RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1758
(1527 letters)
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress response
[Signal transduction mechanisms].
Length = 603
Score = 966 bits (2499), Expect = 0.0
Identities = 352/596 (59%), Positives = 463/596 (77%), Gaps = 6/596 (1%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
AIIAHVDHGKTTL+D LL+QSGTFR+ + + R+MDSN++EKERGITI +KN ++ YNGT
Sbjct: 9 AIIAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGITILAKNTAVNYNGT 68
Query: 986 RINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVN 1045
RINI+DTPGHADFGGEVER+LSMVD VLLL+DA EGPMPQTRFV +KAL LG KPIVV+N
Sbjct: 69 RINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALALGLKPIVVIN 128
Query: 1046 KIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIPLFE 1105
KIDR +ARP+ VVD FDLF +L AT+EQLDFP++Y SA +G A+ + + +M PLFE
Sbjct: 129 KIDRPDARPDEVVDEVFDLFVELGATDEQLDFPIVYASARNGTASLDPEDEADDMAPLFE 188
Query: 1106 AILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPN 1165
IL +VP K + + PLQ+Q+ L+Y+SY+G+IGIGRI G +K Q V ++ D
Sbjct: 189 TILDHVPAPKGDLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALIKS-DGTTE 247
Query: 1166 KAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTL 1225
+I ++ F GL+R+ + EA +GDIV I G+E+I IG TICDP P LP L++DEPTL
Sbjct: 248 NGRITKLLGFLGLERIEIEEAEAGDIVAIAGLEDINIGDTICDPDNPEALPALSVDEPTL 307
Query: 1226 TINFMVNNSPLAGREGKFITTRQIKNRLDHEIKNNIGLRVTQNKHDDSIYEVSGRGELHL 1285
++ F VN+SP AG+EGKF+T+RQI++RL+ E++ N+ LRV + + D+ +EVSGRGELHL
Sbjct: 308 SMTFSVNDSPFAGKEGKFVTSRQIRDRLNKELETNVALRVEETESPDA-FEVSGRGELHL 366
Query: 1286 TILIENMRREGYELSVSRPRVIFKTLNGELYEPYENLFVDIEEINQGIIMQKLNYRGGDL 1345
+ILIENMRREG+EL VSRP VI K ++G EP+E + +D+ E +QG +++KL R G++
Sbjct: 367 SILIENMRREGFELQVSRPEVIIKEIDGVKCEPFEEVTIDVPEEHQGAVIEKLGERKGEM 426
Query: 1346 KNIEINEKERVRLEYRIPSRGLIGFQNEFITLTRGTGLISHVFEEYAPFYNKSKYDLGKR 1405
K++ + K RVRLE+ IP+RGLIGF+ EF+T+TRGTG+++H F+ Y P K ++G R
Sbjct: 427 KDMAPDGKGRVRLEFVIPARGLIGFRTEFLTMTRGTGIMNHSFDHYRPV----KGEIGGR 482
Query: 1406 RNGVLISQYSGKAVAYSLWKLQDRGRLFINHNDLVYEGMIIGIHSRDNDLLVNPIKEKQL 1465
NGVLIS +GKAVAY+L+ LQDRG+LFI VYEGMIIG HSRDNDL VN +K K+L
Sbjct: 483 HNGVLISNETGKAVAYALFNLQDRGKLFIEPGTKVYEGMIIGEHSRDNDLTVNVLKGKKL 542
Query: 1466 TNIRSSGSDEAIQLISPIKITLEYAIEFINDDELVEITPKNIRLRKRFLKENERKK 1521
TN+R+SG DEA+ L PI++TLE A+EFI DDELVE+TP++IRLRK+ L ENERK+
Sbjct: 543 TNMRASGKDEAVTLTPPIRMTLERALEFIADDELVEVTPESIRLRKKILNENERKR 598
Score = 84.6 bits (210), Expect = 2e-16
Identities = 50/129 (38%), Positives = 64/129 (49%), Gaps = 20/129 (15%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAG----------------GITQHIGAYN--VVT 113
+ I+ HVDHGKT+L+D + K + F E GIT I A N V
Sbjct: 8 IAIIAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGIT--ILAKNTAVNY 65
Query: 114 NHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIV 173
N I +DTPGH F R + D V+L+V A +G MPQTR + A G+ IV
Sbjct: 66 NGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALALGLKPIV 125
Query: 174 AINKIDKLD 182
INKID+ D
Sbjct: 126 VINKIDRPD 134
>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 = 901 bits (2330), Expect = 0.0
Identities = 337/596 (56%), Positives = 451/596 (75%), Gaps = 6/596 (1%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
AIIAHVDHGKTTL+D LL+QSGTFR N+ + R+MDSN++E+ERGITI +KN +I YNGT
Sbjct: 5 AIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDLERERGITILAKNTAIRYNGT 64
Query: 986 RINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVN 1045
+INI+DTPGHADFGGEVER+L MVD VLLL+DA EGPMPQTRFV +KAL+LG KPIVV+N
Sbjct: 65 KINIVDTPGHADFGGEVERVLGMVDGVLLLVDASEGPMPQTRFVLKKALELGLKPIVVIN 124
Query: 1046 KIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIPLFE 1105
KIDR +ARP+ VVD FDLF +L A +EQLDFP++Y S G+A+ + NM PLF+
Sbjct: 125 KIDRPSARPDEVVDEVFDLFAELGADDEQLDFPIVYASGRAGWASLDLDDPSDNMAPLFD 184
Query: 1106 AILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPN 1165
AI+++VP K + + PLQ+ + +L+Y YLG+I IGR+ G +K Q V +M D
Sbjct: 185 AIVRHVPAPKGDLDEPLQMLVTNLDYDEYLGRIAIGRVHRGTVKKGQQVALMK-RDGTIE 243
Query: 1166 KAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTL 1225
+I+++ F+GL+RV ++EA +GDIV + G+E+I IG TI DP P LP + +DEPTL
Sbjct: 244 NGRISKLLGFEGLERVEIDEAGAGDIVAVAGLEDINIGETIADPEVPEALPTITVDEPTL 303
Query: 1226 TINFMVNNSPLAGREGKFITTRQIKNRLDHEIKNNIGLRVTQNKHDDSIYEVSGRGELHL 1285
++ F VN+SPLAG+EGK +T+R I++RL E++ N+ LRV + D +EVSGRGELHL
Sbjct: 304 SMTFSVNDSPLAGKEGKKVTSRHIRDRLMRELETNVALRVEDTESADK-FEVSGRGELHL 362
Query: 1286 TILIENMRREGYELSVSRPRVIFKTLNGELYEPYENLFVDIEEINQGIIMQKLNYRGGDL 1345
+ILIE MRREG+EL V RP+VI+K ++G+ EP E L +D+ E + G +++KL R G++
Sbjct: 363 SILIETMRREGFELQVGRPQVIYKEIDGKKLEPIEELTIDVPEEHVGAVIEKLGKRKGEM 422
Query: 1346 KNIEINEKERVRLEYRIPSRGLIGFQNEFITLTRGTGLISHVFEEYAPFYNKSKYDLGKR 1405
++E + R RLE++IPSRGLIGF+ EF+T TRGTG+++HVF+EY P+ K ++ R
Sbjct: 423 VDMEPSGNGRTRLEFKIPSRGLIGFRTEFLTDTRGTGIMNHVFDEYEPW----KGEIETR 478
Query: 1406 RNGVLISQYSGKAVAYSLWKLQDRGRLFINHNDLVYEGMIIGIHSRDNDLLVNPIKEKQL 1465
RNG L+S G A AY+LW LQ+RG +F++ VYEGMIIG HSR+NDL VNP K K+L
Sbjct: 479 RNGSLVSMEDGTATAYALWNLQERGVMFVSPGTEVYEGMIIGEHSRENDLDVNPCKAKKL 538
Query: 1466 TNIRSSGSDEAIQLISPIKITLEYAIEFINDDELVEITPKNIRLRKRFLKENERKK 1521
TN+RSSG DEA++L P K++LE A+E+I DDELVE+TPK+IRLRKR L NERK+
Sbjct: 539 TNVRSSGKDEAVKLTPPRKLSLEQALEYIEDDELVEVTPKSIRLRKRVLDPNERKR 594
Score = 83.5 bits (207), Expect = 3e-16
Identities = 48/135 (35%), Positives = 66/135 (48%), Gaps = 20/135 (14%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAG----------------GITQHIGAYNV-VTN 114
+ I+ HVDHGKT+L+D + K + F GIT I A N +
Sbjct: 4 IAIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDLERERGIT--ILAKNTAIRY 61
Query: 115 HGS-ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIV 173
+G+ I +DTPGH F R + D V+L+V A +G MPQTR + A G+ IV
Sbjct: 62 NGTKINIVDTPGHADFGGEVERVLGMVDGVLLLVDASEGPMPQTRFVLKKALELGLKPIV 121
Query: 174 AINKIDKLDINLDRI 188
INKID+ D +
Sbjct: 122 VINKIDRPSARPDEV 136
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 900 bits (2329), Expect = 0.0
Identities = 319/539 (59%), Positives = 412/539 (76%), Gaps = 10/539 (1%)
Query: 1 MSVKSSVVIKNLMKLGQMVTINQVLDQETAMILVEEMGHVAHASKLNDPESFLLNEYNKN 60
M+VK++ VIK L KLG M TINQ LDQETA +L EE GH L + +
Sbjct: 191 MAVKAAEVIKKLFKLGVMATINQSLDQETAELLAEEFGHEVKLVSLLEDDD--------- 241
Query: 61 ITAESLVRAPIVTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHGSITF 120
+ + R P+VTIMGHVDHGKTSLLD IRKTNV EAGGITQHIGAY V TN G ITF
Sbjct: 242 -EEDLVPRPPVVTIMGHVDHGKTSLLDAIRKTNVAAGEAGGITQHIGAYQVETNGGKITF 300
Query: 121 LDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDK 180
LDTPGHEAFTAMRARGA+VTDIVVLVVAADDGVMPQT EAI HAK +GVP+IVAINKIDK
Sbjct: 301 LDTPGHEAFTAMRARGAQVTDIVVLVVAADDGVMPQTIEAINHAKAAGVPIIVAINKIDK 360
Query: 181 LDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISLQAEILELKAPVT 240
N DR+KQ+L ++PEE+GG + F+ +SAKTG GI++LLE I LQAE+LELKA
Sbjct: 361 PGANPDRVKQELSEYGLVPEEWGGDTIFVPVSAKTGEGIDELLEAILLQAEVLELKANPD 420
Query: 241 TPAKGVIIESRLDKGKGPVATVLIQSGTLRCSDIVVAGASYGRIRSMLNENGKNILEAGP 300
PA+G +IE++LDKG+GPVATVL+Q+GTL+ DIVVAG +YGR+R+M+++NGK + EAGP
Sbjct: 421 RPARGTVIEAKLDKGRGPVATVLVQNGTLKVGDIVVAGTTYGRVRAMVDDNGKRVKEAGP 480
Query: 301 SIPVEIQGLTKVPFSGEELFVILNEKKAREIGLFRQGKFRDVKLSKQKLHKTENMFNDIN 360
S PVEI GL+ VP +G+E V+ +EKKAREI +RQ K R+ KL++Q+ EN+F +
Sbjct: 481 STPVEILGLSGVPQAGDEFVVVEDEKKAREIAEYRQEKAREKKLARQQRVSLENLFEQMK 540
Query: 361 KEKVKNLLIIIKTDVYGSREVLTESLKNLSTDKVKIQVIHNAVGNINESDINLAIASKAI 420
+ +VK L +IIK DV GS E L +SL+ LSTD+VK+ +IH+ VG I ESD+ LA AS AI
Sbjct: 541 EGEVKELNLIIKADVQGSVEALKDSLEKLSTDEVKVNIIHSGVGAITESDVTLAAASNAI 600
Query: 421 IIGFNVRADASTRKLAQINNINIRYHNIIYNIIKEIKSEITNLIPLEKKENLLGLAEIRQ 480
IIGFNVR DA RKLA+ ++IRY++IIY++I ++K+ ++ ++ E +E ++G AE+R+
Sbjct: 601 IIGFNVRPDAKARKLAEQEGVDIRYYSIIYDLIDDVKAAMSGMLEPEYEEEIIGQAEVRE 660
Query: 481 VILVNKVSKIAGCYILEGLIRRDSKIRILRNKNIIWTGELDSLKRFKDNVKEVKAGFEC 539
V V+KV IAGC + EG I+R++K+R+LR+ +I+ GEL+SLKRFKD+VKEV+AG+EC
Sbjct: 661 VFKVSKVGTIAGCMVTEGKIKRNAKVRVLRDGVVIYEGELESLKRFKDDVKEVRAGYEC 719
Score = 67.2 bits (165), Expect = 5e-11
Identities = 50/144 (34%), Positives = 70/144 (48%), Gaps = 46/144 (31%)
Query: 927 IIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKE-RGIT--I--FSKNCSIE 981
I+ HVDHGKT+L+D + RK +N E GIT I + +E
Sbjct: 254 IMGHVDHGKTSLLDAI-------RK----------TNVAAGEAGGITQHIGAY----QVE 292
Query: 982 YNGTRINIIDTPGHADF------GGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKAL- 1034
NG +I +DTPGH F G +V I V+L++ A +G MPQ T +A+
Sbjct: 293 TNGGKITFLDTPGHEAFTAMRARGAQVTDI------VVLVVAADDGVMPQ----TIEAIN 342
Query: 1035 --KLGFKPIVV-VNKIDRSNARPE 1055
K PI+V +NKID+ A P+
Sbjct: 343 HAKAAGVPIIVAINKIDKPGANPD 366
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 685 bits (1768), Expect = 0.0
Identities = 335/598 (56%), Positives = 452/598 (75%), Gaps = 5/598 (0%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
AIIAHVDHGKTTL+D LL+QSGTF R+MDSN++EKERGITI +KN +I++N
Sbjct: 9 AIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTAIKWNDY 68
Query: 986 RINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVN 1045
RINI+DTPGHADFGGEVER++SMVD+VLL++DA +GPMPQTRFVT+KA G KPIVV+N
Sbjct: 69 RINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIVVIN 128
Query: 1046 KIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIPLFE 1105
K+DR ARP+WVVD FDLF L AT+EQLDFP++Y SAL+G A + + +M PL++
Sbjct: 129 KVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNGIAGLDHEDMAEDMTPLYQ 188
Query: 1106 AILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPN 1165
AI+ +VP + + P Q+QI L+Y+SY+G IGIGRI G++K Q V I++ + K
Sbjct: 189 AIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQVTIIDS-EGKTR 247
Query: 1166 KAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTL 1225
AK+ ++ GL+R+ + A +GDIV ITG+ E+ I T+CD LP L++DEPT+
Sbjct: 248 NAKVGKVLGHLGLERIETDLAEAGDIVAITGLGELNISDTVCDTQNVEALPALSVDEPTV 307
Query: 1226 TINFMVNNSPLAGREGKFITTRQIKNRLDHEIKNNIGLRVTQNKHDDSIYEVSGRGELHL 1285
++ F VN SP G+EGKF+T+RQI +RL+ E+ +N+ LRV + + D+ + VSGRGELHL
Sbjct: 308 SMFFCVNTSPFCGKEGKFVTSRQILDRLNKELVHNVALRVEETEDADA-FRVSGRGELHL 366
Query: 1286 TILIENMRREGYELSVSRPRVIFKTLNGELYEPYENLFVDIEEINQGIIMQKLNYRGGDL 1345
++LIENMRREG+EL+VSRP+VIF+ ++G EPYEN+ +D+EE +QG +MQ L R GDL
Sbjct: 367 SVLIENMRREGFELAVSRPKVIFREIDGRKQEPYENVTLDVEEQHQGSVMQALGERKGDL 426
Query: 1346 KNIEINEKERVRLEYRIPSRGLIGFQNEFITLTRGTGLISHVFEEYAPFYNKSKYDLGKR 1405
KN+ + K RVRL+Y IPSRGLIGF++EF+T+T GTGL+ F Y + ++G+R
Sbjct: 427 KNMNPDGKGRVRLDYVIPSRGLIGFRSEFMTMTSGTGLLYSTFSHYD---DVRPGEVGQR 483
Query: 1406 RNGVLISQYSGKAVAYSLWKLQDRGRLFINHNDLVYEGMIIGIHSRDNDLLVNPIKEKQL 1465
+NGVLIS GKAVA++L+ LQDRG+LF+ H VYEG IIGIHSR NDL VN + K+L
Sbjct: 484 QNGVLISNGQGKAVAFALFGLQDRGKLFLGHGAEVYEGQIIGIHSRSNDLTVNCLTGKKL 543
Query: 1466 TNIRSSGSDEAIQLISPIKITLEYAIEFINDDELVEITPKNIRLRKRFLKENERKKKL 1523
TN+R+SG+DEA+ L+ PI++TLE A+EFI+DDELVE+TP +IR+RKR L EN+R++
Sbjct: 544 TNMRASGTDEAVVLVPPIRMTLEQALEFIDDDELVEVTPTSIRIRKRHLTENDRRRAN 601
Score = 65.9 bits (160), Expect = 1e-10
Identities = 43/125 (34%), Positives = 58/125 (46%), Gaps = 16/125 (12%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHGSITFL---------- 121
+ I+ HVDHGKT+L+D + + + F + + N + IT L
Sbjct: 8 IAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTAIKWND 67
Query: 122 ------DTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAI 175
DTPGH F R + D V+LVV A DG MPQTR A G+ IV I
Sbjct: 68 YRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPIVVI 127
Query: 176 NKIDK 180
NK+D+
Sbjct: 128 NKVDR 132
>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 = 683 bits (1763), Expect = 0.0
Identities = 300/540 (55%), Positives = 398/540 (73%), Gaps = 3/540 (0%)
Query: 1 MSVKSSVVIKNLMKLGQMVTINQVLDQETAMILVEEMGHVAHASKLNDPESFLLNEYNKN 60
M++K S +IK LM LG MVTINQVLD+ETA ++ EE G E E +++
Sbjct: 21 MNIKVSDIIKKLMLLGVMVTINQVLDKETAELVAEEFGV--KVEVRVTLEETEAEEQDED 78
Query: 61 ITAESLVRAPIVTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHGS-IT 119
+ R P+VTIMGHVDHGKTSLLD IRKT V EAGGITQHIGAY+V G IT
Sbjct: 79 SGDLLVERPPVVTIMGHVDHGKTSLLDSIRKTKVAQGEAGGITQHIGAYHVENEDGKMIT 138
Query: 120 FLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKID 179
FLDTPGHEAFT+MRARGAKVTDIVVLVVAADDGVMPQT EAI+HAK + VP+IVAINKID
Sbjct: 139 FLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVPIIVAINKID 198
Query: 180 KLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISLQAEILELKAPV 239
K + N DR+KQ+L ++PE++GG + F+ +SA TG GI++LL+ I LQ+E+ ELKA
Sbjct: 199 KPEANPDRVKQELSEYGLVPEDWGGDTIFVPVSALTGDGIDELLDMILLQSEVEELKANP 258
Query: 240 TTPAKGVIIESRLDKGKGPVATVLIQSGTLRCSDIVVAGASYGRIRSMLNENGKNILEAG 299
A GV+IE++LDKG+GPVATVL+QSGTLR DIVV GA+YGR+R+M++ENGK++ EAG
Sbjct: 259 NGQASGVVIEAQLDKGRGPVATVLVQSGTLRVGDIVVVGAAYGRVRAMIDENGKSVKEAG 318
Query: 300 PSIPVEIQGLTKVPFSGEELFVILNEKKAREIGLFRQGKFRDVKLSKQKLHKTENMFNDI 359
PS PVEI GL+ VP +G+E V +EK AR + R GK R LS+ +N+F I
Sbjct: 319 PSKPVEILGLSDVPAAGDEFIVFKDEKDARLVAEKRAGKLRQKALSRSVKVTLDNLFEQI 378
Query: 360 NKEKVKNLLIIIKTDVYGSREVLTESLKNLSTDKVKIQVIHNAVGNINESDINLAIASKA 419
+ ++K L II+K DV GS E + SL+ L+ ++VK++VIH+ VG I E+DI+LA AS A
Sbjct: 379 KEGELKELNIILKADVQGSLEAIKNSLEKLNNEEVKVKVIHSGVGGITETDISLASASNA 438
Query: 420 IIIGFNVRADASTRKLAQINNINIRYHNIIYNIIKEIKSEITNLIPLEKKENLLGLAEIR 479
IIIGFNVR DA+ + +A+ N++IRY+++IY +I EI++ + ++ E +E ++G AE+R
Sbjct: 439 IIIGFNVRPDATAKNVAEAENVDIRYYSVIYKLIDEIRAAMKGMLDPEYEEEIIGQAEVR 498
Query: 480 QVILVNKVSKIAGCYILEGLIRRDSKIRILRNKNIIWTGELDSLKRFKDNVKEVKAGFEC 539
QV V K+ IAGCY+ EG+I+R + +R++R+ +I+ GE+DSLKRFKD+VKEV G+EC
Sbjct: 499 QVFNVPKIGNIAGCYVTEGVIKRGNPLRVIRDGVVIFEGEIDSLKRFKDDVKEVSNGYEC 558
Score = 65.9 bits (161), Expect = 9e-11
Identities = 44/133 (33%), Positives = 59/133 (44%), Gaps = 19/133 (14%)
Query: 927 IIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKER-GITIFSKNCSIEYN-G 984
I+ HVDHGKT+L+D I + + E GIT +E G
Sbjct: 92 IMGHVDHGKTSLLDS-----------------IRKTKVAQGEAGGITQHIGAYHVENEDG 134
Query: 985 TRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVV 1044
I +DTPGH F R + D V+L++ A +G MPQT A IV +
Sbjct: 135 KMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVPIIVAI 194
Query: 1045 NKIDRSNARPEWV 1057
NKID+ A P+ V
Sbjct: 195 NKIDKPEANPDRV 207
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 652 bits (1685), Expect = 0.0
Identities = 263/476 (55%), Positives = 350/476 (73%), Gaps = 4/476 (0%)
Query: 68 RAPIVTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHGS---ITFLDTP 124
R P+VTIMGHVDHGKT+LLD IRKTNV EAGGITQHIGAY V + ITF+DTP
Sbjct: 4 RPPVVTIMGHVDHGKTTLLDKIRKTNVAAGEAGGITQHIGAYQVPLDVIKIPGITFIDTP 63
Query: 125 GHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLDIN 184
GHEAFTAMRARGA VTDI +LVVAADDGVMPQT EAI HAK +GVP++VAINKIDK + N
Sbjct: 64 GHEAFTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAAGVPIVVAINKIDKPEAN 123
Query: 185 LDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISLQAEILELKAPVTTPAK 244
D++KQ+L ++PEE+GG F+ +SAKTG GI++LLE I L AE+LELKA PA+
Sbjct: 124 PDKVKQELQEYGLVPEEWGGDVIFVPVSAKTGEGIDELLELILLLAEVLELKANPEGPAR 183
Query: 245 GVIIESRLDKGKGPVATVLIQSGTLRCSDIVVAGASYGRIRSMLNENGKNILEAGPSIPV 304
G +IE +LDKG GPVATV++Q GTL+ DI+VAG YGR+R+M+++ GK I EAGPS PV
Sbjct: 184 GTVIEVKLDKGLGPVATVIVQDGTLKKGDIIVAGGEYGRVRTMVDDLGKPIKEAGPSKPV 243
Query: 305 EIQGLTKVPFSGEELFVILNEKKAREIGLFRQGKFRDVKLSKQKLHKTENMFNDINKEK- 363
EI GL++VP +G+ V+ +EKKAR I R R+ +L+ +K + E + +I
Sbjct: 244 EILGLSEVPAAGDVFIVVKDEKKARAIAELRVVLLREAELASKKKGELEELIAEIKIRGE 303
Query: 364 VKNLLIIIKTDVYGSREVLTESLKNLSTDKVKIQVIHNAVGNINESDINLAIASKAIIIG 423
+K L +I+K D GS E L SLK L D+VK+++IH VG I ESD+ LA AS A+IIG
Sbjct: 304 LKELNVILKADTQGSLEALKGSLKKLGVDEVKVRIIHAGVGGITESDVMLAAASDAVIIG 363
Query: 424 FNVRADASTRKLAQINNINIRYHNIIYNIIKEIKSEITNLIPLEKKENLLGLAEIRQVIL 483
FNVR D R+LA+ + IRY+++IY +I+++++ + ++ EKKE ++GLAE+R V
Sbjct: 364 FNVRVDPEARRLAESEGVKIRYYDVIYKLIEDVEAAMKGMLEPEKKERVIGLAEVRAVFK 423
Query: 484 VNKVSKIAGCYILEGLIRRDSKIRILRNKNIIWTGELDSLKRFKDNVKEVKAGFEC 539
+ KV IAGC + EG+I+R + +R++R+ +I+ GE++SLKRFKD+VKEV+ G EC
Sbjct: 424 LPKVGAIAGCMVTEGVIKRGAPVRVVRDGVVIYEGEVESLKRFKDDVKEVRKGQEC 479
Score = 66.0 bits (162), Expect = 7e-11
Identities = 43/136 (31%), Positives = 61/136 (44%), Gaps = 25/136 (18%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
I+ HVDHGKTTL+D +R++ N+ A ++ I + G +
Sbjct: 9 TIMGHVDHGKTTLLDK-IRKT-------NVAAG--EAGGITQHIGAYQVPLD---VIKIP 55
Query: 986 RINIIDTPGHADF------GGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFK 1039
I IDTPGH F G V I +L++ A +G MPQT A G
Sbjct: 56 GITFIDTPGHEAFTAMRARGASVTDI------AILVVAADDGVMPQTIEAINHAKAAGVP 109
Query: 1040 PIVVVNKIDRSNARPE 1055
+V +NKID+ A P+
Sbjct: 110 IVVAINKIDKPEANPD 125
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 463 bits (1193), Expect = e-145
Identities = 231/538 (42%), Positives = 338/538 (62%), Gaps = 11/538 (2%)
Query: 8 VIKNLMKLGQMVTINQVLDQETAMILVEEMGHVAHASKLNDPESFLLNEYNKNITAESLV 67
+IK+L G VT+NQ++D + ++ G + + N+ N N + E+ +
Sbjct: 182 IIKSLFLKGISVTVNQIIDISIISQVADDFGINIISEEKNNINEKTSNLDNTSAFTENSI 241
Query: 68 -RAPIVTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHGS----ITFLD 122
R PIVTI+GHVDHGKT+LLD IRKT + EAGGITQ IGAY V + I FLD
Sbjct: 242 NRPPIVTILGHVDHGKTTLLDKIRKTQIAQKEAGGITQKIGAYEVEFEYKDENQKIVFLD 301
Query: 123 TPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLD 182
TPGHEAF++MR+RGA VTDI +L++AADDGV PQT EAI + + + VP+IVAINKIDK +
Sbjct: 302 TPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVPIIVAINKIDKAN 361
Query: 183 INLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISLQAEILELKAPVTTP 242
N +RIKQ L +IPE++GG +P I ISA G I+KLLE I L AEI +LKA T
Sbjct: 362 ANTERIKQQLAKYNLIPEKWGGDTPMIPISASQGTNIDKLLETILLLAEIEDLKADPTQL 421
Query: 243 AKGVIIESRLDKGKGPVATVLIQSGTLRCSDIVVAGASYGRIRSMLNENGKNILEAGPSI 302
A+G+I+E+ LDK KGPVAT+L+Q+GTL DI+V G SY +IR M+N G I A PS
Sbjct: 422 AQGIILEAHLDKTKGPVATILVQNGTLHIGDIIVIGTSYAKIRGMINSLGNKINLATPSS 481
Query: 303 PVEIQGLTKVPFSGEELFVILNEKKAREIGLFRQGKFRDVK-LSKQKLHKTENMFNDINK 361
VEI GL+ VP +GE V +EK+A+ + K + K +K+ T N +
Sbjct: 482 VVEIWGLSSVPATGEHFQVFNSEKEAKL--KIIKNKENNKKDTTKRITLSTTKTINKKDN 539
Query: 362 EKVKNLLIIIKTDVYGSREVLTESLKNLSTDKVKIQVIHNAVGNINESDINLAIASKAII 421
+K NL IIKTD GS E + S+ + KV++ +++ ++G + E+D+ A + A I
Sbjct: 540 KKQINL--IIKTDTQGSIEAIINSISQIPQKKVQLNILYASLGEVTETDVEFASTTNAEI 597
Query: 422 IGFNVRADASTRKLAQINNINIRYHNIIYNIIKEIKSEITNLIPLEKKENLLGLAEIRQV 481
+ FN +K A+ NI I+ + +IY++++ I++ + +L+ E K+ +G AE++ V
Sbjct: 598 LAFNTNLAPGAKKAARKLNIIIKEYQVIYDLLEYIEALMEDLLDPEYKKVPIGEAEVKTV 657
Query: 482 ILVNKVSKIAGCYILEGLIRRDSKIRILRNKNIIWTGELDSLKRFKDNVKEVKAGFEC 539
+ K +AGC + EG I +++ I+++R +I+ G++ SLKR K++V+E + G EC
Sbjct: 658 FPLAK-RFVAGCRVTEGKITKNALIKVIRENKLIYEGKITSLKRVKEDVEEAQEGNEC 714
Score = 60.6 bits (147), Expect = 5e-09
Identities = 45/134 (33%), Positives = 58/134 (43%), Gaps = 20/134 (14%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGIT--IFSKNCSIEYN 983
I+ HVDHGKTTL+D + RK Q GIT I + EY
Sbjct: 248 TILGHVDHGKTTLLDKI-------RKTQIAQKEA---------GGITQKIGAYEVEFEYK 291
Query: 984 GTRINII--DTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPI 1041
I+ DTPGH F R ++ D +L+I A +G PQT I
Sbjct: 292 DENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVPII 351
Query: 1042 VVVNKIDRSNARPE 1055
V +NKID++NA E
Sbjct: 352 VAINKIDKANANTE 365
>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 = 350 bits (901), Expect = e-112
Identities = 126/187 (67%), Positives = 156/187 (83%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
AIIAHVDHGKTTL+D LL+QSGTFR+N+ + R+MDSN++E+ERGITI +KN +I Y T
Sbjct: 6 AIIAHVDHGKTTLVDALLKQSGTFRENEEVGERVMDSNDLERERGITILAKNTAITYKDT 65
Query: 986 RINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVN 1045
+INIIDTPGHADFGGEVER+LSMVD VLLL+DA EGPMPQTRFV +KAL+ G KPIVV+N
Sbjct: 66 KINIIDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALEAGLKPIVVIN 125
Query: 1046 KIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIPLFE 1105
KIDR +ARPE VVD FDLF +L AT+EQLDFP++Y SA +G+A+ N ++ PLFE
Sbjct: 126 KIDRPDARPEEVVDEVFDLFLELNATDEQLDFPIVYASAKNGWASLNLDDPSEDLDPLFE 185
Query: 1106 AILKYVP 1112
I+++VP
Sbjct: 186 TIIEHVP 192
Score = 85.0 bits (211), Expect = 1e-18
Identities = 56/167 (33%), Positives = 76/167 (45%), Gaps = 24/167 (14%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAG----------------GITQHIGAYNVVTNH 115
+ I+ HVDHGKT+L+D + K + F E GIT I A N +
Sbjct: 5 IAIIAHVDHGKTTLVDALLKQSGTFRENEEVGERVMDSNDLERERGIT--ILAKNTAITY 62
Query: 116 GSITF--LDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIV 173
+DTPGH F R + D V+L+V A +G MPQTR + A +G+ IV
Sbjct: 63 KDTKINIIDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALEAGLKPIV 122
Query: 174 AINKIDKLDINLDRIK---QDLISEQVIPEEYGGASPFISISAKTGV 217
INKID+ D + + DL E +E P + SAK G
Sbjct: 123 VINKIDRPDARPEEVVDEVFDLFLELNATDEQLDF-PIVYASAKNGW 168
>gnl|CDD|234986 PRK01851, truB, tRNA pseudouridine synthase B; Provisional.
Length = 303
Score = 351 bits (902), Expect = e-110
Identities = 137/258 (53%), Positives = 182/258 (70%), Gaps = 1/258 (0%)
Query: 659 KNIIHGVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSN 718
+ + GVLLLDKP GLSSN+AL++ K LL AKK G+TGTLDP ATGLLPLCFGEATKFS
Sbjct: 12 RRPVDGVLLLDKPLGLSSNDALQRAKRLLRAKKAGHTGTLDPLATGLLPLCFGEATKFSQ 71
Query: 719 YLSEADKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMY 778
L +ADK YEA + LG+ T TGD EG+++ + + +E L F G+I Q+PPMY
Sbjct: 72 DLLDADKTYEATLRLGVRTSTGDAEGEVLA-TRPVDCDPAALEAALARFTGEIRQVPPMY 130
Query: 779 SALKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSED 838
SALK G PLY+YAR+GIT++R+ R + I+ + ++ +P +T+R+ CSKGTYIR L+ED
Sbjct: 131 SALKKDGKPLYEYARAGITVEREARDVTIHALDLLACDLPDVTIRVTCSKGTYIRTLAED 190
Query: 839 IGKMLGCGAHLKYLRRIGIDKLTLDKCLNIDTIIKYSEYERISSLIPIDILLSSFGIIYL 898
IG+ LGCGAHL LRR G+ LTL++ + ++ + E ER + L P+D LLS+F + L
Sbjct: 191 IGEALGCGAHLTALRRTGVGGLTLEQAVTLEALEAADEAERDALLAPVDALLSTFPRVTL 250
Query: 899 SDLLSKRFLHGQNLFLSD 916
+ RFLHGQ L LSD
Sbjct: 251 DADAAGRFLHGQRLRLSD 268
>gnl|CDD|235333 PRK05033, truB, tRNA pseudouridine synthase B; Provisional.
Length = 312
Score = 344 bits (885), Expect = e-108
Identities = 116/265 (43%), Positives = 167/265 (63%), Gaps = 12/265 (4%)
Query: 656 KKNKNIIHGVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATK 715
++ ++I +GVLLLDKP G+SSN+AL+K+K L NA K G+TG LDP ATG+LP+C GEATK
Sbjct: 4 RRGRDI-NGVLLLDKPQGMSSNDALQKVKRLFNANKAGHTGALDPLATGMLPICLGEATK 62
Query: 716 FSNYLSEADKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIP 775
FS YL ++DK Y LG T+T D +G++++ + + S E +E L F G I Q+P
Sbjct: 63 FSQYLLDSDKRYRVTARLGQRTDTSDADGEVVE-ERPVTLSAEQLEAALEKFRGDIEQVP 121
Query: 776 PMYSALKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVL 835
MYSALKY+G PLY+YAR GI ++R+ R I IY++ +I + L L +HCSKGTYIR L
Sbjct: 122 SMYSALKYQGQPLYEYARQGIEVEREARPITIYELELIRFEGDELELEVHCSKGTYIRTL 181
Query: 836 SEDIGKMLGCGAHLKYLRRIGIDKLTLDKCLNIDTIIKYSEYERISS----------LIP 885
+D+G+ LGCGAH+ YLRR + L++ + ++ + E L+P
Sbjct: 182 VDDLGEKLGCGAHVIYLRRTQVAPYPLERMVTLEQLEALVEQAEQQEIPPAELLDPLLLP 241
Query: 886 IDILLSSFGIIYLSDLLSKRFLHGQ 910
+D +S + L + + F GQ
Sbjct: 242 MDSAVSDLPEVNLPEESAYYFKQGQ 266
>gnl|CDD|211339 cd02573, PseudoU_synth_EcTruB, Pseudouridine synthase, Escherichia
coli TruB like. This group consists of bacterial
pseudouridine synthases similar to E. coli TruB and
Mycobacterium tuberculosis TruB. Pseudouridine synthases
catalyze the isomerization of specific uridines in an
RNA molecule to pseudouridines (5-ribosyluracil, psi).
E. coli TruB and M. tuberculosis TruB make psi55 in the
T loop of tRNAs. Psi55 is nearly universally conserved.
E. coli TruB is not inhibited by RNA containing
5-fluorouridine.
Length = 213
Score = 302 bits (777), Expect = 2e-94
Identities = 101/210 (48%), Positives = 140/210 (66%), Gaps = 2/210 (0%)
Query: 664 GVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEA 723
G+LLLDKP GL+S++ ++K++ LL KKVG+TGTLDP ATG+LP+ GEATK S YL +A
Sbjct: 1 GILLLDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDA 60
Query: 724 DKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKY 783
DK Y A + LG T+T D EG+II+ + + E IE L F G+I Q+PPMYSA+K
Sbjct: 61 DKTYRATVRLGEATDTDDAEGEIIETSPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKV 120
Query: 784 KGIPLYKYARSGITIKRKLRYIKIYKITIIDYT--IPYLTLRIHCSKGTYIRVLSEDIGK 841
G LY+ AR+G ++R R + IY + ++ + P +HCSKGTYIR L+ D+GK
Sbjct: 121 DGKRLYELARAGEEVERPPRKVTIYSLELLSFDPENPEADFEVHCSKGTYIRSLARDLGK 180
Query: 842 MLGCGAHLKYLRRIGIDKLTLDKCLNIDTI 871
LGCGAHL LRR TL++ + ++ +
Sbjct: 181 ALGCGAHLSALRRTRSGPFTLEQAITLEEL 210
>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 = 284 bits (730), Expect = 1e-88
Identities = 109/169 (64%), Positives = 128/169 (75%), Gaps = 5/169 (2%)
Query: 70 PIVTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNH--GSITFLDTPGHE 127
P+VT+MGHVDHGKT+LLD IRKTNV EAGGITQHIGAY V + ITF+DTPGHE
Sbjct: 1 PVVTVMGHVDHGKTTLLDKIRKTNVAAGEAGGITQHIGAYQVPIDVKIPGITFIDTPGHE 60
Query: 128 AFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKL---DIN 184
AFT MRARGA VTDI +LVVAADDGVMPQT EAI HAK + VP+IVAINKIDK + +
Sbjct: 61 AFTNMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAANVPIIVAINKIDKPYGTEAD 120
Query: 185 LDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISLQAEIL 233
+R+K +L ++ EE+GG + ISAKTG GI+ LLE I L AE+L
Sbjct: 121 PERVKNELSELGLVGEEWGGDVSIVPISAKTGEGIDDLLEAILLLAEVL 169
Score = 82.9 bits (206), Expect = 5e-18
Identities = 51/166 (30%), Positives = 69/166 (41%), Gaps = 21/166 (12%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKE-RGIT--IFSKNCSIEY 982
++ HVDHGKTTL+D + RK +N E GIT I + I+
Sbjct: 4 TVMGHVDHGKTTLLDKI-------RK----------TNVAAGEAGGITQHIGAYQVPIDV 46
Query: 983 NGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIV 1042
I IDTPGH F R S+ D +L++ A +G MPQT A IV
Sbjct: 47 KIPGITFIDTPGHEAFTNMRARGASVTDIAILVVAADDGVMPQTIEAINHAKAANVPIIV 106
Query: 1043 VVNKIDRSNARPEWVVDATFDLFDKLCATEEQL-DFPVIYTSALHG 1087
+NKID+ +L + EE D ++ SA G
Sbjct: 107 AINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVPISAKTG 152
>gnl|CDD|129523 TIGR00431, TruB, tRNA pseudouridine(55) synthase. TruB, the tRNA
pseudouridine 55 synthase, converts uracil to
pseudouridine in the T loop of most tRNAs in all three
domains of life. This model is built on a seed alignment
of bacterial proteins only. Saccharomyces cerevisiae
protein YNL292w (Pus4) has been shown to be the
pseudouridine 55 synthase of both cytosolic and
mitochondrial compartments, active at no other position
on tRNA and the only enzyme active at that position in
the species. A distinct yeast protein YLR175w,
(centromere/microtubule-binding protein CBF5) is an rRNA
pseudouridine synthase, and the archaeal set is much
more similar to CBF5 than to Pus4. It is unclear whether
the archaeal proteins found by this model are tRNA
pseudouridine 55 synthases like TruB, rRNA pseudouridine
synthases like CBF5, or (as suggested by the absence of
paralogs in the Archaea) both. CBF5 likely has
additional, eukaryotic-specific functions. The trusted
cutoff is set above the scores for the archaeal homologs
of unknown function, so yeast Pus4p scores between
trusted and noise [Protein synthesis, tRNA and rRNA base
modification].
Length = 209
Score = 265 bits (679), Expect = 3e-81
Identities = 108/208 (51%), Positives = 147/208 (70%), Gaps = 1/208 (0%)
Query: 662 IHGVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLS 721
I+GVLLLDKP G++S +AL K++ LLN KKVG+TGTLDPFATG+LP+ G+ATK S YL+
Sbjct: 1 INGVLLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLT 60
Query: 722 EADKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSAL 781
+ DK Y A I LG+ T+T D +G+I++ P E +E L F G+I QIPPMYSAL
Sbjct: 61 DLDKEYRAEIRLGVRTDTLDPDGQIVETRPVNPT-TEDVEAALPTFRGEIEQIPPMYSAL 119
Query: 782 KYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGK 841
K G LY+YAR GI ++RK R + +Y + + Y P LTL +HCSKGTYIR L+ D+G+
Sbjct: 120 KVNGKRLYEYARQGIEVERKARPVTVYDLQFLKYEGPELTLEVHCSKGTYIRTLARDLGE 179
Query: 842 MLGCGAHLKYLRRIGIDKLTLDKCLNID 869
LGCGA++ +LRR + LD+ + ++
Sbjct: 180 KLGCGAYVSHLRRTAVGDFPLDQSVTLE 207
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal
structure and biogenesis].
Length = 271
Score = 232 bits (595), Expect = 5e-69
Identities = 88/251 (35%), Positives = 132/251 (52%), Gaps = 32/251 (12%)
Query: 660 NIIHGVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNY 719
I GV+ LDKP G +S+ + +K +L +K G+ GTLDP ATG+LP+C GEATK Y
Sbjct: 12 EIYIGVINLDKPPGPTSHEVVAWVKRILGVEKAGHGGTLDPLATGVLPICLGEATKLVQY 71
Query: 720 LSEADKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYS 779
L +ADK Y A + LG T++ E + L F G+I QIPPM+S
Sbjct: 72 LLDADKEYVATVRLGDQTDS-----------------EEEVRAALEAFTGEIYQIPPMFS 114
Query: 780 ALKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDI 839
A+K ++R R I IY + +D+ +TLR+ CSKGTYIR L+ D+
Sbjct: 115 AVK-------------REVER--RKITIYDLLELDFDRNLVTLRVECSKGTYIRTLARDL 159
Query: 840 GKMLGCGAHLKYLRRIGIDKLTLDKCLNIDTIIKYSEYERISSLIPIDILLSSFGIIYLS 899
G+ LGCGAH+ LRR + + + + ++ + + + L+P++ LS + L
Sbjct: 160 GEALGCGAHMSELRRTRVGPFSEEDAVTLELLDELDAESLLRLLLPLESALSDLPRLVLK 219
Query: 900 DLLSKRFLHGQ 910
D + +G
Sbjct: 220 DSAANAIKYGA 230
>gnl|CDD|216540 pfam01509, TruB_N, TruB family pseudouridylate synthase (N terminal
domain). Members of this family are involved in
modifying bases in RNA molecules. They carry out the
conversion of uracil bases to pseudouridine. This family
includes TruB, a pseudouridylate synthase that
specifically converts uracil 55 to pseudouridine in most
tRNAs. This family also includes Cbf5p that modifies
rRNA.
Length = 149
Score = 227 bits (581), Expect = 7e-69
Identities = 74/149 (49%), Positives = 104/149 (69%)
Query: 684 KYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEAIIHLGITTETGDIE 743
K +L AKKVG+TGTLDP ATG+LP+C G+ATK YL +ADK Y A I LG+ T+T D E
Sbjct: 1 KRILGAKKVGHTGTLDPLATGVLPVCVGKATKLLQYLLDADKEYRATIRLGVATDTLDAE 60
Query: 744 GKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPLYKYARSGITIKRKLR 803
G+I++ + E IE++L +F G+I Q+PPMYSA+K G LY+ AR GI ++R R
Sbjct: 61 GEIVEEPPVDHITEEKIEEVLASFTGEIEQVPPMYSAVKVNGKRLYELAREGIEVERPPR 120
Query: 804 YIKIYKITIIDYTIPYLTLRIHCSKGTYI 832
+ IY + ++++ +P +T + CSKGTYI
Sbjct: 121 PVTIYSLELLEFDLPEVTFEVSCSKGTYI 149
>gnl|CDD|178886 PRK00130, truB, tRNA pseudouridine synthase B; Provisional.
Length = 290
Score = 232 bits (595), Expect = 1e-68
Identities = 100/251 (39%), Positives = 152/251 (60%), Gaps = 3/251 (1%)
Query: 664 GVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEA 723
G+L + KP G++S + ++KI+ + KKVG+TGTLDP A+G+LP+C G+ATK +YL E
Sbjct: 3 GILNILKPPGMTSFDVVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGKATKIVDYLMEG 62
Query: 724 DKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKY 783
K Y A I LG+ T+T D EG+I+ + + E I + +++F G+I Q+PPMYSALK
Sbjct: 63 KKTYRAEIKLGVETDTYDREGEILKEKEVSHLTEEEIREAILSFQGEIDQVPPMYSALKI 122
Query: 784 KGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKML 843
G LY+ AR GI ++R+ R I IY I I++ +PY+ + CSKGTYIR L DIG+ L
Sbjct: 123 NGKKLYELARQGIEVEREARKITIYDIEILEIDLPYVIFDVKCSKGTYIRSLCFDIGEKL 182
Query: 844 GCGAHLKYLRRIGIDKLTLDKCLNIDTIIKYSEYERISSLIPIDILLSSFGIIYLSDLLS 903
CGA++ L R ++ + ++ + +E +IPID L + + L +
Sbjct: 183 NCGAYMWNLIRTETGPFNIENSITLEDL---NEENIEDYIIPIDKALKHYPKVSLDEKFE 239
Query: 904 KRFLHGQNLFL 914
K L+G +
Sbjct: 240 KLLLNGVKIKD 250
>gnl|CDD|179870 PRK04642, truB, tRNA pseudouridine synthase B; Provisional.
Length = 300
Score = 225 bits (574), Expect = 8e-66
Identities = 110/254 (43%), Positives = 160/254 (62%), Gaps = 4/254 (1%)
Query: 662 IHGVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLS 721
+ G+LLLDKP GLSSNNAL+ + LL A+K G+TG+LDP ATGLLPLCFGEATK + L
Sbjct: 9 LDGILLLDKPAGLSSNNALQAARRLLRAEKGGHTGSLDPLATGLLPLCFGEATKIAGLLL 68
Query: 722 EADKYYEAIIHLGITTETGDIEGKIIDFNKNIPN-SIEIIEKILINFHGKISQIPPMYSA 780
+ K Y+A I LG+TT+T D +G+++ + +P+ S ++ L G+I Q P+YSA
Sbjct: 69 GSAKAYDAEIVLGVTTDTDDADGQVL-RERPVPDLSAAALQAALAPLIGRIRQRAPIYSA 127
Query: 781 LKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIG 840
LK G PLY AR G I+ +R ++++ I ++ Y P L LR+ C GTYIR L+ D+G
Sbjct: 128 LKQGGEPLYAKARRGEVIEAPVREVEVHAIEVLGYAAPRLRLRVTCGSGTYIRSLARDLG 187
Query: 841 KMLGCGAHLKYLRRIGIDKLTLDKCLNIDTIIKYSEY--ERISSLIPIDILLSSFGIIYL 898
++LGCGAH+ LRR+ ++ + + ++ + E E + L+P+ L+ F I L
Sbjct: 188 EVLGCGAHIAALRRLWVEPFRAPQMITLEALEAALEAGAEADTLLLPLAAGLADFPRIEL 247
Query: 899 SDLLSKRFLHGQNL 912
L+ RF GQ L
Sbjct: 248 DATLAARFRMGQRL 261
>gnl|CDD|134035 PRK00020, truB, tRNA pseudouridine synthase B; Provisional.
Length = 244
Score = 214 bits (547), Expect = 4e-63
Identities = 102/221 (46%), Positives = 141/221 (63%), Gaps = 8/221 (3%)
Query: 656 KKNKNIIHGVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATK 715
K+ + GVLLLDKP GLSSN+AL++ K ++A K G+TGTLDPFATGLL C G ATK
Sbjct: 3 KRRGLALDGVLLLDKPVGLSSNHALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGRATK 62
Query: 716 FSNYLSEADKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEK-----ILINFHGK 770
S + EADK Y+A + G T++GD+ G I+ P+ +E+ +L F G
Sbjct: 63 ISGRMLEADKTYQATLQFGEETDSGDLTGHIV---ARAPDGFAGVEEAALRDVLSRFVGT 119
Query: 771 ISQIPPMYSALKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGT 830
I QIPPMYSALK G PLY+YAR+GI + R R + I I ++ ++ + + CSKGT
Sbjct: 120 IEQIPPMYSALKRDGKPLYEYARAGIELDRPPRQVTIRHIELLSFSGMQAQIDVACSKGT 179
Query: 831 YIRVLSEDIGKMLGCGAHLKYLRRIGIDKLTLDKCLNIDTI 871
YIR L++DIG+ LGC AHL LRR + +LD+ + ++ +
Sbjct: 180 YIRTLAQDIGRALGCHAHLAALRRTHVGPFSLDRAVTLEAL 220
>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 = 209 bits (535), Expect = 3e-62
Identities = 79/189 (41%), Positives = 96/189 (50%), Gaps = 12/189 (6%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
II HVDHGKTTL D LL +G K AR++D + E+ERGITI S E
Sbjct: 7 GIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSFETKKR 66
Query: 986 RINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVN 1045
INIIDTPGH DF E+ R S D +L++DAVEG MPQTR A LG IV +N
Sbjct: 67 LINIIDTPGHVDFTKEMIRGASQADGAILVVDAVEGVMPQTREHLLLAKTLGVPIIVFIN 126
Query: 1046 KIDR-SNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIPLF 1104
KIDR +A E VV+ + PV+ SAL G + L
Sbjct: 127 KIDRVDDAELEEVVEEISRELLEK-YGFGGETVPVVPGSALTGE----------GIDELL 175
Query: 1105 EAILKYVPV 1113
EA+ Y+P
Sbjct: 176 EALDLYLPS 184
Score = 189 bits (483), Expect = 4e-55
Identities = 71/182 (39%), Positives = 95/182 (52%), Gaps = 18/182 (9%)
Query: 68 RAPIVTIMGHVDHGKTSLLDYIRKTNVVFSE----------------AGGITQHIGAYNV 111
R + I+GHVDHGKT+L D + S+ GIT I A +
Sbjct: 2 RHRNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSF 61
Query: 112 VTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPL 171
T I +DTPGH FT RGA D +LVV A +GVMPQTRE + AK GVP+
Sbjct: 62 ETKKRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAVEGVMPQTREHLLLAKTLGVPI 121
Query: 172 IVAINKIDKLDI-NLDRIKQDLISEQVIPEEYGG-ASPFISISAKTGVGINKLLENISLQ 229
IV INKID++D L+ + +++ E + +GG P + SA TG GI++LLE + L
Sbjct: 122 IVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTGEGIDELLEALDLY 181
Query: 230 AE 231
Sbjct: 182 LP 183
>gnl|CDD|234959 PRK01550, truB, tRNA pseudouridine synthase B; Provisional.
