus       142 ~~piilv~nK~Dl~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~g~gi~~l~~~l~~~i~  204 (228)
T 2qu8_A          142 NKSIVIGFNKIDKCNM-DSLSIDNKLLIKQILDNVKNPIKFSSFSTLTGVGVEQAKITACELLK  204 (228)
T ss_dssp             CCCEEEEEECGGGCC---CCCHHHHHHHHHHHHHCCSCEEEEECCTTTCTTHHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCcccCCc-hhhHHHHHHHHHHHHHhcCCCceEEEEecccCCCHHHHHHHHHHHHH
Confidence            6788999999653221 122221  1122222222  278999999999999999999988764

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=88.09  E-value=0.56  Score=34.98  Aligned_cols=60  Identities=8%  Similarity=0.001  Sum_probs=36.1

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhc-cccc---cCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG-AFKK---NHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~-~~~~---~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|++......+-....+... ....   ...|++..||++|.||++|++.|.+.+
T Consensus       106 ~~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~l~~~l~~~~  169 (178)
T 2lkc_A          106 ANVPIIVAINKMDKPEANPDRVMQELMEYNLVPEEWGGDTIFCKLSAKTKEGLDHLLEMILLVS  169 (178)
T ss_dssp             GSCCEEEEEETTTSSCSCHHHHHHHHTTTTCCBTTTTSSEEEEECCSSSSHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECccCCcCCHHHHHHHHHhcCcChhHcCCcccEEEEecCCCCCHHHHHHHHHHhh
Confidence            35688888899543321111111111111 1111   126899999999999999999988654

>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=88.08  E-value=0.37  Score=36.32  Aligned_cols=59  Identities=14%  Similarity=-0.034  Sum_probs=35.7

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+-|++...+|.+.... .++..+.+.+-... ..+|++..||++|.||+++++.|.+.+.
T Consensus       112 ~~~piilv~nK~Dl~~~-~~v~~~~~~~~~~~-~~~~~~~~Sa~~~~~i~~l~~~l~~~i~  170 (183)
T 2fu5_C          112 ADVEKMILGNKCDVNDK-RQVSKERGEKLALD-YGIKFMETSAKANINVENAFFTLARDIK  170 (183)
T ss_dssp             TTCEEEEEEEC--CCSC-CCSCHHHHHHHHHH-HTCEEEECCC---CCHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECccCCcc-CcCCHHHHHHHHHH-cCCeEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            35688899999654322 23334443332222 2368999999999999999999987764

>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=87.90  E-value=0.36  Score=36.90  Aligned_cols=58  Identities=9%  Similarity=-0.104  Sum_probs=38.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+.... .++..+....-. +....+++..||++|.||+++++.|.+.+
T Consensus       125 ~~~piilv~nK~Dl~~~-~~v~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i  182 (191)
T 2a5j_A          125 SNMVIMLIGNKSDLESR-RDVKREEGEAFA-REHGLIFMETSAKTACNVEEAFINTAKEI  182 (191)
T ss_dssp             TTCEEEEEEECTTCGGG-CCSCHHHHHHHH-HHHTCEEEEECTTTCTTHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECcccCCc-cccCHHHHHHHH-HHcCCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence            35678888899653321 233333333222 22245899999999999999999998765

>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=87.74  E-value=0.64  Score=34.98  Aligned_cols=59  Identities=17%  Similarity=0.043  Sum_probs=39.7

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|.+.... .++......+.. +....|++..||++|.||+++++.|.+.+.
T Consensus       114 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~~  172 (186)
T 2bme_A          114 QNIVIILCGNKKDLDAD-REVTFLEASRFA-QENELMFLETSALTGENVEEAFVQCARKIL  172 (186)
T ss_dssp             TTCEEEEEEECGGGGGG-CCSCHHHHHHHH-HHTTCEEEECCTTTCTTHHHHHHHHHHHHH
T ss_pred             CCCcEEEEEECcccccc-cccCHHHHHHHH-HHcCCEEEEecCCCCCCHHHHHHHHHHHHH
Confidence            45688899999754322 233333333322 223468999999999999999999887664

>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=87.67  E-value=0.91  Score=38.11  Aligned_cols=60  Identities=12%  Similarity=0.037  Sum_probs=39.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcccc-ccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFK-KNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~-~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|.+..++|++...  .+-......+...+ ....+++..||++|.|+++|++.|...+|.
T Consensus       115 ~~~P~ilvlNK~D~~~--~~~~~~~~l~~l~~~~~~~~~i~iSA~~g~~v~~l~~~i~~~l~~  175 (301)
T 1ega_A          115 GKAPVILAVNKVDNVQ--EKADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHLPE  175 (301)
T ss_dssp             SSSCEEEEEESTTTCC--CHHHHHHHHHHHHTTSCCSEEEECCTTTTTTHHHHHHHHHTTCCB
T ss_pred             cCCCEEEEEECcccCc--cHHHHHHHHHHHHHhcCcCceEEEECCCCCCHHHHHHHHHHhCCc
Confidence            4678999999954322  11122222222222 123368899999999999999999998874

>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=87.66  E-value=0.34  Score=35.68  Aligned_cols=57  Identities=9%  Similarity=-0.025  Sum_probs=37.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++...+|.+.... .++..+.+.+.. +...+|++..||++|.||+++++.|.+.+
T Consensus       109 ~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~~i~~l~~~l~~~~  165 (168)
T 1z2a_A          109 DIPTALVQNKIDLLDD-SCIKNEEAEGLA-KRLKLRFYRTSVKEDLNVSEVFKYLAEKH  165 (168)
T ss_dssp             SCCEEEEEECGGGGGG-CSSCHHHHHHHH-HHHTCEEEECBTTTTBSSHHHHHHHHHHH
T ss_pred             CCCEEEEEECcccCcc-cccCHHHHHHHH-HHcCCeEEEEecCCCCCHHHHHHHHHHHH
Confidence            5688888999653221 123333333322 22245899999999999999999998654

>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=87.62  E-value=0.41  Score=37.32  Aligned_cols=59  Identities=15%  Similarity=0.106  Sum_probs=39.1

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|.+.... -++....+.+-. +...+|++..||++|.||++|++.|.+.+.
T Consensus       140 ~~~piilV~NK~Dl~~~-~~v~~~~~~~~~-~~~~~~~~~~Sa~~g~gi~~l~~~l~~~i~  198 (217)
T 2f7s_A          140 ENPDIVLIGNKADLPDQ-REVNERQARELA-DKYGIPYFETSAATGQNVEKAVETLLDLIM  198 (217)
T ss_dssp             TCCEEEEEEECTTCGGG-CCSCHHHHHHHH-HHTTCCEEEEBTTTTBTHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCccccc-cccCHHHHHHHH-HHCCCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45688899999653321 123333333222 222468999999999999999999987653

>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=87.28  E-value=0.95  Score=38.07  Aligned_cols=57  Identities=11%  Similarity=0.007  Sum_probs=38.6

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.|++..++|++....... ....+ +..  ....+++..||++|.|+++|++.|...+|.
T Consensus       117 ~~p~ilV~NK~Dl~~~~~~-~~~~~-~~~--~~~~~~~~iSA~~g~gv~~l~~~l~~~l~~  173 (301)
T 1wf3_A          117 KVPILLVGNKLDAAKYPEE-AMKAY-HEL--LPEAEPRMLSALDERQVAELKADLLALMPE  173 (301)
T ss_dssp             TSCEEEEEECGGGCSSHHH-HHHHH-HHT--STTSEEEECCTTCHHHHHHHHHHHHTTCCB
T ss_pred             CCCEEEEEECcccCCchHH-HHHHH-HHh--cCcCcEEEEeCCCCCCHHHHHHHHHHhccc
Confidence            6789999999653321111 12222 212  234578999999999999999999998763

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=87.16  E-value=0.62  Score=36.00  Aligned_cols=59  Identities=17%  Similarity=0.031  Sum_probs=39.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|++.... .++......+.. +....+++..||++|.||+++++.|.+.+.
T Consensus       129 ~~~piilv~nK~Dl~~~-~~v~~~~~~~~~-~~~~~~~~~~SA~~g~gi~~l~~~l~~~i~  187 (200)
T 2o52_A          129 PNIVVILCGNKKDLDPE-REVTFLEASRFA-QENELMFLETSALTGENVEEAFLKCARTIL  187 (200)
T ss_dssp             TTCEEEEEEECGGGGGG-CCSCHHHHHHHH-HHTTCEEEEECTTTCTTHHHHHHHHHHHHH
T ss_pred             CCCcEEEEEECCCcccc-cccCHHHHHHHH-HHcCCEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            35688899999754322 223333333222 223468999999999999999999887653

>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A*

Probab=87.11  E-value=0.42  Score=39.76  Aligned_cols=62  Identities=15%  Similarity=0.129  Sum_probs=39.9

Q ss_pred             CCceeeeeeeeccccc-----------CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKH-----------RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~-----------~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.|++...+|++....           .-.+......+........|++..||++|.||++|++.|.+.+..|
T Consensus       259 ~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~~~~  331 (332)
T 2wkq_A          259 NTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCP  331 (332)
T ss_dssp             TSCEEEEEECHHHHTCHHHHHHHHHTTCCCCCHHHHHHHHHHTTCSEEEECCTTTCTTHHHHHHHHHHHHHC-
T ss_pred             CCcEEEEEEchhcccccchhhhccccccccccHHHHHHHHHHcCCcEEEEecCCCCcCHHHHHHHHHHHHhcC
Confidence            5688888999753221           1123333333322223334899999999999999999998876443

>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=86.95  E-value=0.2  Score=43.24  Aligned_cols=60  Identities=15%  Similarity=0.070  Sum_probs=38.4

Q ss_pred             Cceeeeeeeeccccc-CCcchHHHHhhcc--cc----ccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          25 DSLCARAFKVVHDKH-RGAVTFFRIYSGA--FK----KNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~-~g~l~~~~l~~~~--~~----~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.+..+||++.... ........+.+..  ..    +-..||+..||++|.||++|++.|.++++.
T Consensus       218 ~p~ivVlNK~Dl~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~iSA~~g~Gi~~L~~~i~~~~~~  284 (355)
T 3p32_A          218 LADIVVVNKADGEHHKEARLAARELSAAIRLIYPREALWRPPVLTMSAVEGRGLAELWDTVERHRQV  284 (355)
T ss_dssp             GCSEEEEECCCGGGHHHHHHHHHHHHHHHHHHSTTCCSCCCCEEEEBGGGTBSHHHHHHHHHHHHHH
T ss_pred             cCCEEEEECCCCcChhHHHHHHHHHHHHHhhccccccCCCCceEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            477888899654322 1112222332221  10    114689999999999999999999988753

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=86.76  E-value=0.31  Score=37.92  Aligned_cols=64  Identities=13%  Similarity=0.093  Sum_probs=40.5

Q ss_pred             CCceeeeeeeecccccCC-------cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRG-------AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTE   87 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g-------~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~   87 (221)
                      +.|++...+|.+......       .+......+........|++..||++|.||+++++.|.+.+..+..
T Consensus       113 ~~piilv~nK~Dl~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~~~~~~~~  183 (212)
T 2j0v_A          113 NVPIVLVGTKLDLRDDKGYLADHTNVITSTQGEELRKQIGAAAYIECSSKTQQNVKAVFDTAIKVVLQPPR  183 (212)
T ss_dssp             TCCEEEEEECHHHHTCHHHHHTCSSCCCHHHHHHHHHHHTCSEEEECCTTTCTTHHHHHHHHHHHHHCC--
T ss_pred             CCCEEEEEeCHHhhhCccccccccCCCCHHHHHHHHHHcCCceEEEccCCCCCCHHHHHHHHHHHHhhhhh
Confidence            568888888865322111       1233333322222233589999999999999999999988866543

>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=86.65  E-value=0.42  Score=39.25  Aligned_cols=58  Identities=16%  Similarity=0.217  Sum_probs=40.1

Q ss_pred             CCCCceeeeeeeecccccC-CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          22 HFGDSLCARAFKVVHDKHR-GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~-g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.+.|++..++|++..... .......+.+.    ..+|++..||++|.||++|++.|.+.+.
T Consensus       108 ~~~~pvilv~NK~Dl~~~~~i~~~~~~l~~~----lg~~vi~~SA~~g~gi~el~~~i~~~~~  166 (258)
T 3a1s_A          108 EMEKKVILAMTAIDEAKKTGMKIDRYELQKH----LGIPVVFTSSVTGEGLEELKEKIVEYAQ  166 (258)
T ss_dssp             TTTCCEEEEEECHHHHHHTTCCBCHHHHHHH----HCSCEEECCTTTCTTHHHHHHHHHHHHH
T ss_pred             hcCCCEEEEEECcCCCCccchHHHHHHHHHH----cCCCEEEEEeeCCcCHHHHHHHHHHHhh
Confidence            3567899999997532211 12223333332    2369999999999999999999998764

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=86.35  E-value=0.64  Score=35.87  Aligned_cols=57  Identities=14%  Similarity=0.060  Sum_probs=37.9

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|++...  ..+.......- .+...+|++..||++|.||+++++.|.+.++
T Consensus       125 ~~piilv~nK~Dl~~--~~~~~~~~~~~-~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~~  181 (213)
T 3cph_A          125 EAQLLLVGNKSDMET--RVVTADQGEAL-AKELGIPFIESSAKNDDNVNEIFFTLAKLIQ  181 (213)
T ss_dssp             CSEEEEEEECTTCSS--CCSCHHHHHHH-HHHHTCCEEECBTTTTBSSHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCcc--cccCHHHHHHH-HHHcCCEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            568888899965422  22233322221 1222358999999999999999999987764

>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=86.25  E-value=0.67  Score=35.23  Aligned_cols=59  Identities=12%  Similarity=-0.086  Sum_probs=36.6

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCcc---ccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKN---IGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~---~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|++.... -++.......-. +....|++..||++|   .||.++++.|.+.++
T Consensus       126 ~~~piilv~nK~Dl~~~-~~v~~~~~~~~~-~~~~~~~~~~Sa~~~~~~~~i~~l~~~l~~~i~  187 (189)
T 1z06_A          126 NDIPRILVGNKCDLRSA-IQVPTDLAQKFA-DTHSMPLFETSAKNPNDNDHVEAIFMTLAHKLK  187 (189)
T ss_dssp             SCCCEEEEEECTTCGGG-CCSCHHHHHHHH-HHTTCCEEECCSSSGGGGSCHHHHHHHHC----
T ss_pred             CCCCEEEEEECcccccc-ceeCHHHHHHHH-HHcCCEEEEEeCCcCCcccCHHHHHHHHHHHHh
Confidence            45788899999654222 123333332222 223458999999999   999999999987764

>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=86.23  E-value=0.78  Score=35.01  Aligned_cols=58  Identities=14%  Similarity=-0.170  Sum_probs=38.9

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCC-CccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSS-YKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa-~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|++.... .+++.+...+-..+ ..+|++..|| ++|.||+++++.|.+.+
T Consensus       126 ~~~piilv~nK~Dl~~~-~~v~~~~~~~~~~~-~~~~~~e~Sa~~~g~gv~~lf~~l~~~i  184 (187)
T 3c5c_A          126 RSIPALLLGNKLDMAQY-RQVTKAEGVALAGR-FGCLFFEVSACLDFEHVQHVFHEAVREA  184 (187)
T ss_dssp             CCCCEEEEEECGGGGGG-CSSCHHHHHHHHHH-HTCEEEECCSSSCSHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECcchhhc-CccCHHHHHHHHHH-cCCcEEEEeecCccccHHHHHHHHHHHH
Confidence            46788999999654322 23343333332222 2358999999 89999999999998754

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=86.22  E-value=0.5  Score=35.71  Aligned_cols=53  Identities=11%  Similarity=-0.059  Sum_probs=34.7

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      +.|++...+|++......+         ..+....|++..||++|.||++|++.|.+.+...
T Consensus       115 ~~p~ilv~NK~Dl~~~~~~---------~~~~~~~~~~~~SA~~g~gv~~l~~~l~~~~~~~  167 (172)
T 2gj8_A          115 KLPITVVRNKADITGETLG---------MSEVNGHALIRLSARTGEGVDVLRNHLKQSMGFD  167 (172)
T ss_dssp             TCCEEEEEECHHHHCCCCE---------EEEETTEEEEECCTTTCTTHHHHHHHHHHHC---
T ss_pred             CCCEEEEEECccCCcchhh---------hhhccCCceEEEeCCCCCCHHHHHHHHHHHhhhc
Confidence            4577788888653221111         1111246899999999999999999999887653

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=86.14  E-value=0.75  Score=36.10  Aligned_cols=62  Identities=8%  Similarity=0.033  Sum_probs=41.1

Q ss_pred             CCceeeeeeeeccccc-----------CCcchHHHHhhccccccCceeEecCCCcccc-HHHHHHHHHhhCCCC
Q psy5461          24 GDSLCARAFKVVHDKH-----------RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIG-VQKLMDAIVDILPSP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~-----------~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~G-i~~LLd~I~~~~PsP   85 (221)
                      +.|++...+|.+....           .-.+......+-.......|++..||++|.| |++|++.|...+...
T Consensus       131 ~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~e~SA~~g~g~v~~lf~~l~~~~~~~  204 (214)
T 3q3j_B          131 STRVLLIGCKTDLRTDLSTLMELSHQKQAPISYEQGCAIAKQLGAEIYLEGSAFTSEKSIHSIFRTASMLCLNK  204 (214)
T ss_dssp             TSEEEEEEECGGGGGCHHHHHHHHHTTCCCCCHHHHHHHHHHHTCSEEEECCTTTCHHHHHHHHHHHHHHHHC-
T ss_pred             CCCEEEEEEChhhccchhhhhhhcccccCccCHHHHHHHHHHcCCCEEEEeccCCCcccHHHHHHHHHHHHhcc
Confidence            5688888899654321           1234444443333333334899999999998 999999998876543

>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=85.78  E-value=0.5  Score=36.91  Aligned_cols=58  Identities=16%  Similarity=-0.035  Sum_probs=38.5

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|++.... .++..+....-. +....|++..||++|.||+++++.|...+.
T Consensus       131 ~~piilv~NK~Dl~~~-~~v~~~~~~~~~-~~~~~~~~~~Sa~~g~gv~~l~~~l~~~i~  188 (201)
T 2ew1_A          131 KVITVLVGNKIDLAER-REVSQQRAEEFS-EAQDMYYLETSAKESDNVEKLFLDLACRLI  188 (201)
T ss_dssp             TCEEEEEEECGGGGGG-CSSCHHHHHHHH-HHHTCCEEECCTTTCTTHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCccc-cccCHHHHHHHH-HHcCCEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            5678888899654321 233333332222 222368999999999999999999987664

>3th5_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTPase, GTP binding, protein binding, signali protein; HET: GNP; 2.30A {Homo sapiens}

Probab=85.87  E-value=0.15  Score=39.51  Aligned_cols=58  Identities=14%  Similarity=0.131  Sum_probs=35.5

Q ss_pred             CCceeeeeeeecccccCC-----------cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRG-----------AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g-----------~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +.|++...+|++......           .+...............|++..||++|.||++|++.|.+.
T Consensus       134 ~~piilv~NK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~vSA~~g~gi~~l~~~l~~~  202 (204)
T 3th5_A          134 NTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRA  202 (204)
Confidence            567788888865322110           2222222222222223488999999999999999988754

>3cb4_D GTP-binding protein LEPA; GTPase, OB-fold, membrane, nucleotide-binding, translation; 2.80A {Escherichia coli} PDB: 3deg_C*

Probab=85.61  E-value=0.21  Score=46.56  Aligned_cols=54  Identities=22%  Similarity=0.337  Sum_probs=45.2

Q ss_pred             ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEe
Q psy5461           1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLC   62 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~   62 (221)
                      ++.+++++|+|..        +.+.|+.+++|++..|++.|.+++.++.+|+++.+..+.+.
T Consensus       173 l~~I~~~lp~p~~--------~~~~p~~alI~d~~~d~~~G~v~~~rV~sG~l~~Gd~v~~~  226 (599)
T 3cb4_D          173 LERLVRDIPPPEG--------DPEGPLQALIIDSWFDNYLGVVSLIRIKNGTLRKGDKVKVM  226 (599)
T ss_dssp             HHHHHHHSCCCCC--------CTTSCCEEEEEEEEEETTTEEEEEEEEEESCEESSCEEEET
T ss_pred             HHHHhhcCCCccc--------cccCCceeeeeeccccccccEEEEEEEEeCEEecCCEEEec
Confidence            3667888888853        46789999999999999999999999999999987765444

