RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3751
(967 letters)
>gnl|CDD|235375 PRK05253, PRK05253, sulfate adenylyltransferase subunit 2;
Provisional.
Length = 301
Score = 560 bits (1447), Expect = 0.0
Identities = 166/291 (57%), Positives = 215/291 (73%), Gaps = 1/291 (0%)
Query: 18 YLDWLESEAIHIMREVSAECNNPVLLFSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTGH 77
+LD LE+E+IHI+REV+AE NPV+L+S GKDS V+L LA KAF P + PFP++H+DTG
Sbjct: 8 HLDQLEAESIHILREVAAEFENPVMLYSIGKDSSVMLHLARKAFYPGKLPFPLLHVDTGW 67
Query: 78 NFPEVISFRDNCISKLGETLIVRSVEDSIMKGTVRLRKPNTDSRNAAQSITLLETIKEFK 137
FPE+I FRD +LG LIV S + I +G R + NA ++ L + ++++
Sbjct: 68 KFPEMIEFRDRRAKELGLELIVHSNPEGIARGINPFRHGSAKHTNAMKTEGLKQALEKYG 127
Query: 138 FDACIGGARRDEEKARAKERIFSFRDKFGQWNPKSQRPELWNLYNTRVHPGENIRVFPIS 197
FDA GGARRDEEK+RAKERIFSFRD+FGQW+PK+QRPELWNLYN R++ GE+IRVFP+S
Sbjct: 128 FDAAFGGARRDEEKSRAKERIFSFRDEFGQWDPKNQRPELWNLYNGRINKGEHIRVFPLS 187
Query: 198 NWTELDIWQYIEREKIILPSLYFAHKRKIIKRKGLLIPFTNLTPAHPGEIIENLMVRFRT 257
NWTELDIWQYIERE I + LYFAH+R +++R G+LI + P PGE++E MVRFRT
Sbjct: 188 NWTELDIWQYIERENIPIVPLYFAHERPVVERDGMLIMVDDRMPLRPGEVVEERMVRFRT 247
Query: 258 VGDILCTCPILSNATTVEDIIKEISVTQITERGATRIDDQNSEASMEKRKK 308
+G CT + S A T+E+II E+ VT+ +ERG IDD EASMEKRK+
Sbjct: 248 LGCYPCTGAVESEAATLEEIIAEMLVTRTSERGGRAIDDD-QEASMEKRKR 297
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 551 bits (1422), Expect = 0.0
Identities = 216/426 (50%), Positives = 279/426 (65%), Gaps = 11/426 (2%)
Query: 323 SLLRFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGL 382
SLLRFIT GSVDDGKSTLIGRLL+DSK IF DQL A+ R K G IDL+LL DGL
Sbjct: 23 SLLRFITCGSVDDGKSTLIGRLLYDSKMIFEDQLAALERDSKKVGTQGDEIDLALLVDGL 82
Query: 383 ESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKF 442
+EREQGITIDVAYRYF TPKRKFI+ADTPGHEQYTRNM+TGASTAD IIL+DA K
Sbjct: 83 AAEREQGITIDVAYRYFATPKRKFIVADTPGHEQYTRNMVTGASTADLAIILVDARK--- 139
Query: 443 NPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQN 502
+LTQT+RHS IA LL I+H+++AVNKMDL++Y+Q + IV Y+ FA + +
Sbjct: 140 ----GVLTQTRRHSFIASLLGIRHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGLHD 195
Query: 503 INTIPISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLRFPVQLVARHCGH 562
+ IPISAL GDN+++ S M WY GP+L+ LE++ + K RFPVQ V R
Sbjct: 196 VTFIPISALKGDNVVTRSARMPWYEGPSLLEHLETVEIASDRNLKDFRFPVQYVNRP--- 252
Query: 563 ISKDFRGYMGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDMAITGQSVTLIIKEY 622
+ DFRG+ G + SG+++ D ++V PSGK + +K I + LD A GQ+VTL + +
Sbjct: 253 -NLDFRGFAGTVASGVVRPGDEVVVLPSGKTSRVKRIVTPDGDLDEAFAGQAVTLTLADE 311
Query: 623 LDISRGNMLVSPFKRPVSLRSINANLCWLSEESLDLRRKYLLKHSTNQILSRILKINALL 682
+DISRG+ML RP +A + W++EE L R YLLKH T + + + I +
Sbjct: 312 IDISRGDMLARADNRPEVADQFDATVVWMAEEPLLPGRPYLLKHGTRTVPASVAAIKYRV 371
Query: 683 NINTQKWCPPKLLDLNDIGCVTINIYEPISVDSYDNIRSTGSFILIDEITFQTVAAVYII 742
++NT + K L+LN+IG ++ PI+ D Y R+TGSFILID +T TV A I
Sbjct: 372 DVNTLERLAAKTLELNEIGRCNLSTDAPIAFDPYARNRTTGSFILIDRLTNATVGAGMID 431
Query: 743 GAGPGA 748
A A
Sbjct: 432 FALRRA 437
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 531 bits (1371), Expect = 0.0
Identities = 216/439 (49%), Positives = 292/439 (66%), Gaps = 12/439 (2%)
Query: 323 SLLRFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGL 382
SLLRFIT GSVDDGKSTLIGRLL+D+K I+ DQL ++ R ++ G IDL+LL DGL
Sbjct: 5 SLLRFITCGSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDGL 64
Query: 383 ESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKF 442
E+EREQGITIDVAYRYF+T KRKFIIADTPGHEQYTRNM TGASTAD I+L+DA K
Sbjct: 65 EAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARK--- 121
Query: 443 NPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQN 502
+L QT+RHS IA LL I+H+++AVNKMDL++Y++ ++ IV Y FA + ++
Sbjct: 122 ----GVLEQTRRHSFIASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAAQLGLKD 177
Query: 503 INTIPISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLRFPVQLVARHCGH 562
+ IPISAL GDN++S S NM WY GPTL+ +LE++ + K RFPVQ V R
Sbjct: 178 VRFIPISALLGDNVVSKSENMPWYKGPTLLEILETVEIADDRSAKAFRFPVQYVNRP--- 234
Query: 563 ISKDFRGYMGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDMAITGQSVTLIIKEY 622
+ DFRGY G I SG +K D ++V PSGK + +K I + L A G++VTL++ +
Sbjct: 235 -NLDFRGYAGTIASGSVKVGDEVVVLPSGKTSRVKRIVTFDGELAQASAGEAVTLVLADE 293
Query: 623 LDISRGNMLVSPFKRPVSLRSINANLCWLSEESLDLRRKYLLKHSTNQILSRILKINALL 682
+DISRG+++V+ P + +A++ W+ EE L R Y LK +T + +R+ +I L
Sbjct: 294 IDISRGDLIVAADAPPAVADAFDADVVWMDEEPLLPGRSYDLKIATRTVRARVEEIKHQL 353
Query: 683 NINTQKWCPPKLLDLNDIGCVTINIYEPISVDSYDNIRSTGSFILIDEITFQTVAAVYII 742
++NT + + L LN+IG V I+ +PI+ D+Y R+TGSFILID +T TV A +I
Sbjct: 354 DVNTLEQEGAESLPLNEIGRVRISFDKPIAFDAYAENRATGSFILIDRLTNGTVGA-GMI 412
Query: 743 GAGPGAADLITVRGARLLR 761
A A I V+ + L
Sbjct: 413 LASLSANTGIPVQFSELEL 431
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 516 bits (1330), Expect = e-174
Identities = 202/452 (44%), Positives = 285/452 (63%), Gaps = 25/452 (5%)
Query: 299 SEASMEKRKKTEAPEKKQSVFKKHSLLRFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDA 358
+ EA Q + SLLRF+T GSVDDGKSTLIGRLL D+K I+ DQL +
Sbjct: 5 IAQQIANEGGVEAYLHAQ---QHKSLLRFLTCGSVDDGKSTLIGRLLHDTKQIYEDQLAS 61
Query: 359 VSRTKYKRVMSGHNIDLSLLTDGLESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYT 418
+ + G +DL+LL DGL++EREQGITIDVAYRYF+T KRKFIIADTPGHEQYT
Sbjct: 62 LHNDSKRHGTQGEKLDLALLVDGLQAEREQGITIDVAYRYFSTEKRKFIIADTPGHEQYT 121
Query: 419 RNMITGASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLIN 478
RNM TGAST D I+LIDA K +L QT+RHS IA LL IKH+++AVNKMDL++
Sbjct: 122 RNMATGASTCDLAILLIDARK-------GVLDQTRRHSFIATLLGIKHLVVAVNKMDLVD 174
Query: 479 YNQIFYKRIVYAYKKFAE------DIHFQNINTIPISALNGDNIISASNNMLWYNGPTLI 532
Y++ ++RI Y FAE DI F +P+SAL GDN++S S +M WY+GPTL+
Sbjct: 175 YSEEVFERIREDYLTFAEQLPGNLDIRF-----VPLSALEGDNVVSQSESMPWYSGPTLL 229
Query: 533 SLLESLNTNEKIDKKPLRFPVQLVARHCGHISKDFRGYMGRIESGIIKKNDCLIVEPSGK 592
+LE+++ +D +P RFPVQ V R + DFRGY G + SG++K D + V PSGK
Sbjct: 230 EVLETVDIQRVVDAQPFRFPVQYVNRP----NLDFRGYAGTLASGVVKVGDRVKVLPSGK 285
Query: 593 KATIKDIQMLNKSLDMAITGQSVTLIIKEYLDISRGNMLVSPFKRPVSLRSINANLCWLS 652
++ + I + L+ A G+++TL++++ +DISRG++LV+ + +++ +A++ W++
Sbjct: 286 ESNVARIVTFDGDLEEAFAGEAITLVLEDEIDISRGDLLVAADEALQAVQHASADVVWMA 345
Query: 653 EESLDLRRKYLLKHSTNQILSRILKINALLNINTQKWCPPKLLDLNDIGCVTINIYEPIS 712
E+ L + Y +K + + +R+ I ++INT + L LN IG V + EP+
Sbjct: 346 EQPLQPGQSYDIKIAGKKTRARVDAIRYQVDINTLTQREAENLPLNGIGLVELTFDEPLV 405
Query: 713 VDSYDNIRSTGSFILIDEITFQTVAAVYIIGA 744
+D Y R TG FI ID +T TV A +
Sbjct: 406 LDPYQQNRVTGGFIFIDRLTNVTVGAGMVREP 437
>gnl|CDD|213679 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. 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) [Central intermediary metabolism, Sulfur
metabolism].
Length = 406
Score = 500 bits (1289), Expect = e-169
Identities = 202/414 (48%), Positives = 276/414 (66%), Gaps = 11/414 (2%)
Query: 325 LRFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLES 384
LRF+T GSVDDGKSTLIGRLL D+K I+ DQL A+ R K G IDL+LL DGL++
Sbjct: 1 LRFLTCGSVDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQGGEIDLALLVDGLQA 60
Query: 385 EREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNP 444
EREQGITIDVAYRYF+T KRKFI+ADTPGHEQYTRNM TGASTAD ++L+DA K
Sbjct: 61 EREQGITIDVAYRYFSTDKRKFIVADTPGHEQYTRNMATGASTADLAVLLVDARK----- 115
Query: 445 SVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNIN 504
+L QT+RHS IA LL I+H+++AVNKMDL++Y++ ++ I Y FAE + F+++
Sbjct: 116 --GVLEQTRRHSYIASLLGIRHVVLAVNKMDLVDYDEEVFENIKKDYLAFAEQLGFRDVT 173
Query: 505 TIPISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLRFPVQLVARHCGHIS 564
IP+SAL GDN++S S +M WY+GPTL+ +LE++ PLRFPVQ V R +
Sbjct: 174 FIPLSALKGDNVVSRSESMPWYSGPTLLEILETVEVERDAQDLPLRFPVQYVNRP----N 229
Query: 565 KDFRGYMGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDMAITGQSVTLIIKEYLD 624
DFRGY G I SG + D ++V PSG+ + + I + L+ A GQ+VTL + + +D
Sbjct: 230 LDFRGYAGTIASGSVHVGDEVVVLPSGRSSRVARIVTFDGDLEQARAGQAVTLTLDDEID 289
Query: 625 ISRGNMLVSPFKRPVSLRSINANLCWLSEESLDLRRKYLLKHSTNQILSRILKINALLNI 684
ISRG++L + P A L W++EE L R Y LK T ++ + + I +++
Sbjct: 290 ISRGDLLAAADSAPEVADQFAATLVWMAEEPLLPGRSYDLKLGTRKVRASVAAIKHKVDV 349
Query: 685 NTQKWCPPKLLDLNDIGCVTINIYEPISVDSYDNIRSTGSFILIDEITFQTVAA 738
NT + K L+LN+IG V +++ EPI+ D Y R+TG+FILID ++ +TV A
Sbjct: 350 NTLEKGAAKSLELNEIGRVNLSLDEPIAFDPYAENRTTGAFILIDRLSNRTVGA 403
>gnl|CDD|237138 PRK12563, PRK12563, sulfate adenylyltransferase subunit 2;
Provisional.
Length = 312
Score = 438 bits (1129), Expect = e-147
Identities = 161/292 (55%), Positives = 209/292 (71%), Gaps = 2/292 (0%)
Query: 18 YLDWLESEAIHIMREVSAECNNPVLLFSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTGH 77
+LD LE+E+IHI+REV AEC+ PV+L+S GKDSVV+L LA KAFRP+R PFP++H+DT
Sbjct: 18 HLDRLEAESIHILREVVAECSKPVMLYSIGKDSVVMLHLAMKAFRPTRPPFPLLHVDTTW 77
Query: 78 NFPEVISFRDNCISKLGETLIVRSVEDSIMKGTVRLRKPNTDSRNAAQSITLLETIKEFK 137
F E+I FRD +LG L+V D I +G V R + + A++ L + +
Sbjct: 78 KFREMIDFRDRRAKELGLDLVVHHNPDGIARGIVPFRHGSALHTDVAKTQGLKQALDHHG 137
Query: 138 FDACIGGARRDEEKARAKERIFSFRDKFGQWNPKSQRPELWNLYNTRVHPGENIRVFPIS 197
FDA IGGARRDEEK+RAKERIFSFR F +W+PK+QRPELW+LYN R+ GE++RVFP+S
Sbjct: 138 FDAAIGGARRDEEKSRAKERIFSFRSAFHRWDPKAQRPELWSLYNARLRRGESLRVFPLS 197
Query: 198 NWTELDIWQYIEREKIILPSLYFAHKRKIIKRKGLLIPF-TNLTPAHPGEIIENLMVRFR 256
NWTELD+WQYI REKI L LYFA +R +++R GLLI TP PGE + VRFR
Sbjct: 198 NWTELDVWQYIAREKIPLVPLYFAKRRPVVERDGLLIMVDDERTPLRPGETPQQRKVRFR 257
Query: 257 TVGDILCTCPILSNATTVEDIIKEISVTQITERGATRIDDQNSEASMEKRKK 308
T+G T + S+A TVE II+E++VT+I+ER R+ DQ+S ASMEK+KK
Sbjct: 258 TLGCYPLTGAVESDADTVEKIIQEMAVTRISERQG-RMIDQDSAASMEKKKK 308
>gnl|CDD|131094 TIGR02039, CysD, sulfate adenylyltransferase, small subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. 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 [Central intermediary
metabolism, Sulfur metabolism].
Length = 294
Score = 414 bits (1067), Expect = e-138
Identities = 151/291 (51%), Positives = 199/291 (68%), Gaps = 2/291 (0%)
Query: 19 LDWLESEAIHIMREVSAECNNPVLLFSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTGHN 78
L LESEAIHI+REV+AE PV+L+S GKDS VLL LA KAF P PFP++H+DTG
Sbjct: 1 LRALESEAIHIIREVAAEFERPVMLYSIGKDSSVLLHLARKAFYPGPLPFPLLHVDTGWK 60
Query: 79 FPEVISFRDNCISKLGETLIVRSVEDSIMKGTVRLRKPNTDSRNAAQSITLLETIKEFKF 138
F E+I+FRD+ ++K G LIV S E+ I G + + + ++ L + + + +F
Sbjct: 61 FREMIAFRDHMVAKYGLRLIVHSNEEGIADGINPFTEGSALHTDIMKTEALRQALDKNQF 120
Query: 139 DACIGGARRDEEKARAKERIFSFRDKFGQWNPKSQRPELWNLYNTRVHPGENIRVFPISN 198
DA GGARRDEEK+RAKERIFSFR+ F QW+PK QRPELWNLYN R+ GE++RVFP+SN
Sbjct: 121 DAAFGGARRDEEKSRAKERIFSFRNAFHQWDPKKQRPELWNLYNGRISKGESVRVFPLSN 180
Query: 199 WTELDIWQYIEREKIILPSLYFAHKRKIIKRKGLLI-PFTNLTPAHPGEIIENLMVRFRT 257
WTELDIW+YI E I + LYFA KR +++R G+LI P PGE+++ MVRFRT
Sbjct: 181 WTELDIWRYIAAENIPIVPLYFAAKRPVVQRDGMLIMVDDVRMPLAPGEVVKERMVRFRT 240
Query: 258 VGDILCTCPILSNATTVEDIIKEISVTQITERGATRIDDQNSEASMEKRKK 308
+G T I S+A TVE+II E + + +ER R D++ ASME +K+
Sbjct: 241 LGCYPLTGAIESDAATVEEIIAETAAARTSER-QGRAIDRDQAASMEDKKR 290
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 353 bits (907), Expect = e-115
Identities = 132/213 (61%), Positives = 164/213 (76%), Gaps = 8/213 (3%)
Query: 326 RFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESE 385
RFIT GSVDDGKSTLIGRLL+DSK+IF DQL A+ R+K G +DL+LL DGL++E
Sbjct: 1 RFITCGSVDDGKSTLIGRLLYDSKSIFEDQLAALERSKSSGT-QGEKLDLALLVDGLQAE 59
Query: 386 REQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPS 445
REQGITIDVAYRYF+TPKRKFIIADTPGHEQYTRNM+TGASTAD I+L+DA K
Sbjct: 60 REQGITIDVAYRYFSTPKRKFIIADTPGHEQYTRNMVTGASTADLAILLVDARK------ 113
Query: 446 VNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINT 505
+L QT+RHS IA LL I+H+++AVNKMDL++Y++ ++ I Y FA + ++I
Sbjct: 114 -GVLEQTRRHSYIASLLGIRHVVVAVNKMDLVDYDEEVFEEIKADYLAFAASLGIEDITF 172
Query: 506 IPISALNGDNIISASNNMLWYNGPTLISLLESL 538
IPISAL GDN++S S NM WY GPTL+ LE++
Sbjct: 173 IPISALEGDNVVSRSENMPWYKGPTLLEHLETV 205
>gnl|CDD|235711 PRK06136, PRK06136, uroporphyrin-III C-methyltransferase; Reviewed.
Length = 249
Score = 270 bits (694), Expect = 4e-84
Identities = 101/231 (43%), Positives = 136/231 (58%), Gaps = 10/231 (4%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELL-MLCPKAKHIFVGKRFKKHSI 797
VY++GAGPG DLIT++G RLL +ADVVLYD L++ E+L P A+ I+VGKR +HS
Sbjct: 5 VYLVGAGPGDPDLITLKGVRLLEQADVVLYDDLVSPEILAYAKPDAELIYVGKRAGRHST 64
Query: 798 AQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGITAALAAA 857
Q INR++V A K +VVRLKGGDP +FGR EEL AL+ I +V+PGITAA+AAA
Sbjct: 65 KQEEINRLLVDYARKGKVVVRLKGGDPFVFGRGGEELEALEAAGIPYEVVPGITAAIAAA 124
Query: 858 SESKQSLTKRNISRSVVLFTSSTMLKNNYLKNIPIS------DTLVEYMGGNNIFLTAKK 911
+ + LT R ++RSV T + S DTLV YMG N+ A +
Sbjct: 125 AYAGIPLTHRGVARSVTFVTGHEA-AGKLEPEVNWSALADGADTLVIYMGVRNLPYIAAQ 183
Query: 912 LLKLGFLPTTPVIVVENCSLSNQKITRLILLDL--KKKIFQFEKPVLFMIG 960
LL G P TPV ++EN + Q++ R L + + P + +IG
Sbjct: 184 LLAAGRAPDTPVAIIENGTTPEQRVVRGTLGTIAEGAAAEDIQSPAIIVIG 234
>gnl|CDD|212501 cd11642, SUMT, Uroporphyrin-III C-methyltransferase
(S-Adenosyl-L-methionine:uroporphyrinogen III
methyltransferase, SUMT). SUMT, an enzyme of the
cobalamin and siroheme biosynthetic pathway, catalyzes
the transformation of uroporphyrinogen III into
precorrin-2. It transfers two methyl groups from
S-adenosyl-L-methionine to the C-2 and C-7 atoms of
uroporphyrinogen III to yield precorrin-2 via the
intermediate formation of precorrin-1. SUMT is the first
enzyme committed to the biosynthesis of siroheme or
cobalamin (vitamin B12), and precorrin-2 is a common
intermediate in the biosynthesis of corrinoids such as
vitamin B12, siroheme and coenzyme F430. In some
organisms, the SUMT domain is fused to the precorrin-2
oxidase/ferrochelatase domain to form siroheme synthase
or to uroporphyrinogen-III synthase to form bifunctional
uroporphyrinogen-III methylase/uroporphyrinogen-III
synthase.
Length = 233
Score = 260 bits (668), Expect = 1e-80
Identities = 92/229 (40%), Positives = 139/229 (60%), Gaps = 6/229 (2%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCPK-AKHIFVGKRFKKHSI 797
VY++GAGPG +L+T++ RLL++ADVVLYD L++ E+L L P A+ I+VGKR KHS+
Sbjct: 2 VYLVGAGPGDPELLTLKALRLLQEADVVLYDRLVSPEILDLAPPDAELIYVGKRPGKHSL 61
Query: 798 AQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGITAALAAA 857
Q IN ++V+ A + VVRLKGGDP +FGR EE+ AL++ I +V+PGIT+A+AA
Sbjct: 62 PQEEINELLVEYAREGKRVVRLKGGDPFVFGRGGEEIEALREAGIPFEVVPGITSAIAAP 121
Query: 858 SESKQSLTKRNISRSVVLFT---SSTMLKNNYLKNIPISDTLVEYMGGNNIFLTAKKLLK 914
+ + LT R ++ SV T +++ TLV YMG N+ A +L+
Sbjct: 122 AYAGIPLTHRGVASSVTFVTGHEKDGKDPSDWAALAKSGGTLVIYMGVKNLPEIAAELIA 181
Query: 915 LGFLPTTPVIVVENCSLSNQKITRLILLDLKKKI--FQFEKPVLFMIGK 961
G P TPV ++EN + +Q++ L DL + + P L ++G+
Sbjct: 182 AGRPPDTPVAIIENATTPDQRVVVGTLADLAELAAEAGVKPPALIVVGE 230
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 266 bits (683), Expect = 3e-80
Identities = 144/431 (33%), Positives = 217/431 (50%), Gaps = 27/431 (6%)
Query: 320 KKHSLLRFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNID---LS 376
K H L FI G VD GKSTL+GRLL+D I D + K ++ + +
Sbjct: 5 KPHLNLVFI--GHVDAGKSTLVGRLLYDLGEI-----DKRTMEKLEKEAKELGKESFKFA 57
Query: 377 LLTDGLESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILID 436
+ D + ERE+G+TIDVA+ F T K F I D PGH + +NMITGAS AD ++++D
Sbjct: 58 WVLDKTKEERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVD 117
Query: 437 ASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAE 496
A +F + QT+ H+ +A L IK +I+AVNKMDL+++++ ++ IV K +
Sbjct: 118 ARDGEFEAGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLK 177
Query: 497 DIHFQ--NINTIPISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLRFPVQ 554
+ + ++ IPIS GDN+ S NM WY GPTL+ L+ L E+ KPLR P+Q
Sbjct: 178 MVGYNPKDVPFIPISGFKGDNLTKKSENMPWYKGPTLLEALDQLEPPERPLDKPLRLPIQ 237
Query: 555 LVARHCGHISKDFRGYM--GRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDMAITG 612
V G G + GR+ESG+IK + P+G +K I+M ++ + A G
Sbjct: 238 DVYSISG------IGTVPVGRVESGVIKPGQKVTFMPAGVVGEVKSIEMHHEEISQAEPG 291
Query: 613 QSVTLIIK--EYLDISRGNMLVSPFKRPVSLRSINANLCWLSEESLDLRRKYLLKHS-TN 669
+V ++ E DI RG+++ P A + L + + H+ T
Sbjct: 292 DNVGFNVRGVEKNDIRRGDVIGHSDNPPTVSPEFTAQIIVLWHPGIITSGYTPVLHAHTA 351
Query: 670 QILSRILKINALLNINTQKWC--PPKLLDLNDIGCVTINIYEPISVDSYDNIRSTGSFIL 727
Q+ RI ++ + L+ T K P+ L D V I +P+ ++ I G F L
Sbjct: 352 QVACRIAELLSKLDPRTGKKLEENPQFLKRGDAAIVKIEPEKPLCLEKVSEIPQLGRFAL 411
Query: 728 IDEITFQTVAA 738
D QT+AA
Sbjct: 412 RDM--GQTIAA 420
>gnl|CDD|233426 TIGR01469, cobA_cysG_Cterm, uroporphyrin-III C-methyltransferase.
This model represents enzymes, or enzyme domains, with
uroporphyrin-III C-methyltransferase activity. This
enzyme catalyzes the first step committed to the
biosynthesis of either siroheme or cobalamin (vitamin
B12) rather than protoheme (heme). Cobalamin contains
cobalt while siroheme contains iron. Siroheme is a
cofactor for nitrite and sulfite reductases and
therefore plays a role in cysteine biosynthesis; many
members of this family are CysG, siroheme synthase, with
an additional N-terminal domain and with additional
oxidation and iron insertion activities [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 236
Score = 234 bits (600), Expect = 5e-71
Identities = 98/230 (42%), Positives = 141/230 (61%), Gaps = 7/230 (3%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCP-KAKHIFVGKRFKKHSI 797
VY++GAGPG +L+T++ RLL++ADVVLYDAL++ E+L P +A+ I VGKR HS
Sbjct: 2 VYLVGAGPGDPELLTLKALRLLQEADVVLYDALVSPEILAYAPPQAELIDVGKRPGCHSK 61
Query: 798 AQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGITAALAAA 857
Q INR++V+ A + VVRLKGGDP +FGR EE AL + I +V+PG+T+A+AAA
Sbjct: 62 KQEEINRLLVELAREGKKVVRLKGGDPFVFGRGGEEAEALAEAGIPFEVVPGVTSAIAAA 121
Query: 858 SESKQSLTKRNISRSVVLFTS----STMLKNNYLKNIPISDTLVEYMGGNNIFLTAKKLL 913
+ + LT R ++ SV T L+ ++ + TLV YMG N+ AK+L+
Sbjct: 122 AYAGIPLTHRGVASSVTFVTGHEADDKALEVDWEALAKGAGTLVIYMGVRNLPEIAKELI 181
Query: 914 KLGFLPTTPVIVVENCSLSNQKITRLILLDLKKKI--FQFEKPVLFMIGK 961
+ G P TPV VVE + NQ++ L DL +K + P L +IG+
Sbjct: 182 EHGRSPDTPVAVVEWATTPNQRVLIGTLGDLAEKAAEANLKSPALIVIGE 231
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 240 bits (615), Expect = 1e-70
Identities = 140/451 (31%), Positives = 220/451 (48%), Gaps = 72/451 (15%)
Query: 320 KKHSLLRFITAGSVDDGKSTLIGRLLFDSKNI---FIDQLDAVSRTKYKR------VMSG 370
K H L I G VD GKSTL+GRLL+++ I I++L ++ K K VM
Sbjct: 4 KPHLNLAVI--GHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVM-- 59
Query: 371 HNIDLSLLTDGLESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADA 430
D L+ ERE+G+TID+A++ F T K F I D PGH + +NMITGAS ADA
Sbjct: 60 ---------DRLKEERERGVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMITGASQADA 110
Query: 431 VIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYA 490
++++ A + + ++ QT+ H +A L I +I+A+NKMD +NY++ Y+ +
Sbjct: 111 AVLVVAA-----DDAGGVMPQTREHVFLARTLGINQLIVAINKMDAVNYDEKRYEEVKEE 165
Query: 491 YKKFAEDIHFQ--NINTIPISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKP 548
K + + ++ +I IP+SA GDN++ S NM WYNGPTL+ L++L EK KP
Sbjct: 166 VSKLLKMVGYKPDDIPFIPVSAFEGDNVVKKSENMPWYNGPTLLEALDNLKPPEKPTDKP 225
Query: 549 LRFPVQLVARHCGHISKDFRGYMGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDM 608
LR P+Q V IS +GR+E+G++K D ++ P+G +K I+M ++ L
Sbjct: 226 LRIPIQDVYS----ISGVGTVPVGRVETGVLKVGDKVVFMPAGVVGEVKSIEMHHEELPQ 281
Query: 609 AITGQSVTLIIK--EYLDISRGNMLVSPFKRPVSLRSINANLCWLSEESLDLRRKYLLKH 666
A G ++ ++ DI RG++ P P A + +L+H
Sbjct: 282 AEPGDNIGFNVRGVGKKDIKRGDVCGHPDNPPTVAEEFTA-------------QIVVLQH 328
Query: 667 S--------------TNQILSRILKINALLNINT-----QKWCPPKLLDLNDIGCVTINI 707
T Q+ ++ L+ T + P+ + D V I
Sbjct: 329 PSAITVGYTPVFHAHTAQVACTFEELVKKLDPRTGQVAEEN---PQFIKTGDAAIVKIKP 385
Query: 708 YEPISVDSYDNIRSTGSFILIDEITFQTVAA 738
+P+ ++ I G F + D QT+AA
Sbjct: 386 TKPLVIEKVKEIPQLGRFAIRD--MGQTIAA 414
>gnl|CDD|223086 COG0007, CysG, Uroporphyrinogen-III methylase [Coenzyme
metabolism].