Length = 304
Score = 211 bits (540), Expect = 4e-61
Identities = 103/268 (38%), Positives = 157/268 (58%), Gaps = 14/268 (5%)
Query: 664 GVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEA 723
GVLLL KP G++S++ + K++ +L KKVG+TGTLDP +G+LP+C G ATK + YL++
Sbjct: 3 GVLLLHKPRGMTSHDCVFKLRKILRTKKVGHTGTLDPEVSGVLPICVGRATKIAEYLTDE 62
Query: 724 DKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSI--EIIEKILINFHGKISQIPPMYSAL 781
K YE + LG +T T D +G++++ K + I E IE L + G I QIPPMYSA+
Sbjct: 63 GKTYEGEVTLGFSTTTEDADGEVVE-TKPVDRPITREEIEAALASLTGTIEQIPPMYSAV 121
Query: 782 KYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYT------IPYLTLRIHCSKGTYIRVL 835
K G LY+YAR+GI ++R +R I I++ ++D R+ CSKGTY+R L
Sbjct: 122 KVNGKKLYEYARAGIEVERPVRQITIHEFVLLDSREDFEGETQSFRFRVTCSKGTYVRTL 181
Query: 836 SEDIGKMLGCGAHLKYLRRIGIDKLTLDKCLNIDTIIKYSEYERISS-LIPIDILLSSFG 894
+ IG+ LG AH+ +L R TL+ CL + I + + + S L PID LS
Sbjct: 182 AVMIGEKLGYPAHMSHLVRTASGGFTLEDCLTFEEIEENVQAGTVESILYPIDRALSHLP 241
Query: 895 IIYLSDLLSKRFLHG----QNLFLSDEN 918
+ + + +++ +G LF++ E
Sbjct: 242 KLVIDEKQAEKVKNGAFLKNPLFITVEA 269
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 219 bits (560), Expect = 1e-60
Identities = 164/558 (29%), Positives = 254/558 (45%), Gaps = 118/558 (21%)
Query: 67 VRAPIVTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGA----YNVVTN-------- 114
+R PIV ++GHVDHGKT+LLD IR T V EAGGITQHIGA +V+
Sbjct: 4 LRQPIVVVLGHVDHGKTTLLDKIRGTAVAAKEAGGITQHIGATEVPIDVIEKIAGPLKKP 63
Query: 115 -HGSIT-----FLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISG 168
+ F+DTPGHEAFT +R RG + DI +LVV ++G PQT EAI K
Sbjct: 64 LPIKLKIPGLLFIDTPGHEAFTNLRKRGGALADIAILVVDINEGFQPQTIEAINILKRRK 123
Query: 169 VPLIVAINKIDKL-------------DINL--DRIKQDLISEQVIPE------EYGGAS- 206
P +VA NKID++ I R++Q+L E+ + E E G ++
Sbjct: 124 TPFVVAANKIDRIPGWKSTEDAPFLESIEKQSQRVQQEL--EEKLYELIGQLSELGFSAD 181
Query: 207 ------------PFISISAKTGVGINKLLENIS-LQAEILE--LKAPVTTPAKGVIIESR 251
+ +SAKTG GI LL ++ L LE LK V P KG ++E +
Sbjct: 182 RFDRVKDFTKTVAIVPVSAKTGEGIPDLLMVLAGLAQRYLEERLKIDVEGPGKGTVLEVK 241
Query: 252 LDKGKGPVATVLIQSGTLRCSDIVVAGASYG----RIRSML-----------NENGKNIL 296
++G G V++ GTLR D +V G G ++R++L + K +
Sbjct: 242 EERGLGTTIDVILYDGTLRKGDTIVVGGKDGPIVTKVRALLKPRPLDEMRDPEDKFKPVD 301
Query: 297 E--AGPSIPVEIQGLTKVPFSGEELFVILNEKKAREIGLFRQGKFRDVKLSKQKLHKTEN 354
E A + + L +G L V+ R +VK ++ + E
Sbjct: 302 EVVAAAGVKISAPDLEDA-LAGSPLRVV------------RDEDVEEVK--EEVEEEIEE 346
Query: 355 MFNDINKEKVKNLLIIIKTDVYGSREVLTESLKNLSTDKVKIQVIHNAVGNINESDINLA 414
+ + ++E V ++K D GS E L L+ + I + VG+I++ D+ A
Sbjct: 347 IRIETDEEGV-----VVKADTLGSLEALVNELR-----EEGIPIRKADVGDISKRDVIEA 396
Query: 415 IASK------AIIIGFNVRADASTRKLAQINNINIRYHNIIYNIIKEIKSEITNLIPLEK 468
+I+ FNV+ + A+ +++ I ++IY +I++ + + EK
Sbjct: 397 STVAEKDPLYGVILAFNVKVLPDAEEEAEKSDVKIFTGDVIYQLIEDYEKWVKEQKEAEK 456
Query: 469 K---ENLLGLAEIRQVILVNKV---SK--IAGCYILEGLIRRDSKIRILRNKNIIWTGEL 520
+ E ++ A+IR IL V S I G +L G I+ + I + + G +
Sbjct: 457 EKILEKIVRPAKIR--ILPGYVFRQSDPAIVGVEVLGGTIKPGVPL-IKEDGKRV--GTI 511
Query: 521 DSLKRFKDNVKEVKAGFE 538
++ +NVKE KAG E
Sbjct: 512 KQIQDQGENVKEAKAGME 529
Score = 57.9 bits (141), Expect = 3e-08
Identities = 47/150 (31%), Positives = 68/150 (45%), Gaps = 41/150 (27%)
Query: 923 IKSAIIA---HVDHGKTTLIDHLLRQSGTFRK-----NQNINARIMDSNEIEKERGITIF 974
++ I+ HVDHGKTTL+D +R + K Q+I A + + IEK G
Sbjct: 4 LRQPIVVVLGHVDHGKTTLLDK-IRGTAVAAKEAGGITQHIGATEVPIDVIEKIAG---- 58
Query: 975 SKNCSIEYNGTRINI-----IDTPGHADF------GGEVERILSMVDNVLLLIDAVEGPM 1023
+ ++ I IDTPGH F GG ++ D +L++D EG
Sbjct: 59 ---PLKKPLPIKLKIPGLLFIDTPGHEAFTNLRKRGG------ALADIAILVVDINEGFQ 109
Query: 1024 PQTRFVTRKALKL--GFK-P-IVVVNKIDR 1049
PQ T +A+ + K P +V NKIDR
Sbjct: 110 PQ----TIEAINILKRRKTPFVVAANKIDR 135
>gnl|CDD|179199 PRK00989, truB, tRNA pseudouridine synthase B; Provisional.
Length = 230
Score = 204 bits (520), Expect = 1e-59
Identities = 85/207 (41%), Positives = 137/207 (66%), Gaps = 3/207 (1%)
Query: 662 IHGVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEA-TKFSNYL 720
G+LL+DKP G +S + ++ + L+ KK+G+ GTLDPFATG++ + G T+ S+ L
Sbjct: 8 KEGILLVDKPQGRTSFSLIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGRKFTRLSDIL 67
Query: 721 SEADKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSA 780
DK Y A+ HLG TT++ D +GKI+ +K IP ++E + F G+I Q+PPM+SA
Sbjct: 68 LFEDKEYAAVAHLGTTTDSYDCDGKIVGRSKKIP-TLEEVLSAASYFQGEIQQVPPMFSA 126
Query: 781 LKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIG 840
K +G LY+YAR G++I+R+ ++++ + + Y P L + CSKGTYIR ++ ++G
Sbjct: 127 KKVQGKKLYEYARQGLSIERRPSTVQVH-LQLTKYEYPLLHFVVQCSKGTYIRSIAHELG 185
Query: 841 KMLGCGAHLKYLRRIGIDKLTLDKCLN 867
MLGCGA+L+ LRR+ ++D+C++
Sbjct: 186 NMLGCGAYLEELRRLRSGSFSIDQCID 212
>gnl|CDD|179469 PRK02755, truB, tRNA pseudouridine synthase B; Provisional.
Length = 295
Score = 200 bits (510), Expect = 3e-57
Identities = 96/257 (37%), Positives = 145/257 (56%), Gaps = 7/257 (2%)
Query: 664 GVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEA 723
G L LDKP GL+S++ + +++ LL K+VG+ GTLDP ATG+LP+ G+AT+ YL
Sbjct: 4 GFLNLDKPAGLTSHDCVARLRRLLRLKRVGHGGTLDPAATGVLPIALGKATRLLPYLPG- 62
Query: 724 DKYYEAIIHLGITTETGDIEGKIIDFNKNIPN-SIEIIEKILINFHGKISQIPPMYSALK 782
+K Y I G+ T T D++G+I+ ++ P+ S+ IE L F GKI Q PP YSA++
Sbjct: 63 EKTYRGTIRFGVRTSTDDLQGEILS-SQPWPHLSLAEIETALPQFRGKIEQRPPQYSAIQ 121
Query: 783 YKGIPLYKYARSGITIKRKLRYIKIYKITIIDY---TIPYLTLRIHCSKGTYIRVLSEDI 839
G LY AR G T++ R + I+++ ++D+ P L L IHC GTYIR L+ D+
Sbjct: 122 VDGERLYALARRGETMELPARTVTIFRLQLLDWRPGDQPELDLEIHCGAGTYIRSLARDL 181
Query: 840 GKMLGCGAHLKYLRRIGIDKLTLDKCLNIDTIIKYSEYERISSLIPIDILLSSFGIIYLS 899
G +LG G L LRR L + L + + + L+P D+ L + LS
Sbjct: 182 GAVLGTGGTLAALRRTQSLGFHLAQSLPLPELENQLQAGTF-PLLPPDLALQHLPRVQLS 240
Query: 900 DLLSKRFLHGQNLFLSD 916
++R+ GQ + L +
Sbjct: 241 AEEAQRWCCGQRIPLEN 257
>gnl|CDD|211323 cd00506, PseudoU_synth_TruB_like, Pseudouridine synthase, TruB
family. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases similar to
Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M.
tuberculosis TruB, S. cerevisiae Cbf5 and human
dyskerin. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. E. coli TruB, M. tuberculosis TruB and S.
cerevisiae Pus4, make psi55 in the T loop of tRNAs.
Pus4 catalyses the formation of psi55 in both
cytoplasmic and mitochondrial tRNAs. Psi55 is almost
universally conserved. S. cerevisiae Cbf5 and human
dyskerin are nucleolar proteins that, with the help of
guide RNAs, make the hundreds of psueudouridnes present
in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin
is the catalytic subunit of eukaryotic box H/ACA small
nucleolar ribonucleoprotein (snoRNP) particles.
Mutations in human dyskerin cause X-linked dyskeratosis
congenitas.
Length = 210
Score = 196 bits (499), Expect = 6e-57
Identities = 79/208 (37%), Positives = 120/208 (57%), Gaps = 2/208 (0%)
Query: 664 GVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEA 723
G+ +DKP G SS++ + I+ + A+KVG+ GTLDPFATG+L + G+ATK +L A
Sbjct: 1 GLFAVDKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKATKLLKHLLAA 60
Query: 724 DKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKY 783
K Y AI LG T+T D G++I+ + E +E+ L G I Q+PP+YSA+K
Sbjct: 61 TKDYTAIGRLGQATDTFDATGQVIEETPYDHITHEQLERALETLTGDIQQVPPLYSAVKR 120
Query: 784 KGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPY--LTLRIHCSKGTYIRVLSEDIGK 841
+G Y+ AR G+ + + R IY++ I + P+ L + + C GTYIR L D+G
Sbjct: 121 QGQRAYELARRGLLVPDEARPPTIYELLCIRFNPPHFLLEVEVVCETGTYIRTLIHDLGL 180
Query: 842 MLGCGAHLKYLRRIGIDKLTLDKCLNID 869
LG GAH+ LRR + ++ + +
Sbjct: 181 ELGVGAHVTELRRTRVGPFKVENAVTLH 208
>gnl|CDD|235442 PRK05389, truB, tRNA pseudouridine synthase B; Provisional.
Length = 305
Score = 197 bits (502), Expect = 5e-56
Identities = 87/268 (32%), Positives = 146/268 (54%), Gaps = 3/268 (1%)
Query: 651 MQFHIKKNKNIIHGVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCF 710
M +K I G L+LDKP G++S A+ K+K+L +A+K G+ GTLDP A+G+LP+
Sbjct: 1 MARQRRKKGRPISGWLILDKPAGMTSTEAVSKVKWLFDAQKAGHAGTLDPLASGVLPIAL 60
Query: 711 GEATKFSNYLSEADKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGK 770
GEATK Y+ + K Y + G +T D+EG++ + P + E I L F G+
Sbjct: 61 GEATKTVPYVMDGTKRYRFTVAWGEERDTDDLEGEVTATSDVRP-TDEEIRAALPAFTGE 119
Query: 771 ISQIPPMYSALKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIP-YLTLRIHCSKG 829
I Q+PP +SA+K G Y AR G T++ R ++I ++T+++ + + C KG
Sbjct: 120 IMQVPPQFSAIKIDGERAYDLAREGETVELPARPVEIDRLTLVERPDADHAVFEVECGKG 179
Query: 830 TYIRVLSEDIGKMLGCGAHLKYLRRIGIDKLTLDKCLNIDTIIKYSEYERISS-LIPIDI 888
TY+R L+ D+G+ LGC H+ LRR + T + + ++ + + + + + L+P++
Sbjct: 180 TYVRSLARDLGRALGCYGHIAALRRTRVGPFTEEDAITLEKLEALARFAALDALLLPVET 239
Query: 889 LLSSFGIIYLSDLLSKRFLHGQNLFLSD 916
L + L+D + R G + L
Sbjct: 240 ALDDLPALALTDEQAARLRQGNPVLLRG 267
>gnl|CDD|235042 PRK02484, truB, tRNA pseudouridine synthase B; Provisional.
Length = 294
Score = 194 bits (494), Expect = 4e-55
Identities = 91/263 (34%), Positives = 154/263 (58%), Gaps = 7/263 (2%)
Query: 662 IHGVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLS 721
I+G++ L K G++S++A+ K++ +L KK+G+ GTLDP G+LP+ G+AT+ Y++
Sbjct: 2 INGIINLKKEAGMTSHDAVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKATRLIEYMT 61
Query: 722 EADKYYEAIIHLGITTETGDIEGKIIDFNK-NIPNSIEIIEKILINFHGKISQIPPMYSA 780
EA K YE I LG +T T D G+++ P + E +++ + +F GKI+QIPPMYSA
Sbjct: 62 EAGKVYEGEITLGYSTTTEDASGEVVAETPLTQPLTEEEVDQAMTSFTGKITQIPPMYSA 121
Query: 781 LKYKGIPLYKYARSGITIKRKLRYIKIY------KITIIDYTIPYLTLRIHCSKGTYIRV 834
+K G LY+YAR+G ++R R + IY ++ + + + R+ CSKGTY+R
Sbjct: 122 VKVNGKKLYEYARAGEEVERPKRQVTIYQFERTSPLSFDEDGLCRFSFRVACSKGTYVRT 181
Query: 835 LSEDIGKMLGCGAHLKYLRRIGIDKLTLDKCLNIDTIIKYSEYERISSLIPIDILLSSFG 894
L+ D+G+ LG AH+ +L R LTL++ + ++ I + E +S L PI+ ++
Sbjct: 182 LAVDLGEKLGYAAHMSFLTRTASAGLTLEQAVTLEEIAEKVEAGELSFLQPIEYGVADLP 241
Query: 895 IIYLSDLLSKRFLHGQNLFLSDE 917
+ L+ G+ + L +
Sbjct: 242 KVDLTPEQFTEVSFGRFISLDSQ 264
>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 = 192 bits (490), Expect = 7e-51
Identities = 148/519 (28%), Positives = 241/519 (46%), Gaps = 109/519 (21%)
Query: 927 IIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSI--EYNG 984
I+AH+DHGKTTL D+LL +G + +D +E E+ERGITI + N S+ EY G
Sbjct: 24 IVAHIDHGKTTLSDNLLAGAGMISEELAGQQLYLDFDEQEQERGITINAANVSMVHEYEG 83
Query: 985 TR--INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIV 1042
IN+IDTPGH DFGG+V R + VD ++++ AVEG MPQT V R+ALK KP++
Sbjct: 84 NEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCAVEGVMPQTETVLRQALKENVKPVL 143
Query: 1043 VVNKIDRSNARPEWVVDATFDLFDKLCATEEQL------------------DFPVIYTSA 1084
+NK+DR + + F K+ +L D V + SA
Sbjct: 144 FINKVDRLINELKLTPQELQERFIKIITEVNKLIKAMAPEEFRDKWKVRVEDGSVAFGSA 203
Query: 1085 LHGYA--------------------NENSKARQGNMIPLFEAILKYVPVH---------- 1114
+ +A E+ + PL + +L V H
Sbjct: 204 YYNWAISVPSMKKTGIGFKDIYKYCKEDKQKELAKKSPLHQVVLDMVIRHLPSPIEAQKY 263
Query: 1115 -------------------KDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVV 1155
+ PL L I + + G++ +GR+ SG I+ +V
Sbjct: 264 RIPVIWKGDLNSEVGKAMLNCDPKGPLALMITKIVVDKHAGEVAVGRLYSGTIRPGMEVY 323
Query: 1156 IMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGL 1215
I++ + KA+I Q+ V+ G +RV V+E +G+IV + G+++ G TIC + N
Sbjct: 324 IVD----RKAKARIQQVGVYMGPERVEVDEIPAGNIVAVIGLKDAVAGETICTTVE-NIT 378
Query: 1216 P---MLNIDEPTLTINFMVNNS---PLAGREGKFITT-RQIKNRLDHEIKNNIGLRVTQN 1268
P + +I EP +T+ N+ P K I RQ+ K + + V N
Sbjct: 379 PFESIKHISEPVVTVAIEAKNTKDLP------KLIEVLRQVA-------KEDPTVHVEIN 425
Query: 1269 KHDDSIYEVSGRGELHLTILIENMRRE-GYELSVSRPRVIFK-TLNG-----ELYEP--Y 1319
+ + +SG GELHL I++E +R + G ++ S P V+++ T+ G E P +
Sbjct: 426 EETGE-HLISGMGELHLEIIVEKIREDYGLDVETSPPIVVYRETVTGTSPVVEGKSPNKH 484
Query: 1320 ENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRL 1358
++ +E + + +I ++ G + ++++ +KER RL
Sbjct: 485 NRFYIVVEPLEESVIQA---FKEGKIVDMKMKKKERRRL 520
Score = 62.2 bits (151), Expect = 2e-09
Identities = 64/235 (27%), Positives = 96/235 (40%), Gaps = 61/235 (25%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSE--AG--------------GITQHIGAYNVVTNH 115
+ I+ H+DHGKT+L D + + SE AG GIT I A NV H
Sbjct: 22 IGIVAHIDHGKTTLSDNLLAGAGMISEELAGQQLYLDFDEQEQERGIT--INAANVSMVH 79
Query: 116 GS------ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGV 169
I +DTPGH F R + D ++VV A +GVMPQT + A V
Sbjct: 80 EYEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCAVEGVMPQTETVLRQALKENV 139
Query: 170 PLIVAINKIDKLDINLDRIKQDLISEQVI--------------PEEYG---------GAS 206
++ INK+D+L IN ++ + E+ I PEE+ G+
Sbjct: 140 KPVLFINKVDRL-INELKLTPQELQERFIKIITEVNKLIKAMAPEEFRDKWKVRVEDGSV 198
Query: 207 PF----------ISISAKTGVGINKLLENIS--LQAEILELKAPVTTPAKGVIIE 249
F + KTG+G + + Q E+ + K+P+ ++I
Sbjct: 199 AFGSAYYNWAISVPSMKKTGIGFKDIYKYCKEDKQKELAK-KSPLHQVVLDMVIR 252
>gnl|CDD|172614 PRK14124, PRK14124, tRNA pseudouridine synthase B; Provisional.
Length = 308
Score = 181 bits (461), Expect = 1e-50
Identities = 90/256 (35%), Positives = 145/256 (56%), Gaps = 5/256 (1%)
Query: 661 IIHGVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYL 720
+ HG L+ KP G +S++ + +++ L +KVG+ GTLDPFATG+L + +AT+ YL
Sbjct: 1 MKHGFLVAYKPKGPTSHDVVDEVRKKLKTRKVGHAGTLDPFATGVLIVGVNKATRLLEYL 60
Query: 721 SEADKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSA 780
K Y + LG+ TET DI G++++ + + E I + + +F G+ Q+PP YSA
Sbjct: 61 KNEKKVYYVKMRLGLITETFDITGEVVE-ERECNVTEEEIREAIFSFVGEYKQVPPAYSA 119
Query: 781 LKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIG 840
KYKG LYK AR G I + +KIY+I I P ++ R+ S GTYIR L DIG
Sbjct: 120 KKYKGERLYKLAREGKIINLPPKEVKIYEIWDISIEGPDVSFRVEVSPGTYIRSLCMDIG 179
Query: 841 KMLGCGAHLKYLRRIGIDKLTLDKCLNIDTIIKYSEYERISSLIPIDILLSSFGIIYLSD 900
LGCGA L R+ + K +++ +N+ + S E + +IP++ +L + +
Sbjct: 180 YKLGCGATAVELVRLSVGKFSIEDSINVFEV---SPEEIENRIIPMEEIL-DLPKVVIHQ 235
Query: 901 LLSKRFLHGQNLFLSD 916
+++ L+G ++L
Sbjct: 236 ESTEKILNGSQIYLEM 251
>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 = 174 bits (442), Expect = 1e-49
Identities = 74/189 (39%), Positives = 97/189 (51%), Gaps = 12/189 (6%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
+I HVDHGKTTL LL Q+G + +D+ + E+ERGITI + E+
Sbjct: 3 GVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWPKR 62
Query: 986 RINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVN 1045
RIN IDTPGH DF E R L+ D LL++DA EG PQTR AL G IV VN
Sbjct: 63 RINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGVEPQTREHLNIALAGGLPIIVAVN 122
Query: 1046 KIDR-SNARPEWVVDATFDLFDKLCAT-EEQLDFPVIYTSALHGYANENSKARQGNMIPL 1103
KIDR + V+ +L + T + D P+I SAL G E L
Sbjct: 123 KIDRVGEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGEGIE----------EL 172
Query: 1104 FEAILKYVP 1112
+AI++++P
Sbjct: 173 LDAIVEHLP 181
Score = 128 bits (325), Expect = 6e-34
Identities = 63/176 (35%), Positives = 85/176 (48%), Gaps = 20/176 (11%)
Query: 71 IVTIMGHVDHGKTSLLDYIRKTNVVFSEAG----------------GITQHIGAYNVVTN 114
V ++GHVDHGKT+L + G GIT G
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWP 60
Query: 115 HGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVA 174
I F+DTPGHE F+ RG D +LVV A++GV PQTRE + A G+P+IVA
Sbjct: 61 KRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGVEPQTREHLNIALAGGLPIIVA 120
Query: 175 INKIDKLD-INLDRIKQ---DLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
+NKID++ + D + + +L+ G P I ISA TG GI +LL+ I
Sbjct: 121 VNKIDRVGEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGEGIEELLDAI 176
>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 = 185 bits (471), Expect = 3e-49
Identities = 150/556 (26%), Positives = 249/556 (44%), Gaps = 114/556 (20%)
Query: 67 VRAPIVTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNH----------- 115
+R+PIV+++GHVDHGKT+LLD IR + V EAGGITQHIGA + +
Sbjct: 2 LRSPIVSVLGHVDHGKTTLLDKIRGSAVAKREAGGITQHIGATEIPMDVIEGICGDLLKK 61
Query: 116 -------GSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISG 168
+ F+DTPGHEAFT +R RG + D+ +L+V ++G PQT+EA+ ++
Sbjct: 62 FKIRLKIPGLLFIDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYK 121
Query: 169 VPLIVAINKIDKL---------------DINLDRIKQDL---ISEQVI--------PEEY 202
P +VA NKID++ +++Q+L + VI E +
Sbjct: 122 TPFVVAANKIDRIPGWRSHEGRPFMESFSKQEIQVQQNLDTKVYNLVIKLHEEGFEAERF 181
Query: 203 GGASPF------ISISAKTGVGINKLLENIS-LQAEILE--LKAPVTTPAKGVIIESRLD 253
+ F I ISA TG GI +LL ++ L + LE LK PA+G I+E + +
Sbjct: 182 DRVTDFTKTVAIIPISAITGEGIPELLTMLAGLAQQYLEEQLKLEEEGPARGTILEVKEE 241
Query: 254 KGKGPVATVLIQSGTLRCSDIVVAGASYG----RIRSML-------------NENGKNIL 296
G G +I G LR D + S R+R++L + +
Sbjct: 242 TGLGMTIDAVIYDGILRKGDTIAMAGSDDVIVTRVRALLKPRPLEEMRESRKKFQKVDEV 301
Query: 297 EAGPSIPVEIQGLTKVPFSGEELFVILNE--KKAREIGLFRQGKFRDVKLSKQKLHKTEN 354
A + + GL V +G + V+ +E +K +E + ++K+
Sbjct: 302 VAAAGVKIAAPGLDDV-MAGSPIRVVTDEEIEKVKEE---ILKEVEEIKI---------- 347
Query: 355 MFNDINKEKVKNLLIIIKTDVYGSREVLTESLKNLSTDKVKIQVIHNAVGNINESDINLA 414
+++K D GS E L L+++ V I+ +G++++ D+ A
Sbjct: 348 --------DTDEEGVVVKADTLGSLEALVNELRDMG---VPIKKAD--IGDVSKRDVVEA 394
Query: 415 IASK------AIIIGFNVRADASTRKLAQINNINIRYHNIIYNIIKEIKSEITNLIPLEK 468
+K II FNV+ + + +I + NIIY +++E + I + +K
Sbjct: 395 GIAKQEDRVYGAIIAFNVKVLPGAEQELKKYDIKLFSDNIIYRLMEEFEEWIEGIEEEKK 454
Query: 469 K---ENLLGLAEIR---QVILVNKVSKIAGCYILEGLIRRDSKIRILRNKNIIWTGELDS 522
+ E ++ A+IR +++ I G +L G+IR+ L + G + S
Sbjct: 455 RKWMEAIIKPAKIRLIPKLVFRQSKPAIVGVEVLTGVIRQGYP---LMKDDGETVGTVRS 511
Query: 523 LKRFKDNVKEVKAGFE 538
++ +NVK AG E
Sbjct: 512 MQDKGENVKSASAGQE 527
Score = 59.1 bits (143), Expect = 1e-08
Identities = 44/133 (33%), Positives = 64/133 (48%), Gaps = 12/133 (9%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRK-----NQNINARIMDSNEIEKERGITIFSKNCSI 980
+++ HVDHGKTTL+D + R S ++ Q+I A + + IE G K I
Sbjct: 8 SVLGHVDHGKTTLLDKI-RGSAVAKREAGGITQHIGATEIPMDVIEGICGD--LLKKFKI 64
Query: 981 EYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTR--KALKLGF 1038
+ IDTPGH F +R ++ D +L++D EG PQT+ + K F
Sbjct: 65 RLKIPGLLFIDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYKTPF 124
Query: 1039 KPIVVVNKIDRSN 1051
+V NKIDR
Sbjct: 125 --VVAANKIDRIP 135
>gnl|CDD|184522 PRK14123, PRK14123, tRNA pseudouridine synthase B; Provisional.
Length = 305
Score = 174 bits (442), Expect = 5e-48
Identities = 94/276 (34%), Positives = 147/276 (53%), Gaps = 14/276 (5%)
Query: 664 GVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEA 723
G+L + K GL+S++ + K++ +L KK+G+TGTLDP G+LP+C G AT+ S+Y+ +
Sbjct: 4 GILPVYKERGLTSHDVVFKLRKILKTKKIGHTGTLDPEVAGVLPVCIGNATRVSDYVMDM 63
Query: 724 DKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEI--IEKILINFHGKISQIPPMYSAL 781
K YEA + +G +T T D G ++ I+++L F G I QIPPMYS++
Sbjct: 64 GKAYEATVSIGRSTTTEDQTGDTLETKGVHSADFNKDDIDRLLEQFKGIIEQIPPMYSSV 123
Query: 782 KYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYT-----IPYLTLRIHCSKGTYIRVLS 836
K G LY+YAR+ T++R R + I I I + +R+ C KGTYIR L+
Sbjct: 124 KVNGKKLYEYARNNETVERPKRKVNIKDIGRISELDFKENECHFKIRVICGKGTYIRTLA 183
Query: 837 EDIGKMLGCGAHLKYLRRIGIDKLTLDKCLNIDTIIKYSEYERI-SSLIPIDILLSSFGI 895
DIG LG AH+ L RI L L ++ I + E + + + L P++ L
Sbjct: 184 TDIGVKLGFPAHMSKLTRIESGGFVLKDSLTLEQIKELHEQDSLQNKLFPLEYGLKGLPS 243
Query: 896 IYLSDL-LSKRFLHGQNLFLSD-----ENIYILIKS 925
I + D + KR L+GQ ++ ++ + I
Sbjct: 244 IKIKDSHIKKRILNGQKFNKNEFDNKIKDQIVFIDD 279
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 181 bits (462), Expect = 4e-47
Identities = 133/477 (27%), Positives = 205/477 (42%), Gaps = 127/477 (26%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSI--EYN 983
IIAH+DHGKTTL D+LL +G + +D +E E+ RGITI + N S+ EY
Sbjct: 24 GIIAHIDHGKTTLSDNLLAGAGMISEELAGEQLALDFDEEEQARGITIKAANVSMVHEYE 83
Query: 984 GTR--INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKP- 1040
G IN+IDTPGH DFGG+V R + VD ++++DAVEG MPQT V R+AL+ KP
Sbjct: 84 GKEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQTETVLRQALRERVKPV 143
Query: 1041 ---------------------------IVVVNKIDRSNARPE----WVVDATFDLFDKLC 1069
I VNK+ + A E W VD
Sbjct: 144 LFINKVDRLIKELKLTPQEMQQRLLKIIKDVNKLIKGMAPEEFKEKWKVDVE-------- 195
Query: 1070 ATEEQLDFPVIYTSALHGYANENSKA--------------RQGNM------IPLFEAIL- 1108
D V + SAL+ +A +G PL E +L
Sbjct: 196 ------DGTVAFGSALYNWAISVPMMQKTGIKFKDIIDYYEKGKQKELAEKAPLHEVVLD 249
Query: 1109 -------------KY-VPV--HKD------------NSNNPLQLQIISLEYSSYLGKIGI 1140
KY +P D + N PL + + + + G++
Sbjct: 250 MVVKHLPNPIEAQKYRIPKIWKGDLNSEVGKAMLNCDPNGPLVMMVTDIIVDPHAGEVAT 309
Query: 1141 GRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEI 1200
GR+ SG ++ Q+V ++ K ++ Q+ ++ G +R V E +G+I +TG+++
Sbjct: 310 GRVFSGTLRKGQEVYLVGAK----KKNRVQQVGIYMGPEREEVEEIPAGNIAAVTGLKDA 365
Query: 1201 CIGSTICDPSKPNGLP---MLNIDEPTLTINFMVNNS---PLAGREGKFITT-RQIKNRL 1253
G T+ + P + +I EP +T+ N P K I RQ+
Sbjct: 366 RAGETVVSVE--DMTPFESLKHISEPVVTVAIEAKNPKDLP------KLIEVLRQLA--- 414
Query: 1254 DHEIKNNIGLRVTQNKHDDSIYEVSGRGELHLTILIENMRRE-GYELSVSRPRVIFK 1309
K + L V N+ + + +SG GELHL ++ ++R+ G E+ S P V+++
Sbjct: 415 ----KEDPTLVVKINE-ETGEHLLSGMGELHLEVITYRIKRDYGIEVVTSEPIVVYR 466
Score = 63.3 bits (155), Expect = 8e-10
Identities = 50/151 (33%), Positives = 68/151 (45%), Gaps = 36/151 (23%)
Query: 74 IMGHVDHGKTSLLDYIRKTNVVFSE--AG--------------GITQHIGAYNVVTNHGS 117
I+ H+DHGKT+L D + + SE AG GIT I A NV H
Sbjct: 25 IIAHIDHGKTTLSDNLLAGAGMISEELAGEQLALDFDEEEQARGIT--IKAANVSMVHEY 82
Query: 118 ------ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPL 171
I +DTPGH F R + D ++VV A +GVMPQT + A V
Sbjct: 83 EGKEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQTETVLRQALRERVKP 142
Query: 172 IVAINKIDKLDINLDRIKQDLISE-QVIPEE 201
++ INK+D+ LI E ++ P+E
Sbjct: 143 VLFINKVDR-----------LIKELKLTPQE 162
Score = 31.8 bits (73), Expect = 3.5
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 1315 LYEPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQNEF 1374
L EP + + +++ + G + +++ R G + ++E E + +E P + GF E
Sbjct: 623 LLEPIQKVDINVPQDYMGAVTREIQGRRGKILDME-QEGDMAIIEAEAPVAEMFGFAGEI 681
Query: 1375 ITLTRGTGLISHVFEEYAP 1393
+ T G L S F + P
Sbjct: 682 RSATEGRALWSTEFAGFEP 700
>gnl|CDD|179739 PRK04099, truB, tRNA pseudouridine synthase B; Provisional.
Length = 273
Score = 161 bits (409), Expect = 5e-44
Identities = 87/260 (33%), Positives = 123/260 (47%), Gaps = 28/260 (10%)
Query: 670 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 729
KP G+SSN L ++K KK G++GTLDPFA G+L + FG+ TK +L + K Y A
Sbjct: 9 KPAGMSSNAFLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQYTKLFRFLKKTPKTYRA 68
Query: 730 IIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPLY 789
+ LG ++ + DIE I P ++IEKIL + G+IS PP +SA K G Y
Sbjct: 69 TLWLGASSPSLDIE-NIESIQIIKPFDKDLIEKILKSLQGEISYTPPKFSAKKINGKRAY 127
Query: 790 KYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAHL 849
+ AR G + K ++I+ ++ Y P+LT I S+G YIR L E I K LG L
Sbjct: 128 ELARKGEEFELKPITMEIFDCKLLSYNHPFLTFEITVSEGAYIRSLGELIAKKLGVNGTL 187
Query: 850 KYLRRIGIDKLTLD--KCLNIDTIIKYSEYERISSLIPIDILLSSFGIIYLSDLLSKRFL 907
L R+ K + K LN + + YL D
Sbjct: 188 SSLERLSEGKFVYENEKALNPLEYLNLPQ------------------NFYLGD--KNNLE 227
Query: 908 HGQNLFLSD-----ENIYIL 922
G+ LF+ D + IY +
Sbjct: 228 LGKKLFVEDLENKEDGIYYI 247
>gnl|CDD|221359 pfam11987, IF-2, Translation-initiation factor 2. IF-2 is a
translation initiator in each of the three main
phylogenetic domains (Eukaryotes, Bacteria and Archaea).
IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3
and both ribosomal subunits. Through these interactions,
IF2 promotes the binding of the initiator tRNA to the A
site in the smaller ribosomal subunit and catalyzes the
hydrolysis of GTP following initiation-complex
formation.
Length = 109
Score = 149 bits (379), Expect = 4e-42
Identities = 56/105 (53%), Positives = 78/105 (74%)
Query: 353 ENMFNDINKEKVKNLLIIIKTDVYGSREVLTESLKNLSTDKVKIQVIHNAVGNINESDIN 412
E++F I + +VK L +I+K DV GS E + +SL+ LSTD+VK+ +IH VG I ESD+
Sbjct: 4 EDLFEQIKEGEVKELNLILKADVQGSLEAIKDSLEKLSTDEVKVNIIHAGVGAITESDVM 63
Query: 413 LAIASKAIIIGFNVRADASTRKLAQINNINIRYHNIIYNIIKEIK 457
LA AS AIIIGFNVR DA RKLA+ ++IRY++IIY++I ++K
Sbjct: 64 LASASNAIIIGFNVRPDAKARKLAEQEGVDIRYYSIIYDLIDDVK 108
>gnl|CDD|235113 PRK03287, truB, tRNA pseudouridine synthase B; Provisional.
Length = 298
Score = 152 bits (386), Expect = 1e-40
Identities = 74/214 (34%), Positives = 114/214 (53%), Gaps = 10/214 (4%)
Query: 664 GVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEA 723
G++++DKP G++S++ + + + L +KVG+ GTLDP ATG+L L ATK +L+
Sbjct: 10 GLVVVDKPAGMTSHDVVARCRRLFGTRKVGHAGTLDPMATGVLVLGVERATKLLGHLTLT 69
Query: 724 DKYYEAIIHLGITTETGDIEGKIIDFNKNIPNS---IEIIEKILINFHGKISQIPPMYSA 780
DK Y A I LG T T D EG+++ + S E I + G+I Q+P SA
Sbjct: 70 DKSYTATIRLGQATTTDDAEGEVL---ASADASAVTDEAIAAAVAALTGEIMQVPSAVSA 126
Query: 781 LKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDY--TIPYLTL--RIHCSKGTYIRVLS 836
+K G Y R+G ++ R + + + ++ ++ L + CS GTYIR L+
Sbjct: 127 IKVDGKRAYARVRAGEEVELPARPVTVSRFEVLAVRRDGDFIDLDVEVDCSSGTYIRALA 186
Query: 837 EDIGKMLGCGAHLKYLRRIGIDKLTLDKCLNIDT 870
D+G LG G HL LRR + TLD+ +D
Sbjct: 187 RDLGAALGVGGHLTALRRTRVGPFTLDQARTLDE 220
>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 = 148 bits (376), Expect = 3e-40
Identities = 63/132 (47%), Positives = 81/132 (61%), Gaps = 9/132 (6%)
Query: 927 IIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY---- 982
IIAHVDHGKTTL D LL +G + AR +D+ E E+ERGITI S S+ +
Sbjct: 5 IIAHVDHGKTTLSDSLLASAGIISEKLAGKARYLDTREDEQERGITIKSSAISLYFEYEE 64
Query: 983 -----NGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLG 1037
N IN+ID+PGH DF EV L + D L+++DAVEG QT V R+AL+
Sbjct: 65 EKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDAVEGVCVQTETVLRQALEER 124
Query: 1038 FKPIVVVNKIDR 1049
KP++V+NKIDR
Sbjct: 125 VKPVLVINKIDR 136
Score = 69.6 bits (171), Expect = 6e-13
Identities = 42/141 (29%), Positives = 64/141 (45%), Gaps = 29/141 (20%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSE--AG--------------GITQHIGAYNVVTNH 115
+ I+ HVDHGKT+L D + + + SE AG GIT I + +
Sbjct: 3 ICIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYLDTREDEQERGIT--IKSSAISLYF 60
Query: 116 G-----------SITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHA 164
I +D+PGH F++ ++TD ++VV A +GV QT + A
Sbjct: 61 EYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDAVEGVCVQTETVLRQA 120
Query: 165 KISGVPLIVAINKIDKLDINL 185
V ++ INKID+L + L
Sbjct: 121 LEERVKPVLVINKIDRLILEL 141
>gnl|CDD|239673 cd03702, IF2_mtIF2_II, This family represents the domain II of
bacterial Initiation Factor 2 (IF2) and its eukaryotic
mitochondrial homologue mtIF2. IF2, the largest
initiation factor is an essential GTP binding protein.
In E. coli three natural forms of IF2 exist in the cell,
IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is
structurally and functionally related to eukaryotic
mitochondrial mtIF-2.
Length = 95
Score = 143 bits (364), Expect = 3e-40
Identities = 54/94 (57%), Positives = 78/94 (82%)
Query: 243 AKGVIIESRLDKGKGPVATVLIQSGTLRCSDIVVAGASYGRIRSMLNENGKNILEAGPSI 302
A+GV+IES+LDKG+GPVATVL+Q+GTL+ D++VAG +YG++R+M +ENGK + EAGPS
Sbjct: 1 AEGVVIESKLDKGRGPVATVLVQNGTLKVGDVLVAGTTYGKVRAMFDENGKRVKEAGPST 60
Query: 303 PVEIQGLTKVPFSGEELFVILNEKKAREIGLFRQ 336
PVEI GL VP +G++ V+ +EK+A+EI +R+
Sbjct: 61 PVEILGLKGVPQAGDKFLVVESEKEAKEIAEYRK 94
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 162 bits (412), Expect = 3e-40
Identities = 157/537 (29%), Positives = 241/537 (44%), Gaps = 111/537 (20%)
Query: 83 TSLLDYIRKTNVVFSEAGGITQHIGAYNVVTN-------------HGSIT-----FLDTP 124
T+LLD IRKT V EAGGITQHIGA + + I F+DTP
Sbjct: 475 TTLLDKIRKTRVAKKEAGGITQHIGATEIPIDVIKKICGPLLKLLKAEIKIPGLLFIDTP 534
Query: 125 GHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLD-- 182
GHEAFT++R RG + D+ VLVV ++G PQT EAI + P +VA NKID +
Sbjct: 535 GHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQYKTPFVVAANKIDLIPGW 594
Query: 183 ---------INLDRIKQDLISE------QVIPE--EYG-GASPF------------ISIS 212
+N + Q ++E ++I + E G A F + +S
Sbjct: 595 NISEDEPFLLNFNEQDQHALTELEIKLYELIGKLYELGFDADRFDRVQDFTRTVAIVPVS 654
Query: 213 AKTGVGINKLLENIS-LQAEILE--LKAPVTTPAKGVIIESRLDKGKGPVATVLIQSGTL 269
AKTG GI +LL ++ L + LE LK V AKG I+E + +KG G +I GTL
Sbjct: 655 AKTGEGIPELLMMVAGLAQKYLEERLKLNVEGYAKGTILEVKEEKGLGTTIDAIIYDGTL 714
Query: 270 RCSDIVVAG----ASYGRIRSMLNE-------------NGKNILEAGPSIPVEIQGLTKV 312
R D +V G ++R++L + + + A + + GL +V
Sbjct: 715 RRGDTIVVGGPDDVIVTKVRALLKPKPLDEIRDPRDKFDPVDEVTAAAGVKIAAPGLEEV 774
Query: 313 PFSGEELFVILNEKKAREIGLFRQGKFRDVKLSKQKLHKTENMFNDINKEKVKNLLIIIK 372
+G + ++ ++K + ++ ++V+ +K I +K I+IK
Sbjct: 775 -LAGSPIRIVPTKEKIEK---AKEEVMKEVEEAK------------IETDKEG---ILIK 815
Query: 373 TDVYGSREVLTESLKNLSTDKVKIQVIHNAVGNINESDINLAIASK------AIIIGFNV 426
D GS E L L+ K I + VG+I + D+ A++ K +I+GFNV
Sbjct: 816 ADTLGSLEALANELR-----KAGIPIKKAEVGDITKKDVIEALSYKQENPLYGVILGFNV 870
Query: 427 RADASTRKLAQINNINIRYHNIIYNIIKE----IKSEITNLIPLEKKENLLGLAEIR--- 479
+ ++ A+ + I NIIY ++++ +K E E E L+ IR
Sbjct: 871 KVLPEAQEEAEKYGVKIFVDNIIYKLVEDYTEWVKEE-EEKKKRELFEKLIKPGIIRLLP 929
Query: 480 QVILVNKVSKIAGCYILEGLIRRDSKIRILRNKNIIWTGELDSLKRFKDNVKEVKAG 536
I I G +LEG +R L ++ + G + S+K +NVKE KAG
Sbjct: 930 DCIFRRSNPAIVGVEVLEGTLRVGVT---LIKEDGMKVGTVRSIKDRGENVKEAKAG 983
Score = 37.6 bits (87), Expect = 0.067
Identities = 27/71 (38%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 989 IIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV-VNKI 1047
IDTPGH F +R S+ D +L++D EG PQT L+ P VV NKI
Sbjct: 530 FIDTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQT-IEAINILRQYKTPFVVAANKI 588
Query: 1048 DRSNARPEWVV 1058
D P W +
Sbjct: 589 DLI---PGWNI 596
Score = 34.1 bits (78), Expect = 0.66
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 10/48 (20%)
Query: 56 EYNKNITAESLVRAPIVTIMGHVDHGKTSLLDYIRKTNVVFSEAGGIT 103
+ K + R PIV ++GHVDHGK L + V+ E G IT
Sbjct: 3 KKEKRL------RCPIVAVLGHVDHGKCLLPE----EKVILPEHGLIT 40
>gnl|CDD|179381 PRK02193, truB, tRNA pseudouridine synthase B; Provisional.
Length = 279
Score = 149 bits (379), Expect = 5e-40
Identities = 86/213 (40%), Positives = 119/213 (55%), Gaps = 5/213 (2%)
Query: 665 VLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEAD 724
+ LL KP G+SS +K N KK+G+TGTLDP A+GLL + E TK +YL + D
Sbjct: 2 IKLLYKPKGISSFKFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDEDTKLIDYLDQKD 61
Query: 725 KYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYK 784
K Y A I G + T D EG+II+ ++NI + E +E+ L N G Q+PP++SA K
Sbjct: 62 KTYIAKIKFGFISTTYDSEGQIINVSQNIKVTKENLEEALNNLVGSQKQVPPVFSAKKVN 121
Query: 785 GIPLYKYARSGITIKRKLRYIKIYKITIIDYTIP--YLTLRIHCSKGTYIRVLSEDIGKM 842
G Y AR G I+ K IKI KI ++++ S+GTYIR L D+GKM
Sbjct: 122 GKRAYDLARQGKQIELKPIEIKISKIELLNFDEKLQNCVFMWVVSRGTYIRSLIHDLGKM 181
Query: 843 LGCGAHLKYLRRI---GIDKLTLDKCLNIDTII 872
L GA++ L R +DK L++ LN +I
Sbjct: 182 LKTGAYMSDLERTKIGNLDKNFLNQSLNPLDLI 214
>gnl|CDD|184521 PRK14122, PRK14122, tRNA pseudouridine synthase B; Provisional.
Length = 312
Score = 151 bits (382), Expect = 5e-40
Identities = 81/283 (28%), Positives = 130/283 (45%), Gaps = 44/283 (15%)
Query: 665 VLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEAD 724
V +DKP GL+S++ + + + L ++VG+TGTLDP ATG+L LC ++TK +LS D
Sbjct: 3 VYAVDKPLGLTSHDVVNRARRALGTRRVGHTGTLDPLATGVLVLCTDDSTKLVPFLSAED 62
Query: 725 KYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYK 784
K Y A + G TT T D EG I + P + +E L F G Q+PP YSA+K
Sbjct: 63 KEYLAWVSFGATTPTLDAEGPISEEAPVSPLDEKDLEAALPGFLGLTEQVPPQYSAIKVG 122
Query: 785 GIPLYKYARSGITIKRKLRYIKIYKITIIDY----------------------------- 815
G+ Y+ AR+G ++ R + +++ ++ +
Sbjct: 123 GVRAYEAARAGGALELPARPVVYHELELLAFEPSVAPIPRPIAPSAEGWTPDPRGRPVTL 182
Query: 816 -----TIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAHLKYLRRIGIDKLTLDKCLNIDT 870
P LR+ GTY+R + D+G LG AHL L R + + L+ +++
Sbjct: 183 PEPLGEYPTALLRLVVGSGTYVRSFARDLGAALGVPAHLSGLVRTRVGRYGLEDAVSL-- 240
Query: 871 IIKYSEYERISSLIPIDILLS-SFGIIYLSDLLSKRFLHGQNL 912
E ++ I L + F + LS ++R G+
Sbjct: 241 -------EDLAEAPGIPELDALDFPRVELSHAEARRVRQGKPP 276
>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 = 139 bits (353), Expect = 5e-37
Identities = 68/136 (50%), Positives = 85/136 (62%), Gaps = 4/136 (2%)
Query: 927 IIAHVDHGKTTLIDHLLRQSGTFRKN---QNINARIMDSNEIEKERGITIFSKNCSIEYN 983
I+AHVD GKTTL + LL SG R+ R DS E+E++RGITIFS S ++
Sbjct: 4 ILAHVDAGKTTLTESLLYTSGAIRELGSVDKGTTR-TDSMELERQRGITIFSAVASFQWE 62
Query: 984 GTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV 1043
T++NIIDTPGH DF EVER LS++D +L+I AVEG QTR + R KL I+
Sbjct: 63 DTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILFRLLRKLNIPTIIF 122
Query: 1044 VNKIDRSNARPEWVVD 1059
VNKIDR+ A E V
Sbjct: 123 VNKIDRAGADLEKVYQ 138
Score = 71.5 bits (176), Expect = 1e-13
Identities = 47/175 (26%), Positives = 77/175 (44%), Gaps = 24/175 (13%)
Query: 74 IMGHVDHGKTSLLDYIRKTNVVFSEAG------------------GITQHIGAYNVVTNH 115
I+ HVD GKT+L + + T+ E G GIT +
Sbjct: 4 ILAHVDAGKTTLTESLLYTSGAIRELGSVDKGTTRTDSMELERQRGITIFSAVASFQWED 63
Query: 116 GSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHA-KISGVPLIVA 174
+ +DTPGH F A R V D +LV++A +GV QTR + + +P I+
Sbjct: 64 TKVNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTR-ILFRLLRKLNIPTIIF 122
Query: 175 INKIDKLDINLDRIKQDL---ISEQVIPEEYGGASPFISISAKTGVG-INKLLEN 225
+NKID+ +L+++ Q++ +S ++P + G P I + I + E
Sbjct: 123 VNKIDRAGADLEKVYQEIKEKLSPDIVPMQKVGLYPNICDTNNIDDEQIETVAEG 177
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis, outer
membrane].
Length = 603
Score = 148 bits (377), Expect = 5e-37
Identities = 95/300 (31%), Positives = 154/300 (51%), Gaps = 38/300 (12%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
+IIAH+DHGK+TL D LL +G + + + A+++DS +IE+ERGITI ++ + Y
Sbjct: 13 SIIAHIDHGKSTLADRLLELTGGLSERE-MRAQVLDSMDIERERGITIKAQAVRLNYKAK 71
Query: 986 R-----INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKP 1040
+N+IDTPGH DF EV R L+ + LL++DA +G QT AL+ +
Sbjct: 72 DGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLALENNLEI 131
Query: 1041 IVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNM 1100
I V+NKID A PE V D+ + A++ + SA K G
Sbjct: 132 IPVLNKIDLPAADPERVKQEIEDIIG-IDASD------AVLVSA---------KTGIG-- 173
Query: 1101 IP-LFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNG 1159
I + EAI++ +P K + + PL+ I Y +YLG + + RI G +K + +M+
Sbjct: 174 IEDVLEAIVEKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKGDKIRMMS- 232
Query: 1160 PDDKPNKAK--INQIRVFKGLDRVLVNEALSGDI-VLITGIEEIC---IGSTICDPSKPN 1213
+ ++++ +F V V+E +G++ +I GI+++ +G TI S P
Sbjct: 233 -----TGKEYEVDEVGIFTP-KMVKVDELKAGEVGYIIAGIKDVRDARVGDTITLASNPA 286
Score = 78.0 bits (193), Expect = 2e-14
Identities = 83/285 (29%), Positives = 125/285 (43%), Gaps = 52/285 (18%)
Query: 74 IMGHVDHGKTSLLDYIRKTNVVFSEAG---------------GITQHIGAYNV----VTN 114
I+ H+DHGK++L D + + SE GIT I A V
Sbjct: 14 IIAHIDHGKSTLADRLLELTGGLSEREMRAQVLDSMDIERERGIT--IKAQAVRLNYKAK 71
Query: 115 HGS---ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKIS---G 168
G + +DTPGH F+ +R + +LVV A GV QT +A+ ++
Sbjct: 72 DGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQT---LANVYLALENN 128
Query: 169 VPLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISL 228
+ +I +NKID + +R+KQ++ E +I + AS + +SAKTG+GI +LE I
Sbjct: 129 LEIIPVLNKIDLPAADPERVKQEI--EDIIGID---ASDAVLVSAKTGIGIEDVLEAIV- 182
Query: 229 QAEILELKAPVTTPAKGVIIESRLDKGKGPVATVLIQSGTLRCSDIVVAGASYGRIRSML 288
+I K P K +I +S D G V V I GTL+ D +IR M
Sbjct: 183 -EKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKGD---------KIRMMS 232
Query: 289 NENGKNILEAGPSIP--VEIQGLTKVPFSGEELFVILNEKKAREI 331
+ E G P V++ L +GE ++I K R+
Sbjct: 233 TGKEYEVDEVGIFTPKMVKVDELK----AGEVGYIIAGIKDVRDA 273
Score = 33.7 bits (78), Expect = 0.81
Identities = 25/104 (24%), Positives = 44/104 (42%), Gaps = 21/104 (20%)
Query: 1281 GELHLTILIENMRRE-GYELSVSRPRVIFK--TLNGE------------------LYEPY 1319
G LH+ I+ E + RE +L + P V++K +GE + EPY
Sbjct: 349 GLLHMEIIQERLEREFDLDLITTAPSVVYKVELTDGEEIEVDNPSDLPDPNKIEEIEEPY 408
Query: 1320 ENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIP 1363
+ + G +M+ + G ++E ++ RV L Y +P
Sbjct: 409 VKATIITPQEYLGNVMELCQEKRGIQIDMEYLDQNRVMLTYELP 452
>gnl|CDD|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p;
Reviewed.