>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=85.48  E-value=0.72  Score=37.80  Aligned_cols=56  Identities=14%  Similarity=0.125  Sum_probs=39.7

Q ss_pred             CCCCceeeeeeeeccc-ccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          22 HFGDSLCARAFKVVHD-KHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d-~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +.+.|++..++|++.- ..........+.+..    .+|++..||++|.|+++|++.|.+.
T Consensus       108 ~~~~pvilv~NK~Dl~~~~~~~~~~~~l~~~l----g~~vi~~SA~~g~gi~el~~~i~~~  164 (256)
T 3iby_A          108 ELGKPVVVALNMMDIAEHRGISIDTEKLESLL----GCSVIPIQAHKNIGIPALQQSLLHC  164 (256)
T ss_dssp             TSCSCEEEEEECHHHHHHTTCEECHHHHHHHH----CSCEEECBGGGTBSHHHHHHHHHTC
T ss_pred             HcCCCEEEEEEChhcCCcCCcHHHHHHHHHHc----CCCEEEEECCCCCCHHHHHHHHHhh
Confidence            3567999999997522 211223344443322    3689999999999999999999987

>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=85.40  E-value=0.73  Score=40.99  Aligned_cols=61  Identities=16%  Similarity=0.103  Sum_probs=41.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcc----ccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.+++..++|.+.... .+...+.+.+..    ......|++..||++|.||++|++.|.+.+..
T Consensus       305 ~~~~~ilv~NK~Dl~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~g~gv~~l~~~i~~~~~~  369 (456)
T 4dcu_A          305 AGKAVVIVVNKWDAVDK-DESTMKEFEENIRDHFQFLDYAPILFMSALTKKRIHTLMPAIIKASEN  369 (456)
T ss_dssp             TTCEEEEEEECGGGSCC-CSSHHHHHHHHHHHHCGGGTTSCEEECCTTTCTTGGGHHHHHHHHHHH
T ss_pred             cCCCEEEEEEChhcCCC-chHHHHHHHHHHHHhcccCCCCCEEEEcCCCCcCHHHHHHHHHHHHHH
Confidence            56789999999753322 223333333222    22235799999999999999999999877643

>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=85.26  E-value=0.65  Score=35.58  Aligned_cols=58  Identities=10%  Similarity=-0.087  Sum_probs=39.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccc-cHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNI-GVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~-Gi~~LLd~I~~~~   82 (221)
                      .+-|++...+|.+.... -++......+.... ...|++..||++|. ||+++++.|.+.+
T Consensus       131 ~~~piilv~NK~Dl~~~-~~v~~~~~~~~~~~-~~~~~~~~Sa~~g~~gi~~l~~~l~~~i  189 (196)
T 2atv_A          131 KNVTLILVGNKADLDHS-RQVSTEEGEKLATE-LACAFYECSACTGEGNITEIFYELCREV  189 (196)
T ss_dssp             SCCCEEEEEECGGGGGG-CCSCHHHHHHHHHH-HTSEEEECCTTTCTTCHHHHHHHHHHHH
T ss_pred             CCCcEEEEEECcccccc-cccCHHHHHHHHHH-hCCeEEEECCCcCCcCHHHHHHHHHHHH
Confidence            46688999999654332 23333333322212 24689999999999 9999999998765

>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=85.01  E-value=0.68  Score=39.91  Aligned_cols=59  Identities=15%  Similarity=0.063  Sum_probs=40.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      .+.|++..++|++....  +-....+.+....  ..|++..||+++.||++|++.|.+.+...
T Consensus       273 ~~~p~ilV~NK~Dl~~~--~e~~~~l~~~l~~--~~~v~~iSA~tg~gi~eL~~~l~~~l~~~  331 (342)
T 1lnz_A          273 TERPQIIVANKMDMPEA--AENLEAFKEKLTD--DYPVFPISAVTREGLRELLFEVANQLENT  331 (342)
T ss_dssp             TTSCBCBEEECTTSTTH--HHHHHHHHHHCCS--CCCBCCCSSCCSSTTHHHHHHHHHHHTSC
T ss_pred             cCCCEEEEEECccCCCC--HHHHHHHHHHhhc--CCCEEEEECCCCcCHHHHHHHHHHHHhhC
Confidence            36788899999643221  1122333333221  16789999999999999999999988653

>2ywe_A GTP-binding protein LEPA; G domain, beta-barrel, ferredoxin-like domain, structural GE NPPSFA; 2.05A {Aquifex aeolicus} PDB: 2ywf_A* 2ywg_A* 2ywh_A*

Probab=84.98  E-value=0.26  Score=45.91  Aligned_cols=55  Identities=35%  Similarity=0.519  Sum_probs=45.1

Q ss_pred             ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecC
Q psy5461           1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGS   64 (221)
Q Consensus         1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gS   64 (221)
                      |+.+++++|+|..        +.+.|+.+++||+..|++.|.+++.++++|+++.+.. |+..+
T Consensus       175 le~I~~~lp~p~~--------~~~~pl~~lV~~~~~d~~~G~v~~~rV~sG~l~~Gd~-I~~~~  229 (600)
T 2ywe_A          175 LEAIVNRIPPPKG--------DPQKPLKALIFDSYYDPYRGAVAFVRIFDGEVKPGDK-IMLMS  229 (600)
T ss_dssp             HHHHHHHSCCCCC--------CTTSCCEEEEEEEEEETTTEEEEEEEEEESEECTTCE-EEETT
T ss_pred             HHHHHHhcccccc--------cccCCcceeEEEEeecccceEEEEEEEEeCEEecCCE-EEecc
Confidence            3677888998853        4578999999999999999999999999999998765 55433

>2hjg_A GTP-binding protein ENGA; GTPase ENGA KH-domain, hydrolase; HET: GDP; 2.50A {Bacillus subtilis}

Probab=84.76  E-value=0.95  Score=39.98  Aligned_cols=60  Identities=18%  Similarity=0.104  Sum_probs=39.7

Q ss_pred             CCCceeeeeeeecccccCCcchHH----HHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFF----RIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~----~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.+++..++|.+.... .+....    .+.+........|++..||++|.||++|++.+...+.
T Consensus       285 ~~~~iiiv~NK~Dl~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~SA~tg~~v~~l~~~i~~~~~  348 (436)
T 2hjg_A          285 AGKAVVIVVNKWDAVDK-DESTMKEFEENIRDHFQFLDYAPILFMSALTKKRIHTLMPAIIKASE  348 (436)
T ss_dssp             TTCEEEEEEECGGGSCC-CTTHHHHHHHHHHHHCGGGTTSCEEECCTTTCTTGGGHHHHHHHHHH
T ss_pred             cCCcEEEEEECccCCCc-chHHHHHHHHHHHHhcccCCCCCEEEEecccCCCHHHHHHHHHHHHH
Confidence            46789999999753222 122222    2333333334579999999999999999888876553

>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=84.73  E-value=0.7  Score=35.55  Aligned_cols=59  Identities=5%  Similarity=-0.223  Sum_probs=37.9

Q ss_pred             CCceeeeeeeecccc-----cCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDK-----HRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~-----~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++...+|.+...     ..-++......+- .+....|++..||++|.||+++++.|.+.+.
T Consensus       133 ~~piilv~NK~Dl~~~~~~~~~~~v~~~~~~~~-~~~~~~~~~~~SA~~g~gv~el~~~l~~~i~  196 (199)
T 2p5s_A          133 TVPIMLVGNKADIRDTAATEGQKCVPGHFGEKL-AMTYGALFCETSAKDGSNIVEAVLHLAREVK  196 (199)
T ss_dssp             -CCEEEEEECGGGHHHHHHTTCCCCCHHHHHHH-HHHHTCEEEECCTTTCTTHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECcccccccccccccccCHHHHHHH-HHHcCCeEEEeeCCCCCCHHHHHHHHHHHHH
Confidence            568889999975321     1123333322221 1222458999999999999999999987653

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=84.71  E-value=0.72  Score=36.63  Aligned_cols=57  Identities=12%  Similarity=-0.024  Sum_probs=37.4

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +-|++...+|++.... -++....... .......|++..||++|.||+++++.|...+
T Consensus       145 ~~piilVgNK~DL~~~-r~v~~~e~~~-~a~~~~~~~~e~SAk~g~~v~elf~~l~~~i  201 (211)
T 2g3y_A          145 DIPIILVGNKSDLVRC-REVSVSEGRA-CAVVFDCKFIETSAAVQHNVKELFEGIVRQV  201 (211)
T ss_dssp             TSCEEEEEECTTCGGG-CCSCHHHHHH-HHHHHTCEEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             CCcEEEEEEChHHhcC-ceEeHHHHHH-HHHHcCCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence            5688888999754322 1233322211 1112235789999999999999999998765

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=84.45  E-value=0.63  Score=36.63  Aligned_cols=59  Identities=14%  Similarity=0.028  Sum_probs=38.4

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.|++...+|.+.... .++.......-. +....|++..||++|.||+++++.|.+.+..
T Consensus       118 ~~piilv~nK~Dl~~~-~~v~~~~~~~~~-~~~~~~~~~~Sa~~~~gi~~l~~~l~~~i~~  176 (223)
T 3cpj_B          118 NVAVGLIGNKSDLAHL-RAVPTEESKTFA-QENQLLFTETSALNSENVDKAFEELINTIYQ  176 (223)
T ss_dssp             -CEEEEEECCGGGGGG-CCSCHHHHHHHH-HHTTCEEEECCCC-CCCHHHHHHHHHHHHTT
T ss_pred             CCeEEEEEECcccccc-cccCHHHHHHHH-HHcCCEEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence            5678888899654322 233333333222 2234689999999999999999999988754

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=84.33  E-value=0.93  Score=36.17  Aligned_cols=60  Identities=15%  Similarity=0.030  Sum_probs=39.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+-|++.--+|.+.... -+++.+...+-..+ ...+.+-.||++|.||+++++.|...++.
T Consensus       117 ~~~piilVgNK~Dl~~~-r~V~~~e~~~~a~~-~~~~~~e~SAktg~nV~e~F~~i~~~i~~  176 (216)
T 4dkx_A          117 SDVIIMLVGNKTDLADK-RQVSIEEGERKAKE-LNVMFIETSAKAGYNVKQLFRRVAAALPG  176 (216)
T ss_dssp             TSSEEEEEEECTTCGGG-CCSCHHHHHHHHHH-HTCEEEEEBTTTTBSHHHHHHHHHHHC--
T ss_pred             CCCeEEEEeeccchHhc-CcccHHHHhhHHHH-hCCeeEEEeCCCCcCHHHHHHHHHHHHHh
Confidence            45677778889653322 23444443332222 23578889999999999999999998865

>1mky_A Probable GTP-binding protein ENGA; GTPase, DER, KH-domain, tandem G-domains, ligand binding protein; HET: GDP; 1.90A {Thermotoga maritima} SCOP: c.37.1.8 c.37.1.8 d.52.5.1

Probab=84.28  E-value=1.3  Score=39.20  Aligned_cols=61  Identities=16%  Similarity=0.107  Sum_probs=40.0

Q ss_pred             CCCceeeeeeeecccccCCcchHH----HHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFF----RIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~----~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.+++..++|.+..+.. +.+..    .+.+........|+++.||++|.||++|++.|.+.++.
T Consensus       291 ~~~~~ilv~NK~Dl~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~g~gv~~l~~~i~~~~~~  355 (439)
T 1mky_A          291 RGRASVVVFNKWDLVVHR-EKRYDEFTKLFREKLYFIDYSPLIFTSADKGWNIDRMIDAMNLAYAS  355 (439)
T ss_dssp             TTCEEEEEEECGGGSTTG-GGCHHHHHHHHHHHCGGGTTSCEEECBTTTTBSHHHHHHHHHHHHHH
T ss_pred             cCCCEEEEEECccCCCch-hhHHHHHHHHHHHHhccCCCCcEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            467888999997532211 22222    22222223345689999999999999999999876543

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=84.25  E-value=0.92  Score=35.01  Aligned_cols=61  Identities=10%  Similarity=-0.074  Sum_probs=40.7

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      .+.|++...+|++.... .+++.+...+-. +....+++..||++|.||+++++.|...+...
T Consensus       129 ~~~piilv~nK~Dl~~~-~~v~~~~~~~~a-~~~~~~~~e~Sa~~~~~v~~lf~~l~~~i~~~  189 (195)
T 3cbq_A          129 HDLPVILVGNKSDLARS-REVSLEEGRHLA-GTLSCKHIETSAALHHNTRELFEGAVRQIRLR  189 (195)
T ss_dssp             SCCCEEEEEECTTCTTT-CCSCHHHHHHHH-HHTTCEEEEEBTTTTBSHHHHHHHHHHHHHTT
T ss_pred             CCCCEEEEeechhcccc-CCcCHHHHHHHH-HHhCCEEEEEcCCCCCCHHHHHHHHHHHHHHh
Confidence            36688888999654322 233333332221 12235889999999999999999999887543

>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=83.65  E-value=0.89  Score=34.19  Aligned_cols=61  Identities=8%  Similarity=-0.064  Sum_probs=38.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhcccc---ccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFK---KNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~---~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|++...+|.+..... +-....+.+....   ....+++..||++|.||+++++.|.+.++.
T Consensus       121 ~~~piilv~nK~Dl~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~~v~~l~~~l~~~~~~  184 (190)
T 2cxx_A          121 LDIPTIVAVNKLDKIKNV-QEVINFLAEKFEVPLSEIDKVFIPISAKFGDNIERLKNRIFEVIRE  184 (190)
T ss_dssp             TTCCEEEEEECGGGCSCH-HHHHHHHHHHHTCCGGGHHHHEEECCTTTCTTHHHHHHHHHHHHHH
T ss_pred             cCCceEEEeehHhccCcH-HHHHHHHHHHhhhhhhccCCcEEEEecCCCCCHHHHHHHHHHhcch
Confidence            467889999996543321 1112222221111   002368999999999999999999987654

>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=82.99  E-value=1.3  Score=36.59  Aligned_cols=58  Identities=16%  Similarity=0.127  Sum_probs=39.2

Q ss_pred             CCCceeeeeeeecccccC-CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHR-GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~-g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|++...+|++..... .......+.+.    ..+|++..||++|.||++|++.|.+.+..
T Consensus       106 ~~~p~ilv~NK~Dl~~~~~~~~~~~~l~~~----lg~~vi~~SA~~g~gi~el~~~i~~~~~~  164 (272)
T 3b1v_A          106 TGIPVTIALNMIDVLDGQGKKINVDKLSYH----LGVPVVATSALKQTGVDQVVKKAAHTTTS  164 (272)
T ss_dssp             TCSCEEEEEECHHHHHHTTCCCCHHHHHHH----HTSCEEECBTTTTBSHHHHHHHHHHSCTT
T ss_pred             cCCCEEEEEEChhhCCcCCcHHHHHHHHHH----cCCCEEEEEccCCCCHHHHHHHHHHHHhh
Confidence            467888888886532211 12222333322    23689999999999999999999987754

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=82.77  E-value=0.74  Score=36.11  Aligned_cols=54  Identities=13%  Similarity=0.026  Sum_probs=34.2

Q ss_pred             eeeeeeecccccCCcchHHHHhhcccc-ccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          28 CARAFKVVHDKHRGAVTFFRIYSGAFK-KNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        28 ~~~vfk~~~d~~~g~l~~~~l~~~~~~-~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +..++|++.... .+.....+.+.... +...|++..||++|.|+++|++.|...+
T Consensus       168 iiv~NK~Dl~~~-~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~~l~~~l~~~~  222 (226)
T 2hf9_A          168 LIVINKIDLADA-VGADIKKMENDAKRINPDAEVVLLSLKTMEGFDKVLEFIEKSV  222 (226)
T ss_dssp             EEEEECGGGHHH-HTCCHHHHHHHHHHHCTTSEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             EEEEeccccCch-hHHHHHHHHHHHHHhCCCCeEEEEEecCCCCHHHHHHHHHHHH
Confidence            778888643221 11233333332221 2246899999999999999999987654

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=82.66  E-value=1.2  Score=33.63  Aligned_cols=58  Identities=9%  Similarity=-0.021  Sum_probs=37.3

Q ss_pred             CCceeeeeeeeccccc-----------CCcchHHHHhhccccccCceeEecCCC-ccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKH-----------RGAVTFFRIYSGAFKKNHVPVLCGSSY-KNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~-----------~g~l~~~~l~~~~~~~~~~Pv~~gSa~-~~~Gi~~LLd~I~~~   81 (221)
                      +.|++...+|.+....           .-.+..+...+-.......|++..||+ ++.||+++++.|.+.
T Consensus       111 ~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~e~Sa~~~~~gi~~l~~~i~~~  180 (184)
T 1m7b_A          111 NTKMLLVGCKSDLRTDVSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSENSVRDIFHVATLA  180 (184)
T ss_dssp             TCEEEEEEECGGGGGCHHHHHHHHTTTCCCCCHHHHHHHHHHHTCSEEEECBTTTBHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEcchhhcchhhHhhhhhcccCCCCHHHHHHHHHHcCCcEEEEeeecCCCcCHHHHHHHHHHH
Confidence            5688888899653321           122333333332222234689999999 689999999998764

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=82.31  E-value=1.3  Score=34.58  Aligned_cols=58  Identities=9%  Similarity=-0.021  Sum_probs=37.3

Q ss_pred             CCceeeeeeeeccccc-----------CCcchHHHHhhccccccCceeEecCCC-ccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKH-----------RGAVTFFRIYSGAFKKNHVPVLCGSSY-KNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~-----------~g~l~~~~l~~~~~~~~~~Pv~~gSa~-~~~Gi~~LLd~I~~~   81 (221)
                      +.|++...+|++....           .-.+..+...+-.......+++..||+ +|.||+++++.|.+.
T Consensus       132 ~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~e~SAk~~~~gv~~lf~~l~~~  201 (205)
T 1gwn_A          132 NTKMLLVGCKSDLRTDVSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSENSVRDIFHVATLA  201 (205)
T ss_dssp             TCEEEEEEECGGGGGCHHHHHHHHTTTCCCCCHHHHHHHHHHHTCSEEEECCTTTCHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEechhhccchhhhhhhcccccCCCCHHHHHHHHHHcCCCEEEEeeeccCCcCHHHHHHHHHHH
Confidence            5688888899754321           123343433332222234689999999 689999999998865

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C

Probab=82.11  E-value=0.85  Score=34.86  Aligned_cols=60  Identities=13%  Similarity=-0.109  Sum_probs=31.9

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCc-cccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYK-NIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~-~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++...+|++......++....+.+-... ...|++..||++ |.||+++++.|.+.+.
T Consensus       131 ~~~piilv~nK~Dl~~~~~~v~~~~~~~~~~~-~~~~~~~~Sa~~~~~gi~~l~~~i~~~~~  191 (208)
T 2yc2_C          131 RPLRAVLVANKTDLPPQRHQVRLDMAQDWATT-NTLDFFDVSANPPGKDADAPFLSIATTFY  191 (208)
T ss_dssp             SCCEEEEEEECC-------CCCHHHHHHHHHH-TTCEEEECCC-------CHHHHHHHHHHH
T ss_pred             cCCcEEEEEECcccchhhccCCHHHHHHHHHH-cCCEEEEeccCCCCcCHHHHHHHHHHHHH
Confidence            36688999999653320123444444332222 236899999999 9999999999987653

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=81.99  E-value=1.3  Score=34.05  Aligned_cols=57  Identities=12%  Similarity=-0.026  Sum_probs=36.1