Length = 244
Score = 228 bits (583), Expect = 2e-68
Identities = 89/227 (39%), Positives = 131/227 (57%), Gaps = 4/227 (1%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELL-MLCPKAKHIFVGKRFKKHSI 797
VY++GAGPG L+T+R R L++ADVVLYD L+ E+L + A+ I+VGKR HS
Sbjct: 6 VYLVGAGPGDPGLLTLRALRALQEADVVLYDRLVPEEVLALARRDAERIYVGKRPGGHSK 65
Query: 798 AQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGITAALAAA 857
Q IN ++V+ A + VVRLKGGDP +FGR EE+ AL + I+ +V+PGIT+A+AA
Sbjct: 66 PQDEINALLVELAREGKRVVRLKGGDPYIFGRGGEEIEALAEAGIEFEVVPGITSAIAAP 125
Query: 858 SESKQSLTKRNISRSVVLFTSSTM-LKNNYLKNIPISDTLVEYMGGNNIFLTAKKLLKLG 916
+ + LT R ++ S T K ++ TLV MG + + A++L+ G
Sbjct: 126 AYAGIPLTHRGVASSFTFVTGHDRDGKLDWEALARSVGTLVILMGASRLAEIARELIAHG 185
Query: 917 FLPTTPVIVVENCSLSNQKITRLILLDLKKKI--FQFEKPVLFMIGK 961
P TPV V+EN + +Q++ L DL + P L +IG+
Sbjct: 186 RSPDTPVAVIENGTTPDQRVVVGTLGDLAELAEEAGLTPPALIVIGE 232
>gnl|CDD|129574 TIGR00483, EF-1_alpha, translation elongation factor EF-1 alpha.
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 [Protein synthesis, Translation
factors].
Length = 426
Score = 233 bits (597), Expect = 3e-68
Identities = 133/434 (30%), Positives = 216/434 (49%), Gaps = 21/434 (4%)
Query: 320 KKHSLLRFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLT 379
K+H + FI G VD GKST +G LL+ I ++ + ++ + + + +
Sbjct: 5 KEHINVAFI--GHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKAS--FEFAWVM 60
Query: 380 DGLESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASK 439
D L+ ERE+G+TIDVA+ F T K + I D PGH + +NMITGAS ADA ++++
Sbjct: 61 DRLKEERERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGD 120
Query: 440 IKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIH 499
+F + QT+ H+ +A L I +I+A+NKMD +NY++ ++ I + +
Sbjct: 121 GEF----EVQPQTREHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVG 176
Query: 500 FQ--NINTIPISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLRFPVQLVA 557
+ + IPISA NGDN+I S N WY G TL+ L++L EK KPLR P+Q V
Sbjct: 177 YNPDTVPFIPISAWNGDNVIKKSENTPWYKGKTLLEALDALEPPEKPTDKPLRIPIQDVY 236
Query: 558 RHCGHISKDFRGYMGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDMAITGQSVTL 617
I+ +GR+E+G++K D ++ EP+G +K I+M ++ ++ A G ++
Sbjct: 237 S----ITGVGTVPVGRVETGVLKPGDKVVFEPAGVSGEVKSIEMHHEQIEQAEPGDNIGF 292
Query: 618 IIK--EYLDISRGNMLVSPFKRPVSLRSINANLCWLSEES-LDLRRKYLLKHSTNQILSR 674
++ DI RG++ P P + A + L + + + T QI R
Sbjct: 293 NVRGVSKKDIRRGDVCGHPDNPPKVAKEFTAQIVVLQHPGAITVGYTPVFHCHTAQIACR 352
Query: 675 ILKINALLNINTQKWCP--PKLLDLNDIGCVTINIYEPISVDSYDNIRSTGSFILIDEIT 732
++ + T + P+ L D V +P+ +++ I G F + D
Sbjct: 353 FDELLKKNDPRTGQVLEENPQFLKTGDAAIVKFKPTKPMVIEAVKEIPPLGRFAIRD--M 410
Query: 733 FQTVAAVYIIGAGP 746
QTVAA II P
Sbjct: 411 GQTVAAGMIIDVDP 424
>gnl|CDD|206670 cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein
family. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3 of
breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation in yeast, and to associate with Dom34. It has
been speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 219
Score = 201 bits (514), Expect = 3e-59
Identities = 86/221 (38%), Positives = 124/221 (56%), Gaps = 16/221 (7%)
Query: 327 FITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRT--KYKR---VMSGHNIDLSLLTDG 381
+ G VD GKSTL G LL+ + D+ RT KY++ M + + + D
Sbjct: 2 LVVIGHVDAGKSTLTGHLLYKLGGV--DK-----RTIEKYEKEAKEMGKESFKYAWVLDK 54
Query: 382 LESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIK 441
L+ ERE+G+TIDV F T K +F I D PGH + +NMITGAS AD ++++ A K +
Sbjct: 55 LKEERERGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMITGASQADVAVLVVSARKGE 114
Query: 442 FNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLI--NYNQIFYKRIVYAYKKFAEDIH 499
F QT+ H+++A L +K +I+AVNKMD + N++Q Y I F + +
Sbjct: 115 FEAGFEKGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVG 174
Query: 500 FQ--NINTIPISALNGDNIISASNNMLWYNGPTLISLLESL 538
+ ++ IPIS GDN+I S NM WY GPTL+ L+SL
Sbjct: 175 YNPKDVPFIPISGFTGDNLIEKSENMPWYKGPTLLEALDSL 215
>gnl|CDD|223253 COG0175, CysH, 3'-phosphoadenosine 5'-phosphosulfate
sulfotransferase (PAPS reductase)/FAD synthetase and
related enzymes [Amino acid transport and metabolism /
Coenzyme metabolism].
Length = 261
Score = 190 bits (484), Expect = 1e-54
Identities = 95/297 (31%), Positives = 133/297 (44%), Gaps = 65/297 (21%)
Query: 19 LDWLESEA-IHIMREVSAECNNP-VLLFSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTG 76
LD LE+E+ I I+R + E +NP V+ FSGGKDS VLL LA KAF FP++ +DTG
Sbjct: 19 LDKLEAESPIEILRWAAEEFSNPVVVSFSGGKDSTVLLHLAAKAFPD----FPVIFLDTG 74
Query: 77 HNFPEVISFRDNCISKLGETLIVRSVEDSI---MKGTVRLRKPNTDSR--NAAQSITLLE 131
++FPE FRD + G L V +D + K +L +P+ + + + L
Sbjct: 75 YHFPETYEFRDRLAEEYGLDLKVYRPDDEVAEGEKYGGKLWEPSVERWCCDIRKVEPLKR 134
Query: 132 TIKEFKFDACIGGARRDEEKARAKERIFSFRDKFGQWNPKSQRPELWNLYNTRVHPGENI 191
+ E+ FDA G RRDE RAK + SF +FG E+I
Sbjct: 135 ALDEYGFDAWFTGLRRDESPTRAKLPVVSFDSEFG----------------------ESI 172
Query: 192 RVFPISNWTELDIWQYIEREKIILPSLYFAHKRKIIKRKGLLIPFTNLTPAHPGEIIENL 251
RV P+++WTELD+W YI + LY
Sbjct: 173 RVNPLADWTELDVWLYILANNLPYNPLYDQG----------------------------- 203
Query: 252 MVRFRTVGDILCTCPILSNATTVEDIIKEISVTQITERGATRIDDQNSEASMEKRKK 308
+R++G CT P+ A E + + TE G R DD +S SME K+
Sbjct: 204 ---YRSIGCWPCTRPVEPLAEDERAGRWEGELAEKTECGLHRADDPDSALSMELLKR 257
>gnl|CDD|178232 PLN02625, PLN02625, uroporphyrin-III C-methyltransferase.
Length = 263
Score = 188 bits (479), Expect = 6e-54
Identities = 87/232 (37%), Positives = 131/232 (56%), Gaps = 10/232 (4%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELL-MLCPKAKHIFVGKRFKKHSI 797
V+++G GPG DL+T++ RLL+ ADVVLYD L++ ++L ++ P A+ ++VGKR HS
Sbjct: 17 VFLVGTGPGDPDLLTLKALRLLQTADVVLYDRLVSPDILDLVPPGAELLYVGKRGGYHSR 76
Query: 798 AQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGITAALAAA 857
Q I+ +++ A VVRLKGGDP++FGR EE++AL+K I V V+PGITAA+ A
Sbjct: 77 TQEEIHELLLSFAEAGKTVVRLKGGDPLVFGRGGEEMDALRKNGIPVTVVPGITAAIGAP 136
Query: 858 SESKQSLTKRNISRSVVLFT------SSTMLKNNYLKNIPISDTLVEYMGGNNIFLTAKK 911
+E LT R ++ SV T + L P TLV YMG + A+K
Sbjct: 137 AELGIPLTHRGVATSVRFLTGHDREGGTDPLDVAEAAADPD-TTLVVYMGLGTLPSLAEK 195
Query: 912 LLKLGFLPTTPVIVVENCSLSNQKITRLILLDLKKKIFQ--FEKPVLFMIGK 961
L+ G P TP VE + Q++ L D+ + + P + ++G+
Sbjct: 196 LIAAGLPPDTPAAAVERGTTPEQRVVFGTLEDIAEDVAAAGLVSPTVIVVGE 247
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 193 bits (493), Expect = 9e-54
Identities = 114/321 (35%), Positives = 174/321 (54%), Gaps = 24/321 (7%)
Query: 320 KKHSLLRFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRT--KYKR---VMSGHNID 374
K H L I G VD GKST G L++ K ID+ RT K+++ M +
Sbjct: 5 KTHINLVVI--GHVDSGKSTTTGHLIY--KCGGIDK-----RTIEKFEKEAAEMGKGSFK 55
Query: 375 LSLLTDGLESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIIL 434
+ + D L++ERE+GITID+A F TPK F I D PGH + +NMITG S AD I++
Sbjct: 56 YAWVLDKLKAERERGITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILV 115
Query: 435 IDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDL--INYNQIFYKRIVYAYK 492
+ ++ +F ++ QT+ H+++A L +K +I+ +NKMD +NY+Q Y I
Sbjct: 116 VASTAGEFEAGISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVS 175
Query: 493 KFAEDIHFQ--NINTIPISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLR 550
+ + + + + IPIS GDN+I S+NM WY GPTL+ L++L ++ KPLR
Sbjct: 176 AYLKKVGYNPEKVPFIPISGWQGDNMIEKSDNMPWYKGPTLLEALDTLEPPKRPVDKPLR 235
Query: 551 FPVQLVARHCGHISKDFRGYMGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDMAI 610
P+Q V + I +GR+E+GI+K + PSG +K ++M ++ L A+
Sbjct: 236 LPLQDVYK----IGGIGTVPVGRVETGILKPGMVVTFAPSGVTTEVKSVEMHHEQLAEAV 291
Query: 611 TGQSVTLIIKEYL--DISRGN 629
G +V +K DI RG
Sbjct: 292 PGDNVGFNVKNVSVKDIKRGY 312
>gnl|CDD|201832 pfam01507, PAPS_reduct, Phosphoadenosine phosphosulfate reductase
family. This domain is found in phosphoadenosine
phosphosulfate (PAPS) reductase enzymes or PAPS
sulfotransferase. PAPS reductase is part of the adenine
nucleotide alpha hydrolases superfamily also including N
type ATP PPases and ATP sulphurylases. The enzyme uses
thioredoxin as an electron donor for the reduction of
PAPS to phospho-adenosine-phosphate (PAP). It is also
found in NodP nodulation protein P from Rhizobium which
has ATP sulfurylase activity (sulfate adenylate
transferase).
Length = 173
Score = 160 bits (407), Expect = 2e-45
Identities = 71/191 (37%), Positives = 87/191 (45%), Gaps = 29/191 (15%)
Query: 39 NPVLLFSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTGHNFPEVISFRDNCISKLGETLI 98
V+ FSGGKDS+VLL LA KAF P P++ IDTG+ FPE F D K G L
Sbjct: 1 ELVVSFSGGKDSLVLLHLASKAFPP----GPVIFIDTGYEFPETYEFVDELEEKYGLNLK 56
Query: 99 VRSVEDSIMKGTVRLRKPNTDSRNAAQSI---TLLETIKEFKFDACIGGARRDEEKARAK 155
V EDS +G P++ R + L +KE FDA G RRDE +RAK
Sbjct: 57 VYLPEDSFAEGINPEGIPSSLYRRCCRLRKVEPLKRALKELGFDAWFTGLRRDESPSRAK 116
Query: 156 ERIFSFRDKFGQWNPKSQRPELWNLYNTRVHPGENIRVFPISNWTELDIWQYIEREKIIL 215
I S F + I+VFP+ NWTE D+WQYI +
Sbjct: 117 LPIVSIDGDFPK----------------------VIKVFPLLNWTETDVWQYILANNVPY 154
Query: 216 PSLYFAHKRKI 226
LY R I
Sbjct: 155 NPLYDQGYRSI 165
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 167 bits (424), Expect = 1e-44
Identities = 124/423 (29%), Positives = 205/423 (48%), Gaps = 18/423 (4%)
Query: 325 LRFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLES 384
+ + G VD GKST G L++ I D+ K M+ + + + D L++
Sbjct: 8 INIVVIGHVDSGKSTTTGHLIYKLGGI--DKRVIERFEKEAAEMNKRSFKYAWVLDKLKA 65
Query: 385 EREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNP 444
ERE+GITID+A F T K + D PGH + +NMITG S AD +++ID++ F
Sbjct: 66 ERERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGGFEA 125
Query: 445 SVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLIN--YNQIFYKRIVYAYKKFAEDIHFQ- 501
++ QT+ H+++A L +K +I NKMD Y++ Y IV + + + +
Sbjct: 126 GISKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGYNP 185
Query: 502 -NINTIPISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLRFPVQLVARHC 560
I +PIS GDN+I S N+ WY GPTL+ L+ +N ++ KPLR P+Q V +
Sbjct: 186 DKIPFVPISGFEGDNMIERSTNLDWYKGPTLLEALDQINEPKRPSDKPLRLPLQDVYKIG 245
Query: 561 GHISKDFRGYMGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDMAITGQSVTLIIK 620
G + +GR+E+G+IK + P+G +K ++M ++SL A+ G +V +K
Sbjct: 246 GIGTVP----VGRVETGVIKPGMVVTFGPTGLTTEVKSVEMHHESLQEALPGDNVGFNVK 301
Query: 621 EYL--DISRGNMLVSPFKRPVSLRSINANLCWLSEESLDLRRKY--LLKHSTNQILSRIL 676
D+ RG + + P + + + + Y +L T+ I +
Sbjct: 302 NVAVKDLKRGYVASNSKDDPAKEAANFTSQVIIMNHPGQIGNGYAPVLDCHTSHIAVKFA 361
Query: 677 KINALLNINTQKWC--PPKLLDLNDIGCVTINIYEPISVDSYDNIRSTGSFILIDEITFQ 734
+I ++ + K PK L D G V + +P+ V+++ G F + D Q
Sbjct: 362 EILTKIDRRSGKELEKEPKFLKNGDAGFVKMIPTKPMVVETFSEYPPLGRFAVRD--MRQ 419
Query: 735 TVA 737
TVA
Sbjct: 420 TVA 422
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. 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
Score = 156 bits (398), Expect = 7e-44
Identities = 65/200 (32%), Positives = 98/200 (49%), Gaps = 32/200 (16%)
Query: 320 KKHSLLRFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLT 379
K+H G VD GK+TL LL+ + I K RV+
Sbjct: 1 KRH--RNIGIIGHVDHGKTTLTDALLYVTGAISK------ESAKGARVL----------- 41
Query: 380 DGLESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASK 439
D L+ ERE+GITI +A F T KR I DTPGH +T+ MI GAS AD I+++DA +
Sbjct: 42 DKLKEERERGITIKIAAVSFETKKRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAVE 101
Query: 440 IKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIV-YAYKKFAEDI 498
++ QT+ H ++A L + II+ +NK+D ++ + + +V ++ E
Sbjct: 102 -------GVMPQTREHLLLAKTLGVP-IIVFINKIDRVDDAE--LEEVVEEISRELLEKY 151
Query: 499 HFQ--NINTIPISALNGDNI 516
F + +P SAL G+ I
Sbjct: 152 GFGGETVPVVPGSALTGEGI 171
>gnl|CDD|182606 PRK10637, cysG, siroheme synthase; Provisional.
Length = 457
Score = 159 bits (404), Expect = 7e-42
Identities = 88/228 (38%), Positives = 131/228 (57%), Gaps = 7/228 (3%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCPK-AKHIFVGKRFKKHSI 797
V ++GAGPG A L+T++G + +++ADVV+YD L++++++ L + A +FVGKR H +
Sbjct: 218 VVLVGAGPGDAGLLTLKGLQQIQQADVVVYDRLVSDDIMNLVRRDADRVFVGKRAGYHCV 277
Query: 798 AQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGITAALAAA 857
Q IN+I+++ A K VVRLKGGDP +FGR EEL L I V+PGITAA +
Sbjct: 278 PQEEINQILLREAQKGKRVVRLKGGDPFIFGRGGEELETLCNAGIPFSVVPGITAASGCS 337
Query: 858 SESKQSLTKRNISRSVVLFTSSTMLKNNY---LKNIPIS-DTLVEYMGGNNIFLTAKKLL 913
+ S LT R+ ++SV L T LK +N+ TLV YMG N +KL+
Sbjct: 338 AYSGIPLTHRDYAQSVRLVTGH--LKTGGELDWENLAAEKQTLVFYMGLNQAATIQQKLI 395
Query: 914 KLGFLPTTPVIVVENCSLSNQKITRLILLDLKKKIFQFEKPVLFMIGK 961
+ G PV +VEN + Q++ L L + Q P L ++G+
Sbjct: 396 EHGMPADMPVALVENGTSVTQRVVSGTLTQLGELAQQVNSPSLIIVGR 443
>gnl|CDD|216012 pfam00590, TP_methylase, Tetrapyrrole (Corrin/Porphyrin)
Methylases. This family uses S-AdoMet in the
methylation of diverse substrates. This family includes
a related group of bacterial proteins of unknown
function. This family includes the methylase Dipthine
synthase.
Length = 202
Score = 151 bits (383), Expect = 9e-42
Identities = 64/206 (31%), Positives = 99/206 (48%), Gaps = 6/206 (2%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCPKAKHIFVGKRFKKHSIA 798
+YI+G GPG +L+T+R R L++ADVV+ D LL L IA
Sbjct: 2 LYIVGIGPGDPELLTLRALRALKEADVVIGDDRALEILLDLLRPMGKELELLEGAYEEIA 61
Query: 799 QYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGITAALAAAS 858
+ + +++ VV L GDP+++G + AL+ I+V+VIPGI++ AAA+
Sbjct: 62 ELLEAAALLR---AGKDVVVLVSGDPLVYGTGSYLVEALEAAGIEVEVIPGISSLQAAAA 118
Query: 859 ESKQSLTKRNISRSVVLFTSSTMLKNNYLKNIPISDTLVEYMGGNNIFLTAKKLLKLGFL 918
LT + L+ L+ + DTLV + + A+ LL+LG
Sbjct: 119 RLGIPLTDGGVVSLH--GRGLETLRARLLEALLAGDTLVLLTDPHRLAEIAELLLELGD- 175
Query: 919 PTTPVIVVENCSLSNQKITRLILLDL 944
TPV VVEN +++I R L +L
Sbjct: 176 DDTPVAVVENLGTPDERIIRGTLAEL 201
>gnl|CDD|212500 cd11641, Precorrin-4_C11-MT, Precorrin-4 C11-methyltransferase
(CbiF/CobM). Precorrin-4 C11-methyltransferase
participates in the pathway toward the biosynthesis of
cobalamin (vitamin B12). There are two distinct
cobalamin biosynthetic pathways in bacteria. The aerobic
pathway requires oxygen, and cobalt is inserted late in
the pathway; the anaerobic pathway does not require
oxygen, and cobalt insertion is the first committed step
towards cobalamin synthesis. In the aerobic pathway,
CobM catalyzes the methylation of precorrin-4 at C-11 to
yield precorrin-5. In the anaerobic pathway, CibF
catalyzes the methylation of cobalt-precorrin-4 to
cobalt-precorrin-5. Both CibF and CobM, which are
homologous, are included in this model. There are about
30 enzymes involved in vitamin B12 synthetic pathway.
The enzymes involved in the aerobic pathway are prefixed
Cob and those of the anaerobic pathway Cbi. Most of the
enzymes are shared in both pathways and several of these
enzymes are pathway-specific.
Length = 228
Score = 149 bits (379), Expect = 8e-41
Identities = 72/233 (30%), Positives = 123/233 (52%), Gaps = 12/233 (5%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLY-DALITNELLMLCPKAKHIFVGKRFKKHSI 797
VY +GAGPG +LITV+G RLL +ADVV+Y +L+ ELL I+ ++
Sbjct: 1 VYFVGAGPGDPELITVKGRRLLEEADVVIYAGSLVPPELLEYARPDAEIY---DSASMTL 57
Query: 798 AQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGITAALAAA 857
+ I ++ + A + VVRL GDP L+G E++ L I +V+PG+++ AAA
Sbjct: 58 EE--IIALMKEAAREGKDVVRLHTGDPSLYGAIREQMRELDALGIPYEVVPGVSSFFAAA 115
Query: 858 SESKQSLTKRNISRSVVL---FTSSTMLKNNYLKNIPISD-TLVEYMGGNNIFLTAKKLL 913
+ + LT +S++V+L + + + L ++ T+ ++ + I ++LL
Sbjct: 116 AALGRELTLPEVSQTVILTRAAGRTPVPEGESLASLARHGATMAIFLSVHLIEEVVEELL 175
Query: 914 KLGFLPTTPVIVVENCSLSNQKITRLILLDLKKKI--FQFEKPVLFMIGKSLK 964
+ G+ P TPV VV S ++KI R L D+ +K+ + L ++G +L
Sbjct: 176 EGGYPPDTPVAVVYRASWPDEKIIRGTLADIAEKVKEAGITRTALILVGPALD 228
>gnl|CDD|225430 COG2875, CobM, Precorrin-4 methylase [Coenzyme metabolism].
Length = 254
Score = 146 bits (370), Expect = 3e-39
Identities = 80/240 (33%), Positives = 122/240 (50%), Gaps = 18/240 (7%)
Query: 735 TVAAVYIIGAGPGAADLITVRGARLLRKADVVLY-DALITNELLMLCPKAKHIFVGKRFK 793
VY IGAGPG DLITV+G RLL KADVV+Y +L+ ELL C I
Sbjct: 1 MAMKVYFIGAGPGDPDLITVKGQRLLEKADVVIYAGSLVPPELLEYCRPDAEI------- 53
Query: 794 KHSIAQYIINRII---VKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGI 850
+ A + II V + VVRL GDP ++G E++ L+ I +V+PG+
Sbjct: 54 -VNSASLTLEEIIDLMVDAVREGKDVVRLHSGDPSIYGALAEQMRELEALGIPYEVVPGV 112
Query: 851 TAALAAASESKQSLTKRNISRSVVLFTSST---MLKNNYLKNIPISD-TLVEYMGGNNIF 906
++ AAA+ LT +S++V+L S + + L + T+V ++G + I
Sbjct: 113 SSFAAAAAALGIELTVPGVSQTVILTRPSGRTPVPEKESLAALAKHGATMVIFLGVHAID 172
Query: 907 LTAKKLLKLGFLPTTPVIVVENCSLSNQKITRLILLDLKKKIFQ--FEKPVLFMIGKSLK 964
++LL+ G+ P TPV VV S ++KI R L D+ +K+ + + L ++G L
Sbjct: 173 KVVEELLEGGYPPDTPVAVVYRASWPDEKIIRGTLEDIAEKVKEAGIRRTALIIVGDVLD 232
>gnl|CDD|238846 cd01713, PAPS_reductase, This domain is found in phosphoadenosine
phosphosulphate (PAPS) reductase enzymes or PAPS
sulphotransferase. PAPS reductase is part of the adenine
nucleotide alpha hydrolases superfamily also including N
type ATP PPases and ATP sulphurylases. A highly modified
version of the P loop, the fingerprint peptide of
mononucleotide-binding proteins, is present in the
active site of the protein, which appears to be a
positively charged cleft containing a number of
conserved arginine and lysine residues. Although PAPS
reductase has no ATPase activity, it shows a striking
similarity to the structure of the ATP pyrophosphatase
(ATP PPase) domain of GMP synthetase, indicating that
both enzyme families have evolved from a common
ancestral nucleotide-binding fold. The enzyme uses
thioredoxin as an electron donor for the reduction of
PAPS to phospho-adenosine-phosphate (PAP) . It is also
found in NodP nodulation protein P from Rhizobium
meliloti which has ATP sulphurylase activity (sulphate
adenylate transferase) .
Length = 173
Score = 139 bits (352), Expect = 7e-38
Identities = 59/195 (30%), Positives = 77/195 (39%), Gaps = 30/195 (15%)
Query: 39 NPVLLFSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTGHNFPEVISFRDNCISKLGETLI 98
N V+ FSGGKDS VLL LA KA P P++ +DTG+ FPE F D + G L+
Sbjct: 1 NVVVSFSGGKDSTVLLHLALKALPE-LKPVPVIFLDTGYEFPETYEFVDRVAERYGLPLV 59
Query: 99 VRSVEDSIMKGTVRLRKPNTDSRNAAQSIT-------LLETIKEFKFDACIGGARRDEEK 151
V DS +G K + L +KE A I G RRDE
Sbjct: 60 VVRPPDSPAEGLALGLKGFPLPSPDRRWCCRILKVEPLRRALKELGVVAWITGIRRDESA 119
Query: 152 ARAKERIFSFRDKFGQWNPKSQRPELWNLYNTRVHPGENIRVFPISNWTELDIWQYIERE 211
RA + T G ++V P+ +WT D+W Y+ R
Sbjct: 120 RRALLPVV----------------------WTDDGKGGILKVNPLLDWTYEDVWAYLARH 157
Query: 212 KIILPSLYFAHKRKI 226
+ LY R I
Sbjct: 158 GLPYNPLYDQGYRSI 172
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor 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.
Length = 183
Score = 133 bits (336), Expect = 1e-35
Identities = 59/197 (29%), Positives = 92/197 (46%), Gaps = 34/197 (17%)
Query: 326 RFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESE 385
G VD GK+TL G LL+ + I D L+ E
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRK-----------------ETFLDTLKEE 43
Query: 386 REQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASK-IKFNP 444
RE+GITI F PKR+ DTPGHE +++ + G + AD ++++DA++ ++
Sbjct: 44 RERGITIKTGVVEFEWPKRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGVE--- 100
Query: 445 SVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHF---- 500
QT+ H IA L II+AVNK+D + + + ++ K+ + I F
Sbjct: 101 -----PQTREHLNIA-LAGGLPIIVAVNKIDRV--GEEDFDEVLREIKELLKLIGFTFLK 152
Query: 501 -QNINTIPISALNGDNI 516
+++ IPISAL G+ I
Sbjct: 153 GKDVPIIPISALTGEGI 169
>gnl|CDD|200107 TIGR01465, cobM_cbiF, precorrin-4 C11-methyltransferase. This
model represents precorrin-4 C11-methyltransferase, one
of two methyltransferases commonly referred to as
precorrin-3 methylase (the other is precorrin-3B
C17-methyltransferase, EC 2.1.1.131). This enzyme
participates in the pathway toward the biosynthesis of
cobalamin and related products [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 247
Score = 132 bits (335), Expect = 9e-35
Identities = 69/239 (28%), Positives = 117/239 (48%), Gaps = 18/239 (7%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLY-DALITNELLMLCPKAKHIFVGKRFKKHSI 797
VY IGAGPG DLITV+G +L+ ADV+LY +L+ ELL C + +
Sbjct: 1 VYFIGAGPGDPDLITVKGRKLIESADVILYAGSLVPPELLAHCRPGAEV--------VNS 52
Query: 798 AQYIINRI---IVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGITAAL 854
A + I + + V RL GDP ++G E++ L+ I +V+PG+++
Sbjct: 53 AGMSLEEIVDIMSDAHREGKDVARLHSGDPSIYGAIAEQMRLLEALGIPYEVVPGVSSFF 112
Query: 855 AAASESKQSLTKRNISRSVVLFTSS---TMLKNNYLKNIP-ISDTLVEYMGGNNIFLTAK 910
AAA+ LT +S++V+L +S M + L ++ T+ ++ + + K
Sbjct: 113 AAAAALGAELTVPEVSQTVILTRASGRTPMPEGEKLADLAKHGATMAIFLSAHILDKVVK 172
Query: 911 KLLKLGFLPTTPVIVVENCSLSNQKITRLILLDLKKKIFQ--FEKPVLFMIGKSLKSHY 967
+L++ G+ TPV VV + ++KI R L DL + + + L ++G +L
Sbjct: 173 ELIEHGYSEDTPVAVVYRATWPDEKIVRGTLADLADLVREEGIYRTTLILVGPALDPRI 231
>gnl|CDD|180864 PRK07168, PRK07168, bifunctional uroporphyrinogen-III
methyltransferase/uroporphyrinogen-III synthase;
Reviewed.