Length = 300
Score = 141 bits (357), Expect = 7e-37
Identities = 70/195 (35%), Positives = 98/195 (50%), Gaps = 35/195 (17%)
Query: 661 IIHGVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYL 720
I GV+ LDKP G +S+ ++ +L +K G+ GTLDP TG+LP+ G+ATK L
Sbjct: 20 IKFGVVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQAL 79
Query: 721 SEADKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSA 780
E+ K Y ++HL GD+ E I K+ F G+I Q PP+ SA
Sbjct: 80 LESGKEYVCVMHL-----HGDV-------------PEEDIRKVFKEFTGEIYQKPPLKSA 121
Query: 781 LKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIG 840
+KR+LR IY++ I++ + R+ C GTYIR L DIG
Sbjct: 122 -----------------VKRRLRVRTIYELEILEIDGRDVLFRVRCESGTYIRKLCHDIG 164
Query: 841 KMLGCGAHLKYLRRI 855
LG GAH++ LRR
Sbjct: 165 LALGTGAHMQELRRT 179
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases) [Translation,
ribosomal structure and biogenesis].
Length = 697
Score = 149 bits (378), Expect = 1e-36
Identities = 64/138 (46%), Positives = 85/138 (61%), Gaps = 3/138 (2%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRK--NQNINARIMDSNEIEKERGITIFSKNCSIEYN 983
I+AH+D GKTTL + +L +G K + A MD E E+ERGITI S ++ +
Sbjct: 14 GIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQERGITITSAATTLFWK 73
Query: 984 GT-RINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIV 1042
G RIN+IDTPGH DF EVER L ++D ++++DAVEG PQT V R+A K G I+
Sbjct: 74 GDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETVWRQADKYGVPRIL 133
Query: 1043 VVNKIDRSNARPEWVVDA 1060
VNK+DR A VV+
Sbjct: 134 FVNKMDRLGADFYLVVEQ 151
Score = 95.0 bits (237), Expect = 1e-19
Identities = 44/140 (31%), Positives = 63/140 (45%), Gaps = 19/140 (13%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAG------------------GITQHIGAYNVVT 113
+ I+ H+D GKT+L + I + S+ G GIT A +
Sbjct: 13 IGIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQERGITITSAATTLFW 72
Query: 114 N-HGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLI 172
I +DTPGH FT R +V D V+VV A +GV PQT A GVP I
Sbjct: 73 KGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETVWRQADKYGVPRI 132
Query: 173 VAINKIDKLDINLDRIKQDL 192
+ +NK+D+L + + + L
Sbjct: 133 LFVNKMDRLGADFYLVVEQL 152
Score = 87.3 bits (217), Expect = 3e-17
Identities = 67/262 (25%), Positives = 117/262 (44%), Gaps = 47/262 (17%)
Query: 1070 ATEEQLDFPVIYTSALHGYANENSKARQGNMIPLFEAILKYVP----------------- 1112
T PV+ SA K Q PL +A++ Y+P
Sbjct: 246 GTIAGKIVPVLCGSAFKN------KGVQ----PLLDAVVDYLPSPLDVPPIKGDLDDEIE 295
Query: 1113 ---VHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKI 1169
+ K + PL + + ++GK+ R+ SG +KS +V+ N K K ++
Sbjct: 296 KAVLRKASDEGPLSALVFKIMTDPFVGKLTFVRVYSGTLKSGSEVL--NSTKGK--KERV 351
Query: 1170 NQIRVFKGLDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTLTINF 1229
++ + G +R V+E +GDIV + G+++ G T+CD +KP L + EP +++
Sbjct: 352 GRLLLMHGNEREEVDEVPAGDIVALVGLKDATTGDTLCDENKPVILESMEFPEPVISV-- 409
Query: 1230 MVNNSPLAGRE-GKFITTRQIKNRLDHEIKNNIGLRVTQNKHDDSIYEVSGRGELHLTIL 1288
V P + K N+L E RV ++ + +SG GELHL I+
Sbjct: 410 AVE--PKTKADQEKLSEAL---NKLAEEDP---TFRVETDE-ETGETIISGMGELHLEII 460
Query: 1289 IENMRRE-GYELSVSRPRVIFK 1309
++ ++RE G E+ V +P+V ++
Sbjct: 461 VDRLKREFGVEVEVGKPQVAYR 482
Score = 37.6 bits (88), Expect = 0.061
Identities = 17/84 (20%), Positives = 33/84 (39%), Gaps = 1/84 (1%)
Query: 1315 LYEPYENLFVDIEEINQGIIMQKLNYRGGDLKNIE-INEKERVRLEYRIPSRGLIGFQNE 1373
L EP + + E G ++ LN R G + +E ++ +P + G+ +
Sbjct: 599 LLEPIMKVEITTPEEYMGDVIGDLNSRRGQILGMEQRPGGGLDVIKAEVPLAEMFGYATD 658
Query: 1374 FITLTRGTGLISHVFEEYAPFYNK 1397
+ T+G S F+ Y +
Sbjct: 659 LRSATQGRASFSMEFDHYEEVPSS 682
>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 = 134 bits (339), Expect = 9e-36
Identities = 69/193 (35%), Positives = 101/193 (52%), Gaps = 25/193 (12%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY--- 982
+IIAH+DHGK+TL D LL +GT + + +++DS ++E+ERGITI ++ + Y
Sbjct: 4 SIIAHIDHGKSTLADRLLELTGTVSEREM-KEQVLDSMDLERERGITIKAQAVRLFYKAK 62
Query: 983 NGTR--INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKP 1040
+G +N+IDTPGH DF EV R L+ + LL++DA +G QT AL+ +
Sbjct: 63 DGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQGVEAQTLANFYLALENNLEI 122
Query: 1041 IVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNM 1100
I V+NKID A P+ V D+ E I SA K G
Sbjct: 123 IPVINKIDLPAADPDRVKQEIEDVLG--LDASE-----AILVSA---------KTGLG-- 164
Query: 1101 IP-LFEAILKYVP 1112
+ L EAI++ +P
Sbjct: 165 VEDLLEAIVERIP 177
Score = 71.4 bits (176), Expect = 6e-14
Identities = 56/180 (31%), Positives = 81/180 (45%), Gaps = 39/180 (21%)
Query: 74 IMGHVDHGKTSLLD-YIRKTNVVFSEAG--------------GITQHIGAYNVVTNHGSI 118
I+ H+DHGK++L D + T V GIT I A V + +
Sbjct: 5 IIAHIDHGKSTLADRLLELTGTVSEREMKEQVLDSMDLERERGIT--IKAQAVRLFYKAK 62
Query: 119 T-------FLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAH---AKISG 168
+DTPGH F+ +R + +LVV A GV QT +A+ A +
Sbjct: 63 DGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQGVEAQT---LANFYLALENN 119
Query: 169 VPLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPF--ISISAKTGVGINKLLENI 226
+ +I INKID + DR+KQ++ E+ G I +SAKTG+G+ LLE I
Sbjct: 120 LEIIPVINKIDLPAADPDRVKQEI-------EDVLGLDASEAILVSAKTGLGVEDLLEAI 172
>gnl|CDD|239672 cd03701, IF2_IF5B_II, IF2_IF5B_II: This family represents the
domain II of prokaryotic Initiation Factor 2 (IF2) and
its archeal and eukaryotic homologue aeIF5B. IF2, the
largest initiation factor is an essential GTP binding
protein. In E. coli three natural forms of IF2 exist in
the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption
of the eIF5B gene (FUN12) in yeast causes a severe
slow-growth phenotype, associated with a defect in
translation. eIF5B has a function analogous to
prokaryotic IF2 in mediating the joining of the 60S
ribosomal subunit. The eIF5B consists of three
N-terminal domains (I, II, II) connected by a long
helix to domain IV. Domain I is a G domain, domain II
and IV are beta-barrels and domain III has a novel
alpha-beta-alpha sandwich fold. The G domain and the
beta-barrel domain II display a similar structure and
arrangement to the homologous domains in EF1A, eEF1A and
aeIF2gamma.
Length = 95
Score = 129 bits (327), Expect = 2e-35
Identities = 55/94 (58%), Positives = 79/94 (84%)
Query: 243 AKGVIIESRLDKGKGPVATVLIQSGTLRCSDIVVAGASYGRIRSMLNENGKNILEAGPSI 302
A+G +IES+LDKG+GPVATV++Q+GTL+ D++VAG +YG+IR+M++ENGK +LEAGPS
Sbjct: 1 AEGTVIESKLDKGRGPVATVIVQNGTLKKGDVIVAGGTYGKIRTMVDENGKALLEAGPST 60
Query: 303 PVEIQGLTKVPFSGEELFVILNEKKAREIGLFRQ 336
PVEI GL VP +G+ + V+ +EK+A+EIG +R
Sbjct: 61 PVEILGLKDVPKAGDGVLVVASEKEAKEIGSYRL 94
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 142 bits (362), Expect = 4e-35
Identities = 92/299 (30%), Positives = 153/299 (51%), Gaps = 38/299 (12%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY--- 982
+IIAH+DHGK+TL D L+ +GT + + + A+++DS ++E+ERGITI ++ + Y
Sbjct: 11 SIIAHIDHGKSTLADRLIELTGTLSERE-MKAQVLDSMDLERERGITIKAQAVRLNYKAK 69
Query: 983 NGTR--INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKP 1040
+G +N+IDTPGH DF EV R L+ + LL++DA +G QT AL+ +
Sbjct: 70 DGETYILNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLALENDLEI 129
Query: 1041 IVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNM 1100
I V+NKID A PE V D+ + + SA K G
Sbjct: 130 IPVLNKIDLPAADPERVKQEIEDVIG--IDASD-----AVLVSA---------KTGIG-- 171
Query: 1101 IP-LFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNG 1159
I + EAI++ +P K + + PL+ I Y +Y G + + R++ G +K + +M+
Sbjct: 172 IEEVLEAIVERIPPPKGDPDAPLKALIFDSWYDNYRGVVVLVRVVDGTLKKGDKIKMMS- 230
Query: 1160 PDDKPNKAK--INQIRVFKGLDRVLVNEALSGDI-VLITGIEEIC---IGSTICDPSKP 1212
+ ++++ VF V V+E +G++ +I GI+++ +G TI P
Sbjct: 231 -----TGKEYEVDEVGVFT-PKMVPVDELSAGEVGYIIAGIKDVRDARVGDTITLAKNP 283
Score = 65.1 bits (160), Expect = 2e-10
Identities = 73/235 (31%), Positives = 108/235 (45%), Gaps = 63/235 (26%)
Query: 74 IMGHVDHGKTSLLD-YIRKTNVVFSE---------------AGGITQHIGAYNVVTNHGS 117
I+ H+DHGK++L D I T + SE GIT I A V N+ +
Sbjct: 12 IIAHIDHGKSTLADRLIELTGTL-SEREMKAQVLDSMDLERERGIT--IKAQAVRLNYKA 68
Query: 118 -------ITFLDTPGHEAFT-----AMRA-RGAKVTDIVVLVVAADDGVMPQT----REA 160
+ +DTPGH F+ ++ A GA +LVV A GV QT A
Sbjct: 69 KDGETYILNLIDTPGHVDFSYEVSRSLAACEGA------LLVVDASQGVEAQTLANVYLA 122
Query: 161 IAHAKISGVPLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGG--ASPFISISAKTGVG 218
+ + + +I +NKID + +R+KQ++ E VI G AS + +SAKTG+G
Sbjct: 123 LEN----DLEIIPVLNKIDLPAADPERVKQEI--EDVI-----GIDASDAVLVSAKTGIG 171
Query: 219 INKLLENISLQAEILELKAP---VTTPAKGVIIESRLDKGKGPVATVLIQSGTLR 270
I ++LE I + + P P K +I +S D +G V V + GTL+
Sbjct: 172 IEEVLEAI-----VERIPPPKGDPDAPLKALIFDSWYDNYRGVVVLVRVVDGTLK 221
>gnl|CDD|179300 PRK01528, truB, tRNA pseudouridine synthase B; Provisional.
Length = 292
Score = 132 bits (333), Expect = 8e-34
Identities = 93/262 (35%), Positives = 135/262 (51%), Gaps = 16/262 (6%)
Query: 670 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 729
KP G+SS + +K +L K+G+ GTLD A G+LPL GEATK L +A K Y
Sbjct: 10 KPRGISSAKLVSIVKKILGKVKIGHAGTLDVEAEGVLPLAVGEATKLVQLLIDAKKTYIF 69
Query: 730 IIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPLY 789
+ G T++GD GK+I IP S E + F G I+QIPP +SALK G+ Y
Sbjct: 70 TVKFGKQTDSGDYAGKVIATKDYIP-SKEEAYAVCSKFIGNITQIPPAFSALKVNGVRAY 128
Query: 790 KYARSGITIKRKLRYIKIYKITIIDY-----TIPYLTLRIHCSKGTYIRVLSEDIGKMLG 844
K AR G ++ K R I IY + +++ T Y T CSKGTYIR L+ED+ L
Sbjct: 129 KLAREGKEVELKPRNITIYDLKCLNFDEKNATATYYT---ECSKGTYIRTLAEDLALSLQ 185
Query: 845 CGAHLKYLRRIGIDKLTLDKCLNI---DTIIKYSEYERISSLIPIDILLSSFGIIYLSDL 901
+ LRR + + + I D I K S E+ I I+ +L ++ +D
Sbjct: 186 SLGFVIELRRTQVGIFKEENAIRIKSSDAITKNSLEEKS---IKIEAILDDILVLDATDE 242
Query: 902 LSKRFLHGQN-LFLSDENIYIL 922
+++ +GQ LF ++++ L
Sbjct: 243 QAQKIKYGQKCLFDYEKDVNFL 264
>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 = 138 bits (350), Expect = 1e-33
Identities = 93/296 (31%), Positives = 145/296 (48%), Gaps = 34/296 (11%)
Query: 927 IIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY---- 982
IIAH+DHGK+TL D LL +G + + + +++DS ++E+ERGITI ++ + Y
Sbjct: 8 IIAHIDHGKSTLADRLLEYTGAISERE-MREQVLDSMDLERERGITIKAQAVRLNYKAKD 66
Query: 983 -NGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPI 1041
+N+IDTPGH DF EV R L+ + LLL+DA +G QT AL+ + I
Sbjct: 67 GETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQTLANVYLALENDLEII 126
Query: 1042 VVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMI 1101
V+NKID +A PE V ++ E I SA K G I
Sbjct: 127 PVINKIDLPSADPERVKKEIEEVIG--LDASE-----AILASA---------KTGIG--I 168
Query: 1102 P-LFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGP 1160
+ EAI+K VP K + + PL+ I Y +Y G + + R+ G IK + M+
Sbjct: 169 EEILEAIVKRVPPPKGDPDAPLKALIFDSHYDNYRGVVALVRVFEGTIKPGDKIRFMSTG 228
Query: 1161 DDKPNKAKINQIRVFKGLDRVLVNEALSGDI-VLITGIEEIC---IGSTICDPSKP 1212
+ ++++ VF +E +G++ +I GI+++ +G TI P
Sbjct: 229 KEYE----VDEVGVFT-PKLTKTDELSAGEVGYIIAGIKDVSDVRVGDTITHVKNP 279
Score = 81.6 bits (202), Expect = 1e-15
Identities = 80/288 (27%), Positives = 126/288 (43%), Gaps = 58/288 (20%)
Query: 74 IMGHVDHGKTSLLD-YIRKTNVV--------------FSEAGGITQHIGAYNV----VTN 114
I+ H+DHGK++L D + T + GIT I A V
Sbjct: 8 IIAHIDHGKSTLADRLLEYTGAISEREMREQVLDSMDLERERGIT--IKAQAVRLNYKAK 65
Query: 115 HGS---ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKIS---G 168
G + +DTPGH F+ +R + +L+V A G+ QT +A+ ++
Sbjct: 66 DGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQT---LANVYLALEND 122
Query: 169 VPLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISL 228
+ +I INKID + +R+K+++ E+VI + AS I SAKTG+GI ++LE I
Sbjct: 123 LEIIPVINKIDLPSADPERVKKEI--EEVIGLD---ASEAILASAKTGIGIEEILEAI-- 175
Query: 229 QAEILELKAP---VTTPAKGVIIESRLDKGKGPVATVLIQSGTLRCSDIVVAGASYGRIR 285
+ + P P K +I +S D +G VA V + GT++ D +IR
Sbjct: 176 ---VKRVPPPKGDPDAPLKALIFDSHYDNYRGVVALVRVFEGTIKPGD---------KIR 223
Query: 286 SMLNENGKNILEAGPSIPVEIQGLTKVPF--SGEELFVILNEKKAREI 331
M + E G P LTK +GE ++I K ++
Sbjct: 224 FMSTGKEYEVDEVGVFTP----KLTKTDELSAGEVGYIIAGIKDVSDV 267
Score = 37.7 bits (88), Expect = 0.047
Identities = 33/135 (24%), Positives = 54/135 (40%), Gaps = 22/135 (16%)
Query: 1281 GELHLTILIENMRRE-GYELSVSRPRVIFK--TLNGE------------------LYEPY 1319
G LH+ I+ E + RE +L + P VI++ NGE + EPY
Sbjct: 343 GLLHMEIIQERLEREFNLDLITTAPSVIYRVYLTNGEVIEVDNPSDLPDPGKIEHVEEPY 402
Query: 1320 ENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIP-SRGLIGFQNEFITLT 1378
+ G IM + G N+E + RV L Y +P + + F ++ +++
Sbjct: 403 VKATIITPTEYLGPIMTLCQEKRGVQTNMEYLDPNRVELIYEMPLAEIVYDFFDKLKSIS 462
Query: 1379 RGTGLISHVFEEYAP 1393
RG + Y P
Sbjct: 463 RGYASFDYELIGYRP 477
>gnl|CDD|211338 cd02572, PseudoU_synth_hDyskerin, Pseudouridine synthase, human
dyskerin like. This group consists of eukaryotic and
archeal pseudouridine synthases similar to human
dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila
melanogaster Mfl (minifly protein). Pseudouridine
synthases catalyze the isomerization of specific
uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactor is required. S.
cerevisiae Cbf5 and human dyskerin are nucleolar
proteins that, with the help of guide RNAs, make the
hundreds of psueudouridnes present in rRNA and small
nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic
subunit of eukaryotic box H/ACA small nucleolar
ribonucleoprotein (snoRNP) particles. D. melanogaster
mfl hosts in its fourth intron, a box H/AC snoRNA gene.
In addition dyskerin is likely to have a structural role
in the telomerase complex. Mutations in human dyskerin
cause X-linked dyskeratosis congenitas. Mutations in
Drosophila Mfl results in miniflies that suffer
abnormalities.
Length = 182
Score = 126 bits (320), Expect = 3e-33
Identities = 67/194 (34%), Positives = 94/194 (48%), Gaps = 37/194 (19%)
Query: 664 GVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEA 723
GV+ LDKP G SS+ + IK +L +K G++GTLDP TG LP+C AT+ EA
Sbjct: 3 GVINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEA 62
Query: 724 DKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKY 783
K Y ++ L D+ E + ++L F G I Q PP+ SA
Sbjct: 63 GKEYVCVMRL-----HDDV-------------DEEKVRRVLEEFTGAIFQRPPLISA--- 101
Query: 784 KGIPLYKYARSGITIKRKLRYIKIYKITIIDY--TIPYLTLRIHCSKGTYIRVLSEDIGK 841
+KR+LR IY+ +++Y + R+ C GTYIR L IG
Sbjct: 102 --------------VKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTYIRTLCVHIGL 147
Query: 842 MLGCGAHLKYLRRI 855
+LG GAH++ LRR
Sbjct: 148 LLGVGAHMQELRRT 161
>gnl|CDD|211344 cd02867, PseudoU_synth_TruB_4, Pseudouridine synthase homolog 4.
This group consists of Eukaryotic TruB proteins similar
to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4,
makes psi55 in the T loop of both cytoplasmic and
mitochondrial tRNAs. Psi55 is almost universally
conserved. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi).
Length = 312
Score = 130 bits (329), Expect = 5e-33
Identities = 70/223 (31%), Positives = 95/223 (42%), Gaps = 39/223 (17%)
Query: 664 GVLLLDKPYGLSSNNALKKIKYLLNAK-----------------------------KVGY 694
GV ++KP G++S L +K L K+G+
Sbjct: 1 GVFAINKPSGITSAQVLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGH 60
Query: 695 TGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEAIIHLGITTETGDIEGKIIDFNKNIP 754
GTLDP ATG+L + G TK K YEA G +T T D EGKI+ K P
Sbjct: 61 GGTLDPLATGVLVVGVGAGTKQLQDYLSCSKTYEATGLFGASTTTYDREGKIL---KKKP 117
Query: 755 NSI---EIIEKILINFHGKISQIPPMYSALKYKGIPLYKYARSGI----TIKRKLRYIKI 807
S E IE++L F G I Q+PP+YSALK G LY+YAR G I+R+ +
Sbjct: 118 YSHITREDIEEVLAKFRGDIKQVPPLYSALKMDGKRLYEYAREGKPLPRPIERRQVVVSE 177
Query: 808 YKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIGKMLGCGAHLK 850
+ P T + Y R + + +GK L A +
Sbjct: 178 LLVKDWIEPGPLFTRTVEEEGKQYERSVVKMLGKELKTFAEVT 220
>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 = 127 bits (323), Expect = 2e-32
Identities = 61/135 (45%), Positives = 78/135 (57%), Gaps = 2/135 (1%)
Query: 927 IIAHVDHGKTTLIDHLLRQSGTFRKNQNI--NARIMDSNEIEKERGITIFSKNCSIEYNG 984
IIAH+D GKTT + +L +G K + MD E E+ERGITI S + +
Sbjct: 4 IIAHIDAGKTTTTERILYYTGRIHKIGEVHGGGATMDWMEQERERGITIQSAATTCFWKD 63
Query: 985 TRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVV 1044
RINIIDTPGH DF EVER L ++D + + DAV G PQT V R+A + G I V
Sbjct: 64 HRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVQPQTETVWRQADRYGVPRIAFV 123
Query: 1045 NKIDRSNARPEWVVD 1059
NK+DR+ A VV+
Sbjct: 124 NKMDRTGADFYRVVE 138
Score = 50.6 bits (122), Expect = 2e-06
Identities = 41/139 (29%), Positives = 57/139 (41%), Gaps = 18/139 (12%)
Query: 74 IMGHVDHGKTSL----LDYIRKTNVV-----------FSEAG---GITQHIGAYNVVTNH 115
I+ H+D GKT+ L Y + + + + E GIT A
Sbjct: 4 IIAHIDAGKTTTTERILYYTGRIHKIGEVHGGGATMDWMEQERERGITIQSAATTCFWKD 63
Query: 116 GSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAI 175
I +DTPGH FT R +V D V V A GV PQT A GVP I +
Sbjct: 64 HRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVQPQTETVWRQADRYGVPRIAFV 123
Query: 176 NKIDKLDINLDRIKQDLIS 194
NK+D+ + R+ + +
Sbjct: 124 NKMDRTGADFYRVVEQIRE 142
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative. This
family, found in archaea and eukaryotes, includes the
only archaeal proteins markedly similar to bacterial
TruB, the tRNA pseudouridine 55 synthase. However, among
two related yeast proteins, the archaeal set matches
yeast YLR175w far better than YNL292w. The first, termed
centromere/microtubule binding protein 5 (CBF5), is an
apparent rRNA pseudouridine synthase, while the second
is the exclusive tRNA pseudouridine 55 synthase for both
cytosolic and mitochondrial compartments. It is unclear
whether archaeal proteins found by this model modify
tRNA, rRNA, or both [Protein synthesis, tRNA and rRNA
base modification].
Length = 322
Score = 129 bits (325), Expect = 2e-32
Identities = 80/263 (30%), Positives = 121/263 (46%), Gaps = 45/263 (17%)
Query: 661 IIHGVLLLDKPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYL 720
I +GV+ LDKP G SS+ + ++ +LN +K G+ GTLDP TG+LP+C AT+
Sbjct: 32 ISYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVCIERATRLVKSQ 91
Query: 721 SEADKYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSA 780
EA K Y ++ L D + E I ++L F G+I Q PP+ SA
Sbjct: 92 QEAPKEYVCLMRL-----HRDAKE-------------EDILRVLKEFTGRIFQRPPLKSA 133
Query: 781 LKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGTYIRVLSEDIG 840
+KR+LR IY+ +++ + R+ C GTYIR L DIG
Sbjct: 134 -----------------VKRQLRVRTIYESELLEKDGKDVLFRVSCEAGTYIRKLCVDIG 176
Query: 841 KMLGCGAHLKYLRRIGIDKLTLDKCLNI----DTIIKYSE-----YERISSLIPIDILLS 891
+ LG GAH++ LRR D + + D + + E Y R + P++ LL
Sbjct: 177 EALGTGAHMQELRRTRSGCFGEDDMVTLHDLLDAYVFWKEDGDESYLR-RIIKPMEYLLR 235
Query: 892 SFGIIYLSDLLSKRFLHGQNLFL 914
+ + D HG +L +
Sbjct: 236 HLKRVVVKDSAVDAICHGADLMV 258
>gnl|CDD|239681 cd03710, BipA_TypA_C, BipA_TypA_C: a C-terminal portion of BipA or
TypA having homology to the C terminal domains of the
elongation factors EF-G and EF-2. A member of the
ribosome binding GTPase superfamily, BipA is widely
distributed in bacteria and plants. BipA is a highly
conserved protein with global regulatory properties in
Escherichia coli. BipA is phosphorylated on a tyrosine
residue under some cellular conditions. Mutants show
altered regulation of some pathways. BipA functions as a
translation factor that is required specifically for the
expression of the transcriptional modulator Fis. BipA
binds to ribosomes at a site that coincides with that of
EF-G and has a GTPase activity that is sensitive to high
GDP:GTP ratios and, is stimulated by 70S ribosomes
programmed with mRNA and aminoacylated tRNAs. The growth
rate-dependent induction of BipA allows the efficient
expression of Fis, thereby modulating a range of
downstream processes, including DNA metabolism and type
III secretion.
Length = 79
Score = 119 bits (300), Expect = 6e-32
Identities = 38/78 (48%), Positives = 58/78 (74%)
Query: 1317 EPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQNEFIT 1376
EP E L +D+ E G +++KL R G++ ++E + R RLE++IPSRGLIGF++EF+T
Sbjct: 1 EPIEELTIDVPEEYSGAVIEKLGKRKGEMVDMEPDGNGRTRLEFKIPSRGLIGFRSEFLT 60
Query: 1377 LTRGTGLISHVFEEYAPF 1394
TRGTG+++HVF+ Y P+
Sbjct: 61 DTRGTGIMNHVFDGYEPY 78
>gnl|CDD|237834 PRK14846, truB, tRNA pseudouridine synthase B; Provisional.
Length = 345
Score = 127 bits (319), Expect = 2e-31
Identities = 88/263 (33%), Positives = 134/263 (50%), Gaps = 10/263 (3%)
Query: 670 KPYGLSSNNALKKIKYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEA 729
KP G+SS + +K +L K+G+ GTLD A G+LP GEATK + L +A K Y
Sbjct: 10 KPRGISSAQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEATKLIHLLIDARKTYIF 69
Query: 730 IIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPLY 789
+ G+ T +GD GK+I IP S E + F G ++QIPP +SALK G+ Y
Sbjct: 70 TVKFGMQTNSGDCAGKVIATKDCIP-SQEEAYAVCSKFIGNVTQIPPAFSALKVNGVRAY 128
Query: 790 KYARSGITIKRKLRYIKIYKITIIDY-----TIPYLTLRIHCSKGTYIRVLSEDIGKMLG 844
K AR G ++ K R I IY + +++ T Y T CSKGTYIR L+ED+ L
Sbjct: 129 KLAREGKKVELKPRNITIYDLKCLNFDEKNATATYYT---ECSKGTYIRTLAEDLALSLQ 185
Query: 845 CGAHLKYLRRIGIDKLTLDKCLNIDTIIKYSEYERISSLIPIDILLSSFGIIYLSDLLSK 904
+ LRR + + + I + + ++ I I+ +L ++ +D ++
Sbjct: 186 SLGFVIELRRTQVGIFKEENAIRIKSPDEITKNALEEKSIKIEAILDDILVLDATDSQAQ 245
Query: 905 RFLHGQN-LFLSDENIYILIKSA 926
+ +GQ LF +++ L K A
Sbjct: 246 QIKYGQKCLFNYEKDFRHLAKFA 268
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 130 bits (330), Expect = 8e-31
Identities = 57/142 (40%), Positives = 79/142 (55%), Gaps = 16/142 (11%)
Query: 928 IAHVDHGKTTLIDHLLRQSGTFRKNQNINAR--------IMDSNEIEKERGITIFSKNCS 979
+ H GKTTL + +L +G I+ MD E+ERGI+I S +
Sbjct: 1 VGHSGAGKTTLTEAILFYTGA------IHRIGEVEDGTTTMDFMPEERERGISITSAATT 54
Query: 980 IEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFK 1039
E+ G +IN+IDTPGH DF GEVER L ++D ++++ AV G PQT V R+A K G
Sbjct: 55 CEWKGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTETVWRQAEKYG-V 113
Query: 1040 P-IVVVNKIDRSNARPEWVVDA 1060
P I+ VNK+DR+ A V+
Sbjct: 114 PRIIFVNKMDRAGADFFRVLAQ 135
Score = 87.9 bits (219), Expect = 2e-17
Identities = 65/267 (24%), Positives = 110/267 (41%), Gaps = 66/267 (24%)
Query: 1070 ATEEQLDFPVIYTSALHGYANENSKARQGNMIPLFEAILKYVP-------VHKDNSNN-- 1120
AT PV SAL + L +A++ Y+P V ++
Sbjct: 230 ATLAGEIVPVFCGSALKNKG----------VQRLLDAVVDYLPSPLEVPPVDGEDGEEGA 279
Query: 1121 --------PLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQI 1172
PL + ++GK+ + R+ SG +K + N K K ++ ++
Sbjct: 280 ELAPDPDGPLVALVFKTMDDPFVGKLSLVRVYSGTLKK--GDTLYNSGTGK--KERVGRL 335
Query: 1173 RVFKGLDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTLTINFMVN 1232
G R V+EA++GDIV + +++ G T+CD P L + EP +
Sbjct: 336 YRMHGKQREEVDEAVAGDIVAVAKLKDAATGDTLCDKGDPILLEPMEFPEPVI------- 388
Query: 1233 NSPLAGREGKFITTRQIKNRLDHE-IKNNIG--------LRVTQNKHDDS---IYEVSGR 1280
LA I K++ D E + +G LRV +++ ++ I +SG
Sbjct: 389 --SLA------IEP---KDKGDEEKLSEALGKLAEEDPTLRVERDE--ETGQTI--LSGM 433
Query: 1281 GELHLTILIENMRRE-GYELSVSRPRV 1306
GELHL + +E ++RE G E+ P+V
Sbjct: 434 GELHLDVALERLKREYGVEVETGPPQV 460
Score = 75.2 bits (186), Expect = 2e-13
Identities = 44/139 (31%), Positives = 58/139 (41%), Gaps = 24/139 (17%)
Query: 75 MGHVDHGKTSLLDYI--------RKTNVVFSEAG-------------GITQHIGAYNVVT 113
+GH GKT+L + I R V E G GI+ A
Sbjct: 1 VGHSGAGKTTLTEAILFYTGAIHRIGEV---EDGTTTMDFMPEERERGISITSAATTCEW 57
Query: 114 NHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIV 173
I +DTPGH FT R +V D V+VV A GV PQT A+ GVP I+
Sbjct: 58 KGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTETVWRQAEKYGVPRII 117
Query: 174 AINKIDKLDINLDRIKQDL 192
+NK+D+ + R+ L
Sbjct: 118 FVNKMDRAGADFFRVLAQL 136
Score = 30.9 bits (71), Expect = 6.3
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 3/80 (3%)
Query: 1315 LYEPYENLFVDIEEINQGIIMQKLNYRGGDLKNIE-INEKERVRLEYRIPSRGLIGFQNE 1373
L EP + V + E G ++ L+ R G + +E + VR E +P + G+ +
Sbjct: 580 LLEPIMKVEVSVPEEFVGDVIGDLSSRRGRILGMESRGGGDVVRAE--VPLAEMFGYATD 637
Query: 1374 FITLTRGTGLISHVFEEYAP 1393
+LT+G G S F Y
Sbjct: 638 LRSLTQGRGSFSMEFSHYEE 657
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 130 bits (328), Expect = 1e-30
Identities = 62/152 (40%), Positives = 86/152 (56%), Gaps = 12/152 (7%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNIN--ARIMDSNEIEKERGITIFSKNCSIEYN 983
I+AH+D GKTTL + +L +G K + + D E+ERGITI S S +++
Sbjct: 12 GILAHIDAGKTTLTERILFYTGKIHKMGEVEDGTTVTDWMPQEQERGITIESAATSCDWD 71
Query: 984 GTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV 1043
RIN+IDTPGH DF GEVER L ++D +++ DAV G PQT V R+A + G ++
Sbjct: 72 NHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTGVQPQTETVWRQADRYGIPRLIF 131
Query: 1044 VNKIDRSNARPEWVVDATFDLFDKLCATEEQL 1075
+NK+DR A DLF L EE+
Sbjct: 132 INKMDRVGA----------DLFKVLEDIEERF 153
Score = 85.4 bits (212), Expect = 1e-16
Identities = 65/254 (25%), Positives = 111/254 (43%), Gaps = 47/254 (18%)
Query: 1077 FPVIYTSALHGYANENSKARQGNMIPLFEAILKYVPVHKD------------------NS 1118
PV++ SAL E PL +A++ Y+P + +
Sbjct: 253 VPVLFGSALKNIGIE----------PLLDAVVDYLPSPLEVPPPRGSKDNGKPVKVDPDP 302
Query: 1119 NNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNK-AKINQIRVFKG 1177
PL + ++Y Y GK+ R+ SG ++ + NG K K ++ R+ G
Sbjct: 303 EKPLLALVFKVQYDPYAGKLTYLRVYSGTLR--AGSQLYNGTGGKREKVGRL--FRLQ-G 357
Query: 1178 LDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTLTINFMVNNSPL- 1236
R V+ A +GDIV + G++E+ G T+ D + P L +L EP + P
Sbjct: 358 NKREEVDRAKAGDIVAVAGLKELETGDTLHDSADPVLLELLTFPEPV----VSLAVEPER 413
Query: 1237 AGREGKFITTRQIKNRLDHEIKNNIGLRVTQNKHDDSIYEVSGRGELHLTILIENMRRE- 1295
G E K + L+ + + LRV +++ +SG GELHL + +E +RRE
Sbjct: 414 RGDEQK------LAEALEKLVWEDPSLRVEEDEETGQTI-LSGMGELHLEVALERLRREF 466
Query: 1296 GYELSVSRPRVIFK 1309
E++ +P+V ++
Sbjct: 467 KLEVNTGKPQVAYR 480
Score = 73.4 bits (181), Expect = 5e-13
Identities = 43/142 (30%), Positives = 66/142 (46%), Gaps = 24/142 (16%)
Query: 72 VTIMGHVDHGKTSLLDYI--------RKTNVVFSEAG-------------GITQHIGAYN 110
+ I+ H+D GKT+L + I + V E G GIT A +
Sbjct: 11 IGILAHIDAGKTTLTERILFYTGKIHKMGEV---EDGTTVTDWMPQEQERGITIESAATS 67
Query: 111 VVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVP 170
++ I +DTPGH FT R +V D V+V A GV PQT A G+P
Sbjct: 68 CDWDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTGVQPQTETVWRQADRYGIP 127
Query: 171 LIVAINKIDKLDINLDRIKQDL 192
++ INK+D++ +L ++ +D+
Sbjct: 128 RLIFINKMDRVGADLFKVLEDI 149
>gnl|CDD|234787 PRK00521, rbfA, ribosome-binding factor A; Validated.
Length = 120
Score = 116 bits (293), Expect = 2e-30
Identities = 35/108 (32%), Positives = 66/108 (61%)
Query: 541 RLSRIENQIQRDISEIIAFDIQNPIINIITITEVKITLDYSYAKIFFTTFNKDISIKNIL 600
R R+ QIQR+++EI+ +I++P + ++T+T+V+++ D ++AK++ T + + L
Sbjct: 7 RALRVAEQIQRELAEILQREIKDPRLGMVTVTDVEVSPDLAHAKVYVTVLGDEEDKEEAL 66
Query: 601 DNLSKAKNYIRFKLSKKLHIHTLPILNFFYDNSIENAMMISKLIDGIK 648
L KA ++R +L K+L + +P L F YD S+E I +L+ K
Sbjct: 67 AALKKAAGFLRSELGKRLRLRYVPELRFVYDESLEYGNRIDELLRKAK 114
>gnl|CDD|216854 pfam02033, RBFA, Ribosome-binding factor A.
Length = 104
Score = 115 bits (291), Expect = 2e-30
Identities = 34/104 (32%), Positives = 66/104 (63%)
Query: 541 RLSRIENQIQRDISEIIAFDIQNPIINIITITEVKITLDYSYAKIFFTTFNKDISIKNIL 600
R R+ IQR+++EI+ ++++P + ++T+TEV+++ D S+AK++ + + + L
Sbjct: 1 RTERVAELIQRELAEILQRELKDPRLGLVTVTEVEVSPDLSHAKVYVSVLGDEEEKEETL 60
Query: 601 DNLSKAKNYIRFKLSKKLHIHTLPILNFFYDNSIENAMMISKLI 644
L+KA +IR +L+K+L + P L F YD+S+E I +L+
Sbjct: 61 KALNKAAGFIRSELAKRLRLRYTPELRFVYDDSLEYGARIEELL 104
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 124 bits (314), Expect = 9e-29
Identities = 55/135 (40%), Positives = 79/135 (58%), Gaps = 10/135 (7%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
++IAHVDHGK+TL D L+ ++G +AR D+ E+ERGITI S S+ Y
Sbjct: 23 SVIAHVDHGKSTLTDSLVCKAGIISSKNAGDARFTDTRADEQERGITIKSTGISLYYEHD 82
Query: 986 R----------INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALK 1035
IN+ID+PGH DF EV L + D L+++D VEG QT V R+AL+
Sbjct: 83 LEDGDDKQPFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVEGVCVQTETVLRQALQ 142
Query: 1036 LGFKPIVVVNKIDRS 1050
+P++ +NK+DR+
Sbjct: 143 ERIRPVLFINKVDRA 157
Score = 46.6 bits (111), Expect = 1e-04
Identities = 37/139 (26%), Positives = 61/139 (43%), Gaps = 34/139 (24%)
Query: 73 TIMGHVDHGKTSLLD-YIRKTNVVFSEAGG---------------IT----------QHI 106
+++ HVDHGK++L D + K ++ S+ G IT +H
Sbjct: 23 SVIAHVDHGKSTLTDSLVCKAGIISSKNAGDARFTDTRADEQERGITIKSTGISLYYEHD 82
Query: 107 GAYNVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQT----REAIA 162
I +D+PGH F++ +VTD ++VV +GV QT R+A+
Sbjct: 83 LEDGDDKQPFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVEGVCVQTETVLRQALQ 142
Query: 163 HAKISGVPLIVAINKIDKL 181
+I V + INK+D+
Sbjct: 143 E-RIRPV---LFINKVDRA 157
Score = 30.8 bits (70), Expect = 7.9
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 1117 NSNNPLQLQIISLEYSSYLGKI-GIGRILSGRIKSLQDVVIMNGPDDKPNK 1166
+ N PL + I + +S G+ GR+ SG + + Q V I GP+ P K
Sbjct: 367 DPNGPLMMYISKMVPTSDKGRFYAFGRVFSGTVATGQKVRIQ-GPNYVPGK 416
>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 = 122 bits (308), Expect = 3e-28
Identities = 63/155 (40%), Positives = 88/155 (56%), Gaps = 5/155 (3%)
Query: 927 IIAHVDHGKTTLIDHLLRQSGTFRKNQNIN--ARIMDSNEIEKERGITIFSKNCSIEYNG 984
I AH+D GKTT + +L +G K ++ A MD E EKERGITI S ++ + G
Sbjct: 15 ISAHIDAGKTTTTERILFYTGRIHKIGEVHDGAATMDWMEQEKERGITITSAATTVFWKG 74
Query: 985 TRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVV 1044
RINIIDTPGH DF EVER L ++D + ++DAV G PQ+ V R+A + I V
Sbjct: 75 HRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSETVWRQANRYEVPRIAFV 134
Query: 1045 NKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPV 1079
NK+D++ A VV+ + +L A + P+
Sbjct: 135 NKMDKTGANFLRVVNQ---IKQRLGANAVPIQLPI 166
Score = 61.7 bits (150), Expect = 2e-09
Identities = 41/137 (29%), Positives = 53/137 (38%), Gaps = 18/137 (13%)
Query: 74 IMGHVDHGKTSLLDYIRKTNVVFSEAG------------------GITQHIGAYNVVTNH 115
I H+D GKT+ + I + G GIT A V
Sbjct: 15 ISAHIDAGKTTTTERILFYTGRIHKIGEVHDGAATMDWMEQEKERGITITSAATTVFWKG 74
Query: 116 GSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAI 175
I +DTPGH FT R +V D V V+ A GV PQ+ A VP I +
Sbjct: 75 HRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSETVWRQANRYEVPRIAFV 134
Query: 176 NKIDKLDINLDRIKQDL 192
NK+DK N R+ +
Sbjct: 135 NKMDKTGANFLRVVNQI 151
Score = 56.7 bits (137), Expect = 7e-08
Identities = 54/264 (20%), Positives = 107/264 (40%), Gaps = 66/264 (25%)
Query: 1077 FPVIYTSALHGYANENSKARQGNMIPLFEAILKYVPVHKD---------NSNNPLQLQI- 1126
FPV+ SA + N+ + L +A++ Y+P D ++ ++ +
Sbjct: 254 FPVLCGSA---FKNKGVQL-------LLDAVVDYLPSPTDVPAIKGIDPDTEKEIERKAS 303
Query: 1127 ---------ISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKG 1177
+ ++G++ R+ SG +KS V N +K K ++ ++
Sbjct: 304 DDEPFSALAFKVATDPFVGQLTFVRVYSGVLKSGSYV--KNSRKNK--KERVGRLVKMHA 359
Query: 1178 LDRVLVNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTLTINFMVNNSPLA 1237
+R + E +GDI G+++ G T+CDP L + EP +++
Sbjct: 360 NNREEIKEVRAGDICAAIGLKDTTTGDTLCDPKIDVILERMEFPEPVISLAV-------- 411
Query: 1238 GREGKFITTRQIKNRLDHEIKNNIGLRVTQNKHDDSIYEV-----------SGRGELHLT 1286
+ K + D E +G+ + + +D + +G GELHL
Sbjct: 412 ----------EPKTKADQE---KMGIALGKLAEEDPTFRTFTDPETGQTIIAGMGELHLD 458
Query: 1287 ILIENMRRE-GYELSVSRPRVIFK 1309
I+++ M+RE E +V P+V ++
Sbjct: 459 IIVDRMKREFKVEANVGAPQVAYR 482
>gnl|CDD|239662 cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also called
TypA) having homology to domain II of the elongation
factors (EFs) EF-G and EF-Tu. BipA is a highly conserved
protein with global regulatory properties in Escherichia
coli. BipA is phosphorylated on a tyrosine residue under
some cellular conditions. Mutants show altered regulation
of some pathways. BipA functions as a translation factor
that is required specifically for the expression of the
transcriptional modulator Fis. BipA binds to ribosomes
at a site that coincides with that of EF-G and has a
GTPase activity that is sensitive to high GDP:GTP ratios
and, is stimulated by 70S ribosomes programmed with mRNA
and aminoacylated tRNAs. The growth rate-dependent
induction of BipA allows the efficient expression of Fis,
thereby modulating a range of downstream processes,
including DNA metabolism and type III secretion.
Length = 86
Score = 106 bits (267), Expect = 2e-27
Identities = 44/87 (50%), Positives = 58/87 (66%), Gaps = 1/87 (1%)
Query: 1122 LQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRV 1181
LQ+ + +L+Y Y+G+I IGRI G +K Q V ++ D K KAKI ++ F+GL RV
Sbjct: 1 LQMLVTTLDYDDYVGRIAIGRIFRGTVKVGQQVAVVK-RDGKIEKAKITKLFGFEGLKRV 59
Query: 1182 LVNEALSGDIVLITGIEEICIGSTICD 1208
V EA +GDIV I GIE+I IG TICD
Sbjct: 60 EVEEAEAGDIVAIAGIEDITIGDTICD 86
>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 = 110 bits (277), Expect = 1e-26
Identities = 55/138 (39%), Positives = 79/138 (57%), Gaps = 22/138 (15%)
Query: 926 AIIAHVDHGKTTLIDHLL------RQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCS 979
AII+H D GKTTL + LL +++G + ++ D EIEK+RGI++ S
Sbjct: 6 AIISHPDAGKTTLTEKLLLFGGAIQEAGAVKARKSRKHATSDWMEIEKQRGISVTSSVMQ 65
Query: 980 IEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFK 1039
EY G IN++DTPGH DF + R L+ VD+ +++IDA +G PQTR KL F+
Sbjct: 66 FEYKGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTR-------KL-FE 117
Query: 1040 -------PIV-VVNKIDR 1049
PI+ +NK+DR
Sbjct: 118 VCRLRGIPIITFINKLDR 135
Score = 48.4 bits (116), Expect = 1e-05
Identities = 32/80 (40%), Positives = 46/80 (57%), Gaps = 6/80 (7%)
Query: 118 ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINK 177
I LDTPGHE F+ R D V+V+ A GV PQTR+ ++ G+P+I INK
Sbjct: 73 INLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGIPIITFINK 132
Query: 178 IDK-----LDINLDRIKQDL 192
+D+ L++ LD I+ +L
Sbjct: 133 LDREGRDPLEL-LDEIENEL 151
>gnl|CDD|223927 COG0858, RbfA, Ribosome-binding factor A [Translation, ribosomal
structure and biogenesis].
Length = 118
Score = 103 bits (259), Expect = 6e-26
Identities = 41/109 (37%), Positives = 73/109 (66%), Gaps = 1/109 (0%)
Query: 541 RLSRIENQIQRDISEIIAFDIQNPIINIITITEVKITLDYSYAKIFFTTFN-KDISIKNI 599
R R+ QIQ++++EI+ +I++P + ++T+T+V+++ D S+AK++ T ++ S I
Sbjct: 6 RAKRVAEQIQKELAEILQREIKDPRLGLVTVTDVEVSKDLSHAKVYVTVLGDEESSKAEI 65
Query: 600 LDNLSKAKNYIRFKLSKKLHIHTLPILNFFYDNSIENAMMISKLIDGIK 648
L L+KAK +IR +L K+L + P L+F YD+SIEN I L++ +K
Sbjct: 66 LAALNKAKGFIRSELGKRLRLRKTPELHFVYDDSIENGNKIDALLNDLK 114
>gnl|CDD|239663 cd03692, mtIF2_IVc, mtIF2_IVc: this family represents the C2
subdomain of domain IV of mitochondrial translation
initiation factor 2 (mtIF2) which adopts a beta-barrel
fold displaying a high degree of structural similarity
with domain II of the translation elongation factor
EF-Tu. The C-terminal part of mtIF2 contains the entire
fMet-tRNAfmet binding site of IF-2 and is resistant to
proteolysis. This C-terminal portion consists of two
domains, IF2 C1 and IF2 C2. IF2 C2 been shown to
contain all molecular determinants necessary and
sufficient for the recognition and binding of
fMet-tRNAfMet. Like IF2 from certain prokaryotes such as
Thermus thermophilus, mtIF2lacks domain II which is
thought to be involved in binding of E.coli IF-2 to 30S
subunits.