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.|++...+|.+.... -.+....... .......+++..||++|.||+++++.|...+
T Consensus       114 ~~piilV~NK~Dl~~~-r~v~~~~~~~-~a~~~~~~~~e~SA~~g~~v~~lf~~l~~~~  170 (192)
T 2cjw_A          114 DIPIILVGNKSDLVRX-REVSVSEGRA-XAVVFDXKFIETSAAVQHNVKELFEGIVRQV  170 (192)
T ss_dssp             CCCEEEEEECTTCGGG-CCSCHHHHHH-HHHHTTCEEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             CCeEEEEEechhhhcc-ccccHHHHHH-HHHHhCCceEEeccccCCCHHHHHHHHHHHH
Confidence            5678888889653221 1222222111 1111235788999999999999999998765

>3e3x_A BIPA; MCSG,PSI2, structural genomics, protein struct initiative, midwest center for structural genomics, GTP-BIN nucleotide-binding; HET: MLZ MLY; 1.95A {Vibrio parahaemolyticus}

Probab=81.97  E-value=0.86  Score=39.28  Aligned_cols=27  Identities=4%  Similarity=-0.146  Sum_probs=24.1

Q ss_pred             eehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461         192 VQCSARWTLNLEVGASSPIISKSKRRQ  218 (221)
Q Consensus       192 v~~~~l~~~L~~L~~~Dp~l~~~~~~~  218 (221)
                      ++..+|.++|++|+++||+|.+.++.+
T Consensus        53 vt~~kL~~aL~kl~~eDpsL~v~~~~~   79 (332)
T 3e3x_A           53 VTSRNILERLEKELVHNVALRVEQTDD   79 (332)
T ss_dssp             CSHHHHHHHHHHHHHHCTTCEEEECSS
T ss_pred             chHHHHHHHHHHHhccCCEEEEEEcCC
Confidence            456799999999999999999998864

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=81.53  E-value=0.93  Score=35.38  Aligned_cols=59  Identities=12%  Similarity=0.013  Sum_probs=36.9

Q ss_pred             CceeeeeeeecccccCCcchHHHHhhcccc-ccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          25 DSLCARAFKVVHDKHRGAVTFFRIYSGAFK-KNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~-~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.+..++|++..... +.....+.+...+ +...|++..||++|.|+++|++.|.+.+..
T Consensus       155 ~~~iiv~NK~Dl~~~~-~~~~~~~~~~~~~~~~~~~i~~~Sa~~g~gi~~l~~~l~~~~~~  214 (221)
T 2wsm_A          155 VADLIVINKVALAEAV-GADVEKMKADAKLINPRAKIIEMDLKTGKGFEEWIDFLRGILNV  214 (221)
T ss_dssp             TCSEEEEECGGGHHHH-TCCHHHHHHHHHHHCTTSEEEECBTTTTBTHHHHHHHHHHHHC-
T ss_pred             cCCEEEEecccCCcch-hhHHHHHHHHHHHhCCCCeEEEeecCCCCCHHHHHHHHHHHHHH
Confidence            4667788886432110 1223333322211 234689999999999999999999887644

>2hjg_A GTP-binding protein ENGA; GTPase ENGA KH-domain, hydrolase; HET: GDP; 2.50A {Bacillus subtilis}

Probab=80.27  E-value=1.5  Score=38.66  Aligned_cols=56  Identities=14%  Similarity=0.221  Sum_probs=37.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.|++..++|++..+....+  ..++    +.+.-+++..||++|.|+.+|++.|.+.+|.
T Consensus       110 ~~~pvilv~NK~D~~~~~~~~--~~~~----~lg~~~~~~iSA~~g~gv~~L~~~i~~~l~~  165 (436)
T 2hjg_A          110 TKKPVVLAVNKLDNTEMRANI--YDFY----SLGFGEPYPISGTHGLGLGDLLDAVAEHFKN  165 (436)
T ss_dssp             CCSCEEEEEECCCC-----CC--CSSG----GGSSCCCEECBTTTTBTHHHHHHHHHHTGGG
T ss_pred             cCCCEEEEEECccCccchhhH--HHHH----HcCCCCeEEEeCcCCCChHHHHHHHHHhcCc
Confidence            567999999997643321111  1111    1123367889999999999999999999874

>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=80.20  E-value=1.3  Score=39.89  Aligned_cols=57  Identities=16%  Similarity=0.145  Sum_probs=38.4

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC-CC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP-SP   85 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P-sP   85 (221)
                      +.|++..+||++.... .......+.+.    ...|++..||++|.||++|++.|.+.++ .+
T Consensus       343 ~~piIvV~NK~Dl~~~-~~~~~~~l~~~----~~~~~i~vSAktg~GI~eL~~~i~~~~~~~~  400 (476)
T 3gee_A          343 AAKFLTVANKLDRAAN-ADALIRAIADG----TGTEVIGISALNGDGIDTLKQHMGDLVKNLD  400 (476)
T ss_dssp             TSEEEEEEECTTSCTT-THHHHHHHHHH----HTSCEEECBTTTTBSHHHHHHHHTHHHHSSC
T ss_pred             CCCEEEEEECcCCCCc-cchhHHHHHhc----CCCceEEEEECCCCCHHHHHHHHHHHHhhcc
Confidence            4578888899653322 12222222221    1368999999999999999999999887 44

>3c5h_A Glucocorticoid receptor DNA-binding factor 1; RAS, GTPase, glucorticoid receptor, structural genomics consortium, SGC, alternative splicing; HET: GNP; 1.80A {Homo sapiens}

Probab=80.12  E-value=1.7  Score=35.22  Aligned_cols=57  Identities=14%  Similarity=0.131  Sum_probs=36.6

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|++.... .++  ....+........|++..||++|.||+++++.|.+.+
T Consensus       197 ~~~piilV~NK~Dl~~~-~~v--~~~~~~~~~~~~~~~~e~SAk~g~gv~elf~~l~~~l  253 (255)
T 3c5h_A          197 TKKPIVVVLTKCDEGVE-RYI--RDAHTFALSKKNLQVVETSARSNVNVDLAFSTLVQLI  253 (255)
T ss_dssp             TTCCEEEEEECGGGBCH-HHH--HHHHHHHHTSSSCCEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEccccccc-HHH--HHHHHHHHhcCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            35688888899653221 111  2222212121246899999999999999999998653

---

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	221
d2bv3a1	121	b.43.3.1 (A:283-403) Elongation factor G (EF-G), d	2e-12
d2bv3a1	121	b.43.3.1 (A:283-403) Elongation factor G (EF-G), d	0.002
d2dy1a1	103	b.43.3.1 (A:275-377) Elongation factor G (EF-G), d	3e-12
d2dy1a1	103	b.43.3.1 (A:275-377) Elongation factor G (EF-G), d	4e-06
d2dy1a2	267	c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-t	4e-10
d2bv3a2	276	c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-t	1e-09
d1n0ua1	138	b.43.3.1 (A:344-481) Elongation factor 2 (eEF-2),	5e-09

>d2bv3a1 b.43.3.1 (A:283-403) Elongation factor G (EF-G), domain II {Thermus thermophilus [TaxId: 274]} Length = 121

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor G (EF-G), domain II
species: Thermus thermophilus [TaxId: 274]

 Score = 59.7 bits (144), Expect = 2e-12
 Identities = 34/98 (34%), Positives = 50/98 (51%), Gaps = 12/98 (12%)

Query: 76  DAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYN 135
             +V+I P P               L A AFK++ D + G +TF R+YSG    G   YN
Sbjct: 14  GEVVEIHPDPNG------------PLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYN 61

Query: 136 IHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173
               + E++ RLL   A+  +EV E++ G++ AV GLK
Sbjct: 62  TTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLK 99

>d2bv3a1 b.43.3.1 (A:283-403) Elongation factor G (EF-G), domain II {Thermus thermophilus [TaxId: 274]} Length = 121

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor G (EF-G), domain II
species: Thermus thermophilus [TaxId: 274]

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 13/74 (17%)

Query: 2  DAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVL 61
            +V+I P P               L A AFK++ D + G +TF R+YSG        V 
Sbjct: 14 GEVVEIHPDPNG------------PLAALAFKIMADPYVGRLTFIRVYSGTLTSGS-YVY 60

Query: 62 CGSSYKNIGVQKLM 75
            +  +   V +L+
Sbjct: 61 NTTKGRKERVARLL 74

>d2dy1a1 b.43.3.1 (A:275-377) Elongation factor G (EF-G), domain II {Thermus thermophilus, EF-G-2 [TaxId: 274]} Length = 103

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor G (EF-G), domain II
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

 Score = 58.9 bits (142), Expect = 3e-12
 Identities = 19/73 (26%), Positives = 29/73 (39%), Gaps = 2/73 (2%)

Query: 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNE 160
             A+ FKV  D   G V + R+Y G  K G    +       ++  L +    D  EV E
Sbjct: 10  PLAKVFKVQVDPFMGQVAYLRLYRGRLKPGDSLQSEA--GQVRLPHLYVPMGKDLLEVEE 67

Query: 161 IQCGNIAAVTGLK 173
            + G +  V   +
Sbjct: 68  AEAGFVLGVPKAE 80

>d2dy1a1 b.43.3.1 (A:275-377) Elongation factor G (EF-G), domain II {Thermus thermophilus, EF-G-2 [TaxId: 274]} Length = 103

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor G (EF-G), domain II
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

 Score = 42.0 bits (98), Expect = 4e-06
 Identities = 11/30 (36%), Positives = 14/30 (46%)

Query: 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKN 56
            A+ FKV  D   G V + R+Y G  K  
Sbjct: 10 PLAKVFKVQVDPFMGQVAYLRLYRGRLKPG 39

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]} Length = 267

class: 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]

 Score = 55.7 bits (133), Expect = 4e-10
 Identities = 11/27 (40%), Positives = 16/27 (59%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPS 84
            PV   S  + IGV  L++ I++ LPS
Sbjct: 241 YPVALASGEREIGVLPLLELILEALPS 267

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]} Length = 276

class: 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]

 Score = 54.3 bits (130), Expect = 1e-09
 Identities = 17/27 (62%), Positives = 20/27 (74%)

Query: 58  VPVLCGSSYKNIGVQKLMDAIVDILPS 84
            PV  GS+ KN GVQ L+DA+VD LPS
Sbjct: 250 TPVFLGSALKNKGVQLLLDAVVDYLPS 276

>d1n0ua1 b.43.3.1 (A:344-481) Elongation factor 2 (eEF-2), domain II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 138

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor 2 (eEF-2), domain II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 50.8 bits (121), Expect = 5e-09
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 10/83 (12%)

Query: 101 LCARAFKVVHDKHRGA-VTFFRIYSGAFKKGQKFYNIHLD---------QSEQITRLLLA 150
           L     K+V    +G    F R+++G  K GQK      +           + I R++L 
Sbjct: 35  LMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLM 94

Query: 151 EADDYKEVNEIQCGNIAAVTGLK 173
                + +++   GNI  + G+ 
Sbjct: 95  MGRFVEPIDDCPAGNIIGLVGID 117

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	221
d2bv3a1	121	Elongation factor G (EF-G), domain II {Thermus the	99.91
d2dy1a1	103	Elongation factor G (EF-G), domain II {Thermus the	99.88
d1n0ua1	138	Elongation factor 2 (eEF-2), domain II {Baker's ye	99.85
d1f60a1	94	Elongation factor eEF-1alpha, domain 2 {Baker's ye	99.22
d1jnya1	95	Elongation factor eEF-1alpha, domain 2 {Archaeon S	99.19
d1r5ba1	95	Eukaryotic peptide chain release factor ERF2, post	99.06
d2c78a1	100	Elongation factor Tu (EF-Tu), domain 2 {Thermus th	99.04
d1efca1	92	Elongation factor Tu (EF-Tu), domain 2 {Escherichi	99.04
d1d2ea1	98	Elongation factor Tu (EF-Tu), domain 2 {Cow (Bos t	98.98
d1wb1a1	92	Elongation factor SelB, domains 2 and 4 {Methanoco	98.88
d1zunb1	92	Sulfate adenylate transferase subunit cysN/C, EF-T	98.84
d1xe1a_	91	Hypothetical protein PF0907 {Pyrococcus furiosus [	98.64
d1kk1a1	121	Initiation factor eIF2 gamma subunit, domain II {A	98.62
d1s0ua1	118	Initiation factor eIF2 gamma subunit, domain II {A	98.48
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	98.42
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	98.34
d1g7sa1	101	Initiation factor IF2/eIF5b, domains 2 and 4 {Arch	98.23
d2qn6a1	114	Initiation factor eIF2 gamma subunit, domain II {S	98.12
d1g7sa2	128	Initiation factor IF2/eIF5b, domains 2 and 4 {Arch	98.1
d2bv3a1	121	Elongation factor G (EF-G), domain II {Thermus the	97.34
d2qn6a3	205	Initiation factor eIF2 gamma subunit, N-terminal (	97.33
d2dy1a4	77	Elongation factor G (EF-G) {Thermus thermophilus,	97.24
d2bv3a4	75	Elongation factor G (EF-G) {Thermus thermophilus [	97.2
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	97.04
d1kk1a3	195	Initiation factor eIF2 gamma subunit, N-terminal (	96.86
d1d2ea3	196	Elongation factor Tu (EF-Tu), N-terminal (G) domai	96.65
d1d1na_	99	Initiation factor IF2/eIF5b, domains 2 and 4 {Baci	96.63
d2dy1a1	103	Elongation factor G (EF-G), domain II {Thermus the	96.55
d1n0ua4	79	Elongation factor 2 (eEF-2) {Baker's yeast (Saccha	96.15
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	95.8
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	95.19
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	95.13
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	95.07
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	94.97
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.89
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	94.37
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.28
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.27
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.25
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	93.87
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	93.82
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.8
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.53
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.49
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	93.44
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	93.27
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	93.05
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	92.93
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.42
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	92.16
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.16
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	92.13
d1n0ua1	138	Elongation factor 2 (eEF-2), domain II {Baker's ye	92.03
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	91.54
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	91.25
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	91.05
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	90.34
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	90.29
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	90.05
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	89.94
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	89.34
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	89.31
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	89.26
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	89.18
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	88.96
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	88.76
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	88.69
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	88.61
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	88.27
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	88.25
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	88.09
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	87.92
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	87.8
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	87.73
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	87.36
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	87.28
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	86.94
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	86.31
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	86.24
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	86.21
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	86.06
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	85.89
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	85.63
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	85.17
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	83.44
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	82.86
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	82.75
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	82.29

>d2bv3a1 b.43.3.1 (A:283-403) Elongation factor G (EF-G), domain II {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor G (EF-G), domain II
species: Thermus thermophilus [TaxId: 274]

Probab=99.91  E-value=1.2e-24  Score=162.66  Aligned_cols=90  Identities=34%  Similarity=0.541  Sum_probs=86.9

Q ss_pred             CCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCC
Q psy5461          95 QHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKR  174 (221)
Q Consensus        95 ~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~  174 (221)
                      +++++||+|+|||+++|+++|+++|+|||||+|++||+|++.+++++++|.+|+.++|.++++++++.||||+++.|+++
T Consensus        21 pd~~~p~~a~Vfk~~~d~~~G~i~~~RV~sG~l~~g~~v~~~~~~~~~rv~~l~~~~g~~~~~v~~~~aGdI~~i~gl~~  100 (121)
T d2bv3a1          21 PDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKE  100 (121)
T ss_dssp             CCTTSCCEEEEEEEEEETTTEEEEEEEEEESEEETTEEEEETTTTEEEEECEEEEECSSCEEEESEEETTCEEEEESCSS
T ss_pred             CCCCCCEEEEEEeeeecCCCCeEEeeeecccccCCCCEEEEccCCCEEEEeeeeeeecccccEeeEeccccceEEeccCC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccCcEEecC
Q psy5461         175 ERGKDKRTRV  184 (221)
Q Consensus       175 ~~~Gdtl~~~  184 (221)
                      +++|||||+.
T Consensus       101 ~~~GDTl~~~  110 (121)
T d2bv3a1         101 TITGDTLVGE  110 (121)
T ss_dssp             CCTTCEEEET
T ss_pred             ceeCCEEecC
Confidence            9999999975

>d2dy1a1 b.43.3.1 (A:275-377) Elongation factor G (EF-G), domain II {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor G (EF-G), domain II
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=99.88  E-value=7.2e-23  Score=148.90  Aligned_cols=87  Identities=22%  Similarity=0.262  Sum_probs=81.9

Q ss_pred             CCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC
Q psy5461          96 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE  175 (221)
Q Consensus        96 ~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~  175 (221)
                      +.++||+|+|||+++|+++|+++|+|||||+|++||+|++.+.  .+++.+++.+++.+.++++++.||||++|.|++++
T Consensus         5 ~~d~p~~a~Vfk~~~d~~~G~i~~~RV~sG~l~~g~~v~~~~~--~~~~~~~~~~~~~~~~~v~~~~aGdI~~v~g~~~~   82 (103)
T d2dy1a1           5 FGDGPPLAKVFKVQVDPFMGQVAYLRLYRGRLKPGDSLQSEAG--QVRLPHLYVPMGKDLLEVEEAEAGFVLGVPKAEGL   82 (103)
T ss_dssp             HCSCSCEEEEEEEEEETTTEEEEEEEEEESEECTTEEEBCTTS--CEEESSEEEEETTEEEEESCEETTCEEEESSCTTC
T ss_pred             CCCCCcEEEEEEEEecCCCCEEEEEEEeccccCCCCEEEEeec--ccccceeeeeecCcceecCEecCCCEEEEeCCCCC
Confidence            5689999999999999999999999999999999999987644  47899999999999999999999999999999999


Q ss_pred             ccCcEEecC
Q psy5461         176 RGKDKRTRV  184 (221)
Q Consensus       176 ~~Gdtl~~~  184 (221)
                      ++||||++.
T Consensus        83 ~iGDTl~~~   91 (103)
T d2dy1a1          83 HRGMVLWQG   91 (103)
T ss_dssp             CTTCEEESS
T ss_pred             ccCCEEcCC
Confidence            999999986

>d1n0ua1 b.43.3.1 (A:344-481) Elongation factor 2 (eEF-2), domain II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor 2 (eEF-2), domain II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=4.5e-21  Score=146.19  Aligned_cols=91  Identities=21%  Similarity=0.250  Sum_probs=82.7

Q ss_pred             cCCCCCCcEEEEEEEeecCCCce-EEEEEEEceEEcCCCEEEeccCC---------ceeeeceeEeeecCCeeeeCcccc
Q psy5461          94 FQHFGDSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKGQKFYNIHLD---------QSEQITRLLLAEADDYKEVNEIQC  163 (221)
Q Consensus        94 ~~~~~~~~~~~Vfk~~~d~~~G~-i~~~RV~sG~L~~gd~v~~~~~~---------~~~~v~~i~~~~g~~~~~v~~a~a  163 (221)
                      +|++++||+++|+|+.++++.|+ ++++|||||+|++||+|++.+.+         ...+|++||.++|.++++++++.|
T Consensus        28 ~cd~~~Pl~~~v~k~~~~~~~g~~~~~gRV~SGtl~~G~~v~vl~~~~~~~~~~~~~~~~i~~i~~~~g~~~~~v~~a~A  107 (138)
T d1n0ua1          28 NCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPA  107 (138)
T ss_dssp             TTCTTSSCEEEEEEEEEBSSTTCEEEEEEEEESEEETTCEEEEECTTCCSSSCTTEEEEECCEEEEEETTEEEEESEEET
T ss_pred             ccCCCCCEEEEEEeeccCCCCCEEEEEEEEEeceEcCCCEEEEecCCcccccccccceeeeeeeEEEecCceeeEeEEec
Confidence            35788999999999999999998 69999999999999999998643         236899999999999999999999


Q ss_pred             CCEEEEcCCCC-CccCcEEecC
Q psy5461         164 GNIAAVTGLKR-ERGKDKRTRV  184 (221)
Q Consensus       164 GdIv~i~gl~~-~~~Gdtl~~~  184 (221)
                      ||||+|.|+++ +..|+|||+.
T Consensus       108 GdIvai~Gl~~~i~k~~Tl~~~  129 (138)
T d1n0ua1         108 GNIIGLVGIDQFLLKTGTLTTS  129 (138)
T ss_dssp             TCEEEEESCTTTCCSSEEEESC
T ss_pred             CcEEEEeccccceeccceecCC
Confidence            99999999998 5669999986

>d1f60a1 b.43.3.1 (A:241-334) Elongation factor eEF-1alpha, domain 2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor eEF-1alpha, domain 2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.22  E-value=3.7e-11  Score=84.69  Aligned_cols=84  Identities=13%  Similarity=0.079  Sum_probs=74.0