Length = 474
Score = 138 bits (349), Expect = 1e-34
Identities = 78/205 (38%), Positives = 112/205 (54%), Gaps = 10/205 (4%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLC-PKAKHIFVGKRFKKHSI 797
VY++GAGPG LIT + L++AD+VLYD L+ L + ++ GK K H +
Sbjct: 5 VYLVGAGPGDEGLITKKAIECLKRADIVLYDRLLNPFFLSYTKQTCELMYCGKMPKNHIM 64
Query: 798 AQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGITAALAAA 857
Q +IN +++ A + +VVRLKGGDP +FGR EE L NI +++PGIT+++AA+
Sbjct: 65 RQEMINAHLLQFAKEGKIVVRLKGGDPSIFGRVGEEAETLAAANIPYEIVPGITSSIAAS 124
Query: 858 SESKQSLTKRNISRSVVLFTSST------MLKNNYLKNIPISDTLVEYMGGNNIFLTAKK 911
S + LT RN S SV L T K N N SDT+ YMG N+ +
Sbjct: 125 SYAGIPLTHRNYSNSVTLLTGHAKGPLTDHGKYNSSHN---SDTIAYYMGIKNLPTICEN 181
Query: 912 LLKLGFLPTTPVIVVENCSLSNQKI 936
L + G TPV V+E + Q++
Sbjct: 182 LRQAGKKEDTPVAVIEWGTTGKQRV 206
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 128 bits (324), Expect = 1e-31
Identities = 90/368 (24%), Positives = 150/368 (40%), Gaps = 70/368 (19%)
Query: 327 FITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESER 386
TAG +D GK+TL+ + ++G TD L E+
Sbjct: 3 IGTAGHIDHGKTTLL------------------------KALTGGV------TDRLPEEK 32
Query: 387 EQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSV 446
++GITID+ + Y D PGH + N++ G D ++++ A +
Sbjct: 33 KRGITIDLGFYYRKLEDGVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADE------- 85
Query: 447 NLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTI 506
L+ QT H +I LL IK+ II + K D ++ +I K K+ D+ N
Sbjct: 86 GLMAQTGEHLLILDLLGIKNGIIVLTKADRVDEARIEQKI-----KQILADLSLANAKIF 140
Query: 507 PISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLRFPVQLVARHCGHISKD 566
SA G I N L++ L E+ ++KP R + +
Sbjct: 141 KTSAKTGRGIEELKN-----------ELIDLLEEIERDEQKPFRIAID----RAFTV--- 182
Query: 567 FRGY----MGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDMAITGQSVTLIIK-- 620
+G G + SG +K D L + P K+ ++ IQ + ++ A GQ V L +K
Sbjct: 183 -KGVGTVVTGTVLSGEVKVGDKLYLSPINKEVRVRSIQAHDVDVEEAKAGQRVGLALKGV 241
Query: 621 EYLDISRGNMLVSPFKRPVSLR-SINANLCWLSEESLDLRRKYLLKHSTNQILSRI--LK 677
E +I RG+ L+ P V+ R + + L +++L + + + RI L+
Sbjct: 242 EKEEIERGDWLLKPEPLEVTTRLIVELEIDPLFKKTLKQGQPVHIHVGLRSVTGRIVPLE 301
Query: 678 INALLNIN 685
NA LN+
Sbjct: 302 KNAELNLV 309
>gnl|CDD|212499 cd09815, TP_methylase, S-AdoMet dependent tetrapyrrole methylases.
This family uses S-AdoMet (S-adenosyl-L-methionine or
SAM) in the methylation of diverse substrates. Most
members catalyze various methylation steps in cobalamin
(vitamin B12) biosynthesis. There are two distinct
cobalamin biosynthetic pathways in bacteria. The aerobic
pathway requires oxygen, and cobalt is inserted late in
the pathway; the anaerobic pathway does not require
oxygen, and cobalt insertion is the first committed step
towards cobalamin synthesis. The enzymes involved in the
aerobic pathway are prefixed Cob and those of the
anaerobic pathway Cbi. Most of the enzymes are shared by
both pathways and a few enzymes are pathway-specific.
Diphthine synthase and Ribosomal RNA small subunit
methyltransferase I (RsmI) are two superfamily members
that are not involved in cobalamin biosynthesis.
Diphthine synthase participates in the posttranslational
modification of a specific histidine residue in
elongation factor 2 (EF-2) of eukaryotes and archaea to
diphthamide. RsmI catalyzes the 2-O-methylation of the
ribose of cytidine 1402 (C1402) in 16S rRNA using
S-adenosylmethionine (Ado-Met) as the methyl donor.
Length = 224
Score = 118 bits (298), Expect = 4e-30
Identities = 60/229 (26%), Positives = 97/229 (42%), Gaps = 12/229 (5%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCPKAKH------IFVGKRF 792
+Y +GAGPG DL+T+R +LR ADVV+ D +ELL L P+A + +
Sbjct: 1 LYFVGAGPGDPDLLTLRAVEVLRSADVVVVDDK-VSELLRLKPRAHLPDGAEIVELVDEE 59
Query: 793 KKHSIAQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGITA 852
+ + R +++ A + VVRL GDP+L G E + + V+V+PG+++
Sbjct: 60 EDDHGVLAEVARTLLEAARQGRDVVRLVAGDPLLAGPGAELRAVAEDAGVDVEVVPGVSS 119
Query: 853 ALAAASESKQSLTKRNISRSVVLFTSSTMLKNNYLKNIPISDTLVEYMGGNNIFLTAKKL 912
A A + + L + V TLV Y + K
Sbjct: 120 ATAVPAYAGIPLGQSVTFADVRDDEPGAEAAALAAA----PQTLVLYADPASALADIAKE 175
Query: 913 LKLGFLPTTPVIVVENCSLSNQKITRLILLDLKKKIFQFEK-PVLFMIG 960
L+ TPV+V N + Q+I L +L + P + ++G
Sbjct: 176 LREALPDDTPVVVTANGTTRGQRIRTGTLAELAAAREEELPGPTIILVG 224
>gnl|CDD|239762 cd04095, CysN_NoDQ_III, TCysN_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. 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 shows no aa sequence similarity to
CysN or NodQ. CysN and the N-terminal portion of NodQ
show similarity to GTPases involved in translation, in
particular, EF-Tu and EF-1alpha.
Length = 103
Score = 111 bits (279), Expect = 5e-29
Identities = 40/100 (40%), Positives = 57/100 (57%)
Query: 642 RSINANLCWLSEESLDLRRKYLLKHSTNQILSRILKINALLNINTQKWCPPKLLDLNDIG 701
A L W+ EE L RKYLLK T + + + I +++NT + L+LNDIG
Sbjct: 4 DQFAATLVWMDEEPLRPGRKYLLKLGTRTVRATVTAIKYRVDVNTLEHEAADTLELNDIG 63
Query: 702 CVTINIYEPISVDSYDNIRSTGSFILIDEITFQTVAAVYI 741
V +++ +P++ D Y R+TGSFILID +T TV A I
Sbjct: 64 RVELSLSKPLAFDPYRENRATGSFILIDRLTNATVGAGMI 103
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
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 [Protein synthesis, Translation factors].
Length = 581
Score = 117 bits (294), Expect = 4e-27
Identities = 80/300 (26%), Positives = 124/300 (41%), Gaps = 62/300 (20%)
Query: 327 FITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESER 386
TAG VD GK+TL+ L ++ D L E+
Sbjct: 3 IATAGHVDHGKTTLL------------KALTGIA------------------ADRLPEEK 32
Query: 387 EQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSV 446
++G+TID+ + YF P + D PGHE++ N I G DA ++++DA +
Sbjct: 33 KRGMTIDLGFAYFPLPDYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADE------- 85
Query: 447 NLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHF-QNINT 505
++TQT H + LL I H I+ + K D +N +I KR K+ F +N
Sbjct: 86 GVMTQTGEHLAVLDLLGIPHTIVVITKADRVNEEEI--KRTEMFMKQILNSYIFLKNAKI 143
Query: 506 IPISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLRFPVQLVARHCGHISK 565
SA G I L +LLESL+ +KPLR + +
Sbjct: 144 FKTSAKTGQGIGELKKE--------LKNLLESLDIKRI--QKPLRMAIDRAFK------- 186
Query: 566 DFRGY----MGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDMAITGQSVTLIIKE 621
+G G SG +K D L + P + +K IQ N+ +++A GQ + L + +
Sbjct: 187 -VKGAGTVVTGTAFSGEVKVGDNLRLLPINHEVRVKAIQAQNQDVEIAYAGQRIALNLMD 245
>gnl|CDD|239666 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. 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 shows no aa sequence similarity to
CysN or NodQ. CysN and the N-terminal portion of NodQ
show similarity to GTPases involved in translation, in
particular, EF-Tu and EF-1alpha.
Length = 81
Score = 103 bits (260), Expect = 1e-26
Identities = 38/85 (44%), Positives = 56/85 (65%), Gaps = 4/85 (4%)
Query: 549 LRFPVQLVARHCGHISKDFRGYMGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDM 608
RFPVQ V R + DFRGY G I SG I+ D ++V PSGK + +K I+ + LD
Sbjct: 1 FRFPVQYVIRP----NADFRGYAGTIASGSIRVGDEVVVLPSGKTSRVKSIETFDGELDE 56
Query: 609 AITGQSVTLIIKEYLDISRGNMLVS 633
A G+SVTL +++ +D+SRG+++V+
Sbjct: 57 AGAGESVTLTLEDEIDVSRGDVIVA 81
>gnl|CDD|185370 PRK15473, cbiF, cobalt-precorrin-4 C(11)-methyltransferase;
Provisional.
Length = 257
Score = 101 bits (254), Expect = 7e-24
Identities = 77/255 (30%), Positives = 121/255 (47%), Gaps = 37/255 (14%)
Query: 732 TFQTVAAVYIIGAGPGAADLITVRGARLLRKADVVLY-DALITNELLMLCPKAKHIFVGK 790
TF V+ +GAGPG +LIT++G RLL++A VV+Y +LI ELL CP
Sbjct: 4 TFDP-RCVWFVGAGPGDKELITLKGYRLLQQAQVVIYAGSLINTELLDYCPAQAEC---- 58
Query: 791 RFKKHSIAQYIINRII------VKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKV 844
H A+ + +II VK VVRL+ GD L+G E+ L K I
Sbjct: 59 ----HDSAELHLEQIIDLMEAGVKAG---KTVVRLQTGDVSLYGSIREQGEELTKRGIDF 111
Query: 845 KVIPGITAALAAASESKQSLTKRNISRSVVLFTSSTMLKNNYLKNIPISDTLVEYMGGNN 904
+V+PG+++ L AA+E T +S+S+++ T ++ +P + L +
Sbjct: 112 QVVPGVSSFLGAAAELGVEYTVPEVSQSLII----TRMEGR--TPVPAREQLESFASHQT 165
Query: 905 ---IFLT-------AKKLLKLGFLPTTPVIVVENCSLSNQKITRLILLDLKKKIFQ--FE 952
IFL+ A++L+ G+ TTPV V+ + + R L D+ +K+
Sbjct: 166 SMAIFLSVQRIHRVAERLIAGGYPATTPVAVIYKATWPESQTVRGTLADIAEKVRDAGIR 225
Query: 953 KPVLFMIGKSLKSHY 967
K L ++G L Y
Sbjct: 226 KTALILVGNFLGEEY 240
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. 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 eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 93.4 bits (233), Expect = 6e-22
Identities = 49/153 (32%), Positives = 75/153 (49%), Gaps = 42/153 (27%)
Query: 329 TAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQ 388
TAG +D GK+TLI L +G TD L E+++
Sbjct: 4 TAGHIDHGKTTLIKAL------------------------TGIE------TDRLPEEKKR 33
Query: 389 GITIDVAYRYFNTPKRK---FIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPS 445
GITID+ + Y + P K FI D PGHE++ +NM+ GA DAV++++ A +
Sbjct: 34 GITIDLGFAYLDLPDGKRLGFI--DVPGHEKFVKNMLAGAGGIDAVLLVVAADE------ 85
Query: 446 VNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLIN 478
++ QT+ H I LL IK ++ + K DL++
Sbjct: 86 -GIMPQTREHLEILELLGIKKGLVVLTKADLVD 117
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 98.5 bits (246), Expect = 9e-22
Identities = 85/330 (25%), Positives = 144/330 (43%), Gaps = 74/330 (22%)
Query: 329 TAGSVDDGKSTLI----GRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLES 384
T G VD GK+TL L Y ++ D
Sbjct: 17 TIGHVDHGKTTLTAAITTVLAKKGGAEAKA---------YDQI------------DNAPE 55
Query: 385 EREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNP 444
E+ +GITI+ A+ + T R + D PGH Y +NMITGA+ D I+++ A+ P
Sbjct: 56 EKARGITINTAHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATD---GP 112
Query: 445 SVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNIN 504
+ QT+ H ++A + + +I++ +NK+D+++ ++ + + ++ + F +
Sbjct: 113 ----MPQTREHILLARQVGVPYIVVFLNKVDMVDDEELL-ELVEMEVRELLSEYGFPGDD 167
Query: 505 TIPI------SALNGDNIISASNNMLWYNGPTLISLLESLN----TNEKIDKKPLRFPVQ 554
T PI AL GD A + L+++++ T E+ KP PV+
Sbjct: 168 T-PIIRGSALKALEGDAKWEAK----------IEELMDAVDSYIPTPERDIDKPFLMPVE 216
Query: 555 LVARHCGHISKDFRGYM--GRIESGIIKKNDCLIVEPSG----KKATIKDIQMLNKSLDM 608
V G RG + GR+E GI+K + VE G +K T+ ++M K LD
Sbjct: 217 DVFSISG------RGTVVTGRVERGILKVGE--EVEIVGIKETQKTTVTGVEMFRKLLDE 268
Query: 609 AITGQSVTL----IIKEYLDISRGNMLVSP 634
G +V + + +E D+ RG +L P
Sbjct: 269 GQAGDNVGVLLRGVKRE--DVERGQVLAKP 296
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
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
[Protein synthesis, Translation factors].
Length = 394
Score = 96.8 bits (241), Expect = 3e-21
Identities = 80/324 (24%), Positives = 144/324 (44%), Gaps = 62/324 (19%)
Query: 329 TAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQ 388
T G VD GK+TL + + + + Y ++ D E+ +
Sbjct: 17 TIGHVDHGKTTLTAAI-----TTVLAKEGGAAARAYDQI------------DNAPEEKAR 59
Query: 389 GITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNL 448
GITI+ A+ + T R + D PGH Y +NMITGA+ D I+++ A+
Sbjct: 60 GITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATD-------GP 112
Query: 449 LTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIF------YKRIVYAYKKFAEDIHFQN 502
+ QT+ H ++A + + +I++ +NK D+++ ++ + ++ Y +D
Sbjct: 113 MPQTREHILLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSEYDFPGDDTPI-- 170
Query: 503 INTIPISALNGDNIISASNNMLWYNGPTLISLLESLNTN----EKIDKKPLRFPVQLVAR 558
I + AL GD A ++ L+++++ E+ KP P++ V
Sbjct: 171 IRGSALKALEGDAEWEAK----------ILELMDAVDEYIPTPERETDKPFLMPIEDVFS 220
Query: 559 HCGHISKDFRGYM--GRIESGIIKKNDCLIVEPSG----KKATIKDIQMLNKSLDMAITG 612
G RG + GR+E GI+K + VE G +K T+ ++M K LD G
Sbjct: 221 ITG------RGTVVTGRVERGIVKVGE--EVEIVGLKDTRKTTVTGVEMFRKELDEGRAG 272
Query: 613 QSVTLIIK--EYLDISRGNMLVSP 634
+V L+++ + +I RG +L P
Sbjct: 273 DNVGLLLRGIKREEIERGMVLAKP 296
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 97.0 bits (242), Expect = 3e-21
Identities = 75/278 (26%), Positives = 128/278 (46%), Gaps = 45/278 (16%)
Query: 380 DGLESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASK 439
D E+ +GITI+ A+ + T R + D PGH Y +NMITGA+ D I+++ A+
Sbjct: 51 DSAPEEKARGITINTAHVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAAD 110
Query: 440 IKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFY------KRIVYAYKK 493
P + QTK H ++A + + +I++ +NK D ++ ++ + ++ Y
Sbjct: 111 ---GP----MPQTKEHILLAKQVGVPNIVVFLNKEDQVDDEELLELVELEVRELLSKYDF 163
Query: 494 FAEDIHFQNINTIPISALNGDNIISASNNMLWYNGP---TLISLLESLN----TNEKIDK 546
+DI + SAL ++ + + + +L+++++ T E+
Sbjct: 164 PGDDIPI-----VSGSALLALEALTENPKIKRGENKWVDKIYNLMDAVDSYIPTPERDTD 218
Query: 547 KPLRFPVQLVARHCGHISKDFRG--YMGRIESGIIKKNDCLIVEPSG----KKATIKDIQ 600
KP ++ V G RG GRIE G +K D VE G K T+ ++
Sbjct: 219 KPFLMAIEDVFSITG------RGTVATGRIERGTVKVGD--TVEIVGLRETKTTTVTGLE 270
Query: 601 MLNKSLDMAITGQSVTL----IIKEYLDISRGNMLVSP 634
M K+LD + G +V + I KE DI RG +L P
Sbjct: 271 MFQKTLDEGLAGDNVGILLRGIQKE--DIERGMVLAKP 306
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 94.5 bits (235), Expect = 3e-20
Identities = 86/331 (25%), Positives = 147/331 (44%), Gaps = 72/331 (21%)
Query: 329 TAGSVDDGKSTL---IGRLLFD---SKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGL 382
T G VD GK+TL I ++L + +K + D++D
Sbjct: 66 TIGHVDHGKTTLTAAITKVLAEEGKAKAVAFDEIDKAPE--------------------- 104
Query: 383 ESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKF 442
E+ +GITI A+ + T KR + D PGH Y +NMITGA+ D I+++ A
Sbjct: 105 --EKARGITIATAHVEYETAKRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPD--- 159
Query: 443 NPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQI-----FYKRIVYAYKKFAED 497
P + QTK H ++A + + +++ +NK+D+++ ++ R + ++ KF D
Sbjct: 160 GP----MPQTKEHILLARQVGVPSLVVFLNKVDVVDDEELLELVEMELRELLSFYKFPGD 215
Query: 498 IHFQNINTIPI------SALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLRF 551
IPI SAL G N N +L + ++ E + ++ KP
Sbjct: 216 -------EIPIIRGSALSALQGTNDEIGKNAIL----KLMDAVDEYIPEPVRVLDKPFLM 264
Query: 552 PVQLVARHCGHISKDFRGYM--GRIESGIIKKNDCL----IVEPSGKKATIKDIQMLNKS 605
P++ V S RG + GR+E G IK + + + K T+ ++M K
Sbjct: 265 PIEDV------FSIQGRGTVATGRVEQGTIKVGEEVEIVGLRPGGPLKTTVTGVEMFKKI 318
Query: 606 LDMAITGQSVTLIIK--EYLDISRGNMLVSP 634
LD G +V L+++ + D+ RG ++ P
Sbjct: 319 LDQGQAGDNVGLLLRGLKREDVQRGQVICKP 349
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 89.2 bits (222), Expect = 9e-19
Identities = 86/330 (26%), Positives = 149/330 (45%), Gaps = 74/330 (22%)
Query: 329 TAGSVDDGKSTL---IGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESE 385
T G VD GK+TL I ++L + Y + D E
Sbjct: 17 TIGHVDHGKTTLTAAITKVLAER--------GLNQAKDYDSI------------DAAPEE 56
Query: 386 REQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPS 445
+E+GITI+ A+ + T KR + D PGH Y +NMITGA+ D I+++ A+ P
Sbjct: 57 KERGITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATD---GP- 112
Query: 446 VNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIF------YKRIVYAYKKFAEDIH 499
+ QT+ H ++A + + ++++ +NK+DL++ ++ + ++ Y F D
Sbjct: 113 ---MPQTREHILLARQVGVPYLVVFLNKVDLVDDEELLELVEMEVRELLSEY-DFPGD-- 166
Query: 500 FQNINTIPIS---ALNGDNIISASNNMLWYNGPTLISLLESLN----TNEKIDKKPLRFP 552
+I I S AL GD + ++ L+++++ T E+ KP P
Sbjct: 167 --DIPVIRGSALKALEGDPKWEDA----------IMELMDAVDEYIPTPERDTDKPFLMP 214
Query: 553 VQLVARHCGHISKDFRGYM--GRIESGIIKKNDCLIVEPSG----KKATIKDIQMLNKSL 606
V+ V G RG + GR+E G +K D VE G +K + ++M K L
Sbjct: 215 VEDVFTITG------RGTVVTGRVERGTVKVGD--EVEIVGIKETQKTVVTGVEMFRKLL 266
Query: 607 DMAITGQSVTLIIK--EYLDISRGNMLVSP 634
D G +V ++++ + ++ RG +L P
Sbjct: 267 DEGQAGDNVGVLLRGVDRDEVERGQVLAKP 296
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 88.5 bits (219), Expect = 3e-18
Identities = 78/319 (24%), Positives = 146/319 (45%), Gaps = 42/319 (13%)
Query: 329 TAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQ 388
T G VD GK+TL L + + + + KY + D ER +
Sbjct: 86 TIGHVDHGKTTLTAAL-----TMALASMGGSAPKKYDEI------------DAAPEERAR 128
Query: 389 GITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNL 448
GITI+ A + T R + D PGH Y +NMITGA+ D I+++ + P
Sbjct: 129 GITINTATVEYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGAD---GP---- 181
Query: 449 LTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIF------YKRIVYAYKKFAEDIHFQN 502
+ QTK H ++A + + ++++ +NK D ++ ++ + ++ +Y+ +DI +
Sbjct: 182 MPQTKEHILLAKQVGVPNMVVFLNKQDQVDDEELLELVELEVRELLSSYEFPGDDIPIIS 241
Query: 503 INTI-PISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLRFPVQLVARHCG 561
+ + + AL + I +N W + + L++++++ I ++ P L
Sbjct: 242 GSALLALEALMENPNIKRGDNK-WVD--KIYELMDAVDSYIPIPQRQTDLPFLLAVEDVF 298
Query: 562 HISKDFRGYMGRIESGIIKKNDCLIVEPSG----KKATIKDIQMLNKSLDMAITGQSVTL 617
I+ GR+E G +K + V+ G + T+ ++M K LD A+ G +V L
Sbjct: 299 SITGRGTVATGRVERGTVKVGE--TVDIVGLRETRSTTVTGVEMFQKILDEALAGDNVGL 356
Query: 618 IIK--EYLDISRGNMLVSP 634
+++ + DI RG +L P
Sbjct: 357 LLRGIQKADIQRGMVLAKP 375
>gnl|CDD|212504 cd11645, Precorrin_2_C20_MT, Precorrin-2 C20-methyltransferase,
also named CobI or CbiL. Precorrin-2
C20-methyltransferase participates in the pathway toward
the biosynthesis of cobalamin (vitamin B12). There are
two distinct cobalamin biosynthetic pathways in
bacteria. The aerobic pathway requires oxygen, and
cobalt is inserted late in the pathway; the anaerobic
pathway does not require oxygen, and cobalt insertion is
the first committed step towards cobalamin synthesis.
Precorrin-2 C20-methyltransferase catalyzes methylation
at the C-20 position of a cyclic tetrapyrrole ring of
precorrin-2 using S-adenosylmethionine as a methyl group
source to produce precorrin-3A. In the anaerobic
pathway, cobalt is inserted into precorrin-2 by CbiK to
generate cobalt-precorrin-2, which is the substrate for
CbiL, a C20 methyltransferase. In Clostridium difficile,
CbiK and CbiL are fused into a bifunctional enzyme. In
the aerobic pathway, the precorrin-2
C20-methyltransferase is named CobI. This family
includes CbiL and CobI precorrin-2
C20-methyltransferases, both as stand-alone enzymes and
when CbiL forms part of a bifunctional enzyme.
Length = 226
Score = 81.8 bits (203), Expect = 2e-17
Identities = 53/223 (23%), Positives = 93/223 (41%), Gaps = 23/223 (10%)
Query: 740 YIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLM-LCPKAKHIFVGKRF------ 792
Y +G GPG +L+T++ R+LR+ADV+ E L ++ K
Sbjct: 3 YGVGVGPGDPELLTLKAVRILREADVIAVPGSKAGEGSAALIIVVAYLIPEKEILPLEFP 62
Query: 793 ----KKHSIAQYIIN-RIIVKCAFKYNLVVRLKGGDPML---FGRTDEELNALKKYNIKV 844
K+ + I V L GDP L F L L++ ++V
Sbjct: 63 MTKDKEVLEEAWDEAAAEIAAELEAGKDVAFLTLGDPSLYSTFSYL---LRRLREPGVEV 119
Query: 845 KVIPGITAALAAASESKQSLTKRNISRSVVLFTSSTMLKNNYLKNIPISDTLVEYMGGNN 904
+ IPGIT+ AAA+ L + + +++ +T+ + + + + DT+V G N
Sbjct: 120 ETIPGITSFSAAAARLGIPLAEGDERLAIL---PATLGEEELEEALELFDTVVLMKVGRN 176
Query: 905 IFLTAKKLLKLGFLPTTPVIVVENCSLSNQKITRLILLDLKKK 947
+ + L + G L + VE C + ++I R + D +K
Sbjct: 177 LDEVRELLEEAGLLDR--AVYVERCGMEGERIVRDLEADPEKL 217
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 82.6 bits (205), Expect = 1e-16
Identities = 87/338 (25%), Positives = 145/338 (42%), Gaps = 88/338 (26%)
Query: 329 TAGSVDDGKSTL---IGRLL---FDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGL 382
T G VD GK+TL I ++L + DQ+D
Sbjct: 17 TIGHVDHGKTTLTAAITKVLAKKGGGEAKAYDQIDNAPE--------------------- 55
Query: 383 ESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKF 442
E+ +GITI+ ++ + T R + D PGH Y +NMITGA+ D I+++ A+
Sbjct: 56 --EKARGITINTSHVEYETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAAD--- 110
Query: 443 NPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMD------LINYNQIFYKRIVYAYKKFAE 496
P + QT+ H ++A + + +I++ +NK D L+ ++ + ++ Y F
Sbjct: 111 GP----MPQTREHILLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSKY-DFPG 165
Query: 497 DIHFQNINTIPI------SALNGDNIISASNNMLWYNGPTLISLLESLNTN----EKIDK 546
D PI AL GD+ ++ L++++++ E+
Sbjct: 166 D-------DTPIIRGSALKALEGDDD--------EEWEAKILELMDAVDSYIPEPERAID 210
Query: 547 KPLRFPVQLVARHCGHISKDFRGYM--GRIESGIIKKNDCLIVEPSGKKATIK----DIQ 600
KP P++ V G RG + GR+E GI+K D VE G K T K ++
Sbjct: 211 KPFLMPIEDVFSISG------RGTVVTGRVERGIVKVGD--EVEIVGIKETQKTTVTGVE 262
Query: 601 MLNKSLDMAITGQSVTLII----KEYLDISRGNMLVSP 634
M K LD G +V +++ +E D+ RG +L P
Sbjct: 263 MFRKLLDEGQAGDNVGVLLRGTKRE--DVERGQVLAKP 298
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 80.6 bits (200), Expect = 6e-16
Identities = 86/332 (25%), Positives = 150/332 (45%), Gaps = 76/332 (22%)
Query: 329 TAGSVDDGKSTL---IGRLL---FDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGL 382
T G VD GK+TL I ++L ++ DQ+D
Sbjct: 17 TIGHVDHGKTTLTAAITKVLAKKGGAEAKAYDQIDKAP---------------------- 54
Query: 383 ESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKF 442
E+ +GITI+ A+ + T KR + D PGH Y +NMITGA+ D I+++ A+
Sbjct: 55 -EEKARGITINTAHVEYETEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAAD--- 110
Query: 443 NPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIF------YKRIVYAYKKFAE 496
P + QT+ H ++A + + +I++ +NK D+++ ++ + ++ Y F
Sbjct: 111 GP----MPQTREHILLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSKY-DFPG 165
Query: 497 DIHFQNINTIPISALNGDNIISASNNMLWYNGPTLISLLESLNTN----EKIDKKPLRFP 552
D + I SAL + ++ W ++ L++++++ E+ KP P
Sbjct: 166 D----DTPIIRGSALKA---LEGDDDEEWE--KKILELMDAVDSYIPTPERAIDKPFLMP 216
Query: 553 VQLVARHCGHISKDFRGYM--GRIESGIIKKNDCLIVEPSG----KKATIKDIQMLNKSL 606
++ V G RG + GR+E GIIK + VE G +K T+ ++M K L
Sbjct: 217 IEDVFSISG------RGTVVTGRVERGIIKVGE--EVEIVGIRDTQKTTVTGVEMFRKLL 268
Query: 607 DMAITGQSVTLII----KEYLDISRGNMLVSP 634
D G +V ++ +E D+ RG +L P
Sbjct: 269 DEGQAGDNVGALLRGIKRE--DVERGQVLAKP 298
>gnl|CDD|206671 cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.
EF-Tu subfamily. 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.
Length = 195
Score = 76.5 bits (189), Expect = 9e-16
Identities = 42/152 (27%), Positives = 73/152 (48%), Gaps = 30/152 (19%)
Query: 329 TAGSVDDGKSTL---IGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESE 385
T G VD GK+TL I ++L ++ + ID + E
Sbjct: 7 TIGHVDHGKTTLTAAITKVL--------------AKKGGAKAKKYDEIDKAP------EE 46
Query: 386 REQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPS 445
+ +GITI+ A+ + T R + D PGH Y +NMITGA+ D I+++ A+
Sbjct: 47 KARGITINTAHVEYETANRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATD------ 100
Query: 446 VNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLI 477
+ QT+ H ++A + + +I++ +NK D++
Sbjct: 101 -GPMPQTREHLLLARQVGVPYIVVFLNKADMV 131
>gnl|CDD|225152 COG2243, CobF, Precorrin-2 methylase [Coenzyme metabolism].