Length = 84
Score = 102 bits (256), Expect = 7e-26
Identities = 37/66 (56%), Positives = 53/66 (80%)
Query: 474 GLAEIRQVILVNKVSKIAGCYILEGLIRRDSKIRILRNKNIIWTGELDSLKRFKDNVKEV 533
G AE+R V ++KV IAGCY+ +G I+R++K+R+LRN +I+ G++ SLKRFKD+VKEV
Sbjct: 1 GEAEVRAVFKISKVGNIAGCYVTDGKIKRNAKVRVLRNGEVIYEGKISSLKRFKDDVKEV 60
Query: 534 KAGFEC 539
K G+EC
Sbjct: 61 KKGYEC 66
>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 = 106 bits (267), Expect = 8e-26
Identities = 49/133 (36%), Positives = 76/133 (57%), Gaps = 10/133 (7%)
Query: 926 AIIAHVDHGKTTLIDHLL----RQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIE 981
I H+ HGKT+L+D L+ +++ + + R D+ + E+ERGI+I S S+
Sbjct: 4 CIAGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPL-RYTDTRKDEQERGISIKSNPISLV 62
Query: 982 YNGTR-----INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKL 1036
++ INIIDTPGH +F EV L + D V+L++D VEG T + R A++
Sbjct: 63 LEDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVEGLTSVTERLIRHAIQE 122
Query: 1037 GFKPIVVVNKIDR 1049
G ++V+NKIDR
Sbjct: 123 GLPMVLVINKIDR 135
Score = 70.0 bits (172), Expect = 4e-13
Identities = 43/138 (31%), Positives = 62/138 (44%), Gaps = 24/138 (17%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAY----------------NVVT-- 113
V I GH+ HGKTSLLD + + + + + Y N ++
Sbjct: 3 VCIAGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPLRYTDTRKDEQERGISIKSNPISLV 62
Query: 114 ----NHGS--ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKIS 167
S I +DTPGH F A ++ D VVLVV +G+ T I HA
Sbjct: 63 LEDSKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVVEGLTSVTERLIRHAIQE 122
Query: 168 GVPLIVAINKIDKLDINL 185
G+P+++ INKID+L + L
Sbjct: 123 GLPMVLVINKIDRLILEL 140
>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 = 106 bits (268), Expect = 3e-25
Identities = 47/153 (30%), Positives = 75/153 (49%), Gaps = 14/153 (9%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINAR--------IMDSNEIEKERGITIFSKN 977
A++ H GKTTL + LL +G I+ + D + EK+R ++I +
Sbjct: 3 ALVGHSGSGKTTLAEALLYATGA------IDRLGRVEDGNTVSDYDPEEKKRKMSIETSV 56
Query: 978 CSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLG 1037
+E+NG +IN+IDTPG+ADF GE L VD L++++A G T V
Sbjct: 57 APLEWNGHKINLIDTPGYADFVGETLSALRAVDAALIVVEAQSGVEVGTEKVWEFLDDAK 116
Query: 1038 FKPIVVVNKIDRSNARPEWVVDATFDLFDKLCA 1070
I+ +NK+DR+ A + + A + F +
Sbjct: 117 LPRIIFINKMDRARADFDKTLAALREAFGRPVV 149
Score = 58.4 bits (142), Expect = 6e-09
Identities = 38/168 (22%), Positives = 62/168 (36%), Gaps = 39/168 (23%)
Query: 72 VTIMGHVDHGKTSLLDYI--------RKTNVVFSEAG-------------GITQHIGAYN 110
+ ++GH GKT+L + + R V E G ++
Sbjct: 2 IALVGHSGSGKTTLAEALLYATGAIDRLGRV---EDGNTVSDYDPEEKKRKMSIETSVAP 58
Query: 111 VVTNHGSITFLDTPG-----HEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAK 165
+ N I +DTPG E +A+R D ++VV A GV T +
Sbjct: 59 LEWNGHKINLIDTPGYADFVGETLSALR-----AVDAALIVVEAQSGVEVGTEKVWEFLD 113
Query: 166 ISGVPLIVAINKIDKLDINLDRIKQDL---ISEQVIPEEY--GGASPF 208
+ +P I+ INK+D+ + D+ L V+P + G F
Sbjct: 114 DAKLPRIIFINKMDRARADFDKTLAALREAFGRPVVPIQLPIGEGDEF 161
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 112 bits (283), Expect = 5e-25
Identities = 55/140 (39%), Positives = 77/140 (55%), Gaps = 16/140 (11%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY--- 982
++IAHVDHGK+TL D L+ +G + + R+ D+ E ERGITI S S+ Y
Sbjct: 23 SVIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRMTDTRADEAERGITIKSTGISLYYEMT 82
Query: 983 -------------NGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFV 1029
N IN+ID+PGH DF EV L + D L+++D +EG QT V
Sbjct: 83 DESLKDFKGERDGNEYLINLIDSPGHVDFSSEVTAALRITDGALVVVDCIEGVCVQTETV 142
Query: 1030 TRKALKLGFKPIVVVNKIDR 1049
R+AL +P++ VNK+DR
Sbjct: 143 LRQALGERIRPVLTVNKMDR 162
Score = 37.0 bits (86), Expect = 0.094
Identities = 39/149 (26%), Positives = 67/149 (44%), Gaps = 34/149 (22%)
Query: 72 VTIMGHVDHGKTSLLDYI---------------RKTNVVFSEAG-GIT---QHIGAYNVV 112
++++ HVDHGK++L D + R T+ EA GIT I Y +
Sbjct: 22 MSVIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRMTDTRADEAERGITIKSTGISLYYEM 81
Query: 113 T-------------NHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTRE 159
T N I +D+PGH F++ ++TD ++VV +GV QT
Sbjct: 82 TDESLKDFKGERDGNEYLINLIDSPGHVDFSSEVTAALRITDGALVVVDCIEGVCVQTET 141
Query: 160 AIAHAKISGVPLIVAINKIDK--LDINLD 186
+ A + ++ +NK+D+ L++ +D
Sbjct: 142 VLRQALGERIRPVLTVNKMDRCFLELQVD 170
Score = 35.5 bits (82), Expect = 0.30
Identities = 52/218 (23%), Positives = 98/218 (44%), Gaps = 37/218 (16%)
Query: 1117 NSNNPLQLQIISLEYSSYLGK-IGIGRILSGRIKSLQDVVIMNGPDDKPNKAK------I 1169
+ N PL L + + +S G+ GR+ SG + + V IM GP+ P + K +
Sbjct: 371 DPNGPLMLYVSKMIPASDKGRFFAFGRVFSGTVATGMKVRIM-GPNYVPGEKKDLYVKSV 429
Query: 1170 NQIRVFKGLDRVLVNEALSGDIVLITGIEEICIGS-TICDPSKPNGLPMLNIDEPTLTIN 1228
+ ++ G + V + G+ V + G+++ + T+ + + + P+ +
Sbjct: 430 QRTVIWMGKKQESVEDVPCGNTVAMVGLDQFITKNATLTNEKEVDAHPIKAM-------K 482
Query: 1229 FMVNNSPLAGREGKFITTRQIKNRLDHEIKNNIGLR-------VTQNKHDDS-IYEVSGR 1280
F V SP+ Q KN D K GL+ + Q ++S + ++G
Sbjct: 483 FSV--SPVVRV------AVQCKNASDLP-KLVEGLKRLAKSDPMVQCTIEESGEHIIAGA 533
Query: 1281 GELHLTILIENMRRE---GYELSVSRPRVIFK-TLNGE 1314
GELHL I +++++ + G E+ VS P V F+ T+ +
Sbjct: 534 GELHLEICLKDLQDDFMGGAEIKVSDPVVSFRETVLEK 571
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 111 bits (281), Expect = 8e-25
Identities = 63/138 (45%), Positives = 80/138 (57%), Gaps = 8/138 (5%)
Query: 927 IIAHVDHGKTTLIDHLLRQSGTFRKNQNIN-----ARIMDSNEIEKERGITIFSKNCSIE 981
I+AH+D GKTT + +L +G K+ I A MD E E+ERGITI S +
Sbjct: 13 IMAHIDAGKTTTTERILYYTG---KSHKIGEVHDGAATMDWMEQEQERGITITSAATTCF 69
Query: 982 YNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPI 1041
+ G RINIIDTPGH DF EVER L ++D + + DAV G PQ+ V R+A K G I
Sbjct: 70 WKGHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQSETVWRQADKYGVPRI 129
Query: 1042 VVVNKIDRSNARPEWVVD 1059
V VNK+DR A V+
Sbjct: 130 VFVNKMDRIGADFFRSVE 147
Score = 47.5 bits (114), Expect = 6e-05
Identities = 44/132 (33%), Positives = 55/132 (41%), Gaps = 18/132 (13%)
Query: 74 IMGHVDHGKTS----LLDY---IRKTNVVFSEAG-----------GITQHIGAYNVVTNH 115
IM H+D GKT+ +L Y K V A GIT A
Sbjct: 13 IMAHIDAGKTTTTERILYYTGKSHKIGEVHDGAATMDWMEQEQERGITITSAATTCFWKG 72
Query: 116 GSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAI 175
I +DTPGH FT R +V D V V A GV PQ+ A GVP IV +
Sbjct: 73 HRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQSETVWRQADKYGVPRIVFV 132
Query: 176 NKIDKLDINLDR 187
NK+D++ + R
Sbjct: 133 NKMDRIGADFFR 144
Score = 45.2 bits (108), Expect = 3e-04
Identities = 38/139 (27%), Positives = 61/139 (43%), Gaps = 33/139 (23%)
Query: 1183 VNEALSGDIVLITGIEEICIGSTICDPSKPNGLPMLNIDEPTLTINFMVNNSPLAGREGK 1242
+ E +GDI G+++ G T+CD P L + EP I+ V P
Sbjct: 364 IKEVYAGDIAAAVGLKDTTTGDTLCDEKAPIILESMEFPEPV--ISLAV--EP------- 412
Query: 1243 FITTRQIKNRLDHEIKNNIGL----------RVTQNKHD-DSIYEVSGRGELHLTILIEN 1291
K + D + K + L RV ++ +I +SG GELHL I+++
Sbjct: 413 -------KTKADQD-KMGLALQKLAEEDPTFRVETDEETGQTI--ISGMGELHLDIIVDR 462
Query: 1292 MRRE-GYELSVSRPRVIFK 1309
M+RE E +V P+V ++
Sbjct: 463 MKREFKVEANVGAPQVAYR 481
>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 = 101 bits (254), Expect = 1e-24
Identities = 48/165 (29%), Positives = 81/165 (49%), Gaps = 18/165 (10%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAG-GITQHIGAYNVVTNHGSITF--LDTPGHEA 128
+ I+G + GK++LL+ + + +E G T++ + + + F LDT G E
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQED 63
Query: 129 FTAMR-------ARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKL 181
+ A+R +V DIV+LV+ ++ + QT+E I HA+ SGVP+I+ NKID
Sbjct: 64 YDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAE-SGVPIILVGNKIDLR 122
Query: 182 DINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
D L L ++ P I +SA+TG I+ + +
Sbjct: 123 DAKLKTHVAFLFAKL-------NGEPIIPLSAETGKNIDSAFKIV 160
Score = 68.9 bits (169), Expect = 3e-13
Identities = 37/141 (26%), Positives = 57/141 (40%), Gaps = 37/141 (26%)
Query: 923 IKSAIIAHVDHGKTTLIDHLL--------RQSGTFRKNQNINARIMDSNEIEKERGITIF 974
IK I+ + GK+TL++ LL + GT R + +E G T
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTR---------NYVTTVIEEDGKTY- 51
Query: 975 SKNCSIEYNGTRINIIDTPGHADF-------GGEVERILSMVDNVLLLIDAVEGPMPQTR 1027
+ N++DT G D+ VE L + D V+L++D E QT+
Sbjct: 52 -----------KFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTK 100
Query: 1028 FVTRKALKLGFKPIVVVNKID 1048
+ + G I+V NKID
Sbjct: 101 EIIH-HAESGVPIILVGNKID 120
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 110 bits (277), Expect = 2e-24
Identities = 64/150 (42%), Positives = 83/150 (55%), Gaps = 11/150 (7%)
Query: 927 IIAHVDHGKTTLIDHLLRQSGTFRKNQNI-----NARIMDSNEIEKERGITIFSKNCSIE 981
I+AH+D GKTT + +L +G N I A MD E E+ERGITI S +
Sbjct: 15 IMAHIDAGKTTTTERILFYTG---VNHKIGEVHDGAATMDWMEQEQERGITITSAATTCF 71
Query: 982 YNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPI 1041
+ RINIIDTPGH DF EVER L ++D + + DAV G PQ+ V R+A K I
Sbjct: 72 WKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVGGVEPQSETVWRQADKYKVPRI 131
Query: 1042 VVVNKIDRSNARPEWVVDATFDLFDKLCAT 1071
VNK+DR+ A VV+ + D+L A
Sbjct: 132 AFVNKMDRTGADFYRVVE---QIKDRLGAN 158
Score = 44.3 bits (106), Expect = 5e-04
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 118 ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQT----REAIAHAKISGVPLIV 173
I +DTPGH FT R +V D V V A GV PQ+ R+A + VP I
Sbjct: 77 INIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVGGVEPQSETVWRQADKY----KVPRIA 132
Query: 174 AINKIDKLDINLDRIKQDLI 193
+NK+D+ + R+ + +
Sbjct: 133 FVNKMDRTGADFYRVVEQIK 152
Score = 41.6 bits (99), Expect = 0.003
Identities = 52/190 (27%), Positives = 81/190 (42%), Gaps = 47/190 (24%)
Query: 1134 YLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVL 1193
++GK+ R+ SG ++S V +N K K +I +I R + E +GDI
Sbjct: 322 FVGKLTFFRVYSGVLESGSYV--LNSTKGK--KERIGRILQMHANKREEIKEVRAGDIAA 377
Query: 1194 ITGIEEICIGSTICDPSKPNGLPMLNIDEPTLTINFMVNNSPLAGREGKFITTRQIKNRL 1253
G+++ G T+CD P L + EP I+ V P K +
Sbjct: 378 AVGLKDTTTGDTLCDEKNPIILESMEFPEP--VISVAV--EP--------------KTKA 419
Query: 1254 DHEIKNNIGL----------RVTQNKHDDSIYEVSGR------GELHLTILIENMRRE-G 1296
D E K I L RV+ + E +G+ GELHL I+++ M+RE
Sbjct: 420 DQE-KMGIALQKLAEEDPSFRVSTD-------EETGQTIIAGMGELHLDIIVDRMKREFK 471
Query: 1297 YELSVSRPRV 1306
E +V +P+V
Sbjct: 472 VEANVGKPQV 481
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 107 bits (269), Expect = 3e-24
Identities = 86/322 (26%), Positives = 130/322 (40%), Gaps = 41/322 (12%)
Query: 923 IKSAIIAHVDHGKTTLIDHLLRQSGTF---------RKNQNIN------ARIMDSNEIEK 967
+ I HVD GK+TL+ LL G ++ + + A ++D + E+
Sbjct: 8 LNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKTKEER 67
Query: 968 ERGITIFSKNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEG------ 1021
ERG+TI + E + IID PGH DF + S D +L++DA +G
Sbjct: 68 ERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEFEAGF 127
Query: 1022 -PMPQTRFVTRKALKLGFKP-IVVVNKIDR---SNARPEWVVDATFDLFDKLCATEEQLD 1076
QTR A LG K IV VNK+D R E +V L K+ + D
Sbjct: 128 GVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLL-KMVGYNPK-D 185
Query: 1077 FPVIYTSALHG-YANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYL 1135
P I S G + S+ P L + + + PL+L I + S +
Sbjct: 186 VPFIPISGFKGDNLTKKSENMPWYKGPTLLEALDQLEPPERPLDKPLRLPIQDVYSISGI 245
Query: 1136 GKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--L 1193
G + +GR+ SG IK Q V M P +++ + +++A GD V
Sbjct: 246 GTVPVGRVESGVIKPGQKVTFM------PAGVV-GEVKSIEM-HHEEISQAEPGDNVGFN 297
Query: 1194 ITGIE--EICIGSTICDPSKPN 1213
+ G+E +I G I P
Sbjct: 298 VRGVEKNDIRRGDVIGHSDNPP 319
Score = 80.4 bits (199), Expect = 2e-15
Identities = 73/293 (24%), Positives = 118/293 (40%), Gaps = 58/293 (19%)
Query: 75 MGHVDHGKTSLLDY------------IRKTNVVFSEAG-------------------GIT 103
+GHVD GK++L+ + K E G G+T
Sbjct: 13 IGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKTKEERERGVT 72
Query: 104 QHIGAYNVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDG-------VMPQ 156
+ T+ + T +D PGH F GA D+ VLVV A DG V Q
Sbjct: 73 IDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEFEAGFGVGGQ 132
Query: 157 TREAIAHAKISGVP-LIVAINKIDKLDINLDRIKQDLISEQVIP--EEYG---GASPFIS 210
TRE A+ G+ LIVA+NK+D ++ D + + I +V + G PFI
Sbjct: 133 TREHAFLARTLGIKQLIVAVNKMD--LVSWDEERFEEIVSEVSKLLKMVGYNPKDVPFIP 190
Query: 211 ISAKTGVGINKLLENI------SLQAEILELKAP---VTTPAKGVIIESRLDKGKGPVAT 261
IS G + K EN+ +L + +L+ P + P + I + G G V
Sbjct: 191 ISGFKGDNLTKKSENMPWYKGPTLLEALDQLEPPERPLDKPLRLPIQDVYSISGIGTVPV 250
Query: 262 VLIQSGTLRCSDIVVAGASY--GRIRS-MLNENGKNILEAGPSIPVEIQGLTK 311
++SG ++ V + G ++S ++ + E G ++ ++G+ K
Sbjct: 251 GRVESGVIKPGQKVTFMPAGVVGEVKSIEMHHEEISQAEPGDNVGFNVRGVEK 303
>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 = 99.2 bits (248), Expect = 9e-24
Identities = 56/161 (34%), Positives = 88/161 (54%), Gaps = 6/161 (3%)
Query: 71 IVTIMGHVDHGKTSLLDYI--RKTNVVFSE-AGGITQHIG-AYNVVTNHGSITFLDTPGH 126
I+ GH+DHGKT+L+ + +T+ + E GIT +G AY + + + F+D PGH
Sbjct: 1 IIGTAGHIDHGKTTLIKALTGIETDRLPEEKKRGITIDLGFAYLDLPDGKRLGFIDVPGH 60
Query: 127 EAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVP-LIVAINKIDKLDINL 185
E F GA D V+LVVAAD+G+MPQTRE + ++ G+ +V + K D +D +
Sbjct: 61 EKFVKNMLAGAGGIDAVLLVVAADEGIMPQTREHLEILELLGIKKGLVVLTKADLVDEDR 120
Query: 186 DRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
+ ++ I E + A P +S+ TG GI +L +
Sbjct: 121 LELVEEEILELLAGTFLADA-PIFPVSSVTGEGIEELKNYL 160
Score = 78.8 bits (195), Expect = 1e-16
Identities = 52/169 (30%), Positives = 74/169 (43%), Gaps = 36/169 (21%)
Query: 930 HVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY----NGT 985
H+DHGKTTLI + + D EK+RGITI + Y +G
Sbjct: 7 HIDHGKTTLI-------------KALTGIETDRLPEEKKRGITI---DLGFAYLDLPDGK 50
Query: 986 RINIIDTPGHADFGGEVERILSMV------DNVLLLIDAVEGPMPQTRFVTRKALKLGFK 1039
R+ ID PGH F + +M+ D VLL++ A EG MPQTR LG K
Sbjct: 51 RLGFIDVPGHEKF------VKNMLAGAGGIDAVLLVVAADEGIMPQTREHLEILELLGIK 104
Query: 1040 P-IVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHG 1087
+VV+ K D + + ++ + L T D P+ S++ G
Sbjct: 105 KGLVVLTKADL--VDEDRLELVEEEILELLAGTFLA-DAPIFPVSSVTG 150
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 105 bits (265), Expect = 3e-23
Identities = 54/135 (40%), Positives = 79/135 (58%), Gaps = 16/135 (11%)
Query: 926 AIIAHVDHGKTTLIDHLL------RQSGTFR-KNQNINARIMDSNEIEKERGITIFSKNC 978
AII+H D GKTTL + LL +++GT + + +A+ D EIEK+RGI++ S
Sbjct: 16 AIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGKHAK-SDWMEIEKQRGISVTSSVM 74
Query: 979 SIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTR--F-VTRKALK 1035
+Y +N++DTPGH DF + R L+ VD+ +++IDA +G PQT F V R
Sbjct: 75 QFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCR---- 130
Query: 1036 LGFKPIV-VVNKIDR 1049
L PI +NK+DR
Sbjct: 131 LRDIPIFTFINKLDR 145
Score = 46.9 bits (112), Expect = 8e-05
Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 118 ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINK 177
+ LDTPGHE F+ R D V+V+ A G+ PQT + ++ +P+ INK
Sbjct: 83 VNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCRLRDIPIFTFINK 142
Query: 178 IDK-----LDINLDRIKQDL 192
+D+ L++ LD I+++L
Sbjct: 143 LDREGRDPLEL-LDEIEEEL 161
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 102 bits (257), Expect = 1e-22
Identities = 88/300 (29%), Positives = 141/300 (47%), Gaps = 35/300 (11%)
Query: 928 IAHVDHGKTTL---IDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNG 984
I HVDHGKTTL I +L + G K + + +D EK RGITI + + E
Sbjct: 67 IGHVDHGKTTLTAAITKVLAEEG---KAKAVAFDEIDKAPEEKARGITIATAHVEYETAK 123
Query: 985 TRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV- 1043
+D PGHAD+ + + +D +L++ A +GPMPQT+ A ++G +VV
Sbjct: 124 RHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVVF 183
Query: 1044 VNKIDRSNARPEWVVDATFDLFDKLCATE--EQLDF--------PVIYTSALHGYANENS 1093
+NK+D VVD +L + L E E L F P+I SAL N
Sbjct: 184 LNKVD--------VVDDE-ELLE-LVEMELRELLSFYKFPGDEIPIIRGSALSALQGTND 233
Query: 1094 KARQGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQD 1153
+ + ++ L +A+ +Y+P + P + I + G + GR+ G IK ++
Sbjct: 234 EIGKNAILKLMDAVDEYIPEPVRVLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEE 293
Query: 1154 VVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LITGI--EEICIGSTICDP 1209
V I+ P K + + +FK ++++ +GD V L+ G+ E++ G IC P
Sbjct: 294 VEIVGLRPGGPLKTTVTGVEMFKK----ILDQGQAGDNVGLLLRGLKREDVQRGQVICKP 349
Score = 73.7 bits (181), Expect = 3e-13
Identities = 50/134 (37%), Positives = 64/134 (47%), Gaps = 29/134 (21%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAG-------------------GIT---QHIGAY 109
V +GHVDHGKT+L I K V +E G GIT H+ Y
Sbjct: 64 VGTIGHVDHGKTTLTAAITK---VLAEEGKAKAVAFDEIDKAPEEKARGITIATAHV-EY 119
Query: 110 NVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGV 169
H +D PGH + GA D +LVV+A DG MPQT+E I A+ GV
Sbjct: 120 ETAKRH--YAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGV 177
Query: 170 P-LIVAINKIDKLD 182
P L+V +NK+D +D
Sbjct: 178 PSLVVFLNKVDVVD 191
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 101 bits (254), Expect = 8e-22
Identities = 74/218 (33%), Positives = 105/218 (48%), Gaps = 25/218 (11%)
Query: 71 IVTIMGHVDHGKTSLLDYIRKTN---VVFSEAGGITQHIG-AYNVVTNHGSITFLDTPGH 126
I+ GHVDHGKT+LL I N + + G+T +G AY + + F+D PGH
Sbjct: 2 IIATAGHVDHGKTTLLQAITGVNADRLPEEKKRGMTIDLGYAYWPQPDGRVLGFIDVPGH 61
Query: 127 EAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVP-LIVAINKIDKLDINL 185
E F + G D +LVVA DDGVM QTRE +A +++G P L VA+ K D++D
Sbjct: 62 EKFLSNMLAGVGGIDHALLVVACDDGVMAQTREHLAILQLTGNPMLTVALTKADRVDE-- 119
Query: 186 DRIKQDLISEQVIPE--EYG-GASPFISISAKTGVGINKLLENISLQAEILELKAPVTTP 242
RI + + QV EYG + +A G GI+ +L+ +L+L P
Sbjct: 120 ARIAE--VRRQVKAVLREYGFAEAKLFVTAATEGRGID------ALREHLLQL--PEREH 169
Query: 243 AKGVIIESRLD-----KGKGPVATVLIQSGTLRCSDIV 275
A +D KG G V T SG ++ D +
Sbjct: 170 AAQHRFRLAIDRAFTVKGAGLVVTGTALSGEVKVGDTL 207
Score = 55.4 bits (134), Expect = 2e-07
Identities = 41/118 (34%), Positives = 54/118 (45%), Gaps = 43/118 (36%)
Query: 927 IIA---HVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY- 982
IIA HVDHGKTTL+ Q+ T +NA D EK+RG+TI + Y
Sbjct: 2 IIATAGHVDHGKTTLL-----QAIT-----GVNA---DRLPEEKKRGMTI-----DLGYA 43
Query: 983 -----NGTRINIIDTPGHADF--------GGEVERILSMVDNVLLLIDAVEGPMPQTR 1027
+G + ID PGH F GG +D+ LL++ +G M QTR
Sbjct: 44 YWPQPDGRVLGFIDVPGHEKFLSNMLAGVGG--------IDHALLVVACDDGVMAQTR 93
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 100 bits (252), Expect = 1e-21
Identities = 56/142 (39%), Positives = 78/142 (54%), Gaps = 30/142 (21%)
Query: 926 AIIAHVDHGKTTLIDHLL------RQSGTF--RKNQNINARIMDSN--EIEKERGITIFS 975
AII+H D GKTTL + LL +++GT RK+ R S+ E+EK+RGI++ S
Sbjct: 14 AIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSG----RHATSDWMEMEKQRGISVTS 69
Query: 976 KNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALK 1035
Y IN++DTPGH DF + R L+ VD+ L++IDA +G PQTR K
Sbjct: 70 SVMQFPYRDCLINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKGVEPQTR-------K 122
Query: 1036 LGFK-------PIVV-VNKIDR 1049
L + PI +NK+DR
Sbjct: 123 L-MEVCRLRDTPIFTFINKLDR 143
Score = 39.7 bits (94), Expect = 0.011
Identities = 30/88 (34%), Positives = 45/88 (51%), Gaps = 22/88 (25%)
Query: 118 ITFLDTPGHEAF--------TAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGV 169
I LDTPGHE F TA+ D ++V+ A GV PQTR+ + ++
Sbjct: 81 INLLDTPGHEDFSEDTYRTLTAV--------DSALMVIDAAKGVEPQTRKLMEVCRLRDT 132
Query: 170 PLIVAINKIDK-----LDINLDRIKQDL 192
P+ INK+D+ L++ LD I++ L
Sbjct: 133 PIFTFINKLDRDGREPLEL-LDEIEEVL 159
>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 = 100 bits (251), Expect = 2e-21
Identities = 65/227 (28%), Positives = 108/227 (47%), Gaps = 7/227 (3%)
Query: 71 IVTIMGHVDHGKTSLLDYIRKTNVVF---SEAGGITQHIGAYNVVTNHGSITFLDTPGHE 127
I+ GHVDHGKT+LL + + G+T +G + F+D PGHE
Sbjct: 2 IIATAGHVDHGKTTLLKALTGIAADRLPEEKKRGMTIDLGFAYFPLPDYRLGFIDVPGHE 61
Query: 128 AFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVP-LIVAINKIDKLDINLD 186
F + G D +LVV AD+GVM QT E +A + G+P IV I K D+++
Sbjct: 62 KFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPHTIVVITKADRVNEEEI 121
Query: 187 RIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISLQAEILELKAPVTTPAKGV 246
+ + + + + + + SAKTG GI +L + + E L++K + P +
Sbjct: 122 KRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKELKNLLESLDIK-RIQKPLRMA 180
Query: 247 IIESRLDKGKGPVATVLIQSGTLRCSD-IVVAGASY-GRIRSMLNEN 291
I + KG G V T SG ++ D + + ++ R++++ +N
Sbjct: 181 IDRAFKVKGAGTVVTGTAFSGEVKVGDNLRLLPINHEVRVKAIQAQN 227
Score = 73.0 bits (179), Expect = 6e-13
Identities = 46/127 (36%), Positives = 54/127 (42%), Gaps = 14/127 (11%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
A HVDHGKTTL+ L I A D EK+RG+TI
Sbjct: 4 ATAGHVDHGKTTLLKAL----------TGIAA---DRLPEEKKRGMTIDLGFAYFPLPDY 50
Query: 986 RINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKP-IVVV 1044
R+ ID PGH F +D LL++DA EG M QT LG IVV+
Sbjct: 51 RLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPHTIVVI 110
Query: 1045 NKIDRSN 1051
K DR N
Sbjct: 111 TKADRVN 117
>gnl|CDD|129191 TIGR00082, rbfA, ribosome-binding factor A. Associates with free
30S ribosomal subunits (but not with 30S subunits that
are part of 70S ribosomes or polysomes). Essential for
efficient processing of 16S rRNA. May interact with the
5'terminal helix region of 16S rRNA. Mutants lacking
rbfA have a cold-sensitive phenotype [Transcription, RNA
processing].
Length = 114
Score = 90.1 bits (224), Expect = 3e-21
Identities = 35/109 (32%), Positives = 68/109 (62%)
Query: 540 ERLSRIENQIQRDISEIIAFDIQNPIINIITITEVKITLDYSYAKIFFTTFNKDISIKNI 599
R R+E+ I R+I+ I+ +I++P + ++T+T+V+++ D +AK+F + + +I +
Sbjct: 4 YRKERVESDIIREINRILIREIKDPRVGMLTVTKVEVSKDLQHAKVFVDCYGDEEAIDRV 63
Query: 600 LDNLSKAKNYIRFKLSKKLHIHTLPILNFFYDNSIENAMMISKLIDGIK 648
+ L+KAK +IR L + + + P L+F DNS++ M I LI+ +K
Sbjct: 64 VKALNKAKGFIRSLLGQAMRLRKTPELHFVKDNSLDKGMRIENLINSLK 112
>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 = 94.9 bits (236), Expect = 4e-20
Identities = 72/259 (27%), Positives = 115/259 (44%), Gaps = 31/259 (11%)
Query: 923 IKSAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINAR---------------IMDSNEIEK 967
I A I HVDHGK+T + HLL + G + +MD + E+
Sbjct: 8 INVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVMDRLKEER 67
Query: 968 ERGITIFSKNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGP---MP 1024
ERG+TI + E + + I+D PGH DF + S D +L++ +G P
Sbjct: 68 ERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEFEVQP 127
Query: 1025 QTRFVTRKALKLGFKPIVV-VNKIDRSN---ARPEWVVDATFDLFDKLCATEEQLDFPVI 1080
QTR A LG ++V +NK+D N E + +L K+ + + F I
Sbjct: 128 QTREHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTVPF--I 185
Query: 1081 YTSALHG----YANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLG 1136
SA +G +EN+ +G L EA+ P K ++ PL++ I + + +G
Sbjct: 186 PISAWNGDNVIKKSENTPWYKGKT--LLEALDALEPPEKP-TDKPLRIPIQDVYSITGVG 242
Query: 1137 KIGIGRILSGRIKSLQDVV 1155
+ +GR+ +G +K VV
Sbjct: 243 TVPVGRVETGVLKPGDKVV 261
Score = 69.5 bits (170), Expect = 5e-12
Identities = 77/266 (28%), Positives = 112/266 (42%), Gaps = 51/266 (19%)
Query: 72 VTIMGHVDHGKTSLLDY------------IRKTNVVFSEAG------------------- 100
V +GHVDHGK++ + + I K E G
Sbjct: 10 VAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVMDRLKEERER 69
Query: 101 GITQHIGAYNVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDG---VMPQT 157
G+T + + T+ +T +D PGH F GA D VLVVA DG V PQT
Sbjct: 70 GVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEFEVQPQT 129
Query: 158 REAIAHAKISGV-PLIVAINKIDKLDINLDRIKQ--DLISEQVIPEEYGGAS-PFISISA 213
RE A+ G+ LIVAINK+D ++ + + + +S + Y + PFI ISA
Sbjct: 130 REHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTVPFIPISA 189
Query: 214 KTGVGINKLLENI------SLQAEILELKAP---VTTPAKGVIIESRLDKGKGPVATVLI 264
G + K EN +L + L+ P P + I + G G V +
Sbjct: 190 WNGDNVIKKSENTPWYKGKTLLEALDALEPPEKPTDKPLRIPIQDVYSITGVGTVPVGRV 249
Query: 265 QSGTLRCSDIVV---AGASYGRIRSM 287
++G L+ D VV AG S G ++S+
Sbjct: 250 ETGVLKPGDKVVFEPAGVS-GEVKSI 274
>gnl|CDD|201388 pfam00679, EFG_C, Elongation factor G C-terminus. This domain
includes the carboxyl terminal regions of Elongation
factor G, elongation factor 2 and some tetracycline
resistance proteins and adopt a ferredoxin-like fold.
Length = 89
Score = 85.3 bits (212), Expect = 7e-20
Identities = 26/80 (32%), Positives = 40/80 (50%)
Query: 1314 ELYEPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQNE 1373
L EP + + + E G ++ LN R G++ ++E + RV +E +P L GF E
Sbjct: 1 VLLEPIMKVEITVPEEYLGDVIGDLNQRRGEILDMEPDGGGRVVIEAEVPLAELFGFSTE 60
Query: 1374 FITLTRGTGLISHVFEEYAP 1393
+LT+G G S F Y P
Sbjct: 61 LRSLTQGRGSFSMEFSGYEP 80
>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 = 91.8 bits (228), Expect = 3e-19
Identities = 87/293 (29%), Positives = 139/293 (47%), Gaps = 25/293 (8%)
Query: 928 IAHVDHGKTTL---IDHLLRQSG--TFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 982
I HVDHGKTTL I +L + G R I D+ EK RGITI + + E
Sbjct: 18 IGHVDHGKTTLTAAITTVLAKEGGAAARAYDQI-----DNAPEEKARGITINTAHVEYET 72
Query: 983 NGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIV 1042
+D PGHAD+ + + +D +L++ A +GPMPQTR A ++G IV
Sbjct: 73 ENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMPQTREHILLARQVGVPYIV 132
Query: 1043 V-VNKIDRSNARPEWVVDATFDLFDKLCATE-EQLDFPVIYTSALHGYANENSKARQGNM 1100
V +NK D + E + ++ + L + D P+I SAL A E + +
Sbjct: 133 VFLNKCDMVD-DEELLELVEMEVRELLSEYDFPGDDTPIIRGSALK--ALEGDAEWEAKI 189
Query: 1101 IPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGP 1160
+ L +A+ +Y+P + ++ P + I + + G + GR+ G +K ++V I+
Sbjct: 190 LELMDAVDEYIPTPERETDKPFLMPIEDVFSITGRGTVVTGRVERGIVKVGEEVEIVGLK 249
Query: 1161 DDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LITGI--EEICIGSTICDP 1209
D + K + + +F R ++E +GD V L+ GI EEI G + P
Sbjct: 250 DTR--KTTVTGVEMF----RKELDEGRAGDNVGLLLRGIKREEIERGMVLAKP 296
Score = 78.7 bits (194), Expect = 6e-15
Identities = 82/250 (32%), Positives = 108/250 (43%), Gaps = 66/250 (26%)
Query: 71 IVTIMGHVDHGKTSLLDYIRKTNVVFSEAG------------------GIT---QHIGAY 109
I TI GHVDHGKT+L I T V+ E G GIT H+ Y
Sbjct: 15 IGTI-GHVDHGKTTLTAAI--TTVLAKEGGAAARAYDQIDNAPEEKARGITINTAHV-EY 70
Query: 110 NVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGV 169
H +D PGH + GA D +LVV+A DG MPQTRE I A+ GV
Sbjct: 71 ETENRH--YAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMPQTREHILLARQVGV 128
Query: 170 P-LIVAINKIDKLDINLDRIKQDLISEQV--IPEEY---GGASPFISISAKTGVGINKLL 223
P ++V +NK D +D D +L+ +V + EY G +P I SA K L
Sbjct: 129 PYIVVFLNKCDMVD---DEELLELVEMEVRELLSEYDFPGDDTPIIRGSAL------KAL 179
Query: 224 ENISL-QAEILELKAPVT----TPAKGVIIESRLDK-------------GKGPVATVLIQ 265
E + +A+ILEL V TP E DK G+G V T ++
Sbjct: 180 EGDAEWEAKILELMDAVDEYIPTP------ERETDKPFLMPIEDVFSITGRGTVVTGRVE 233
Query: 266 SGTLRCSDIV 275
G ++ + V
Sbjct: 234 RGIVKVGEEV 243
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 91.1 bits (227), Expect = 6e-19
Identities = 85/269 (31%), Positives = 126/269 (46%), Gaps = 54/269 (20%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINAR---------------IMDSNEIEKERG 970
A+I HVDHGK+TL+ LL ++G ++ R +MD + E+ERG
Sbjct: 10 AVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDRLKEERERG 69
Query: 971 ITI---FSKNCSIEYNGTRINIIDTPGHADFGGEVERIL---SMVDNVLLLIDA--VEGP 1022
+TI K + +Y T I+D PGH DF V+ ++ S D +L++ A G
Sbjct: 70 VTIDLAHKKFETDKYYFT---IVDCPGHRDF---VKNMITGASQADAAVLVVAADDAGGV 123
Query: 1023 MPQTR---FVTRKALKLGFKP-IVVVNKIDRSN---ARPEWVVDATFDLFDKLCATEEQL 1075
MPQTR F+ R LG IV +NK+D N R E V + L + +
Sbjct: 124 MPQTREHVFLAR---TLGINQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPD-- 178
Query: 1076 DFPVIYTSALHGYANENSKARQGNMIP------LFEAILKYVPVHKDNSNNPLQLQIISL 1129
D P I SA G +N + NM P L EA L + + ++ PL++ I +
Sbjct: 179 DIPFIPVSAFEG---DNVVKKSENM-PWYNGPTLLEA-LDNLKPPEKPTDKPLRIPIQDV 233
Query: 1130 EYS-SYLGKIGIGRILSGRIKSLQDVVIM 1157
YS S +G + +GR+ +G +K VV M
Sbjct: 234 -YSISGVGTVPVGRVETGVLKVGDKVVFM 261
Score = 83.4 bits (207), Expect = 2e-16
Identities = 77/270 (28%), Positives = 118/270 (43%), Gaps = 62/270 (22%)
Query: 72 VTIMGHVDHGKTSL---------------LDYIRKTNVVFSEAG---------------- 100
+ ++GHVDHGK++L ++ +R+ +
Sbjct: 9 LAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDRLKEERER 68
Query: 101 GITQHIGAYNVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADD--GVMPQTR 158
G+T + T+ T +D PGH F GA D VLVVAADD GVMPQTR
Sbjct: 69 GVTIDLAHKKFETDKYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAADDAGGVMPQTR 128
Query: 159 EAIAHAKISGVP-LIVAINKIDKLDINLDRIKQDLISEQVI---------PEEYGGASPF 208
E + A+ G+ LIVAINK+D ++ + R ++ + E+V P++ PF
Sbjct: 129 EHVFLARTLGINQLIVAINKMDAVNYDEKRYEE--VKEEVSKLLKMVGYKPDD----IPF 182
Query: 209 ISISAKTGVGINKLLENIS-------LQA--EILELKAPVTTPAKGVIIESRLDKGKGPV 259
I +SA G + K EN+ L+A + + P P + I + G G V
Sbjct: 183 IPVSAFEGDNVVKKSENMPWYNGPTLLEALDNLKPPEKPTDKPLRIPIQDVYSISGVGTV 242
Query: 260 ATVLIQSGTLRCSDIVV---AGASYGRIRS 286
+++G L+ D VV AG G ++S
Sbjct: 243 PVGRVETGVLKVGDKVVFMPAGVV-GEVKS 271
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors [Translation,
ribosomal structure and biogenesis].
Length = 394
Score = 88.5 bits (220), Expect = 3e-18
Identities = 83/303 (27%), Positives = 136/303 (44%), Gaps = 45/303 (14%)
Query: 928 IAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEI---EKERGITIFSKNCSIEYNG 984
I HVDHGKTTL + + K A+ D + EK RGITI + + E
Sbjct: 18 IGHVDHGKTTLTAAI---TTVLAKKGGAEAKAYDQIDNAPEEKARGITINTAHVEYETAN 74
Query: 985 TRINIIDTPGHADFGGEVERILSMV------DNVLLLIDAVEGPMPQTRFVTRKALKLGF 1038
+D PGHAD+ + +M+ D +L++ A +GPMPQTR A ++G
Sbjct: 75 RHYAHVDCPGHADY------VKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVGV 128
Query: 1039 KPIVV-VNKIDRSNARP--EWVVDATFDLFDKLCATEEQLDF-----PVIYTSALHGYAN 1090
IVV +NK+D + E V +L + F P+I SAL A
Sbjct: 129 PYIVVFLNKVDMVDDEELLELVEMEVRELL-------SEYGFPGDDTPIIRGSALK--AL 179
Query: 1091 ENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKS 1150
E + + L +A+ Y+P + + + P + + + S G + GR+ G +K
Sbjct: 180 EGDAKWEAKIEELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVTGRVERGILKV 239
Query: 1151 LQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LITGI--EEICIGSTI 1206
++V I+ + + K + + +F R L++E +GD V L+ G+ E++ G +
Sbjct: 240 GEEVEIVGIKETQ--KTTVTGVEMF----RKLLDEGQAGDNVGVLLRGVKREDVERGQVL 293
Query: 1207 CDP 1209
P
Sbjct: 294 AKP 296
Score = 82.0 bits (203), Expect = 4e-16
Identities = 75/241 (31%), Positives = 110/241 (45%), Gaps = 46/241 (19%)
Query: 71 IVTIMGHVDHGKTSL----------------LDYIRKTNVVFSEAGGIT---QHIGAYNV 111
+ TI GHVDHGKT+L Y + N +A GIT H+ Y
Sbjct: 15 VGTI-GHVDHGKTTLTAAITTVLAKKGGAEAKAYDQIDNAPEEKARGITINTAHV-EYET 72
Query: 112 VTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVP- 170
H + +D PGH + GA D +LVVAA DG MPQTRE I A+ GVP
Sbjct: 73 ANRHYA--HVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVGVPY 130
Query: 171 LIVAINKIDKLDINLDRIKQDLISEQV--IPEEY---GGASPFISISA-KTGVGINKLLE 224
++V +NK+D +D D +L+ +V + EY G +P I SA K G K
Sbjct: 131 IVVFLNKVDMVD---DEELLELVEMEVRELLSEYGFPGDDTPIIRGSALKALEGDAKWEA 187
Query: 225 NISLQAEILE-LKAPVTTPAKGVI------IES--RLDKGKGPVATVLIQSGTLRCSDIV 275
I E+++ + + + TP + + +E + G+G V T ++ G L+ + V
Sbjct: 188 KIE---ELMDAVDSYIPTPERDIDKPFLMPVEDVFSIS-GRGTVVTGRVERGILKVGEEV 243
Query: 276 V 276
Sbjct: 244 E 244
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 87.7 bits (218), Expect = 6e-18
Identities = 84/254 (33%), Positives = 109/254 (42%), Gaps = 69/254 (27%)
Query: 70 PIVTI--MGHVDHGKTSLLDYIRKTNVVFSEAG-------------------GIT---QH 105
P V I +GHVDHGKT+L I K V +E G GIT H
Sbjct: 11 PHVNIGTIGHVDHGKTTLTAAITK---VLAERGLNQAKDYDSIDAAPEEKERGITINTAH 67
Query: 106 IGAYNVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAK 165
+ Y H +D PGH + GA D +LVVAA DG MPQTRE I A+
Sbjct: 68 V-EYETEKRH--YAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLAR 124
Query: 166 ISGVP-LIVAINKIDKLD----INLDRIK-QDLISEQVIPEEYGGASPFISISAKTGVGI 219
GVP L+V +NK+D +D + L ++ ++L+SE P G P I SA
Sbjct: 125 QVGVPYLVVFLNKVDLVDDEELLELVEMEVRELLSEYDFP---GDDIPVIRGSAL----- 176
Query: 220 NKLLENISLQAE-ILELKAPVT----TPAKGVIIESRLDK-------------GKGPVAT 261
K LE + I+EL V TP E DK G+G V T
Sbjct: 177 -KALEGDPKWEDAIMELMDAVDEYIPTP------ERDTDKPFLMPVEDVFTITGRGTVVT 229
Query: 262 VLIQSGTLRCSDIV 275
++ GT++ D V
Sbjct: 230 GRVERGTVKVGDEV 243
Score = 79.2 bits (196), Expect = 3e-15
Identities = 92/311 (29%), Positives = 148/311 (47%), Gaps = 61/311 (19%)
Query: 928 IAHVDHGKTTL---IDHLL--RQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCS-IE 981
I HVDHGKTTL I +L R + +I D+ EKERGITI N + +E
Sbjct: 18 IGHVDHGKTTLTAAITKVLAERGLNQAKDYDSI-----DAAPEEKERGITI---NTAHVE 69
Query: 982 YN-GTR-INIIDTPGHADFGGEVERILSMV------DNVLLLIDAVEGPMPQTRFVTRKA 1033
Y R +D PGHAD+ + +M+ D +L++ A +GPMPQTR A
Sbjct: 70 YETEKRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVAATDGPMPQTREHILLA 123
Query: 1034 LKLGFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCATE--EQL--------DFPVIYT 1082
++G +VV +NK+D +VD +L + L E E L D PVI
Sbjct: 124 RQVGVPYLVVFLNKVD--------LVDDE-ELLE-LVEMEVRELLSEYDFPGDDIPVIRG 173
Query: 1083 SALHGYANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGR 1142
SAL A E + ++ L +A+ +Y+P + +++ P + + + + G + GR
Sbjct: 174 SALK--ALEGDPKWEDAIMELMDAVDEYIPTPERDTDKPFLMPVEDVFTITGRGTVVTGR 231
Query: 1143 ILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LITGI--E 1198
+ G +K +V I+ + + K + + +F R L++E +GD V L+ G+ +
Sbjct: 232 VERGTVKVGDEVEIVGIKETQ--KTVVTGVEMF----RKLLDEGQAGDNVGVLLRGVDRD 285
Query: 1199 EICIGSTICDP 1209
E+ G + P
Sbjct: 286 EVERGQVLAKP 296
>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 = 88.8 bits (220), Expect = 6e-18
Identities = 50/141 (35%), Positives = 76/141 (53%), Gaps = 8/141 (5%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINAR------IMDSNEIEKERGITIFSKNCS 979
AII+H D GKTT+ + +L G + + R D E+EK+RGI+I +
Sbjct: 15 AIISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGISITTSVMQ 74
Query: 980 IEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFK 1039
Y +N++DTPGH DF + R L+ VDN L++IDA +G +TR + + +L
Sbjct: 75 FPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLM-EVTRLRDT 133
Query: 1040 PIVV-VNKIDRSNARPEWVVD 1059
PI +NK+DR P ++D
Sbjct: 134 PIFTFMNKLDRDIRDPLELLD 154
Score = 46.4 bits (110), Expect = 1e-04
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 118 ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINK 177
+ LDTPGHE F+ R D ++V+ A GV +TR+ + ++ P+ +NK
Sbjct: 82 VNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTRLRDTPIFTFMNK 141
Query: 178 IDKLDIN-----LDRIKQDL 192
+D+ DI LD ++ +L
Sbjct: 142 LDR-DIRDPLELLDEVENEL 160
>gnl|CDD|238772 cd01514, Elongation_Factor_C, Elongation factor G C-terminus. This
domain includes the carboxyl terminal regions of
elongation factors (EFs) bacterial EF-G, eukaryotic and
archeal EF-2 and eukaryotic mitochondrial mtEFG1s and
mtEFG2s. This group also includes proteins similar to the
ribosomal protection proteins Tet(M) and Tet(O), BipA,
LepA and, spliceosomal proteins: human 116kD U5 small
nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and
yeast counterpart Snu114p. This domain adopts a
ferredoxin-like fold consisting of an alpha-beta sandwich
with anti-parallel beta-sheets, resembling the topology
of domain III found in the elongation factors EF-G and
eukaryotic EF-2, with which it forms the C-terminal
block. The two domains however are not superimposable and
domain III lacks some of the characteristics of this
domain. EF-2/EF-G in complex with GTP, promotes the
translocation step of translation. During translocation
the peptidyl-tRNA is moved from the A site to the P site,
the uncharged tRNA from the P site to the E-site and, the
mRNA is shifted one codon relative to the ribosome.
Tet(M) and Tet(O) mediate Tc resistance. Typical Tcs bind
to the ribosome and inhibit the elongation phase of
protein synthesis, by inhibiting the occupation of site A
by aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release
of tetracycline (Tc) from the ribosome in a GTP-dependent
manner. BipA is a highly conserved protein with global
regulatory properties in Escherichia coli. Yeast Snu114p
is essential for cell viability and for splicing in vivo.
Experiments suggest that GTP binding and probably GTP
hydrolysis is important for the function of the U5-116
kD/Snu114p. The function of LepA proteins is unknown.