Q ss_pred             CCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--
Q psy5461          98 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--  173 (221)
Q Consensus        98 ~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--  173 (221)
                      ++||.+.|-.++..++.|+++.+||.+|++++||++.+...+.+.+|++|+..    ..++++|.|||-++  |.|++  
T Consensus         1 dkP~rmpI~~vf~i~g~GtVvtG~v~~G~i~~Gd~v~i~P~~~~~~VksI~~~----~~~~~~a~aG~~v~l~l~~i~~~   76 (94)
T d1f60a1           1 DKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMH----HEQLEQGVPGDNVGFNVKNVSVK   76 (94)
T ss_dssp             TSCCEEEEEEEEEETTTEEEEEEECCBSCBCTTCEEEEETTTEEEEEEEEEET----TEECSCBCTTCEEEEEESSCCTT
T ss_pred             CCCEEEEEEEEEEeCCeeEEEEEeeecccCCCCCEEEECcCCceEEEEEEEEc----CcCcCEecCCCeEEEEEeCccHH
Confidence            47999999999999999999999999999999999999999988999999743    35789999999995  56765  


Q ss_pred             CCccCcEEecCC
Q psy5461         174 RERGKDKRTRVI  185 (221)
Q Consensus       174 ~~~~Gdtl~~~~  185 (221)
                      +++.|+.+++..
T Consensus        77 ~i~rG~vl~~~~   88 (94)
T d1f60a1          77 EIRRGNVCGDAK   88 (94)
T ss_dssp             TSCTTCEEEETT
T ss_pred             hcCCCCEEECCC
Confidence            789999999763

>d1jnya1 b.43.3.1 (A:228-322) Elongation factor eEF-1alpha, domain 2 {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor eEF-1alpha, domain 2
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=99.19  E-value=5.3e-11  Score=84.05  Aligned_cols=87  Identities=17%  Similarity=0.176  Sum_probs=76.2

Q ss_pred             CCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEE--EEcCCC--
Q psy5461          98 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA--AVTGLK--  173 (221)
Q Consensus        98 ~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv--~i~gl~--  173 (221)
                      ++||++.|..++..++.|+++.+||.+|++++||++.+...+.+.+|++|...    ..+++++.|||.+  .|.|++  
T Consensus         3 d~Plr~pI~~vf~~~g~G~vv~G~v~~G~i~~gd~v~i~P~~~~~~VksI~~~----~~~~~~a~aG~~v~l~l~~i~~~   78 (95)
T d1jnya1           3 DKPLRIPIQDVYSISGVGTVPVGRVESGVLKVGDKIVFMPAGKVGEVRSIETH----HTKMDKAEPGDNIGFNVRGVEKK   78 (95)
T ss_dssp             GSCCBEEEEEEEEETTTEEEEEEECCBSCEETTCEEEEETTTEEEEEEEEEET----TEEESEECTTCEEEEEEESSCGG
T ss_pred             CcCEEEEEEEEEEcCCceeEEEEEEeeccccCCCEEEEEeCCceEEEEEEEec----CCccCEEeCCCcEEEEEEcCcHH
Confidence            47999999999999999999999999999999999999999988999998754    3478999999999  466765  


Q ss_pred             CCccCcEEecCCCCC
Q psy5461         174 RERGKDKRTRVIPKP  188 (221)
Q Consensus       174 ~~~~Gdtl~~~~~~p  188 (221)
                      +++.||.|++....|
T Consensus        79 ~i~rG~vl~~~~~~p   93 (95)
T d1jnya1          79 DIKRGDVVGHPNNPP   93 (95)
T ss_dssp             GCCTTCEEECTTSCC
T ss_pred             hcCCCCEEECCCccC
Confidence            689999999876555

>d1r5ba1 b.43.3.1 (A:460-554) Eukaryotic peptide chain release factor ERF2, post-G domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Eukaryotic peptide chain release factor ERF2, post-G domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=99.06  E-value=2.7e-10  Score=80.28  Aligned_cols=84  Identities=14%  Similarity=0.164  Sum_probs=70.1

Q ss_pred             CCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc--CC-C
Q psy5461          97 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT--GL-K  173 (221)
Q Consensus        97 ~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~--gl-~  173 (221)
                      .++||++.|..++.  ..|+++++||.+|++++||+|.+...+...+|.+|+.+.   ..++++|.|||.+.+.  |. +
T Consensus         6 ~~~PlR~pV~d~~k--g~G~vv~G~v~sG~i~~gd~v~i~P~~~~~~Vk~I~~~~---~~~v~~a~aGd~V~l~l~~~~~   80 (95)
T d1r5ba1           6 VNAPFIMPIASKYK--DLGTILEGKIEAGSIKKNSNVLVMPINQTLEVTAIYDEA---DEEISSSICGDQVRLRVRGDDS   80 (95)
T ss_dssp             HTSCCEEECCEEEE--SSSEEEEEECCBSEEETTEEEEEETTTEEEEEEEEECTT---CCEESEEETTCEEEEEEESCCT
T ss_pred             CCCCEEEEEEEEEc--CCCEEEEEEEeeCeEeCCCEEEEecCCCEEEEEEEEEEc---cccccCcCCCCEEEEEEcCccc
Confidence            46899999988884  578999999999999999999999999888999986432   3468999999999654  53 3


Q ss_pred             CCccCcEEecCC
Q psy5461         174 RERGKDKRTRVI  185 (221)
Q Consensus       174 ~~~~Gdtl~~~~  185 (221)
                      ++++||++|+..
T Consensus        81 di~rG~vl~~~~   92 (95)
T d1r5ba1          81 DVQTGYVLTSTK   92 (95)
T ss_dssp             TCCTTCEEECSS
T ss_pred             ccCCCCEEEcCC
Confidence            789999999753

>d2c78a1 b.43.3.1 (A:213-312) Elongation factor Tu (EF-Tu), domain 2 {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor Tu (EF-Tu), domain 2
species: Thermus thermophilus [TaxId: 274]

Probab=99.04  E-value=5.8e-10  Score=79.29  Aligned_cols=85  Identities=16%  Similarity=0.159  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEec---cCCceeeeceeEeeecCCeeeeCccccCCEEE--Ec
Q psy5461          96 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNI---HLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VT  170 (221)
Q Consensus        96 ~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~---~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~  170 (221)
                      +.++||++.|..++..++.|+++.+||.+|+++.||.+.+.   ..++..+|.+|..    ...++++|.|||-++  |.
T Consensus         4 ~~~~p~r~~Id~vf~~~g~Gtvv~G~v~~G~i~~gd~v~i~~~~p~~~~~~V~sI~~----~~~~~~~a~aG~~v~l~l~   79 (100)
T d2c78a1           4 DVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEM----HRKTLQEGIAGDNVGVLLR   79 (100)
T ss_dssp             CCSSCCEEECCEEEEETTTEEEEEEECCBSEEETTCEEEEESSSSSCEEEEEEEEEE----TTEEESEEETTCEEEEEES
T ss_pred             CCCCCEEEEEEEEEEcCCcEEEEEEEEeccEEECCCEeEEEeecCCCcEEEEEEEEE----CCccccEEeCCCeEEEEEc
Confidence            45789999999999999999999999999999999999997   3455677888863    245789999999995  56


Q ss_pred             CCC--CCccCcEEecC
Q psy5461         171 GLK--RERGKDKRTRV  184 (221)
Q Consensus       171 gl~--~~~~Gdtl~~~  184 (221)
                      |++  +++.|+.||+.
T Consensus        80 gi~~~~i~rG~vl~~p   95 (100)
T d2c78a1          80 GVSREEVERGQVLAKP   95 (100)
T ss_dssp             SCCTTTCCTTCEEEST
T ss_pred             CCCHHHccCcCEEECC
Confidence            765  68999999864

>d1efca1 b.43.3.1 (A:205-296) Elongation factor Tu (EF-Tu), domain 2 {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor Tu (EF-Tu), domain 2
species: Escherichia coli [TaxId: 562]

Probab=99.04  E-value=4.7e-10  Score=78.58  Aligned_cols=82  Identities=18%  Similarity=0.189  Sum_probs=68.8

Q ss_pred             CCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC--ceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC
Q psy5461          98 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD--QSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK  173 (221)
Q Consensus        98 ~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~--~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~  173 (221)
                      ++||++.|-.++..++.|+++++|+.+|++++||++.....+  .+.+|.+|...    ..++++|.|||.++  +.|++
T Consensus         3 d~P~rlpId~vf~i~G~GtVvtG~v~~G~i~~Gd~v~i~p~~~~~~~~vksi~~~----~~~~~~a~aG~~v~l~L~gi~   78 (92)
T d1efca1           3 DKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMF----RKLLDEGRAGENVGVLLRGIK   78 (92)
T ss_dssp             GSCCEEECCEEEECTTSCEEEEEECCBSEEETTCEEEEESSSSCEEEEEEEEEET----TEEESEEETTCEEEEEETTCC
T ss_pred             CCCEEEEEEEEEEcCCeEEEEEEEeccCeEcCCCEEEEEcCCCCcEEEEEEEEEC----CcCccccCCCCEEEEEEcCCC
Confidence            579999999999999999999999999999999999886543  45678887633    36789999999995  56765


Q ss_pred             --CCccCcEEec
Q psy5461         174 --RERGKDKRTR  183 (221)
Q Consensus       174 --~~~~Gdtl~~  183 (221)
                        +++.|+.++.
T Consensus        79 ~~~i~rG~vl~~   90 (92)
T d1efca1          79 REEIERGQVLAK   90 (92)
T ss_dssp             GGGCCTTCEEEC
T ss_pred             HHHcCCccEEeC
Confidence              6899999985

>d1d2ea1 b.43.3.1 (A:251-348) Elongation factor Tu (EF-Tu), domain 2 {Cow (Bos taurus), mitochondrial [TaxId: 9913]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor Tu (EF-Tu), domain 2
species: Cow (Bos taurus), mitochondrial [TaxId: 9913]

Probab=98.98  E-value=1.2e-09  Score=77.36  Aligned_cols=85  Identities=19%  Similarity=0.157  Sum_probs=69.7

Q ss_pred             CCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC--ceeeeceeEeeecCCeeeeCccccCCEEE--EcC
Q psy5461          96 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD--QSEQITRLLLAEADDYKEVNEIQCGNIAA--VTG  171 (221)
Q Consensus        96 ~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~--~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~g  171 (221)
                      +.++||.+.|-.++..++.|+++++|+.+|+++.||++......  ...+|..|..    ...++++|.|||-++  |.|
T Consensus         3 ~~d~Pfr~pId~vf~i~G~GtVvtG~v~~G~i~~gd~v~~~~~~~~~~~~V~si~~----~~~~~~~a~aG~~v~l~l~g   78 (98)
T d1d2ea1           3 DLEKPFLLPVESVYSIPGRGTVVTGTLERGILKKGDECEFLGHSKNIRTVVTGIEM----FHKSLDRAEAGDNLGALVRG   78 (98)
T ss_dssp             CTTSCCEEECCEEEEETTTEEEEEEECCBSEEETTCEEEEEETTEEEEEEEEEEEE----TTEEESEEETTCEEEEEESS
T ss_pred             CCCCCEEEEEEEEEEeCCcEEEEecceeeeeEeCCCEEEEccCCCCeeEEEEEEEE----eccEeccCCCCCEEEEEEcC
Confidence            56799999999999999999999999999999999999655433  3346777653    345789999999995  567


Q ss_pred             CC--CCccCcEEecC
Q psy5461         172 LK--RERGKDKRTRV  184 (221)
Q Consensus       172 l~--~~~~Gdtl~~~  184 (221)
                      ++  +++.|+.|++.
T Consensus        79 i~~~~i~rG~vl~~p   93 (98)
T d1d2ea1          79 LKREDLRRGLVMAKP   93 (98)
T ss_dssp             CCGGGCCTTCEEEST
T ss_pred             CCHHHccCccEEeCC
Confidence            75  78999999975

>d1wb1a1 b.43.3.1 (A:180-271) Elongation factor SelB, domains 2 and 4 {Methanococcus maripaludis [TaxId: 39152]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor SelB, domains 2 and 4
species: Methanococcus maripaludis [TaxId: 39152]

Probab=98.88  E-value=7e-11  Score=82.92  Aligned_cols=85  Identities=15%  Similarity=0.093  Sum_probs=72.8

Q ss_pred             CCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC
Q psy5461          96 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK  173 (221)
Q Consensus        96 ~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~  173 (221)
                      +.++||.+.|-.++..++.|+++.+||.+|++++||+|.+...+.+.+|.+|. ++   .+++++|.|||.+++  .|++
T Consensus         2 ~~~~~fr~~I~~vf~i~g~G~VvtG~v~sG~i~~gd~v~i~P~~~~~~VksI~-~~---~~~~~~a~aGd~v~l~L~gi~   77 (92)
T d1wb1a1           2 NTESYFKMPLDHAFPIKGAGTVVTGTINKGIVKVGDELKVLPINMSTKVRSIQ-YF---KESVMEAKAGDRVGMAIQGVD   77 (92)
T ss_dssp             CSSSCCBCBCSCEECCSSCCCEECCCCCBSCCCSSEEECCTTTCCCEEECCBC-GG---GSCBCCCCSSCCCCEECSSCC
T ss_pred             CCCCCEEEEEEEEEEeCCcEEEEEeEEeeceEecCCeEEEeccCCceEEEeee-Ec---CceeeEeCCCCEEEEEEcCCC
Confidence            45789999999999889999999999999999999999999988888999986 33   346899999999954  5654


Q ss_pred             --CCccCcEEecC
Q psy5461         174 --RERGKDKRTRV  184 (221)
Q Consensus       174 --~~~~Gdtl~~~  184 (221)
                        +++.||.|++.
T Consensus        78 ~~~i~rG~vl~~~   90 (92)
T d1wb1a1          78 AKQIYRGCILTSK   90 (92)
T ss_dssp             SSCCCSSCBCCCT
T ss_pred             HHHcCCcCEEeCC
Confidence              78999998864

>d1zunb1 b.43.3.1 (B:238-329) Sulfate adenylate transferase subunit cysN/C, EF-Tu domain 2-like domain {Pseudomonas syringae pv. tomato [TaxId: 323]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Sulfate adenylate transferase subunit cysN/C, EF-Tu domain 2-like domain
species: Pseudomonas syringae pv. tomato [TaxId: 323]

Probab=98.84  E-value=7.3e-09  Score=72.31  Aligned_cols=87  Identities=14%  Similarity=0.024  Sum_probs=69.0

Q ss_pred             CCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc--CCCCC
Q psy5461          98 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT--GLKRE  175 (221)
Q Consensus        98 ~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~--gl~~~  175 (221)
                      +.+|.+.|-.+....+.++...+||.+|++++||+|.+...++..+|++|+.. +   .++++|.||+.++|.  +-.++
T Consensus         4 ~~~fr~pVQ~V~r~~~~~r~~~G~v~sG~v~~Gd~v~i~Psg~~~~Vk~I~~~-~---~~~~~a~~G~~v~l~L~~~~di   79 (92)
T d1zunb1           4 YTDLRFPVQYVNRPNLNFRGFAGTLASGIVHKGDEIVVLPSGKSSRVKSIVTF-E---GELEQAGPGQAVTLTMEDEIDI   79 (92)
T ss_dssp             SSSCEEECCEEECSSSSCCEEEEECCBSCEETTCEEEETTTCCEEEEEEEEET-T---EEESEECTTCEEEEEESSCCCC
T ss_pred             CCCeEEeEEEEEccCCCccEEEEEEcccEEecCCEEEECCCCceEEEeEEEEc-C---cccCEEcCCCEEEEEEcCcccc
Confidence            35788877666654445677889999999999999999999999999999743 3   478899999999754  43478


Q ss_pred             ccCcEEecCCCCC
Q psy5461         176 RGKDKRTRVIPKP  188 (221)
Q Consensus       176 ~~Gdtl~~~~~~p  188 (221)
                      ..||+|+.....|
T Consensus        80 ~RGdvl~~~~~~P   92 (92)
T d1zunb1          80 SRGDLLVHADNVP   92 (92)
T ss_dssp             CTTCEEEETTSCC
T ss_pred             CCCCEEecCCCCC
Confidence            9999999875444

>d1xe1a_ b.43.3.1 (A:) Hypothetical protein PF0907 {Pyrococcus furiosus [TaxId: 2261]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Hypothetical protein PF0907
species: Pyrococcus furiosus [TaxId: 2261]

Probab=98.64  E-value=1.6e-07  Score=65.18  Aligned_cols=80  Identities=16%  Similarity=0.021  Sum_probs=64.9

Q ss_pred             CCCCc-EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC
Q psy5461          97 FGDSL-CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK  173 (221)
Q Consensus        97 ~~~~~-~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~  173 (221)
                      ..+|+ .++|-.++..++ |++.+++|.+|++++||+|.....  +.+|.+|...    ..++++|.|||-+++  .|-.
T Consensus         5 ~~kp~~R~~Id~vf~i~G-gtVvtGtV~sG~i~~Gd~v~~~p~--~~~VksIq~~----~~~v~~a~~G~~v~l~L~~~~   77 (91)
T d1xe1a_           5 SKKPAGKVVVEEVVNIMG-KDVIIGTVESGMIGVGFKVKGPSG--IGGIVRIERN----REKVEFAIAGDRIGISIEGKI   77 (91)
T ss_dssp             CSSCSEEEEEEEEEEETT-EEEEEEEEEEEEEETTCEEECSSC--EEEEEEEEET----TEEESEEETTCEEEEEEESCC
T ss_pred             cCCCccEeeEEEEEEECC-cEEEEEEEeeCCcCCCCEEEECCc--cEEEEEEEEc----ceEhhhhhhcceeEEEEcCCc
Confidence            34676 899999999898 999999999999999999988753  4678888743    347899999999964  4633


Q ss_pred             -CCccCcEEec
Q psy5461         174 -RERGKDKRTR  183 (221)
Q Consensus       174 -~~~~Gdtl~~  183 (221)
                       +++.||.|..
T Consensus        78 ~di~rGdvL~~   88 (91)
T d1xe1a_          78 GKVKKGDVLEI   88 (91)
T ss_dssp             CCCCTTCEEEE
T ss_pred             CCcCCCCEEEe
Confidence             6899999864

>d1kk1a1 b.43.3.1 (A:201-321) Initiation factor eIF2 gamma subunit, domain II {Archaeon Pyrococcus abyssi [TaxId: 29292]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Initiation factor eIF2 gamma subunit, domain II
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

Probab=98.62  E-value=1.1e-07  Score=69.33  Aligned_cols=86  Identities=16%  Similarity=0.009  Sum_probs=66.0

Q ss_pred             CCCCCcEEEEEEEeec--------CCCceEEEEEEEceEEcCCCEEEeccCCc------------eeeeceeEeeecCCe
Q psy5461          96 HFGDSLCARAFKVVHD--------KHRGAVTFFRIYSGAFKKGQKFYNIHLDQ------------SEQITRLLLAEADDY  155 (221)
Q Consensus        96 ~~~~~~~~~Vfk~~~d--------~~~G~i~~~RV~sG~L~~gd~v~~~~~~~------------~~~v~~i~~~~g~~~  155 (221)
                      +.++||++.|..++.-        ..+|.++.++|.+|+|++||+|.+...++            +.+|.+|...    .
T Consensus         4 ~~~~p~r~~Idr~F~v~g~Gt~~~~~~G~VvtGtv~sG~ik~GD~v~i~P~~~~~~~~~~~~~~~~~~V~sI~~~----~   79 (121)
T d1kk1a1           4 DPNKPPKMLVLRSFDVNKPGTPPEKLVGGVLDGSIVQGKLKVGDEIEIRPGVPYEEHGRIKYEPITTEIVSLQAG----G   79 (121)
T ss_dssp             CTTSCCEEEEEEEECCSCCC----CCCCCEEEEEEEESCEETTCEEEEEEEEEEEETTEEEEEEEEEEEEEEEET----T
T ss_pred             CCCCCcEEEEEEEEEecCCCCccccCcceEEEeeecCCEEecCCEEEECCCCccccccceeceeeeeEEEEEEEC----C
Confidence            5678999999998865        34456999999999999999999987553            2467777632    3