Length = 234
Score = 76.6 bits (189), Expect = 2e-15
Identities = 58/233 (24%), Positives = 90/233 (38%), Gaps = 57/233 (24%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCPKAKHIFVGKRFKKHSIA 798
+Y +G GPG +L+T++ R L+KADVV P K K S+A
Sbjct: 4 LYGVGLGPGDPELLTLKAIRALKKADVVYV------------PSKKG--------KGSLA 43
Query: 799 QYIINR------IIVKCAFKYNLVVR------------------LKG--------GDPML 826
+ I+ IV+ F +R G GDP
Sbjct: 44 REIVEDYLTPGSRIVELHFPMTTDMREELEDAWEEAAAEVAAELEAGRDVAFLTLGDPTF 103
Query: 827 FGRTDEELNALKKYNIKVKVIPGITAALAAASESKQSLTKRNISRSVVLFTSSTMLKNNY 886
+ L L++ +V+V+PG+++ A A+ L + + S SV+ T
Sbjct: 104 YSTFMYLLERLRERGFEVEVVPGVSSFSACAARLGVPLVEGDDSLSVLPATRPDEELERA 163
Query: 887 LKNIPISDTLVEYMGGNNIFLTAKKLLKLGFLPTTPVIVVENCSLSNQKITRL 939
L + DT V G N + L KLG L + VE +++ +KI RL
Sbjct: 164 LADF---DTAVVMKVGRNFEKLRRLLAKLGLL--DRAVYVERATMAGEKIVRL 211
>gnl|CDD|237510 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 80.0 bits (198), Expect = 2e-15
Identities = 66/216 (30%), Positives = 94/216 (43%), Gaps = 40/216 (18%)
Query: 14 LNNLYLDWLESEAIHIMREVSAECNNPVLL-FSGGKDSVVLLRLAEKAFRPSRFPFPMVH 72
N +L+ E EA++ +R V+ + N PV + FSGGKDS+V+L LA +A + + F
Sbjct: 219 ANRKHLEEKEKEAVNFIRGVAEKYNLPVSVSFSGGKDSLVVLDLAREALKDFKAFF---- 274
Query: 73 IDTGHNFPEVISFRDNCISKLGETLIVRSVEDSIMKGTVRLRKPNTDSRNAAQ-----SI 127
+TG FPE + + G LI D+ + + P D R + I
Sbjct: 275 NNTGLEFPETVENVKEVAEEYGIELIEADAGDAFWRAVEKFGPPARDYRWCCKVCKLGPI 334
Query: 128 TLLETIKEFKFDACIG--GARRDEEKARAKERIFSFRDKFGQWNPKSQRPELWNLYNTRV 185
T IKE C+ G R+ E +RAK P +W N V
Sbjct: 335 TRA--IKENFPKGCLTFVGQRKYESFSRAK------------------SPRVWR--NPWV 372
Query: 186 HPGENIRVFPISNWTELDIWQYIEREKIILP--SLY 219
P + I PI +WT L++W YI K LP LY
Sbjct: 373 -PNQ-IGASPIQDWTALEVWLYIFWRK--LPYNPLY 404
>gnl|CDD|235512 PRK05576, PRK05576, cobalt-precorrin-2 C(20)-methyltransferase;
Validated.
Length = 229
Score = 73.4 bits (181), Expect = 2e-14
Identities = 53/215 (24%), Positives = 92/215 (42%), Gaps = 22/215 (10%)
Query: 737 AAVYIIGAGPGAADLITVRGARLLRKADVVLY--DALITNELLML------CPKAKHIFV 788
+Y IG GPG +L+TV+ AR+L +ADVV Y + L L + I
Sbjct: 2 GKLYGIGLGPGDPELLTVKAARILEEADVV-YAPASRKGGGSLALNIVRPYLKEETEIVE 60
Query: 789 -----GKRFKKHSIAQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIK 843
K ++ I A + V + GDP L+ L LK ++I+
Sbjct: 61 LHFPMSKDEEEKEAVWKENAEEIAAEAEEGKNVAFITLGDPNLYSTFSHLLEYLKCHDIE 120
Query: 844 VKVIPGITAALAAASESKQSLTKRNISRSVVLFTSSTMLKNNYLKNIPISDTLVEYMGGN 903
V+ +PGI++ A AS + L + S +++ T ++ + + D++V M
Sbjct: 121 VETVPGISSFTAIASRAGVPLAMGDESLAIIPATREALI----EQALTDFDSVV-LMKVY 175
Query: 904 NIFLTAKKLLKLGFLPTTPVIVVENCSLSNQKITR 938
F ++LL+ G+L + V + ++I R
Sbjct: 176 KNFALIEELLEEGYL---DALYVRRAYMEGEQILR 207
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). 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 selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is
a member of the same family as eubacterial IF2, but the
two proteins are only distantly related. This family
includes translation initiation, elongation, and release
factors.
Length = 197
Score = 71.1 bits (175), Expect = 7e-14
Identities = 56/218 (25%), Positives = 81/218 (37%), Gaps = 69/218 (31%)
Query: 329 TAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQ 388
T G V GK+TL+ K + SG + T + E ++
Sbjct: 5 TIGHVAHGKTTLV-------KAL-----------------SG------VWTVRHKEELKR 34
Query: 389 GITIDVAYR----------YFNTP-----------------KRKFIIADTPGHEQYTRNM 421
ITI + Y P R D PGHE M
Sbjct: 35 NITIKLGYANAKIYKCPNCGCPRPYDTPECECPGCGGETKLVRHVSFVDCPGHEILMATM 94
Query: 422 ITGASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQ 481
++GA+ D ++LI A++ P QT H ++ +KHIII NK+DL+ Q
Sbjct: 95 LSGAAVMDGALLLIAANEPCPQP------QTSEHLAALEIMGLKHIIILQNKIDLVKEEQ 148
Query: 482 IF--YKRIVYAYKKFAEDIHFQNINTIPISALNGDNII 517
Y++I K+F + +N IPISA NI
Sbjct: 149 ALENYEQI----KEFVKGTIAENAPIIPISAQLKYNID 182
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 73.7 bits (182), Expect = 1e-13
Identities = 59/222 (26%), Positives = 88/222 (39%), Gaps = 78/222 (35%)
Query: 328 ITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESERE 387
G VD GK+TL+ + ++G + TD E +
Sbjct: 13 GMVGHVDHGKTTLV------------------------QALTG------VWTDRHSEELK 42
Query: 388 QGITIDVAY---------------RYFNTPK-----------RKFIIADTPGHEQYTRNM 421
+GITI + Y Y PK R+ D PGHE M
Sbjct: 43 RGITIRLGYADATIRKCPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGHETLMATM 102
Query: 422 ITGASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLI---- 477
++GA+ D I++I A++ P QTK H + ++ IK+I+I NK+DL+
Sbjct: 103 LSGAALMDGAILVIAANEPCPQP------QTKEHLMALDIIGIKNIVIVQNKIDLVSKER 156
Query: 478 ---NYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
NY QI K+F + +N IP+SAL+ NI
Sbjct: 157 ALENYEQI---------KEFVKGTVAENAPIIPVSALHKVNI 189
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 73.2 bits (180), Expect = 2e-13
Identities = 54/222 (24%), Positives = 86/222 (38%), Gaps = 78/222 (35%)
Query: 328 ITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESERE 387
G VD GK+TL + ++G + TD E +
Sbjct: 8 GMVGHVDHGKTTLT------------------------KALTG------VWTDTHSEELK 37
Query: 388 QGITIDVAY---------------RYFNTPK-----------RKFIIADTPGHEQYTRNM 421
+GI+I + Y Y P R+ D PGHE M
Sbjct: 38 RGISIRLGYADAEIYKCPECDGPECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMATM 97
Query: 422 ITGASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLI---- 477
++GA+ D +++I A++ P QT+ H + ++ IK+I+I NK+DL+
Sbjct: 98 LSGAALMDGALLVIAANEPCPQP------QTREHLMALEIIGIKNIVIVQNKIDLVSKEK 151
Query: 478 ---NYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
NY +I K+F + +N IP+SAL+ NI
Sbjct: 152 ALENYEEI---------KEFVKGTIAENAPIIPVSALHNANI 184
>gnl|CDD|233425 TIGR01467, cobI_cbiL, precorrin-2 C20-methyltransferase. This
model represents precorrin-2 C20-methyltransferase, one
of several closely related
S-adenosylmethionine-dependent methyltransferases
involved in cobalamin (vitamin B12) biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 230
Score = 68.9 bits (169), Expect = 6e-13
Identities = 56/233 (24%), Positives = 92/233 (39%), Gaps = 56/233 (24%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCPKAKHIFVGKRFKKHSIA 798
+Y +G GPG +LITV+ LR ADV+ K+ ++ S+A
Sbjct: 3 LYGVGVGPGDPELITVKALEALRSADVIAV------------------PASKKGRE-SLA 43
Query: 799 QYIINRI-------IVKCAF-----------KYNLVVR-----LKG---------GDPML 826
+ I+ I++ F ++ L+ GDP L
Sbjct: 44 RKIVEDYLKPNDTRILELVFPMTKDRDELEKAWDEAAEAVAAELEEGRDVAFLTLGDPSL 103
Query: 827 FGRTDEELNALKKYNIKVKVIPGITAALAAASESKQSLTKRNISRSVVLFTSSTMLKNNY 886
+ L L+ I+V+V+PGIT+ A AS + L + + +T +
Sbjct: 104 YSTFSYLLQRLQGMGIEVEVVPGITSFAACASAAGLPLVE---GDESLAILPATAGEAEL 160
Query: 887 LKNIPISDTLVEYMGGNNIFLTAKKLLKLGFLPTTPVIVVENCSLSNQKITRL 939
K + DT+V G N+ + L KLG L +VVE ++ ++KI L
Sbjct: 161 EKALAEFDTVVLMKVGRNLPQIKEALAKLGRLDAA--VVVERATMPDEKIVDL 211
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 70.4 bits (173), Expect = 1e-12
Identities = 59/221 (26%), Positives = 86/221 (38%), Gaps = 78/221 (35%)
Query: 329 TAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQ 388
G VD GK+TL + +SG + TD E ++
Sbjct: 15 MVGHVDHGKTTLT------------------------KALSG------VWTDRHSEELKR 44
Query: 389 GITIDVAY---------------RYFNTPK-----------RKFIIADTPGHEQYTRNMI 422
GITI + Y Y PK R+ D PGHE M+
Sbjct: 45 GITIKLGYADAKIYKCPECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATML 104
Query: 423 TGASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLI----- 477
+GA+ D +++I A++ P QT+ H + ++ IK+III NK+DL+
Sbjct: 105 SGAALMDGALLVIAANEPCPQP------QTREHLMALEIIGIKNIIIVQNKIDLVSRERA 158
Query: 478 --NYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
NY QI K+F + +N IPISA + NI
Sbjct: 159 LENYEQI---------KEFVKGTVAENAPIIPISAQHKANI 190
>gnl|CDD|239664 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. 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.
Length = 91
Score = 59.9 bits (146), Expect = 4e-11
Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 6/85 (7%)
Query: 547 KPLRFPVQLVARHCGHISKDFRGYMGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSL 606
KPLR P+Q V + I +GR+E+G++K + P+G +K ++M ++ L
Sbjct: 3 KPLRLPIQDVYK----IGGIGTVPVGRVETGVLKPGMVVTFAPAGVTGEVKSVEMHHEPL 58
Query: 607 DMAITGQSVTLIIK--EYLDISRGN 629
+ A+ G +V +K DI RG+
Sbjct: 59 EEALPGDNVGFNVKNVSKKDIKRGD 83
>gnl|CDD|235609 PRK05787, PRK05787, cobalt-precorrin-6Y C(5)-methyltransferase;
Validated.
Length = 210
Score = 63.0 bits (154), Expect = 5e-11
Identities = 53/224 (23%), Positives = 89/224 (39%), Gaps = 40/224 (17%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVV--------LYDALITNELLMLCPKAKHIFVGK 790
+YI+G GPG + +T++ +RKADVV L+ LI E +L
Sbjct: 2 IYIVGIGPGDPEYLTLKALEAIRKADVVVGSKRVLELFPELIDGEAFVL----------- 50
Query: 791 RFKKHSIAQYIINRIIVKCAFKYNLVVRLKGGDPML--FGRTDEELNALKKYNIKVKVIP 848
+ +++ K VV L GDP+ G+ + A+ + V+VIP
Sbjct: 51 TAGLRDLLEWLELAA------KGKNVVVLSTGDPLFSGLGKLLKVRRAVAE---DVEVIP 101
Query: 849 GITAALAAASESKQSLTKRNIS---RSVVLFTSSTMLKNNYLKNIPISDTLVEYMGGNNI 905
GI++ AA+ + + F L N K I + D
Sbjct: 102 GISSVQYAAARLGIDMNDVVFTTSHGRGPNFEELEDLLKNGRKVIMLPDP------RFGP 155
Query: 906 FLTAKKLLKLGFLPTTPVIVVENCSLSNQKITRLILLDLKKKIF 949
A +LL+ G ++V EN S +++I +L L +++ F
Sbjct: 156 KEIAAELLERG-KLERRIVVGENLSYPDERIHKLTLSEIEPLEF 198
>gnl|CDD|238652 cd01342, Translation_Factor_II_like, Translation_Factor_II_like:
Elongation factor Tu (EF-Tu) domain II-like proteins.
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
Score = 58.5 bits (142), Expect = 1e-10
Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 549 LRFPVQLVARHCGHISKDFRGYMGRIESGIIKKNDCLIVEP--SGKKATIKDIQMLNKSL 606
LR V V + GR+ESG +KK D + V P G K +K ++ +
Sbjct: 1 LRALVFKVFK----DKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFKGEV 56
Query: 607 DMAITGQSVTLIIKEYLDISRGNMLVS 633
D A+ G V +++K+ DI G+ L
Sbjct: 57 DEAVAGDIVGIVLKDKDDIKIGDTLTD 83
>gnl|CDD|237509 PRK13794, PRK13794, hypothetical protein; Provisional.
Length = 479
Score = 63.9 bits (156), Expect = 2e-10
Identities = 57/204 (27%), Positives = 90/204 (44%), Gaps = 32/204 (15%)
Query: 15 NNLYLDWLESEAIHIMREVSAECNNPVLL-FSGGKDSVVLLRLAEKAFRPSRFPFPMVHI 73
N LD E +I +R + + N PV + +SGGKDS+ L LA KA FP++
Sbjct: 224 NKNVLDKYERNSIGFIRNTAEKINKPVTVAYSGGKDSLATLLLALKAL---GINFPVLFN 280
Query: 74 DTGHNFPEVISFRDNCISKLGETLIVRSVEDSIMKGTVRLRKPNTDSRNAAQSITLL--- 130
DTG FPE + ++ + K I+R+ + + P D+R ++ L
Sbjct: 281 DTGLEFPETLENVED-VEKHYGLEIIRTKSEEFWEKLEEYGPPARDNRWCSEVCKLEPLG 339
Query: 131 ETIKEFKFDACIG--GARRDEEKARAKERIFSFRDKFGQWNPKSQRPELWNLYNTRVHPG 188
+ I E C+ G R+ E SF +S++P +W N +
Sbjct: 340 KLIDEKYEGECLSFVGQRKYE----------SFN--------RSKKPRIWR--NPYIK-- 377
Query: 189 ENIRVFPISNWTELDIWQYIEREK 212
+ I PI +WT + +W Y+ REK
Sbjct: 378 KQILAAPILHWTAMHVWIYLFREK 401
>gnl|CDD|223942 COG1010, CobJ, Precorrin-3B methylase [Coenzyme metabolism].
Length = 249
Score = 61.5 bits (150), Expect = 3e-10
Identities = 40/124 (32%), Positives = 65/124 (52%), Gaps = 12/124 (9%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVL-YDALITNELLMLCPKAKHIFVGKRFKKHSI 797
+Y++G GPG +L+T R L +ADV++ Y + +L+ L P + I G R ++
Sbjct: 5 LYVVGIGPGDPELMTPEARRALEEADVIVGYTTYL--DLIELRPGKEVIRSGMR-EEIER 61
Query: 798 AQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTD---EELNALKKYNIKVKVIPGITAAL 854
A+ I A + V + GDP ++G E Y++ V+V+PG+TAAL
Sbjct: 62 AKEAIEL-----AAEGRDVALVSSGDPGVYGMAGLVLEAAEEEGWYDVDVEVVPGVTAAL 116
Query: 855 AAAS 858
AAA+
Sbjct: 117 AAAA 120
>gnl|CDD|225150 COG2241, CobL, Precorrin-6B methylase 1 [Coenzyme metabolism].
Length = 210
Score = 60.3 bits (147), Expect = 4e-10
Identities = 47/231 (20%), Positives = 77/231 (33%), Gaps = 56/231 (24%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVV--------LYDALITNELLMLCPKAKHIFVGK 790
+ ++G GPG + +T+ +R+ADVV L LI E ++
Sbjct: 2 ITVVGIGPGGPEGLTLAAIEAIRRADVVAGSKRHLELLPPLIKAERIIWPYPFDAE---- 57
Query: 791 RFKKHSIAQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIK--VKVIP 848
I R VV L GDP+ G L++ V++IP
Sbjct: 58 --SLEEILAERKGR----------DVVVLASGDPLFSGV----GRLLRRKFSCEEVEIIP 101
Query: 849 GITAALAAASESKQSLTKRNISRSVVLFTSSTMLKNNYLKNIPISDTLVEYMGGNNIFL- 907
GI++ AA+ L S L+ + G + +
Sbjct: 102 GISSVQLAAARLGWPLQD-------TEVISLHGRPVELLRPL--------LENGRRLVIL 146
Query: 908 ---------TAKKLLKLGFLPTTPVIVVENCSLSNQKITRLILLDLKKKIF 949
AK L + G + V V+EN +++IT D+ + F
Sbjct: 147 TPDDFGPAEIAKLLTENGI-GDSRVTVLENLGYPDERITDGTAEDIAAEEF 196
>gnl|CDD|239669 cd03698, eRF3_II_like, eRF3_II_like: domain similar to domain II of
the eukaryotic class II release factor (eRF3). 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-like protein with
the property of aggregating into polymer-like fibrils.
This group also contains proteins similar to S.
cerevisiae Hbs1, a G protein known to be important for
efficient growth and protein synthesis under conditions
of limiting translation initiation and, to associate
with Dom34. It has been speculated that yeast Hbs1 and
Dom34 proteins may function as part of a complex with a
role in gene expression.
Length = 83
Score = 56.8 bits (138), Expect = 4e-10
Identities = 31/90 (34%), Positives = 49/90 (54%), Gaps = 11/90 (12%)
Query: 548 PLRFPVQLVARHCGHISKDFRGY--MGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKS 605
P R P+ KD G G++ESG I+K D L+V PS + +K I + ++
Sbjct: 1 PFRLPIS-------DKYKDQGGTVVSGKVESGSIQKGDTLLVMPSKESVEVKSIYVDDEE 53
Query: 606 LDMAITGQSVTLIIK--EYLDISRGNMLVS 633
+D A+ G++V L +K + DIS G++L S
Sbjct: 54 VDYAVAGENVRLKLKGIDEEDISPGDVLCS 83
>gnl|CDD|212510 cd11724, TP_methylase_like, Uncharacterized subfamily of S-AdoMet
dependent tetrapyrrole methylases. TP-methylases use
S-AdoMet (S-adenosyl-L-methionine or SAM) in the
methylation of diverse substrates. Most members catalyze
various methylation steps in cobalamin (vitamin B12)
biosynthesis, other members like Diphthine synthase and
Ribosomal RNA small subunit methyltransferase I (RsmI)
act on other substrates. The function of this subfamily
is not known.
Length = 255
Score = 60.8 bits (148), Expect = 5e-10
Identities = 60/253 (23%), Positives = 105/253 (41%), Gaps = 41/253 (16%)
Query: 740 YIIGAGPGAADLITVRGARLLRKADVVL--------YDALITN--------ELLMLCPKA 783
Y++G GPG D IT+R ++ KAD++ + + +L
Sbjct: 4 YLVGVGPGDPDNITLRALEVIAKADIIFCPKEIVKRFADYLKGKPVLEDPWKLFWHYGGK 63
Query: 784 KH------IFVGKRFKKHSIAQY--IINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELN 835
+ F++ Q + I A N V L GGDP ++G + +
Sbjct: 64 PWENLEAEKSPREAFEEEKKRQREEFVKVIREALAQGKN-VALLDGGDPTIYGPSHWLME 122
Query: 836 ALKKYNIKVKVIPGI---TAALAAASESKQSLTKRNISRSVVLFTSSTMLKNNYLKNIP- 891
++ ++IPG+ AA AA K+S+T +RSV+L T+ L+ N +
Sbjct: 123 GFD--DLDPEIIPGVSCFNAANAAL---KRSITTGGDARSVIL-TAPYGLEENEDRLDAE 176
Query: 892 ----ISDTLVEYMGGNNIFLTAKKLLKLGFLPTTPVIVVENCSLSN-QKITRLILLDLKK 946
TLV +M + + K L K + P TPV +V + + +K+ R L + +
Sbjct: 177 DLAKYPATLVFFMMLSELPKLVKLLKKH-YPPDTPVAIVYHAGYPDKEKVVRGTLDTILE 235
Query: 947 KIFQFEKPVLFMI 959
K+ ++P +I
Sbjct: 236 KLKGEKEPFEGLI 248
>gnl|CDD|233424 TIGR01466, cobJ_cbiH, precorrin-3B C17-methyltransferase. This
model represents precorrin-3B C17-methyltransferase, one
of two methyltransferases commonly referred to as
precorrin-3 methylase (the other is precorrin-4
C11-methyltransferase, EC 2.1.1.133). This enzyme
participates in the pathway toward the biosynthesis of
cobalamin and related products. Members of this family
may appear as fusion proteins with other enzymes of
cobalamin biosynthesis [Biosynthesis of cofactors,
prosthetic groups, and carriers, Heme, porphyrin, and
cobalamin].
Length = 239
Score = 60.0 bits (146), Expect = 8e-10
Identities = 39/128 (30%), Positives = 57/128 (44%), Gaps = 20/128 (15%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVV----LYDALITNELLMLCPKAKHIFVGKRFKK 794
+Y++G GPGA +L+T L +ADV+ Y LI + + GK
Sbjct: 1 LYVVGIGPGAEELMTPEAKEALAEADVIVGYKTYLDLI-----------EDLIPGKEVVT 49
Query: 795 HSIAQYI--INRIIVKCAFKYNLVVRLKGGDPMLFGRTDE--ELNALKKYNIKVKVIPGI 850
+ + I I A + V + GDP ++G E K + ++VIPGI
Sbjct: 50 SGMREEIARAELAIEL-AAEGRTVALVSSGDPGIYGMAALVFEALEKKGAEVDIEVIPGI 108
Query: 851 TAALAAAS 858
TAA AAAS
Sbjct: 109 TAASAAAS 116
>gnl|CDD|212503 cd11644, Precorrin-6Y-methylase, Precorrin-6Y methyltransferase,
the cobalamin biosynthesis enzyme CbiE. Precorrin-6Y
methyltransferase participates in the pathway toward the
biosynthesis of cobalamin (vitamin B12). There are two
distinct cobalamin biosynthetic pathways in bacteria.
The aerobic pathway requires oxygen, and cobalt is
inserted late in the pathway; the anaerobic pathway does
not requires oxygen, and cobalt insertion is the first
committed step towards cobalamin synthesis. This model
represents the CbiE subunit of precorrin-6Y
C5,15-methyltransferase from the anaerobic pathway, a
bifunctional enzyme that catalyzes two methylations (at
C-5 and C-15) in precorrin-6Y, as well as the
decarboxylation of the acetate side chain located in
ring C, in order to generate precorrin-8X. In the
anaerobic pathway, two enzymes are required to produce
precorrin-8X: CbiE and CbiT, which can be fused as CbiET
(sometimes called CobL). In the aerobic pathway, the
bifunctional enzyme is called CobL.
Length = 201
Score = 58.7 bits (143), Expect = 1e-09
Identities = 45/227 (19%), Positives = 83/227 (36%), Gaps = 51/227 (22%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCPKAKHIFVGKR----FKK 794
+ ++G GPG D +T + +ADV + GKR F
Sbjct: 1 ITVVGIGPGGPDGLTPAAREAIEEADV--------------------LVGGKRHLELFPD 40
Query: 795 HSIAQYIIN-----RIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKY--NIKVKVI 847
+ + ++ + A VV L GDP+ +G L + +V+VI
Sbjct: 41 LGAEKIPLPSDDLAELLERLAAAGRRVVVLASGDPLFYGI----GATLARRLGAEEVEVI 96
Query: 848 PGITAALAAASESKQSLTK-RNIS---RSVVLFTSSTMLKNNYLKNIPI-SDTLVEYMGG 902
PGI++ A + +S R + L+ + + + +D
Sbjct: 97 PGISSVQLAFARLGWPWQDAAVVSLHGRDLEELLR--ALRPG--RKVAVLTD------DE 146
Query: 903 NNIFLTAKKLLKLGFLPTTPVIVVENCSLSNQKITRLILLDLKKKIF 949
N A+ LL+ G + + V EN +++IT+ +L ++ F
Sbjct: 147 NTPAEIARLLLERGLGDSR-LTVGENLGYPDERITKGTAEELAEEDF 192
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. 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 eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 58.5 bits (142), Expect = 1e-09
Identities = 42/154 (27%), Positives = 67/154 (43%), Gaps = 32/154 (20%)
Query: 380 DGLESEREQGITIDVAYRYFNTPKRK--------------FIIADTPGHEQYTRNMITGA 425
D +E+GIT+D+ + F K K + D PGH R +I GA
Sbjct: 30 DKNPQSQERGITLDLGFSSFEVDKPKHLEDNENPQIENYQITLVDCPGHASLIRTIIGGA 89
Query: 426 STADAVIILIDASK-IKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQI-- 482
D +++++DA K I+ TQT +I LL +I+ +NK+DLI +
Sbjct: 90 QIIDLMLLVVDAKKGIQ--------TQTAECLVIGELLCKP-LIVVLNKIDLIPEEERKR 140
Query: 483 ---FYKRIVYAYKKFAEDIHFQNINTIPISALNG 513
K+ + +K E ++ IP+SA G
Sbjct: 141 KIEKMKKRL---QKTLEKTRLKDSPIIPVSAKPG 171
>gnl|CDD|235597 PRK05765, PRK05765, precorrin-3B C17-methyltransferase;
Provisional.
Length = 246
Score = 59.0 bits (143), Expect = 2e-09
Identities = 34/127 (26%), Positives = 61/127 (48%), Gaps = 18/127 (14%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVL----YDALITNELLMLCPKAKHIFVGKRFKK 794
+YI+G GPG+ + T++ + K++V++ Y LI + GK
Sbjct: 4 LYIVGIGPGSKEQRTIKAQEAIEKSNVIIGYNTYLRLI-----------SDLLDGKEVIG 52
Query: 795 HSIAQYIIN-RIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKV--KVIPGIT 851
+ + I ++ A + N+V + GDP ++G + + + V +VIPG+T
Sbjct: 53 ARMKEEIFRANTAIEKALEGNIVALVSSGDPQVYGMAGLVFELISRRKLDVDVEVIPGVT 112
Query: 852 AALAAAS 858
AALAAA+
Sbjct: 113 AALAAAA 119
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 60.4 bits (147), Expect = 3e-09
Identities = 39/123 (31%), Positives = 55/123 (44%), Gaps = 22/123 (17%)
Query: 401 TPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAH 460
T KR D PGH+ M+ GA+ DA ++LI A++ P QT H
Sbjct: 114 TLKRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAANESCPQP------QTSEHLAAVE 167
Query: 461 LLRIKHIIIAVNKMDLI-------NYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNG 513
++++KHIII NK+DL+ Y +I + F + N IPISA
Sbjct: 168 IMKLKHIIILQNKIDLVKEAQAQDQYEEI---------RNFVKGTIADNAPIIPISAQLK 218
Query: 514 DNI 516
NI
Sbjct: 219 YNI 221
>gnl|CDD|212505 cd11646, Precorrin_3B_C17_MT, Precorrin-3B C(17)-methyltransferase
(CobJ/CbiH). Precorrin-3B C(17)-methyltransferase
participates in the pathway toward the biosynthesis of
cobalamin (vitamin B12). There are two distinct
cobalamin biosynthetic pathways. The aerobic pathway
requires oxygen, and cobalt is inserted late in the
pathway; the anaerobic pathway does not require oxygen,
and cobalt insertion is the first committed step towards
cobalamin synthesis. This model includes CobJ of the
aerobic pathway and CbiH of the anaerobic pathway, both
as stand-alone enzymes and when CobJ forms part of a
bifunctional enzyme. In the aerobic pathway, once CobG
has generated precorrin-3b, CobJ catalyzes the
methylation of precorrin-3b at C-17 to form precorrin-4
(the extruded methylated C-20 fragment is left attached
as an acyl group at C-1). In the corresponding anaerobic
pathway, CbiH carries out this ring contraction, using
cobalt-precorrin-3b as a substrate to generate a
tetramethylated delta-lactone.
Length = 240
Score = 58.2 bits (142), Expect = 3e-09
Identities = 39/130 (30%), Positives = 62/130 (47%), Gaps = 24/130 (18%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVV----LYDALITNELLMLCPKAKHIFVGKRFKK 794
+Y++G GPG DL+T R + +ADVV Y LI + + GK
Sbjct: 3 LYVVGIGPGDPDLMTPRAREAIEEADVVVGYKTYLDLI-----------EDLLEGKEVIS 51
Query: 795 HSIAQYIINRIIVKCAFKYNL----VVRLKGGDPMLFGRTDE--ELNALKKYNIKVKVIP 848
+ + + R + A + V + GDP ++G EL + +++V+VIP
Sbjct: 52 SGMGEEV-ER--ARLAVELAREGKTVALVSSGDPGVYGMAGLVLELAEKEGDDVEVEVIP 108
Query: 849 GITAALAAAS 858
G+TAALAAA+
Sbjct: 109 GVTAALAAAA 118
>gnl|CDD|233878 TIGR02467, CbiE, precorrin-6y C5,15-methyltransferase
(decarboxylating), CbiE subunit. This model recognizes
the CbiE methylase which is responsible, in part (along
with CbiT), for methylating precorrin-6y (or
cobalt-precorrin-6y) at both the 5 and 15 positions as
well as the concomitant decarbozylation at C-12. In many
organisms, this protein is fused to the CbiT subunit.
The fused protein, when found in organisms catalyzing
the oxidative version of the cobalamin biosynthesis
pathway, is called CobL.
Length = 204
Score = 57.7 bits (140), Expect = 3e-09
Identities = 52/232 (22%), Positives = 91/232 (39%), Gaps = 45/232 (19%)
Query: 741 IIGAGPGAADLITVRGARLLRKADVV--------LYDALITNELLMLCPKAKHIFVGKRF 792
++G GPG +L+T +RKAD+V L LI K + I K
Sbjct: 1 VVGIGPGGPELLTPAAIEAIRKADLVVGGERHLELLAELIG-------EKREIILTYKDL 53
Query: 793 KKHSIAQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNALKKYNIKVKVIPGITA 852
+ + ++I K +VV L GDP+ +G L K + ++IPGI++
Sbjct: 54 DE--LLEFIAATRKEK-----RVVV-LASGDPLFYGIGRTLAERLGKERL--EIIPGISS 103
Query: 853 ALAAASESK--------QSLTKRNISRSVVLFTSSTMLKNNYLKNIPISDTLVEYMGGNN 904
A + SL R + ++ L + K ++D N
Sbjct: 104 VQYAFARLGLPWQDAVVISLHGRELDELLLA------LLRGHRKVAVLTD------PRNG 151
Query: 905 IFLTAKKLLKLGFLPTTPVIVVENCSLSNQKITRLILLDLKKKIFQFEKPVL 956
A++L++LG + + V EN +++IT L ++ F F ++
Sbjct: 152 PAEIARELIELGIGGSYELTVGENLGYEDERITEGTLEEIAAAQFDFSPLLV 203
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. 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.