Length = 79
Score = 78.7 bits (195), Expect = 1e-17
Identities = 20/77 (25%), Positives = 36/77 (46%)
Query: 1317 EPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQNEFIT 1376
EP + + + E G ++ L+ R G++ +E RV ++ +P + GF + +
Sbjct: 1 EPIMKVEITVPEEYLGAVIGDLSKRRGEILGMEPRGTGRVVIKAELPLAEMFGFATDLRS 60
Query: 1377 LTRGTGLISHVFEEYAP 1393
LT+G S F Y P
Sbjct: 61 LTQGRASFSMEFSHYEP 77
>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 = 82.9 bits (206), Expect = 1e-17
Identities = 60/209 (28%), Positives = 85/209 (40%), Gaps = 45/209 (21%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGT--------FRKN-QNIN------ARIMDSNEIEKERG 970
+I HVD GK+TL HLL + G + K + + A ++D + E+ERG
Sbjct: 3 VVIGHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKYAWVLDKLKEERERG 62
Query: 971 ITIFSKNCSIEYNGTRINIIDTPGHADFGGEVERILSMV------DNVLLLIDAVEG--- 1021
+TI E R IID PGH DF + +M+ D +L++ A +G
Sbjct: 63 VTIDVGLAKFETEKYRFTIIDAPGHRDF------VKNMITGASQADVAVLVVSARKGEFE 116
Query: 1022 ----PMPQTRFVTRKALKLGFKP-IVVVNKIDR-----SNARPEWVVDATFDLFDKLCAT 1071
QTR A LG K IV VNK+D S R + + K+
Sbjct: 117 AGFEKGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVGYN 176
Query: 1072 EEQLDFPVIYTSALHGYANENSKARQGNM 1100
+ D P I S G +N + NM
Sbjct: 177 PK--DVPFIPISGFTG---DNLIEKSENM 200
Score = 69.8 bits (172), Expect = 4e-13
Identities = 63/199 (31%), Positives = 84/199 (42%), Gaps = 45/199 (22%)
Query: 71 IVTIMGHVDHGKTSL---LDY---------IRKTNVVFSEAG------------------ 100
+V I GHVD GK++L L Y I K E G
Sbjct: 2 LVVI-GHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKYAWVLDKLKEERE 60
Query: 101 -GITQHIGAYNVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDG------- 152
G+T +G T T +D PGH F GA D+ VLVV+A G
Sbjct: 61 RGVTIDVGLAKFETEKYRFTIIDAPGHRDFVKNMITGASQADVAVLVVSARKGEFEAGFE 120
Query: 153 VMPQTREAIAHAKISGVP-LIVAINKIDKLDINLDRIKQDLISEQVIP--EEYGGAS--- 206
QTRE A+ GV LIVA+NK+D + +N + + D I ++V P ++ G
Sbjct: 121 KGGQTREHALLARTLGVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVGYNPKDV 180
Query: 207 PFISISAKTGVGINKLLEN 225
PFI IS TG + + EN
Sbjct: 181 PFIPISGFTGDNLIEKSEN 199
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 87.1 bits (216), Expect = 2e-17
Identities = 66/228 (28%), Positives = 98/228 (42%), Gaps = 14/228 (6%)
Query: 71 IVTIMGHVDHGKTSLLDYIRKTNV-VFSEAG--GITQHIGAYNVVTNHGSITFLDTPGHE 127
I+ GH+DHGKT+LL + E GIT +G Y G + F+D PGH
Sbjct: 2 IIGTAGHIDHGKTTLLKALTGGVTDRLPEEKKRGITIDLGFYYRKLEDGVMGFIDVPGHP 61
Query: 128 AFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVP-LIVAINKIDKLDINLD 186
F + G D +LVVAAD+G+M QT E + + G+ I+ + K D++D
Sbjct: 62 DFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKNGIIVLTKADRVDEARI 121
Query: 187 RIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISLQAEILELKAPVTTPAKGV 246
K I + + SAKTG GI +L + E +E P +
Sbjct: 122 EQKIKQILADLSLAN----AKIFKTSAKTGRGIEELKNELIDLLEEIERD--EQKPFRIA 175
Query: 247 IIESRLDKGKGPVATVLIQSGTLRCSDIVVAGASYG---RIRSMLNEN 291
I + KG G V T + SG ++ D + R+RS+ +
Sbjct: 176 IDRAFTVKGVGTVVTGTVLSGEVKVGDKLYLS-PINKEVRVRSIQAHD 222
Score = 61.6 bits (150), Expect = 2e-09
Identities = 51/175 (29%), Positives = 74/175 (42%), Gaps = 22/175 (12%)
Query: 929 AHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGTRIN 988
H+DHGKTTL+ + + + D EK+RGITI + +
Sbjct: 7 GHIDHGKTTLL-------------KALTGGVTDRLPEEKKRGITIDLGFYYRKLEDGVMG 53
Query: 989 IIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFK-PIVVVNKI 1047
ID PGH DF + L +D LL++ A EG M QT LG K I+V+ K
Sbjct: 54 FIDVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGIKNGIIVLTKA 113
Query: 1048 DRSN-ARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMI 1101
DR + AR E + ++ A + + TSA G E K +++
Sbjct: 114 DRVDEARIEQKI-------KQILADLSLANAKIFKTSAKTGRGIEELKNELIDLL 161
>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 = 78.9 bits (195), Expect = 2e-16
Identities = 55/188 (29%), Positives = 87/188 (46%), Gaps = 28/188 (14%)
Query: 72 VTIMGHVDHGKTSL---LDYIRKTNVV----FSEAGGITQHIG--------AYNVVTNHG 116
V ++GHVD GKTSL L I T S+ GIT +G ++ N
Sbjct: 3 VGLLGHVDSGKTSLAKALSEIASTAAFDKNPQSQERGITLDLGFSSFEVDKPKHLEDNEN 62
Query: 117 S------ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVP 170
IT +D PGH + GA++ D+++LVV A G+ QT E + ++ P
Sbjct: 63 PQIENYQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDAKKGIQTQTAECLVIGELLCKP 122
Query: 171 LIVAINKIDKLDIN-----LDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLEN 225
LIV +NKID + ++++K+ L ++ + + SP I +SAK G G +L
Sbjct: 123 LIVVLNKIDLIPEEERKRKIEKMKKRL--QKTLEKTRLKDSPIIPVSAKPGEGEAELGGE 180
Query: 226 ISLQAEIL 233
+ +
Sbjct: 181 LKNLIVLP 188
Score = 55.1 bits (133), Expect = 3e-08
Identities = 42/139 (30%), Positives = 62/139 (44%), Gaps = 29/139 (20%)
Query: 927 IIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITI---FS-------- 975
++ HVD GKT+L L + T D N +ERGIT+ FS
Sbjct: 5 LLGHVDSGKTSLAKALSEIAST---------AAFDKNPQSQERGITLDLGFSSFEVDKPK 55
Query: 976 ---KNCSIEYNGTRINIIDTPGHADFGGEVERILS---MVDNVLLLIDAVEGPMPQTRFV 1029
N + + +I ++D PGHA + I+ ++D +LL++DA +G QT
Sbjct: 56 HLEDNENPQIENYQITLVDCPGHASL---IRTIIGGAQIIDLMLLVVDAKKGIQTQTAEC 112
Query: 1030 TRKALKLGFKPIVVVNKID 1048
L IVV+NKID
Sbjct: 113 LVIGELLCKPLIVVLNKID 131
>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 = 77.2 bits (191), Expect = 8e-16
Identities = 58/187 (31%), Positives = 85/187 (45%), Gaps = 41/187 (21%)
Query: 71 IVTIMGHVDHGKTSLLDYIRKTNVVFSEAG-------------------GIT---QHIGA 108
+ TI GHVDHGKT+L I K V ++ G GIT H+
Sbjct: 5 VGTI-GHVDHGKTTLTAAITK---VLAKKGGAKAKKYDEIDKAPEEKARGITINTAHVE- 59
Query: 109 YNVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISG 168
Y H + D PGH + GA D +LVV+A DG MPQTRE + A+ G
Sbjct: 60 YETANRHYAHV--DCPGHADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVG 117
Query: 169 VP-LIVAINKIDKLDIN--LDRIKQDLISEQVIPEEYGG-ASPFISISA-------KTGV 217
VP ++V +NK D +D L+ ++ + + E + + G +P + SA
Sbjct: 118 VPYIVVFLNKADMVDDEELLELVEME-VRELLSKYGFDGDDTPIVRGSALKALEGDDPNK 176
Query: 218 GINKLLE 224
++K+LE
Sbjct: 177 WVDKILE 183
Score = 66.8 bits (164), Expect = 3e-12
Identities = 51/135 (37%), Positives = 68/135 (50%), Gaps = 27/135 (20%)
Query: 928 IAHVDHGKTTL---IDHLLRQSG--TFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 982
I HVDHGKTTL I +L + G +K I D EK RGITI + +EY
Sbjct: 8 IGHVDHGKTTLTAAITKVLAKKGGAKAKKYDEI-----DKAPEEKARGITINT--AHVEY 60
Query: 983 NGTRINI--IDTPGHADFGGEVERILSMV------DNVLLLIDAVEGPMPQTRFVTRKAL 1034
+ +D PGHAD+ I +M+ D +L++ A +GPMPQTR A
Sbjct: 61 ETANRHYAHVDCPGHADY------IKNMITGAAQMDGAILVVSATDGPMPQTREHLLLAR 114
Query: 1035 KLGFKPIVV-VNKID 1048
++G IVV +NK D
Sbjct: 115 QVGVPYIVVFLNKAD 129
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 81.2 bits (201), Expect = 9e-16
Identities = 89/321 (27%), Positives = 137/321 (42%), Gaps = 64/321 (19%)
Query: 930 HVDHGKTTLIDHLLRQSGTFRKNQ-----NINAR------------IMDSNEIEKERGIT 972
VD GK+TLI LL + ++Q + R ++D E E+E+GIT
Sbjct: 14 SVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDGLEAEREQGIT 73
Query: 973 I------FS--KNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMP 1024
I FS K I I DTPGH + + S D +LL+DA +G +
Sbjct: 74 IDVAYRYFSTEKRKFI--------IADTPGHEQYTRNMATGASTADLAILLVDARKGVLE 125
Query: 1025 QTRFVTRKALKLGFKPIVV-VNKID---RSNARPEWVVDATFDLFDKLCATEEQLDFPVI 1080
QTR + A LG + +VV VNK+D S E +V +L + + I
Sbjct: 126 QTRRHSFIASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAAQLGLKDVR----FI 181
Query: 1081 YTSALHGYANENSKARQGNMIPLFE-----AILKYVPVHKDNSNNPLQL--QIISLEYSS 1133
SAL G +N ++ NM P ++ IL+ V + D S + Q ++
Sbjct: 182 PISALLG---DNVVSKSENM-PWYKGPTLLEILETVEIADDRSAKAFRFPVQYVNRPNLD 237
Query: 1134 YLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVL 1193
+ G G I SG +K +VV++ P K +++ +I F G + +A +G+ V
Sbjct: 238 FRGY--AGTIASGSVKVGDEVVVL--PSGK--TSRVKRIVTFDG----ELAQASAGEAVT 287
Query: 1194 ITGIEEICI--GSTICDPSKP 1212
+ +EI I G I P
Sbjct: 288 LVLADEIDISRGDLIVAADAP 308
Score = 58.5 bits (142), Expect = 2e-08
Identities = 38/122 (31%), Positives = 60/122 (49%), Gaps = 29/122 (23%)
Query: 122 DTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKIS---GVP-LIVAINK 177
DTPGHE +T A GA D+ +L+V A GV+ QTR H+ I+ G+ ++VA+NK
Sbjct: 92 DTPGHEQYTRNMATGASTADLAILLVDARKGVLEQTRR---HSFIASLLGIRHVVVAVNK 148
Query: 178 IDKLDINLDRIKQDLISEQVIPEEYGGASP--------FISISAKTGVGINKLLENISLQ 229
+D +D + + + I +Y + FI ISA G +N+ +
Sbjct: 149 MDLVDYSEEVFEA-------IVADYLAFAAQLGLKDVRFIPISALLG-------DNVVSK 194
Query: 230 AE 231
+E
Sbjct: 195 SE 196
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 80.4 bits (199), Expect = 1e-15
Identities = 90/301 (29%), Positives = 135/301 (44%), Gaps = 55/301 (18%)
Query: 928 IAHVDHGKTTL---IDHLLRQSGT--FRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 982
I HVDHGKTTL I L G +K I DS EK RGITI + + E
Sbjct: 18 IGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEI-----DSAPEEKARGITINTAHVEYET 72
Query: 983 NGTRINIIDTPGHADFGGEVERILSM------VDNVLLLIDAVEGPMPQTRFVTRKALKL 1036
+D PGHAD+ + +M +D +L++ A +GPMPQT+ A ++
Sbjct: 73 ENRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQV 126
Query: 1037 GFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCATE--EQLDF-----PVIYTSALHG- 1087
G IVV +NK D+ V D +L E + DF P++ SAL
Sbjct: 127 GVPNIVVFLNKEDQ-------VDDEELLELVELEVRELLSKYDFPGDDIPIVSGSALLAL 179
Query: 1088 -YANENSKARQGN------MIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGI 1140
EN K ++G + L +A+ Y+P + +++ P + I + + G +
Sbjct: 180 EALTENPKIKRGENKWVDKIYNLMDAVDSYIPTPERDTDKPFLMAIEDVFSITGRGTVAT 239
Query: 1141 GRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVF-KGLDRVLVNEALSGDIV--LITGI 1197
GRI G +K + D V + G + + + +F K LD E L+GD V L+ GI
Sbjct: 240 GRIERGTVK-VGDTVEIVGLRETKT-TTVTGLEMFQKTLD-----EGLAGDNVGILLRGI 292
Query: 1198 E 1198
+
Sbjct: 293 Q 293
Score = 69.6 bits (171), Expect = 5e-12
Identities = 78/251 (31%), Positives = 108/251 (43%), Gaps = 58/251 (23%)
Query: 71 IVTIMGHVDHGKTSLLDYIRKTNVVFS----------------EAGGI---TQHIGAYNV 111
I TI GHVDHGKT+L I T +A GI T H+ Y
Sbjct: 15 IGTI-GHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARGITINTAHV-EYET 72
Query: 112 VTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVP- 170
H + +D PGH + GA D +LVV+A DG MPQT+E I AK GVP
Sbjct: 73 ENRHYA--HVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVGVPN 130
Query: 171 LIVAINKIDKL-DINLDRIKQDLISEQVIPEEYGGAS-PFISISA-----------KTGV 217
++V +NK D++ D L + + + E + ++ G P +S SA K
Sbjct: 131 IVVFLNKEDQVDDEELLELVELEVRELLSKYDFPGDDIPIVSGSALLALEALTENPKIKR 190
Query: 218 GINKLLENISLQAEILELKAPVTTPAKGVIIESRLDK-------------GKGPVATVLI 264
G NK ++ I + ++ P TP E DK G+G VAT I
Sbjct: 191 GENKWVDKIYNLMDAVDSYIP--TP------ERDTDKPFLMAIEDVFSITGRGTVATGRI 242
Query: 265 QSGTLRCSDIV 275
+ GT++ D V
Sbjct: 243 ERGTVKVGDTV 253
>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 = 74.4 bits (183), Expect = 3e-15
Identities = 41/163 (25%), Positives = 72/163 (44%), Gaps = 15/163 (9%)
Query: 74 IMGHVDHGKTSLLDYIRKTNVVF-SEAGGITQHIGAYNVVTNHG--SITFLDTPGHEAFT 130
++G GK+SLL+ + V S+ G T+ Y + G + +DTPG + F
Sbjct: 2 VVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFG 61
Query: 131 AMRARG-----AKVTDIVVLVVAADDGVMPQTREAIAHAKIS--GVPLIVAINKIDKLDI 183
+ + D+++LVV + D + + + ++ G+P+I+ NKID L+
Sbjct: 62 GLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNKIDLLEE 121
Query: 184 NLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
L I P +SAKTG G+++L E +
Sbjct: 122 REVEELLRLEELAKILGV-----PVFEVSAKTGEGVDELFEKL 159
Score = 67.9 bits (166), Expect = 7e-13
Identities = 39/191 (20%), Positives = 75/191 (39%), Gaps = 37/191 (19%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
++ GK++L++ LL S+ R ++ K ++
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEV-----------SDVPGTTRDPDVYVK--ELDKGKV 47
Query: 986 RINIIDTPGHADFGG-----EVERILSMVDNVLLLIDAVEGPMPQT-RFVTRKALKLGFK 1039
++ ++DTPG +FGG +L D +LL++D+ + + + + + L+
Sbjct: 48 KLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGI 107
Query: 1040 PIVVV-NKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQG 1098
PI++V NKID R + +L + L PV SA G
Sbjct: 108 PIILVGNKIDLLEEREVEELLRLEEL-------AKILGVPVFEVSAKTGE---------- 150
Query: 1099 NMIPLFEAILK 1109
+ LFE +++
Sbjct: 151 GVDELFEKLIE 161
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 78.9 bits (194), Expect = 8e-15
Identities = 76/287 (26%), Positives = 137/287 (47%), Gaps = 19/287 (6%)
Query: 928 IAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGTRI 987
I HVDHGKTTL L + + +D+ E+ RGITI + E
Sbjct: 87 IGHVDHGKTTLTAALTMALASMGGSAPKKYDEIDAAPEERARGITINTATVEYETENRHY 146
Query: 988 NIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV-VNK 1046
+D PGHAD+ + + +D +L++ +GPMPQT+ A ++G +VV +NK
Sbjct: 147 AHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNK 206
Query: 1047 IDRSNARPEWVVDATFDLFDKLCATE-EQLDFPVIYTSALHGYAN--ENSKARQGN---- 1099
D+ + E + ++ + L + E D P+I SAL EN ++G+
Sbjct: 207 QDQVDDE-ELLELVELEVRELLSSYEFPGDDIPIISGSALLALEALMENPNIKRGDNKWV 265
Query: 1100 --MIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIM 1157
+ L +A+ Y+P+ + ++ P L + + + G + GR+ G +K + + V +
Sbjct: 266 DKIYELMDAVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVERGTVK-VGETVDI 324
Query: 1158 NGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LITGIEEICI 1202
G + + + + +F+ +++EAL+GD V L+ GI++ I
Sbjct: 325 VGLRETRS-TTVTGVEMFQK----ILDEALAGDNVGLLLRGIQKADI 366
Score = 66.2 bits (161), Expect = 7e-11
Identities = 73/250 (29%), Positives = 116/250 (46%), Gaps = 47/250 (18%)
Query: 68 RAPIVTI--MGHVDHGKTSLLDYI------------RKTNVVFS----EAGGITQHIGAY 109
+ P V I +GHVDHGKT+L + +K + + + A GIT +
Sbjct: 78 KKPHVNIGTIGHVDHGKTTLTAALTMALASMGGSAPKKYDEIDAAPEERARGITINTATV 137
Query: 110 NVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGV 169
T + +D PGH + GA D +LVV+ DG MPQT+E I AK GV
Sbjct: 138 EYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGV 197
Query: 170 P-LIVAINKIDKLD----INLDRIK-QDLISEQVIPEEYGGASPFISISAKTGVGINKLL 223
P ++V +NK D++D + L ++ ++L+S P G P IS SA + + L+
Sbjct: 198 PNMVVFLNKQDQVDDEELLELVELEVRELLSSYEFP---GDDIPIISGSAL--LALEALM 252
Query: 224 ENISLQA-------EILELKAPVTT----PAKG------VIIESRLD-KGKGPVATVLIQ 265
EN +++ +I EL V + P + + +E G+G VAT ++
Sbjct: 253 ENPNIKRGDNKWVDKIYELMDAVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVE 312
Query: 266 SGTLRCSDIV 275
GT++ + V
Sbjct: 313 RGTVKVGETV 322
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 76.0 bits (188), Expect = 4e-14
Identities = 50/135 (37%), Positives = 65/135 (48%), Gaps = 30/135 (22%)
Query: 71 IVTIMGHVDHGKTSLLDYIRKTNVVFSEAG-------------------GIT---QHIGA 108
+ TI GHVDHGKT+L I K V ++ G GIT H+
Sbjct: 15 VGTI-GHVDHGKTTLTAAITK---VLAKKGGAEAKAYDQIDKAPEEKARGITINTAHV-E 69
Query: 109 YNVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISG 168
Y H + +D PGH + GA D +LVV+A DG MPQTRE I A+ G
Sbjct: 70 YETEKRHYA--HVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVG 127
Query: 169 VP-LIVAINKIDKLD 182
VP ++V +NK D +D
Sbjct: 128 VPYIVVFLNKCDMVD 142
Score = 68.7 bits (169), Expect = 8e-12
Identities = 93/316 (29%), Positives = 143/316 (45%), Gaps = 69/316 (21%)
Query: 928 IAHVDHGKTTL---IDHLL--RQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCS-IE 981
I HVDHGKTTL I +L + + I D EK RGITI N + +E
Sbjct: 18 IGHVDHGKTTLTAAITKVLAKKGGAEAKAYDQI-----DKAPEEKARGITI---NTAHVE 69
Query: 982 YNGTRINI--IDTPGHADFGGEVERILSMV------DNVLLLIDAVEGPMPQTRFVTRKA 1033
Y + + +D PGHAD+ + +M+ D +L++ A +GPMPQTR A
Sbjct: 70 YETEKRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSAADGPMPQTREHILLA 123
Query: 1034 LKLGFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCATE--EQL--------DFPVIYT 1082
++G IVV +NK D V D +L + L E E L D P+I
Sbjct: 124 RQVGVPYIVVFLNKCDM-------VDDE--ELLE-LVEMEVRELLSKYDFPGDDTPIIRG 173
Query: 1083 SALHGYANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQI-----ISLEYSSYLGK 1137
SAL ++ + + ++ L +A+ Y+P + + P + I IS G
Sbjct: 174 SALKALEGDDDEEWEKKILELMDAVDSYIPTPERAIDKPFLMPIEDVFSISGR-----GT 228
Query: 1138 IGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LIT 1195
+ GR+ G IK ++V I+ D + K + + +F R L++E +GD V L+
Sbjct: 229 VVTGRVERGIIKVGEEVEIVGIRDTQ--KTTVTGVEMF----RKLLDEGQAGDNVGALLR 282
Query: 1196 GI--EEICIGSTICDP 1209
GI E++ G + P
Sbjct: 283 GIKREDVERGQVLAKP 298
>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 = 75.5 bits (186), Expect = 5e-14
Identities = 65/223 (29%), Positives = 98/223 (43%), Gaps = 50/223 (22%)
Query: 68 RAPIVTI--MGHVDHGKTSLLDYIRKTNV---VFSEA--GGITQHIG------------- 107
R P V I +GHVDHGKT+L + T V SE GI+ +G
Sbjct: 1 RQPEVNIGMVGHVDHGKTTLTKAL--TGVWTDTHSEELKRGISIRLGYADAEIYKCPECD 58
Query: 108 ---AYNV---VTNHGS-------ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGV- 153
Y N GS ++F+D PGHE A GA + D +LV+AA++
Sbjct: 59 GPECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALLVIAANEPCP 118
Query: 154 MPQTREAIAHAKISGVP-LIVAINKIDKLDI-----NLDRIKQDLISEQVIPEEYGGASP 207
PQTRE + +I G+ +++ NKID + N + IK+ + + I E +P
Sbjct: 119 QPQTREHLMALEIIGIKNIVIVQNKIDLVSKEKALENYEEIKEFV--KGTIAEN----AP 172
Query: 208 FISISAKTGVGINKLLENISLQAEILELKAPVTTPAKGVIIES 250
I +SA I+ LLE +++ I + + P + S
Sbjct: 173 IIPVSALHNANIDALLE--AIEKFIPTPERDLDKPPLMYVARS 213
Score = 60.1 bits (146), Expect = 5e-09
Identities = 63/228 (27%), Positives = 92/228 (40%), Gaps = 52/228 (22%)
Query: 927 IIAHVDHGKTTLIDHL-----LRQSGTFRKNQNI-----NARIMDSNEIEKERGITIFSK 976
++ HVDHGKTTL L S ++ +I +A I E + T
Sbjct: 9 MVGHVDHGKTTLTKALTGVWTDTHSEELKRGISIRLGYADAEIYKCPECDGPECYTTEPV 68
Query: 977 --NCSIEYNGTR-INIIDTPGHADFGGEVERILSMVDNVLLLIDAVEG-PMPQTRFVTRK 1032
NC E R ++ +D PGH + +++D LL+I A E P PQTR
Sbjct: 69 CPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALLVIAANEPCPQPQTREHLMA 128
Query: 1033 ALKLGFKPIVVV-NKIDRSNARPEWVVDATFDLFDKLCATE--EQL----------DFPV 1079
+G K IV+V NKID L K A E E++ + P+
Sbjct: 129 LEIIGIKNIVIVQNKID---------------LVSKEKALENYEEIKEFVKGTIAENAPI 173
Query: 1080 IYTSALHGYANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQII 1127
I SALH N+ L EAI K++P + + + P + +
Sbjct: 174 IPVSALHN----------ANIDALLEAIEKFIPTPERDLDKPPLMYVA 211
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 74.5 bits (184), Expect = 1e-13
Identities = 50/135 (37%), Positives = 65/135 (48%), Gaps = 30/135 (22%)
Query: 71 IVTIMGHVDHGKTSLLDYIRKTNVVFSEAG-------------------GIT---QHIGA 108
+ TI GHVDHGKT+L I K V ++ G GIT H+
Sbjct: 15 VGTI-GHVDHGKTTLTAAITK---VLAKKGGGEAKAYDQIDNAPEEKARGITINTSHV-E 69
Query: 109 YNVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISG 168
Y H + +D PGH + GA D +LVV+A DG MPQTRE I A+ G
Sbjct: 70 YETANRHYA--HVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVG 127
Query: 169 VP-LIVAINKIDKLD 182
VP ++V +NK D +D
Sbjct: 128 VPYIVVFLNKCDMVD 142
Score = 74.1 bits (183), Expect = 1e-13
Identities = 92/311 (29%), Positives = 142/311 (45%), Gaps = 59/311 (18%)
Query: 928 IAHVDHGKTTL---IDHLLRQSG--TFRKNQNINARIMDSNEIEKERGITIFSKNCS-IE 981
I HVDHGKTTL I +L + G + I D+ EK RGITI N S +E
Sbjct: 18 IGHVDHGKTTLTAAITKVLAKKGGGEAKAYDQI-----DNAPEEKARGITI---NTSHVE 69
Query: 982 YNGTRINI--IDTPGHADFGGEVERILSMV------DNVLLLIDAVEGPMPQTRFVTRKA 1033
Y + +D PGHAD+ + +M+ D +L++ A +GPMPQTR A
Sbjct: 70 YETANRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSAADGPMPQTREHILLA 123
Query: 1034 LKLGFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCATE--EQL--------DFPVIYT 1082
++G IVV +NK D V D +L + L E E L D P+I
Sbjct: 124 RQVGVPYIVVFLNKCDM-------VDDE--ELLE-LVEMEVRELLSKYDFPGDDTPIIRG 173
Query: 1083 SALHGYANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQIISLEYSSYLGKIGIGR 1142
SAL ++ + + ++ L +A+ Y+P + + P + I + S G + GR
Sbjct: 174 SALKALEGDDDEEWEAKILELMDAVDSYIPEPERAIDKPFLMPIEDVFSISGRGTVVTGR 233
Query: 1143 ILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIV--LITGI--E 1198
+ G +K +V I+ G + K + + +F R L++E +GD V L+ G E
Sbjct: 234 VERGIVKVGDEVEIV-GIKE-TQKTTVTGVEMF----RKLLDEGQAGDNVGVLLRGTKRE 287
Query: 1199 EICIGSTICDP 1209
++ G + P
Sbjct: 288 DVERGQVLAKP 298
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 74.3 bits (183), Expect = 1e-13
Identities = 71/257 (27%), Positives = 109/257 (42%), Gaps = 54/257 (21%)
Query: 63 AESLVRAPIVTI--MGHVDHGKTSLLDYIRKTNVV-FSEA--GGITQHIG---------- 107
A+ P V I +GHVDHGKT+L + SE GIT +G
Sbjct: 2 ADPKHIQPEVNIGMVGHVDHGKTTLTKALSGVWTDRHSEELKRGITIKLGYADAKIYKCP 61
Query: 108 ---AYNVVT------NHGS-------ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADD 151
T N G+ ++F+D PGHE A GA + D +LV+AA++
Sbjct: 62 ECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGAALMDGALLVIAANE 121
Query: 152 GV-MPQTREAIAHAKISGVP-LIVAINKID-----KLDINLDRIKQDLISEQVIPEEYGG 204
PQTRE + +I G+ +I+ NKID + N ++IK+ + + + E
Sbjct: 122 PCPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRERALENYEQIKEFV--KGTVAEN--- 176
Query: 205 ASPFISISAKTGVGINKLLENISLQAEILELKAPVTTPAKGVIIES--------RLDKGK 256
+P I ISA+ I+ L+E I + I + + P + + S ++ K
Sbjct: 177 -APIIPISAQHKANIDALIEAI--EKYIPTPERDLDKPPRMYVARSFDVNKPGTPPEELK 233
Query: 257 GPVATVLIQSGTLRCSD 273
G V + G LR D
Sbjct: 234 GGVIGGSLVQGVLRVGD 250
Score = 63.1 bits (154), Expect = 5e-10
Identities = 66/233 (28%), Positives = 97/233 (41%), Gaps = 64/233 (27%)
Query: 928 IAHVDHGKTTLIDHL-----LRQSGTFRKNQNI-----NARIMDSNEIEKERGITI--FS 975
+ HVDHGKTTL L R S ++ I +A+I E + T
Sbjct: 16 VGHVDHGKTTLTKALSGVWTDRHSEELKRGITIKLGYADAKIYKCPECYRPECYTTEPKC 75
Query: 976 KNCSIEYNGTR-INIIDTPGHADFGGEVERILS---MVDNVLLLIDAVEG-PMPQTR--F 1028
NC E R ++ +D PGH + +LS ++D LL+I A E P PQTR
Sbjct: 76 PNCGAETELVRRVSFVDAPGHETL---MATMLSGAALMDGALLVIAANEPCPQPQTREHL 132
Query: 1029 VTRKALK-LGFKPIVVV-NKID---RSNARPEWVVDATFDLFDKLCATEEQLDF------ 1077
+ AL+ +G K I++V NKID R A + E+ +F
Sbjct: 133 M---ALEIIGIKNIIIVQNKIDLVSRERALENY---------------EQIKEFVKGTVA 174
Query: 1078 ---PVIYTSALHGYANENSKARQGNMIPLFEAILKYVPVHKDNSNNPLQLQII 1127
P+I SA H N+ L EAI KY+P + + + P ++ +
Sbjct: 175 ENAPIIPISAQHKA----------NIDALIEAIEKYIPTPERDLDKPPRMYVA 217
>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 = 69.2 bits (170), Expect = 2e-13
Identities = 42/168 (25%), Positives = 69/168 (41%), Gaps = 27/168 (16%)
Query: 74 IMGHVDHGKTSLL-----DYIRKTNVVFSEAGGITQHIGAYNVVTNH-GSITFLDTPG-H 126
I G + GK+SLL + S G T+ G + +DTPG
Sbjct: 2 IFGRPNVGKSSLLNALLGQNVGIV----SPIPGTTRDPVRKEWELLPLGPVVLIDTPGLD 57
Query: 127 EAFTAMRARG------AKVTDIVVLVVAADDGVMPQTREAIAHAKI--SGVPLIVAINKI 178
E R R A D+V+LVV +D + E + G P+++ +NKI
Sbjct: 58 EEGGLGRERVEEARQVADRADLVLLVVDSD---LTPVEEEAKLGLLRERGKPVLLVLNKI 114
Query: 179 DKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
D + + + +++P+ P I++SA G GI++L + I
Sbjct: 115 DLVPESEEEELLRERKLELLPDL-----PVIAVSALPGEGIDELRKKI 157
Score = 39.9 bits (94), Expect = 0.002
Identities = 45/194 (23%), Positives = 70/194 (36%), Gaps = 57/194 (29%)
Query: 934 GKTTLIDHLLRQ--------SGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
GK++L++ LL Q GT R + + E+ +
Sbjct: 9 GKSSLLNALLGQNVGIVSPIPGTTR---DPVRKEW---ELLPLGPVV------------- 49
Query: 986 RINIIDTPGHADFGGE----VERILSM---VDNVLLLIDAVEGPMPQTRFVTRKALKLGF 1038
+IDTPG + GG VE + D VLL++D+ P+ + + +
Sbjct: 50 ---LIDTPGLDEEGGLGRERVEEARQVADRADLVLLVVDSDLTPVEEEAKLGLLRERG-- 104
Query: 1039 KPIVVV-NKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQ 1097
KP+++V NKID E KL D PVI SAL G
Sbjct: 105 KPVLLVLNKIDLVPESEE----EELLRERKLELL---PDLPVIAVSALPG---------- 147
Query: 1098 GNMIPLFEAILKYV 1111
+ L + I + +
Sbjct: 148 EGIDELRKKIAELL 161
>gnl|CDD|184345 PRK13818, PRK13818, ribosome-binding factor A; Provisional.
Length = 121
Score = 66.2 bits (161), Expect = 9e-13
Identities = 36/109 (33%), Positives = 67/109 (61%), Gaps = 1/109 (0%)
Query: 541 RLSRIENQIQRDISEIIAFDIQNPIINIITITEVKITLDYSYAKIFFTTFNKDISI-KNI 599
R+ R+E +I R++++I+ +I++P ++ +TIT V+ T D SYA ++++ +D + K +
Sbjct: 4 RIGRVEGEILRELTKILRKNIRDPRLSDVTITAVECTNDLSYATVYYSLLTEDEAKEKEV 63
Query: 600 LDNLSKAKNYIRFKLSKKLHIHTLPILNFFYDNSIENAMMISKLIDGIK 648
+ L KAK +R L + L ++ +P L F DNS+ I +LI +K
Sbjct: 64 QEGLEKAKGMMRHLLGQTLTVYKVPELIFKRDNSVAYGSKIDRLIAEVK 112
>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 = 67.6 bits (166), Expect = 2e-12
Identities = 60/206 (29%), Positives = 86/206 (41%), Gaps = 57/206 (27%)
Query: 930 HVDHGKTTLIDHLLRQSG----------TFRKNQNINAR------IMDSNEIEKERGITI 973
VD GK+TLI LL S K+ ++D + E+E+GITI
Sbjct: 7 SVDDGKSTLIGRLLYDSKSIFEDQLAALERSKSSGTQGEKLDLALLVDGLQAEREQGITI 66
Query: 974 ------FS--KNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQ 1025
FS K I I DTPGH + + S D +LL+DA +G + Q
Sbjct: 67 DVAYRYFSTPKRKFI--------IADTPGHEQYTRNMVTGASTADLAILLVDARKGVLEQ 118
Query: 1026 TR---FVTRKALKLGFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCA----TEEQLDF 1077
TR ++ LG + +VV VNK+D +VD ++F+++ A L
Sbjct: 119 TRRHSYIAS---LLGIRHVVVAVNKMD--------LVDYDEEVFEEIKADYLAFAASLGI 167
Query: 1078 PVIY---TSALHGYANENSKARQGNM 1100
I SAL G +N +R NM
Sbjct: 168 EDITFIPISALEG---DNVVSRSENM 190
Score = 58.7 bits (143), Expect = 2e-09
Identities = 37/105 (35%), Positives = 54/105 (51%), Gaps = 18/105 (17%)
Query: 122 DTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKIS---GVP-LIVAINK 177
DTPGHE +T GA D+ +L+V A GV+ QTR H+ I+ G+ ++VA+NK
Sbjct: 84 DTPGHEQYTRNMVTGASTADLAILLVDARKGVLEQTRR---HSYIASLLGIRHVVVAVNK 140
Query: 178 IDKLDIN---LDRIKQD---LISEQVIPEEYGGASPFISISAKTG 216
+D +D + + IK D + I + FI ISA G
Sbjct: 141 MDLVDYDEEVFEEIKADYLAFAASLGIEDIT-----FIPISALEG 180
>gnl|CDD|172345 PRK13815, PRK13815, ribosome-binding factor A; Provisional.
Length = 122
Score = 65.2 bits (159), Expect = 2e-12
Identities = 36/108 (33%), Positives = 55/108 (50%)
Query: 540 ERLSRIENQIQRDISEIIAFDIQNPIINIITITEVKITLDYSYAKIFFTTFNKDISIKNI 599
+R ++ I IS ++ +++P I +TIT VK+T D A I+FT D + K+
Sbjct: 3 KRSEKVAEAIHELISGLLVKGLKDPRIGFVTITGVKVTDDLHLATIYFTVIGDDEAKKST 62
Query: 600 LDNLSKAKNYIRFKLSKKLHIHTLPILNFFYDNSIENAMMISKLIDGI 647
L+ A+ +IR +L K L + P L F YD S E I L+ I
Sbjct: 63 EAGLNSARGFIRKELGKVLRMRYAPELIFKYDESQEYGNRIDSLLKEI 110
>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 = 66.9 bits (164), Expect = 3e-12
Identities = 58/194 (29%), Positives = 84/194 (43%), Gaps = 44/194 (22%)
Query: 71 IVTIMGHVDHGKTSLLDYIRKTNVV-FSEA--GGITQHIGAYN----------------- 110
I TI GHV HGKT+L+ + V E IT +G N
Sbjct: 3 IGTI-GHVAHGKTTLVKALSGVWTVRHKEELKRNITIKLGYANAKIYKCPNCGCPRPYDT 61
Query: 111 ---VVTNHGS-------ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGV-MPQTRE 159
G ++F+D PGHE A GA V D +L++AA++ PQT E
Sbjct: 62 PECECPGCGGETKLVRHVSFVDCPGHEILMATMLSGAAVMDGALLLIAANEPCPQPQTSE 121
Query: 160 AIAHAKISGVP-LIVAINKIDKLDI-----NLDRIKQDLISEQVIPEEYGGASPFISISA 213
+A +I G+ +I+ NKID + N ++IK+ + + I E +P I ISA
Sbjct: 122 HLAALEIMGLKHIIILQNKIDLVKEEQALENYEQIKEFV--KGTIAEN----APIIPISA 175
Query: 214 KTGVGINKLLENIS 227
+ I+ L E I
Sbjct: 176 QLKYNIDVLCEYIV 189
Score = 54.6 bits (132), Expect = 4e-08
Identities = 55/238 (23%), Positives = 80/238 (33%), Gaps = 101/238 (42%)
Query: 928 IAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITI--------FSK--- 976
I HV HGKTTL+ + ++ ++ E +R ITI K
Sbjct: 6 IGHVAHGKTTLV-------------KALSGVWTVRHKEELKRNITIKLGYANAKIYKCPN 52
Query: 977 ----NCSIEYNGTR------------INIIDTPGHADFGGEVERIL--------SMVDNV 1012
++ +D PGH IL +++D
Sbjct: 53 CGCPRPYDTPECECPGCGGETKLVRHVSFVDCPGH--------EILMATMLSGAAVMDGA 104
Query: 1013 LLLIDAVEG-PMPQTR--FVTRKALK-LGFKPIVVV-NKID---RSNARPEWVVDATFDL 1064
LLLI A E P PQT AL+ +G K I+++ NKID A +
Sbjct: 105 LLLIAANEPCPQPQTSEHLA---ALEIMGLKHIIILQNKIDLVKEEQALENY-------- 153
Query: 1065 FDKLCATEEQLDF---------PVIYTSALHGYANENSKARQGNMIPLFEAILKYVPV 1113
E+ +F P+I SA Y N+ L E I+K +P
Sbjct: 154 -------EQIKEFVKGTIAENAPIIPISAQLKY----------NIDVLCEYIVKKIPT 194
>gnl|CDD|184344 PRK13816, PRK13816, ribosome-binding factor A; Provisional.
Length = 131
Score = 64.1 bits (156), Expect = 6e-12
Identities = 33/110 (30%), Positives = 65/110 (59%), Gaps = 10/110 (9%)
Query: 540 ERLSRIENQIQRDISEIIAFDIQNP-IINIITITEVKITLDYSYAKIFFTTFNKDI---- 594
+RL R+ + +QR++SE+I ++++P + ++TI+ VK++ D YA ++ T +++
Sbjct: 3 QRLKRMADSVQRELSELIRQELKDPRLGGLVTISSVKVSPDLGYADVYVTVMGRELSDDQ 62
Query: 595 ---SIKNILDNLSKAKNYIRFKLSKKLHIHTLPILNFFYD--NSIENAMM 639
+ + LD L+KA ++R +LS+++ P L F YD N+ N M
Sbjct: 63 NEVAHRETLDVLNKASGFLRTELSRRIKTRITPRLRFHYDKTNAYGNYMF 112
>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 = 68.6 bits (168), Expect = 9e-12
Identities = 84/301 (27%), Positives = 136/301 (45%), Gaps = 46/301 (15%)
Query: 931 VDHGKTTLIDHLLRQSGTFRKNQ----------------NIN-ARIMDSNEIEKERGITI 973
VD GK+TLI LL + ++Q I+ A ++D + E+E+GITI
Sbjct: 9 VDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQGGEIDLALLVDGLQAEREQGITI 68
Query: 974 FSKNCSIEYNGT--RINII-DTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVT 1030
+ + Y T R I+ DTPGH + + S D +LL+DA +G + QTR +
Sbjct: 69 ---DVAYRYFSTDKRKFIVADTPGHEQYTRNMATGASTADLAVLLVDARKGVLEQTRRHS 125
Query: 1031 RKALKLGFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYA 1089
A LG + +V+ VNK+D + E V + + D I SAL G
Sbjct: 126 YIASLLGIRHVVLAVNKMDLVDYDEE-VFENIKKDYLAFAEQLGFRDVTFIPLSALKG-- 182
Query: 1090 NENSKARQGNMIPLFEA-----ILKYVPVHKDNSNNPLQL--QIISLEYSSYLGKIGIGR 1142
+N +R +M P + IL+ V V +D + PL+ Q ++ + G G
Sbjct: 183 -DNVVSRSESM-PWYSGPTLLEILETVEVERDAQDLPLRFPVQYVNRPNLDFRGYAGT-- 238
Query: 1143 ILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEICI 1202
I SG + +VV++ P + +++ +I F G + +A +G V +T +EI I
Sbjct: 239 IASGSVHVGDEVVVL--PSGR--SSRVARIVTFDG----DLEQARAGQAVTLTLDDEIDI 290
Query: 1203 G 1203
Sbjct: 291 S 291
Score = 57.4 bits (139), Expect = 3e-08
Identities = 31/77 (40%), Positives = 47/77 (61%), Gaps = 10/77 (12%)
Query: 122 DTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKIS---GVP-LIVAINK 177
DTPGHE +T A GA D+ VL+V A GV+ QTR H+ I+ G+ +++A+NK
Sbjct: 86 DTPGHEQYTRNMATGASTADLAVLLVDARKGVLEQTRR---HSYIASLLGIRHVVLAVNK 142
Query: 178 IDKLDIN---LDRIKQD 191
+D +D + + IK+D
Sbjct: 143 MDLVDYDEEVFENIKKD 159
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 67.2 bits (165), Expect = 3e-11
Identities = 62/213 (29%), Positives = 98/213 (46%), Gaps = 48/213 (22%)
Query: 76 GHVDHGKTSLLDYIRKTNV---VFSE--AGGITQHIG----------------AYNV--- 111
GHVDHGKT+L+ + T V SE GIT +G AY
Sbjct: 16 GHVDHGKTTLVQAL--TGVWTDRHSEELKRGITIRLGYADATIRKCPDCEEPEAYTTEPK 73
Query: 112 VTNHGS-------ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGV-MPQTREAIAH 163
N GS ++F+D PGHE A GA + D +LV+AA++ PQT+E +
Sbjct: 74 CPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGAILVIAANEPCPQPQTKEHLMA 133
Query: 164 AKISGVP-LIVAINKIDKLDI-----NLDRIKQDLISEQVIPEEYGGASPFISISAKTGV 217
I G+ +++ NKID + N ++IK+ + + + E +P I +SA V
Sbjct: 134 LDIIGIKNIVIVQNKIDLVSKERALENYEQIKEFV--KGTVAEN----APIIPVSALHKV 187
Query: 218 GINKLLENISLQAEILELKAPVTTPAKGVIIES 250
I+ L+E +++ EI + + P + + S
Sbjct: 188 NIDALIE--AIEEEIPTPERDLDKPPRMYVARS 218
Score = 54.9 bits (133), Expect = 2e-07
Identities = 64/229 (27%), Positives = 92/229 (40%), Gaps = 90/229 (39%)
Query: 930 HVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITI--------FSK--NC- 978
HVDHGKTTL+ L +G + D + E +RGITI K +C
Sbjct: 17 HVDHGKTTLVQAL---TGVW----------TDRHSEELKRGITIRLGYADATIRKCPDCE 63
Query: 979 ---------SIEYNGT------RINIIDTPGHADFGGEV--ERILS---MVDNVLLLIDA 1018
G+ R++ +D PGH E +LS ++D +L+I A
Sbjct: 64 EPEAYTTEPKCPNCGSETELLRRVSFVDAPGH-----ETLMATMLSGAALMDGAILVIAA 118
Query: 1019 VEG-PMPQTR--FVTRKALK-LGFKPIVVV-NKIDRSNARPEWVVDATFDLFDKLCATEE 1073
E P PQT+ + AL +G K IV+V NKID +V ++ E
Sbjct: 119 NEPCPQPQTKEHLM---ALDIIGIKNIVIVQNKID--------LVSK-----ERALENYE 162
Query: 1074 QL----------DFPVIYTSALHGYANENSKARQGNMIPLFEAILKYVP 1112
Q+ + P+I SALH N+ L EAI + +P
Sbjct: 163 QIKEFVKGTVAENAPIIPVSALHKV----------NIDALIEAIEEEIP 201
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 65.1 bits (158), Expect = 2e-10
Identities = 70/259 (27%), Positives = 106/259 (40%), Gaps = 37/259 (14%)
Query: 923 IKSAIIAHVDHGKTTLIDHLLRQSGTFRKN---------QNINAR------IMDSNEIEK 967
I +I HVD GK+T HL+ + G K +N R ++D + E+
Sbjct: 8 INIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFEKEAAEMNKRSFKYAWVLDKLKAER 67
Query: 968 ERGITIFSKNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMP--- 1024
ERGITI E +ID PGH DF + S D +L+ID+ G
Sbjct: 68 ERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGGFEAGI 127
Query: 1025 ----QTRFVTRKALKLGFKPIV-VVNKIDR-----SNARPEWVVDATFDLFDKLCATEEQ 1074
QTR A LG K ++ NK+D S AR + +V K+ ++
Sbjct: 128 SKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGYNPDK 187
Query: 1075 LDFPVIYTSALHGYANENSKARQGNMI----PLFEAILKYVPVHKDNSNNPLQLQIISLE 1130
+ F I G+ +N R N+ P L + K S+ PL+L + +
Sbjct: 188 IPFVPI-----SGFEGDNMIERSTNLDWYKGPTLLEALDQINEPKRPSDKPLRLPLQDVY 242
Query: 1131 YSSYLGKIGIGRILSGRIK 1149
+G + +GR+ +G IK
Sbjct: 243 KIGGIGTVPVGRVETGVIK 261
Score = 35.5 bits (81), Expect = 0.26
Identities = 30/105 (28%), Positives = 41/105 (39%), Gaps = 8/105 (7%)
Query: 101 GITQHIGAYNVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMP----- 155
GIT I + T T +D PGH F G D VL++ + G
Sbjct: 70 GITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGGFEAGISK 129
Query: 156 --QTREAIAHAKISGVP-LIVAINKIDKLDINLDRIKQDLISEQV 197
QTRE A GV +I NK+D + + D I ++V
Sbjct: 130 DGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEV 174
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 64.5 bits (158), Expect = 2e-10
Identities = 88/348 (25%), Positives = 139/348 (39%), Gaps = 89/348 (25%)
Query: 931 VDHGKTTLIDHLLRQSGTFRKNQ-----NINARI------------MDSNEIEKERGITI 973
VD GK+TLI LL + ++Q N + R +D + E+E+GITI
Sbjct: 36 VDDGKSTLIGRLLHDTKQIYEDQLASLHNDSKRHGTQGEKLDLALLVDGLQAEREQGITI 95
Query: 974 ------FSKNCSIEYNGTRINII-DTPGHADF------GGEVERILSMVDNVLLLIDAVE 1020
FS R II DTPGH + G S D +LLIDA +
Sbjct: 96 DVAYRYFSTE-------KRKFIIADTPGHEQYTRNMATGA------STCDLAILLIDARK 142
Query: 1021 GPMPQTRFVTRKALKLGFKPIVV-VNKID---RSNARPEWVVDATFDLFDKLCATEEQLD 1076
G + QTR + A LG K +VV VNK+D S E + + ++L LD
Sbjct: 143 GVLDQTRRHSFIATLLGIKHLVVAVNKMDLVDYSEEVFERIREDYLTFAEQL---PGNLD 199
Query: 1077 FPVIYTSALHGYANENSKARQGNM-----IPLFEAILKYVPVHKDNSNNPLQL--QIIS- 1128
+ SAL G +N ++ +M L E +L+ V + + P + Q ++
Sbjct: 200 IRFVPLSALEG---DNVVSQSESMPWYSGPTLLE-VLETVDIQRVVDAQPFRFPVQYVNR 255
Query: 1129 --LEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEA 1186
L++ Y G + SG +K V ++ P K ++ + +I F G D EA
Sbjct: 256 PNLDFRGYAGTLA-----SGVVKVGDRVKVL--PSGK--ESNVARIVTFDG-DL---EEA 302
Query: 1187 LSGDIVLITGIEEICI--GSTICDPSKPNGLPMLNIDEPTLTINFMVN 1232
+G+ + + +EI I G + + + +
Sbjct: 303 FAGEAITLVLEDEIDISRGDLLVAAD----------EALQAVQHASAD 340
Score = 59.5 bits (145), Expect = 8e-09
Identities = 31/77 (40%), Positives = 48/77 (62%), Gaps = 10/77 (12%)
Query: 122 DTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKIS---GVP-LIVAINK 177
DTPGHE +T A GA D+ +L++ A GV+ QTR H+ I+ G+ L+VA+NK
Sbjct: 113 DTPGHEQYTRNMATGASTCDLAILLIDARKGVLDQTRR---HSFIATLLGIKHLVVAVNK 169
Query: 178 IDKLDIN---LDRIKQD 191
+D +D + +RI++D
Sbjct: 170 MDLVDYSEEVFERIRED 186
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 62.1 bits (151), Expect = 1e-09
Identities = 68/256 (26%), Positives = 105/256 (41%), Gaps = 39/256 (15%)
Query: 927 IIAHVDHGKTTLIDHLLRQSG-----TFRKNQNINARI----------MDSNEIEKERGI 971
+I HVD GK+T HL+ + G T K + A + +D + E+ERGI
Sbjct: 12 VIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGI 71
Query: 972 TIFSKNCSIEYNGTRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMP------- 1024
TI E IID PGH DF + S D +L++ + G
Sbjct: 72 TIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFEAGISKDG 131
Query: 1025 QTRFVTRKALKLGFKPIVV-VNKIDR-----SNARPEWVVDATFDLFDKLCATEEQLDFP 1078
QTR A LG K ++V +NK+D S R + + K+ E++ F
Sbjct: 132 QTREHALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYNPEKVPFI 191
Query: 1079 VIYTSALHGYANENSKARQGNMI-----PLFEAILKYVPVHKDNSNNPLQLQIISLEYSS 1133
I G+ +N + NM L EA+ P K + PL+L + +
Sbjct: 192 PI-----SGWQGDNMIEKSDNMPWYKGPTLLEALDTLEP-PKRPVDKPLRLPLQDVYKIG 245
Query: 1134 YLGKIGIGRILSGRIK 1149
+G + +GR+ +G +K
Sbjct: 246 GIGTVPVGRVETGILK 261
Score = 50.9 bits (122), Expect = 3e-06
Identities = 43/133 (32%), Positives = 56/133 (42%), Gaps = 21/133 (15%)
Query: 101 GITQHIGAYNVVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMP----- 155
GIT I + T T +D PGH F G D+ +LVVA+ G
Sbjct: 70 GITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFEAGISK 129
Query: 156 --QTREAIAHAKISGVP-LIVAINKIDKLDINLDRIKQDLISEQVI---------PEEYG 203
QTRE A GV +IV INK+D +N + + D I ++V PE+
Sbjct: 130 DGQTREHALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYNPEKV- 188
Query: 204 GASPFISISAKTG 216
PFI IS G
Sbjct: 189 ---PFIPISGWQG 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 = 55.4 bits (134), Expect = 2e-09
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 8/89 (8%)
Query: 1122 LQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRV 1181
L+ + + G + GR+ SG +K V + P K K+ ++ FKG
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVG--PGGGGVKGKVKSLKRFKG---- 54
Query: 1182 LVNEALSGDIVLITG--IEEICIGSTICD 1208
V+EA++GDIV I ++I IG T+ D
Sbjct: 55 EVDEAVAGDIVGIVLKDKDDIKIGDTLTD 83
Score = 51.9 bits (125), Expect = 3e-08
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 1/66 (1%)
Query: 474 GLAEIRQVILVNKVSKIAGCYILEGLIRRDSKIRILRNKNIIWTGELDSLKRFKDNVKEV 533
A + +V +A + G +++ K+R+ + G++ SLKRFK V E
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGV-KGKVKSLKRFKGEVDEA 59
Query: 534 KAGFEC 539
AG
Sbjct: 60 VAGDIV 65
Score = 48.9 bits (117), Expect = 4e-07
Identities = 22/90 (24%), Positives = 42/90 (46%), Gaps = 12/90 (13%)
Query: 243 AKGVIIESRLDKGKGPVATVLIQSGTLRCSDIVVAGASYGRIRSMLNENGKNILEAGPSI 302
+ ++ + DKG+G VAT ++SGTL+ D V G G ++ + K++
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKV----KSLKRFK--- 53
Query: 303 PVEIQGLTKVPFSGEELFVILNEKKAREIG 332
G +G+ + ++L +K +IG
Sbjct: 54 -----GEVDEAVAGDIVGIVLKDKDDIKIG 78
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase subunit
1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 61.1 bits (149), Expect = 3e-09
Identities = 72/279 (25%), Positives = 121/279 (43%), Gaps = 66/279 (23%)
Query: 931 VDHGKTTLIDHLL------------------RQSGTFRKNQNIN-ARIMDSNEIEKERGI 971
VD GK+TLI LL ++ GT + I+ A ++D E+E+GI
Sbjct: 33 VDDGKSTLIGRLLYDSKMIFEDQLAALERDSKKVGT--QGDEIDLALLVDGLAAEREQGI 90
Query: 972 TIFSKNCSIEYNGT--RINII-DTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRF 1028
TI + + Y T R I+ DTPGH + + S D ++L+DA +G + QTR
Sbjct: 91 TI---DVAYRYFATPKRKFIVADTPGHEQYTRNMVTGASTADLAIILVDARKGVLTQTRR 147
Query: 1029 VTRKALKLGFKPIVV-VNKIDRSNARPEWVVDATFDLFDKLCAT----EEQLDFPVIYT- 1082
+ A LG + +V+ VNK+D +VD ++FD++ A +L +
Sbjct: 148 HSFIASLLGIRHVVLAVNKMD--------LVDYDQEVFDEIVADYRAFAAKLGLHDVTFI 199
Query: 1083 --SALHGYANENSKARQGNMIPLFE-----AILKYVPVHKDNSNNPLQL--QII---SLE 1130
SAL G +N R M P +E L+ V + D + + Q + +L+
Sbjct: 200 PISALKG---DNVVTRSARM-PWYEGPSLLEHLETVEIASDRNLKDFRFPVQYVNRPNLD 255
Query: 1131 YSSYLGKIGIGRIL---------SGRIKSLQDVVIMNGP 1160
+ + G + G + SG+ ++ +V +G
Sbjct: 256 FRGFAGTVASGVVRPGDEVVVLPSGKTSRVKRIVTPDGD 294
Score = 53.4 bits (129), Expect = 9e-07
Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 10/77 (12%)
Query: 122 DTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKIS---GVPLIV-AINK 177
DTPGHE +T GA D+ +++V A GV+ QTR H+ I+ G+ +V A+NK
Sbjct: 110 DTPGHEQYTRNMVTGASTADLAIILVDARKGVLTQTRR---HSFIASLLGIRHVVLAVNK 166
Query: 178 IDKLDIN---LDRIKQD 191
+D +D + D I D
Sbjct: 167 MDLVDYDQEVFDEIVAD 183
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 60.9 bits (148), Expect = 3e-09
Identities = 51/190 (26%), Positives = 77/190 (40%), Gaps = 37/190 (19%)
Query: 118 ITFLDTPGHEAF--TAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAI 175
++F+DT GHE + T +R + D +LVVAADDGV T+E + A +P+IV +
Sbjct: 203 VSFVDTVGHEPWLRTTIRGLLGQKVDYGLLVVAADDGVTKMTKEHLGIALAMELPVIVVV 262
Query: 176 NKIDKLDINLDRIKQ-----------------------DLISEQVIPEEYGGASPFISIS 212
KID + DR + D++ + G P S
Sbjct: 263 TKIDMVPD--DRFQGVVEEISALLKRVGRIPLIVKDTDDVVLAAKAMKAGRGVVPIFYTS 320
Query: 213 AKTGVGINKLLENISLQAEILELKAPVTTPAKGV----IIESRLDKGKGPVATVLIQSGT 268
+ TG G++ L E L L +G I + G G V + ++SG
Sbjct: 321 SVTGEGLDLLDEFFLL------LPKRRRWDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGI 374
Query: 269 LRCSDIVVAG 278
L D V+ G
Sbjct: 375 LHVGDTVLLG 384
Score = 40.9 bits (96), Expect = 0.006
Identities = 69/323 (21%), Positives = 116/323 (35%), Gaps = 68/323 (21%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITI--------FS-- 975
+ HVDHGK+TL+ L+ +G +D + E ERG++ F
Sbjct: 121 GVAGHVDHGKSTLVGVLV--TGRLDDGDGATRSYLDVQKHEVERGLSADISLRVYGFDDG 178
Query: 976 -------------KNCSIEYNGTRINIIDTPGHADFGGEVERIL--SMVDNVLLLIDAVE 1020
K ++ ++ +DT GH + R L VD LL++ A +
Sbjct: 179 KVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQKVDYGLLVVAADD 238
Query: 1021 GPMPQTRFVTRKALKLGFKPIVVVNKID------------------RSNARPEWVVDATF 1062
G T+ AL + IVVV KID + R +V T
Sbjct: 239 GVTKMTKEHLGIALAMELPVIVVVTKIDMVPDDRFQGVVEEISALLKRVGRIPLIVKDTD 298
Query: 1063 DLFDKLCATE-EQLDFPVIYTSA--LHGYANENSKARQGNMIPLFEAILKYVPVHKDNSN 1119
D+ A + + P+ YTS+ G L + +P + +
Sbjct: 299 DVVLAAKAMKAGRGVVPIFYTSSVTGEGLD-------------LLDEFFLLLPKRRRWDD 345
Query: 1120 NPLQLQIISLEYS-SYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGL 1178
L I YS + +G + G + SG + V++ D K + + I +
Sbjct: 346 EGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDTVLLGPFKDGKFREVVVKSIEM---- 401
Query: 1179 DRVLVNEALSGDIV--LITGIEE 1199
V+ A +G I+ + G+E+
Sbjct: 402 HHYRVDSAKAGSIIGIALKGVEK 424
>gnl|CDD|139879 PRK13817, PRK13817, ribosome-binding factor A; Provisional.