Q ss_pred             eeeCccccCCEEEEc-----CCC--CCccCcEEecCC
Q psy5461         156 KEVNEIQCGNIAAVT-----GLK--RERGKDKRTRVI  185 (221)
Q Consensus       156 ~~v~~a~aGdIv~i~-----gl~--~~~~Gdtl~~~~  185 (221)
                      .++++|.|||.+++.     +++  ++..|++++...
T Consensus        80 ~~v~~A~~G~~Vgv~l~~d~~i~r~Dv~rG~Vl~~pg  116 (121)
T d1kk1a1          80 QFVEEAYPGGLVGVGTKLDPYLTKGDLMAGNVVGKPG  116 (121)
T ss_dssp             EEESEECSSSCEEEEESSCGGGTGGGTTTTCEEECTT
T ss_pred             CCcCEEeCCCeEEEEecccCCcchhHhcceeEEECCC
Confidence            579999999988653     332  677899888753

>d1s0ua1 b.43.3.1 (A:230-347) Initiation factor eIF2 gamma subunit, domain II {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Initiation factor eIF2 gamma subunit, domain II
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=98.48  E-value=3.9e-07  Score=66.11  Aligned_cols=85  Identities=14%  Similarity=0.028  Sum_probs=65.2

Q ss_pred             CCCCCcEEEEEEEeecCC--------CceEEEEEEEceEEcCCCEEEeccCCc------------eeeeceeEeeecCCe
Q psy5461          96 HFGDSLCARAFKVVHDKH--------RGAVTFFRIYSGAFKKGQKFYNIHLDQ------------SEQITRLLLAEADDY  155 (221)
Q Consensus        96 ~~~~~~~~~Vfk~~~d~~--------~G~i~~~RV~sG~L~~gd~v~~~~~~~------------~~~v~~i~~~~g~~~  155 (221)
                      +.++||.++|..+..-..        .|.++.++|.+|+|++||+|.+...++            +.+|.+|+..    .
T Consensus         2 ~~~~p~~~~I~r~F~i~~~gt~~~~~~G~VvtGtv~sG~i~~GD~v~i~P~~~~~~~~~~~~~~~~t~V~sI~~~----~   77 (118)
T d1s0ua1           2 DPDATPRMYVARSFDINKPGTEIKDLKGGVLGGAIIQGVFKVGDEIEIRPGIKVTEGNKTFWKPLTTKIVSLAAG----N   77 (118)
T ss_dssp             CTTSCCEEEEEEEECCCCSSCCGGGCCCCEEEEEEEESCEETTCEEEEEEEEEECCTTCCEEEEEEEECCEEEET----T
T ss_pred             CCCCCcEEEEEeEEcccCCCCccccccccEEEeeecccEEeeCCEEEECCCCcccccceeeeeeeeEEEEEEEEC----C
Confidence            567899999998875443        455999999999999999999987543            3578888743    3


Q ss_pred             eeeCccccCCEEEEc-----CCC--CCccCcEEecC
Q psy5461         156 KEVNEIQCGNIAAVT-----GLK--RERGKDKRTRV  184 (221)
Q Consensus       156 ~~v~~a~aGdIv~i~-----gl~--~~~~Gdtl~~~  184 (221)
                      .++++|.|||-++|.     +++  ++..|++|+..
T Consensus        78 ~~v~~A~aG~~V~i~l~~d~~i~r~Di~~G~Vl~~p  113 (118)
T d1s0ua1          78 TILRKAHPGGLIGVGTTLDPYLTKSDALTGSVVGLP  113 (118)
T ss_dssp             EEESEECSSSCEEEECSSCGGGTGGGTTTTCEEEST
T ss_pred             cccCEEeCCCEEEEEeccCCCccHHHheeeeEEeCC
Confidence            578999999999764     221  56778888764

>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=98.42  E-value=3e-08  Score=82.40  Aligned_cols=61  Identities=33%  Similarity=0.506  Sum_probs=49.4

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.|+.+...++.  .+....+-....+++++.++.++|||+|||.++.||++|||+|++++||
T Consensus       216 e~Dd~L~e~yle--~~e~~~eel~~~l~~a~~~g~i~PV~~GSA~~n~GV~~LLD~i~~~~PS  276 (276)
T d2bv3a2         216 DFDENIMLKYLE--GEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPS  276 (276)
T ss_dssp             TTCHHHHHHHHH--TCCCCHHHHHHHHHHHHHTTSCEEEEECBTTTTBSHHHHHHHHHHHSCC
T ss_pred             cccHHHHHHHhc--CCCCCHHHHHHHHHHHHhcCcEEEEEEeECCCCcCHHHHHHHHHHhCCC
Confidence            456677666665  2333445556777889999999999999999999999999999999996

>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=98.34  E-value=6.2e-08  Score=80.05  Aligned_cols=61  Identities=21%  Similarity=0.282  Sum_probs=48.9

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.|+.+...++.  .+....+.....+++++.++.++|||||||.++.||++|||+|++++||
T Consensus       207 e~Dd~Lle~yle--~~~l~~eel~~~l~~ai~~g~i~PV~~GSA~~n~GV~~LLd~i~~~~Ps  267 (267)
T d2dy1a2         207 ETDEGLLEKYLE--GEEVTGEALEKAFHEAVRRGLLYPVALASGEREIGVLPLLELILEALPS  267 (267)
T ss_dssp             TTCHHHHHHHHH--TCCCCHHHHHHHHHHHHHTTSCEEEEECBTTTTBSHHHHHHHHHHHSCC
T ss_pred             hcCHHHHHHHhC--CCcccHHHHHHHHHHHHHcCcEEEEEeCcCCCCcCHHHHHHHHHHhCCC
Confidence            355666666665  2333455556777889999999999999999999999999999999996

>d1g7sa1 b.43.3.1 (A:228-328) Initiation factor IF2/eIF5b, domains 2 and 4 {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Initiation factor IF2/eIF5b, domains 2 and 4
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=98.23  E-value=8.6e-06  Score=56.96  Aligned_cols=85  Identities=15%  Similarity=0.224  Sum_probs=70.6

Q ss_pred             CCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCc--eeeeceeEe--------eecCCeeeeCccccCCEE
Q psy5461          98 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ--SEQITRLLL--------AEADDYKEVNEIQCGNIA  167 (221)
Q Consensus        98 ~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~--~~~v~~i~~--------~~g~~~~~v~~a~aGdIv  167 (221)
                      ++|..+.|.....|+++|.++.+-|++|+|+.||.+.......  ..+|+.|+.        ....+.++++++.|..-+
T Consensus         2 d~~a~G~VlEs~~dkg~G~~atviv~~GtLk~GD~iv~g~~~G~i~~~iraLl~p~pl~emr~~~~~~~~vke~~aa~gV   81 (101)
T d1g7sa1           2 DSPARGTILEVKEETGLGMTIDAVIYDGILRKDDTIAMMTSKDVISTRIRSLLKPRPLEEMRESRKKFQKVDEVVAAAGI   81 (101)
T ss_dssp             TSBCEEEEEEEEEETTEEEEEEEEEEESEEETTCEEEEEBSSSEEEEECCEEEEECCCC----CCCSEEECSEEESSEEE
T ss_pred             CCCcEEEEEEEEEcCCCCeeEEEEEEcCEEccCCEEEEecCcCCEEEEeecccCCcchhhhhccccCCeECcEEeCCCce
Confidence            5788999999999999999999999999999999999976542  346777664        345678899999999988


Q ss_pred             EEc--CCCCCccCcEEe
Q psy5461         168 AVT--GLKRERGKDKRT  182 (221)
Q Consensus       168 ~i~--gl~~~~~Gdtl~  182 (221)
                      -|.  |++.+-.|+.|.
T Consensus        82 kI~a~gLe~v~aG~~~~   98 (101)
T d1g7sa1          82 KIVAPGIDDVMAGSPLR   98 (101)
T ss_dssp             EEECSSCTTBCTTCEEE
T ss_pred             EEEcCCCCcCCCCCEEE
Confidence            665  888877999874

>d2qn6a1 b.43.3.1 (A:207-320) Initiation factor eIF2 gamma subunit, domain II {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Initiation factor eIF2 gamma subunit, domain II
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.12  E-value=5.3e-06  Score=59.58  Aligned_cols=71  Identities=17%  Similarity=0.183  Sum_probs=55.5

Q ss_pred             CCCCCcEEEEEEEeec--------CCCceEEEEEEEceEEcCCCEEEeccCCc------------eeeeceeEeeecCCe
Q psy5461          96 HFGDSLCARAFKVVHD--------KHRGAVTFFRIYSGAFKKGQKFYNIHLDQ------------SEQITRLLLAEADDY  155 (221)
Q Consensus        96 ~~~~~~~~~Vfk~~~d--------~~~G~i~~~RV~sG~L~~gd~v~~~~~~~------------~~~v~~i~~~~g~~~  155 (221)
                      +.+.|++++|...+.-        .++|.++.+++.+|+++.||+|.+...++            +.+|.+|+..    .
T Consensus         2 d~~~~p~~~V~R~F~vn~pgt~~~~~~G~VvtGtv~~G~ikvGD~i~i~P~~~~~~~~~~~~~~~~t~V~sI~~~----~   77 (114)
T d2qn6a1           2 DLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIRFG----D   77 (114)
T ss_dssp             CTTSCCEEEEEEEECCCCTTCBGGGCCCCEEEEEEEESCEETTCEEEEEEEEEEEETTEEEEEEEEEEEEEEEET----T
T ss_pred             CCCCCceEEEeccccccCCCCCcccccceEEEEEEccccEEeCCEEEEcCCCccccCceeeeeecceEEEEEEEC----C
Confidence            4567888888877543        34667999999999999999999987653            2578887643    3


Q ss_pred             eeeCccccCCEEEEc
Q psy5461         156 KEVNEIQCGNIAAVT  170 (221)
Q Consensus       156 ~~v~~a~aGdIv~i~  170 (221)
                      .++++|.||+.++|.
T Consensus        78 ~~v~~A~aG~~V~i~   92 (114)
T d2qn6a1          78 EEFKEAKPGGLVAIG   92 (114)
T ss_dssp             EEESEECSSSCEEEE
T ss_pred             cccCEEeCCCEEEEE
Confidence            578999999999874

>d1g7sa2 b.43.3.1 (A:460-587) Initiation factor IF2/eIF5b, domains 2 and 4 {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Initiation factor IF2/eIF5b, domains 2 and 4
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=98.10  E-value=8.4e-06  Score=59.67  Aligned_cols=68  Identities=12%  Similarity=0.102  Sum_probs=54.3

Q ss_pred             ceEEEE-EEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC---CCccCcEEecCCC
Q psy5461         115 GAVTFF-RIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK---RERGKDKRTRVIP  186 (221)
Q Consensus       115 G~i~~~-RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~---~~~~Gdtl~~~~~  186 (221)
                      +.++++ ||.+|+|++|+.|.+...+...+|.+|. .   +.+++++|.+|+-|++  .|..   ++..||+|++..+
T Consensus        19 ~p~ivgv~V~sG~ik~G~~l~~~p~~~~g~VksIq-~---~~~~v~~A~~G~~Vai~I~g~~~gr~i~~gD~L~s~i~   92 (128)
T d1g7sa2          19 KPAIGGVEVLTGVIRQGYPLMNDDGETVGTVESMQ-D---KGENLKSASRGQKVAMAIKDAVYGKTIHEGDTLYVDIP   92 (128)
T ss_dssp             SSEEEEEEEEEEEEETTCEEECTTSCEEEEEEEEE-E---TTEEESEEETTCCEEEEEETCCBTTTBCTTCEEEECCC
T ss_pred             CCeEEEEEEeeeeecCCCEEEECCCCceEEEEEEE-E---CCccccEEcCCCEEEEEEcCcccCCCCCCCCEEEEeCC
Confidence            455555 9999999999999999888777888875 3   3458999999999965  4643   7899999987644

>d2bv3a1 b.43.3.1 (A:283-403) Elongation factor G (EF-G), domain II {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor G (EF-G), domain II
species: Thermus thermophilus [TaxId: 274]

Probab=97.34  E-value=2.3e-05  Score=56.65  Aligned_cols=43  Identities=33%  Similarity=0.507  Sum_probs=37.0

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCC
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSS   65 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa   65 (221)
                      ++++||+++|||++.|++.|++++.|+++|+++.+.. +++.+.
T Consensus        22 d~~~p~~a~Vfk~~~d~~~G~i~~~RV~sG~l~~g~~-v~~~~~   64 (121)
T d2bv3a1          22 DPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSY-VYNTTK   64 (121)
T ss_dssp             CTTSCCEEEEEEEEEETTTEEEEEEEEEESEEETTEE-EEETTT
T ss_pred             CCCCCEEEEEEeeeecCCCCeEEeeeecccccCCCCE-EEEccC
Confidence            5688999999999999999999999999999998664 555443

>d2qn6a3 c.37.1.8 (A:2-206) Initiation factor eIF2 gamma subunit, N-terminal (G) domain {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor eIF2 gamma subunit, N-terminal (G) domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=97.33  E-value=8e-05  Score=57.91  Aligned_cols=61  Identities=20%  Similarity=0.266  Sum_probs=40.9

Q ss_pred             Cceeeeeeeecc-cccCCcchHHHHhhc--cccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          25 DSLCARAFKVVH-DKHRGAVTFFRIYSG--AFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        25 ~~~~~~vfk~~~-d~~~g~l~~~~l~~~--~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      .+++..++|.+. +..........+.+.  ......+|++++||++|.||++|++.|.+++|.|
T Consensus       141 ~~iIV~vNK~Dl~~~~~~~~~~~~~~~~l~~~~~~~~p~ipiSA~~g~nI~~L~e~i~~~ip~P  204 (205)
T d2qn6a3         141 KNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTP  204 (205)
T ss_dssp             CCEEEEEECGGGSCHHHHHHHHHHHHHHHTTSTTTTCCEEECBTTTTBSHHHHHHHHHHHSCCC
T ss_pred             ceeeeccccCCCccchHHHHHHHHHHHHhccccCCCCeEEEEeCCCCCChHHHHHHHHhhCCCC
Confidence            478889999642 211011111111111  1223468999999999999999999999999987

>d2dy1a4 d.58.11.1 (A:378-454) Elongation factor G (EF-G) {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: EF-G C-terminal domain-like
family: EF-G/eEF-2 domains III and V
domain: Elongation factor G (EF-G)
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=97.24  E-value=9.8e-05  Score=48.95  Aligned_cols=27  Identities=4%  Similarity=-0.015  Sum_probs=24.8

Q ss_pred             ehHHHHHHHHHHhhcCCceEEEccccc
Q psy5461         193 QCSARWTLNLEVGASSPIISKSKRRQN  219 (221)
Q Consensus       193 ~~~~l~~~L~~L~~~Dp~l~~~~~~~~  219 (221)
                      |.++|.+||++|+++||++.+.+|.++
T Consensus        17 d~~kl~~aL~~L~~eDPsl~v~~d~et   43 (77)
T d2dy1a4          17 DEARLGEALRKLLEEDPSLKLERQEET   43 (77)
T ss_dssp             HHHHHHHHHHHHHHHCTTSEEEECTTT
T ss_pred             HHHHHHHHHHHHHhhcCeEEEEEcCCc
Confidence            889999999999999999999998653

>d2bv3a4 d.58.11.1 (A:404-478) Elongation factor G (EF-G) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: EF-G C-terminal domain-like
family: EF-G/eEF-2 domains III and V
domain: Elongation factor G (EF-G)
species: Thermus thermophilus [TaxId: 274]

Probab=97.20  E-value=6.2e-05  Score=49.73  Aligned_cols=27  Identities=15%  Similarity=0.067  Sum_probs=10.3

Q ss_pred             ehHHHHHHHHHHhhcCCceEEEccccc
Q psy5461         193 QCSARWTLNLEVGASSPIISKSKRRQN  219 (221)
Q Consensus       193 ~~~~l~~~L~~L~~~Dp~l~~~~~~~~  219 (221)
                      |.++|++||++|+++||++++.+|..+
T Consensus        17 D~~kl~~aL~~L~~EDPsl~~~~d~et   43 (75)
T d2bv3a4          17 DQEKLSQALARLAEESPTFSVSTHPET   43 (75)
T ss_dssp             ---------------CCSCEEEECSSS
T ss_pred             HHHHHHHHHHHHHhhCCceEEEEcCcC
Confidence            889999999999999999999998753

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=97.04  E-value=0.00015  Score=54.94  Aligned_cols=64  Identities=14%  Similarity=0.165  Sum_probs=45.0

Q ss_pred             CCCceeeeeeeecccc-cC---CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461          23 FGDSLCARAFKVVHDK-HR---GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT   86 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~-~~---g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~   86 (221)
                      .+-|++..++|++.-. ..   ......++.+........|+++.||++|.|+++|++.|.+.+|.+.
T Consensus       110 ~~~p~iiv~NKiD~~~~~~~~~~~~~~~~~~~~~~~~~~~~iv~iSA~~g~gi~eL~~~I~~~l~~~e  177 (179)
T d1wb1a4         110 FNIPIIVVITKSDNAGTEEIKRTEMIMKSILQSTHNLKNSSIIPISAKTGFGVDELKNLIITTLNNAE  177 (179)
T ss_dssp             TTCCBCEEEECTTSSCHHHHHHHHHHHHHHHHHSSSGGGCCEEECCTTTCTTHHHHHHHHHHHHHHSC
T ss_pred             cCCcceeccccccccCHHHHHHHHHHHHHHHHHhhcCCCCeEEEEEccCCcCHHHHHHHHHhcCCccc
Confidence            4678899999964211 10   1122333444445556789999999999999999999999998763

>d1kk1a3 c.37.1.8 (A:6-200) Initiation factor eIF2 gamma subunit, N-terminal (G) domain {Archaeon Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor eIF2 gamma subunit, N-terminal (G) domain
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

Probab=96.86  E-value=0.0004  Score=53.21  Aligned_cols=60  Identities=18%  Similarity=0.265  Sum_probs=39.5

Q ss_pred             Cceeeeeeeec-ccccCCcchHHHHhhcc--ccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          25 DSLCARAFKVV-HDKHRGAVTFFRIYSGA--FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        25 ~~~~~~vfk~~-~d~~~g~l~~~~l~~~~--~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+++..++|.+ .|+..-...+..+.+..  .....+|++.+||++|.||++|+++|.+++|+
T Consensus       133 ~~iiv~inK~D~~d~~~~~~~~~~~~~~~~~~~~~~~~iIpiSA~~G~ni~~Ll~~I~~~iPt  195 (195)
T d1kk1a3         133 KNIIIAQNKIELVDKEKALENYRQIKEFIEGTVAENAPIIPISALHGANIDVLVKAIEDFIPT  195 (195)
T ss_dssp             CCEEEEEECGGGSCHHHHHHHHHHHHHHHTTSTTTTCCEEECBTTTTBSHHHHHHHHHHHSCC
T ss_pred             ccceeeeecccchhhHHHHHHHHHHHHHhccccCCCCeEEEEECCCCCCHHHHHHHHHHHCcC
Confidence            35778899964 22211111222222222  22346799999999999999999999999996

>d1d2ea3 c.37.1.8 (A:55-250) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Cow (Bos taurus), mitochondrial [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Cow (Bos taurus), mitochondrial [TaxId: 9913]

Probab=96.65  E-value=0.00031  Score=54.45  Aligned_cols=61  Identities=25%  Similarity=0.357  Sum_probs=41.2