Length = 169
Score = 56.3 bits (137), Expect = 4e-09
Identities = 35/116 (30%), Positives = 52/116 (44%), Gaps = 18/116 (15%)
Query: 406 FIIADTPGHEQYTRNMIT-GASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRI 464
FI DTPGHE +T NM GAS D I+++ A ++ QT I H
Sbjct: 53 FI--DTPGHEAFT-NMRARGASVTDIAILVVAADD-------GVMPQT--IEAINHAKAA 100
Query: 465 K-HIIIAVNKMDLINYNQIF---YKRIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
II+A+NK+D + K + E+ +++ +PISA G+ I
Sbjct: 101 NVPIIVAINKIDKPYGTEADPERVKNELSELGLVGEEWG-GDVSIVPISAKTGEGI 155
>gnl|CDD|129526 TIGR00434, cysH, phosophoadenylyl-sulfate reductase (thioredoxin).
This enzyme, involved in the assimilation of inorganic
sulfate, is designated cysH in Bacteria and MET16 in
Saccharomyces cerevisiae. Synonyms include
phosphoadenosine phosphosulfate reductase, PAPS
reductase, and PAPS reductase, thioredoxin-dependent. In
a reaction requiring reduced thioredoxin and NADPH, it
converts 3(prime)-phosphoadenylylsulfate (PAPS) to
sulfite and adenosine 3(prime),5(prime) diphosphate
(PAP). A related family of plant enzymes, scoring below
the trusted cutoff, differs in having a thioredoxin-like
C-terminal domain, not requiring thioredoxin, and in
having a preference for 5(prime)-adenylylsulfate (APS)
over PAPS [Central intermediary metabolism, Sulfur
metabolism].
Length = 212
Score = 55.2 bits (133), Expect = 2e-08
Identities = 42/175 (24%), Positives = 71/175 (40%), Gaps = 32/175 (18%)
Query: 41 VLLFSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTGHNFPEVISFRDNCISKLGETLIVR 100
V S G VLL L K P P++ +DTG++FPE D + + V
Sbjct: 17 VYSTSFGIQGAVLLDLVSK-ISPD---IPVIFLDTGYHFPETYELIDELTERYPLNIKVY 72
Query: 101 ----SVEDSIMKGTVRLRKPNTDSRNAAQSIT-LLETIKEFKFDACIGGARRDEEKARAK 155
S+ + K +L + + + + + + + +KE A G RRD+ +RA
Sbjct: 73 KPDLSLAEQAAKYGDKLWEQDPNKYDYLRKVEPMHRALKELHASAWFTGLRRDQGPSRAN 132
Query: 156 ERIFSFRDKFGQWNPKSQRPELWNLYNTRVHPGENIRVFPISNWTELDIWQYIER 210
I + +KFG ++V P+ +WT D++QYI+
Sbjct: 133 LSILNIDEKFGI-----------------------LKVLPLIDWTWKDVYQYIDA 164
>gnl|CDD|217388 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2. 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
Score = 49.9 bits (120), Expect = 7e-08
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 572 GRIESGIIKKNDCLIVEPS--GKKATIKDIQMLNKSLDMAITGQSVTLI--IKEYLDISR 627
GR+ESG +KK D +++ P+ GKK + ++M + L A+ G + +I DI R
Sbjct: 6 GRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGLKDIKR 65
Query: 628 GNMLV 632
G+ L
Sbjct: 66 GDTLT 70
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. 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.
Length = 168
Score = 52.8 bits (128), Expect = 7e-08
Identities = 43/195 (22%), Positives = 69/195 (35%), Gaps = 66/195 (33%)
Query: 336 GKSTLIGRLLFDSKNIFIDQLDAVSR----TKYKRVMSGHNIDLSLLTDGLESEREQGIT 391
GKSTL+ L+ K I I VS T+ + I +GI
Sbjct: 15 GKSTLLNALV-GQK-ISI-----VSPKPQTTR-------NRI--------------RGI- 45
Query: 392 IDVAYRYFNTPKRKFIIADTPG-HEQYTRNM-------ITGASTADAVIILIDASKIKFN 443
+ + I DTPG H+ + + D V+ ++DAS+
Sbjct: 46 -------YTDDDAQIIFVDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASE---- 94
Query: 444 PSVNLLTQTKRHSIIAHLLRIKH--IIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQ 501
+ I LL+ +I+ +NK+DL+ + + + F
Sbjct: 95 ------WIGEGDEFILELLKKSKTPVILVLNKIDLVKDKEDLLPLLEKLKELHP----FA 144
Query: 502 NINTIPISALNGDNI 516
I PISAL G+N+
Sbjct: 145 EI--FPISALKGENV 157
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 52.4 bits (126), Expect = 8e-08
Identities = 50/203 (24%), Positives = 72/203 (35%), Gaps = 58/203 (28%)
Query: 331 GSVDDGKSTLIGRLLFDSKNIFIDQLDA-VSRTKYKRVMSGHNIDLSLLTDGLESEREQG 389
G + GKSTL+ RLL + I I + +R E G
Sbjct: 8 GDPNVGKSTLLNRLLGNK--ISITEYKPGTTRN-----------------YVTTVIEEDG 48
Query: 390 ITIDVAYRYFNTPKRKFIIADTPGHE-------QYTRNMITGASTADAVIILIDASKIKF 442
T KF + DT G E Y R + + D VI+++D +I
Sbjct: 49 KTY------------KFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEI-- 94
Query: 443 NPSVNLLTQTKRHSIIAHLLRIK-HIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQ 501
L QTK I H II+ NK+DL + ++ ++ +
Sbjct: 95 -----LEKQTK---EIIHHAESGVPIILVGNKIDLRD------AKLKTHVAFLFAKLNGE 140
Query: 502 NINTIPISALNGDNIISASNNML 524
I IP+SA G NI SA +
Sbjct: 141 PI--IPLSAETGKNIDSAFKIVE 161
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 55.7 bits (135), Expect = 8e-08
Identities = 40/150 (26%), Positives = 61/150 (40%), Gaps = 33/150 (22%)
Query: 331 GSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGI 390
+D GK+TL R+LF + I K V G + TD + E+E+GI
Sbjct: 15 AHIDAGKTTLTERILFYTGKI----------HKMGEVEDGTTV-----TDWMPQEQERGI 59
Query: 391 TIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLLT 450
TI+ A + + + DTPGH +T + D +++ DA V T
Sbjct: 60 TIESAATSCDWDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDA-----VTGVQPQT 114
Query: 451 QT-----KRHSIIAHLLRIKHIIIAVNKMD 475
+T R+ I +I +NKMD
Sbjct: 115 ETVWRQADRYGIP--------RLIFINKMD 136
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 54.8 bits (132), Expect = 1e-07
Identities = 93/417 (22%), Positives = 172/417 (41%), Gaps = 73/417 (17%)
Query: 268 LSNATTVE--DIIKEISVTQITERGATRIDDQNSE------ASMEKRKKTEAPEKKQSVF 319
LS+ VE ++++E++ E GA+ + E A + R+KTE + V
Sbjct: 66 LSDEKLVESIEVLRELA----REVGASIYIVRVHEGTDGYVAEVLVRRKTEEAPEHVLV- 120
Query: 320 KKHSLLRFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKR----VMSGHNIDL 375
AG VD GKSTL+G L+ +D D +R+ V G + D+
Sbjct: 121 --------GVAGHVDHGKSTLVGVLVTGR----LDDGDGATRSYLDVQKHEVERGLSADI 168
Query: 376 SLLTDGLESEREQGIT--IDVA--YRYFNTPKRKFIIADTPGHEQYTRNMITG--ASTAD 429
SL G + + + +D A + DT GHE + R I G D
Sbjct: 169 SLRVYGFDDGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQKVD 228
Query: 430 AVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVY 489
++++ A + TK H IA + + +I+ V K+D++ ++
Sbjct: 229 YGLLVVAADD-------GVTKMTKEHLGIALAMELP-VIVVVTKIDMVPDDRF------- 273
Query: 490 AYKKFAEDIH--FQNINTIPISALNGDNIISASNNMLWYNG--PTLISLLESLNTNEKID 545
+ E+I + + IP+ + D+++ A+ M G P + + + +D
Sbjct: 274 --QGVVEEISALLKRVGRIPLIVKDTDDVVLAAKAMKAGRGVVPIFYTSSVTGEGLDLLD 331
Query: 546 KKPLRFPVQLVARHCG----HISKDF--RGY----MGRIESGIIKKNDCLIVEP----SG 591
+ L P + G +I K + G G ++SGI+ D +++ P
Sbjct: 332 EFFLLLPKRRRWDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTVLLGPFKDGKF 391
Query: 592 KKATIKDIQMLNKSLDMAITGQSVTLIIK--EYLDISRGNMLVSPFKRPVSLRSINA 646
++ +K I+M + +D A G + + +K E ++ RG M++S P ++R +A
Sbjct: 392 REVVVKSIEMHHYRVDSAKAGSIIGIALKGVEKEELERG-MVLSAGADPKAVREFDA 447
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 54.7 bits (132), Expect = 2e-07
Identities = 40/154 (25%), Positives = 66/154 (42%), Gaps = 42/154 (27%)
Query: 327 FITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESER 386
TAG VD GK+TL+ + ++G N D L E+
Sbjct: 3 IATAGHVDHGKTTLL------------------------QAITGVN------ADRLPEEK 32
Query: 387 EQGITIDVAYRYFNTPKRK---FIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFN 443
++G+TID+ Y Y+ P + FI D PGHE++ NM+ G D ++++
Sbjct: 33 KRGMTIDLGYAYWPQPDGRVLGFI--DVPGHEKFLSNMLAGVGGIDHALLVVACDD---- 86
Query: 444 PSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLI 477
++ QT+ H I L + +A+ K D +
Sbjct: 87 ---GVMAQTREHLAILQLTGNPMLTVALTKADRV 117
>gnl|CDD|235231 PRK04160, PRK04160, diphthine synthase; Provisional.
Length = 258
Score = 52.9 bits (128), Expect = 2e-07
Identities = 40/130 (30%), Positives = 57/130 (43%), Gaps = 22/130 (16%)
Query: 740 YIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCPKAKHIFVGKRFKK----- 794
Y IG G IT++G LR AD V + T+ L+ + +GK
Sbjct: 3 YFIGLGLYDERDITLKGLEALRNADKVYAEFY-TSILMGTTIEKLEELIGKEIIVLDRED 61
Query: 795 ---HSIAQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRT---DEELNALKKYNIKVKVIP 848
S +II++ A + N V L GDPM+ T D L A K+ I+V+VI
Sbjct: 62 VEQESE------KIILEEAKEKN-VAFLTAGDPMV--ATTHVDLRLEAKKR-GIEVRVIH 111
Query: 849 GITAALAAAS 858
G++ AA S
Sbjct: 112 GVSIYSAAIS 121
>gnl|CDD|206731 cd04168, TetM_like, Tet(M)-like family includes Tet(M), Tet(O),
Tet(W), and OtrA, containing tetracycline resistant
proteins. 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.
Length = 237
Score = 52.6 bits (127), Expect = 2e-07
Identities = 48/155 (30%), Positives = 68/155 (43%), Gaps = 29/155 (18%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITI 392
VD GK+TL LL+ S I + V G TD +E ER++GITI
Sbjct: 8 VDAGKTTLTESLLYTSGAI----------RELGSVDKGTTR-----TDSMELERQRGITI 52
Query: 393 DVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLLTQT 452
A F K I DTPGH + + S D I++I A + + QT
Sbjct: 53 FSAVASFQWEDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVE-------GVQAQT 105
Query: 453 KRHSIIAHLLRIKHI--IIAVNKMDL--INYNQIF 483
+ I+ LLR +I II VNK+D + +++
Sbjct: 106 R---ILFRLLRKLNIPTIIFVNKIDRAGADLEKVY 137
>gnl|CDD|131112 TIGR02057, PAPS_reductase, phosphoadenosine phosphosulfate
reductase, thioredoxin dependent. Requiring thioredoxin
as an electron donor, phosphoadenosine phosphosulfate
reductase catalyzes the reduction of
3'-phosphoadenylylsulfate (PAPS) to sulfite and
phospho-adenosine-phosphate (PAP). Found in
enterobacteria, cyanobacteria, and yeast, PAPS reductase
is related to a group of plant (TIGR00424) and bacterial
(TIGR02055) enzymes preferring 5'-adenylylsulfate (APS)
over PAPS as a substrate for reduction to sulfite
[Central intermediary metabolism, Sulfur metabolism].
Length = 226
Score = 51.8 bits (124), Expect = 4e-07
Identities = 37/181 (20%), Positives = 71/181 (39%), Gaps = 33/181 (18%)
Query: 41 VLLFSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTGHNFPEVISFRDNCISKLGETLIVR 100
V + G ++V L L P P++ IDT ++FP+ ++ +D K +TL +
Sbjct: 29 VQTSAFGIQALVTLHLLSSISEP---MIPVIFIDTLYHFPQTLTLKDELTKKYYQTLNLY 85
Query: 101 ------SVEDSIMKGTVRLRKPNTDSRNAAQSITLLE-TIKEFKFDACIGGARRDEEKAR 153
S D K L + + + + + ++ +KE A G RRD+ AR
Sbjct: 86 KYDGCESEADFEAKYGKLLWQKDIEKYDYIAKVEPMQRALKELNASAWFTGRRRDQGSAR 145
Query: 154 AKERIFSFRDKFGQWNPKSQRPELWNLYNTRVHPGENIRVFPISNWTELDIWQYIEREKI 213
A + ++ G ++V P+ +WT ++QY++ +
Sbjct: 146 ANLPVIEIDEQNGI-----------------------LKVNPLIDWTFEQVYQYLDAHNV 182
Query: 214 I 214
Sbjct: 183 P 183
>gnl|CDD|224711 COG1798, DPH5, Diphthamide biosynthesis methyltransferase
[Translation, ribosomal structure and biogenesis].
Length = 260
Score = 52.3 bits (126), Expect = 4e-07
Identities = 37/142 (26%), Positives = 59/142 (41%), Gaps = 5/142 (3%)
Query: 740 YIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCPKAKHIFVGKRFKKHSIAQ 799
Y++G G IT++G +RKAD V + T+ LL + +GK
Sbjct: 3 YLVGLGLYDEGDITLKGLEAVRKADRVYAEFY-TSILLGSNLEKLEELIGKEVILLDRED 61
Query: 800 YIIN-RIIVKCAFKYNLVVRLKGGDPMLFGRTDEELNAL-KKYNIKVKVIPGITAALAAA 857
N R I+ A + V L GDPM T +L K+ I+V+VI G + AA
Sbjct: 62 LEENSRSILDRAKDKD-VALLVAGDPM-VATTHVDLRIEAKRRGIEVRVIHGASIINAAI 119
Query: 858 SESKQSLTKRNISRSVVLFTSS 879
+ K + ++ + +
Sbjct: 120 GLTGLQNYKFGKTVTLPFPSEN 141
>gnl|CDD|239668 cd03697, EFTU_II, EFTU_II: Elongation factor Tu domain II.
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 affinity for GDP than for GTP.
Length = 87
Score = 48.3 bits (116), Expect = 4e-07
Identities = 27/72 (37%), Positives = 37/72 (51%), Gaps = 12/72 (16%)
Query: 571 MGRIESGIIKKNDCLIVEPSG----KKATIKDIQMLNKSLDMAITGQSVTLII----KEY 622
GRIE G IK D VE G K T+ I+M K+LD A G +V +++ +E
Sbjct: 19 TGRIERGTIKVGD--EVEIVGFGETLKTTVTGIEMFRKTLDEAEAGDNVGVLLRGVKRE- 75
Query: 623 LDISRGNMLVSP 634
D+ RG +L P
Sbjct: 76 -DVERGMVLAKP 86
>gnl|CDD|206678 cd01891, TypA_BipA, Tyrosine phosphorylated protein A (TypA)/BipA
family belongs to ribosome-binding GTPases. 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.
coli has been shown to be phosphorylated on a tyrosine
residue, while BipA from Salmonella and from E. coli K12
strains is not phosphorylated under the conditions
assayed. The phosphorylation apparently modifies the
rate of nucleotide hydrolysis, with the phosphorylated
form showing greatly increased GTPase activity.
Length = 194
Score = 51.1 bits (123), Expect = 4e-07
Identities = 46/149 (30%), Positives = 71/149 (47%), Gaps = 37/149 (24%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITI 392
VD GK+TL+ LL S F + + +RVM +++ ERE+GITI
Sbjct: 11 VDHGKTTLVDALLKQSG-TFRE-----NEEVGERVMDSNDL-----------ERERGITI 53
Query: 393 ---DVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLL 449
+ A Y +T K I DTPGH + + S D V++L+DAS+ P +
Sbjct: 54 LAKNTAITYKDT---KINIIDTPGHADFGGEVERVLSMVDGVLLLVDASE---GP----M 103
Query: 450 TQTK---RHSIIAHLLRIKHIIIAVNKMD 475
QT+ + ++ A L I+ +NK+D
Sbjct: 104 PQTRFVLKKALEAGLK----PIVVINKID 128
>gnl|CDD|212506 cd11647, Diphthine_synthase, Diphthine synthase, also known as
DPH5. Diphthine synthase, also known as diphthamide
biosynthesis S-adenosylmethionine-dependent
methyltransferase, participates in the posttranslational
modification of a specific histidine residue in
elongation factor 2 (EF-2) of eukaryotes and archaea to
diphthamide. It catalyzes the trimethylation step in
diphthamide biosynthesis. Diphthamide is the target of
diphtheria toxin, which ADP-ribosylates diphthamide and
inhibits protein synthesis, leading to host cell death.
Length = 241
Score = 51.7 bits (125), Expect = 4e-07
Identities = 37/132 (28%), Positives = 58/132 (43%), Gaps = 23/132 (17%)
Query: 740 YIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCPKAKHIFVGKRFKKHSIAQ 799
Y++G G G IT++G ++KAD V +A T+ L+ +A F GK
Sbjct: 3 YLVGLGLGDEKDITLKGLEAVKKADKVYLEAY-TSILMGGTLEALEEFYGKEII------ 55
Query: 800 YIINR--------IIVKCAFKYNLVVRLKGGDPMLFGRT---DEELNALKKYNIKVKVIP 848
+ +R I++ A + + V L GDP T D L A ++ I+V+VI
Sbjct: 56 -VADREDVEEESDEILEEAKEKD-VALLVVGDPF--IATTHSDLRLRAKER-GIEVRVIH 110
Query: 849 GITAALAAASES 860
+ A S S
Sbjct: 111 NASILNAVGSCS 122
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 53.4 bits (129), Expect = 4e-07
Identities = 45/203 (22%), Positives = 75/203 (36%), Gaps = 31/203 (15%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITI 392
+D GK+TL R+LF + I +K V G D +E E+E+GITI
Sbjct: 19 IDAGKTTLTERILFYTGII----------SKIGEVHDGAAT-----MDWMEQEQERGITI 63
Query: 393 DVAYRYFNT-PKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLLTQ 451
A + + DTPGH +T + D ++++DA V T+
Sbjct: 64 TSAATTLFWKGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDA-----VEGVEPQTE 118
Query: 452 TKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTIPISAL 511
T + + I+ VNKMD + + FY + ++ + + +PI A
Sbjct: 119 TVWRQADKY--GVPR-ILFVNKMDRLGAD--FYLVVEQLKERLGANPV--PVQ-LPIGAE 170
Query: 512 N--GDNIISASNNMLWYNGPTLI 532
I + +
Sbjct: 171 EEFEGVIDLVEMKAVAFGDGAKY 193
>gnl|CDD|181465 PRK08557, PRK08557, hypothetical protein; Provisional.
Length = 417
Score = 52.4 bits (126), Expect = 7e-07
Identities = 57/222 (25%), Positives = 85/222 (38%), Gaps = 51/222 (22%)
Query: 15 NNLYLDWLESEAIHIMREVSAECNNPVLL----FSGGKDSVVLLRLAEKAFRPSRFPFPM 70
N ++ LE ++ I+++ + N FSGGKDS V LA++ +
Sbjct: 155 NKERIEKLEENSLSILKDYIEKYKNKGYAINASFSGGKDSSVSTLLAKEVIP----DLEV 210
Query: 71 VHIDTGHNFPEVISFRDNCISKLGETLIV---RSVEDSIMKGTVRLRKPNTDSRNAAQSI 127
+ IDTG +PE I++ + K L + +++ K + P D+R S
Sbjct: 211 IFIDTGLEYPETINYVKDFAKKYDLNLDTLDGDNFWENLEKEGI----PTKDNR-WCNSA 265
Query: 128 TLLETIKEF-------KFDACIGGARRDEEKARAK---ERIFSFRDKFGQWNPKSQRPEL 177
L +KE+ K I G+R+ E RA ER F D
Sbjct: 266 CKLMPLKEYLKKKYGNKKVLTIDGSRKYESFTRANLDYERKSGFIDF------------- 312
Query: 178 WNLYNTRVHPGENIRVFPISNWTELDIWQYIEREKIILPSLY 219
VFPI +W LDIW YI I+ LY
Sbjct: 313 ------------QTNVFPILDWNSLDIWSYIYLNDILYNPLY 342
>gnl|CDD|234997 PRK02090, PRK02090, phosphoadenosine phosphosulfate reductase;
Provisional.
Length = 241
Score = 51.0 bits (123), Expect = 8e-07
Identities = 41/189 (21%), Positives = 63/189 (33%), Gaps = 56/189 (29%)
Query: 38 NNPVLLFSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTGHNFPEVISFRDNCISKLGETL 97
L+ S G + VLL L + P P++ +DTG+ FPE F D +L L
Sbjct: 41 GRLALVSSFGAEDAVLLHLVAQV-DPD---IPVIFLDTGYLFPETYRFIDELTERLLLNL 96
Query: 98 IVRSVEDSIMKGTVRLRKPNTDSRNAAQSITLLE-------------TIKEFKFDACIGG 144
V + S + R QS+ + + DA I G
Sbjct: 97 KVYRPDASAAEQEARYGGLW------EQSVEDRDECCRIRKVEPLNRALAG--LDAWITG 148
Query: 145 ARRDEEKARAKERIFSF---RDKFGQWNPKSQRPELWNLYNTRVHPGENIRVFPISNWTE 201
RR++ RA + R K N P+++WT
Sbjct: 149 LRREQSGTRANLPVLEIDGGRFKI---N-------------------------PLADWTN 180
Query: 202 LDIWQYIER 210
D+W Y++
Sbjct: 181 EDVWAYLKE 189
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 50.8 bits (123), Expect = 1e-06
Identities = 34/126 (26%), Positives = 58/126 (46%), Gaps = 24/126 (19%)
Query: 400 NTPKRKFIIADTPG-HEQYT---RNMITGASTA----DAVIILIDASKIKFNPSVNLLTQ 451
+ I DTPG H+ R M A ++ D V+ ++DA + K P
Sbjct: 49 TEDDAQIIFVDTPGIHKPKRALNRAMNKAAWSSLKDVDLVLFVVDADE-KIGPGDEF--- 104
Query: 452 TKRHSIIAHLLRIKH-IIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTIPISA 510
I+ L ++K +I+ +NK+DL+ + + ++ +E + F I +PISA
Sbjct: 105 -----ILEKLKKVKTPVILVLNKIDLVKDKEELLPLL----EELSELMDFAEI--VPISA 153
Query: 511 LNGDNI 516
L GDN+
Sbjct: 154 LKGDNV 159
>gnl|CDD|239667 cd03696, selB_II, selB_II: this subfamily represents the domain of
elongation factor SelB, homologous to domain II of
EF-Tu. 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.
Length = 83
Score = 46.7 bits (112), Expect = 1e-06
Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 572 GRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDMAITGQSVTLIIK--EYLDISRGN 629
G + SG +K D + + P G++ ++ IQ+ K ++ A G V L + + D+ RG+
Sbjct: 20 GTVLSGSVKVGDKVEILPLGEETRVRSIQVHGKDVEEAKAGDRVALNLTGVDAKDLERGD 79
Query: 630 MLVS 633
+L S
Sbjct: 80 VLSS 83
>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. 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
Score = 50.8 bits (122), Expect = 3e-06
Identities = 46/149 (30%), Positives = 70/149 (46%), Gaps = 37/149 (24%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITI 392
VD GK+TL+ LL S +AV+ +RVM +++ ERE+GITI
Sbjct: 10 VDHGKTTLVDALLKQSGT--FRANEAVA----ERVMDSNDL-----------ERERGITI 52
Query: 393 ---DVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLL 449
+ A RY T K I DTPGH + + D V++L+DAS+ P +
Sbjct: 53 LAKNTAIRYNGT---KINIVDTPGHADFGGEVERVLGMVDGVLLLVDASE---GP----M 102
Query: 450 TQTK---RHSIIAHLLRIKHIIIAVNKMD 475
QT+ + ++ L I+ +NK+D
Sbjct: 103 PQTRFVLKKALELGL----KPIVVINKID 127
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. 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
Score = 50.4 bits (121), Expect = 3e-06
Identities = 48/193 (24%), Positives = 82/193 (42%), Gaps = 45/193 (23%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITI 392
+D GKSTL RL ++ A+S R M + D ++ ERE+GITI
Sbjct: 12 IDHGKSTLADRL--------LEYTGAISE----REMR------EQVLDSMDLERERGITI 53
Query: 393 D-----VAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVN 447
+ Y+ + + DTPGH ++ + + + ++L+DA++
Sbjct: 54 KAQAVRLNYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQ-------G 106
Query: 448 LLTQTKRHSIIAHL-LRIKH---IIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNI 503
+ QT +A++ L +++ II +NK+DL + + K K+ E I
Sbjct: 107 IEAQT-----LANVYLALENDLEIIPVINKIDLPSADPERVK------KEIEEVIGLDAS 155
Query: 504 NTIPISALNGDNI 516
I SA G I
Sbjct: 156 EAILASAKTGIGI 168
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 49.9 bits (120), Expect = 5e-06
Identities = 51/199 (25%), Positives = 77/199 (38%), Gaps = 65/199 (32%)
Query: 331 GSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGI 390
G VD GK+TL LD + +T V +G GI
Sbjct: 12 GHVDHGKTTL---------------LDKIRKTN---VAAGE---------------AGGI 38
Query: 391 TIDV-AYRY-FNTPKRKFIIA-DTPGHEQYTRNMIT-GASTADAVIILIDASKIKFNPSV 446
T + AY+ + K I DTPGHE +T M GAS D I+++ A + V
Sbjct: 39 TQHIGAYQVPLDVIKIPGITFIDTPGHEAFT-AMRARGASVTDIAILVVAA-----DDGV 92
Query: 447 NLLTQTKRHSIIAHLLRIKH-------IIIAVNKMDLINYN--QIFYKRIVYAYKKFAED 497
+ QT I H I++A+NK+D N ++ + Y E+
Sbjct: 93 --MPQTI--------EAINHAKAAGVPIVVAINKIDKPEANPDKVKQELQEYGL--VPEE 140
Query: 498 IHFQNINTIPISALNGDNI 516
++ +P+SA G+ I
Sbjct: 141 W-GGDVIFVPVSAKTGEGI 158
>gnl|CDD|233701 TIGR02055, APS_reductase, thioredoxin-dependent adenylylsulfate APS
reductase. This model describes recently identified
adenosine 5'-phosphosulfate (APS) reductase activity
found in sulfate-assimilatory prokaryotes, thus
separating it from the traditionally described
phosphoadenosine 5'-phosphosulfate (PAPS) reductases
found in bacteria and fungi. Homologous to PAPS
reductase in enterobacteria, cyanobacteria, and yeast,
APS reductase here clusters with, and demonstrates
greater homology to plant APS reductase. Additionally,
the presence of two conserved C-terminal motifs
(CCXXRKXXPL & SXGCXXCT) distinguishes APS substrate
specificity and serves as a FeS cluster [Central
intermediary metabolism, Sulfur metabolism].
Length = 191
Score = 47.1 bits (112), Expect = 1e-05
Identities = 38/178 (21%), Positives = 65/178 (36%), Gaps = 32/178 (17%)
Query: 47 GKDSVVLLRLAEKAFRPSRFPFPMVHIDTGHNFPEVISFRDNCISKLGETLIVRSVEDSI 106
G + VVL+ LA K + F +DTG F E D + + V S
Sbjct: 2 GAEDVVLVDLAAKVRPDVKVFF----LDTGRLFKETYETIDQVRERYDILIDVLSPPPLT 57
Query: 107 MKGTVRLRKPNTDSRNAAQSITLLETIKEFK-----FDACIGGARRDEEKARAKERIFSF 161
++ V+ N R+ + ++ K A I G RRD+ RA+
Sbjct: 58 VEEQVKEYGLNLFYRSVPHECCGIRKVEPLKRALAGVSAWITGLRRDQSPTRAQAPFLEI 117
Query: 162 RDKFGQWNPKSQRPELWNLYNTRVHPGENIRVFPISNWTELDIWQYIEREKIILPSLY 219
+ FG +++ P+++WT D+W+YI ++ L+
Sbjct: 118 DEAFGL-----------------------VKINPLADWTSEDVWEYIADNELPYNPLH 152
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 46.3 bits (110), Expect = 1e-05
Identities = 32/193 (16%), Positives = 62/193 (32%), Gaps = 49/193 (25%)
Query: 330 AGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQG 389
G GKS+L+ LL +
Sbjct: 3 VGRGGVGKSSLLNALL--GGEVGEV----------------------------SDVPGTT 32
Query: 390 ITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITG-----ASTADAVIILIDASKIKFNP 444
DV + + K K ++ DTPG +++ AD +++++D++
Sbjct: 33 RDPDVYVKELDKGKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTD----- 87
Query: 445 SVNLLTQTKRHSIIAHLLRI-KHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNI 503
+ + I+ L + II+ NK+DL+ +R V + E +
Sbjct: 88 --RESEEDAKLLILRRLRKEGIPIILVGNKIDLLE------EREVEELLRLEELAKILGV 139
Query: 504 NTIPISALNGDNI 516
+SA G+ +
Sbjct: 140 PVFEVSAKTGEGV 152
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 49.0 bits (118), Expect = 1e-05
Identities = 33/149 (22%), Positives = 54/149 (36%), Gaps = 31/149 (20%)
Query: 331 GSVDDGKSTLIGRLLFDSKNIF----IDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESER 386
G GK+TL +LF + I ++ D + ER
Sbjct: 2 GHSGAGKTTLTEAILFYTGAIHRIGEVEDGTTTM-------------------DFMPEER 42
Query: 387 EQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSV 446
E+GI+I A K + DTPGH +T + D ++++ A +
Sbjct: 43 ERGISITSAATTCEWKGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTE 102
Query: 447 NLLTQTKRHSIIAHLLRIKHIIIAVNKMD 475
+ Q +++ + II VNKMD
Sbjct: 103 TVWRQAEKYG-VPR-------IIFVNKMD 123
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family 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.