Length = 119
Score = 55.5 bits (133), Expect = 4e-09
Identities = 32/106 (30%), Positives = 63/106 (59%), Gaps = 1/106 (0%)
Query: 540 ERLSRIENQIQRDISEIIAFDIQNPIINIITITEVKITLDYSYAKIFFTTFNKDISIKNI 599
+R R+ + I + ++E++ ++++ ++ I++T V I+ D AK+F++ ++ + K +
Sbjct: 3 QRQQRVADLIHQQLAELLKKEVRDSRLSKISLTAVSISPDLKQAKVFYSLL-ENQNEKEV 61
Query: 600 LDNLSKAKNYIRFKLSKKLHIHTLPILNFFYDNSIENAMMISKLID 645
L+KA Y+R L++ + +P L F YD SIE A IS LI+
Sbjct: 62 QKALNKATGYLRHLLAQATVLRYVPKLEFVYDESIERAHRISLLIE 107
>gnl|CDD|239671 cd03700, eEF2_snRNP_like_II, EF2_snRNP_like_II: this subfamily
represents domain II of elongation factor (EF) EF-2 found
eukaryotes and archaea and, the C-terminal portion of the
spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. During the process of peptide
synthesis and tRNA site changes, the ribosome is moved
along the mRNA a distance equal to one codon with the
addition of each amino acid. This translocation step is
catalyzed by EF-2_GTP, which is hydrolyzed to provide the
required energy. Thus, this action releases the uncharged
tRNA from the P site and transfers the newly formed
peptidyl-tRNA from the A site to the P site. Yeast
Snu114p is essential for cell viability and for splicing
in vivo. U5-116 kD binds GTP. Experiments suggest that
GTP binding and probably GTP hydrolysis is important for
the function of the U5-116 kD/Snu114p.
Length = 93
Score = 52.6 bits (127), Expect = 2e-08
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 1136 GKIGIGRILSGRIKSLQDVVIMN-----GPDDKPNKAKINQIRVFKGLDRVLVNEALSGD 1190
G I GR+ SG I+ Q V ++ ++ +K I ++ + G R V+E +G+
Sbjct: 16 GFIAFGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYREPVDEVPAGN 75
Query: 1191 IVLITGIEEICIGSTICD 1208
IVLI G++++ G+T
Sbjct: 76 IVLIVGLDQLKSGTTATI 93
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 57.0 bits (139), Expect = 3e-08
Identities = 34/117 (29%), Positives = 57/117 (48%), Gaps = 13/117 (11%)
Query: 118 ITFLDTPG-HEAFTA-----MRA--RGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGV 169
I F+DTPG H+ A +A K D+V+ VV AD+ + P + K
Sbjct: 55 IIFVDTPGIHKPKRALNRAMNKAAWSSLKDVDLVLFVVDADEKIGPGDEFILEKLKKVKT 114
Query: 170 PLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
P+I+ +NKID + D+ + + E++ E + + ISA G +++LL+ I
Sbjct: 115 PVILVLNKIDLVK---DKEELLPLLEEL--SELMDFAEIVPISALKGDNVDELLDVI 166
Score = 49.7 bits (120), Expect = 5e-06
Identities = 33/107 (30%), Positives = 46/107 (42%), Gaps = 19/107 (17%)
Query: 1009 VDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKL 1068
VD VL ++DA E P F+ K K+ I+V+NKID + E L L
Sbjct: 85 VDLVLFVVDADEKIGPGDEFILEKLKKVKTPVILVLNKIDLVKDKEE--------LLPLL 136
Query: 1069 CATEEQLDF-PVIYTSALHGYANENSKARQGNMIPLFEAILKYVPVH 1114
E +DF ++ SAL G N+ L + I KY+P
Sbjct: 137 EELSELMDFAEIVPISALKGD----------NVDELLDVIAKYLPEG 173
>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 = 51.1 bits (123), Expect = 5e-08
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 1136 GKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLIT 1195
G + GR+ SG +K VVI P+ K ++ + +F G R V A +G I+
Sbjct: 1 GTVATGRVESGTLKKGDKVVIG--PNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGI 58
Query: 1196 GIEEICIGSTIC 1207
G+++I G T+
Sbjct: 59 GLKDIKRGDTLT 70
Score = 37.2 bits (87), Expect = 0.003
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 257 GPVATVLIQSGTLRCSDIVVAGASY----GRIRSMLNENGKN---ILEAGPSIPVEIQGL 309
G VAT ++SGTL+ D VV G + GR+ S+ +G + A I + GL
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGIGL 60
Query: 310 TKV 312
+
Sbjct: 61 KDI 63
Score = 31.8 bits (73), Expect = 0.30
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 490 IAGCYILEGLIRRDSKIRILRNKNIIWTGELDSLKRFKDNVKEVKAGFEC 539
+A + G +++ K+ I N G + SL+ F +++E AG
Sbjct: 3 VATGRVESGTLKKGDKVVIGPNGT-GKKGRVTSLEMFHGDLREAVAGANA 51
>gnl|CDD|239755 cd04088, EFG_mtEFG_II, EFG_mtEFG_II: this subfamily represents the
domain II of elongation factor G (EF-G) in bacteria and,
the C-terminus of mitochondrial Elongation factor G1
(mtEFG1) and G2 (mtEFG2)_like proteins found in
eukaryotes. During the process of peptide synthesis and
tRNA site changes, the ribosome is moved along the mRNA a
distance equal to one codon with the addition of each
amino acid. In bacteria this translocation step is
catalyzed by EF-G_GTP, which is hydrolyzed to provide the
required energy. Thus, this action releases the uncharged
tRNA from the P site and transfers the newly formed
peptidyl-tRNA from the A site to the P site. Eukaryotic
cells harbor 2 protein synthesis systems: one localized
in the cytoplasm, the other in the mitochondria. Most
factors regulating mitochondrial protein synthesis are
encoded by nuclear genes, translated in the cytoplasm,
and then transported to the mitochondria. The eukaryotic
system of elongation factor (EF) components is more
complex than that in prokaryotes, with both cytoplasmic
and mitochondrial elongation factors and multiple
isoforms being expressed in certain species. mtEFG1 and
mtEFG2 show significant homology to bacterial EF-Gs.
Mutants in yeast mtEFG1 have impaired mitochondrial
protein synthesis, respiratory defects and a tendency to
lose mitochondrial DNA. No clear phenotype has been found
for mutants in the yeast homologue of mtEFG2, MEF2.
Length = 83
Score = 51.3 bits (124), Expect = 6e-08
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 1134 YLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVL 1193
++GK+ R+ SG +K+ + N K K ++ ++ G + V EA +GDI
Sbjct: 13 FVGKLSFVRVYSGTLKA--GSTLYNSTKGK--KERVGRLLRMHGKKQEEVEEAGAGDIGA 68
Query: 1194 ITGIEEICIGSTICD 1208
+ G+++ G T+CD
Sbjct: 69 VAGLKDTATGDTLCD 83
>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 = 56.0 bits (136), Expect = 7e-08
Identities = 39/139 (28%), Positives = 58/139 (41%), Gaps = 20/139 (14%)
Query: 116 GSITFLDTPGHE---AFTAMR-ARGAKV---TDIVVLVVAADDGVMPQTREAIAHAKISG 168
G + +DT G + +R + +V TD+ +LVV A G E I K
Sbjct: 55 GPVVLIDTAGLDDEGELGELRVEKTREVLDKTDLALLVVDAGVGPGEYELELIEELKERK 114
Query: 169 VPLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISL 228
+P IV INKID + + + K + P I +SA TG GI++L E I
Sbjct: 115 IPYIVVINKIDLGEESAELEKLEKKFGL----------PPIFVSALTGEGIDELKEAI-- 162
Query: 229 QAEILELKAPVTTPAKGVI 247
E+L T ++
Sbjct: 163 -IELLPEDFEEPTIVGDLV 180
Score = 47.9 bits (115), Expect = 3e-05
Identities = 35/121 (28%), Positives = 50/121 (41%), Gaps = 19/121 (15%)
Query: 989 IIDTPGHADFG--GE--VER---ILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPI 1041
+IDT G D G GE VE+ +L D LL++DA GP + + + I
Sbjct: 59 LIDTAGLDDEGELGELRVEKTREVLDKTDLALLVVDAGVGPGEYELELIEELKERKIPYI 118
Query: 1042 VVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMI 1101
VV+NKID E E++ P I+ SAL G + K ++
Sbjct: 119 VVINKIDLGEESAELEKL------------EKKFGLPPIFVSALTGEGIDELKEAIIELL 166
Query: 1102 P 1102
P
Sbjct: 167 P 167
>gnl|CDD|211345 cd02868, PseudoU_synth_hTruB2_like, Pseudouridine synthase,
humanTRUB2_like. This group consists of eukaryotic
pseudouridine synthases similar to human TruB
pseudouridine synthase homolog 2 (TRUB2). Pseudouridine
synthases catalyze the isomerization of specific
uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi).
Length = 226
Score = 54.3 bits (131), Expect = 1e-07
Identities = 54/229 (23%), Positives = 85/229 (37%), Gaps = 24/229 (10%)
Query: 664 GVLLLDKPYGLSSNNALKKI-----KYLLNAKKVGYTGTLDPFATGLLPLCFGEATKFSN 718
G+ + KP G+ + I KY K + LD F++G+L L K +
Sbjct: 1 GLFAVYKPPGVHWKHVRDTIESNLLKYFPEDKVLVGVHRLDAFSSGVLVLGVNHGNKLLS 60
Query: 719 YLSEAD--KYYEAIIHLGITTETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPP 776
+L + Y LG TE G++I+ + E IE++L Q
Sbjct: 61 HLYSNHPTRVYTIRGLLGKATENFFHTGRVIEKTTYDHITREKIERLLAVIQSGHQQ--- 117
Query: 777 MYSALKYKGIPL-----YKYARSGITIKRKLRYIKIYKITIIDYTIPYLTLRIHCSKGT- 830
A + + + A G+ IY I ++++ P TL + C T
Sbjct: 118 --KAFELCSVDDQSQQAAELAARGLIRPADKSPPIIYGIRLLEFRPPEFTLEVQCINETQ 175
Query: 831 -YIRVLSEDIGKMLGCGAHLKYLRRI-----GIDKLTLDKCLNIDTIIK 873
Y+R L +IG L A +RR +D L K N+ II
Sbjct: 176 EYLRKLIHEIGLELRSSAVCTQVRRTRDGPFTVDDALLRKQWNLQNIIS 224
>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 = 1e-07
Identities = 34/117 (29%), Positives = 55/117 (47%), Gaps = 13/117 (11%)
Query: 118 ITFLDTPG-HEAFTAMR------ARGA-KVTDIVVLVVAADDGVMPQTREAIAHAKISGV 169
I F+DTPG H+ + A A K D+V+ VV A + + + K S
Sbjct: 53 IIFVDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEWIGEGDEFILELLKKSKT 112
Query: 170 PLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
P+I+ +NKID + D+ + E++ +E + ISA G +++LLE I
Sbjct: 113 PVILVLNKIDLVK---DKEDLLPLLEKL--KELHPFAEIFPISALKGENVDELLEYI 164
Score = 45.1 bits (108), Expect = 5e-05
Identities = 45/165 (27%), Positives = 61/165 (36%), Gaps = 36/165 (21%)
Query: 934 GKTTLIDHLLRQ--SGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGTRINIID 991
GK+TL++ L+ Q S K Q RI RGI +I +D
Sbjct: 15 GKSTLLNALVGQKISIVSPKPQTTRNRI---------RGIYTDDD--------AQIIFVD 57
Query: 992 TPG-HADFGG-------EVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVV 1043
TPG H L VD VL ++DA E F+ K I+V
Sbjct: 58 TPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEWIGEGDEFILELLKKSKTPVILV 117
Query: 1044 VNKIDRSNARPEWVVDATFDLFDKLCATEEQLDF-PVIYTSALHG 1087
+NKID + + L +KL +E F + SAL G
Sbjct: 118 LNKIDLVKDKEDL-----LPLLEKL---KELHPFAEIFPISALKG 154
>gnl|CDD|218250 pfam04760, IF2_N, Translation initiation factor IF-2, N-terminal
region. This conserved feature at the N-terminus of
bacterial translation initiation factor IF2 has
recently had its structure solved. It shows structural
similarity to the tRNA anticodon Stem Contact Fold
domains of the methionyl-tRNA and glutaminyl-tRNA
synthetases, and a similar fold is also found in the B5
domain of the phenylalanine-tRNA synthetase.
Length = 52
Score = 48.2 bits (116), Expect = 3e-07
Identities = 20/39 (51%), Positives = 24/39 (61%)
Query: 1 MSVKSSVVIKNLMKLGQMVTINQVLDQETAMILVEEMGH 39
+ V S +IK L KLG M T N LD+ETA +L EE G
Sbjct: 13 LGVSSKELIKKLFKLGIMKTHNSTLDEETAELLAEEFGV 51
>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 = 51.3 bits (124), Expect = 4e-07
Identities = 44/171 (25%), Positives = 77/171 (45%), Gaps = 21/171 (12%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTN--VVFSEAGGITQHIGAYNVVTNHG-SITFLDTPG--- 125
+ I+G + GK+SLL+ + +V AG T G T +DT G
Sbjct: 5 IAIIGRPNVGKSSLLNALLGEERVIVSDIAG--TTRDSIDVPFEYDGQKYTLIDTAGIRK 62
Query: 126 -------HEAFTAMRARGA-KVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINK 177
E ++ +R A + D+V+LV+ A +G+ Q G LI+ +NK
Sbjct: 63 KGKVTEGIEKYSVLRTLKAIERADVVLLVLDASEGITEQDLRIAGLILEEGKALIIVVNK 122
Query: 178 IDKLDINLDRIKQ--DLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
D ++ + +K+ + ++ +Y +P + ISA TG G++KL + I
Sbjct: 123 WDLVEKDEKTMKEFEKELRRKLPFLDY---APIVFISALTGQGVDKLFDAI 170
Score = 48.2 bits (116), Expect = 5e-06
Identities = 51/181 (28%), Positives = 77/181 (42%), Gaps = 37/181 (20%)
Query: 923 IKSAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 982
IK AII + GK++L++ LL + R++ S+ G T S + EY
Sbjct: 3 IKIAIIGRPNVGKSSLLNALLGEE-----------RVIVSDI----AGTTRDSIDVPFEY 47
Query: 983 NGTRINIIDTPG-----HADFGGE------VERILSMVDNVLLLIDAVEGPMPQTRFVTR 1031
+G + +IDT G G E + + D VLL++DA EG Q +
Sbjct: 48 DGQKYTLIDTAGIRKKGKVTEGIEKYSVLRTLKAIERADVVLLVLDASEGITEQDLRIAG 107
Query: 1032 KALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDF----PVIYTSALHG 1087
L+ G I+VVNK D + T F+K +L F P+++ SAL G
Sbjct: 108 LILEEGKALIIVVNKWDLVEKDEK-----TMKEFEKE--LRRKLPFLDYAPIVFISALTG 160
Query: 1088 Y 1088
Sbjct: 161 Q 161
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 52.6 bits (127), Expect = 1e-06
Identities = 41/191 (21%), Positives = 81/191 (42%), Gaps = 29/191 (15%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTN--VVFSEAG----GITQHIGAYNVVTNHGSITFLDTPG 125
+ I+G + GK+SL++ I +V AG I + +DT G
Sbjct: 181 IAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSIDIEF-----ERDGRKYVLIDTAG 235
Query: 126 ----------HEAFTAMRARGA-KVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVA 174
E ++ R A + D+V+LV+ A +G+ Q + +G +++
Sbjct: 236 IRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDLRIAGLIEEAGRGIVIV 295
Query: 175 INKIDKLDINLDRIKQDLISEQVIPEEYG--GASPFISISAKTGVGINKLLENISLQAEI 232
+NK D ++ + +++ ++ + + +P + ISA TG G++KL E I E
Sbjct: 296 VNKWDLVEEDEATMEE---FKKKLRRKLPFLDFAPIVFISALTGQGLDKLFEAIKEIYEC 352
Query: 233 LELKAPVTTPA 243
+ ++T
Sbjct: 353 ATRR--ISTSL 361
Score = 51.0 bits (123), Expect = 3e-06
Identities = 30/119 (25%), Positives = 50/119 (42%), Gaps = 21/119 (17%)
Query: 118 ITFLDTPGHEAF------TAMRA---RGAKVTDIVVLVVAADDGVMPQTREAIAHAKISG 168
+DT G + +R + D+++ VV +G+ P E + S
Sbjct: 53 FILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIAKILRRSK 112
Query: 169 VPLIVAINKIDKLDINLDRIKQDLISEQVIPEEYG-GASPFISISAKTGVGINKLLENI 226
P+I+ +NKID L +E++ E Y G + ISA+ G GI LL+ +
Sbjct: 113 KPVILVVNKIDNLK-----------AEELAYEFYSLGFGEPVPISAEHGRGIGDLLDAV 160
Score = 49.9 bits (120), Expect = 8e-06
Identities = 61/231 (26%), Positives = 92/231 (39%), Gaps = 49/231 (21%)
Query: 894 GIIYLSDLLSKRFLHGQNLFLSDENIYILIKSAIIAHVDHGKTTLIDHLLRQSGTFRKNQ 953
GI L D + + L +E IK AII + GK++LI+ +L +
Sbjct: 152 GIGDLLDAVLE-LLPPDEEE-EEEEETDPIKIAIIGRPNVGKSSLINAILGEE------- 202
Query: 954 NINARIMDSNEIEKERGITIFSKNCSIEYNGTRINIIDTPG---HADFGGEVE------- 1003
R++ S+ G T S + E +G + +IDT G VE
Sbjct: 203 ----RVIVSDI----AGTTRDSIDIEFERDGRKYVLIDTAGIRRKGKITESVEKYSVART 254
Query: 1004 -RILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVNKIDRSNARPEWVVDATF 1062
+ + D VLL+IDA EG Q + + G ++VVNK D +AT
Sbjct: 255 LKAIERADVVLLVIDATEGISEQDLRIAGLIEEAGRGIVIVVNKWDLVEED-----EATM 309
Query: 1063 DLFDKLCATEEQLDF----PVIYTSALHGYANENSKARQGNMIPLFEAILK 1109
+ F K +L F P+++ SAL G + LFEAI +
Sbjct: 310 EEFKKK--LRRKLPFLDFAPIVFISALTGQ----------GLDKLFEAIKE 348
Score = 43.7 bits (104), Expect = 7e-04
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 9/79 (11%)
Query: 979 SIEYNGTRINIIDTPGHADFGGE---------VERILSMVDNVLLLIDAVEGPMPQTRFV 1029
E+ G +IDT G D + + D +L ++D EG P +
Sbjct: 45 DAEWLGREFILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEI 104
Query: 1030 TRKALKLGFKPIVVVNKID 1048
+ + I+VVNKID
Sbjct: 105 AKILRRSKKPVILVVNKID 123
>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 = 51.7 bits (125), Expect = 2e-06
Identities = 39/160 (24%), Positives = 62/160 (38%), Gaps = 35/160 (21%)
Query: 980 IEYNGTRINIIDTPGHADFGGE--------VERILSMVDNVLLLIDAVEGPMPQTRFVTR 1031
E+ G +IDT G + E + D +L ++D EG P+ + +
Sbjct: 42 AEWGGREFILIDTGGIEEDDDGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEEIAK 101
Query: 1032 KALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFP-VIYTSALHGYAN 1090
K G I+V NKID + + V A F L F I SA HG
Sbjct: 102 WLRKSGKPVILVANKID--GKKED-AVAAEF----------YSLGFGEPIPISAEHGR-- 146
Query: 1091 ENSKARQGNMIPLFEAILKYVP---VHKDNSNNPLQLQII 1127
+ L +AIL+ +P ++ + P+++ II
Sbjct: 147 --------GIGDLLDAILELLPEEEEEEEEEDGPIKIAII 178
Score = 47.8 bits (115), Expect = 3e-05
Identities = 40/162 (24%), Positives = 75/162 (46%), Gaps = 22/162 (13%)
Query: 81 GKTSLLDYIRKTN--VVFSEAGGITQHIGAYNVVTNHG-SITFLDTPG----------HE 127
GK++L++ + +V AG T +G T +DT G E
Sbjct: 184 GKSTLVNALLGEERVIVSDIAG--TTRDSIDIPFERNGKKYTLIDTAGIRRKGKVTEGVE 241
Query: 128 AFTAMRARGA-KVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLDIN-- 184
++ +R A + D+V+LV+ A +G+ Q A +G L++ +NK D +
Sbjct: 242 KYSVLRTLKAIERADVVLLVLDATEGITEQDLRIAGLALEAGKALVIVVNKWDLVKDEKT 301
Query: 185 LDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
+ K++ + ++ ++ +P + ISA TG G++KLL+ I
Sbjct: 302 REEFKKE-LRRKLPFLDF---APIVFISALTGQGVDKLLDAI 339
Score = 47.4 bits (114), Expect = 5e-05
Identities = 28/87 (32%), Positives = 40/87 (45%), Gaps = 12/87 (13%)
Query: 141 DIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLDINLDRIKQDLISEQVIPE 200
D+++ VV +G+ P+ E + SG P+I+ NKID + V E
Sbjct: 80 DVILFVVDGREGLTPEDEEIAKWLRKSGKPVILVANKIDGKK-----------EDAVAAE 128
Query: 201 EYG-GASPFISISAKTGVGINKLLENI 226
Y G I ISA+ G GI LL+ I
Sbjct: 129 FYSLGFGEPIPISAEHGRGIGDLLDAI 155
Score = 47.1 bits (113), Expect = 6e-05
Identities = 55/187 (29%), Positives = 77/187 (41%), Gaps = 52/187 (27%)
Query: 923 IKSAIIAHVDHGKTTLIDHLLRQ--------SGTFRKNQNINARIMDSNEIEKERGITIF 974
IK AII + GK+TL++ LL + +GT R DS +I
Sbjct: 173 IKIAIIGRPNVGKSTLVNALLGEERVIVSDIAGTTR----------DSIDIP-------- 214
Query: 975 SKNCSIEYNGTRINIIDTPG-----HADFGGE------VERILSMVDNVLLLIDAVEGPM 1023
E NG + +IDT G G E + + D VLL++DA EG
Sbjct: 215 -----FERNGKKYTLIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEGIT 269
Query: 1024 PQTRFVTRKALKLGFKPIVVVNKID--RSNARPEWVVDATFDLFDKLCATEEQLDF-PVI 1080
Q + AL+ G ++VVNK D + E +L KL LDF P++
Sbjct: 270 EQDLRIAGLALEAGKALVIVVNKWDLVKDEKTREEFKK---ELRRKL----PFLDFAPIV 322
Query: 1081 YTSALHG 1087
+ SAL G
Sbjct: 323 FISALTG 329
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 50.8 bits (122), Expect = 4e-06
Identities = 51/182 (28%), Positives = 80/182 (43%), Gaps = 41/182 (22%)
Query: 118 ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGV-MPQTREAIAHAKISGVP-LIVAI 175
++F+D PGH+ A GA V D +L++AA++ PQT E +A +I + +I+
Sbjct: 119 VSFVDCPGHDILMATMLNGAAVMDAALLLIAANESCPQPQTSEHLAAVEIMKLKHIIILQ 178
Query: 176 NKIDKLDINLDRIKQDLISEQVIPEEY-----------GGASPFISISAKTGVGINKLLE 224
NKI DL+ E ++Y +P I ISA+ I+ +LE
Sbjct: 179 NKI------------DLVKEAQAQDQYEEIRNFVKGTIADNAPIIPISAQLKYNIDVVLE 226
Query: 225 NISLQAEILELKAPV---TTPAKGVIIES--------RLDKGKGPVATVLIQSGTLRCSD 273
I Q I P T+P + ++I S ++ KG VA I G L+ D
Sbjct: 227 YICTQIPI-----PKRDLTSPPRMIVIRSFDVNKPGEDIENLKGGVAGGSILQGVLKVGD 281
Query: 274 IV 275
+
Sbjct: 282 EI 283
>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 = 47.8 bits (115), Expect = 5e-06
Identities = 27/87 (31%), Positives = 41/87 (47%), Gaps = 12/87 (13%)
Query: 141 DIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLDINLDRIKQDLISEQVIPE 200
D+++ VV +G+ P E + + S P+I+ +NKID + E+ E
Sbjct: 78 DVILFVVDGREGLTPADEEIAKYLRKSKKPVILVVNKIDNIK-----------EEEEAAE 126
Query: 201 EYG-GASPFISISAKTGVGINKLLENI 226
Y G I ISA+ G GI LL+ I
Sbjct: 127 FYSLGFGEPIPISAEHGRGIGDLLDAI 153
Score = 45.5 bits (109), Expect = 3e-05
Identities = 30/117 (25%), Positives = 42/117 (35%), Gaps = 22/117 (18%)
Query: 980 IEYNGTRINIIDTPGHADFGGE--------VERILSMVDNVLLLIDAVEGPMPQTRFVTR 1031
E+ G +IDT G E + D +L ++D EG P + +
Sbjct: 40 AEWGGREFILIDTGGIEPDDEGISKEIREQAEIAIEEADVILFVVDGREGLTPADEEIAK 99
Query: 1032 KALKLGFKPIVVVNKIDRSNARPEWVVDATFDL-FDKLCATEEQLDFPVIYTSALHG 1087
K I+VVNKID N + E + L F + I SA HG
Sbjct: 100 YLRKSKKPVILVVNKID--NIKEEEEAAEFYSLGFGE-----------PIPISAEHG 143
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 48.3 bits (116), Expect = 2e-05
Identities = 37/119 (31%), Positives = 57/119 (47%), Gaps = 17/119 (14%)
Query: 118 ITFLDTPG-HEAFTAM------RARGA-KVTDIVVLVVAADDGVMPQTREAIAHAKISGV 169
I F+DTPG H+ A+ AR A K D+++ VV AD+G P + K +
Sbjct: 56 IIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKKTKT 115
Query: 170 PLIVAINKIDKL--DINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
P+I+ +NKIDK+ L ++ L ++ + ISA G ++ LLE I
Sbjct: 116 PVILVVNKIDKVKPKTVLLKLIAFL-------KKLLPFKEIVPISALKGDNVDTLLEII 167
Score = 44.5 bits (106), Expect = 3e-04
Identities = 49/173 (28%), Positives = 67/173 (38%), Gaps = 36/173 (20%)
Query: 926 AIIAHVDHGKTTLIDHLLRQ--SGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYN 983
AII + GK+TL++ L+ Q S K Q RI RGI I
Sbjct: 10 AIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRI---------RGIVTTDNAQII--- 57
Query: 984 GTRINIIDTPG----HADFG----GEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALK 1035
+DTPG G L VD +L ++DA EG P F+ + K
Sbjct: 58 -----FVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKK 112
Query: 1036 LGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDF-PVIYTSALHG 1087
I+VVNKID+ V L + ++ L F ++ SAL G
Sbjct: 113 TKTPVILVVNKIDK--------VKPKTVLLKLIAFLKKLLPFKEIVPISALKG 157
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily of
the Ras GTPases. This family represents archaeal GTPase
typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 46.2 bits (110), Expect = 2e-05
Identities = 34/109 (31%), Positives = 52/109 (47%), Gaps = 20/109 (18%)
Query: 1002 VERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVNKIDRSNARPEWVVDAT 1061
V RI+ D VL ++DA + + ++R + R AL+LG K I+V+NK D P V++
Sbjct: 5 VRRIIKEADVVLEVVDARDPELTRSRKLERMALELGKKLIIVLNKADLV---PREVLEKW 61
Query: 1062 FDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQGNMIPLFEAILKY 1110
++F E PV+Y SA + R G I L I +
Sbjct: 62 KEVF-------ESEGLPVVYVSA---------RERLGTRI-LRRTIKEL 93
Score = 31.1 bits (71), Expect = 2.0
Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 12/91 (13%)
Query: 138 KVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKID--KLDINLDRIKQDLISE 195
K D+V+ VV A D + ++R+ A G LI+ +NK D ++ L++ K+ SE
Sbjct: 10 KEADVVLEVVDARDPELTRSRKLERMALELGKKLIIVLNKADLVPREV-LEKWKEVFESE 68
Query: 196 QVIPEEYGGASPFISISAKTGVGINKLLENI 226
+ P + +SA+ +G L I
Sbjct: 69 GL---------PVVYVSARERLGTRILRRTI 90
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 49.0 bits (117), Expect = 2e-05
Identities = 39/168 (23%), Positives = 78/168 (46%), Gaps = 19/168 (11%)
Query: 69 APIVTIMGHVDHGKTSLLDYI-RKTNVVFSEAGGITQHIGAYNVVTNHGSITFLDTPG-- 125
V ++G + GK+SLL+ + + V ++ G T+ V + F+DT G
Sbjct: 450 LRRVALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRDPVDEIVEIDGEDWLFIDTAGIK 509
Query: 126 --------HEAFTAMRARGA-KVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAIN 176
E ++++R + A + +++ + + A + Q + ++ A +G L++ N
Sbjct: 510 RRQHKLTGAEYYSSLRTQAAIERSELALFLFDASQPISEQDLKVMSMAVDAGRALVLVFN 569
Query: 177 KIDKLDINLDRIKQDLISEQVIPEEYGGA--SPFISISAKTGVGINKL 222
K D +D R Q L E++ E+ + +++SAKTG N+L
Sbjct: 570 KWDLMD-EFRR--QRL--ERLWKTEFDRVTWARRVNLSAKTGWHTNRL 612
Score = 45.9 bits (109), Expect = 2e-04
Identities = 66/258 (25%), Positives = 109/258 (42%), Gaps = 49/258 (18%)
Query: 20 TINQVLDQETAMI-LVEEMGHVAHASK-LNDPESFLLNEYNKNITAESLVRAP------- 70
++ LD +I LVE+ + + E + L+E ++++ S A
Sbjct: 217 DFDETLD---LLIGLVEDAIEEQEYDQYAANLEGYELDEGDEDLLEGSGFVAGDEKAGPK 273
Query: 71 ---IVTIMGHVDHGKTSLLDYI--RKTNVVFSEAGGITQHIGAYNVVTNHGSITFLDTPG 125
+V I+G + GK++L++ I R+ VV + G+T+ +Y+ +DT G
Sbjct: 274 AVGVVAIVGRPNVGKSTLVNRILGRREAVV-EDTPGVTRDRVSYDAEWAGTDFKLVDTGG 332
Query: 126 HE-------AFTAMRARGA-KVTDIVVLVVAADDGVMPQTREAIAHA-KISGVPLIVAIN 176
E + A +A+ A + D VV VV G + T E I + +G P+++A+N
Sbjct: 333 WEADVEGIDSAIASQAQIAVSLADAVVFVVDGQVG-LTSTDERIVRMLRRAGKPVVLAVN 391
Query: 177 KIDKLDINLDRIKQDLISEQVIPE--EYGGASPFISISAKTGVGINKLLENISLQAEILE 234
KID D SE E + G P+ ISA G G+ LL+ E L+
Sbjct: 392 KID-----------DQASEYDAAEFWKLGLGEPY-PISAMHGRGVGDLLD------EALD 433
Query: 235 LKAPVTTPAKGVIIESRL 252
V G + S L
Sbjct: 434 -SLKVAEKTSGFLTPSGL 450
Score = 35.9 bits (83), Expect = 0.20
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 10/77 (12%)
Query: 981 EYNGTRINIIDTPG--------HADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRK 1032
E+ GT ++DT G + + + +S+ D V+ ++D G T +
Sbjct: 319 EWAGTDFKLVDTGGWEADVEGIDSAIASQAQIAVSLADAVVFVVDGQVGLT-STDERIVR 377
Query: 1033 ALKLGFKPI-VVVNKID 1048
L+ KP+ + VNKID
Sbjct: 378 MLRRAGKPVVLAVNKID 394
>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 = 46.0 bits (110), Expect = 3e-05
Identities = 35/197 (17%), Positives = 66/197 (33%), Gaps = 38/197 (19%)
Query: 926 AIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGT 985
A++ GK+TL++ LL + E+ + + Y G
Sbjct: 4 AVVGEFSAGKSTLLNALLGE------------------EVLPTGVTPTTAVITVLRY-GL 44
Query: 986 R--INIIDTPG-------HADFGGEVERILSMVDNVLLLIDAVEGPMPQT--RFVTRKAL 1034
+ ++DTPG H + E L D V+ ++ A + P+ ++ F+
Sbjct: 45 LKGVVLVDTPGLNSTIEHHTE---ITESFLPRADAVIFVLSA-DQPLTESEREFLKEILK 100
Query: 1035 KLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTS---ALHGYANE 1091
G K V+NKID + E + + + + S AL
Sbjct: 101 WSGKKIFFVLNKIDLL-SEEELEEVLEYSREELGVLELGGGEPRIFPVSAKEALEARLQG 159
Query: 1092 NSKARQGNMIPLFEAIL 1108
+ + + + E L
Sbjct: 160 DEELLEQSGFEELEEHL 176
Score = 34.4 bits (80), Expect = 0.20
Identities = 42/184 (22%), Positives = 72/184 (39%), Gaps = 32/184 (17%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVT------NHGSITFLDTPG 125
+ ++G GK++LL+ + V+ + T V+T G + +DTPG
Sbjct: 3 LAVVGEFSAGKSTLLNALLGEEVLPTGVTPTT------AVITVLRYGLLKG-VVLVDTPG 55
Query: 126 HEAFTAMRARGAKVT-------DIVVLVVAADDGVMPQTREAIA----HAKISGVPLIVA 174
+ ++T D V+ V++AD P T K SG +
Sbjct: 56 ---LNSTIEHHTEITESFLPRADAVIFVLSADQ---PLTESEREFLKEILKWSGKKIFFV 109
Query: 175 INKIDKL-DINLDRIKQDLISEQVIPEEYGGASPFISISAKTG-VGINKLLENISLQAEI 232
+NKID L + L+ + + E + E GG +SAK + E + Q+
Sbjct: 110 LNKIDLLSEEELEEVLEYSREELGVLELGGGEPRIFPVSAKEALEARLQGDEELLEQSGF 169
Query: 233 LELK 236
EL+
Sbjct: 170 EELE 173
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 48.2 bits (116), Expect = 3e-05
Identities = 30/86 (34%), Positives = 44/86 (51%), Gaps = 16/86 (18%)
Query: 141 DIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLDINLDRIKQDLISEQVIPE 200
D+V+LV+ A + + + E + ++ P+IV +NK D L E + E
Sbjct: 296 DLVLLVLDASEPLTEEDDEILE--ELKDKPVIVVLNKAD------------LTGEIDLEE 341
Query: 201 EYGGASPFISISAKTGVGINKLLENI 226
E G P I ISAKTG GI++L E I
Sbjct: 342 ENG--KPVIRISAKTGEGIDELREAI 365
Score = 38.9 bits (92), Expect = 0.022
Identities = 31/117 (26%), Positives = 45/117 (38%), Gaps = 26/117 (22%)
Query: 979 SIEYNGTRINIIDTPGHADFGGEVERI--------LSMVDNVLLLIDAVEGPMPQTRFVT 1030
I +G + +IDT G + EVE+I + D VLL++DA E + +
Sbjct: 257 HINLDGIPLRLIDTAGIRETDDEVEKIGIERSREAIEEADLVLLVLDASEPLTEEDDEIL 316
Query: 1031 RKALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHG 1087
+ IVV+NK D + EE+ PVI SA G
Sbjct: 317 EELKDKPV--IVVLNKADLTGEIDL----------------EEENGKPVIRISAKTG 355
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 46.5 bits (110), Expect = 3e-05
Identities = 33/174 (18%), Positives = 63/174 (36%), Gaps = 18/174 (10%)
Query: 81 GKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHGSITF--LDTPGHEAFTAMRARGAK 138
GKT+LL+ + I A + +I DT G E + ++R +
Sbjct: 17 GKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYR 76
Query: 139 VTDIVVLVVAAD-----DGVMPQTREAIAHAKISGVPLIVAINKID---------KLDIN 184
+ +++V + D + + E + VP+++ NKID ++
Sbjct: 77 GANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFDEQSSSEEILNQ 136
Query: 185 LDRIKQDLISEQVIPEEYGGASPFISISAK--TGVGINKLLENISLQAEILELK 236
L+R L+ + SAK TG +N+L + + + K
Sbjct: 137 LNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKELLRKLLEEIEK 190
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 47.6 bits (114), Expect = 3e-05
Identities = 45/195 (23%), Positives = 86/195 (44%), Gaps = 36/195 (18%)
Query: 67 VRAPIVTIMGHVDHGKTSLLDYIRKTNV-----VFSEAGGITQHIGAYNVVTNHGSITFL 121
P+V ++G+ + GK++L + + +V +F+ T+ I + + +
Sbjct: 190 SGIPLVALVGYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRI----ELGDGRKVLLT 245
Query: 122 DTPG------HEAFTAMRARGAKVT--DIVVLVV-AADDGV---MPQTREAIAHAKISGV 169
DT G H A ++ +V D+++ VV A+D + + + +A +
Sbjct: 246 DTVGFIRDLPHPLVEAFKSTLEEVKEADLLLHVVDASDPEILEKLEAVEDVLAEIGADEI 305
Query: 170 PLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISLQ 229
P+I+ +NKID L+ E+++ E G+ + ISAKTG G++ L E I
Sbjct: 306 PIILVLNKIDLLE-----------DEEILAELERGSPNPVFISAKTGEGLDLLRERIIEL 354
Query: 230 A----EILELKAPVT 240
+ L+ P T
Sbjct: 355 LSGLRTEVTLELPYT 369
>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 = 46.3 bits (111), Expect = 3e-05
Identities = 26/90 (28%), Positives = 41/90 (45%), Gaps = 15/90 (16%)
Query: 141 DIVVLVV-AADDGV---MPQTREAIAHAKISGVPLIVAINKIDKLDINLDRIKQDLISEQ 196
D+++ VV A+D + E + +P+I+ +NKID LD E+
Sbjct: 122 DLLLHVVDASDPDREEQIETVEEVLKELGADDIPIILVLNKIDLLD-----------DEE 170
Query: 197 VIPEEYGGASPFISISAKTGVGINKLLENI 226
+ G + ISAKTG G++ L E I
Sbjct: 171 LEERLRAGRPDAVFISAKTGEGLDLLKEAI 200
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 47.7 bits (115), Expect = 4e-05
Identities = 58/205 (28%), Positives = 85/205 (41%), Gaps = 55/205 (26%)
Query: 923 IKSAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEY 982
IK AII + GK++LI+ LL + R++ S+ G T S + E
Sbjct: 174 IKIAIIGRPNVGKSSLINALLGEE-----------RVIVSDI----AGTTRDSIDTPFER 218
Query: 983 NGTRINIIDTPG-------HADFGGEVE--------RILSMVDNVLLLIDAVEGPMPQTR 1027
+G + +IDT G VE + + D VLL+IDA EG Q
Sbjct: 219 DGQKYTLIDTAGIRRKGKVTEG----VEKYSVIRTLKAIERADVVLLVIDATEGITEQDL 274
Query: 1028 FVTRKALKLGFKPIV-VVNKIDRSNARPEWVVDATFDLFDKLCATE-EQLDF-PVIYTSA 1084
+ AL+ G + +V VVNK D V + T + F K LD+ P+++ SA
Sbjct: 275 RIAGLALEAG-RALVIVVNKWDL-------VDEKTMEEFKKELRRRLPFLDYAPIVFISA 326
Query: 1085 LHGYANENSKARQGNMIPLFEAILK 1109
L G + L EAI +
Sbjct: 327 LTGQ----------GVDKLLEAIDE 341
Score = 47.4 bits (114), Expect = 5e-05
Identities = 49/204 (24%), Positives = 85/204 (41%), Gaps = 51/204 (25%)
Query: 53 LLNEYNKNITAESLVRAPIVTIMGHVDHGKTSLLDYIRKTN--VVFSEAGGITQHIGAYN 110
+L E + + + I+G + GK+SL++ + +V AG T + +
Sbjct: 157 ILEELPEEEEEDEEDEPIKIAIIGRPNVGKSSLINALLGEERVIVSDIAG-TT--RDSID 213
Query: 111 VVTNHG--SITFLDTPGHEAFTAMRARGAKVT------------------DIVVLVVAAD 150
T +DT G +R +G KVT D+V+LV+ A
Sbjct: 214 TPFERDGQKYTLIDTAG------IRRKG-KVTEGVEKYSVIRTLKAIERADVVLLVIDAT 266
Query: 151 DGVMPQTREAIAHAKI------SGVPLIVAINKIDKLDIN-LDRIKQDLISE-QVIPEEY 202
+G+ Q +I +G L++ +NK D +D ++ K++L +
Sbjct: 267 EGITEQ------DLRIAGLALEAGRALVIVVNKWDLVDEKTMEEFKKELRRRLPFLDY-- 318
Query: 203 GGASPFISISAKTGVGINKLLENI 226
+P + ISA TG G++KLLE I
Sbjct: 319 ---APIVFISALTGQGVDKLLEAI 339
Score = 43.5 bits (104), Expect = 7e-04
Identities = 38/159 (23%), Positives = 62/159 (38%), Gaps = 34/159 (21%)
Query: 980 IEYNGTRINIIDTPG----HADFGGEV----ERILSMVDNVLLLIDAVEGPMPQTRFVTR 1031
E+ G +IDT G F ++ E + D +L ++D G P + +
Sbjct: 44 AEWLGREFILIDTGGIEPDDDGFEKQIREQAELAIEEADVILFVVDGRAGLTPADEEIAK 103
Query: 1032 KALKLGFKP-IVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYAN 1090
K KP I+VVNK+D + ++ F L E SA HG
Sbjct: 104 ILRKSN-KPVILVVNKVDGPDEE-----ADAYE-FYSLGLGE------PYPISAEHGR-- 148
Query: 1091 ENSKARQGNMIPLFEAILKYVPVHK--DNSNNPLQLQII 1127
+ L +AIL+ +P + D + P+++ II
Sbjct: 149 --------GIGDLLDAILEELPEEEEEDEEDEPIKIAII 179
Score = 42.3 bits (101), Expect = 0.002
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 12/85 (14%)
Query: 141 DIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLDINLDRIKQDLISEQVIPE 200
D+++ VV G+ P E + S P+I+ +NK+D D E E
Sbjct: 82 DVILFVVDGRAGLTPADEEIAKILRKSNKPVILVVNKVDGPDE-----------EADAYE 130
Query: 201 EYG-GASPFISISAKTGVGINKLLE 224
Y G ISA+ G GI LL+
Sbjct: 131 FYSLGLGEPYPISAEHGRGIGDLLD 155
>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 = 45.2 bits (108), Expect = 4e-05
Identities = 28/87 (32%), Positives = 40/87 (45%), Gaps = 15/87 (17%)
Query: 141 DIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLDINLDRIKQDLISEQVIPE 200
D+V+LVV D + + P+IV +NK D L+S+
Sbjct: 84 DLVLLVV--DASEGLDEEDLEILELPAKKPVIVVLNKSD------------LLSDAEGIS 129
Query: 201 EYGGASPFISISAKTGVGINKLLENIS 227
E G P I+ISAKTG GI++L E +
Sbjct: 130 ELNG-KPIIAISAKTGEGIDELKEALL 155
Score = 32.5 bits (75), Expect = 0.92
Identities = 31/118 (26%), Positives = 43/118 (36%), Gaps = 27/118 (22%)
Query: 979 SIEYNGTRINIIDTPGHADFGGEVERI-----LSMVDN---VLLLIDAVEGPMPQTRFVT 1030
I+ G + +IDT G + E+E+I ++ VLL++DA EG
Sbjct: 45 EIDLGGIPVRLIDTAGLRETEDEIEKIGIERAREAIEEADLVLLVVDASEG---LDEEDL 101
Query: 1031 RKALKLGFKP-IVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHG 1087
KP IVV+NK DL E P+I SA G
Sbjct: 102 EILELPAKKPVIVVLNKS---------------DLLSDAEGISELNGKPIIAISAKTG 144
>gnl|CDD|239682 cd03711, Tet_C, Tet_C: C-terminus of ribosomal protection proteins
Tet(M) and Tet(O). This domain has homology to the C
terminal domains of the elongation factors EF-G and EF-2.
Tet(M) and Tet(O) catalyze the release of tetracycline
(Tc) from the ribosome in a GTP-dependent manner thereby
mediating Tc resistance. Tcs are broad-spectrum
antibiotics. Typical Tcs bind to the ribosome and
inhibit the elongation phase of protein synthesis, by
inhibiting the occupation of site A by aminoacyl-tRNA.
Length = 78
Score = 41.8 bits (99), Expect = 9e-05
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 9/81 (11%)
Query: 1317 EPYENLFVDIE-EINQ---GIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQN 1372
EPY E E+ Q G M L G ++ +I + V LE IP +Q+
Sbjct: 1 EPYL----RFELEVPQDALGRAMSDLAKMGATFEDPQIKG-DEVTLEGTIPVATSQDYQS 55
Query: 1373 EFITLTRGTGLISHVFEEYAP 1393
E + T G G++ F+ Y P
Sbjct: 56 ELPSYTHGEGVLETEFKGYRP 76
>gnl|CDD|206728 cd04165, GTPBP1_like, GTP binding protein 1 (GTPBP1)-like family
includes GTPBP2. Mammalian GTP binding protein 1
(GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1
are GTPases whose specific functions remain unknown. In
mouse, GTPBP1 is expressed in macrophages, in smooth
muscle cells of various tissues and in some neurons of
the cerebral cortex; GTPBP2 tissue distribution appears
to overlap that of GTPBP1. In human leukemia and
macrophage cell lines, expression of both GTPBP1 and
GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The
chromosomal location of both genes has been identified
in humans, with GTPBP1 located in chromosome 22q12-13.1
and GTPBP2 located in chromosome 6p21-12. Human
glioblastoma multiforme (GBM), a highly-malignant
astrocytic glioma and the most common cancer in the
central nervous system, has been linked to chromosomal
deletions and a translocation on chromosome 6. The GBM
translocation results in a fusion of GTPBP2 and PTPRZ1,
a protein involved in oligodendrocyte differentiation,
recovery, and survival. This fusion product may
contribute to the onset of GBM.