Q ss_pred             Cceeeeeeeecc--cccCCcchHHHHhhc----cccccCceeEecCCCcc----------ccHHHHHHHHHhhCCCC
Q psy5461          25 DSLCARAFKVVH--DKHRGAVTFFRIYSG----AFKKNHVPVLCGSSYKN----------IGVQKLMDAIVDILPSP   85 (221)
Q Consensus        25 ~~~~~~vfk~~~--d~~~g~l~~~~l~~~----~~~~~~~Pv~~gSa~~~----------~Gi~~LLd~I~~~~PsP   85 (221)
                      .+++..+||.+.  |...-+.....++..    -.....+|++++||++|          .|+.+|||+|.+++|+|
T Consensus       120 ~~iIv~iNK~D~~~~~~~~~~i~~~i~~~l~~~~~~~~~~pii~iSa~~g~~~~~~~~~~~~~~~Lldai~~~iP~P  196 (196)
T d1d2ea3         120 EHVVVYVNKADAVQDSEMVELVELEIRELLTEFGYKGEETPIIVGSALCALEQRDPELGLKSVQKLLDAVDTYIPVP  196 (196)
T ss_dssp             CCEEEEEECGGGCSCHHHHHHHHHHHHHHHHHTTSCTTTSCEEECCHHHHHTTCCTTTTHHHHHHHHHHHHHHSCCC
T ss_pred             CcEEEEEecccccccHHHHHHHHHHHHHHHHHhCCCcccCEEEEEEccccccccCcccccCCHHHHHHHHHhhCCCC
Confidence            578899999652  221111122222222    12345689999999999          49999999999999987

>d1d1na_ b.43.3.1 (A:) Initiation factor IF2/eIF5b, domains 2 and 4 {Bacillus stearothermophilus [TaxId: 1422]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Initiation factor IF2/eIF5b, domains 2 and 4
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.63  E-value=0.0023  Score=44.12  Aligned_cols=77  Identities=14%  Similarity=0.125  Sum_probs=58.7

Q ss_pred             EEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCce---eeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCcc
Q psy5461         103 ARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQS---EQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERG  177 (221)
Q Consensus       103 ~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~---~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~  177 (221)
                      |.|-++..-...|.+|=+||.+|.++++..+++.+.++.   .++.+|..    ....+.++..|.=|.|  .+..+++.
T Consensus         9 A~V~~vF~~~k~~~iAGc~V~~G~i~~~~~vrv~R~~~~I~~G~i~sLk~----~K~~V~eV~~G~ECGi~l~~~~d~~~   84 (99)
T d1d1na_           9 AEVRQTFKVSKVGTIAGCYVTDGKITRDSKVRLIRQGIVVYEGEIDSLKR----YKDDVREVAQGYECGLTIKNFNDIKE   84 (99)
T ss_dssp             EEECCCCCCSSSCCCEEEEECSSBCCSSSEEEEECSSSEEEEEECSEEEC----SSSCCSCCBTTCEEEEECTTCSSCSS
T ss_pred             EEEEEEEEcCCCcEEEEEEEEeCeEccCCceEEecCCEEEEEeEEeeecc----cccccCEecCCeEEEEEecCccCCCC
Confidence            344444444566899999999999999999999988753   46666653    3457899999999965  45668899


Q ss_pred             CcEEec
Q psy5461         178 KDKRTR  183 (221)
Q Consensus       178 Gdtl~~  183 (221)
                      ||+|-.
T Consensus        85 GD~ie~   90 (99)
T d1d1na_          85 GDVIEA   90 (99)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            999843

>d2dy1a1 b.43.3.1 (A:275-377) Elongation factor G (EF-G), domain II {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor G (EF-G), domain II
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=96.55  E-value=0.00015  Score=50.70  Aligned_cols=39  Identities=28%  Similarity=0.448  Sum_probs=34.7

Q ss_pred             CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeE
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVL   61 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~   61 (221)
                      +.+.||+++|||+.+|++.|++++.|+++|+++.... |+
T Consensus         5 ~~d~p~~a~Vfk~~~d~~~G~i~~~RV~sG~l~~g~~-v~   43 (103)
T d2dy1a1           5 FGDGPPLAKVFKVQVDPFMGQVAYLRLYRGRLKPGDS-LQ   43 (103)
T ss_dssp             HCSCSCEEEEEEEEEETTTEEEEEEEEEESEECTTEE-EB
T ss_pred             CCCCCcEEEEEEEEecCCCCEEEEEEEeccccCCCCE-EE
Confidence            3578999999999999999999999999999998664 54

>d1n0ua4 d.58.11.1 (A:482-560) Elongation factor 2 (eEF-2) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: EF-G C-terminal domain-like
family: EF-G/eEF-2 domains III and V
domain: Elongation factor 2 (eEF-2)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.15  E-value=0.0021  Score=42.38  Aligned_cols=24  Identities=8%  Similarity=-0.081  Sum_probs=22.0

Q ss_pred             ehHHHHHHHHHHhhcCCceEEEcc
Q psy5461         193 QCSARWTLNLEVGASSPIISKSKR  216 (221)
Q Consensus       193 ~~~~l~~~L~~L~~~Dp~l~~~~~  216 (221)
                      |.++|.+||++|+++||++.+..+
T Consensus        19 d~~kL~~aL~kl~~eDpsl~v~~~   42 (79)
T d1n0ua4          19 DLPKLVEGLKRLSKSDPCVLTYMS   42 (79)
T ss_dssp             GHHHHHHHHHHHHHHCTTCEEEEC
T ss_pred             HHHHHHHHHHHHHHhCCcEEEEEc
Confidence            889999999999999999988654

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=95.80  E-value=0.0027  Score=47.48  Aligned_cols=57  Identities=16%  Similarity=0.095  Sum_probs=40.7

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +.|++..++|++...  ..-..+.+++...  ...|++..||++|.||++|++.|.+.++.
T Consensus       117 ~kp~ivv~NK~Dl~~--~~~~~~~~~~~~~--~~~~v~~iSA~~g~Gi~~L~~~i~~~L~~  173 (185)
T d1lnza2         117 ERPQIIVANKMDMPE--AAENLEAFKEKLT--DDYPVFPISAVTREGLRELLFEVANQLEN  173 (185)
T ss_dssp             TSCBCBEEECTTSTT--HHHHHHHHHHHCC--SCCCBCCCSSCCSSTTHHHHHHHHHHHTS
T ss_pred             CCcchhhccccchHh--HHHHHHHHHHHhc--cCCcEEEEECCCCCCHHHHHHHHHHhhhh
Confidence            457788899964322  1222344444332  35789999999999999999999999875

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.19  E-value=0.016  Score=42.39  Aligned_cols=29  Identities=17%  Similarity=0.266  Sum_probs=26.4

Q ss_pred             cCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          56 NHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      ...|++..||++|.||++|++.|.+++|.
T Consensus       144 ~~~~~~~vSA~~g~gi~~L~~~i~~~lpe  172 (179)
T d1egaa1         144 NFLDIVPISAETGLNVDTIAAIVRKHLPE  172 (179)
T ss_dssp             CCSEEEECCTTTTTTHHHHHHHHHTTCCB
T ss_pred             CCCCEEEEeCcCCCCHHHHHHHHHHhCCC
Confidence            45689999999999999999999999975

>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=95.13  E-value=0.0098  Score=44.63  Aligned_cols=60  Identities=15%  Similarity=-0.002  Sum_probs=41.1

Q ss_pred             CCCceeeeeeeeccc-ccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHD-KHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d-~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ...|++..++|.+.- +..-.-....+++........|+++.||++|.|+++|++.|.+++
T Consensus       133 ~~~piivv~NK~D~~~~~~~~~~~~~~~~~l~~~~~~~~~~~SA~~~~gi~el~~~i~~~l  193 (195)
T d1svia_         133 YGIPVIVIATKADKIPKGKWDKHAKVVRQTLNIDPEDELILFSSETKKGKDEAWGAIKKMI  193 (195)
T ss_dssp             TTCCEEEEEECGGGSCGGGHHHHHHHHHHHHTCCTTSEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             ccCcceechhhccccCHHHHHHHHHHHHHHhcccCCCCEEEEeCCCCCCHHHHHHHHHHHh
Confidence            457888999996521 111111233344444445677899999999999999999998764

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=95.07  E-value=0.0069  Score=44.54  Aligned_cols=59  Identities=12%  Similarity=0.017  Sum_probs=39.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP   85 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP   85 (221)
                      .+.|++..+||++.....    ...+.....+....++++.||++|.||++|++.|.+++|..
T Consensus       108 ~~~pviiv~NK~Dl~~~~----~~~~~~~~~~~~~~~~i~iSAk~g~gid~L~~~i~~~l~e~  166 (171)
T d1mkya1         108 STVDTILVANKAENLREF----EREVKPELYSLGFGEPIPVSAEHNINLDTMLETIIKKLEEK  166 (171)
T ss_dssp             HTCCEEEEEESCCSHHHH----HHHTHHHHGGGSSCSCEECBTTTTBSHHHHHHHHHHHHHHT
T ss_pred             ccccccccchhhhhhhhh----hhHHHHHHHhcCCCCeEEEecCCCCCHHHHHHHHHHhCCCC
Confidence            456888889996533211    11222222222344567799999999999999999988754

>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=94.97  E-value=0.011  Score=43.77  Aligned_cols=57  Identities=16%  Similarity=0.114  Sum_probs=38.0

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      ..|++..++|++  ... +-....+.+. +.....|++..||++|.||++|++.|.+.+++
T Consensus       113 ~~p~iiv~NK~D--~~~-~~~~~~~~~~-~~~~~~~~~~iSA~tg~gid~L~~~i~~~l~~  169 (180)
T d1udxa2         113 RRPSLVALNKVD--LLE-EEAVKALADA-LAREGLAVLPVSALTGAGLPALKEALHALVRS  169 (180)
T ss_dssp             HSCEEEEEECCT--TSC-HHHHHHHHHH-HHTTTSCEEECCTTTCTTHHHHHHHHHHHHHT
T ss_pred             hhhhhhhhhhhh--hhh-HHHHHHHHHH-HHhcCCeEEEEEcCCCCCHHHHHHHHHHHHhh
Confidence            357888889954  221 1112222222 23346799999999999999999999777743

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=94.89  E-value=0.019  Score=42.00  Aligned_cols=60  Identities=12%  Similarity=-0.092  Sum_probs=38.9

Q ss_pred             CCCceeeeeeeecccccCC-cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRG-AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g-~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+...... +...+.+.....+....+++..||++|.||+++++.|++.+
T Consensus       116 ~~~pillv~nK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~tg~gv~e~~~~l~~~i  176 (176)
T d1fzqa_         116 SCVPVLIFANKQDLLTAAPASEIAEGLNLHTIRDRVWQIQSCSALTGEGVQDGMNWVCKNV  176 (176)
T ss_dssp             TTCCEEEEEECTTSTTCCCHHHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHTC
T ss_pred             CCCeEEEEEEeccccccccHHHHHHHHHHHHHHhcCCEEEEEeCCCCCCHHHHHHHHHhcC
Confidence            3568888889964322211 12222222233344567899999999999999999998753

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.37  E-value=0.024  Score=41.32  Aligned_cols=60  Identities=15%  Similarity=-0.001  Sum_probs=42.1

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.+++...+|.+.+.. -.++.....+ ..+....|.+..||++|.||++++..|++.+|+
T Consensus       108 ~~~~iilvgnK~Dl~~~-~~v~~~~~~~-~~~~~~~~~~e~SAk~~~nV~e~f~~l~~~i~~  167 (167)
T d1z0ja1         108 PSIVVAIAGNKCDLTDV-REVMERDAKD-YADSIHAIFVETSAKNAININELFIEISRRIPS  167 (167)
T ss_dssp             TTSEEEEEEECTTCGGG-CCSCHHHHHH-HHHHTTCEEEECBTTTTBSHHHHHHHHHHHCCC
T ss_pred             CcceEEEecccchhccc-cchhHHHHHH-HHHHcCCEEEEEecCCCCCHHHHHHHHHHhCCC
Confidence            46678788888654332 2344444333 223335688999999999999999999999986

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=94.28  E-value=0.034  Score=39.39  Aligned_cols=31  Identities=10%  Similarity=0.138  Sum_probs=25.6

Q ss_pred             cccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          52 AFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        52 ~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..+....+++..||++|.||++++|.|++.+
T Consensus       130 ~~~~~~~~~~~~SAktg~gi~e~~~~l~~~l  160 (160)
T d1r8sa_         130 SLRHRNWYIQATCATSGDGLYEGLDWLSNQL  160 (160)
T ss_dssp             GCSSCCEEEEECBTTTTBTHHHHHHHHHHHC
T ss_pred             HHhhCCCEEEEeECCCCCCHHHHHHHHHhcC
Confidence            3444567899999999999999999998753

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=94.27  E-value=0.031  Score=40.88  Aligned_cols=60  Identities=7%  Similarity=-0.138  Sum_probs=39.5

Q ss_pred             CCCceeeeeeeeccccc-CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKH-RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~-~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+.+.. ...-....+.....+....+++..||++|.||+++++.|.+.+
T Consensus       112 ~~~piiiv~NK~Dl~~~~~~~~i~~~~~~~~~~~~~~~~~e~SA~tg~gv~e~~~~l~~~~  172 (173)
T d1e0sa_         112 RDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY  172 (173)
T ss_dssp             TTCEEEEEEECTTSTTCCCHHHHHHHTTGGGCCSSCEEEEECBTTTTBTHHHHHHHHHHHC
T ss_pred             ccceeeeeeecccccccccHHHHHHHHHHHHHHhCCCEEEEeeCCCCcCHHHHHHHHHHhc
Confidence            46788899999654332 1111222222222344456789999999999999999998764

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=94.25  E-value=0.024  Score=40.99  Aligned_cols=60  Identities=13%  Similarity=-0.001  Sum_probs=38.3

Q ss_pred             CCCceeeeeeeecccccCC-cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRG-AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g-~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|.+...... .-....+.....+...++++..||++|.||.++++.|.+.+
T Consensus       102 ~~~p~iiv~nK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~e~~~~l~~~i  162 (165)
T d1ksha_         102 AGATLLIFANKQDLPGALSCNAIQEALELDSIRSHHWRIQGCSAVTGEDLLPGIDWLLDDI  162 (165)
T ss_dssp             TTCEEEEEEECTTSTTCCCHHHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             CCCceEEEEeccccccccCHHHHHHHHHhhhhhcCCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            4568888889955322211 11111111222344467899999999999999999988654

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=93.87  E-value=0.02  Score=41.74  Aligned_cols=60  Identities=17%  Similarity=0.035  Sum_probs=37.0

Q ss_pred             CCCceeeeeeeec-ccccCCcchHHHHhhccc-cccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVV-HDKHRGAVTFFRIYSGAF-KKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~-~d~~~g~l~~~~l~~~~~-~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ...+.+.-++|.+ .++..-......+.+... .....|+++.||++|.||++|++.|.+++
T Consensus       126 ~~~~~~~v~~k~D~~~~~~~~~~~~~~~~~l~~~~~~~~~i~vSA~~g~Gid~L~~~i~~~~  187 (188)
T d1puia_         126 SNIAVLVLLTKADKLASGARKAQLNMVREAVLAFNGDVQVETFSSLKKQGVDKLRQKLDTWF  187 (188)
T ss_dssp             TTCCEEEEEECGGGSCHHHHHHHHHHHHHHHGGGCSCEEEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             ccccccchhhhhhccCHHHHHHHHHHHHHHHHhhCCCCcEEEEeCCCCCCHHHHHHHHHHHh
Confidence            3456666667753 222211222233333222 23467899999999999999999998764

>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=93.82  E-value=0.044  Score=40.21  Aligned_cols=56  Identities=11%  Similarity=0.013  Sum_probs=37.1

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      +.|++..++|++..+. .+.....+.. ..  ....++..||++|.||++|++.|.+.+|
T Consensus       115 ~~piilv~NK~Dl~~~-~~~~~~~~~~-~~--~~~~~~~iSA~~~~gi~~L~~~i~~~lp  170 (178)
T d1wf3a1         115 KVPILLVGNKLDAAKY-PEEAMKAYHE-LL--PEAEPRMLSALDERQVAELKADLLALMP  170 (178)
T ss_dssp             TSCEEEEEECGGGCSS-HHHHHHHHHH-TS--TTSEEEECCTTCHHHHHHHHHHHHTTCC
T ss_pred             chhhhhhhcccccccC-HHHHHHHHHh-hc--ccCceEEEecCCCCCHHHHHHHHHHhCC
Confidence            5688888999654322 1211222222 21  2334677899999999999999999997

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=93.80  E-value=0.038  Score=40.13  Aligned_cols=60  Identities=12%  Similarity=-0.048  Sum_probs=38.4

Q ss_pred             CCCceeeeeeeeccccc-CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKH-RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~-~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ...|++...+|.+.... ..+-....+..........+++..||++|.||+++++.|.+.+
T Consensus       115 ~~~p~iiv~nK~Dl~~~~~~~~i~~~~~~~~~~~~~~~~~~~Sa~tg~Gi~e~~~~L~~~l  175 (177)
T d1zj6a1         115 RKAGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRL  175 (177)
T ss_dssp             TTCEEEEEEECTTSTTCCCHHHHHHHHTGGGCCSSCEEEEECBTTTTBTHHHHHHHHHHHH
T ss_pred             cceEEEEEEEcccccccCcHHHHHHHHHHHhhHhcCCEEEEEeCCCCCCHHHHHHHHHHHh
Confidence            45678888888543221 1111122222222344567899999999999999999998754

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.53  E-value=0.03  Score=40.88  Aligned_cols=58  Identities=14%  Similarity=0.086  Sum_probs=38.5

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +-|++...+|.+.......+..+...+-..+....|++..||++|.||+++++.|+..
T Consensus       112 ~~piilv~nK~Dl~~~~~~v~~~~~~~~~~~~~~~~~~e~SA~~g~gv~e~f~~l~~~  169 (175)
T d1ky3a_         112 TFPFVILGNKIDAEESKKIVSEKSAQELAKSLGDIPLFLTSAKNAINVDTAFEEIARS  169 (175)
T ss_dssp             TCCEEEEEECTTSCGGGCCSCHHHHHHHHHHTTSCCEEEEBTTTTBSHHHHHHHHHHH
T ss_pred             cCcEEEEecccchhhhhcchhHHHHHHHHHHcCCCeEEEEeCCCCcCHHHHHHHHHHH
Confidence            4578888899764332222333333332333346788889999999999999988753

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.49  E-value=0.038  Score=40.82  Aligned_cols=57  Identities=18%  Similarity=0.185  Sum_probs=39.8

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +-|++...+|.+.+.  .++......+...+....|.+..||++|.||+++++.|++.+
T Consensus       111 ~ip~ilv~nK~Dl~~--~~~~~~~~~~~~~~~~~~~~~e~Sak~~~gI~e~f~~l~~~i  167 (184)
T d1vg8a_         111 NFPFVVLGNKIDLEN--RQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNA  167 (184)
T ss_dssp             GSCEEEEEECTTSSC--CCSCHHHHHHHHHHTTSCCEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             CCCEEEEEEeecccc--cchhHHHHHHHHHHhcCCeEEEEcCCCCcCHHHHHHHHHHHH
Confidence            347888889955332  344444444444444567899999999999999999987643

>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=93.44  E-value=0.013  Score=43.12  Aligned_cols=60  Identities=8%  Similarity=-0.029  Sum_probs=37.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhh---ccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYS---GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~---~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      .+.|++..++|++.-+. .+.....+..   ........+++..||++|.||++|++.|.+.+|
T Consensus       120 ~~~p~iiv~NK~D~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~vSA~~g~gi~~L~~~i~~~l~  182 (184)
T d2cxxa1         120 LDIPTIVAVNKLDKIKN-VQEVINFLAEKFEVPLSEIDKVFIPISAKFGDNIERLKNRIFEVIR  182 (184)
T ss_dssp             TTCCEEEEEECGGGCSC-HHHHHHHHHHHHTCCGGGHHHHEEECCTTTCTTHHHHHHHHHHHHH
T ss_pred             cCCCEEEEEeeeehhhh-HHHHHHHHHHHhcccccccCCeEEEEECCCCCCHHHHHHHHHHHcc
Confidence            45688889999642111 1222222211   122223445778999999999999999998876

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=93.27  E-value=0.052  Score=39.85  Aligned_cols=59  Identities=15%  Similarity=0.057  Sum_probs=37.5