Length = 179
Score = 46.0 bits (110), Expect = 1e-05
Identities = 38/155 (24%), Positives = 70/155 (45%), Gaps = 39/155 (25%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITI 392
+D GKSTL RLL ++ T +R M + D ++ ERE+GITI
Sbjct: 9 IDHGKSTLADRLL------------ELTGTVSEREMKEQ------VLDSMDLERERGITI 50
Query: 393 D-----VAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVN 447
+ Y+ + + + DTPGH ++ + + + ++++DA++
Sbjct: 51 KAQAVRLFYKAKDGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQ-------G 103
Query: 448 LLTQTKRHSIIAHL-LRIKH---IIIAVNKMDLIN 478
+ QT +A+ L +++ II +NK+DL
Sbjct: 104 VEAQT-----LANFYLALENNLEIIPVINKIDLPA 133
>gnl|CDD|239756 cd04089, eRF3_II, eRF3_II: domain II of the eukaryotic class II
release factor (eRF3). 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-like protein with the property of
aggregating into polymer-like fibrils.
Length = 82
Score = 43.7 bits (104), Expect = 2e-05
Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 571 MGRIESGIIKKNDCLIVEPSGKKATIKDIQMLNKSLDMAITGQSVTLIIK--EYLDISRG 628
+G++ESG IKK D L+V P+ + + I + + A G++V L +K E DIS G
Sbjct: 18 LGKVESGTIKKGDKLLVMPNKTQVEVLSIYNEDVEVRYARPGENVRLRLKGIEEEDISPG 77
Query: 629 NMLVS 633
+L S
Sbjct: 78 FVLCS 82
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 47.9 bits (114), Expect = 2e-05
Identities = 65/260 (25%), Positives = 97/260 (37%), Gaps = 67/260 (25%)
Query: 271 ATTVEDIIKEISVTQITERGATRIDDQNSEASMEKRKKTEAPEKKQSVFKKHSLLR--FI 328
+ TV II ++Q+ + I + EK S F ++S+ R +
Sbjct: 192 SVTVNQIIDISIISQVADDFGINIISEEKNNINEKTSN----LDNTSAFTENSINRPPIV 247
Query: 329 TA-GSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESERE 387
T G VD GK+TL LD + +T+ + +G
Sbjct: 248 TILGHVDHGKTTL---------------LDKIRKTQIAQKEAG----------------- 275
Query: 388 QGITIDV-AYRY---FNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFN 443
GIT + AY + +K + DTPGHE ++ GA+ D I++I A
Sbjct: 276 -GITQKIGAYEVEFEYKDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADD---- 330
Query: 444 PSVNLLTQTKRHSIIAHLLRIKHI-------IIAVNKMDLINYNQIFYKRIVYAYKKFAE 496
K +I A I +I I+A+NK+D N N K+ + Y E
Sbjct: 331 -------GVKPQTIEA----INYIQAANVPIIVAINKIDKANANTERIKQQLAKYNLIPE 379
Query: 497 DIHFQNINTIPISALNGDNI 516
IPISA G NI
Sbjct: 380 KWGGD-TPMIPISASQGTNI 398
>gnl|CDD|206732 cd04169, RF3, Release Factor 3 (RF3) protein involved in the
terminal step of translocation in bacteria. 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
Score = 46.8 bits (112), Expect = 3e-05
Identities = 40/144 (27%), Positives = 66/144 (45%), Gaps = 23/144 (15%)
Query: 334 DDGKSTLIGRLLFDSKNIFIDQL-DAV-SRTKYKRVMSGHNIDLSLLTDGLESEREQGIT 391
D GK+TL +LL I Q AV +R K S D +E E+++GI+
Sbjct: 12 DAGKTTLTEKLLLFGGAI---QEAGAVKARKSRKHATS----------DWMEIEKQRGIS 58
Query: 392 IDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLLTQ 451
+ + F + DTPGHE ++ + + D+ +++IDA+K + Q
Sbjct: 59 VTSSVMQFEYKGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAK-------GVEPQ 111
Query: 452 TKRHSIIAHLLRIKHIIIAVNKMD 475
T++ + L I II +NK+D
Sbjct: 112 TRKLFEVCRLRGIP-IITFINKLD 134
>gnl|CDD|236300 PRK08576, PRK08576, hypothetical protein; Provisional.
Length = 438
Score = 47.4 bits (113), Expect = 3e-05
Identities = 55/213 (25%), Positives = 85/213 (39%), Gaps = 37/213 (17%)
Query: 14 LNNLYLDWLESEAIHIMREVSAECNNPVLLFSGGKDSVVLLRLAEKAFRPSRFPFPMVHI 73
N L+ E +I +R+ E ++ +SGGKDS L LA+KAF V++
Sbjct: 213 ANREVLEAFEKASIKFLRKF--EEWTVIVPWSGGKDSTAALLLAKKAFGDVT----AVYV 266
Query: 74 DTGHNFPEVISFRDNCISKLGETLIVRSVEDSIMKGTVRLRK---PNTDSR--NAAQSIT 128
DTG+ P + + KLG LI V+ + + K P +R +
Sbjct: 267 DTGYEMPLTDEYVEKVAEKLGVDLIRAGVDVPMP-----IEKYGMPTHSNRWCTKLKVEA 321
Query: 129 LLETIKEFKFDACIGGARRDEEKARAKERIFSFRDKFGQWNPKSQRPELWNLYNTRVHPG 188
L E I+E + + G RD E AR + R P +R + G
Sbjct: 322 LEEAIRELEDGLLVVG-DRDGESARRRLR-----------PPVVERKTNF---------G 360
Query: 189 ENIRVFPISNWTELDIWQYIEREKIILPSLYFA 221
+ + V PI W+ + YI + L LY+
Sbjct: 361 KILVVMPIKFWSGAMVQLYILMNGLELNPLYYK 393
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. 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.
Length = 213
Score = 45.7 bits (109), Expect = 4e-05
Identities = 34/155 (21%), Positives = 62/155 (40%), Gaps = 30/155 (19%)
Query: 330 AGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQG 389
AG + GK++L+ L+ + +Y TD + E+E+G
Sbjct: 6 AGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPLRY--------------TDTRKDEQERG 51
Query: 390 ITIDVAYRYFNTPKRK-----FIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNP 444
I+I K I DTPGH + + D V++++D +
Sbjct: 52 ISIKSNPISLVLEDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVE----- 106
Query: 445 SVNLLTQTKRHSIIAHLLRIK-HIIIAVNKMD-LI 477
L + T+R +I H ++ +++ +NK+D LI
Sbjct: 107 --GLTSVTER--LIRHAIQEGLPMVLVINKIDRLI 137
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 44.4 bits (106), Expect = 4e-05
Identities = 29/138 (21%), Positives = 57/138 (41%), Gaps = 30/138 (21%)
Query: 389 GITIDVAYRYFNTPKRKFIIADTPG---------HEQYTRNMITGASTADAVIILIDASK 439
G+T++ F ++ I D PG E+ R+ + G D ++ ++DA+
Sbjct: 29 GVTVEKKEGEFKLGGKEIEIVDLPGTYSLTPYSEDEKVARDFLLGEE-PDLIVNVVDATN 87
Query: 440 IKFNPSVNLLTQTKRHSIIAHLLRI-KHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDI 498
++ N + L Q LL + +++A+N +D + I K +E +
Sbjct: 88 LERN--LYLTLQ---------LLELGLPVVVALNMIDEAE-----KRGIKIDLDKLSELL 131
Query: 499 HFQNINTIPISALNGDNI 516
+ +P SA G+ I
Sbjct: 132 ---GVPVVPTSARKGEGI 146
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 44.8 bits (106), Expect = 5e-05
Identities = 25/131 (19%), Positives = 47/131 (35%), Gaps = 20/131 (15%)
Query: 410 DTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIK---H 466
TPG E++ + A I+L+D+S+ T I L +
Sbjct: 74 GTPGQERFKFMWEILSRGAVGAIVLVDSSR----------PITFHAEEIIDFLTSRNPIP 123
Query: 467 IIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNGDNIISASNNMLWY 526
+++A+NK DL F ++ A + ++ I I A G+ + +L
Sbjct: 124 VVVAINKQDL------FDALPPEKIRE-ALKLELLSVPVIEIDATEGEGARDQLDVLLLK 176
Query: 527 NGPTLISLLES 537
+ + S
Sbjct: 177 DLLGSANEEAS 187
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. 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 [Protein
synthesis, Translation factors].
Length = 587
Score = 45.9 bits (109), Expect = 8e-05
Identities = 52/194 (26%), Positives = 75/194 (38%), Gaps = 57/194 (29%)
Query: 331 GSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGI 390
G VD GK++L LD++ +TK + +G GI
Sbjct: 94 GHVDHGKTSL---------------LDSIRKTKVAQGEAG------------------GI 120
Query: 391 TIDV-AYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLL 449
T + AY N + DTPGHE +T GA D V++++ A ++
Sbjct: 121 TQHIGAYHVENEDGKMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADD-------GVM 173
Query: 450 TQTKRHSIIAHLLRIKH-------IIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQN 502
QT I H II+A+NK+D N K+ + Y ED
Sbjct: 174 PQTIE--------AISHAKAANVPIIVAINKIDKPEANPDRVKQELSEYGLVPEDWGGDT 225
Query: 503 INTIPISALNGDNI 516
I +P+SAL GD I
Sbjct: 226 I-FVPVSALTGDGI 238
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), 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 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.
Length = 161
Score = 43.0 bits (102), Expect = 1e-04
Identities = 39/192 (20%), Positives = 65/192 (33%), Gaps = 61/192 (31%)
Query: 336 GKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITID-V 394
GKS+L+ LL +N+ I VS G T D V
Sbjct: 9 GKSSLLNALL--GQNVGI-----VSPIP-------------------------GTTRDPV 36
Query: 395 AYRYFNTPKRKFIIADTPG-----HEQYTRN--MITGASTADAVIILIDASKIKFNPSVN 447
+ P ++ DTPG R A AD V++++D+
Sbjct: 37 RKEWELLPLGPVVLIDTPGLDEEGGLGRERVEEARQVADRADLVLLVVDSDLTPVEEEAK 96
Query: 448 LLTQTKRHSIIAHLLRIKHIIIAVNKMDLIN---YNQIFYKRIVYAYKKFAEDIHFQNIN 504
L +R K +++ +NK+DL+ ++ +R + +
Sbjct: 97 LGLLRERG---------KPVLLVLNKIDLVPESEEEELLRERKLELLPD---------LP 138
Query: 505 TIPISALNGDNI 516
I +SAL G+ I
Sbjct: 139 VIAVSALPGEGI 150
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. 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
Score = 44.5 bits (105), Expect = 2e-04
Identities = 31/144 (21%), Positives = 65/144 (45%), Gaps = 23/144 (15%)
Query: 334 DDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITID 393
D GK+T+ ++L ++ + K + +D +E E+++GI+I
Sbjct: 21 DAGKTTITEKVL-----LYGGAIQTAGAVKGRGSQR------HAKSDWMEMEKQRGISIT 69
Query: 394 VAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLLTQTK 453
+ F + DTPGHE ++ + + D +++IDA+K + T+T+
Sbjct: 70 TSVMQFPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAK-------GVETRTR 122
Query: 454 RHSIIAHLLRIKH--IIIAVNKMD 475
+ + + R++ I +NK+D
Sbjct: 123 K---LMEVTRLRDTPIFTFMNKLD 143
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 43.5 bits (102), Expect = 5e-04
Identities = 39/143 (27%), Positives = 66/143 (46%), Gaps = 25/143 (17%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITI 392
VD GK+TL+ +LL S D+ + T+ +RVM +++ E+E+GITI
Sbjct: 14 VDHGKTTLVDKLLQQSGT-----FDSRAETQ-ERVMDSNDL-----------EKERGITI 56
Query: 393 DVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLLTQT 452
+ I DTPGH + + S D+V++++DA P +T+
Sbjct: 57 LAKNTAIKWNDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPM-PQTRFVTKK 115
Query: 453 KRHSIIAHLLRIKHIIIAVNKMD 475
A+ L+ I+ +NK+D
Sbjct: 116 A----FAYGLK---PIVVINKVD 131
>gnl|CDD|185375 PRK15478, cbiH, cobalt-precorrin-3B C(17)-methyltransferase;
Provisional.
Length = 241
Score = 42.6 bits (100), Expect = 5e-04
Identities = 33/127 (25%), Positives = 64/127 (50%), Gaps = 18/127 (14%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVL----YDALITNELLMLCPKAKHIFVGKRFKK 794
+ +IG GPG+ ++T+ L+ A++V+ Y L+ K K+ K
Sbjct: 2 LSVIGIGPGSQAMMTMEAIEALQAAEIVVGYKTYTHLV-----------KAFTGDKQVIK 50
Query: 795 HSIAQYIIN-RIIVKCAFKYNLVVRLKGGDPMLFGRTDE--ELNALKKYNIKVKVIPGIT 851
+ + I + ++ A + V + GD ++G EL + +K +++V++IPG+T
Sbjct: 51 TGMCKEIERCQAAIELAQAGHNVALISSGDAGIYGMAGLVLELVSKQKLDVEVRLIPGMT 110
Query: 852 AALAAAS 858
A++AAAS
Sbjct: 111 ASIAAAS 117
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. 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. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 41.7 bits (99), Expect = 5e-04
Identities = 32/138 (23%), Positives = 56/138 (40%), Gaps = 30/138 (21%)
Query: 389 GITIDVAYRYFNTPKRKFIIADTPG---------HEQYTRNMITGASTADAVIILIDASK 439
G+T++ F + I D PG E+ R+ + D +I ++DA+
Sbjct: 32 GVTVEKKEGTFKYKGYEIEIVDLPGTYSLSPYSEEEKVARDYLLEEK-PDVIINVVDATN 90
Query: 440 IKFNPSVNLLTQTKRHSIIAHLLRI-KHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDI 498
++ N + L Q LL + +++A+N MD K I KK +E +
Sbjct: 91 LERN--LYLTLQ---------LLELGIPVVVALNMMDEAE-----KKGIKIDIKKLSELL 134
Query: 499 HFQNINTIPISALNGDNI 516
+ +P SA G+ I
Sbjct: 135 ---GVPVVPTSARKGEGI 149
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily 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.
Length = 174
Score = 41.3 bits (98), Expect = 6e-04
Identities = 39/149 (26%), Positives = 61/149 (40%), Gaps = 41/149 (27%)
Query: 389 GITIDVAYRYFNTPKRKFIIADTPG----------HEQY----TRNMITGASTADAVIIL 434
G T D F +K+ + DT G E+Y T I AD V+++
Sbjct: 35 GTTRDSIDVPFEYDGQKYTLIDTAGIRKKGKVTEGIEKYSVLRTLKAI---ERADVVLLV 91
Query: 435 IDASKIKFNPSVNLLTQTKRHSIIAHLL--RIKHIIIAVNKMDLINYNQIFYKRIVYAYK 492
+DAS+ + Q R IA L+ K +II VNK DL+ ++ K
Sbjct: 92 LDASEG-------ITEQDLR---IAGLILEEGKALIIVVNKWDLVEKDE-------KTMK 134
Query: 493 KFAEDI--HFQNINTIP---ISALNGDNI 516
+F +++ ++ P ISAL G +
Sbjct: 135 EFEKELRRKLPFLDYAPIVFISALTGQGV 163
>gnl|CDD|180320 PRK05948, PRK05948, precorrin-2 methyltransferase; Provisional.
Length = 238
Score = 41.9 bits (99), Expect = 7e-04
Identities = 17/40 (42%), Positives = 25/40 (62%)
Query: 735 TVAAVYIIGAGPGAADLITVRGARLLRKADVVLYDALITN 774
T+ +Y I GPG +LIT++G RLL+ A VV + A +
Sbjct: 2 TLGTLYGISVGPGDPELITLKGLRLLQSAPVVAFPAGLAG 41
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 42.2 bits (100), Expect = 8e-04
Identities = 30/128 (23%), Positives = 50/128 (39%), Gaps = 26/128 (20%)
Query: 399 FNTPKRKFIIADTPG-HEQYT-------RNMITGASTADAVIILIDASKIKFNPSVNLLT 450
T + I DTPG H+ + + D ++ ++DA + + P
Sbjct: 49 VTTDNAQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADE-GWGPGDE--- 104
Query: 451 QTKRHSIIAHLLRIKHI--IIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTIPI 508
I L+ I+ VNK+D + + K I + + F+ I +PI
Sbjct: 105 ------FILEQLKKTKTPVILVVNKIDKVKPKTVLLKLI----AFLKKLLPFKEI--VPI 152
Query: 509 SALNGDNI 516
SAL GDN+
Sbjct: 153 SALKGDNV 160
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 42.6 bits (101), Expect = 0.001
Identities = 44/149 (29%), Positives = 71/149 (47%), Gaps = 37/149 (24%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITI 392
VD GK+TL+ LL S F + + V+ +RVM +++ E+E+GITI
Sbjct: 14 VDHGKTTLVDALLKQS-GTF-REREEVA----ERVMDSNDL-----------EKERGITI 56
Query: 393 ---DVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLL 449
+ A Y T + I DTPGH + + S D V++L+DAS+ P +
Sbjct: 57 LAKNTAVNYNGT---RINIVDTPGHADFGGEVERVLSMVDGVLLLVDASE---GP----M 106
Query: 450 TQTK---RHSIIAHLLRIKHIIIAVNKMD 475
QT+ + ++ L I+ +NK+D
Sbjct: 107 PQTRFVLKKALALGL----KPIVVINKID 131
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 42.2 bits (100), Expect = 0.001
Identities = 36/146 (24%), Positives = 61/146 (41%), Gaps = 35/146 (23%)
Query: 389 GITIDVAYRYFNTPKRKFIIADTPG----------HEQYTRNMITGA-STADAVIILIDA 437
G T D F RK+++ DT G E+Y+ A AD V+++IDA
Sbjct: 211 GTTRDSIDIEFERDGRKYVLIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDA 270
Query: 438 SKIKFNPSVNLLTQTKRHSIIAHLL--RIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFA 495
++ + Q R IA L+ + I+I VNK DL+ ++ ++F
Sbjct: 271 TE-------GISEQDLR---IAGLIEEAGRGIVIVVNKWDLVEEDE-------ATMEEFK 313
Query: 496 EDI--HFQNIN---TIPISALNGDNI 516
+ + ++ + ISAL G +
Sbjct: 314 KKLRRKLPFLDFAPIVFISALTGQGL 339
Score = 33.7 bits (78), Expect = 0.47
Identities = 31/138 (22%), Positives = 53/138 (38%), Gaps = 30/138 (21%)
Query: 389 GITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMI---------TGASTADAVIILIDASK 439
G+T D Y R+FI+ DT G + + + AD ++ ++D +
Sbjct: 36 GVTRDRIYGDAEWLGREFILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGRE 95
Query: 440 IKFNPSVNLLTQTKRHSIIAHLLRI-KHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDI 498
+T I L R K +I+ VNK+D + ++ Y+ Y +
Sbjct: 96 G--------ITPADEE-IAKILRRSKKPVILVVNKIDNLKAEELAYE----FYSLGFGEP 142
Query: 499 HFQNINTIPISALNGDNI 516
+PISA +G I
Sbjct: 143 -------VPISAEHGRGI 153
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. 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
Score = 41.7 bits (98), Expect = 0.002
Identities = 41/157 (26%), Positives = 59/157 (37%), Gaps = 33/157 (21%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNI----DLSLLTDGLESEREQ 388
+D GK+T R+LF + I H I D + D +E E+E+
Sbjct: 19 IDAGKTTTTERILFYTGRI-------------------HKIGEVHDGAATMDWMEQEKER 59
Query: 389 GITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNL 448
GITI A + I DTPGH +T + D + ++DA S +
Sbjct: 60 GITITSAATTVFWKGHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSETV 119
Query: 449 LTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYK 485
Q R+ + I VNKMD N F +
Sbjct: 120 WRQANRYEVPR--------IAFVNKMDKTGAN--FLR 146
>gnl|CDD|206673 cd01886, EF-G, Elongation factor G (EF-G) family involved in both
the elongation and ribosome recycling phases of protein
synthesis. 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
Score = 40.9 bits (97), Expect = 0.002
Identities = 24/86 (27%), Positives = 33/86 (38%), Gaps = 23/86 (26%)
Query: 333 VDDGKSTLIGRLLFDSKNIF----IDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQ 388
+D GK+T R+L+ + I + A D +E ERE+
Sbjct: 8 IDAGKTTTTERILYYTGRIHKIGEVHGGGAT-------------------MDWMEQERER 48
Query: 389 GITIDVAYRYFNTPKRKFIIADTPGH 414
GITI A + I DTPGH
Sbjct: 49 GITIQSAATTCFWKDHRINIIDTPGH 74
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 39.8 bits (94), Expect = 0.002
Identities = 28/115 (24%), Positives = 44/115 (38%), Gaps = 27/115 (23%)
Query: 408 IADTPG-------HEQYTRNMITGASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAH 460
+ DTPG H + T + + ADAVI ++ A LT+++R +
Sbjct: 50 LVDTPGLNSTIEHHTEITESFL---PRADAVIFVLSAD--------QPLTESEREFLKEI 98
Query: 461 LLR-IKHIIIAVNKMDLIN----YNQIFYKRIVYAYKKFAEDIHFQNINTIPISA 510
L K I +NK+DL++ + Y R I P+SA
Sbjct: 99 LKWSGKKIFFVLNKIDLLSEEELEEVLEYSR--EELGVLELGGGEPRI--FPVSA 149
>gnl|CDD|180341 PRK05990, PRK05990, precorrin-2 C(20)-methyltransferase; Reviewed.
Length = 241
Score = 40.0 bits (94), Expect = 0.003
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 742 IGAGPGAADLITVRGARLLRKADVVLY 768
+G GPG +L+T++ RLL+ A VV Y
Sbjct: 8 LGVGPGDPELLTLKALRLLQAAPVVAY 34
Score = 31.5 bits (72), Expect = 1.8
Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 5/95 (5%)
Query: 845 KVIPGITAALAAASESKQSLTKRNISRSVVLFTSSTMLKNNYLKNIPISDTLVEYMGGNN 904
+VIPG+ + L S L RN S SV+ S + + + + +D V G N
Sbjct: 129 EVIPGVCSMLGCWSVLGAPLVYRNQSLSVL---SGVLPEEELRRRLADADAAVIMKLGRN 185
Query: 905 IFLTAKKLLKLGFLPTTPVIVVENCSLSNQKITRL 939
+ + L LG L + VE +++NQ+I L
Sbjct: 186 LDKVRRVLAALGLLDRA--LYVERATMANQRIVPL 218
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 40.7 bits (96), Expect = 0.004
Identities = 24/98 (24%), Positives = 50/98 (51%), Gaps = 12/98 (12%)
Query: 380 DGLESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASK 439
D +E E+++GI++ + F+ + DTPGHE ++ + + D+ +++IDA+K
Sbjct: 57 DWMEIEKQRGISVTSSVMQFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAK 116
Query: 440 IKFNPSVNLLTQTKRHSIIAHLLRIKH--IIIAVNKMD 475
+ QT + + + R++ I +NK+D
Sbjct: 117 -------GIEPQTLK---LFEVCRLRDIPIFTFINKLD 144
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 40.6 bits (96), Expect = 0.004
Identities = 57/201 (28%), Positives = 81/201 (40%), Gaps = 72/201 (35%)
Query: 331 GSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGI 390
G VD GK++L LDA+ +T V +G E+ GI
Sbjct: 256 GHVDHGKTSL---------------LDAIRKTN---VAAG------------EA---GGI 282
Query: 391 T--IDVAYRYFNTPKRK--FIIADTPGHEQYT----RNMITGASTADAVIILIDASKIKF 442
T I AY+ T K F+ DTPGHE +T R GA D V++++ A
Sbjct: 283 TQHIG-AYQ-VETNGGKITFL--DTPGHEAFTAMRAR----GAQVTDIVVLVVAA----- 329
Query: 443 NPSVNLLTQTKRHSIIAHLLRIKH-------IIIAVNKMDLINYNQIFYKRIVYAYKKFA 495
+ V + QT A I H II+A+NK+D N K+ + Y
Sbjct: 330 DDGV--MPQTIE----A----INHAKAAGVPIIVAINKIDKPGANPDRVKQELSEYGLVP 379
Query: 496 EDIHFQNINTIPISALNGDNI 516
E+ I +P+SA G+ I
Sbjct: 380 EEWGGDTI-FVPVSAKTGEGI 399
>gnl|CDD|239665 cd03694, GTPBP_II, Domain II of the GP-1 family of GTPase. 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.
Length = 87
Score = 36.8 bits (86), Expect = 0.005
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 8/69 (11%)
Query: 572 GRIESGIIKKNDCLIVEP--SGK--KATIKDIQMLNKSL-DMAITGQSVTLIIKEYLD-- 624
G + G+I+ D L++ P G T+K I N+S + GQS +L +K+
Sbjct: 20 GTVSKGVIRLGDTLLLGPDQDGSFRPVTVKSIHR-NRSPVRVVRAGQSASLALKKIDRSL 78
Query: 625 ISRGNMLVS 633
+ +G +LVS
Sbjct: 79 LRKGMVLVS 87
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 40.0 bits (95), Expect = 0.006
Identities = 36/150 (24%), Positives = 58/150 (38%), Gaps = 45/150 (30%)
Query: 389 GIT---IDVAYRYFNTPKRKFIIADTPG----------HEQY----TRNMITGASTADAV 431
G T ID + +K+ + DT G E+Y T I AD V
Sbjct: 206 GTTRDSIDTPFERDG---QKYTLIDTAGIRRKGKVTEGVEKYSVIRTLKAI---ERADVV 259
Query: 432 IILIDASKIKFNPSVNLLTQTKRHSIIAHLL--RIKHIIIAVNKMDLINYNQIFYKRIVY 489
+++IDA++ + Q R IA L + ++I VNK DL++ +
Sbjct: 260 LLVIDATE-------GITEQDLR---IAGLALEAGRALVIVVNKWDLVDEKTM------E 303
Query: 490 AYKKFAEDIHFQNIN---TIPISALNGDNI 516
+KK ++ + ISAL G +
Sbjct: 304 EFKKELRR-RLPFLDYAPIVFISALTGQGV 332
Score = 33.9 bits (79), Expect = 0.47
Identities = 36/142 (25%), Positives = 51/142 (35%), Gaps = 39/142 (27%)
Query: 389 GITIDVAYRYFNTPKRKFIIADTPG------------HEQYTRNMITGASTADAVIILID 436
G+T D Y R+FI+ DT G EQ I AD ++ ++D
Sbjct: 34 GVTRDRIYGEAEWLGREFILIDTGGIEPDDDGFEKQIREQ-AELAI---EEADVILFVVD 89
Query: 437 ASKIKFNPSVNLLTQTKRHSIIAHLLRI--KHIIIAVNKMDLINYNQIFYKRIVYAYKKF 494
LT IA +LR K +I+ VNK+D + Y+ Y
Sbjct: 90 GR--------AGLTPADEE--IAKILRKSNKPVILVVNKVDGPDEEADAYE----FYSLG 135
Query: 495 AEDIHFQNINTIPISALNGDNI 516
+ PISA +G I
Sbjct: 136 LGEP-------YPISAEHGRGI 150
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. 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
[Protein synthesis, Other].
Length = 429
Score = 39.7 bits (94), Expect = 0.006
Identities = 38/150 (25%), Positives = 60/150 (40%), Gaps = 44/150 (29%)
Query: 389 GITIDVAYRYFNTPKRKFIIADTPG----------HEQY----TRNMITGASTADAVIIL 434
G T D F +K+ + DT G E+Y T I AD V+++
Sbjct: 205 GTTRDSIDIPFERNGKKYTLIDTAGIRRKGKVTEGVEKYSVLRTLKAI---ERADVVLLV 261
Query: 435 IDASKIKFNPSVNLLT-QTKRHSIIAHLLRIKH---IIIAVNKMDLIN--YNQIFYKRIV 488
+DA++ +T Q R IA L ++ ++I VNK DL+ + +K+ +
Sbjct: 262 LDATEG--------ITEQDLR---IAGLA-LEAGKALVIVVNKWDLVKDEKTREEFKKEL 309
Query: 489 YAYKKFAED--IHFQNINTIPISALNGDNI 516
F + I F ISAL G +
Sbjct: 310 RRKLPFLDFAPIVF-------ISALTGQGV 332
Score = 39.0 bits (92), Expect = 0.010
Identities = 36/175 (20%), Positives = 61/175 (34%), Gaps = 43/175 (24%)
Query: 389 GITIDVAYRYFNTPKRKFIIADTPG--------HEQYTRNMITGASTADAVIILIDASKI 440
G+T D Y R+FI+ DT G +Q AD ++ ++D
Sbjct: 32 GVTRDRKYGDAEWGGREFILIDTGGIEEDDDGLDKQIREQAEIAIEEADVILFVVDGR-- 89
Query: 441 KFNPSVNLLTQTKRHSIIAHLLRI-KHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIH 499
LT I L + K +I+ NK+D + + + +
Sbjct: 90 ------EGLTPED-EEIAKWLRKSGKPVILVANKIDGKKEDAVAA------------EFY 130
Query: 500 ---FQNINTIPISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLRF 551
F IPISA +G I ++L ++ LL E+ + P++
Sbjct: 131 SLGFGEP--IPISAEHGRGI----GDLL----DAILELLPEEEEEEEEEDGPIKI 175
>gnl|CDD|223115 COG0037, MesJ, tRNA(Ile)-lysidine synthase MesJ [Cell cycle
control, cell division, chromosome partitioning].