Length = 224
Score = 44.6 bits (106), Expect = 2e-04
Identities = 40/159 (25%), Positives = 60/159 (37%), Gaps = 52/159 (32%)
Query: 72 VTIMGHVDHGKTSL--------LDYIR-----------------KTNVV------FSEAG 100
V ++G+VD GK++L LD R +T+ V F G
Sbjct: 2 VAVVGNVDAGKSTLLGVLTQGELDNGRGKARLNLFRHKHEVESGRTSSVSNDILGFDSDG 61
Query: 101 GITQHIGAYNVVTNHGS-------------ITFLDTPGHEAF--TAMRARGAKVTDIVVL 145
+ N NH +TF+D GHE + T + D +L
Sbjct: 62 EVV------NYPDNHLGELDVEICEKSSKVVTFIDLAGHERYLKTTVFGMTGYAPDYAML 115
Query: 146 VVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLDIN 184
VV A+ G++ T+E + A VP+ V + KID N
Sbjct: 116 VVGANAGIIGMTKEHLGLALALKVPVFVVVTKIDMTPAN 154
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 45.6 bits (109), Expect = 2e-04
Identities = 28/97 (28%), Positives = 43/97 (44%), Gaps = 15/97 (15%)
Query: 132 MRARGA-KVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLDINLDRIKQ 190
RA+ A + D+V+ V+ A + + I P+IV +NK D
Sbjct: 288 ERAKKAIEEADLVLFVLDASQPLDKEDLALIELLP-KKKPIIVVLNKAD----------- 335
Query: 191 DLISEQVIPE-EYGGASPFISISAKTGVGINKLLENI 226
L+S+ + + ISISAKTG G++ L E I
Sbjct: 336 -LVSKIELESEKLANGDAIISISAKTGEGLDALREAI 371
Score = 36.8 bits (86), Expect = 0.098
Identities = 32/152 (21%), Positives = 50/152 (32%), Gaps = 32/152 (21%)
Query: 979 SIEYNGTRINIIDTPGHADFGGEVERI--------LSMVDNVLLLIDAVEGPMPQTRFVT 1030
I NG + ++DT G + VERI + D VL ++DA + + +
Sbjct: 259 DINLNGIPVRLVDTAGIRETDDVVERIGIERAKKAIEEADLVLFVLDASQPLDKEDLALI 318
Query: 1031 RKALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYAN 1090
L IVV+NK D + +L + + +I SA G
Sbjct: 319 EL-LPKKKPIIVVLNKADLVSK-------------IELESEKLANGDAIISISAKTGEGL 364
Query: 1091 ENSKARQGNMIPLFEAILKYVPVHKDNSNNPL 1122
+ L EAI + N
Sbjct: 365 DA----------LREAIKQLFGKGLGNQEGLF 386
>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 = 42.5 bits (101), Expect = 3e-04
Identities = 41/162 (25%), Positives = 71/162 (43%), Gaps = 20/162 (12%)
Query: 81 GKTSLLDYI--RKTNVVFSEAGGITQHIGAYNVVTNHGSITFLDTPG---HEAFTAMRAR 135
GK+SL++ + RK S+ G TQ I +NV +D PG + +R +
Sbjct: 11 GKSSLINALTNRKKLARTSKTPGRTQLINFFNVG---DKFRLVDLPGYGYAKVSKEVREK 67
Query: 136 GAKVTD----------IVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLDINL 185
K+ + VVL++ A G P E + + G+P ++ + K DKL +
Sbjct: 68 WGKLIEEYLENRENLKGVVLLIDARHGPTPIDLEMLEFLEELGIPFLIVLTKADKLKKS- 126
Query: 186 DRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENIS 227
+ K ++ + + P I S+K G GI++L I+
Sbjct: 127 ELAKVLKKIKEEL-NLFNILPPVILFSSKKGTGIDELRALIA 167
Score = 35.2 bits (82), Expect = 0.11
Identities = 36/172 (20%), Positives = 62/172 (36%), Gaps = 42/172 (24%)
Query: 934 GKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGTRINIIDTP 993
GK++LI+ L + AR S + + I F+ G + ++D P
Sbjct: 11 GKSSLINALTNRKK--------LART--SKTPGRTQLINFFN-------VGDKFRLVDLP 53
Query: 994 GHADFGG------EVERILSMVDN----------VLLLIDAVEGPMPQTRFVTRKALKLG 1037
G +G E+ +++ V+LLIDA GP P + +LG
Sbjct: 54 G---YGYAKVSKEVREKWGKLIEEYLENRENLKGVVLLIDARHGPTPIDLEMLEFLEELG 110
Query: 1038 FKPIVVVNKIDRSNARP-EWVVDATFDLFDKLCATEEQLDFPVIYTSALHGY 1088
++V+ K D+ V+ + + PVI S+ G
Sbjct: 111 IPFLIVLTKADKLKKSELAKVLKKIKEELNLFNI-----LPPVILFSSKKGT 157
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate cancer
cells, RalB promotes migration while RalA inhibits it. A
Ral-specific set of GEFs has been identified that are
activated by Ras binding. This RalGEF activity is
enhanced by Ras binding to another of its target
proteins, phosphatidylinositol 3-kinase (PI3K). Ral
effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and
the exocyst (Sec6/8) complex, a heterooctomeric protein
complex that is involved in tethering vesicles to
specific sites on the plasma membrane prior to
exocytosis. In rat kidney cells, RalB is required for
functional assembly of the exocyst and for localizing
the exocyst to the leading edge of migrating cells. In
human cancer cells, RalA is required to support
anchorage-independent proliferation and RalB is required
to suppress apoptosis. RalA has been shown to localize
to the plasma membrane while RalB is localized to the
intracellular vesicles. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 42.4 bits (100), Expect = 4e-04
Identities = 29/109 (26%), Positives = 51/109 (46%), Gaps = 11/109 (10%)
Query: 118 ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADD----GVMPQTREAIAHAKIS-GVPLI 172
+ LDT G E + A+R + + +LV + D + + RE I K VPL+
Sbjct: 50 LNILDTAGQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLL 109
Query: 173 VAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINK 221
+ NK D L+ D+ + + + E++G ++ SAKT ++K
Sbjct: 110 LVGNKCD-LE---DKRQVSVEEAANLAEQWG--VNYVETSAKTRANVDK 152
>gnl|CDD|239661 cd03690, Tet_II, Tet_II: This subfamily represents domain II of
ribosomal protection proteins Tet(M) and Tet(O). This
domain has homology to domain II of the elongation
factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the
release of tetracycline (Tc) from the ribosome in a
GTP-dependent manner thereby mediating Tc resistance.
Tcs are broad-spectrum antibiotics. Typical Tcs bind to
the ribosome and inhibit the elongation phase of protein
synthesis, by inhibiting the occupation of site A by
aminoacyl-tRNA.
Length = 85
Score = 40.3 bits (95), Expect = 4e-04
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 5/65 (7%)
Query: 1142 RILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLITGIEEIC 1201
R+ SG ++ L+D V +N + K KI ++RVF + V + +GDI ++TG++ +
Sbjct: 24 RLYSGTLR-LRDSVRVNREE----KIKITELRVFNNGEVVTADTVTAGDIAILTGLKGLR 78
Query: 1202 IGSTI 1206
+G +
Sbjct: 79 VGDVL 83
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 41.0 bits (97), Expect = 0.001
Identities = 44/169 (26%), Positives = 70/169 (41%), Gaps = 36/169 (21%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHGSITF----LDTPGHE 127
+ ++G GK++L IR + F E T +Y T+ LDT G E
Sbjct: 2 LVVLGAGGVGKSALT--IRFVSGEFVEEYDPTIE-DSYRKQIVVDGETYTLDILDTAGQE 58
Query: 128 AFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIA--HAKISG------VPLIVAINKID 179
F+AMR + + D +LV + ++ E I +I VP+++ NK
Sbjct: 59 EFSAMRDQYIRNGDGFILVYSITS---RESFEEIKNIREQILRVKDKEDVPIVLVGNKC- 114
Query: 180 KLDINLDRIKQDLISEQVIPEEYGGA------SPFISISAKTGVGINKL 222
DL +E+ + E G A PF+ SAKT + I++L
Sbjct: 115 -----------DLENERQVSTEEGEALAEEWGCPFLETSAKTNINIDEL 152
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 43.4 bits (103), Expect = 0.001
Identities = 49/198 (24%), Positives = 73/198 (36%), Gaps = 52/198 (26%)
Query: 81 GKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVT----------NHGSITFLDTPGHEAFT 130
GKT+L F+ G Q +G + VT I +D PG + T
Sbjct: 15 GKTTL----------FNALTGANQKVGNWPGVTVEKKEGKLKYKGHEIEIVDLPGTYSLT 64
Query: 131 AMRARGAKVT---------DIVVLVVAAD--DGVMP---QTREAIAHAKISGVPLIVAIN 176
A + KV D++V VV A + + Q E G+P+I+A+N
Sbjct: 65 A-YSEDEKVARDFLLEGKPDLIVNVVDATNLERNLYLTLQLLEL-------GIPMILALN 116
Query: 177 KIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISLQAEILELK 236
ID+ RI + +S+ G P + AK G G+ +L I AE K
Sbjct: 117 MIDEAKKRGIRIDIEKLSK-----LLG--VPVVPTVAKRGEGLEELKRAIIELAES---K 166
Query: 237 APVTTPAKGVIIESRLDK 254
G IE + +
Sbjct: 167 TTPREVDYGEEIEEEIKE 184
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 41.4 bits (98), Expect = 0.001
Identities = 40/165 (24%), Positives = 66/165 (40%), Gaps = 27/165 (16%)
Query: 81 GKTSLLDYI--RKTNVVFSEAGGITQHIGAYNVVTNHGSITFLDTPGH----------EA 128
GK+SL++ + +K S+ G TQ I + V + +D PG+ E
Sbjct: 36 GKSSLINALTNQKNLARTSKTPGRTQLINFFEVD---DELRLVDLPGYGYAKVPKEVKEK 92
Query: 129 FTAM-------RARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKL 181
+ + RA VVL++ A RE I G+P+IV + K DKL
Sbjct: 93 WKKLIEEYLEKRAN----LKGVVLLIDARHPPKDLDREMIEFLLELGIPVIVVLTKADKL 148
Query: 182 DINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
+ +R KQ + + + + S+ GI++L I
Sbjct: 149 KKS-ERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKGIDELKAKI 192
>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 = 40.5 bits (96), Expect = 0.002
Identities = 40/170 (23%), Positives = 64/170 (37%), Gaps = 46/170 (27%)
Query: 81 GKTSLLDYIRKTNVVFSEAGGITQHIGA----YNVVTNHGSITFL--DTPGHEAFTAMRA 134
GKTSLL +R + FSE T IG + + + DT G E F ++ +
Sbjct: 12 GKTSLL--LRFVDNKFSENYKST--IGVDFKSKTIEVDGKKVKLQIWDTAGQERFRSITS 67
Query: 135 ---RGAKVTDIVVLVVAADDGVMPQT--------REAIAHAKISGVPLIVAINKIDKLDI 183
RGA +LV + ++ E +A +P+I+ NK D
Sbjct: 68 SYYRGA---HGAILVYDVTN---RESFENLDKWLNELKEYAP-PNIPIILVGNKSD---- 116
Query: 184 NLDRIKQDLISEQVIPEEYG------GASPFISISAKTGVGINKLLENIS 227
L E+ + E F SAKTG +++ E+++
Sbjct: 117 --------LEDERQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLA 158
>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 = 40.1 bits (95), Expect = 0.002
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 17/69 (24%)
Query: 168 GVPLIVAINKID-----KLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKL 222
G+P++VA+N ID + I+LD++ + L P + SA+ G GI++L
Sbjct: 102 GLPVVVALNMIDEAEKRGIKIDLDKLSELL------------GVPVVPTSARKGEGIDEL 149
Query: 223 LENISLQAE 231
L+ I+ AE
Sbjct: 150 LDAIAKLAE 158
Score = 34.7 bits (81), Expect = 0.16
Identities = 39/139 (28%), Positives = 54/139 (38%), Gaps = 45/139 (32%)
Query: 970 GITIFSKNCSIEYNGTRINIIDTPG----HA---------DF--GGEVERILSMVD---- 1010
G+T+ K + G I I+D PG DF G E + I+++VD
Sbjct: 29 GVTVEKKEGEFKLGGKEIEIVDLPGTYSLTPYSEDEKVARDFLLGEEPDLIVNVVDATNL 88
Query: 1011 --NVLLLIDAVEGPMPQTRFVTRKALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKL 1068
N+ L + +E LG +V +N ID + R DL DKL
Sbjct: 89 ERNLYLTLQLLE---------------LGLPVVVALNMIDEAEKR-----GIKIDL-DKL 127
Query: 1069 CATEEQLDFPVIYTSALHG 1087
E L PV+ TSA G
Sbjct: 128 ---SELLGVPVVPTSARKG 143
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 40.6 bits (95), Expect = 0.002
Identities = 39/121 (32%), Positives = 50/121 (41%), Gaps = 16/121 (13%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAGGIT---QHIGAYNVVTNHGSITFLDTPGHEA 128
+ MG GKT+L+ R F T H Y V +I LDT G +
Sbjct: 2 LVFMGAAGVGKTALIQ--RFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYS 59
Query: 129 FTAMRARGAKVTDIVVLVVAADDGVMPQT-------REAIAHAK-ISGVPLIVAINKIDK 180
F AMR + D LV + DD P++ RE I K VP++V NKID
Sbjct: 60 FPAMRKLSIQNGDAFALVYSVDD---PESFEEVKRLREEILEVKEDKFVPIVVVGNKIDS 116
Query: 181 L 181
L
Sbjct: 117 L 117
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 41.9 bits (99), Expect = 0.002
Identities = 43/170 (25%), Positives = 79/170 (46%), Gaps = 29/170 (17%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTN-VVFSEAGGITQHIGAYNVVTNHGSIT--FLDTPG--- 125
V ++G + GK+SLL+ + V + G T + + + G T F+DT G
Sbjct: 214 VALVGKPNVGKSSLLNKLAGEERSVVDDVAGTT--VDPVDSLIELGGKTWRFVDTAGLRR 271
Query: 126 -------HEAFTAMRARGA-KVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINK 177
HE + ++R A + ++ V+++ A + + Q + ++ +G L++A NK
Sbjct: 272 RVKQASGHEYYASLRTHAAIEAAEVAVVLIDASEPISEQDQRVLSMVIEAGRALVLAFNK 331
Query: 178 IDKLD----INLDR-IKQDLISEQVIPEEYGGASPFISISAKTGVGINKL 222
D +D L+R I ++L P ++ISAKTG ++KL
Sbjct: 332 WDLVDEDRRYYLEREIDRELAQVPWAPR--------VNISAKTGRAVDKL 373
Score = 41.1 bits (97), Expect = 0.004
Identities = 43/128 (33%), Positives = 65/128 (50%), Gaps = 13/128 (10%)
Query: 63 AESLVRAPIVTIMGHVDHGKTSLLDYI--RKTNVVFSEAGGITQHIGAYNVVTNHGSITF 120
A P+V ++G + GK++L++ I R+ VV + G+T+ +Y+ N T
Sbjct: 32 AAEGGPLPVVAVVGRPNVGKSTLVNRILGRREAVV-EDVPGVTRDRVSYDAEWNGRRFTV 90
Query: 121 LDTPGHE-------AFTAMRARGAKVT-DIVVLVVAADDGVMPQTREAIAHA-KISGVPL 171
+DT G E A A +A A T D V+ VV A G T EA+A + SG P+
Sbjct: 91 VDTGGWEPDAKGLQASVAEQAEVAMRTADAVLFVVDATVGAT-ATDEAVARVLRRSGKPV 149
Query: 172 IVAINKID 179
I+A NK+D
Sbjct: 150 ILAANKVD 157
Score = 35.3 bits (82), Expect = 0.24
Identities = 37/116 (31%), Positives = 51/116 (43%), Gaps = 22/116 (18%)
Query: 981 EYNGTRINIIDTPG--------HADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRK 1032
E+NG R ++DT G A + E + D VL ++DA G V R
Sbjct: 82 EWNGRRFTVVDTGGWEPDAKGLQASVAEQAEVAMRTADAVLFVVDATVGATATDEAVARV 141
Query: 1033 ALKLGFKPIVVV-NKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHG 1087
+ G KP+++ NK+D + R E DA L+ L E PV SALHG
Sbjct: 142 LRRSG-KPVILAANKVD--DERGE--ADAA-ALW-SLGLGEP---HPV---SALHG 184
>gnl|CDD|239757 cd04090, eEF2_II_snRNP, Loc2 eEF2_C_snRNP, cd01514/C terminal
domain:eEF2_C_snRNP: This family includes C-terminal
portion of the spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. This domain is homologous to
domain II of the eukaryotic translational elongation
factor EF-2. Yeast Snu114p is essential for cell
viability and for splicing in vivo. U5-116 kD binds GTP.
Experiments suggest that GTP binding and probably GTP
hydrolysis is important for the function of the U5-116
kD/Snu114p. In complex with GTP, EF-2 promotes the
translocation step of translation. During translocation
the peptidyl-tRNA is moved from the A site to the P site,
the uncharged tRNA from the P site to the E-site and, the
mRNA is shifted one codon relative to the ribosome.
Length = 94
Score = 38.3 bits (90), Expect = 0.003
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 1141 GRILSGRIKSLQDVVIMN---GPDDKPN--KAKINQIRVFKGLDRVLVNEALSGDIVLIT 1195
GRI SG IK Q V ++ DD+ + I ++ + G ++ VNEA +G+ VLI
Sbjct: 21 GRIYSGTIKKGQKVKVLGENYSLDDEEDMTICTIGRLWILGGRYKIEVNEAPAGNWVLIK 80
Query: 1196 GIEEICI-GSTICD 1208
GI+ + +TI
Sbjct: 81 GIDSSIVKTATITS 94
>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 = 40.1 bits (95), Expect = 0.004
Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 18/93 (19%)
Query: 141 DIVVLVVAADDGVMPQTREA-----IAHAKISGVPLIVAINKIDKLDINLDRIKQDLISE 195
D V++V + + P + A+ SG+ ++ +NK D +D D ++L+
Sbjct: 4 DQVLIVFSLKE---PFFNLRLLDRYLVAAEASGIEPVIVLNKADLVD---DEELEELL-- 55
Query: 196 QVIPEEYGGAS-PFISISAKTGVGINKLLENIS 227
E Y P +++SAKTG G+++L E +
Sbjct: 56 ----EIYEKLGYPVLAVSAKTGEGLDELRELLK 84
Score = 38.5 bits (91), Expect = 0.011
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 14/82 (17%)
Query: 1009 VDNVLLLIDAVEGPMPQTRFVTR---KALKLGFKPIVVVNKIDRSNARPEWVVDATFDLF 1065
VD VL++ +++ P R + R A G +P++V+NK D +VD +
Sbjct: 3 VDQVLIVF-SLKEPFFNLRLLDRYLVAAEASGIEPVIVLNKAD--------LVDD--EEL 51
Query: 1066 DKLCATEEQLDFPVIYTSALHG 1087
++L E+L +PV+ SA G
Sbjct: 52 EELLEIYEKLGYPVLAVSAKTG 73
>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 = 38.7 bits (91), Expect = 0.006
Identities = 34/158 (21%), Positives = 62/158 (39%), Gaps = 29/158 (18%)
Query: 81 GKTSLLDYIRKTNVVFSEAGGITQHIGAYNV---VTNHGSITFLDTPGHEAFTAMRARGA 137
GKT++L ++ VV IG +NV + T D G + +
Sbjct: 11 GKTTILYKLKLGEVV-----TTIPTIG-FNVETVEYKNVKFTVWDVGGQDKIRPLWKHYY 64
Query: 138 KVTDIVVLVV-AADDGVMPQTRE----AIAHAKISGVPLIVAINKIDKLDINLDRIKQDL 192
+ TD ++ VV ++D + + + + ++ G PL++ NK D
Sbjct: 65 ENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDLP---------GA 115
Query: 193 ISEQVIPEEYGGASP------FISISAKTGVGINKLLE 224
++E + E G S SA TG G+++ L+
Sbjct: 116 LTESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGLD 153
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 39.0 bits (91), Expect = 0.008
Identities = 34/162 (20%), Positives = 57/162 (35%), Gaps = 21/162 (12%)
Query: 70 PIVTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHGSITFLDTPGHEAF 129
P+V R T V G+ + + G + TPG E F
Sbjct: 34 PLVITEADASSVSGKG---KRPTTVAMD--------FGSIELDEDTG-VHLFGTPGQERF 81
Query: 130 TAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKIS-GVPLIVAINKIDKLDI-NLDR 187
M ++ +++V + + E I +P++VAINK D D ++
Sbjct: 82 KFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVVAINKQDLFDALPPEK 141
Query: 188 IKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISLQ 229
I++ L E + I I A G G L+ + L+
Sbjct: 142 IREALKLELLSVPV-------IEIDATEGEGARDQLDVLLLK 176
Score = 36.3 bits (84), Expect = 0.054
Identities = 41/180 (22%), Positives = 62/180 (34%), Gaps = 21/180 (11%)
Query: 921 ILIKSAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSI 980
I K +I V GKTT + L + I S + +R T+ SI
Sbjct: 9 IETKIVVIGPVGAGKTTFVRALSDKPLV------ITEADASSVSGKGKRPTTVAMDFGSI 62
Query: 981 EYNG-TRINIIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLGFK 1039
E + T +++ TPG F E + ++L+D+ +
Sbjct: 63 ELDEDTGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPI 122
Query: 1040 PIVV-VNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSALHGYANENSKARQG 1098
P+VV +NK D +A P + + E L PVI A E AR
Sbjct: 123 PVVVAINKQDLFDALP---PEKIREALKL-----ELLSVPVIEID-----ATEGEGARDQ 169
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 40.5 bits (95), Expect = 0.008
Identities = 42/169 (24%), Positives = 70/169 (41%), Gaps = 27/169 (15%)
Query: 81 GKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHGSITFLDTPGHEAFTAMR-----AR 135
GK++L + + N G+T + I +D PG + T AR
Sbjct: 6 GKSTLFNALTGANQTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFSLEEEVAR 65
Query: 136 GAKVT---DIVVLVVAAD--DGVMPQTREAIAHAKISGVPLIVAINKID---KLDINLDR 187
+ D+VV VV A + + T + + G+P+I+A+N +D K I R
Sbjct: 66 DYLLNEKPDLVVNVVDASNLERNLYLTLQLLE----LGIPMILALNLVDEAEKKGI---R 118
Query: 188 IKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISLQAEILELK 236
I ++ + E++ P + SA G GI +L + I + ELK
Sbjct: 119 IDEEKLEERL-------GVPVVPTSATEGRGIERLKDAIRKAIGLKELK 160
Score = 35.9 bits (83), Expect = 0.18
Identities = 43/171 (25%), Positives = 73/171 (42%), Gaps = 25/171 (14%)
Query: 970 GITIFSKNCSIEYNGTRINIIDTPGHADFGG-----EVER---ILSMVDNVLLLIDAVEG 1021
G+T+ K + + G I I+D PG EV R + D V+ ++DA
Sbjct: 26 GVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFSLEEEVARDYLLNEKPDLVVNVVDASN- 84
Query: 1022 PMPQTRFVTRKALKLGFKPIVVVNKIDRSNARPEWV-VDATFDLFDKLCATEEQLDFPVI 1080
+ + ++T + L+LG I+ +N +D A + + +D +KL EE+L PV+
Sbjct: 85 -LERNLYLTLQLLELGIPMILALNLVDE--AEKKGIRIDE-----EKL---EERLGVPVV 133
Query: 1081 YTSALHGYANENSKARQGNMIPLFEAILKYVP----VHKDNSNNPLQLQII 1127
TSA G E K I L E + + ++ ++II
Sbjct: 134 PTSATEGRGIERLKDAIRKAIGLKELKKRAIEIVPEAYQVVEVVEGLIEII 184
>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 = 39.7 bits (94), Expect = 0.009
Identities = 26/66 (39%), Positives = 36/66 (54%), Gaps = 12/66 (18%)
Query: 170 PLIVAINKIDKLD-INLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENISL 228
P IV +NKID LD L+ + ++L E G P ISA TG G+++LL +
Sbjct: 275 PRIVVLNKIDLLDEEELEELLKELK------EALGK--PVFPISALTGEGLDELLYAL-- 324
Query: 229 QAEILE 234
AE+LE
Sbjct: 325 -AELLE 329
>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 = 38.6 bits (91), Expect = 0.009
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 6/57 (10%)
Query: 170 PLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
P IV +NKID LD + + + ++++ E G ISA TG G+++LL+ +
Sbjct: 116 PRIVVLNKIDLLD---AEERFEKL-KELLKELKGK--KVFPISALTGEGLDELLKKL 166
>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 = 37.3 bits (87), Expect = 0.011
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 10/74 (13%)
Query: 983 NGTRINIIDTPG------HADFGGEVERILSMVDN---VLLLIDAVEGPMPQTRFVTRKA 1033
G +I ++DTPG R L + +LL++DA EG + +
Sbjct: 44 LGRQIILVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEEL 103
Query: 1034 LKLGFKP-IVVVNK 1046
KL KP I+V+NK
Sbjct: 104 EKLPKKPIILVLNK 117
Score = 36.9 bits (86), Expect = 0.012
Identities = 28/117 (23%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVF-SEAGGITQHIGAYNVVTNHGSITFLDTPG----- 125
V ++G + GK++L++ + V S+ G T+ V+ I +DTPG
Sbjct: 2 VALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDP-ILGVLGLGRQIILVDTPGLIEGA 60
Query: 126 -HEAFTAMRAR---GAKVTDIVVLVVAADDGVMPQTREAIAHA-KISGVPLIVAINK 177
R + D+++LVV A +G+ E + K+ P+I+ +NK
Sbjct: 61 SEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKPIILVLNK 117
>gnl|CDD|215692 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 37.9 bits (89), Expect = 0.013
Identities = 43/166 (25%), Positives = 62/166 (37%), Gaps = 40/166 (24%)
Query: 81 GKTSLLDYIRKTNVVFSEAGGITQHIGAY--NVVTNHGSITF--LDTPGHEAFTAMRA-- 134
GK+SLL IR T F E T + Y + + ++ DT G E F A+R
Sbjct: 11 GKSSLL--IRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERFRALRPLY 68
Query: 135 -RGAKVTDIVVLVVAADDGVMPQT-------REAIAHAKISGVPLIVAINKIDKLDINLD 186
RGA +LV + E I VP+++ NK D
Sbjct: 69 YRGA---QGFLLVYDITS---RDSFENVKKWLEEILRHADENVPIVLVGNKCD------- 115
Query: 187 RIKQDLISEQVIPEEYGGA------SPFISISAKTGVGINKLLENI 226
L ++V+ E G A PF+ SAKT + + E +
Sbjct: 116 -----LEDQRVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEEL 156
>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and RSR1.
The Rap subfamily consists of the Rap1, Rap2, and RSR1.
Rap subfamily proteins perform different cellular
functions, depending on the isoform and its subcellular
localization. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and microsomal
membrane of the pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. Rap1 localizes in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines. Rap1 plays a role in phagocytosis by controlling
the binding of adhesion receptors (typically integrins)
to their ligands. In yeast, Rap1 has been implicated in
multiple functions, including activation and silencing
of transcription and maintenance of telomeres. Rap2 is
involved in multiple functions, including activation of
c-Jun N-terminal kinase (JNK) to regulate the actin
cytoskeleton and activation of the Wnt/beta-catenin
signaling pathway in embryonic Xenopus. A number of
effector proteins for Rap2 have been identified,
including isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK), and the
RalGEFs RalGDS, RGL, and Rlf, which also interact with
Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and
Rap2. In budding yeasts, it is involved in selecting a
site for bud growth, which directs the establishment of
cell polarization. The Rho family GTPase Cdc42 and its
GEF, Cdc24, then establish an axis of polarized growth.
It is believed that Cdc42 interacts directly with RSR1
in vivo. In filamentous fungi such as Ashbya gossypii,
RSR1 is a key regulator of polar growth in the hypha.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 164
Score = 37.5 bits (87), Expect = 0.016
Identities = 35/122 (28%), Positives = 52/122 (42%), Gaps = 26/122 (21%)
Query: 121 LDTPGHEAFTAMRARGAKVTDIVVLVVAADD-----GVMPQTREAIAHAKIS-GVPLIVA 174
LDT G E FTAMR K LV + + RE I K + VP+I+
Sbjct: 54 LDTAGTEQFTAMRDLYIKNGQGFALVYSITAQQSFNDLQD-LREQILRVKDTEDVPMILV 112
Query: 175 INKIDKLDINLDRIKQDLISEQVIPEEYG-------GASPFISISAKTGVGINKLLENIS 227
NK DL E+V+ +E G G PF+ SAK+ + ++++ ++
Sbjct: 113 GNKC------------DLEDERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLV 160
Query: 228 LQ 229
Q
Sbjct: 161 RQ 162
>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 = 38.0 bits (89), Expect = 0.017
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 6/86 (6%)
Query: 143 VVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKL--DINLDRIKQDLISEQVIPE 200
VV VV D P + I P+I+ NKID L D+ +R+KQ + ++ +
Sbjct: 37 VVHVVDIFD--FPGSLIPGLAELIGAKPVILVGNKIDLLPKDVKPNRLKQWV--KKRLKI 92
Query: 201 EYGGASPFISISAKTGVGINKLLENI 226
I +SAK G G+ +L+E I
Sbjct: 93 GGLKIKDVILVSAKKGWGVEELIEEI 118
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 37.5 bits (88), Expect = 0.019
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 10/57 (17%)
Query: 169 VPLIVAINKIDKLDI-NLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLE 224
P+IV +NKID L +L I+++L E I IS T G+++L
Sbjct: 113 KPVIVVLNKIDLLTEEDLSEIEKELEKEGE---------EVIKISTLTEEGVDELKN 160
Score = 29.8 bits (68), Expect = 6.2
Identities = 33/119 (27%), Positives = 46/119 (38%), Gaps = 23/119 (19%)
Query: 980 IEYNGTRINIIDTPGHADFGGE----VER--ILSMV---DNVLLLIDAVE--GPMPQTRF 1028
+Y R +IDTPG D E +E I ++ VL ID E G + +
Sbjct: 42 FDYKYLRWQVIDTPGILDRPLEERNTIEMQAITALAHLRAAVLFFIDPSETCGYSIEEQL 101
Query: 1029 VTRKALKLGFKP--IVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPVIYTSAL 1085
K +K F IVV+NKID T + ++ E+ VI S L
Sbjct: 102 SLFKEIKPLFNKPVIVVLNKIDLL----------TEEDLSEIEKELEKEGEEVIKISTL 150
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are polypeptides
of 30-65kDa with three characteristic GTPase motifs
(G-1, G-3 and G-4) that are similar to those of the Ras
family. The G-4 motif is strictly conserved with a
unique septin consensus of AKAD. Most septins are
thought to have at least one coiled-coil region, which
in some cases is necessary for intermolecular
interactions that allow septins to polymerise to form
rod-shaped complexes. In turn, these are arranged into
tandem arrays to form filaments. They are
multifunctional proteins, with roles in cytokinesis,
sporulation, germ cell development, exocytosis and
apoptosis.
Length = 280
Score = 38.4 bits (90), Expect = 0.022
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 934 GKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGTRIN--IID 991
GKTTLI+ L I R + + ++ + I + IE +G ++N +ID
Sbjct: 16 GKTTLINTLFLTD-------LIPERGIPGPSEKIKKTVEIKATTVEIEEDGVKLNLTVID 68
Query: 992 TPGHADF 998
TPG D
Sbjct: 69 TPGFGDA 75
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 37.6 bits (88), Expect = 0.024
Identities = 32/109 (29%), Positives = 51/109 (46%), Gaps = 16/109 (14%)
Query: 81 GKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHGSITF--LDTPGHEAFTAMRARG-- 136
GKT+LL + K + + T H + + G++ F D GHE A R
Sbjct: 31 GKTTLLHML-KDDRLAQHVP--TLHPTSEELTI--GNVKFTTFDLGGHEQ--ARRVWKDY 83
Query: 137 -AKVTDIVVLVVAADDGVMPQTREAI----AHAKISGVPLIVAINKIDK 180
+V IV LV AAD +++E + +++ VP+++ NKIDK
Sbjct: 84 FPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPILILGNKIDK 132
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 38.6 bits (91), Expect = 0.024
Identities = 36/126 (28%), Positives = 53/126 (42%), Gaps = 24/126 (19%)
Query: 114 NHGSITFLDTPG------HEAFTAMRARGAKVT--DIVVLVV-AADDGVMPQ---TREAI 161
+ G + DT G HE A RA +V D+++ VV A+D Q + +
Sbjct: 235 DGGEVLLTDTVGFIRDLPHELVAAFRATLEEVREADLLLHVVDASDPDREEQIEAVEKVL 294
Query: 162 AHAKISGVPLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINK 221
+P ++ NKID LD E I G + +SAKTG G++
Sbjct: 295 EELGAEDIPQLLVYNKIDLLD------------EPRIERLEEGYPEAVFVSAKTGEGLDL 342
Query: 222 LLENIS 227
LLE I+
Sbjct: 343 LLEAIA 348
>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 = 34.8 bits (81), Expect = 0.032
Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 16/84 (19%)
Query: 1131 YSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNK--AKINQIRVFKGLDRVLVNEALS 1188
Y G + G++ SG I+ +++M P+K ++ I V D V+ A++
Sbjct: 10 YKDQGGTVVSGKVESGSIQKGDTLLVM------PSKESVEVKSIYV----DDEEVDYAVA 59
Query: 1189 GDIVLIT--GIEE--ICIGSTICD 1208
G+ V + GI+E I G +C
Sbjct: 60 GENVRLKLKGIDEEDISPGDVLCS 83
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b and
Arl10c have been solved.
Length = 159
Score = 36.5 bits (85), Expect = 0.034
Identities = 43/164 (26%), Positives = 69/164 (42%), Gaps = 24/164 (14%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYN---VVTNHGSITFLDTPGHEA 128
+T++G + GKT+L++ I + FSE T +N V + +I D G
Sbjct: 2 ITLVGLQNSGKTTLVNVI--ASGQFSED---TIPTVGFNMRKVTKGNVTIKVWDLGGQPR 56
Query: 129 FTAMRARGAKVTDIVVLVV-AADDGVMPQTREAIAHAKIS-----GVPLIVAINKID--- 179
F +M R + + +V VV AAD + + + H + G+PL+V NK D
Sbjct: 57 FRSMWERYCRGVNAIVYVVDAADREKLEVAKNEL-HDLLEKPSLEGIPLLVLGNKNDLPG 115
Query: 180 KLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLL 223
L +LI + + SISAK I+ +L
Sbjct: 116 ALS------VDELIEQMNLKSITDREVSCYSISAKEKTNIDIVL 153
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 37.7 bits (89), Expect = 0.042
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 170 PLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
P I+ +NKID LD +++ ++ E P ISA TG G+++LL +
Sbjct: 273 PRILVLNKIDLLD------EEEEREKRAALELAALGGPVFLISAVTGEGLDELLRAL 323
>gnl|CDD|133375 cd04175, Rap1, Rap1 family GTPase consists of Rap1a and Rap1b
isoforms. The Rap1 subgroup is part of the Rap
subfamily of the Ras family. It can be further divided
into the Rap1a and Rap1b isoforms. In humans, Rap1a and
Rap1b share 95% sequence homology, but are products of
two different genes located on chromosomes 1 and 12,
respectively. Rap1a is sometimes called smg p21 or Krev1
in the older literature. Rap1 proteins are believed to
perform different cellular functions, depending on the
isoform, its subcellular localization, and the effector
proteins it binds. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and the microsomal
membrane of pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. High expression of Rap1 has been observed
in the nucleus of human oropharyngeal squamous cell
carcinomas (SCCs) and cell lines; interestingly, in the
SCCs, the active GTP-bound form localized to the
nucleus, while the inactive GDP-bound form localized to
the cytoplasm. Rap1 plays a role in phagocytosis by
controlling the binding of adhesion receptors (typically
integrins) to their ligands. In yeast, Rap1 has been
implicated in multiple functions, including activation
and silencing of transcription and maintenance of
telomeres. Rap1a, which is stimulated by T-cell receptor
(TCR) activation, is a positive regulator of T cells by
directing integrin activation and augmenting lymphocyte
responses. In murine hippocampal neurons, Rap1b
determines which neurite will become the axon and
directs the recruitment of Cdc42, which is required for
formation of dendrites and axons. In murine platelets,
Rap1b is required for normal homeostasis in vivo and is
involved in integrin activation. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 36.3 bits (84), Expect = 0.045
Identities = 35/120 (29%), Positives = 50/120 (41%), Gaps = 23/120 (19%)
Query: 121 LDTPGHEAFTAMRARGAKVTDIVVLVVA----ADDGVMPQTREAIAHAK-ISGVPLIVAI 175
LDT G E FTAMR K VLV + + + RE I K VP+I+
Sbjct: 54 LDTAGTEQFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVG 113
Query: 176 NKIDKLDINLDRIKQDLISEQVIPEEYGGA------SPFISISAKTGVGINKLLENISLQ 229
NK DL E+V+ +E G F+ SAK + +N++ ++ Q
Sbjct: 114 NKC------------DLEDERVVGKEQGQNLARQWGCAFLETSAKAKINVNEIFYDLVRQ 161
>gnl|CDD|179880 PRK04804, minC, septum formation inhibitor; Reviewed.
Length = 221
Score = 36.9 bits (86), Expect = 0.049
Identities = 18/56 (32%), Positives = 27/56 (48%)
Query: 160 AIAHAKISGVPLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKT 215
A A +G PL+V ++ I DI+ +K+ L S Q+I GA + AK
Sbjct: 37 AQAPQFFAGAPLVVNLSAIQDGDIDFVALKELLESRQLIIVGITGAKDKLQNQAKA 92
>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 = 35.1 bits (81), Expect = 0.050
Identities = 25/115 (21%), Positives = 41/115 (35%), Gaps = 8/115 (6%)
Query: 72 VTIMGHVDHGKTSLLD-YIRKTNVVF-SEAGGITQHIGAYNVVTNHGSITFLDTPGHEAF 129
V ++G GK+SLL + E G T + V + G + D G E
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREEL 61
Query: 130 TAMRARGAKVTDIVVLVVAADDGVMPQTREA----IAHAKISG--VPLIVAINKI 178
K D ++LV D + + + G +P+I+ NK+
Sbjct: 62 KFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNKL 116
>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 = 36.3 bits (85), Expect = 0.054
Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 17/69 (24%)
Query: 168 GVPLIVAINKID-----KLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKL 222
G+P++VA+N +D + I++ ++ + L P + SA+ G GI++L
Sbjct: 105 GIPVVVALNMMDEAEKKGIKIDIKKLSELL------------GVPVVPTSARKGEGIDEL 152
Query: 223 LENISLQAE 231
+ I AE
Sbjct: 153 KDAIIEVAE 161
Score = 35.5 bits (83), Expect = 0.11
Identities = 34/128 (26%), Positives = 57/128 (44%), Gaps = 23/128 (17%)
Query: 970 GITIFSKNCSIEYNGTRINIIDTPGHADFGG--EVERILSMV------DNVLLLIDAV-- 1019
G+T+ K + +Y G I I+D PG E E++ D ++ ++DA
Sbjct: 32 GVTVEKKEGTFKYKGYEIEIVDLPGTYSLSPYSEEEKVARDYLLEEKPDVIINVVDATNL 91
Query: 1020 EGPMPQTRFVTRKALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDFPV 1079
E + ++T + L+LG +V +N +D + + D+ KL E L PV
Sbjct: 92 ERNL----YLTLQLLELGIPVVVALNMMDEAEKK-----GIKIDI-KKL---SELLGVPV 138
Query: 1080 IYTSALHG 1087
+ TSA G
Sbjct: 139 VPTSARKG 146
>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 = 35.8 bits (83), Expect = 0.060
Identities = 28/100 (28%), Positives = 42/100 (42%), Gaps = 7/100 (7%)
Query: 141 DIVVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKLDINLDRIKQDLISEQVIPE 200
D+VV VV A D + + + LI+ +NK D + + + ++E
Sbjct: 1 DVVVEVVDARDPLSSRNPDIEVLINEKNKKLIMVLNKADLVP---KEVLRKWVAELS--- 54
Query: 201 EYGGASPFISISAKTGVGINKLLENISLQAEILELKAPVT 240
E G F ISA G GI KL I+ Q L+ K +
Sbjct: 55 ELYGTKTFF-ISATNGQGILKLKAEITKQKLKLKYKKGIR 93
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 37.2 bits (87), Expect = 0.063
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 9/59 (15%)
Query: 170 PLIVAINKIDKLDINLDRIKQDLISEQV--IPEEYGGASPFISISAKTGVGINKLLENI 226
P + NKID LD ++ E+ I E G P ISA +G+G+ +L ++
Sbjct: 277 PRWLVFNKIDLLD-------EEEAEERAKAIVEALGWEGPVYLISAASGLGVKELCWDL 328
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 37.0 bits (87), Expect = 0.065
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 17/67 (25%)
Query: 170 PLIVAINKIDKLDI--NLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENIS 227
P IV NK+D + NL+ K+ L +V P ISA TG G+++LL +
Sbjct: 276 PQIVVANKMDLPEAEENLEEFKEKL-GPKVFP-----------ISALTGQGLDELLYAV- 322
Query: 228 LQAEILE 234
AE+LE
Sbjct: 323 --AELLE 327
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 35.3 bits (82), Expect = 0.079
Identities = 40/172 (23%), Positives = 68/172 (39%), Gaps = 45/172 (26%)
Query: 70 PIVTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHGSITFLDTPG---- 125
+ ++G GKT+L + + + + TQ I + + +DTPG
Sbjct: 2 KKIMLIGRSGCGKTTLTQALNGEELKYKK----TQAIEFSDNM--------IDTPGEYLE 49
Query: 126 HEAF------TAMRARGAKVTDIVVLVVAADD--GVMPQTREAIAHAKISGVPLIVAINK 177
+ F TA A D++ LV A + V P A + P+I I K
Sbjct: 50 NRRFYSALIVTAADA------DVIALVQDATEPWSVFPP-----GFASMFNKPVIGIITK 98
Query: 178 ID--KLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENIS 227
ID K + N++ +++ L + GA +SA T GI++L +
Sbjct: 99 IDLAKDEANIEMVEEWLNN--------AGAEKIFEVSAVTNEGIDELFAYLE 142
>gnl|CDD|182123 PRK09866, PRK09866, hypothetical protein; Provisional.
Length = 741
Score = 37.1 bits (86), Expect = 0.086
Identities = 44/136 (32%), Positives = 54/136 (39%), Gaps = 31/136 (22%)
Query: 80 HGKTSLLDYIRKTNVV-----FSEAGGITQHIGAYNVVTNH--------GSITFLDTPG- 125
H SL D +R + FS I +HI V H G +T LDTPG
Sbjct: 182 HCLKSLNDLVRLAKALDVDFPFSAYAAI-EHIPVIEVEFVHLAGLESYPGQLTLLDTPGP 240
Query: 126 HEA--------FTAMRARGAKV---TDIVVLVVAADDGVMPQTREAIAHAKISGVPLIVA 174
+EA AR + V D L +D+ V REAI S VPL V
Sbjct: 241 NEAGQPHLQKMLNQQLARASAVLAVLDYTQLKSISDEEV----REAILAVGQS-VPLYVL 295
Query: 175 INKIDKLDINLDRIKQ 190
+NK D+ D N D Q
Sbjct: 296 VNKFDQQDRNSDDADQ 311
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 36.2 bits (84), Expect = 0.11
Identities = 45/184 (24%), Positives = 82/184 (44%), Gaps = 33/184 (17%)
Query: 70 PIVTIMGHVDHGKTSLLDYIRKTNV-----VFSEAGGITQHIGAYNVVTNHGSITFLDTP 124
P V+++G+ + GK++L + I + V +F+ + I +V G DT
Sbjct: 198 PTVSLVGYTNAGKSTLFNRITEARVYAADQLFATLDPTLRRIDVADV----GETVLADTV 253
Query: 125 G------HEAFTAMRA--RGAKVTDIVVLVVAADDGVMPQTREAI----AHAKISGVPLI 172
G H+ A +A + + +++ VV A D + + EA+ +P +
Sbjct: 254 GFIRHLPHDLVAAFKATLQETRQATLLLHVVDAADVRVQENIEAVNTVLEEIDAHEIPTL 313
Query: 173 VAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENIS--LQA 230
+ +NKID LD RI +D E+ P + +SA+TG GI L + ++ L
Sbjct: 314 LVMNKIDMLDDFEPRIDRD---EENKPIR-------VWLSAQTGAGIPLLFQALTERLSG 363
Query: 231 EILE 234
E+ +
Sbjct: 364 EVAQ 367
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like protein)-like
YfjP subfamily includes several uncharacterized bacterial
GTPases that are similar to Era. They 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. Era is characterized by a distinct
derivative of the KH domain (the pseudo-KH domain) which
is located C-terminal to the GTPase domain.
Length = 140
Score = 34.2 bits (79), Expect = 0.16
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 7/48 (14%)
Query: 978 CSIEYNGTRINIIDTPG-------HADFGGEVERILSMVDNVLLLIDA 1018
+ G + ++D PG ++ R+L D VL L+DA
Sbjct: 38 YVWQTGGDGLVLLDLPGVGERGRRDREYEELYRRLLPEADLVLWLLDA 85
>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and
Rap2c. The Rap2 subgroup is part of the Rap subfamily
of the Ras family. It consists of Rap2a, Rap2b, and
Rap2c. Both isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK) are putative
effectors of Rap2 in mediating the activation of c-Jun
N-terminal kinase (JNK) to regulate the actin
cytoskeleton. In human platelets, Rap2 was shown to
interact with the cytoskeleton by binding the actin
filaments. In embryonic Xenopus development, Rap2 is
necessary for the Wnt/beta-catenin signaling pathway.
The Rap2 interacting protein 9 (RPIP9) is highly
expressed in human breast carcinomas and correlates with
a poor prognosis, suggesting a role for Rap2 in breast
cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a,
or Rap1b, is expressed in human red blood cells, where
it is believed to be involved in vesiculation. A number
of additional effector proteins for Rap2 have been
identified, including the RalGEFs RalGDS, RGL, and Rlf,
which also interact with Rap1 and Ras. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 34.4 bits (79), Expect = 0.17
Identities = 37/128 (28%), Positives = 59/128 (46%), Gaps = 19/128 (14%)
Query: 111 VVTNHGSITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQT-------REAIAH 163
V ++ + LDT G E F +MR K ++V + V QT R+ I
Sbjct: 44 VDSSPSVLEILDTAGTEQFASMRDLYIKNGQGFIVVYSL---VNQQTFQDIKPMRDQIVR 100
Query: 164 AKIS-GVPLIVAINKIDKLDINLDRIKQDLISE-QVIPEEYGGASPFISISAKTGVGINK 221
K VP+I+ NK+D L+ ++ +E + + EE+G PF+ SAK+ +N+
Sbjct: 101 VKGYEKVPIILVGNKVD-----LESEREVSSAEGRALAEEWG--CPFMETSAKSKTMVNE 153
Query: 222 LLENISLQ 229
L I Q
Sbjct: 154 LFAEIVRQ 161
>gnl|CDD|133345 cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3. The
M-Ras/R-Ras-like subfamily contains R-Ras2/TC21,
M-Ras/R-Ras3, and related members of the Ras family.
M-Ras is expressed in lympho-hematopoetic cells. It
interacts with some of the known Ras effectors, but
appears to also have its own effectors. Expression of
mutated M-Ras leads to transformation of several types
of cell lines, including hematopoietic cells, mammary
epithelial cells, and fibroblasts. Overexpression of
M-Ras is observed in carcinomas from breast, uterus,
thyroid, stomach, colon, kidney, lung, and rectum. In
addition, expression of a constitutively active M-Ras
mutant in murine bone marrow induces a malignant mast
cell leukemia that is distinct from the monocytic
leukemia induced by H-Ras. TC21, along with H-Ras, has
been shown to regulate the branching morphogenesis of
ureteric bud cell branching in mice. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 34.3 bits (79), Expect = 0.18
Identities = 31/120 (25%), Positives = 50/120 (41%), Gaps = 29/120 (24%)
Query: 121 LDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIA--HAKISGV------PLI 172
LDT G E F+AMR + + + +LV + D + E + H +I V P+I
Sbjct: 55 LDTAGQEEFSAMREQYMRTGEGFLLVFSVTD---RGSFEEVDKFHTQILRVKDRDEFPMI 111
Query: 173 VAINKIDKLDINLDRIKQDLISEQVIPEEYGGAS------PFISISAKTGVGINKLLENI 226
+ NK DL ++ + E G P+I SAK V ++K ++
Sbjct: 112 LVGNKA------------DLEHQRQVSREEGQELARQLKIPYIETSAKDRVNVDKAFHDL 159
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 34.2 bits (79), Expect = 0.19
Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 170 PLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
P+I+ ID+ I + ++++ +S K G GI +L + I
Sbjct: 108 PVILVGTHIDESCDE--DILKKALNKKFPAIIND----IHFVSCKNGKGIAELKKAI 158
>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 = 35.4 bits (82), Expect = 0.19
Identities = 48/205 (23%), Positives = 64/205 (31%), Gaps = 45/205 (21%)
Query: 923 IKSAIIAHVDHGKTTLIDHLLRQ--SGTFRKNQNINARIMDSNEIEKERGITIFSKNCSI 980
AI+ + GK+TL++ L Q S T K Q RI S IF
Sbjct: 1 GFVAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRI--SGIHTTGASQIIF------ 52
Query: 981 EYNGTRINIIDTPG----HADFG----GEVERILSMVDNVLLLIDAVEGPMPQTRFVTRK 1032
IDTPG E + VD +L ++D+ + FV K
Sbjct: 53 ---------IDTPGFHEKKHSLNRLMMKEARSAIGGVDLILFVVDSDQWN-GDGEFVLTK 102
Query: 1033 ALKLGFKPIVVVNKIDRSNARPEWVVDATFDLFDKLCATEEQLDF-PVIYTSALHGYANE 1091
L ++ NK+D D L DK DF ++ SAL G
Sbjct: 103 LQNLKRPVVLTRNKLDNKFK------DKLLPLIDKY---AILEDFKDIVPISALTGDNTS 153
Query: 1092 NSKARQGNMIPLFEAILKYVPVHKD 1116
A E L P
Sbjct: 154 FLAA-------FIEVHLPEGPFRYP 171
Score = 33.9 bits (78), Expect = 0.53
Identities = 42/163 (25%), Positives = 71/163 (43%), Gaps = 20/163 (12%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNV-VFSEAGGITQHIGAYNVVTNHGSITFLDTPG----- 125
V I+G + GK++LL+ + + + S T++ + T I F+DTPG
Sbjct: 3 VAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPGFHEKK 62
Query: 126 HEAFTAM--RARGA-KVTDIVVLVVAADD--GVMPQTREAIAHAKISGVPLIVAINKIDK 180
H M AR A D+++ VV +D G + + K P+++ NK+D
Sbjct: 63 HSLNRLMMKEARSAIGGVDLILFVVDSDQWNGDGEFVLTKLQNLKR---PVVLTRNKLDN 119
Query: 181 LDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLL 223
D++ LI + I E++ + ISA TG + L
Sbjct: 120 --KFKDKLLP-LIDKYAILEDF---KDIVPISALTGDNTSFLA 156
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 35.2 bits (82), Expect = 0.19
Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 9/67 (13%)
Query: 934 GKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYNGTRI--NIID 991
GK+T I+ L + ++ + + + I +E NG ++ +ID
Sbjct: 16 GKSTFINTLF-------GTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVKLKLTVID 68
Query: 992 TPGHADF 998
TPG D
Sbjct: 69 TPGFGDN 75
>gnl|CDD|216219 pfam00965, TIMP, Tissue inhibitor of metalloproteinase. Members of
this family are common in extracellular regions of
vertebrate species.
Length = 174
Score = 34.7 bits (80), Expect = 0.20
Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 13/53 (24%)
Query: 1152 QDVVI---------MNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLIT 1195
D VI + +DK + K+ Q ++FKG + S DI +
Sbjct: 15 ADFVIRAKVVGKKLVEQGNDKRIRYKVKQTKMFKGFSKAG----SSLDIQYVY 63
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 34.3 bits (79), Expect = 0.20
Identities = 34/176 (19%), Positives = 66/176 (37%), Gaps = 37/176 (21%)
Query: 74 IMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHG---SITFLDTPG----- 125
++G + GK++LL + V + T + V G I +D PG
Sbjct: 2 LVGLPNVGKSTLLSALTSAKVEIASYPFTT--LEPNVGVFEFGDGVDIQIIDLPGLLDGA 59
Query: 126 ------HEAFTAMRARGAKVTDIVVLVVAA--DDGVMPQTREAIAHAKISGV-------P 170
E A +D+++ V+ A D P + + ++SG P
Sbjct: 60 SEGRGLGEQILAH----LYRSDLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKNKP 115
Query: 171 LIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
++ NKID + + +K+ + P + SA T +G+++++ I
Sbjct: 116 EMIVANKID--MASENNLKRLK--LDKLKRGI----PVVPTSALTRLGLDRVIRTI 163
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1). This
subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but exhibit
significant differences in tissue distribution and
subcellular localization. Rhes is found primarily in the
striatum of the brain, but is also expressed in other
areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is expressed
primarily in the brain, with low expression levels in
other tissues. Dexras1 localizes primarily to the
cytoplasm, and is a critical regulator of the circadian
master clock to photic and nonphotic input. Most Ras
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins.