Q ss_pred             CCCceeeeeeeecccccC-Ccch--HHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHR-GAVT--FFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~-g~l~--~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      ...+++..++|.+.-... ..+.  ...+.+........|++..||++|.||++|++.|.+.
T Consensus       119 ~~~~~i~v~nK~D~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vSa~~g~gv~~L~~~i~~~  180 (186)
T d1mkya2         119 RGRASVVVFNKWDLVVHREKRYDEFTKLFREKLYFIDYSPLIFTSADKGWNIDRMIDAMNLA  180 (186)
T ss_dssp             TTCEEEEEEECGGGSTTGGGCHHHHHHHHHHHCGGGTTSCEEECBTTTTBSHHHHHHHHHHH
T ss_pred             cCCceeeeccchhhhcchhhhhhhHHHHHHHHhcccCCCeEEEEeCCCCCCHHHHHHHHHHH
Confidence            345777788886422111 1111  2223333333456799999999999999999999764

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=93.05  E-value=0.037  Score=40.78  Aligned_cols=57  Identities=18%  Similarity=0.215  Sum_probs=38.0

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhc----cccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG----AFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.|++...+|++...   ......+.+.    .......+++..||++|.||+++++.|.+.+
T Consensus       117 ~~~piliv~NK~Dl~~---~~~~~~i~~~~~~~~~~~~~~~~~e~SA~~g~gv~e~~~~l~~~i  177 (182)
T d1moza_         117 QDAALLVFANKQDQPG---ALSASEVSKELNLVELKDRSWSIVASSAIKGEGITEGLDWLIDVI  177 (182)
T ss_dssp             SSCEEEEEEECTTSTT---CCCHHHHHHHTTTTTCCSSCEEEEEEBGGGTBTHHHHHHHHHHHH
T ss_pred             CCcceEEEEEeecccc---ccCHHHHHHHHHHHHHhhCCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            3578888889954322   1222222221    2233457899999999999999999988754

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.93  E-value=0.062  Score=39.20  Aligned_cols=56  Identities=11%  Similarity=-0.010  Sum_probs=40.3

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      +-|++.--+|.+..+  -++..+.+++-..+...+|++..||++|.||+++++.++..
T Consensus       115 ~~piilVgnK~Dl~~--~~v~~~~~~~~~~~~~~~~~~e~Sak~~~gI~e~f~~l~~~  170 (174)
T d1wmsa_         115 SFPFVILGNKIDISE--RQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRR  170 (174)
T ss_dssp             TSCEEEEEECTTCSS--CSSCHHHHHHHHHHTTCCCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             CceEEEeccccchhh--ccCcHHHHHHHHHHcCCCeEEEEcCCCCcCHHHHHHHHHHH
Confidence            457888888854322  35566555554444456789999999999999999888764

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=92.42  E-value=0.11  Score=37.48  Aligned_cols=60  Identities=7%  Similarity=-0.068  Sum_probs=39.1

Q ss_pred             CCCceeeeeeeecccccCC-cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRG-AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g-~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+-|++...+|.+...... +-..+.+.....+....+++..||++|.||+++++.|++++
T Consensus       103 ~~~pi~lv~nK~Dl~~~~~~~~i~~~~~~~~~~~~~~~~~e~Sa~~g~gv~e~~~~l~~~~  163 (164)
T d1zd9a1         103 QGIPVLVLGNKRDLPGALDEKELIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHS  163 (164)
T ss_dssp             TTCCEEEEEECTTSTTCCCHHHHHHHTTGGGCCSSCEEEEECCTTTCTTHHHHHHHHHHTC
T ss_pred             cCCcEEEEEeccccchhhhHHHHHHHHHHHHHHhCCCEEEEEeCcCCcCHHHHHHHHHHcc
Confidence            3568888888864332211 11122222223344567899999999999999999999864

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.16  E-value=0.077  Score=38.51  Aligned_cols=59  Identities=22%  Similarity=0.169  Sum_probs=41.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      ++-|++.-.+|.+.... -+++.+...+-. +...+|.+-.||++|.||+++++.|++.++
T Consensus       110 ~~~~iilvgnK~Dl~~~-~~v~~e~~~~~~-~~~~~~~~e~SAk~g~~V~e~f~~l~~~i~  168 (170)
T d1r2qa_         110 PNIVIALSGNKADLANK-RAVDFQEAQSYA-DDNSLLFMETSAKTSMNVNEIFMAIAKKLP  168 (170)
T ss_dssp             TTCEEEEEEECGGGGGG-CCSCHHHHHHHH-HHTTCEEEECCTTTCTTHHHHHHHHHHTSC
T ss_pred             CCceEEeeccccccccc-ccccHHHHHHHH-HhcCCEEEEeeCCCCCCHHHHHHHHHHHHh
Confidence            45677777788653332 244555444333 334568999999999999999999998765

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=92.16  E-value=0.089  Score=37.24  Aligned_cols=60  Identities=18%  Similarity=0.096  Sum_probs=37.0

Q ss_pred             CCCceeeeeeeecccccCC-cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRG-AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g-~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.+++...+|.+...... .-....+..........|++..||++|.||+++++.|.+.+
T Consensus       105 ~~~~i~iv~nk~Dl~~~~~~~~i~~~~~~~~~~~~~~~~~~~SA~~g~gv~e~~~~l~~~l  165 (169)
T d1upta_         105 RKAILVVFANKQDMEQAMTSSEMANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETL  165 (169)
T ss_dssp             TTCEEEEEEECTTSTTCCCHHHHHHHHTGGGCTTSCEEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             ccceEEEEEeeccccccccHHHHHHHHHHHHHhcCCCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence            3456666667744322211 11122222223334567999999999999999999998764

>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=92.13  E-value=0.07  Score=41.13  Aligned_cols=26  Identities=15%  Similarity=0.342  Sum_probs=23.2

Q ss_pred             CceeEecCCCccccHHHHHHHHHhhC
Q psy5461          57 HVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        57 ~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..|+++.||++|.||++|++.|....
T Consensus       191 ~~~i~pvSa~~G~gid~Ll~~l~~l~  216 (227)
T d1g7sa4         191 QVSIIPISAITGEGIPELLTMLMGLA  216 (227)
T ss_dssp             EEEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             CCeEEEeeCCCCCCHHHHHHHHHHHH
Confidence            46899999999999999999998754

>d1n0ua1 b.43.3.1 (A:344-481) Elongation factor 2 (eEF-2), domain II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Elongation factors
domain: Elongation factor 2 (eEF-2), domain II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.03  E-value=0.024  Score=41.00  Aligned_cols=40  Identities=23%  Similarity=0.306  Sum_probs=34.5

Q ss_pred             CCCCceeeeeeeecccccCCcc-hHHHHhhccccccCceeEe
Q psy5461          22 HFGDSLCARAFKVVHDKHRGAV-TFFRIYSGAFKKNHVPVLC   62 (221)
Q Consensus        22 ~~~~~~~~~vfk~~~d~~~g~l-~~~~l~~~~~~~~~~Pv~~   62 (221)
                      |++.||+++|+|+..|++.|++ .+.|+++|+++.+.. ++.
T Consensus        30 d~~~Pl~~~v~k~~~~~~~g~~~~~gRV~SGtl~~G~~-v~v   70 (138)
T d1n0ua1          30 DPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQK-VRI   70 (138)
T ss_dssp             CTTSSCEEEEEEEEEBSSTTCEEEEEEEEESEEETTCE-EEE
T ss_pred             CCCCCEEEEEEeeccCCCCCEEEEEEEEEeceEcCCCE-EEE
Confidence            6789999999999999999995 788999999998664 554

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=91.54  E-value=0.073  Score=37.96  Aligned_cols=50  Identities=12%  Similarity=-0.029  Sum_probs=34.9

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..|++.-.+|++..+....         ..+....|++..||++|.||++|++.|.+.+
T Consensus       112 ~~~iilv~NK~Dl~~~~~~---------~~~~~~~~~~~iSAk~~~gi~~L~~~l~~~l  161 (161)
T d2gj8a1         112 KLPITVVRNKADITGETLG---------MSEVNGHALIRLSARTGEGVDVLRNHLKQSM  161 (161)
T ss_dssp             TCCEEEEEECHHHHCCCCE---------EEEETTEEEEECCTTTCTTHHHHHHHHHHHC
T ss_pred             ccceeeccchhhhhhhHHH---------HHHhCCCcEEEEECCCCCCHHHHHHHHHhhC
Confidence            5677888888652222111         1223457899999999999999999998753

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.25  E-value=0.12  Score=37.10  Aligned_cols=60  Identities=15%  Similarity=0.044  Sum_probs=39.1

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+-|++.--+|.+..+. .+.......+ ..+....+.+..||++|.||+++++.|...+|.
T Consensus       104 ~~~~iilvgnK~Dl~~~-~~~~~~~~~~-~~~~~~~~~~e~SAk~g~~v~e~f~~i~~~l~g  163 (164)
T d1yzqa1         104 SDVIIMLVGNKTDLADK-RQVSIEEGER-KAKELNVMFIETSAKAGYNVKQLFRRVAAALPG  163 (164)
T ss_dssp             TSSEEEEEEECTTCGGG-CCSCHHHHHH-HHHHTTCEEEECCTTTCTTHHHHHHHHHHHSCC
T ss_pred             CCceEEEEecccchhhh-hhhhHHHHHH-HHHHcCCEEEEecCCCCcCHHHHHHHHHHhhCC
Confidence            34566666688653222 2333333322 223334678999999999999999999998873

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.05  E-value=0.17  Score=36.50  Aligned_cols=59  Identities=12%  Similarity=-0.084  Sum_probs=40.7

Q ss_pred             CCceeeeeeeeccc--ccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461          24 GDSLCARAFKVVHD--KHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP   83 (221)
Q Consensus        24 ~~~~~~~vfk~~~d--~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P   83 (221)
                      ..+.+...+|.+..  ...-++......+-..+ ..+|.+..||++|.||++++..|.+.+|
T Consensus       108 ~~~~~~v~nk~d~~~~~~~~~v~~~~~~~~~~~-~~~~~~e~Sak~g~gV~e~F~~i~~~i~  168 (170)
T d1ek0a_         108 DIIIALVGNKIDMLQEGGERKVAREEGEKLAEE-KGLLFFETSAKTGENVNDVFLGIGEKIP  168 (170)
T ss_dssp             TCEEEEEEECGGGGGSSCCCCSCHHHHHHHHHH-HTCEEEECCTTTCTTHHHHHHHHHTTSC
T ss_pred             ccceeeeecccccccccchhhhhHHHHHHHHHH-cCCEEEEecCCCCcCHHHHHHHHHHHhc
Confidence            45676777776422  22235555554443333 3468999999999999999999998876

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=90.34  E-value=0.1  Score=37.56  Aligned_cols=26  Identities=15%  Similarity=0.132  Sum_probs=23.0

Q ss_pred             CceeEecCCCccccHHHHHHHHHhhC
Q psy5461          57 HVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        57 ~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..+++..||++|.||+++++-|.+++
T Consensus       160 ~~~~~~~SA~tg~Gi~e~~~~l~~~i  185 (186)
T d1f6ba_         160 PLEVFMCSVLKRQGYGEGFRWMAQYI  185 (186)
T ss_dssp             CEEEEECBTTTTBSHHHHHHHHHTTC
T ss_pred             CCEEEEEeCCCCCCHHHHHHHHHHhh
Confidence            45788999999999999999998765

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.29  E-value=0.12  Score=37.13  Aligned_cols=57  Identities=9%  Similarity=-0.045  Sum_probs=38.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+-|++.-.+|.+.... -++..+.+.+-. +....|++..||++|.||+++++.|++.
T Consensus       105 ~~~~iilVgnK~Dl~~~-~~v~~~~~~~~~-~~~~~~~~e~Sak~g~~v~e~f~~l~~~  161 (164)
T d1z2aa1         105 GDIPTALVQNKIDLLDD-SCIKNEEAEGLA-KRLKLRFYRTSVKEDLNVSEVFKYLAEK  161 (164)
T ss_dssp             CSCCEEEEEECGGGGGG-CSSCHHHHHHHH-HHHTCEEEECBTTTTBSSHHHHHHHHHH
T ss_pred             CCceEEEeeccCCcccc-eeeeehhhHHHH-HHcCCEEEEeccCCCcCHHHHHHHHHHH
Confidence            35677777789654332 244444444322 2234589999999999999999998764

>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=90.05  E-value=0.065  Score=38.20  Aligned_cols=54  Identities=17%  Similarity=-0.008  Sum_probs=35.7

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      ...++...++|++...   +.....+.....  ...|++..||++|.||++|+++|.+.
T Consensus       106 ~~~~~i~~~~k~d~~~---~~~~~~~~~~~~--~~~~~~~vSA~~g~gi~~L~~~I~ke  159 (160)
T d1xzpa2         106 KNKRYLVVINKVDVVE---KINEEEIKNKLG--TDRHMVKISALKGEGLEKLEESIYRE  159 (160)
T ss_dssp             TTSSEEEEEEECSSCC---CCCHHHHHHHHT--CSTTEEEEEGGGTCCHHHHHHHHHHH
T ss_pred             ccccceeeeeeccccc---hhhhHHHHHHhC--CCCcEEEEECCCCCCHHHHHHHHHhc
Confidence            3456777777754322   222334443332  34689999999999999999999753

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.94  E-value=0.077  Score=37.24  Aligned_cols=25  Identities=16%  Similarity=0.073  Sum_probs=21.9

Q ss_pred             CceeEecCCCccccHHHHHHHHHhh
Q psy5461          57 HVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        57 ~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      ..+++..||++|.||+++++.|.+|
T Consensus       142 ~~~~~~~SA~tg~Gv~e~~~~l~~~  166 (166)
T d2qtvb1         142 PVEVFMCSVVMRNGYLEAFQWLSQY  166 (166)
T ss_dssp             CEEEEEEBTTTTBSHHHHHHHHTTC
T ss_pred             CCEEEEeeCCCCCCHHHHHHHHhCC
Confidence            4578999999999999999998764

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.34  E-value=0.22  Score=35.80  Aligned_cols=58  Identities=14%  Similarity=-0.037  Sum_probs=38.7

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+-|++.--+|.+.+.. .....+.......+...+|.+-.||++|.||+++++.|...
T Consensus       107 ~~~p~ilvgnK~Dl~~~-~~~~~~~~~~~~~~~~~~~~~e~Sak~g~gv~e~F~~l~~~  164 (167)
T d1c1ya_         107 EDVPMILVGNKCDLEDE-RVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQ  164 (167)
T ss_dssp             SCCCEEEEEECTTCGGG-CCSCHHHHHHHHHHTTSCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             CCCeEEEEEEecCcccc-cccchhHHHHHHHHhCCCEEEEEcCCCCcCHHHHHHHHHHH
Confidence            35577888888654332 23444433333333345788999999999999999988754

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.31  E-value=0.25  Score=35.90  Aligned_cols=56  Identities=20%  Similarity=0.058  Sum_probs=37.2

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..+++...+|  .|....++......+-. +...++++..||++|.||+++++.|++.+
T Consensus       113 ~~~i~~~~nk--~d~~~~~v~~~~~~~~~-~~~~~~~~e~Sa~tg~gv~e~f~~l~~~l  168 (177)
T d1x3sa1         113 DIVNMLVGNK--IDKENREVDRNEGLKFA-RKHSMLFIEASAKTCDGVQCAFEELVEKI  168 (177)
T ss_dssp             CCEEEEEEEC--TTSSSCCSCHHHHHHHH-HHTTCEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             ceeeEEEeec--cccccccccHHHHHHHH-HHCCCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence            4556666666  34333455554444433 33456899999999999999999887654

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.26  E-value=0.14  Score=37.15  Aligned_cols=58  Identities=12%  Similarity=0.012  Sum_probs=38.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+-|++...+|.+.... -+........- .+....|.+..||++|.||+++++.|++.+
T Consensus       110 ~~~p~ilvgnK~Dl~~~-~~~~~~~~~~~-~~~~~~~~~e~Sak~g~gv~e~f~~l~~~i  167 (173)
T d2fn4a1         110 DDFPVVLVGNKADLESQ-RQVPRSEASAF-GASHHVAYFEASAKLRLNVDEAFEQLVRAV  167 (173)
T ss_dssp             SCCCEEEEEECGGGGGG-CCSCHHHHHHH-HHHTTCEEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             CCCceEEEEEeechhhc-cccchhhhhHH-HHhcCCEEEEEeCCCCcCHHHHHHHHHHHH
Confidence            35577888889653332 12333333322 233356889999999999999999998754

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=89.18  E-value=0.13  Score=37.21  Aligned_cols=58  Identities=16%  Similarity=0.098  Sum_probs=38.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.+++...+|.+.... -++....+.+ ..+...+|++..||++|.||+++++.|++.+
T Consensus       109 ~~~~iivv~nK~D~~~~-~~v~~~~~~~-~~~~~~~~~~e~Sak~g~gv~e~f~~l~~~i  166 (169)
T d3raba_         109 DNAQVLLVGNKCDMEDE-RVVSSERGRQ-LADHLGFEFFEASAKDNINVKQTFERLVDVI  166 (169)
T ss_dssp             SCCEEEEEEECTTCGGG-CCSCHHHHHH-HHHHHTCEEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             CcceEEEEEeecccccc-cccchhhhHH-HHHHcCCEEEEecCCCCcCHHHHHHHHHHHH
Confidence            34567777788654332 2344444333 2223346899999999999999999988753

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.96  E-value=0.23  Score=35.63  Aligned_cols=56  Identities=14%  Similarity=0.068  Sum_probs=37.0

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +-|++.-.+|.+...  ..++.+.+.+-. +...+|.+..||++|.||+++++.|++.+
T Consensus       108 ~~piilv~nK~Dl~~--~~~~~~~~~~~~-~~~~~~~~e~Sak~g~gi~e~f~~i~~~i  163 (166)
T d1ctqa_         108 DVPMVLVGNKCDLAA--RTVESRQAQDLA-RSYGIPYIETSAKTRQGVEDAFYTLVREI  163 (166)
T ss_dssp             SCCEEEEEECTTCSC--CCSCHHHHHHHH-HHHTCCEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             CCeEEEEeccccccc--ccccHHHHHHHH-HHhCCeEEEEcCCCCcCHHHHHHHHHHHH
Confidence            457878788854322  233444433322 23346899999999999999999987643

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.76  E-value=0.18  Score=36.26  Aligned_cols=57  Identities=14%  Similarity=-0.004  Sum_probs=37.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      ...+++..-+|.+.+.. .....+....-. +....|.+..||++|.||+++++.|++.
T Consensus       108 ~~~~iilvgnK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~e~Saktg~~v~e~f~~i~~~  164 (166)
T d1z0fa1         108 PNTVIILIGNKADLEAQ-RDVTYEEAKQFA-EENGLLFLEASAKTGENVEDAFLEAAKK  164 (166)
T ss_dssp             TTCEEEEEEECTTCGGG-CCSCHHHHHHHH-HHTTCEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             ccceEEEEcccccchhh-cccHHHHHHHHH-HHcCCEEEEEeCCCCCCHHHHHHHHHHH
Confidence            34567766778543332 334443333322 2334689999999999999999988764

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.69  E-value=0.2  Score=36.09  Aligned_cols=57  Identities=11%  Similarity=0.027  Sum_probs=37.9

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +-|++.--+|.+.... -++..+...+ ..+....|.+..||++|.||+++++.|.+.+
T Consensus       108 ~~piilVgnK~Dl~~~-~~v~~~e~~~-~~~~~~~~~~e~Sak~~~~v~e~f~~l~~~~  164 (171)
T d2erxa1         108 SIPIMLVGNKCDESPS-REVQSSEAEA-LARTWKCAFMETSAKLNHNVKELFQELLNLE  164 (171)
T ss_dssp             CCCEEEEEECGGGGGG-CCSCHHHHHH-HHHHHTCEEEECBTTTTBSHHHHHHHHHHTC
T ss_pred             CCcEEEEeeccccccc-ccccHHHHHH-HHHHcCCeEEEEcCCCCcCHHHHHHHHHHHH
Confidence            4567777788653322 2344444333 2233346899999999999999999998754

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.61  E-value=0.17  Score=36.56  Aligned_cols=58  Identities=16%  Similarity=0.047  Sum_probs=39.8