Length = 298
Score = 38.3 bits (89), Expect = 0.012
Identities = 26/79 (32%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 41 VLLFSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTG---HNFPEVISFRDNCISKLGETL 97
++ SGGKDS+ LL L ++ R R VH+D G ++ E C KLG L
Sbjct: 25 LVAVSGGKDSLALLHLLKELGR--RIEVEAVHVDHGLRGYSDQEAELVEKLC-EKLGIPL 81
Query: 98 IVRSVEDSIMKGTVRLRKP 116
IV V D + + T+ +
Sbjct: 82 IVERVTDDLGRETLDGKSI 100
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
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. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins, it
is presumed that modification by the endogenous enzyme
also inhibits eEF2 activity.
Length = 218
Score = 38.0 bits (89), Expect = 0.014
Identities = 42/199 (21%), Positives = 78/199 (39%), Gaps = 47/199 (23%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITI 392
VD GK+TL LL + I S + D E E+E+GITI
Sbjct: 9 VDHGKTTLSDSLLASAGII-----------------SEKLAGKARYLDTREDEQERGITI 51
Query: 393 DVA-------YRYFNTPKRKFII--ADTPGHEQYTRNMITGASTADAVIILIDASKIKFN 443
+ Y ++I D+PGH ++ + D ++++DA +
Sbjct: 52 KSSAISLYFEYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDAVE---- 107
Query: 444 PSVNLLTQTK---RHSIIAHLLRIKHIIIAVNKMD-LINYNQIFYKRIVYAYKKFAEDIH 499
+ QT+ R ++ R+K +++ +NK+D LI ++ + AY++ +
Sbjct: 108 ---GVCVQTETVLRQALEE---RVKPVLV-INKIDRLILELKLSPEE---AYQRLLRIVE 157
Query: 500 FQNINTIPISALNGDNIIS 518
++N I I +
Sbjct: 158 --DVNAI-IETYAPEEFKQ 173
>gnl|CDD|185500 PTZ00175, PTZ00175, diphthine synthase; Provisional.
Length = 270
Score = 38.0 bits (89), Expect = 0.014
Identities = 39/115 (33%), Positives = 55/115 (47%), Gaps = 15/115 (13%)
Query: 740 YIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCPKAK-HIFVGKRFK---KH 795
YIIG G G ITV+G ++ ADVV ++ + +L+ K K F GK +
Sbjct: 4 YIIGLGLGDEKDITVKGLEAVKSADVVYLESYTS--ILINSNKEKLEEFYGKPVIEADRE 61
Query: 796 SIAQYIINRIIVKCAFKYNLVVRLKGGDPMLFGRT---DEELNALKKYNIKVKVI 847
+ + I++ A + N V L GDP F T D L A KK I+V+VI
Sbjct: 62 MVEEG--CDEILEEAKEKN-VAFLVVGDP--FCATTHTDLYLRAKKK-GIEVEVI 110
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily 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.
Length = 157
Score = 36.6 bits (86), Expect = 0.020
Identities = 34/138 (24%), Positives = 50/138 (36%), Gaps = 31/138 (22%)
Query: 389 GITIDVAYRYFNTPKRKFIIADTPG--------HEQYTRNMITGASTADAVIILIDASKI 440
G+T D Y R+FI+ DT G ++ AD ++ ++D +
Sbjct: 30 GVTRDRKYGEAEWGGREFILIDTGGIEPDDEGISKEIREQAEIAIEEADVILFVVDGREG 89
Query: 441 KFNPSVNLLTQTKRHSIIAHLLR--IKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDI 498
LT IA LR K +I+ VNK+D I + Y +
Sbjct: 90 --------LTPADEE--IAKYLRKSKKPVILVVNKIDNIKEEEEAA----EFYSLGFGEP 135
Query: 499 HFQNINTIPISALNGDNI 516
IPISA +G I
Sbjct: 136 -------IPISAEHGRGI 146
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 38.3 bits (90), Expect = 0.021
Identities = 44/193 (22%), Positives = 84/193 (43%), Gaps = 45/193 (23%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITI 392
+D GKSTL RL ++ +S +R M + + D ++ ERE+GITI
Sbjct: 18 IDHGKSTLADRL--------LELTGGLS----EREMR------AQVLDSMDIERERGITI 59
Query: 393 D-----VAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVN 447
+ Y+ + + DTPGH ++ + + + ++++DAS+
Sbjct: 60 KAQAVRLNYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQ-------G 112
Query: 448 LLTQTKRHSIIAHL-LRIKH---IIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNI 503
+ QT +A++ L +++ II +NK+DL + K ++ + I
Sbjct: 113 VEAQT-----LANVYLALENNLEIIPVLNKIDLPAADPERVK------QEIEDIIGIDAS 161
Query: 504 NTIPISALNGDNI 516
+ + +SA G I
Sbjct: 162 DAVLVSAKTGIGI 174
>gnl|CDD|236218 PRK08284, PRK08284, precorrin 6A synthase; Provisional.
Length = 253
Score = 37.1 bits (87), Expect = 0.030
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVL 767
+ +IG G G D +T++ + L +ADV
Sbjct: 4 LLLIGIGAGDPDHLTLQAIKALNRADVFF 32
Score = 35.6 bits (83), Expect = 0.078
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 822 GDPMLFG---RTDEELNALKKYNIKVKVIPGITA--ALAAA 857
GDP L+ R E + A + +VIPGIT+ ALAA
Sbjct: 112 GDPSLYDSTLRILERVRARGRVAFDYEVIPGITSVQALAAR 152
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. 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; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 37.9 bits (88), Expect = 0.031
Identities = 45/217 (20%), Positives = 83/217 (38%), Gaps = 65/217 (29%)
Query: 410 DTPGHEQYTRNMITGASTADAVIILIDASKIKFNP----SVNLLTQTKRHSIIAHLLRIK 465
DTPGHE +T G + AD I+++D ++ F P ++N+L K
Sbjct: 75 DTPGHEAFTNLRKRGGALADLAILIVDINE-GFKPQTQEALNILRMYK-----------T 122
Query: 466 HIIIAVNKMDLIN-------------------------YNQIFYKRIVYAYKKFAEDIH- 499
++A NK+D I +++ I + F +
Sbjct: 123 PFVVAANKIDRIPGWRSHEGRPFMESFSKQEIQVQQNLDTKVYNLVIKLHEEGFEAERFD 182
Query: 500 -----FQNINTIPISALNGDNIISASNNMLWYNGPTLISLLESLNTNEKIDKKPLRFPVQ 554
+ + IPISA+ G+ I P L+++L L ++ ++ L+ +
Sbjct: 183 RVTDFTKTVAIIPISAITGEGI------------PELLTMLAGL--AQQYLEEQLKLEEE 228
Query: 555 LVARHCGHISKDFRGYMGRIES----GIIKKNDCLIV 587
AR K+ G I++ GI++K D + +
Sbjct: 229 GPARGTILEVKEETGLGMTIDAVIYDGILRKGDTIAM 265
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
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
Score = 36.8 bits (86), Expect = 0.035
Identities = 32/142 (22%), Positives = 60/142 (42%), Gaps = 27/142 (19%)
Query: 336 GKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITIDVA 395
GK+TL LL+ + A+ R RV G + ++D E+++ ++I+ +
Sbjct: 11 GKTTLAEALLYATG--------AIDR--LGRVEDG-----NTVSDYDPEEKKRKMSIETS 55
Query: 396 YRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNPSVNLLTQTKRH 455
K + DTPG+ + ++ DA +I+++A V + T+
Sbjct: 56 VAPLEWNGHKINLIDTPGYADFVGETLSALRAVDAALIVVEAQ-----SGVEVGTEK--- 107
Query: 456 SIIAHLLRIKHI--IIAVNKMD 475
+ L + II +NKMD
Sbjct: 108 --VWEFLDDAKLPRIIFINKMD 127
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 35.0 bits (81), Expect = 0.036
Identities = 21/98 (21%), Positives = 37/98 (37%), Gaps = 25/98 (25%)
Query: 389 GITIDVAYRYFNTPKRKFIIADTPG-------------HEQYTRNMITGASTADAVIILI 435
G T D R+ I+ DTPG ++ AD +++++
Sbjct: 32 GTTRDPILGVLG-LGRQIILVDTPGLIEGASEGKGVEGFNRFLEA----IREADLILLVV 86
Query: 436 DASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNK 473
DAS+ +L + ++ L K II+ +NK
Sbjct: 87 DASEGLTEDDEEILEELEK-------LPKKPIILVLNK 117
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. 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 [Protein synthesis, Other].
Length = 329
Score = 36.6 bits (86), Expect = 0.051
Identities = 32/133 (24%), Positives = 52/133 (39%), Gaps = 36/133 (27%)
Query: 402 PKRKFIIADTPGHEQYTRNMITGAST--------------ADAVIILIDASKIKFNPSVN 447
R F+IAD PG +I GAS ++ LID S + +
Sbjct: 203 DGRSFVIADIPG-------LIEGASEGAGLGHRFLKHIERTRVLLHLIDISPEDGSDPIE 255
Query: 448 ----LLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNI 503
+ + K++S L K I+ +NK+DL++ ++ K+ E
Sbjct: 256 DYEIIRNELKKYS---PELAEKPRIVVLNKIDLLDEEELEELL-----KELKEA---LGK 304
Query: 504 NTIPISALNGDNI 516
PISAL G+ +
Sbjct: 305 PVFPISALTGEGL 317
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 36.6 bits (86), Expect = 0.053
Identities = 20/92 (21%), Positives = 32/92 (34%), Gaps = 25/92 (27%)
Query: 425 ASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFY 484
AD V++++DAS+ +L + K K +I+ +NK DL
Sbjct: 292 IEEADLVLLVLDASEPLTEEDDEILEELKD----------KPVIVVLNKADLTGE----- 336
Query: 485 KRIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
+ I ISA G+ I
Sbjct: 337 ----------IDLEEENGKPVIRISAKTGEGI 358
>gnl|CDD|238771 cd01513, Translation_factor_III, Domain III of Elongation factor
(EF) Tu (EF-TU) and EF-G. Elongation factors (EF) EF-Tu
and EF-G participate in the elongation phase during
protein biosynthesis on the ribosome. Their functional
cycles depend on GTP binding and its hydrolysis. The
EF-Tu complexed with GTP and aminoacyl-tRNA delivers
tRNA to the ribosome, whereas EF-G stimulates
translocation, a process in which tRNA and mRNA
movements occur in the ribosome. Experimental data
showed that: (1) intrinsic GTPase activity of EF-G is
influenced by excision of its domain III; (2) that EF-G
lacking domain III has a 1,000-fold decreased GTPase
activity on the ribosome and, a slightly decreased
affinity for GTP; and (3) EF-G lacking domain III does
not stimulate translocation, despite the physical
presence of domain IV which is also very important for
translocation. These findings indicate an essential
contribution of domain III to activation of GTP
hydrolysis. Domains III and V of EF-G have the same fold
(although they are not completely superimposable), the
double split beta-alpha-beta fold. This fold is observed
in a large number of ribonucleotide binding proteins and
is also referred to as the ribonucleoprotein (RNP) or
RNA recognition (RRM) motif. This domain III is found
in several elongation factors, as well as in peptide
chain release factors and in GT-1 family of GTPase
(GTPBP1).
Length = 102
Score = 33.9 bits (78), Expect = 0.061
Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 661 KYLLKHSTNQILSRILKINALLNINTQKWCPPKLLDLNDIGCVTINIYEPISVDSYDNIR 720
K +L T + RI K+ + ++ T++ PP+ L + G V + + +P++++++ +
Sbjct: 24 KPVLNVGTAHVPGRIAKLLSKVDGKTEEKKPPEFLKSGERGIVEVELQKPVALETFSENQ 83
Query: 721 STGSFILIDEITFQTVAA 738
G F L D +TV A
Sbjct: 84 EGGRFALRDGG--RTVGA 99
>gnl|CDD|238951 cd01993, Alpha_ANH_like_II, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily.Adeninosine
nucleotide alpha hydrolases superfamily includes N type
ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins is predicted to bind ATP.
This domainhas a strongly conserved motif SGGKD at the
N terminus.
Length = 185
Score = 35.7 bits (83), Expect = 0.061
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 10/71 (14%)
Query: 44 FSGGKDSVVLLRLAEKAFRPSRFPFP--MVHIDTGHN-----FPEVISFRDNCISKLGET 96
SGGKDS+VLL + +K R + F + +D G EV +LG
Sbjct: 6 LSGGKDSLVLLHVLKKLQRRYPYGFELEALTVDEGIPGYRDESLEV--VERLAE-ELGIE 62
Query: 97 LIVRSVEDSIM 107
L + S ++
Sbjct: 63 LEIVSFKEEYT 73
>gnl|CDD|131487 TIGR02434, CobF, precorrin-6A synthase (deacetylating). In the
aerobic cobalamin biosythesis pathway, four enzymes are
involved in the conversion of precorrin-3A to
precorrin-6A. The first of the four steps is carried out
by EC 1.14.13.83, precorrin-3B synthase (CobG), yielding
precorrin-3B as the product. This is followed by three
methylation reactions, which introduce a methyl group at
C-17 (CobJ; EC 2.1.1.131), C-11 (CobM; EC 2.1.1.133) and
C-1 (CobF; EC 2.1.1.152) of the macrocycle, giving rise
to precorrin-4, precorrin-5 and precorrin-6A,
respectively. This model identifies CobF in High GC gram
positive, alphaproteobacteria and pseudomonas-related
species.
Length = 249
Score = 36.2 bits (84), Expect = 0.062
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 822 GDPMLFG---RTDEELNALKKYNIKVKVIPGITAALAAASE 859
GDP L+ R E L AL +VIPGIT+ A +
Sbjct: 111 GDPSLYDSTLRILERLRALGGVPFDYEVIPGITSVQALTAR 151
Score = 30.4 bits (69), Expect = 4.4
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 738 AVYIIGAGPGAADLITVRGARLLRKADVVL 767
+ +IG G G + +T++ L ADV
Sbjct: 2 TILLIGIGAGDPEQLTLQAVDALNHADVFF 31
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 36.8 bits (85), Expect = 0.065
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 16/72 (22%)
Query: 410 DTPGHEQYTRNMITGASTADAVIILIDASKIKFNP----SVNLLTQTKRHSIIAHLLRIK 465
DTPGHE +T G S AD ++++D ++ F P ++N+L Q K
Sbjct: 532 DTPGHEAFTSLRKRGGSLADLAVLVVDINE-GFKPQTIEAINILRQYK-----------T 579
Query: 466 HIIIAVNKMDLI 477
++A NK+DLI
Sbjct: 580 PFVVAANKIDLI 591
>gnl|CDD|212502 cd11643, Precorrin-6A-synthase, Precorrin-6A synthase, the
cobalamin biosynthesis enzyme CobF. Precorrin-6A
synthase participates in the pathway toward the
biosynthesis of cobalamin (vitamin B12). There are two
distinct cobalamin biosynthetic pathways in bacteria.
The aerobic pathway requires oxygen, and cobalt is
inserted late in the pathway; the anaerobic pathway does
not require oxygen, and cobalt insertion is the first
committed step towards cobalamin synthesis. This model
represents CobF, the precorrin-6A synthase, an enzyme
specific to the aerobic pathway. After precorrin-4 is
methylated at C-11 by CobM to produce precorrin-5, CobF
catalyzes the removal of the extruded acyl group in the
subsequent step, and the addition of a methyl group at
C-1. The product of this reaction is precorrin-6A, which
gets reduced by an NADH-dependent reductase to yield
precorrin-6B. This family includes enzymes in GC-rich
Gram-positive bacteria, alpha proteobacteria and
Pseudomonas-related species.
Length = 247
Score = 36.0 bits (84), Expect = 0.067
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVL 767
+ +IG GPG + +T++ L +ADV
Sbjct: 1 LLLIGIGPGDPEHLTLQAIAALNRADVFF 29
Score = 34.5 bits (80), Expect = 0.22
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 822 GDPMLFGRTDEELNALKKY---NIKVKVIPGITA--ALAAA 857
GDP L+ T L L+ + V+VIPGIT+ ALAA
Sbjct: 109 GDPSLYDSTLRILERLRARGRLDFDVEVIPGITSVQALAAR 149
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. 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.
Length = 170
Score = 35.1 bits (82), Expect = 0.075
Identities = 31/134 (23%), Positives = 49/134 (36%), Gaps = 41/134 (30%)
Query: 403 KRKFIIADTPGHEQYTRNMITGAST--------------ADAVIILIDASKIKFNPSVNL 448
R F+IAD PG +I GAS ++ +ID S + +P +
Sbjct: 47 GRSFVIADIPG-------LIEGASEGKGLGHRFLRHIERTRVLLHVIDLSG-EDDPVEDY 98
Query: 449 LTQTKRHSIIAHLLRIKH------IIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQN 502
T I L I+ +NK+DL++ + F + K +
Sbjct: 99 ET------IRNELEAYNPGLAEKPRIVVLNKIDLLDAEERF--EKLKELLKELKGKKV-- 148
Query: 503 INTIPISALNGDNI 516
PISAL G+ +
Sbjct: 149 ---FPISALTGEGL 159
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. 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.
Length = 159
Score = 34.8 bits (81), Expect = 0.076
Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 24/92 (26%)
Query: 425 ASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFY 484
AD V++++DAS+ + I L K +I+ +NK DL+
Sbjct: 80 IEEADLVLLVVDASE----------GLDEEDLEILELPAKKPVIVVLNKSDLL------- 122
Query: 485 KRIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
I ISA G+ I
Sbjct: 123 -------SDAEGISELNGKPIIAISAKTGEGI 147
>gnl|CDD|206725 cd04160, Arfrp1, Arf-related protein 1 (Arfrp1). 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.
Length = 168
Score = 35.0 bits (81), Expect = 0.077
Identities = 18/99 (18%), Positives = 43/99 (43%), Gaps = 7/99 (7%)
Query: 426 STADAVIILIDAS-KIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFY 484
+ + VI +ID++ + +FN S + + + + + +++ NK DL + +
Sbjct: 73 AESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGV----PLLVLANKQDLPDALSVAE 128
Query: 485 KRIVYAYKKFAEDIHFQNINTIPISALNGDNIISASNNM 523
+ V+ I ++ P+SAL G+ + +
Sbjct: 129 IKEVF--DDCIALIGRRDCLVQPVSALEGEGVEEGIEWL 165
>gnl|CDD|238944 cd01986, Alpha_ANH_like, Adenine nucleotide alpha hydrolases
superfamily including N type ATP PPases and ATP
sulphurylases. The domain forms a apha/beta/apha fold
which binds to Adenosine group..
Length = 103
Score = 33.6 bits (77), Expect = 0.086
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 41 VLLFSGGKDSVVLLRLAEKAF 61
++ FSGGKDS V L +K
Sbjct: 2 LVAFSGGKDSSVAAALLKKLG 22
>gnl|CDD|238950 cd01992, PP-ATPase, N-terminal domain of predicted ATPase of the
PP-loop faimly implicated in cell cycle control [Cell
division and chromosome partitioning]. This is a
subfamily of Adenine nucleotide alpha hydrolases
superfamily.Adeninosine nucleotide alpha hydrolases
superfamily includes N type ATP PPases and ATP
sulphurylases. It forms a apha/beta/apha fold which
binds to Adenosine group. This domain has a strongly
conserved motif SGGXD at the N terminus.
Length = 185
Score = 34.5 bits (80), Expect = 0.14
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 40 PVLL-FSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTGHN 78
+L+ SGG DS+ LL L + VH+D H
Sbjct: 1 KILVAVSGGPDSMALLHLLSELKPRLGLRLVAVHVD--HG 38
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 35.1 bits (82), Expect = 0.16
Identities = 36/146 (24%), Positives = 49/146 (33%), Gaps = 69/146 (47%)
Query: 404 RKFIIADTPGHEQYTRNMITGAS---------------TADAVII-LIDAS--------- 438
R F++AD PG +I GAS T VI+ +ID S
Sbjct: 206 RSFVMADIPG-------LIEGASEGVGLGHQFLRHIERTR--VIVHVIDMSGSEGRDPIE 256
Query: 439 ---KI-----KFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYA 490
KI +NP LL I++A NKMDL + +
Sbjct: 257 DYEKINKELKLYNPR---------------LLERPQIVVA-NKMDLPE----AEENLEEF 296
Query: 491 YKKFAEDIHFQNINTIPISALNGDNI 516
+K + PISAL G +
Sbjct: 297 KEKLGPKV-------FPISALTGQGL 315
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 35.2 bits (82), Expect = 0.19
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 573 RIESGIIKKNDCLIVEPSGKKA-TIKDIQMLNKSLDMAITGQSVTLIIK 620
+ G IK LI E GK+ TIK IQ +++ A G V + I
Sbjct: 488 EVLGGTIKPGVPLIKE-DGKRVGTIKQIQDQGENVKEAKAGMEVAISID 535
Score = 31.7 bits (73), Expect = 2.0
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 18/76 (23%)
Query: 406 FIIADTPGHEQYTRNMITGASTADAVIILIDASKIKFNP----SVNLLTQTKRHSIIAHL 461
FI DTPGHE +T G + AD I+++D ++ F P ++N+L + K
Sbjct: 75 FI--DTPGHEAFTNLRKRGGALADIAILVVDINE-GFQPQTIEAINILKRRK-------- 123
Query: 462 LRIKHIIIAVNKMDLI 477
++A NK+D I
Sbjct: 124 ---TPFVVAANKIDRI 136
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 33.3 bits (77), Expect = 0.33
Identities = 8/50 (16%), Positives = 19/50 (38%), Gaps = 3/50 (6%)
Query: 467 IIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
+I + K D + +++ K + ++ + I S+ G I
Sbjct: 113 FLIVLTKADKLKKSEL-AKVLKKIKEELNLFNILPPV--ILFSSKKGTGI 159
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 33.4 bits (77), Expect = 0.36
Identities = 23/99 (23%), Positives = 42/99 (42%), Gaps = 18/99 (18%)
Query: 390 ITIDVAYRYFNTPKRKFI-IADTPGHEQYTRNMITGASTADAVII-LIDASKI------- 440
I +VA Y N+ K K + + D PGHE+ ++ + I+ ++D++
Sbjct: 32 IEPNVASFYSNSSKGKKLTLVDVPGHEKLRDKLLEYLKASLKAIVFVVDSATFQKNIRDV 91
Query: 441 -KFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLIN 478
+F + + ++ I I+IA NK DL
Sbjct: 92 AEFLYDILTDLEKIKNKI--------PILIACNKQDLFT 122
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 34.2 bits (80), Expect = 0.40
Identities = 29/95 (30%), Positives = 39/95 (41%), Gaps = 39/95 (41%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQL-DAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGIT 391
+D GKSTL RL+ +L +S +R M + + D ++ ERE+GIT
Sbjct: 16 IDHGKSTLADRLI---------ELTGTLS----EREMK------AQVLDSMDLERERGIT 56
Query: 392 ID---VAYRY---------FNTPKRKFIIADTPGH 414
I V Y N I DTPGH
Sbjct: 57 IKAQAVRLNYKAKDGETYILN-----LI--DTPGH 84
>gnl|CDD|233864 TIGR02432, lysidine_TilS_N, tRNA(Ile)-lysidine synthetase,
N-terminal domain. The only examples in which the
wobble position of a tRNA must discriminate between G
and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA
(stop) vs. UGG (Trp). In all bacteria, the wobble
position of the tRNA(Ile) recognizing AUA is lysidine,
a lysine derivative of cytidine. This family describes
a protein domain found, apparently, in all bacteria in
a single copy. Eukaryotic sequences appear to be
organellar. The domain archictecture of this protein
family is variable; some, including characterized
proteins of E. coli and B. subtilis known to be
tRNA(Ile)-lysidine synthetase, include a conserved
50-residue domain that many other members lack. This
protein belongs to the ATP-binding PP-loop family (
pfam01171). It appears in the literature and protein
databases as TilS, YacA, and putative cell cycle
protein MesJ (a misnomer) [Protein synthesis, tRNA and
rRNA base modification].
Length = 189
Score = 33.0 bits (76), Expect = 0.42
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 41 VLLFSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTGHN 78
++ SGG DS+ LL L K + H+D H
Sbjct: 3 LVAVSGGVDSMALLHLLLKLQPKLKIRLIAAHVD--HG 38
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 33.3 bits (77), Expect = 0.55
Identities = 27/117 (23%), Positives = 47/117 (40%), Gaps = 23/117 (19%)
Query: 412 PGHEQYTRNMIT-GASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIA 470
PGH R I D VI ++DA + + R+ +I + K +I
Sbjct: 5 PGHMAKARREIKEKLKLVDVVIEVLDAR----------IPLSSRNPMIDEIRGNKPRLIV 54
Query: 471 VNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNGDN---IISASNNML 524
+NK DL + K+ + +++ + I + I+A G II A+ +L
Sbjct: 55 LNKADLADPAV--TKQWLKYFEE-------KGIKALAINAKKGKGVKKIIKAAKKLL 102
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 33.4 bits (77), Expect = 0.60
Identities = 32/121 (26%), Positives = 49/121 (40%), Gaps = 28/121 (23%)
Query: 130 LETIKEFKFD-ACIGGARRD--------EEKARAKERIFSFRDKFGQWNPKSQRPELWNL 180
LETIKEFK CI D E +AK RIF ++QRP + +
Sbjct: 169 LETIKEFKPKVGCILNITPDHLDRHKTMENYIKAKARIF-----------ENQRPSDYTV 217
Query: 181 YN-----TR-VHPGENIRVFPISNWTELDIWQYIEREKIILPSLYFAHKRKIIKRKGLLI 234
N TR + RV S + L+ +++ KI++ + ++I + I
Sbjct: 218 LNYDDPRTRSLAKKAKARVIFFSRKSLLEEGVFVKNGKIVISLG--GKEEEVIDIDEIFI 275
Query: 235 P 235
P
Sbjct: 276 P 276
>gnl|CDD|226478 COG3969, COG3969, Predicted phosphoadenosine phosphosulfate
sulfotransferase [General function prediction only].
Length = 407
Score = 32.8 bits (75), Expect = 0.90
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 44 FSGGKDSVVLLRL-AEKAFRPSRFPFPMVHIDTGHNFPEVISF 85
FSGGKDS ++L L AE A R ++ ID + I +
Sbjct: 34 FSGGKDSGLMLHLVAEVARENGRDKISVLFIDWEAQYSCTIDY 76
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 30.8 bits (70), Expect = 0.96
Identities = 19/115 (16%), Positives = 34/115 (29%), Gaps = 33/115 (28%)
Query: 326 RFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNI-DLSLLTDGLES 384
+ + G GKS+L+ +L+ + G + +L DG
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPE------------PLEIQGDTLAVDTLEVDG--- 45
Query: 385 EREQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITGASTADAVIILIDASK 439
I D G E+ I ADA++++ D +
Sbjct: 46 -----------------DTGLLNIWDFGGREELKFEHIIFMKWADAILLVYDLTD 83
>gnl|CDD|239460 cd03344, GroEL, GroEL_like type I chaperonin. Chaperonins are
involved in productive folding of proteins. They share a
common general morphology, a double toroid of 2 stacked
rings, each composed of 7-9 subunits. The symmetry of
type I is seven-fold and they are found in eubacteria
(GroEL) and in organelles of eubacterial descent (hsp60
and RBP). With the aid of cochaperonin GroES, GroEL
encapsulates non-native substrate proteins inside the
cavity of the GroEL-ES complex and promotes folding by
using energy derived from ATP hydrolysis.
Length = 520
Score = 32.8 bits (76), Expect = 1.0
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 571 MGRIESGIIKKNDCLIVEPSGKKATIKD-IQMLNKSLDMA 609
+GR + ++ K+D I+ +G KA IK I + K ++
Sbjct: 314 LGRAKKVVVTKDDTTIIGGAGDKAAIKARIAQIRKQIEET 353
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 32.4 bits (74), Expect = 1.1
Identities = 29/141 (20%), Positives = 48/141 (34%), Gaps = 36/141 (25%)
Query: 386 REQGITIDVAYRYFNTPKRKFIIADTPG-----HEQY---TRNMITGASTADAVIILIDA 437
R GI A + I DTPG H + + D ++ ++D+
Sbjct: 38 RISGIHTTGAS--------QIIFIDTPGFHEKKHSLNRLMMKEARSAIGGVDLILFVVDS 89
Query: 438 SKI--KFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFA 495
+ + L KR +++ NK+D +++ YA
Sbjct: 90 DQWNGDGEFVLTKLQNLKRP-----------VVLTRNKLDNKFKDKLLPLIDKYA----- 133
Query: 496 EDIHFQNINTIPISALNGDNI 516
I + +PISAL GDN
Sbjct: 134 --ILEDFKDIVPISALTGDNT 152
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 31.3 bits (72), Expect = 1.1
Identities = 29/118 (24%), Positives = 50/118 (42%), Gaps = 23/118 (19%)
Query: 405 KFIIADTPGHEQYTRNMITGAST----ADAVIILIDASKIK-FNPSVNLLTQTKRHSIIA 459
K I DT G E++ R++ S+ A I++ D + + F L + K ++
Sbjct: 50 KLQIWDTAGQERF-RSI---TSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYA--- 102
Query: 460 HLLRIKHIIIAV-NKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
II V NK DL + Q+ + ++FA++ T SA G+N+
Sbjct: 103 ---PPNIPIILVGNKSDLEDERQVSTEEA----QQFAKENGLLFFET---SAKTGENV 150
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 32.5 bits (75), Expect = 1.2
Identities = 19/99 (19%), Positives = 36/99 (36%), Gaps = 22/99 (22%)
Query: 418 TRNMITGASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLI 477
TR ++ D ++++DA + L+ + K I I+ +NK+DL
Sbjct: 79 TREVL---DKTDLALLVVDAGVGPGEYELELIEELKERKI--------PYIVVINKIDLG 127
Query: 478 NYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
+ + + I +SAL G+ I
Sbjct: 128 E-----------ESAELEKLEKKFGLPPIFVSALTGEGI 155
>gnl|CDD|233007 TIGR00522, dph5, diphthine synthase. Alternate name: diphthamide
biosynthesis S-adenosylmethionine-dependent
methyltransferase. This protein participates in the
modification of a specific His of elongation factor 2 of
eukarotes and Archaea to diphthamide. The protein was
characterized in Saccharomyces cerevisiae and designated
DPH5 [Protein fate, Protein modification and repair].