Length = 247
Score = 35.1 bits (81), Expect = 0.22
Identities = 37/169 (21%), Positives = 68/169 (40%), Gaps = 23/169 (13%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQ---HIGAYNVVTNHGSITFLDTPGHEA 128
+ ++G GKT+++ R F E T H Y++ + LDT G+
Sbjct: 3 MVVLGASKVGKTAIVS--RFLGGRFEEQYTPTIEDFHRKLYSIRGEVYQLDILDTSGNHP 60
Query: 129 FTAMRARGAKVTDIVVLVVAADDG--------VMPQTREAIAHAK-----ISGVPLIVAI 175
F AMR D+ +LV + D+ + Q E + K +P+++
Sbjct: 61 FPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICG 120
Query: 176 NKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLE 224
NK D+ + R Q EQ++ + A + +SAK ++++
Sbjct: 121 NKADR---DFPREVQRDEVEQLVGGDENCA--YFEVSAKKNSNLDEMFR 164
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 34.8 bits (81), Expect = 0.23
Identities = 37/138 (26%), Positives = 57/138 (41%), Gaps = 39/138 (28%)
Query: 122 DTPGH-EAFTAMRARGAKVTDIV-----VLVVAADDGVMPQTRE---------AIAHAKI 166
DTPG E F A R G K+ + + +VV D V+ +T ++
Sbjct: 103 DTPGQMELF-AFRESGRKLVERLSGSSKSVVVFLIDAVLAKTPSDFVSLLLLALSVQLRL 161
Query: 167 SGVPLIVAINKIDKLD--------------------INLDRIKQDLISEQVIP--EEYGG 204
G+P I +NK D L + L++ Q L+S +++ EE G
Sbjct: 162 -GLPQIPVLNKADLLSEEELERILKWLEDPEYLLEELKLEKGLQGLLSLELLRALEETGL 220
Query: 205 ASPFISISAKTGVGINKL 222
I +SAKTG G ++L
Sbjct: 221 PVRVIPVSAKTGEGFDEL 238
Score = 32.9 bits (76), Expect = 1.0
Identities = 26/83 (31%), Positives = 35/83 (42%), Gaps = 15/83 (18%)
Query: 980 IEYNGTRINIIDTPGHA------DFGGEVERILSMVDN--VLLLIDAVEGPMPQTRFVTR 1031
IE ++DTPG + G ++ LS V+ LIDAV P FV+
Sbjct: 92 IESLDADYVLVDTPGQMELFAFRESGRKLVERLSGSSKSVVVFLIDAVLAKTPSD-FVSL 150
Query: 1032 KAL------KLGFKPIVVVNKID 1048
L +LG I V+NK D
Sbjct: 151 LLLALSVQLRLGLPQIPVLNKAD 173
>gnl|CDD|211324 cd01291, PseudoU_synth, Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). Pseudouridine
synthases contains the RsuA/RluD, TruA, TruB and TruD
families. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases. Some psi sites such
as psi55,13,38 and 39 in tRNA are highly conserved,
being in the same position in eubacteria, archeabacteria
and eukaryotes. Other psi sites occur in a more
restricted fashion, for example psi2604in 23S RNA made
by E.coli RluF has only been detected in E.coli. Human
dyskerin with the help of guide RNAs makes the hundreds
of psueudouridnes present in rRNA and small nuclear RNAs
(snRNAs). Mutations in human dyskerin cause X-linked
dyskeratosis congenitas. Missense mutation in human PUS1
causes mitochondrial myopathy and sideroblastic anemia
(MLASA).
Length = 87
Score = 32.5 bits (75), Expect = 0.26
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 668 LDKPYGLSSNNALKKIKYLL--NAKKVGYTGTLDPFATGLLPLC 709
L KP G + A +++ LL K+VGY G D A +
Sbjct: 1 LYKP-GGDTMEAARQLAKLLGIPPKRVGYAGRKDKRAVTTQLVS 43
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 35.7 bits (83), Expect = 0.27
Identities = 73/429 (17%), Positives = 149/429 (34%), Gaps = 41/429 (9%)
Query: 432 TRKLAQINNINIRYHNII---YNIIKEIKSEITNLIPLEKKENLLGLA----EIRQVILV 484
L + ++I +R ++II I I+S++ L+ +EKK+ + L +I
Sbjct: 669 VHILPESSSILVRNNSIIGVDTQITLNIRSKVGGLVRIEKKKKRIELKIFSGDIHFPGET 728
Query: 485 NKVSKIAGCYILEGLIRRDSKIRILRNKNIIWTGELDSLKRFKDNVKEVK---------- 534
+K+S+ +G I G +++SK I + K++ V+ V
Sbjct: 729 DKISRHSGILIPPGTGKKNSKESKKIKNWIYVQRITPTKKKYFVLVRPVVTYEIADGINL 788
Query: 535 AGFECERLSRIENQIQRDISEIIAFDIQNPIINIITITEVKITL------DYSYAKIFFT 588
A + L + ++ +Q + I + PI I +I V+ L D + I
Sbjct: 789 ATLFPQDLLQEKDNLQLRVVNYILYGNGKPIRGISSIQLVRTCLVLNWDQDKKSSSIEEA 848
Query: 589 TFNK-DISIKNILDNLSK---AKNYIRFKLSKKLHIHTLPILNFFYDNSIENAMMISKLI 644
+ ++ ++ + + K+ I + + + + +N +++ + SK
Sbjct: 849 RASFVEVRTNGLIRDFLRINLVKSPISYIRKRNDPSSSGLL--VQSNNFLDSTNIYSKAE 906
Query: 645 DGIKYCMQFH-----IKKNKNIIHGVLLLDK----PYGLSSNNALKKIKYLLNAKKVGYT 695
+ Q + +L+L G + K + +
Sbjct: 907 IQSQSLSQNQGTIRTLLNRNKESQSLLILSSSDCFRIGPFNGKKSKYHNIKESNPLIPIR 966
Query: 696 GTLDPFATGLLPLCFGEATKFSNYLSEADKYYEAIIHLGITTETGDIEGKIIDFNKNIPN 755
+L P T L F + + Y + +L T + ++ +ID N I N
Sbjct: 967 NSLGPLGTVLQIANFSSSYHLLTHNQILVTKYLQLDNLKQTFQVKVLKYYLIDENGKIYN 1026
Query: 756 SIEIIEKILINFHGKISQIPPMYSALKYKGIPLYKYARSGITIKRKLRYIKIYKITIIDY 815
IL F+ + Y I L ++ + I K K +I I+
Sbjct: 1027 PDPCSNIILNPFNLNWYFLHHNYCEETSTIISLGQFICENVCIS-KNGPHKSGQIIIVQV 1085
Query: 816 TIPYLTLRI 824
L +R
Sbjct: 1086 D--SLVIRS 1092
>gnl|CDD|214541 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in
fold and function to the bacterial EF-Tu GTPase. p21Ras
couples receptor Tyr kinases and G protein receptors to
protein kinase cascades.
Length = 164
Score = 34.1 bits (79), Expect = 0.28
Identities = 33/113 (29%), Positives = 50/113 (44%), Gaps = 23/113 (20%)
Query: 121 LDTPGHEAFTAMRARGAKVTDIVVLVVAADD----GVMPQTREAIAHAK-ISGVPLIVAI 175
LDT G E F+AMR + + + +LV + D + + RE I K VP+++
Sbjct: 53 LDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVG 112
Query: 176 NKIDKLDINLDRIKQDLISEQVIPEEYGGA------SPFISISAKTGVGINKL 222
NK DL SE+V+ E G PF+ SAK V +++
Sbjct: 113 NKC------------DLESERVVSTEEGKELARQWGCPFLETSAKERVNVDEA 153
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 34.8 bits (80), Expect = 0.34
Identities = 23/121 (19%), Positives = 47/121 (38%), Gaps = 10/121 (8%)
Query: 71 IVTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHG-SITFLDTPGHE-A 128
V +MG GK+SL++ + + V G+ I ++ G ++ DTPG
Sbjct: 41 NVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDGENLVLWDTPGLGDG 100
Query: 129 FTAMRARGAKV------TDIVVLVVAADDGVMPQTREAIAHAKISGV--PLIVAINKIDK 180
D+V+ ++ ADD + + + I G+ ++ + + D+
Sbjct: 101 KDKDAEHRQLYRDYLPKLDLVLWLIKADDRALGTDEDFLRDVIILGLDKRVLFVVTQADR 160
Query: 181 L 181
Sbjct: 161 A 161
>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 = 31.8 bits (73), Expect = 0.37
Identities = 28/92 (30%), Positives = 47/92 (51%), Gaps = 14/92 (15%)
Query: 1121 PLQLQIISLEYSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDR 1180
PL+L II +Y +G + +G++ SG IK +++M PNK ++ + ++ +
Sbjct: 1 PLRLPIID-KYKD-MGTVVLGKVESGTIKKGDKLLVM------PNKTQVEVLSIYN--ED 50
Query: 1181 VLVNEALSGDIVLI--TGIEE--ICIGSTICD 1208
V V A G+ V + GIEE I G +C
Sbjct: 51 VEVRYARPGENVRLRLKGIEEEDISPGFVLCS 82
>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 = 33.5 bits (77), Expect = 0.39
Identities = 39/162 (24%), Positives = 67/162 (41%), Gaps = 17/162 (10%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHGSIT-------FLDTP 124
V I+G + GKT+ L+ KT + G I V N G+I F D
Sbjct: 2 VLILGLDNAGKTTFLEQT-KTKFSKNYKGLNPSKITP-TVGLNIGTIEVGKARLMFWDLG 59
Query: 125 GHEAFTAMRARG-AKVTDIVVLVVAADDGVMPQTREA----IAHAKISGVPLIVAINKID 179
G E ++ + A+ ++ ++ + D +++ A I + + GVPL+V NK D
Sbjct: 60 GQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQD 119
Query: 180 KLD-INLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGIN 220
D +++ IK+ + I +SA G G+
Sbjct: 120 LPDALSVAEIKEVF--DDCIALIGRRDCLVQPVSALEGEGVE 159
>gnl|CDD|133377 cd04177, RSR1, RSR1/Bud1p family GTPase. RSR1/Bud1p is a member of
the Rap subfamily of the Ras family that is found in
fungi. In budding yeasts, RSR1 is involved in selecting
a site for bud growth on the cell cortex, which directs
the establishment of cell polarization. The Rho family
GTPase cdc42 and its GEF, cdc24, then establish an axis
of polarized growth by organizing the actin cytoskeleton
and secretory apparatus at the bud site. It is believed
that cdc42 interacts directly with RSR1 in vivo. In
filamentous fungi, polar growth occurs at the tips of
hypha and at novel growth sites along the extending
hypha. In Ashbya gossypii, RSR1 is a key regulator of
hyphal growth, localizing at the tip region and
regulating in apical polarization of the actin
cytoskeleton. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 168
Score = 33.6 bits (77), Expect = 0.42
Identities = 31/121 (25%), Positives = 49/121 (40%), Gaps = 24/121 (19%)
Query: 121 LDTPGHEAFTAMRARGAKVTDIVVLVVAADDGV----MPQTREAIAHAKIS-GVPLIVAI 175
LDT G E FTAMR K +LV + + + RE + K S VP+++
Sbjct: 54 LDTAGTEQFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVG 113
Query: 176 NKIDKLDINLDRIKQDLISEQVIPEEYG-------GASPFISISAKTGVGINKLLENISL 228
NK DL ++ + E G G PF SA+ ++++ ++
Sbjct: 114 NKA------------DLEDDRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVR 161
Query: 229 Q 229
Q
Sbjct: 162 Q 162
>gnl|CDD|133356 cd04156, ARLTS1, Arf-like tumor suppressor gene 1 (ARLTS1 or
Arl11). ARLTS1 (Arf-like tumor suppressor gene 1), also
known as Arl11, is a member of the Arf family of small
GTPases that is believed to play a major role in
apoptotic signaling. ARLTS1 is widely expressed and
functions as a tumor suppressor gene in several human
cancers. ARLTS1 is a low-penetrance suppressor that
accounts for a small percentage of familial melanoma or
familial chronic lymphocytic leukemia (CLL). ARLTS1
inactivation seems to occur most frequently through
biallelic down-regulation by hypermethylation of the
promoter. In breast cancer, ARLTS1 alterations were
typically a combination of a hypomorphic polymorphism
plus loss of heterozygosity. In a case of thyroid
adenoma, ARLTS1 alterations were polymorphism plus
promoter hypermethylation. The nonsense polymorphism
Trp149Stop occurs with significantly greater frequency
in familial cancer cases than in sporadic cancer cases,
and the Cys148Arg polymorphism is associated with an
increase in high-risk familial breast cancer.
Length = 160
Score = 33.2 bits (76), Expect = 0.53
Identities = 30/117 (25%), Positives = 52/117 (44%), Gaps = 15/117 (12%)
Query: 72 VTIMGHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVT----NHGSITFLDTPGHE 127
V ++G GK++LL Y K + + + +NV H S+T D G E
Sbjct: 2 VLLLGLDSAGKSTLL-YKLKHAELVTTIPTV-----GFNVEMLQLEKHLSLTVWDVGGQE 55
Query: 128 AFTAMRARGAKVTDIVVLVVAADDGV-MPQTREAIAHA----KISGVPLIVAINKID 179
+ + TD +V VV + D + ++++ + H I GVP+++ NK D
Sbjct: 56 KMRTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQD 112
>gnl|CDD|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21). The localization and
function of Rab21 are not clearly defined, with
conflicting data reported. Rab21 has been reported to
localize in the ER in human intestinal epithelial cells,
with partial colocalization with alpha-glucosidase, a
late endosomal/lysosomal marker. More recently, Rab21
was shown to colocalize with and affect the morphology
of early endosomes. In Dictyostelium, GTP-bound Rab21,
together with two novel LIM domain proteins, LimF and
ChLim, has been shown to regulate phagocytosis. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 162
Score = 33.0 bits (76), Expect = 0.56
Identities = 49/165 (29%), Positives = 69/165 (41%), Gaps = 30/165 (18%)
Query: 76 GHVDHGKTSLLDYIRKTNVVFSEAGGITQHIGAYNVVTNHG----SITFLDTPGHEAFTA 131
G V GKTSL+ +R F+E T + N G + DT G E + A
Sbjct: 9 GRV--GKTSLV--LRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQERYHA 64
Query: 132 ---MRARGAKVTDIVVLVVAAD--DGVMPQTRE--AIAHAKISGVPLIVAINKIDKLDIN 184
+ R A +V + AD V +E + IS L++ NKID
Sbjct: 65 LGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNIS---LVIVGNKID----- 116
Query: 185 LDRIKQDLISEQVIPEEYG---GASPFISISAKTGVGINKLLENI 226
L+R + +S+ EEY GA F SAKTG GI +L ++
Sbjct: 117 LERQRV--VSKSEA-EEYAKSVGAKHF-ETSAKTGKGIEELFLSL 157
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 32.9 bits (76), Expect = 0.64
Identities = 32/116 (27%), Positives = 51/116 (43%), Gaps = 29/116 (25%)
Query: 121 LDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIA--HAKI------SGVPLI 172
LDT G E F+AMR + + + +LV + D Q+ E IA +I VP++
Sbjct: 55 LDTAGQEEFSAMRDQYMRTGEGFLLVYSITD---RQSFEEIAKFREQILRVKDRDDVPIV 111
Query: 173 VAINKIDKLDINLDRIKQDLISEQVIPEEYGGA------SPFISISAKTGVGINKL 222
+ NK DL +E+V+ E G PF+ SAK + +++
Sbjct: 112 LVGNKC------------DLENERVVSTEEGKELARQWGCPFLETSAKERINVDEA 155
>gnl|CDD|187658 cd08955, KR_2_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 2, complex (x).
Ketoreductase, a module of the multidomain polyketide
synthase, has 2 subdomains, each corresponding to a
short-chain dehydrogenases/reductase (SDR) family
monomer. The C-terminal subdomain catalyzes the
NADPH-dependent reduction of the beta-carbonyl of a
polyketide to a hydroxyl group, a step in the
biosynthesis of polyketides, such as erythromycin. The
N-terminal subdomain, an interdomain linker, is a
truncated Rossmann fold which acts to stabilizes the
catalytic subdomain. Unlike typical SDRs, the isolated
domain does not oligomerizes but is composed of 2
subdomains, each resembling an SDR monomer. In some
instances, as in porcine FAS, an enoyl reductase (a
Rossman fold NAD binding domain of the MDR family)
module is inserted between the sub-domains. The active
site resembles that of typical SDRs, except that the
usual positions of the catalytic asparagine and tyrosine
are swapped, so that the canonical YXXXK motif changes
to YXXXN. Modular polyketide synthases are
multifunctional structures in which the makeup
recapitulates that found in (and may have evolved from)
fatty acid synthase. In some instances, such as
porcine FAS , an enoyl reductase module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-ketoacyl reductase (KR), forming
beta-hydroxyacyl-ACP, which is in turn dehydrated by
dehydratase to a beta-enoyl intermediate, which is
reduced by NADP-dependent beta-enoyl reductase (ER).
Polyketide syntheses also proceeds via the addition of
2-carbon units as in fatty acid synthesis. The complex
SDR NADP binding motif, GGXGXXG, is often present, but
is not strictly conserved in each instance of the
module. This subfamily includes the KR domain of the
Lyngbya majuscule Jam J, -K, and #L which are encoded
on the jam gene cluster and are involved in the
synthesis of the Jamaicamides (neurotoxins); Lyngbya
majuscule Jam P belongs to a different KR_FAS_SDR_x
subfamily. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
PGDH numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 376
Score = 33.8 bits (78), Expect = 0.80
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 5/51 (9%)
Query: 121 LDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPL 171
+A A+ GA+V V+AAD A+A + S PL
Sbjct: 185 PSAAARQAIAALEEAGAEVV-----VLAADVSDRDALAAALAQIRASLPPL 230
>gnl|CDD|239683 cd03713, EFG_mtEFG_C, EFG_mtEFG_C: domains similar to the C-terminal
domain of the bacterial translational elongation factor
(EF) EF-G. Included in this group is the C-terminus of
mitochondrial Elongation factor G1 (mtEFG1) and G2
(mtEFG2) proteins. Eukaryotic cells harbor 2 protein
synthesis systems: one localized in the cytoplasm, the
other in the mitochondria. Most factors regulating
mitochondrial protein synthesis are encoded by nuclear
genes, translated in the cytoplasm, and then transported
to the mitochondria. The eukaryotic system of elongation
factor (EF) components is more complex than that in
prokaryotes, with both cytoplasmic and mitochondrial
elongation factors and multiple isoforms being expressed
in certain species. During the process of peptide
synthesis and tRNA site changes, the ribosome is moved
along the mRNA a distance equal to one codon with the
addition of each amino acid. In bacteria this
translocation step is catalyzed by EF-G_GTP, which is
hydrolyzed to provide the required energy. Thus, this
action releases the uncharged tRNA from the P site and
transfers the newly formed peptidyl-tRNA from the A site
to the P site. Eukaryotic mtEFG1 proteins show
significant homology to bacterial EF-Gs. Mutants in
yeast mtEFG1 have impaired mitochondrial protein
synthesis, respiratory defects and a tendency to lose
mitochondrial DNA. No clear phenotype has been found for
mutants in the yeast homologue of mtEFG2, MEF2.
Length = 78
Score = 31.0 bits (71), Expect = 0.81
Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 1/77 (1%)
Query: 1317 EPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIPSRGLIGFQNEFIT 1376
EP + V + E G ++ L+ R G + E +V ++ +P + G+ + +
Sbjct: 1 EPIMKVEVTVPEEYMGDVIGDLSSRRGQILGTESRGGWKV-IKAEVPLAEMFGYSTDLRS 59
Query: 1377 LTRGTGLISHVFEEYAP 1393
LT+G G + F Y
Sbjct: 60 LTQGRGSFTMEFSHYEE 76
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 32.8 bits (76), Expect = 0.84
Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 158 REAIAHAKISGVPLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASP-FISISAKTG 216
+ I K G+P+++ + K DKL +R KQ + + + I S+
Sbjct: 125 LQMIEWLKEYGIPVLIVLTKADKLKKG-ERKKQ----LKKVRKALKFGDDEVILFSSLKK 179
Query: 217 VGINKLLENI 226
GI++L I
Sbjct: 180 QGIDELRAAI 189
>gnl|CDD|180745 PRK06915, PRK06915, acetylornithine deacetylase; Validated.
Length = 422
Score = 33.5 bits (77), Expect = 0.89
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 169 VPLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGA 205
V L++A+ + + I L K D+I + VI EE GGA
Sbjct: 140 VALLLAMEALIESGIEL---KGDVIFQSVIEEESGGA 173
>gnl|CDD|217719 pfam03767, Acid_phosphat_B, HAD superfamily, subfamily IIIB (Acid
phosphatase). This family proteins includes acid
phosphatases and a number of vegetative storage proteins.
Length = 213
Score = 32.7 bits (75), Expect = 0.97
Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 1268 NKHDDSIYEVSGRGELHLTILIENMRREGYELSVSRPRVIFKTLNG 1313
+ I+ VSGR E +EN+++ G+ ++I +
Sbjct: 116 VELGVKIFFVSGRSEDLRAATVENLKKAGFH---GWEKLILRGKKD 158
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 33.3 bits (77), Expect = 1.0
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 12/67 (17%)
Query: 170 PLIVAINKIDKL--DINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENIS 227
P IV +NKID + L+ +K+ L G F ISA T G+++LL +
Sbjct: 277 PRIVVLNKIDLPLDEEELEELKKALAEA-------LGWEVFYLISALTREGLDELLRAL- 328
Query: 228 LQAEILE 234
AE+LE
Sbjct: 329 --AELLE 333
>gnl|CDD|239680 cd03709, lepA_C, lepA_C: This family represents the C-terminal region
of LepA, a GTP-binding protein localized in the
cytoplasmic membrane. LepA is ubiquitous in Bacteria
and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but
is missing from Archaea. LepA exhibits significant
homology to elongation factors (EFs) Tu and G. The
function(s) of the proteins in this family are unknown.
The N-terminal domain of LepA is homologous to a domain
of similar size found in initiation factor 2 (IF2), and
in EF-Tu and EF-G (factors required for translation in
Escherichia coli). Two types of phylogenetic tree, rooted
by other GTP-binding proteins, suggest that eukaryotic
homologs (including S. cerevisiae GUF1) originated within
the bacterial LepA family. LepA has never been observed
in archaea, and eukaryl LepA is organellar. LepA is
therefore a true bacterial GTPase, found only in the
bacterial lineage.
Length = 80
Score = 30.5 bits (70), Expect = 1.1
Identities = 14/47 (29%), Positives = 21/47 (44%)
Query: 1317 EPYENLFVDIEEINQGIIMQKLNYRGGDLKNIEINEKERVRLEYRIP 1363
EP+ + G IM+ R G K++E + RV L Y +P
Sbjct: 1 EPFVKATIITPSEYLGAIMELCQERRGVQKDMEYLDANRVMLTYELP 47
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 33.0 bits (76), Expect = 1.2
Identities = 25/92 (27%), Positives = 46/92 (50%), Gaps = 14/92 (15%)
Query: 141 DIVVLVVAADDGVMPQTREAI-----AHAKISGVPLIVAINKIDKLDINLDRIKQDLISE 195
D ++VV+ V P + A+ G+ ++ +NKID LD + + ++L+ E
Sbjct: 81 DQAIIVVSL---VDPDFNTNLLDRYLVLAEAGGIEPVIVLNKIDLLD-DEEAAVKELLRE 136
Query: 196 QVIPEEYGGASPFISISAKTGVGINKLLENIS 227
E+ G P + +SAK G G+ +L E ++
Sbjct: 137 Y---EDIG--YPVLFVSAKNGDGLEELAELLA 163
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE, also
called MnmE and previously designated ThdF (thiophene and
furan oxidation protein), is a GTPase involved in tRNA
modification to create 5-methylaminomethyl-2-thiouridine
in the wobble position of some tRNAs. This protein and
GidA form an alpha2/beta2 heterotetramer [Protein
synthesis, tRNA and rRNA base modification].
Length = 442
Score = 33.2 bits (76), Expect = 1.3
Identities = 34/134 (25%), Positives = 55/134 (41%), Gaps = 26/134 (19%)
Query: 924 KSAIIAHVDHGKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEKERGITIFSKNCSIEYN 983
K AI+ + GK++L++ LL+Q D + +G T E N
Sbjct: 205 KLAIVGSPNVGKSSLLNALLKQ---------------DRAIVSDIKGTTRDVVEGDFELN 249
Query: 984 GTRINIIDTPGHADFGGEVERI--------LSMVDNVLLLIDAVEGPMPQTR-FVTRKAL 1034
G I ++DT G + VER+ + D V+ ++DA + +
Sbjct: 250 GILIKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIYVLDASQPLTKDDFLIIDLNKS 309
Query: 1035 KLGFKPIVVVNKID 1048
K F I+V+NKID
Sbjct: 310 KKPF--ILVLNKID 321
Score = 31.7 bits (72), Expect = 3.0
Identities = 38/152 (25%), Positives = 61/152 (40%), Gaps = 21/152 (13%)
Query: 48 DPESFLLNEYNKNITAE----------SLVRAPI-VTIMGHVDHGKTSLLD-YIRKTNVV 95
D E LN+ +I AE + + I+G + GK+SLL+ +++ +
Sbjct: 171 DDEQDSLNQLLLSIIAELKDILNSYKLEKLDDGFKLAIVGSPNVGKSSLLNALLKQDRAI 230
Query: 96 FSEAGGITQHIGAYNVVTNHGSITFLDTPG-HEAFTAMRARG-------AKVTDIVVLVV 147
S+ G T+ + + N I LDT G E + G K D+V+ V+
Sbjct: 231 VSDIKGTTRDVVEGDFELNGILIKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIYVL 290
Query: 148 AADDGVMPQTREAIAHAKISGVPLIVAINKID 179
A + I S P I+ +NKID
Sbjct: 291 DASQPLTKDD-FLIIDLNKSKKPFILVLNKID 321
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 32.5 bits (75), Expect = 1.7
Identities = 26/85 (30%), Positives = 36/85 (42%), Gaps = 15/85 (17%)
Query: 1009 VDNVLLLIDAVEGPMPQTRFVTRKALKL----GFKPIVVVNKIDRSNARPEWVVDATFDL 1064
VD +L+ A E P T + R L L G KPI+V+NKID + E
Sbjct: 81 VDQAVLVFAAKE-PDFSTDLLDR-FLVLAEANGIKPIIVLNKIDLLDDLEEA-------- 130
Query: 1065 FDKLCATEEQLDFPVIYTSALHGYA 1089
+L A + + V+ SA G
Sbjct: 131 -RELLALYRAIGYDVLELSAKEGEG 154
Score = 30.6 bits (70), Expect = 6.3
Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 17/90 (18%)
Query: 141 DIVVLVVAADDGVMPQTRE-----AIAHAKISGVPLIVAINKIDKLDINLDRIKQDLISE 195
D VLV AA P + A+ +G+ I+ +NKID LD +L+ ++
Sbjct: 82 DQAVLVFAA---KEPDFSTDLLDRFLVLAEANGIKPIIVLNKIDLLD-DLEEARE----- 132
Query: 196 QVIPEEYGGAS-PFISISAKTGVGINKLLE 224
+ Y + +SAK G G+++L
Sbjct: 133 --LLALYRAIGYDVLELSAKEGEGLDELKP 160
>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 = 31.8 bits (73), Expect = 1.7
Identities = 46/169 (27%), Positives = 69/169 (40%), Gaps = 44/169 (26%)
Query: 81 GKTSLLDYIRKTNVVFSEAGGITQHIGA----YNVVTNHGSITFL--DTPGHEAFTA--- 131
GK+S++ +R FSE T IGA V + ++ F DT G E + +
Sbjct: 13 GKSSIV--LRFVKNEFSENQEST--IGAAFLTQTVNLDDTTVKFEIWDTAGQERYRSLAP 68
Query: 132 MRARGAKVTDIVVLVVAADDGVMPQTREAIAHAK-------ISGVP-LIVAI--NKIDKL 181
M RGA IVV + + E+ AK G P +++A+ NK D
Sbjct: 69 MYYRGAAAA-IVVYDI--------TSEESFEKAKSWVKELQEHGPPNIVIALAGNKADLE 119
Query: 182 DINLDRIKQDLISEQVIPEEYG---GASPFISISAKTGVGINKLLENIS 227
+S + +EY G F+ SAKTG +N+L I+
Sbjct: 120 SKRQ-------VSTEEA-QEYADENGLL-FMETSAKTGENVNELFTEIA 159
>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 = 29.8 bits (68), Expect = 1.8
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 1141 GRILSGRIKSLQDVVIMNGPDDKPNKAKINQIRVFKGLDRVLVNEALSGDIVLIT 1195
G I SG I+ +VV++ P K +++ I F G ++EA +G+ V +T
Sbjct: 20 GTIASGSIRVGDEVVVL--PSGK--TSRVKSIETFDG----ELDEAGAGESVTLT 66
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 32.7 bits (76), Expect = 1.8
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 9/61 (14%)
Query: 189 KQDLISEQV---IPEEYGGASPFISISAKTGV-GINKLLENISLQAEILELKAPVTTPAK 244
K+ L++E+ EEYG AK G I +LL+NI L+AE EL+ +
Sbjct: 146 KKQLLTEEEYREALEEYGD-----EFVAKMGAEAIKELLKNIDLEAEAEELREELKETGS 200
Query: 245 G 245
Sbjct: 201 E 201
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to regulate
cell polarity by interacting with the diaphanous/formin
family protein For3 to control both the actin
cytoskeleton and microtubules. Rho3 is also believed to
have a direct role in exocytosis that is independent of
its role in regulating actin polarity. The function in
exocytosis may be two-pronged: first, in the transport
of post-Golgi vesicles from the mother cell to the bud,
mediated by myosin (Myo2); second, in the docking and
fusion of vesicles to the plasma membrane, mediated by
an exocyst (Exo70) protein. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 185
Score = 31.4 bits (71), Expect = 2.1
Identities = 42/163 (25%), Positives = 69/163 (42%), Gaps = 18/163 (11%)
Query: 72 VTIMGHVDHGKTSLLD-YIRKTNVVFSEAGGITQHIGAYNVVTNHGSITFLDTPGHEAFT 130
V ++G GKTSLL+ + R E +I V ++ DT G E F
Sbjct: 3 VVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQEEFD 62
Query: 131 AMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKIS----GVPLI-VAINKIDKLDINL 185
+R+ T +++L + D+ + E+ A+I GV L+ VA+ K D+
Sbjct: 63 RLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHHCPGVKLVLVAL----KCDLRE 118
Query: 186 DRIKQDLISEQVIPEEYG-------GASPFISISAKTGVGINK 221
R ++D + I E G A ++ SAK G+N+
Sbjct: 119 PRNERDRGT-HTISYEEGLAVAKRINACRYLECSAKLNRGVNE 160
>gnl|CDD|133319 cd04119, RJL, Rab GTPase family J-like (RabJ-like). RJLs are found
in many protists and as chimeras with C-terminal DNAJ
domains in deuterostome metazoa. They are not found in
plants, fungi, and protostome metazoa, suggesting a
horizontal gene transfer between protists and
deuterostome metazoa. RJLs lack any known membrane
targeting signal and contain a degenerate
phosphate/magnesium-binding 3 (PM3) motif, suggesting an
impaired ability to hydrolyze GTP. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization.
Length = 168
Score = 31.2 bits (71), Expect = 2.1
Identities = 30/121 (24%), Positives = 48/121 (39%), Gaps = 21/121 (17%)
Query: 118 ITFLDTPGHEAFTAMRARGAKVTDIVVLVV---------AADDGVMPQTREAIAHAKISG 168
+ F D GH + +R K T V+LV A D + +E H +
Sbjct: 51 VNFFDLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMEN 110
Query: 169 VPLIVAINKIDKLDINLDRIKQDLISEQ---VIPEEYGGASPFISISAKTGVGINKLLEN 225
+ ++V NKID K +SE + E G + SA TG G+N++ +
Sbjct: 111 IVVVVCANKIDLT-------KHRAVSEDEGRLWAESKGFK--YFETSACTGEGVNEMFQT 161
Query: 226 I 226
+
Sbjct: 162 L 162
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 31.4 bits (72), Expect = 2.2
Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 17/67 (25%)
Query: 168 GVPLIVAINKIDKLDINLDRIKQDLISEQVIPEEYGGASP--------FISISAKTGVGI 219
G+P IVA+NK+DK+ N D + ++ E G P ISAK G GI
Sbjct: 130 GIPPIVAVNKMDKIK-NRDEVLDEIA-------ERLGLYPPWRQWQDIIAPISAKKG-GI 180
Query: 220 NKLLENI 226
+L E I
Sbjct: 181 EELKEAI 187
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They are sequestered in the cytosol until activation by
growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active (GTP-bound) Ras interacts with several effector
proteins that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF and NORE/MST1.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 162
Score = 31.2 bits (71), Expect = 2.2
Identities = 30/105 (28%), Positives = 46/105 (43%), Gaps = 14/105 (13%)
Query: 121 LDTPGHEAFTAMRARGAKVTDIVVLVVAAD-----DGVMPQTREAIAHAK-ISGVPLIVA 174
LDT G E ++AMR + + + + V A + + + RE I K VP+++
Sbjct: 54 LDTAGQEEYSAMRDQYMRTGEGFLCVFAINSRKSFEDIH-TYREQIKRVKDSDDVPMVLV 112
Query: 175 INKIDKLDINLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGI 219
NK D L Q + + YG P+I SAKT G+
Sbjct: 113 GNKCD-----LAARTVSTRQGQDLAKSYG--IPYIETSAKTRQGV 150
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 31.9 bits (73), Expect = 2.5
Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 20/73 (27%)
Query: 934 GKTTLIDHLLRQSGTFRKNQNINARIMDSNEIEK------ERGITIFSKNCSIEYNGT-- 985
GKTT I+ L S ++D EI+ + I +E +G
Sbjct: 35 GKTTFINTLFGTS------------LVDETEIDDIRAEGTSPTLEIKITKAELEEDGFHL 82
Query: 986 RINIIDTPGHADF 998
+ +IDTPG DF
Sbjct: 83 NLTVIDTPGFGDF 95
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes [Protein synthesis, Other].
Length = 178
Score = 31.3 bits (72), Expect = 2.6
Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 13/82 (15%)
Query: 143 VVLVVAADDGVMPQTREAIAHAKISGVPLIVAINKIDKL-----DINLDRIKQDLISEQV 197
VVL++ + E I + G+P+++ + K DKL + L +IK+ L
Sbjct: 104 VVLLMDIRHPLKELDLEMIEWLRERGIPVLIVLTKADKLKKSELNKQLKKIKKAL----- 158
Query: 198 IPEEYGGASPFISISAKTGVGI 219
+ S+ GI
Sbjct: 159 ---KKDADDSVQLFSSLKKTGI 177
>gnl|CDD|233543 TIGR01716, RGG_Cterm, transcriptional activator, Rgg/GadR/MutR
family, C-terminal domain. This model describes the
whole, except for a 60 residue N-terminal
helix-turn-helix DNA-binding domain (PFAM pfam01381) of
the family of proteins related to the transcriptional
regulator Rgg, also called RopB. Rgg is required for
secretion of several proteins, including a cysteine
proteinase associated with virulence. GadR (GP|2352485)
is a positive regulator of a glutamate-dependent acid
resistance mechanism. MutR is a transcriptional
activator for mutacin biosynthesis genes in
Streptococcus mutans. This family appears restricted to
the low-GC Gram-positive bacteria, including at least
eight members in Lactococcus lactis [Regulatory
functions, DNA interactions].
Length = 220
Score = 31.5 bits (72), Expect = 2.9
Identities = 43/193 (22%), Positives = 69/193 (35%), Gaps = 17/193 (8%)
Query: 625 ILNFFYDNSIENAMMISKLIDGIKYCMQFHIKKNKNIIHGVL-LLDKPYGLSSNNALKKI 683
I+ FY N I + L+ I + + + NK +I L LD Y LS
Sbjct: 18 IVEAFYSNDIVG---LKSLLSKISETKETYNRLNKAVIKARLHTLDHSYILSEEEVEFLT 74
Query: 684 KYLLNAKKVGY------TGTLDPFATGLLPLCFGEATKFSNYLSEADKYYEAIIHLGITT 737
YL N ++ Y T+ + L E + E ++Y +I L +
Sbjct: 75 DYLFNIEEWTYYELYLFGNTMSILNSEDLEFLGKELLERLKRYRELNRYRRRVIQLLLNI 134
Query: 738 ETGDIEGKIIDFNKNIPNSIEIIEKILINFHGKISQIPPMYSALKYKGIPLYKYARSGIT 797
IE +E +EKIL +I + KGI LYK +
Sbjct: 135 AVLLIEKNEFS---YAQYFLEKLEKILDPEDDLYERILFNF----LKGIILYKEGQKESG 187
Query: 798 IKRKLRYIKIYKI 810
++ + I+I+
Sbjct: 188 EEKIEQAIEIFDE 200
>gnl|CDD|107302 cd06307, PBP1_uncharacterized_sugar_binding, Periplasmic
sugar-binding domain of uncharacterized transport
systems. Periplasmic sugar-binding domain of
uncharacterized transport systems that share homology
with a family of pentose/hexose sugar-binding proteins
of the type I periplasmic binding protein (PBP1)
superfamily. The members of this group are predicted to
be involved in the transport of sugar-containing
molecules across cellular and organellar membranes.
Length = 275
Score = 31.4 bits (72), Expect = 3.2
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 118 ITFLDTPGHEAFTAMRARGAKVTDIVVLVVAADDGVMPQTREAIAHAKISGVPLI 172
I F+++ A A R +D V +VA D PQ R A+A +GVP++
Sbjct: 37 IHFVESFDPAALAAALLRLGARSD-GVALVAPDH---PQVRAAVARLAAAGVPVV 87
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 31.5 bits (72), Expect = 3.3
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 15/59 (25%)
Query: 169 VPLIVAINKIDKLDI-NLDRIKQDLISEQVIPEEYGGASPFISISAKTGVGINKLLENI 226
P + +NKID + L+R+ + + ISAK G+ +++L E I
Sbjct: 240 KPALYVVNKIDLPGLEELERLAR--------------KPNSVPISAKKGINLDELKERI 284
>gnl|CDD|214391 CHL00192, syfB, phenylalanyl-tRNA synthetase beta chain;
Provisional.
Length = 704
Score = 31.6 bits (72), Expect = 3.6
Identities = 36/143 (25%), Positives = 59/143 (41%), Gaps = 31/143 (21%)
Query: 358 DINKEKVKNLLIIIK---TDVYGSREVLTESLKNLS------TDKVKIQVIHNAVGNIN- 407
++ +K+K++L IK Y S + +T +LK L+ + K+ +V+ + +
Sbjct: 306 KLSYKKIKDILGPIKINTNTRYLSPKEITNALKRLNFKITYDSLKLNWEVLIPSYRKDDI 365
Query: 408 --ESDINLAIASKAIIIGFNVRADASTRKLAQINNINIRYHNIIYNIIKEIKSEITNLIP 465
E D+ I A I GFN N I +I YN +I+S + N
Sbjct: 366 VREIDV---IEEIARIYGFN------NFLSKLPNIKFIGRLDIDYNTRDKIRSYLRN--- 413
Query: 466 LEKKENLLGLAEIRQVILVNKVS 488
LGL E+ LV + S
Sbjct: 414 -------LGLTELIHYSLVKQES 429
>gnl|CDD|206740 cd09913, EHD, Eps15 homology domain (EHD), C-terminal domain.
Dynamin-like C-terminal Eps15 homology domain (EHD)
proteins regulate endocytic events; they have been linked
to a number of Rab proteins through their association
with mutual effectors, suggesting a coordinate role in
endocytic regulation. Eukaryotic EHDs comprise four
members (EHD1-4) in mammals and single members in
Caenorhabditis elegans (Rme-1), Drosophila melanogaster
(Past1) as well as several eukaryotic parasites. EHD1
regulates trafficking of multiple receptors from the
endocytic recycling compartment (ERC) to the plasma
membrane; EHD2 regulates trafficking from the plasma
membrane by controlling Rac1 activity; EHD3 regulates
endosome-to-Golgi transport, and preserves Golgi
morphology; EHD4 is involved in the control of
trafficking at the early endosome and regulates exit of
cargo toward the recycling compartment as well as late
endocytic pathway. Rme-1, an ortholog of human EHD1,
controls the recycling of internalized receptors from the
endocytic recycling compartment to the plasma membrane.
In D. melanogaster, deletion of the Past1 gene leads to
infertility as well as premature death of adult flies.
Arabidopsis thaliana also has homologs of EHD proteins
(AtEHD1 and AtEHD2), possibly involved in regulating
endocytosis and signaling.
Length = 241
Score = 30.7 bits (70), Expect = 4.8
Identities = 29/158 (18%), Positives = 45/158 (28%), Gaps = 48/158 (30%)
Query: 934 GKTTLIDHLLRQSGTFRKNQNINAR--------IMDSNEIEKERGITI------------ 973
GK+T I++LL Q +M + G +
Sbjct: 11 GKSTFINYLLGQDYP---GLRTGPEPTTDRFTVVMHGEDDGTIPGNALVVDPDKPFRGLS 67
Query: 974 ------FSKNCSIEYNGT---RINIIDTPGHADFGGEVERIL-------------SMVDN 1011
+K + I+DTPG GE +R D
Sbjct: 68 KFGNGFLNKFEGSTLPHPLLESVTIVDTPGILS--GEKQRQSRGYDFNAVCRWFAERADL 125
Query: 1012 VLLLIDAVE-GPMPQTRFVTRKALKLGFKPIVVVNKID 1048
+ LL D + + R V + K +V+NK D
Sbjct: 126 IFLLFDPHKLDISDEFRRVIEQLKGHESKIRIVLNKAD 163
>gnl|CDD|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase. Members
of this family are involved in modifying bases in RNA
molecules. They carry out the conversion of uracil bases
to pseudouridine. This family includes RluD, a
pseudouridylate synthase that converts specific uracils
to pseudouridine in 23S rRNA. RluA from E. coli converts
bases in both rRNA and tRNA.
Length = 149
Score = 30.1 bits (68), Expect = 5.2
Identities = 20/107 (18%), Positives = 36/107 (33%), Gaps = 18/107 (16%)
Query: 665 VLLLDKPYGL-SSNNALKKIKYLLNAKKVGYTGT--------LDPFATGLLPLCFGEATK 715
++++KP G+ + L V G LD +GL L + +
Sbjct: 1 YIVVNKPAGVPVHPTDPSDLLSLTALLLVAELGKFRLYPVHRLDRNTSGL--LLLAKDGE 58
Query: 716 FSNYLSEA------DKYYEAIIHLGITTETGDIEGKIIDFNKNIPNS 756
+N L++ +K Y A++ E G I+ I
Sbjct: 59 AANKLNKLFPERKVEKEYLALVDGPEEEE-GTIKAPIKKDKAVGFRK 104
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 30.1 bits (68), Expect = 5.3
Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 142 IVVLVVAADDGVMPQTREAIA----HAKISGVPLIVAINKIDK 180
+V +V ++DD + + +E + H ++SG P++V NK DK
Sbjct: 70 LVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDK 112
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 30.4 bits (68), Expect = 6.6
Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 980 IEYNGTRINIIDTPGHADFGGEVERI--------LSMVDNVLLLIDAVEGPMPQTRFVTR 1031
I T++ + DTPG + G +E+ L D VLL+ID+++ T +
Sbjct: 95 ITLKDTQVILYDTPGIFEPKGSLEKAMVRCAWSSLHSADLVLLIIDSLKSFDDITHNILD 154
Query: 1032 KALKLGFKPIVVVNKID 1048
K L PI ++NKID
Sbjct: 155 KLRSLNIVPIFLLNKID 171
>gnl|CDD|179620 PRK03642, PRK03642, putative periplasmic esterase; Provisional.
Length = 432
Score = 30.5 bits (69), Expect = 6.7
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 534 KAGFECERLSRIENQIQRDISEIIAFDIQNPIINIITITEVKITLD--YSYAK 584
KAGF E+L++++ I + I D P +N++ I + +I + YAK
Sbjct: 32 KAGFNSEKLNQMDRWISQQI------DAGYPGVNLLIIKDNQIVYRKAWGYAK 78
>gnl|CDD|130299 TIGR01232, lacD, tagatose 1,6-diphosphate aldolase. This family
consists of Gram-positive proteins. Tagatose
1,6-diphosphate aldolase is part of the
tagatose-6-phosphate pathway of galactose-6-phosphate
degradation [Energy metabolism, Biosynthesis and
degradation of polysaccharides].
Length = 325
Score = 30.4 bits (68), Expect = 7.8
Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 666 LLLDKPYGLSSNNAL-KKIKYLLNAKKVGYTGTLDPFATGLLPLCFGE 712
+LLD YGL +++A K LL +K GY D A G LP C E
Sbjct: 66 ILLDPEYGLPASDARNKDCGLLLAYEKTGY----DVNAKGRLPDCLVE 109
>gnl|CDD|239670 cd03699, lepA_II, lepA_II: This subfamily represents the domain II of
LepA, a GTP-binding protein localized in the cytoplasmic
membrane. The N-terminal domain of LepA shares regions of
homology to translation factors. In terms of interaction
with the ribosome, EF-G, EF-Tu and IF2 have all been
demonstrated to interact at overlapping sites on the
ribosome. Chemical protection studies demonstrate that
they all include the universally conserved alpha-sarcin
loop as part of their binding site. These data indicate
that LepA may bind to this location on the ribosome as
well. LepA has never been observed in archaea, and
eukaryl LepA is organellar. LepA is therefore a true
bacterial GTPase, found only in the bacterial lineage.
Length = 86
Score = 28.2 bits (64), Expect = 8.0
Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 13/84 (15%)
Query: 1131 YSSYLGKIGIGRILSGRIKSLQDVVIMNGPDDKPNKA--KINQIRVFKGLDRVLVNEALS 1188
Y Y G I + R+ G +K + M+ ++ ++ +F+ + +E +
Sbjct: 10 YDPYRGVIALVRVFDGTLKKGDKIRFMS------TGKEYEVEEVGIFR-PEMTPTDELSA 62
Query: 1189 GDI-VLITGI---EEICIGSTICD 1208
G + +I GI ++ +G TI
Sbjct: 63 GQVGYIIAGIKTVKDARVGDTITL 86
>gnl|CDD|185228 PRK15328, PRK15328, invasion protein IagB; Provisional.
Length = 160
Score = 29.4 bits (66), Expect = 8.1
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 836 SEDIGKMLGCGAHLKYLRRIGID--KLTLDKCLNI 868
S D+G M H+K L+++GI +L D C+++
Sbjct: 58 STDLGLMQINSFHMKRLKKMGISEKQLLQDPCISV 92
>gnl|CDD|232987 TIGR00467, lysS_arch, lysyl-tRNA synthetase, archaeal and
spirochete. This model represents the lysyl-tRNA
synthetases that are class I amino-acyl tRNA
synthetases. It includes archaeal and spirochete
examples of the enzyme. All other known examples are
class IIc amino-acyl tRNA synthetases and seem to form a
separate orthologous set [Protein synthesis, tRNA
aminoacylation].
Length = 515
Score = 30.6 bits (69), Expect = 8.1
Identities = 39/184 (21%), Positives = 71/184 (38%), Gaps = 22/184 (11%)
Query: 519 ELDSLKRFKDNVKEVKAGFECERLSRIENQIQRDISEIIAFDIQNPIINIITITEVKITL 578
+ D +RF VK+ + RI Q SE I + + P ++ I++ I
Sbjct: 322 DYDKFERFYYGVKDKDEEKKRAFK-RIYELSQPMPSERIPYQV--PFRHLSVISQ--IFE 376
Query: 579 DYSYAKIFFTTFN-----KDISIKNILDNLSKAKNYIRFKLSKKLHIHTLP----ILNFF 629
+ KI D K I L+ A+N+IR K + + +L +
Sbjct: 377 NNDIEKILEILKRVQYTVDDQKDKLINKRLNCARNWIR-KYAPEDFKFSLRSKFDNMEIL 435
Query: 630 YDNSIENAMMISKLIDGIKYCMQFHIKKNKNIIHGVLLLDKPYGLSSNNALKKIKYLLNA 689
+NS + I++L + +K + I + + + K G+ A + I +L
Sbjct: 436 EENSKK---AINELAEFLKKNF----EVATEIHNLIYKISKENGIEPALAFQAIYKILLG 488
Query: 690 KKVG 693
K+ G
Sbjct: 489 KEYG 492
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 30.4 bits (69), Expect = 8.5
Identities = 31/107 (28%), Positives = 43/107 (40%), Gaps = 23/107 (21%)
Query: 989 IIDTPGHADFGGEVERILSMVDNVLLLIDAVEGPMPQTRFVTRKALKLG---FKPIVVVN 1045
I++T G EV+ I +M D L+++ G Q +K G I+V+N
Sbjct: 148 IVETVGVGQ--SEVD-IANMADTFLVVMIPGAGDDLQ-------GIKAGIMEIADIIVIN 197
Query: 1046 KIDRSNARPEWVVDATFDLFDKLCATEEQLDF-----PVIYTSALHG 1087
K DR A A +L L E PV+ TSAL G
Sbjct: 198 KADRKGAE-----KAARELRSALDLLREVWRENGWRPPVVTTSALEG 239
>gnl|CDD|217326 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding protein.
Members of this family are found in a range of archaea
and eukaryotes and have hypothesised ATP binding
activity.
Length = 235
Score = 30.0 bits (68), Expect = 8.6
Identities = 24/134 (17%), Positives = 42/134 (31%), Gaps = 29/134 (21%)
Query: 122 DTPGHEAFTAMRARGAKVTD--------IVVLVVAADDGVMPQTREAIAHAKIS-----G 168
DTPG A+ + V +V P + +S G
Sbjct: 96 DTPGQIELFTHWESLARGVEALEASLRLGAVYLVDTRRLTDPSDFFSGLLYALSIMLRLG 155
Query: 169 VPLIVAINKID--KLDINLDRIKQDLISEQVIP--------------EEYGGASPFISIS 212
+P +VA+NK D L+ L + ++ + + F+ +
Sbjct: 156 LPFVVALNKFDLLSLEFALKWFTDPDDLQLLLELDPSKLNEAIREALDLFYLVPRFLPDA 215
Query: 213 AKTGVGINKLLENI 226
+TG + LL I
Sbjct: 216 RETGESMEDLLTLI 229
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial cells,
and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the nephron.
It was also shown to be one of several proteins whose
expression is upregulated in human myelodysplastic
syndrome (MDS) patients. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 220
Score = 29.9 bits (67), Expect = 9.5
Identities = 26/73 (35%), Positives = 35/73 (47%), Gaps = 14/73 (19%)
Query: 72 VTIMGHVDHGKTSLLD-YI-RKTNVVFSEAGG--ITQHIGAYNVVTNHGSITFLDTPGHE 127
V ++G ++ GKTSLL Y+ R+ S GG + G YN I+ DT G E
Sbjct: 3 VVLLGDMNVGKTSLLHRYMERRFKDTVSTVGGAFYLKQWGPYN-------ISIWDTAGRE 55
Query: 128 AFT---AMRARGA 137
F +M RGA
Sbjct: 56 QFHGLGSMYCRGA 68
>gnl|CDD|235541 PRK05643, PRK05643, DNA polymerase III subunit beta; Validated.
Length = 367
Score = 30.1 bits (69), Expect = 9.7
Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 388 NLSTDKVKIQVIHNAVGNINESDINLAIASKAIIIGFNVR--ADASTRKLAQINNINIR 444
+LS ++KI + G E + + + + + IGFNV+ D L +++ +R
Sbjct: 285 SLSEGQLKISANNPEQGEAEEE-LEVEYSGEELEIGFNVKYLLDV----LKALDSEEVR 338
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
0.320 0.139 0.389
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 79,684,409
Number of extensions: 8446008
Number of successful extensions: 8823
Number of sequences better than 10.0: 1
Number of HSP's gapped: 8318
Number of HSP's successfully gapped: 491
Length of query: 1527
Length of database: 10,937,602
Length adjustment: 110
Effective length of query: 1417
Effective length of database: 6,058,662
Effective search space: 8585124054
Effective search space used: 8585124054
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 (21.8 bits)
S2: 66 (29.1 bits)