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+-|++.-.+|.+.+.+ .+.......+ ..+...+|.+..||++|.||+++++.|++.+
T Consensus       109 ~~~piivv~nK~D~~~~-~~~~~~~~~~-~~~~~~~~~~e~Sak~~~gi~e~f~~l~~~i  166 (174)
T d2bmea1         109 QNIVIILCGNKKDLDAD-REVTFLEASR-FAQENELMFLETSALTGENVEEAFVQCARKI  166 (174)
T ss_dssp             TTCEEEEEEECGGGGGG-CCSCHHHHHH-HHHHTTCEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             CceEEEEEEecccccch-hchhhhHHHH-HHHhCCCEEEEeeCCCCcCHHHHHHHHHHHH
Confidence            45688888899765544 2333333222 2233457899999999999999998887653

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.27  E-value=0.21  Score=36.28  Aligned_cols=57  Identities=16%  Similarity=0.054  Sum_probs=36.3

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+-|++.-.+|.+..... ....... ....+....|++..||++|.||+++++.+++.
T Consensus       108 ~~~piilvgnK~Dl~~~~-~~~~~~~-~~~~~~~~~~~~e~Sa~~g~~i~e~f~~l~~~  164 (175)
T d2f9la1         108 SNIVIMLVGNKSDLRHLR-AVPTDEA-RAFAEKNNLSFIETSALDSTNVEEAFKNILTE  164 (175)
T ss_dssp             TTCEEEEEEECTTCGGGC-CSCHHHH-HHHHHHTTCEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             CCCcEEEEEeeecccccc-cchHHHH-HHhhcccCceEEEEecCCCcCHHHHHHHHHHH
Confidence            345777777896533221 1222222 22233345789999999999999998887765

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.25  E-value=0.23  Score=36.29  Aligned_cols=57  Identities=16%  Similarity=0.117  Sum_probs=38.4

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..+++...+|.+.... .+++.+...+-..+ ..+|.+..||++|.||+++++.|.+.+
T Consensus       121 ~~~iilv~nK~Dl~~~-~~v~~~e~~~~~~~-~~~~~~e~Sak~~~~i~e~f~~l~~~i  177 (186)
T d2f7sa1         121 NPDIVLIGNKADLPDQ-REVNERQARELADK-YGIPYFETSAATGQNVEKAVETLLDLI  177 (186)
T ss_dssp             CCEEEEEEECTTCGGG-CCSCHHHHHHHHHH-TTCCEEEEBTTTTBTHHHHHHHHHHHH
T ss_pred             CceEEEEeeeccchhh-hcchHHHHHHHHHH-cCCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence            4566677788653332 34555554433323 346899999999999999999988753

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.09  E-value=0.26  Score=35.25  Aligned_cols=56  Identities=18%  Similarity=0.124  Sum_probs=35.2

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..+++...+|  .|........+...+.. ....+|++..||++|.||+++++.|++.+
T Consensus       107 ~~~~i~~~~k--~d~~~~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~~v~e~f~~l~~~i  162 (166)
T d1g16a_         107 EAQLLLVGNK--SDMETRVVTADQGEALA-KELGIPFIESSAKNDDNVNEIFFTLAKLI  162 (166)
T ss_dssp             TCEEEEEEEC--TTCTTCCSCHHHHHHHH-HHHTCCEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             cceeeeecch--hhhhhhhhhHHHHHHHH-HhcCCeEEEECCCCCCCHHHHHHHHHHHH
Confidence            3445544555  33332334444444333 33357899999999999999999988653

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.92  E-value=0.19  Score=36.46  Aligned_cols=58  Identities=12%  Similarity=-0.046  Sum_probs=39.8

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+-|++...+|.+.... -+++.+...+ ..+....|.+..||++|.||+++++.|++.+
T Consensus       110 ~~~piilvgnK~Dl~~~-~~v~~~~~~~-~a~~~~~~~~e~Sak~g~~i~~~f~~l~~~i  167 (172)
T d2g3ya1         110 EDIPIILVGNKSDLVRC-REVSVSEGRA-CAVVFDCKFIETSAAVQHNVKELFEGIVRQV  167 (172)
T ss_dssp             TTSCEEEEEECTTCGGG-CCSCHHHHHH-HHHHHTCEEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             CCceEEEEecccccccc-ccccHHHHHH-HHHHcCCeEEEEeCCCCcCHHHHHHHHHHHH
Confidence            46788899999653332 2344444433 2233346889999999999999999988643

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.80  E-value=0.27  Score=35.42  Aligned_cols=57  Identities=14%  Similarity=-0.001  Sum_probs=38.6

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+.|++...+|.+.+.. ..+..+...+- .+....|.+..||++|.||+++++.|++.
T Consensus       109 ~~~p~ilvgnK~Dl~~~-~~v~~~~~~~~-~~~~~~~~~e~Sak~~~~i~e~f~~l~~~  165 (171)
T d2erya1         109 DEFPMILIGNKADLDHQ-RQVTQEEGQQL-ARQLKVTYMEASAKIRMNVDQAFHELVRV  165 (171)
T ss_dssp             SCCSEEEEEECTTCTTS-CSSCHHHHHHH-HHHTTCEEEECBTTTTBSHHHHHHHHHHH
T ss_pred             CCCCEEEEEeccchhhh-ccchHHHHHHH-HHHcCCEEEEEcCCCCcCHHHHHHHHHHH
Confidence            35677777788654332 34444444433 23334688999999999999999998764

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.73  E-value=0.18  Score=36.55  Aligned_cols=57  Identities=7%  Similarity=-0.133  Sum_probs=36.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+-|++..-+|.+.+.. .....+.... ..+....|.+..||++|.||++++..|.+.
T Consensus       107 ~~~piilv~nK~D~~~~-~~~~~~~~~~-~a~~~~~~~~e~Sa~tg~~V~e~f~~i~~~  163 (173)
T d2a5ja1         107 SNMVIMLIGNKSDLESR-RDVKREEGEA-FAREHGLIFMETSAKTACNVEEAFINTAKE  163 (173)
T ss_dssp             TTCEEEEEEECTTCGGG-CCSCHHHHHH-HHHHHTCEEEEECTTTCTTHHHHHHHHHHH
T ss_pred             CCCeEEEEecCCchhhh-hhhHHHHHHH-HHHHcCCEEEEecCCCCCCHHHHHHHHHHH
Confidence            45677777788653332 2233333222 223335689999999999999998887764

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.36  E-value=0.19  Score=36.32  Aligned_cols=56  Identities=14%  Similarity=-0.072  Sum_probs=35.8

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      .+.+++.-.+|.+..+. -++.......- .+....|++..||++|.||+++++.|+.
T Consensus       109 ~~~~~ilvgnK~D~~~~-~~v~~~~~~~~-~~~~~~~~~~~SAktg~gV~e~f~~l~~  164 (171)
T d2ew1a1         109 NKVITVLVGNKIDLAER-REVSQQRAEEF-SEAQDMYYLETSAKESDNVEKLFLDLAC  164 (171)
T ss_dssp             TTCEEEEEEECGGGGGG-CSSCHHHHHHH-HHHHTCCEEECCTTTCTTHHHHHHHHHH
T ss_pred             ccccEEEEEeecccccc-cchhhhHHHHH-HHhCCCEEEEEccCCCCCHHHHHHHHHH
Confidence            34577777788654332 23444433332 2223468999999999999999877654

>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=87.28  E-value=0.21  Score=37.82  Aligned_cols=60  Identities=23%  Similarity=0.299  Sum_probs=37.0

Q ss_pred             Cceeeeeeeecc-c-ccCCcchHHHHhh----ccccccCceeEecCCCccc------------------cHHHHHHHHHh
Q psy5461          25 DSLCARAFKVVH-D-KHRGAVTFFRIYS----GAFKKNHVPVLCGSSYKNI------------------GVQKLMDAIVD   80 (221)
Q Consensus        25 ~~~~~~vfk~~~-d-~~~g~l~~~~l~~----~~~~~~~~Pv~~gSa~~~~------------------Gi~~LLd~I~~   80 (221)
                      .+++.++||.+. | ++.-+.....++.    .......+|++.+||+++.                  ++.+|||+|.+
T Consensus       121 ~~iiv~iNK~D~~~~~~~~~~~~~~i~~~l~~~~~~~~~i~~i~~sa~~~~~~~~~~~~~~~~~~~~~~~I~eLLdaIde  200 (204)
T d2c78a3         121 PYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAIDE  200 (204)
T ss_dssp             CCEEEEEECGGGCCCHHHHHHHHHHHHHHHHHTTSCTTTSCEEECCHHHHHHHHHHCTTCCTTSCHHHHHHHHHHHHHHH
T ss_pred             CeEEEEEEecccCCCHHHHHHHHHHHHHHHHhcCCCcccceeeeeechhhhhhhhcCccccCCcccchhhHHHHHHHHHH
Confidence            358889999652 2 1111111222222    1233456788999997652                  47789999999


Q ss_pred             hCCC
Q psy5461          81 ILPS   84 (221)
Q Consensus        81 ~~Ps   84 (221)
                      ++|+
T Consensus       201 ~iP~  204 (204)
T d2c78a3         201 YIPT  204 (204)
T ss_dssp             HSCC
T ss_pred             hCcC
Confidence            9996

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.94  E-value=0.35  Score=34.70  Aligned_cols=56  Identities=18%  Similarity=0.007  Sum_probs=37.0

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      ..+++.-.+|..... ...++.+.++....+ ..+|++..||++|.||+++++.|+..
T Consensus       112 ~~~iilv~~k~d~~~-~~~v~~~~~~~~~~~-~~~~~~e~Sak~g~gi~e~f~~l~~~  167 (170)
T d2g6ba1         112 DVALMLLGNKVDSAH-ERVVKREDGEKLAKE-YGLPFMETSAKTGLNVDLAFTAIAKE  167 (170)
T ss_dssp             TCEEEEEEECCSTTS-CCCSCHHHHHHHHHH-HTCCEEECCTTTCTTHHHHHHHHHHH
T ss_pred             CceEEEEEeeechhh-cccccHHHHHHHHHH-cCCEEEEEeCCCCcCHHHHHHHHHHH
Confidence            445555556643332 235555555544433 34689999999999999999998864

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.31  E-value=0.31  Score=35.96  Aligned_cols=60  Identities=13%  Similarity=0.007  Sum_probs=39.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      .+.+++...+|.+.... ..+..+...... .....+.+..||++|.||+++++.|++.++.
T Consensus       110 ~~~~iilv~nK~D~~~~-~~~~~~~~~~~~-~~~~~~~~e~SAk~g~gi~e~f~~l~~~i~~  169 (194)
T d2bcgy1         110 STVLKLLVGNKCDLKDK-RVVEYDVAKEFA-DANKMPFLETSALDSTNVEDAFLTMARQIKE  169 (194)
T ss_dssp             TTCEEEEEEECTTCTTT-CCSCHHHHHHHH-HHTTCCEEECCTTTCTTHHHHHHHHHHHHHH
T ss_pred             CCceEEEEEeccccccc-cchhHHHHhhhh-hccCcceEEEecCcCccHHHHHHHHHHHHHH
Confidence            45677788888543322 334444333333 3335678899999999999999999876643

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.24  E-value=0.37  Score=35.10  Aligned_cols=27  Identities=19%  Similarity=0.287  Sum_probs=22.9

Q ss_pred             cCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          56 NHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      ..++.+-.||++|.||+++++.|+..+
T Consensus       152 ~~~~~~E~SAk~~~~V~e~F~~l~~~i  178 (183)
T d1mh1a_         152 GAVKYLECSALTQRGLKTVFDEAIRAV  178 (183)
T ss_dssp             TCSEEEECCTTTCTTHHHHHHHHHHHH
T ss_pred             CCceEEEcCCCCCcCHHHHHHHHHHHH
Confidence            346788899999999999999888654

>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=86.21  E-value=0.19  Score=37.92  Aligned_cols=26  Identities=23%  Similarity=0.133  Sum_probs=23.2

Q ss_pred             cCceeEecCCCccccHHHHHHHHHhh
Q psy5461          56 NHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      ..+|++..||++|.|+++|+++|.+.
T Consensus       215 ~~~~~v~vSa~~geGi~~L~~~l~e~  240 (244)
T d1yrba1         215 PPVRVLYLSAKTREGFEDLETLAYEH  240 (244)
T ss_dssp             CCCCCEECCTTTCTTHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            46789999999999999999998764

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.06  E-value=0.2  Score=35.93  Aligned_cols=57  Identities=19%  Similarity=0.046  Sum_probs=36.2

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+-|++...+|.+..... .+......... +....|.+..||++|.||+++++.|+..
T Consensus       107 ~~~piilvgnK~Dl~~~~-~~~~~~~~~~~-~~~~~~~~e~Sak~g~~i~e~f~~i~~~  163 (167)
T d1kaoa_         107 EKVPVILVGNKVDLESER-EVSSSEGRALA-EEWGCPFMETSAKSKTMVDELFAEIVRQ  163 (167)
T ss_dssp             SCCCEEEEEECGGGGGGC-CSCHHHHHHHH-HHHTSCEEEECTTCHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEEccchhhcc-cchHHHHHHHH-HHcCCeEEEECCCCCcCHHHHHHHHHHH
Confidence            345788888996533321 22222222222 2224578999999999999999988753

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=85.89  E-value=0.29  Score=35.25  Aligned_cols=57  Identities=12%  Similarity=-0.044  Sum_probs=38.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+-|++.-.+|.+.... -+++.+.+.+-..+ ...+.+..||++|.||+++++.|++.
T Consensus       108 ~~~piiivgnK~Dl~~~-~~v~~~~~~~~~~~-~~~~~~e~Sak~g~gv~e~f~~l~~~  164 (168)
T d1u8za_         108 ENVPFLLVGNKSDLEDK-RQVSVEEAKNRADQ-WNVNYVETSAKTRANVDKVFFDLMRE  164 (168)
T ss_dssp             TTSCEEEEEECGGGGGG-CCSCHHHHHHHHHH-HTCEEEECCTTTCTTHHHHHHHHHHH
T ss_pred             CCCcEEEEecccccccc-ccccHHHHHHHHHH-cCCeEEEEcCCCCcCHHHHHHHHHHH
Confidence            45578888899653332 34555554443322 34678999999999999999988754

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.63  E-value=0.36  Score=34.64  Aligned_cols=57  Identities=14%  Similarity=-0.011  Sum_probs=37.9

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +-|++...+|.+.+.. -+++.....+-. +....|.+..||++|.||+++++.|++.+
T Consensus       105 ~~piilvgnK~Dl~~~-~~v~~~~~~~~~-~~~~~~~~e~Sak~~~~v~~~f~~l~~~i  161 (168)
T d2gjsa1         105 DVPIILVGNKSDLVRS-REVSVDEGRACA-VVFDCKFIETSAALHHNVQALFEGVVRQI  161 (168)
T ss_dssp             CCCEEEEEECTTCGGG-CCSCHHHHHHHH-HHHTSEEEECBTTTTBSHHHHHHHHHHHH
T ss_pred             cceEEEeecccchhhh-cchhHHHHHHHH-HhcCCEEEEEeCCCCcCHHHHHHHHHHHH
Confidence            4577778899654332 244444443322 22345889999999999999999987643

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.17  E-value=0.31  Score=35.19  Aligned_cols=58  Identities=14%  Similarity=-0.030  Sum_probs=33.5

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      .+.+++...+|.+..... ......... .......|++..||++|.||+++++.|+..+
T Consensus       110 ~~~~iilv~~k~D~~~~~-~~~~~~~~~-~~~~~~~~~~e~Sa~~g~gv~e~f~~l~~~i  167 (173)
T d2fu5c1         110 ADVEKMILGNKCDVNDKR-QVSKERGEK-LALDYGIKFMETSAKANINVENAFFTLARDI  167 (173)
T ss_dssp             TTCEEEEEEEC--CCSCC-CSCHHHHHH-HHHHHTCEEEECCC---CCHHHHHHHHHHHH
T ss_pred             CCceEEEEEecccchhhc-ccHHHHHHH-HHHhcCCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence            356777777775433332 233332222 2233457899999999999999999988754

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.44  E-value=0.53  Score=33.57  Aligned_cols=57  Identities=19%  Similarity=0.161  Sum_probs=37.7

Q ss_pred             CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461          24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL   82 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~   82 (221)
                      +.+.+..-+|.+.... -+++.+...+-. +....|.+..||++|.||+++++.|++.+
T Consensus       108 ~~~~ilvgnK~Dl~~~-~~v~~~e~~~~a-~~~~~~~~e~Sak~~~~v~e~F~~l~~~i  164 (167)
T d1z08a1         108 EICLCIVGNKIDLEKE-RHVSIQEAESYA-ESVGAKHYHTSAKQNKGIEELFLDLCKRM  164 (167)
T ss_dssp             GSEEEEEEECGGGGGG-CCSCHHHHHHHH-HHTTCEEEEEBTTTTBSHHHHHHHHHHHH
T ss_pred             ccceeeeccccccccc-cccchHHHHHHH-HHcCCeEEEEecCCCcCHHHHHHHHHHHH
Confidence            4566666688553332 234454444433 33456899999999999999999888653

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.86  E-value=0.6  Score=33.99  Aligned_cols=61  Identities=7%  Similarity=-0.034  Sum_probs=37.0

Q ss_pred             CCceeeeeeeecccc-----------cCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461          24 GDSLCARAFKVVHDK-----------HRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS   84 (221)
Q Consensus        24 ~~~~~~~vfk~~~d~-----------~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps   84 (221)
                      +-+++.-.+|.+...           ..-.++.+...+-..+-...+.+-.||++|.||+++++.++..+-.
T Consensus       113 ~~~~ilvgnK~Dl~~~~~~~~~~~~~~~r~v~~~~~~~~a~~~~~~~~~E~SAk~~~gv~e~F~~li~~il~  184 (185)
T d2atxa1         113 NVPFLLIGTQIDLRDDPKTLARLNDMKEKPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILT  184 (185)
T ss_dssp             TCCEEEEEECTTSTTCHHHHHHHTTTTCCCCCHHHHHHHHHHHTCSCEEECCTTTCTTHHHHHHHHHHHHHC
T ss_pred             CCCeeEeeeccccccchhhhhhhhhcccccccHHHHHHHHHHcCCCEEEEecCCCCcCHHHHHHHHHHHHcC
Confidence            457777778864221           1113344433332222234567778999999999999988775433

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.75  E-value=0.45  Score=33.88  Aligned_cols=57  Identities=11%  Similarity=-0.046  Sum_probs=38.7

Q ss_pred             CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461          23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI   81 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~   81 (221)
                      .+-|++...+|.+.... -+++.+...+-. +....|.+..||++|.||+++++.|+..
T Consensus       108 ~~~piilvgnK~Dl~~~-r~v~~~~~~~~a-~~~~~~~~e~Sak~~~~v~~~f~~li~~  164 (167)
T d1xtqa1         108 VQIPIMLVGNKKDLHME-RVISYEEGKALA-ESWNAAFLESSAKENQTAVDVFRRIILE  164 (167)
T ss_dssp             SCCCEEEEEECTTCGGG-CCSCHHHHHHHH-HHHTCEEEECCTTCHHHHHHHHHHHHHH
T ss_pred             cccceeeeccccccccc-cchhHHHHHHHH-HHcCCEEEEEecCCCCCHHHHHHHHHHH
Confidence            45688888899654332 245555544322 2334578889999999999999988754

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.29  E-value=1.1  Score=31.95  Aligned_cols=58  Identities=10%  Similarity=-0.080  Sum_probs=36.3

Q ss_pred             CCCceeeeeeeeccccc-----------CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461          23 FGDSLCARAFKVVHDKH-----------RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD   80 (221)
Q Consensus        23 ~~~~~~~~vfk~~~d~~-----------~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~   80 (221)
                      .+-|++..-+|.+....           .-.++.+...+-..+-...+.+-.||++|.||+++++.++.
T Consensus       105 ~~~piilvgnK~Dl~~~~~~~~~~~~~~~~~v~~~e~~~~a~~~~~~~~~E~SAkt~~gi~e~F~~i~~  173 (177)
T d1kmqa_         105 PNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATR  173 (177)
T ss_dssp             TTSCEEEEEECGGGTTCHHHHHHHHHTTCCCCCHHHHHHHHHHTTCSEEEECCTTTCTTHHHHHHHHHH
T ss_pred             CCCceEEeeecccccchhhHHHHHHHhhcccccHHHHHHHHHHcCCcEEEEecCCCCcCHHHHHHHHHH
Confidence            35678787889653211           01223333322222334467888999999999999998875