Length = 257
Score = 32.1 bits (73), Expect = 1.2
Identities = 61/246 (24%), Positives = 103/246 (41%), Gaps = 26/246 (10%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDALITNELLMLCPKAKHIFVGKRFKKHSIA 798
+Y+IG G + I+V+G ++KAD V Y T++LL + F GKR +
Sbjct: 2 LYLIGLGLYDENDISVKGLEAIKKADEV-YAEFYTSKLLGSSIEEIEEFFGKRVVVLERS 60
Query: 799 QYIIN-RIIVKCAFKYNLVVRLKGGDPML-FGRTDEELNALKKYNIKVKVIPGITAALAA 856
N +++ A + V L GDPM+ TD +L A K+ I+ ++I G + + A
Sbjct: 61 DVEENSFRLIERAKSKD-VALLVAGDPMVATTHTDLKLEA-KRKGIETRIIHGASISSAV 118
Query: 857 ASESKQSLTKRNISRSVVLFTS---STMLKNNYLKNIPI-SDTLV--EYMGGNNIFLTA- 909
+ L K + ++V FT N +N I TLV + N +T
Sbjct: 119 CGLTGLQLYKFGKTATIVFFTDNYRPQTPYNVIKENRKIGLHTLVLLDIHPKENRAMTIG 178
Query: 910 ---KKLLKL-------GFLPTTPVIVVENCSLSNQKITRLILLDLKKKIFQFEKP--VLF 957
+ LL+ P T +V+ + + +LK + F +P L
Sbjct: 179 EGLENLLEEEEKRKTGAITPDTYAVVIARAGSGKPVVKCDKIENLKN--YDFGEPLHCLV 236
Query: 958 MIGKSL 963
++ K+L
Sbjct: 237 VLAKTL 242
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 32.3 bits (75), Expect = 1.2
Identities = 27/129 (20%), Positives = 48/129 (37%), Gaps = 34/129 (26%)
Query: 404 RKFIIADTPGHEQYTRNMITGAS---------------TADAVIILIDASKIKFNPSVNL 448
+ F+IAD PG +I GAS T ++ L+D +
Sbjct: 206 KSFVIADIPG-------LIEGASEGAGLGHRFLKHIERTR-LLLHLVDIEAVDPVEDYKT 257
Query: 449 LTQT-KRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTIP 507
+ +++S L K I+ +NK+DL++ + KR +
Sbjct: 258 IRNELEKYS---PELADKPRILVLNKIDLLDEEEEREKRAALELAALGGPV-------FL 307
Query: 508 ISALNGDNI 516
ISA+ G+ +
Sbjct: 308 ISAVTGEGL 316
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 32.4 bits (75), Expect = 1.2
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 16/44 (36%)
Query: 379 TDGLESEREQGITIDVA--------YRYFNTPKRKFIIADTPGH 414
D +E E+E+GITI A +R N II DTPGH
Sbjct: 50 MDWMEQEQERGITITSAATTCFWKDHR-IN------II-DTPGH 85
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 32.5 bits (75), Expect = 1.3
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 22/74 (29%)
Query: 377 LLTDGLESEREQGITIDVA-----YRYFNTPKRKFII--ADTPGHEQY----TRNM--IT 423
L D E E+ +GITI A + Y ++I DTPGH + TR M +
Sbjct: 56 LALDFDEEEQARGITIKAANVSMVHEYEGKE---YLINLIDTPGHVDFGGDVTRAMRAVD 112
Query: 424 GASTADAVIILIDA 437
GA I+++DA
Sbjct: 113 GA------IVVVDA 120
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5 and
Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants.
The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 31.0 bits (71), Expect = 1.6
Identities = 30/124 (24%), Positives = 52/124 (41%), Gaps = 33/124 (26%)
Query: 405 KFIIADTPGHEQYT-------RNMITGASTADAVIILID-ASKIKFNPSVNLLTQTKRHS 456
KF I DT G E+Y R A A I++ D S+ F + + + + + H
Sbjct: 51 KFEIWDTAGQERYRSLAPMYYRG-------AAAAIVVYDITSEESFEKAKSWVKELQEHG 103
Query: 457 ---IIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNG 513
I+ I +A NK DL + Q+ + +++A++ + T SA G
Sbjct: 104 PPNIV--------IALAGNKADLESKRQVSTEEA----QEYADENGLLFMET---SAKTG 148
Query: 514 DNII 517
+N+
Sbjct: 149 ENVN 152
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. 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.
Length = 146
Score = 30.8 bits (70), Expect = 1.7
Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 8/58 (13%)
Query: 465 KHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNGDNIISASNN 522
K +I+ +NK DL+ K ++ K AE T ISA NG I+
Sbjct: 29 KKLIMVLNKADLVP------KEVL--RKWVAELSELYGTKTFFISATNGQGILKLKAE 78
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 32.1 bits (74), Expect = 1.7
Identities = 24/94 (25%), Positives = 41/94 (43%), Gaps = 21/94 (22%)
Query: 425 ASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFY 484
AD V+ ++DAS+ L + ++I L + K II+ +NK DL++
Sbjct: 294 IEEADLVLFVLDASQ--------PLDKEDL-ALIELLPKKKPIIVVLNKADLVS------ 338
Query: 485 KRIVYAYKKFAEDIHFQNINTIPISALNGDNIIS 518
+I +K A I ISA G+ + +
Sbjct: 339 -KIELESEKLANGDAI-----ISISAKTGEGLDA 366
>gnl|CDD|224026 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 263
Score = 31.5 bits (72), Expect = 1.7
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 327 FITA-GSVDDGKSTLI----GRLLFDSKNIFIDQLDAVSRTKYKR 366
F+T GS GKSTL+ G L S I ID +D ++ KR
Sbjct: 34 FVTVIGSNGAGKSTLLNAIAGDLKPTSGQILIDGVDVTKKSVAKR 78
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. 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.
Length = 204
Score = 31.3 bits (72), Expect = 1.8
Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 32/97 (32%)
Query: 428 ADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRI--------KHIIIAVNKMDLINY 479
AD ++ ++DAS +P R I + + II+ +NK+DL++
Sbjct: 121 ADLLLHVVDAS----DP--------DREEQIETVEEVLKELGADDIPIILVLNKIDLLDD 168
Query: 480 NQIFYKRIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
++ E + + + ISA G+ +
Sbjct: 169 EEL------------EERLRAGRPDAVFISAKTGEGL 193
>gnl|CDD|216343 pfam01171, ATP_bind_3, PP-loop family. This family of proteins
belongs to the PP-loop superfamily.
Length = 182
Score = 31.0 bits (71), Expect = 1.8
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 2/35 (5%)
Query: 44 FSGGKDSVVLLRLAEKAFRPSRFPFPMVHIDTGHN 78
SGG DS+ LL L +K H+D H
Sbjct: 6 VSGGPDSMALLYLLKKLKPKFGIDLTAAHVD--HG 38
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 31.9 bits (73), Expect = 2.0
Identities = 19/94 (20%), Positives = 38/94 (40%), Gaps = 24/94 (25%)
Query: 427 TADAVIILIDAS----KIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQI 482
AD ++ ++DAS K ++L + I II+ +NK+DL+
Sbjct: 271 EADLLLHVVDASDPEILEKLEAVEDVLAEIGADEI--------PIILVLNKIDLL----- 317
Query: 483 FYKRIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
++ ++ + N + ISA G+ +
Sbjct: 318 -------EDEEILAELERGSPNPVFISAKTGEGL 344
>gnl|CDD|223523 COG0446, HcaD, Uncharacterized NAD(FAD)-dependent dehydrogenases
[General function prediction only].
Length = 415
Score = 31.8 bits (72), Expect = 2.1
Identities = 28/171 (16%), Positives = 51/171 (29%), Gaps = 41/171 (23%)
Query: 739 VYIIGAGPGAADLITVRGARLLRKADVVLYDA---------LITNELLMLCPKAKHIFVG 789
+ I+G G T RLL A++ L ++ + + +
Sbjct: 1 IVIVGGGAAGLSAAT-TLRRLLLAAEITLIGREPKYSYYRCPLSLYVGGGIASLEDLRYP 59
Query: 790 KRFKKHSIAQYIINRIIVKCAFKYNLVVRLKGG-----------------------DPML 826
RF + + + + N VV L G + ++
Sbjct: 60 PRFNRATGIDVRTGTEVTSIDPE-NKVVLLDDGEIEYDYLVLATGARPRPPPISDWEGVV 118
Query: 827 FGRTDEELNALKKYNIKVK---VIPGITAALAAASESKQSLTKRNISRSVV 874
R E+ ALK K V+ L AA ++ KR +++
Sbjct: 119 TLRLREDAEALKGGAEPPKDVVVVGAGPIGLEAA----EAAAKRGKKVTLI 165
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 31.9 bits (73), Expect = 2.1
Identities = 20/98 (20%), Positives = 40/98 (40%), Gaps = 22/98 (22%)
Query: 389 GITIDVAYRYFNTPKRKFIIADTPG---------HEQYTRNMITGASTADAVIILIDASK 439
G+T++ + I D PG E+ R+ + D ++ ++DA+
Sbjct: 35 GVTVEKKEGKLKYKGHEIEIVDLPGTYSLTAYSEDEKVARDFLLEGK-PDLIVNVVDATN 93
Query: 440 IKFNPSVNLLTQTKRHSIIAHLLRI-KHIIIAVNKMDL 476
++ N + L Q LL + +I+A+N +D
Sbjct: 94 LERN--LYLTLQ---------LLELGIPMILALNMIDE 120
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 31.7 bits (73), Expect = 2.5
Identities = 16/40 (40%), Positives = 21/40 (52%)
Query: 379 TDGLESEREQGITIDVAYRYFNTPKRKFIIADTPGHEQYT 418
D +E E+E+GITI A + I DTPGH +T
Sbjct: 48 MDWMEQEQERGITITSAATTCFWKGHRINIIDTPGHVDFT 87
>gnl|CDD|143307 cd05899, IgV_TCR_beta, Immunoglobulin (Ig) variable (V) domain of
T-cell receptor (TCR) bet a chain. IgV_TCR_beta:
immunoglobulin (Ig) variable domain of the beta chain of
alpha/beta T-cell antigen receptors (TCRs). TCRs mediate
antigen recognition by T lymphocytes, and are composed
of alpha and beta, or gamma and delta, polypeptide
chains with variable (V) and constant (C) regions. This
group includes the variable domain of the alpha chain of
alpha/beta TCRs. Alpha/beta TCRs recognize antigen as
peptide fragments presented by major histocompatibility
complex (MHC) molecules. The variable domain of TCRs is
responsible for antigen recognition, and is located at
the N-terminus of the receptor. Gamma/delta TCRs
recognize intact protein antigens; they recognize
proteins antigens directly and without antigen
processing, and MHC independently of the bound peptide.
Length = 110
Score = 29.6 bits (67), Expect = 2.6
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 5/39 (12%)
Query: 521 NNMLWY-----NGPTLISLLESLNTNEKIDKKPLRFPVQ 554
+NM WY G L+ + NE+ RF
Sbjct: 27 DNMYWYRQDPGKGLQLLFYSNGGSLNEEEGDPKDRFSAS 65
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 30.5 bits (69), Expect = 2.8
Identities = 21/116 (18%), Positives = 38/116 (32%), Gaps = 37/116 (31%)
Query: 326 RFITAGSVDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESE 385
I AG D GK++L L + K V S
Sbjct: 5 AVIIAGLCDSGKTSLFTLLTTGTVK--------------KTVTSQEP------------- 37
Query: 386 REQGITIDVAYRYFNTPKRKFIIADTPGHEQYTRNMITG---ASTADAVIILIDAS 438
AY+Y F + D PGH + + ++ +S+ ++ ++D++
Sbjct: 38 -------SAAYKYMLHKGFSFTLIDFPGHVKLRQKLLETIKDSSSLRGIVFVVDST 86
>gnl|CDD|189028 cd09858, PIN_MKT1, PIN domain of Mkt1: A global regulator of mRNAs
encoding mitochondrial proteins and eukaryotic homologs.
The Mkt1 gene product interacts with the
Poly(A)-binding protein associated factor, Pbp1, and is
present at the 3' end of RNA transcripts during
translation. The Mkt1-Pbp1 complex is involved in the
post-transcriptional regulation of HO endonuclease
expression. Mkt1 and eukaryotic homologs are atypical
members of the structure-specific, 5' nuclease family.
Conical members of this family possess a PIN (PilT N
terminus) domain with a helical arch/clamp region/I
domain (approximately 40 to 55 residues in MKT1 PIN
domains) and inserted within the PIN domain is a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Although Mkt1 appears
to possess both a PIN and H3TH domain, the Mkt1 PIN
domain lacks several of the active site residues
necessary to bind essential divalent metal ion cofactors
(Mg2+/Mn2+) required for nuclease activity in this
family. Also, Mkt1 lacks the glycine-rich loop in the
H3TH domain which is proposed to facilitate duplex DNA
binding.
Length = 215
Score = 30.6 bits (70), Expect = 2.8
Identities = 16/76 (21%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 798 AQYIINRIIVKCAFKYNLVVRLKGGDPM-LFGRTDEELNALKKYNIK-VKVIPGITAALA 855
A + ++R++ + L + GG P L + +L K++NIK + V G++
Sbjct: 33 ATHYLSRLLTLKDEQEPLAL---GGLPPSLKSYIESDLRLFKEHNIKPIFVFDGLSPKSQ 89
Query: 856 AASESKQSLTKRNISR 871
S++ + R + +
Sbjct: 90 LEPSSQREQSARQLEQ 105
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 31.0 bits (71), Expect = 2.8
Identities = 29/131 (22%), Positives = 48/131 (36%), Gaps = 34/131 (25%)
Query: 404 RKFIIADTPGHEQYTRNMITGASTA-------------DAVII-LIDASKIKFNPSVN-- 447
F++AD PG +I GAS V++ +ID S I +
Sbjct: 207 ESFVVADIPG-------LIEGASEGVGLGLRFLRHIERTRVLLHVIDLSPIDGRDPIEDY 259
Query: 448 --LLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINT 505
+ + +++S L K I+ +NK+DL + + K AE
Sbjct: 260 QTIRNELEKYS---PKLAEKPRIVVLNKIDLPLDEEELEELK----KALAEA--LGWEVF 310
Query: 506 IPISALNGDNI 516
ISAL + +
Sbjct: 311 YLISALTREGL 321
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. 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. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 30.2 bits (69), Expect = 3.0
Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 13/91 (14%)
Query: 429 DAVIILIDAS-KIKFNPSVNLLTQTKRHSIIAH-LLRIKHIIIAVNKMDLINYNQIF-YK 485
D +I ++D+S + + + N L H ++ L+ ++I NK DL
Sbjct: 68 DGLIFVVDSSDRERIEEAKNEL-----HKLLNEEELKGAPLLILANKQDLPGALTESELI 122
Query: 486 RIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
++ H Q P SA+ GD +
Sbjct: 123 ELLGLESIKGRRWHIQ-----PCSAVTGDGL 148
>gnl|CDD|238942 cd01984, AANH_like, Adenine nucleotide alpha hydrolases superfamily
including N type ATP PPases, ATP sulphurylases
Universal Stress Response protein and electron transfer
flavoprotein (ETF). The domain forms a apha/beta/apha
fold which binds to Adenosine nucleotide.
Length = 86
Score = 28.9 bits (65), Expect = 3.1
Identities = 17/81 (20%), Positives = 25/81 (30%), Gaps = 18/81 (22%)
Query: 41 VLLFSGGKDSVVLLRLA-EKAFRPSRFPFPMVH-----------------IDTGHNFPEV 82
++ SGG DS VLL LA +V I GHN +V
Sbjct: 2 LVALSGGLDSSVLLHLAKRLKSGGPEVVALVVVAFVRILKRLAAEEGADVIILGHNADDV 61
Query: 83 ISFRDNCISKLGETLIVRSVE 103
R + + + +
Sbjct: 62 AGRRLGASANVLVVIKGAGIP 82
>gnl|CDD|180890 PRK07218, PRK07218, replication factor A; Provisional.
Length = 423
Score = 31.1 bits (71), Expect = 3.2
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 11/62 (17%)
Query: 234 IPFTNLTPA---HPGEI--IENLMVR-FRTVGDILCTCPILSNATTVEDIIKEISVTQIT 287
+PFT+ P G IE+ VR FR V + +S TTVE + +E+SV++
Sbjct: 210 LPFTDWDPLPEIEIGASIRIEDAYVREFRGVPSV-----NVSEFTTVEALDREVSVSKDP 264
Query: 288 ER 289
R
Sbjct: 265 PR 266
>gnl|CDD|233376 TIGR01363, strep_his_triad, streptococcal histidine triad protein.
This model represents the N-terminal half of a family of
Streptococcal proteins that contain a signal peptide and
then up to five repeats of a region that includes a
His-X-X-His-X-His (histidine triad) motif. Three repeats
are found in the seed alignment. Members of this family
from Streptococcus pneumoniae are suggested to cleave
human C3, and the member PhpA has been shown in vaccine
studies to be a protective antigen in mice [Cellular
processes, Pathogenesis].
Length = 348
Score = 30.7 bits (69), Expect = 3.6
Identities = 25/74 (33%), Positives = 31/74 (41%), Gaps = 9/74 (12%)
Query: 766 VLYDALITNELLMLCPKAKHIFVGKRFKKHSIAQYIINRIIVKCAFKYNLVVRLKGGDPM 825
V YDA+I+ ELLM P R K I I ++K KY V LK
Sbjct: 93 VPYDAIISEELLMKDPNY-------RLKDSDIVNEIKGGYVIKVNGKY--YVYLKDAAHA 143
Query: 826 LFGRTDEELNALKK 839
RT EE+ K+
Sbjct: 144 DNIRTKEEIARQKQ 157
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 30.5 bits (70), Expect = 3.6
Identities = 27/120 (22%), Positives = 47/120 (39%), Gaps = 29/120 (24%)
Query: 412 PGHEQYTRNMIT-GASTADAVIILIDASKIKF---NPSVNLLTQTKRHSIIAHLLRIKHI 467
PGH R I D VI ++DA +I NP ++ + K
Sbjct: 8 PGHMAKARREIKENLKLVDVVIEVLDA-RIPLSSENPMIDKIIGNKPR------------ 54
Query: 468 IIAVNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNGD---NIISASNNML 524
++ +NK DL + + + ++ E+ Q I + I+A G I+ A+ +L
Sbjct: 55 LLILNKSDLAD------PEVTKKWIEYFEE---QGIKALAINAKKGQGVKKILKAAKKLL 105
>gnl|CDD|215926 pfam00450, Peptidase_S10, Serine carboxypeptidase.
Length = 415
Score = 30.7 bits (70), Expect = 4.0
Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 12 NNLNNLYLDWLESEAIHIMREVSAECNNPVLLFSGGKDSVV 52
+ + N Y D + + I+ ++ VL++SG D +
Sbjct: 305 DEVFNWYGDDISKSMLPILPKLLEG-GLRVLIYSGDHDLIC 344
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 30.8 bits (70), Expect = 4.4
Identities = 46/185 (24%), Positives = 80/185 (43%), Gaps = 41/185 (22%)
Query: 333 VDDGKSTLIGRLLFDSKNIFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQGITI 392
VD GKSTL L V + ++S N + TD E+E+GITI
Sbjct: 28 VDHGKSTLTDSL--------------VCKAG---IISSKNAGDARFTDTRADEQERGITI 70
Query: 393 D---VAYRYFNTP-----KRKFII--ADTPGHEQYTRNMITGASTADAVIILIDASKIKF 442
++ Y + K+ F+I D+PGH ++ + D ++++D +
Sbjct: 71 KSTGISLYYEHDLEDGDDKQPFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVE--- 127
Query: 443 NPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMD-LINYNQIFYKRIVYAYKKFAEDIHFQ 501
V + T+T + RI+ ++ +NK+D I Q+ + I Y+ F + I +
Sbjct: 128 --GVCVQTETVLRQALQE--RIRPVLF-INKVDRAILELQLDPEEI---YQNFVKTI--E 177
Query: 502 NINTI 506
N+N I
Sbjct: 178 NVNVI 182
>gnl|CDD|238953 cd01995, ExsB, ExsB is a transcription regulator related protein.
It is a subfamily of a Adenosine nucleotide binding
superfamily of proteins. This protein family is
represented by a single member in nearly every
completed large (> 1000 genes) prokaryotic genome. In
Rhizobium meliloti, a species in which the exo genes
make succinoglycan, a symbiotically important
exopolysaccharide, exsB is located nearby and affects
succinoglycan levels, probably through polar effects on
exsA expression or the same polycistronic mRNA. In
Arthrobacter viscosus, the homologous gene is
designated ALU1 and is associated with an aluminum
tolerance phenotype. The function is unknown.
Length = 169
Score = 29.5 bits (67), Expect = 4.7
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 41 VLLFSGGKDSVVLLRLAEKAF 61
V+L SGG DS L A+K
Sbjct: 3 VVLLSGGLDSTTCLAWAKKEG 23
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. 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
Score = 30.6 bits (69), Expect = 4.8
Identities = 27/104 (25%), Positives = 49/104 (47%), Gaps = 19/104 (18%)
Query: 383 ESEREQGITIDVA-----YRYFNTPKRKFII--ADTPGHEQYTRNMITGASTADAVIILI 435
E E+E+GITI+ A + Y +++I DTPGH + ++ D I+++
Sbjct: 61 EQEQERGITINAANVSMVHEY---EGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVV 117
Query: 436 DASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMD-LIN 478
A + + +L Q + +K ++ +NK+D LIN
Sbjct: 118 CAVEGVMPQTETVLRQALKE-------NVKPVLF-INKVDRLIN 153
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 29.7 bits (68), Expect = 5.4
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 15/88 (17%)
Query: 429 DAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIV 488
D V+I+ + FN LL R+ + A I+ +I +NK DL+ + + ++
Sbjct: 4 DQVLIVFSLKEPFFNL--RLLD---RYLVAAEASGIE-PVIVLNKADLV--DDEELEELL 55
Query: 489 YAYKKFAEDIHFQNINTIPISALNGDNI 516
Y+K + +SA G+ +
Sbjct: 56 EIYEKL-------GYPVLAVSAKTGEGL 76
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 30.3 bits (69), Expect = 5.5
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 12/38 (31%)
Query: 351 IFIDQLDAVSRTKYKRVMSGHNIDLSLLTDGLESEREQ 388
IFID++DAV R + + G+ EREQ
Sbjct: 151 IFIDEIDAVGRQRGAGLGGGN------------DEREQ 176
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. 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.
Length = 191
Score = 29.5 bits (67), Expect = 6.0
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 8/67 (11%)
Query: 455 HSIIAHLLRIKH---IIIAVNKMDLI--NYNQIFYKRIVYAYKKFAEDIHFQNINTIPIS 509
S+I L + +I+ NK+DL+ + K+ V KK + + + I +S
Sbjct: 48 GSLIPGLAELIGAKPVILVGNKIDLLPKDVKPNRLKQWV---KKRLKIGGLKIKDVILVS 104
Query: 510 ALNGDNI 516
A G +
Sbjct: 105 AKKGWGV 111
>gnl|CDD|212507 cd11648, RsmI, Ribosomal RNA small subunit methyltransferase I,
also known as rRNA (cytidine-2'-O-)-methyltransferase
RsmI. Proteins in this family catalyze the
2-O-methylation of the ribose of cytidine 1402 (C1402)
in 16S rRNA using S-adenosyl-L-methionine (SAM or
Ado-Met) as the methyl donor. RsmI proteins employ the
30S subunit (not the 16S rRNA) as a substrate,
suggesting that the methylation reaction occurs at a
late step during 30S assembly in the cell.
Length = 218
Score = 29.7 bits (68), Expect = 6.0
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 835 NALKKYNIKVKVIPGITAALAAASES 860
A + I V IPG +A + A S S
Sbjct: 94 RAAIEAGIPVVPIPGPSALITALSAS 119
>gnl|CDD|218881 pfam06070, Herpes_UL32, Herpesvirus large structural phosphoprotein
UL32. The large phosphorylated protein (UL32-like) of
herpes viruses is the polypeptide most frequently
reactive in immuno-blotting analyses with antisera when
compared with other viral proteins.
Length = 777
Score = 30.3 bits (68), Expect = 6.3
Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 206 QYIEREKIILPSLY----FAHKRKIIKRKGLLIPFTNLTPAHPGEIIENL 251
+ ++L +L + + + G I F NL E+ ENL
Sbjct: 118 DFRPDVDVVLRALVSLARLSECQPL--AWGTEIGFVNLRAEEVQELEENL 165
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 29.0 bits (66), Expect = 6.9
Identities = 24/106 (22%), Positives = 41/106 (38%), Gaps = 20/106 (18%)
Query: 412 PGHEQYTRNMITG-ASTADAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIA 470
PGH I D VI + DA +I + R+ + +L K +I
Sbjct: 3 PGHMAKALRQIKEKLKLVDVVIEVRDA-RIPL---------SSRNPDLDKILGNKPRLIV 52
Query: 471 VNKMDLINYNQIFYKRIVYAYKKFAEDIHFQNINTIPISALNGDNI 516
+NK DL + + K+ + +K Q + ++A NG +
Sbjct: 53 LNKADLADPAKT--KKWLKYFKS-------QGEPVLFVNAKNGKGV 89
>gnl|CDD|236887 PRK11259, solA, N-methyltryptophan oxidase; Provisional.
Length = 376
Score = 29.8 bits (68), Expect = 6.9
Identities = 12/29 (41%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 398 YFNTPKRKFIIADTPGHEQYTRNMITGAS 426
Y NTP FII PGH + +G S
Sbjct: 313 YTNTPDEHFIIDTLPGHPNVL--VASGCS 339
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 30.1 bits (68), Expect = 7.1
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 20/82 (24%)
Query: 404 RKFIIADTPG--------HEQYTRNMITGASTADAVIILIDASKIKFNPSVNLLTQTKRH 455
F + DT G S ADAV+ ++D ++ LT T
Sbjct: 323 TDFKLVDTGGWEADVEGIDSAIASQAQIAVSLADAVVFVVD-GQVG-------LTSTD-- 372
Query: 456 SIIAHLLRI--KHIIIAVNKMD 475
I +LR K +++AVNK+D
Sbjct: 373 ERIVRMLRRAGKPVVLAVNKID 394
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC class
I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows a
circular permutation of the GTPase signature motifs so
that the C-terminal strands 5, 6, and 7 (strand 6
contains the G4 box with sequence NKXD) are relocated to
the N-terminus.
Length = 140
Score = 28.7 bits (65), Expect = 7.9
Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 15/88 (17%)
Query: 429 DAVIILIDASKIKFNPSVNLLTQTKRHSIIAHLLRIKHIIIAVNKMDLINYNQIFYKRIV 488
D V+ ++DA F +L K + K ++ +NK DL+ +
Sbjct: 13 DVVVQIVDARNPLFFRCPDLEKYVKE------VDPSKENVLLLNKADLVT------EEQR 60
Query: 489 YAYKKFAEDIHFQNINTIPISALNGDNI 516
A+ ++ + + I + SALN I
Sbjct: 61 KAWARYFKK---EGIVVLFFSALNEATI 85
>gnl|CDD|223676 COG0603, COG0603, Predicted PP-loop superfamily ATPase [General
function prediction only].
Length = 222
Score = 29.1 bits (66), Expect = 8.0
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 41 VLLFSGGKDSVVLLRLAEKAF 61
V+L SGG DS L A+K
Sbjct: 6 VVLLSGGLDSTTCLAWAKKEG 26
>gnl|CDD|185455 PTZ00114, PTZ00114, Heat shock protein 60; Provisional.
Length = 555
Score = 29.9 bits (68), Expect = 8.3
Identities = 9/41 (21%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 570 YMGRIESGIIKKNDCLIVEPSGKKATIKD-IQMLNKSLDMA 609
+G + + K++ +I+ G KA IK+ +++L ++
Sbjct: 328 MLGSAKKVTVTKDETVILTGGGDKAEIKERVELLRSQIERT 368
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 29.5 bits (67), Expect = 9.4
Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 460 HLLRIKHIIIAVNKMDL-INYNQIFYKRIVYAYKKFAEDIHFQNINTIPISA 510
+LL K ++ N + + + KR+ K+ A + + +P+SA
Sbjct: 202 NLLTAKPMLYVANVSEDDLANLNEYVKRL----KELAAKENAE---VVPVSA 246
>gnl|CDD|238954 cd01996, Alpha_ANH_like_III, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily.Adeninosine
nucleotide alpha hydrolases superfamily includes N
type ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins is predicted to bind ATP.
This domain has a strongly conserved motif SGGKD at
the N terminus.
Length = 154
Score = 28.4 bits (64), Expect = 9.8
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 13/46 (28%)
Query: 41 VLLFSGGKDSVVLL-RLAEKAFRPSRFPFPM----VHIDTGHNFPE 81
++ SGGKDS L L EK + + V +D G N E
Sbjct: 5 IIGVSGGKDSSYALYLLKEK--------YGLNPLAVTVDNGFNSEE 42
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.137 0.397
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 49,745,129
Number of extensions: 5081136
Number of successful extensions: 5318
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5042
Number of HSP's successfully gapped: 258
Length of query: 967
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 861
Effective length of database: 6,236,078
Effective search space: 5369263158
Effective search space used: 5369263158
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 64 (28.5 bits)