RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16810
(755 letters)
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 1080 bits (2794), Expect = 0.0
Identities = 401/560 (71%), Positives = 457/560 (81%)
Query: 196 RVFDSIMNYKKEEAESLLSKLGIELKPEDKEKDGKALLKVVMRTWLPAGEALLQMIAIHL 255
++FD++MN KE+ + +L L I L EDKE GK LLK VM+ WLPA + LL+MI HL
Sbjct: 277 QLFDAVMNEDKEKYDKMLKSLNISLTGEDKELTGKPLLKAVMQKWLPAADTLLEMIVDHL 336
Query: 256 PSPVVAQKYRMEMLYEGPHDDEAAIGIKNCDPNAPLMMYVSKMVPTSDKGRFYAFGRVFS 315
PSP AQKYR+E LYEGP DDEAA I+NCDPN PLMMY+SKMVPTSDKGRFYAFGRVFS
Sbjct: 337 PSPKEAQKYRVENLYEGPMDDEAANAIRNCDPNGPLMMYISKMVPTSDKGRFYAFGRVFS 396
Query: 316 GKVATGQKARIMGPNYIPGKKEDLYEKAIQRTILMMGRYVEAIEDVPSGNICGLVGVDQF 375
G VATGQK RI GPNY+PGKKEDL+EK IQRT+LMMGRYVE IEDVP GN GLVGVDQ+
Sbjct: 397 GTVATGQKVRIQGPNYVPGKKEDLFEKNIQRTVLMMGRYVEQIEDVPCGNTVGLVGVDQY 456
Query: 376 LVKTGTITTFKDAHNLRVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLSKSDPMVQCII 435
LVK+GTITT + AHN+R MK+SVSPVVRVAVEPKNP DLPKLVEGLKRL+KSDP+V C
Sbjct: 457 LVKSGTITTSETAHNIRDMKYSVSPVVRVAVEPKNPKDLPKLVEGLKRLAKSDPLVVCTT 516
Query: 436 EESGEHIVAGAGELHLEICLKDLEEDHACIPIKKSDPVVSYRETVSEESDQVCLSKSPNK 495
EESGEHIVAG GELH+EICLKDLE+D+A I I SDPVVSYRETV+EES Q CLSKSPNK
Sbjct: 517 EESGEHIVAGCGELHVEICLKDLEDDYANIDIIVSDPVVSYRETVTEESSQTCLSKSPNK 576
Query: 496 HNRLFMKAAPLPDGLPEDIDKGEVNPRDDFKIRGRYLADKYEFDVTEARKIWSFGPDGTG 555
HNRL+MKA PL + L E I++G+V P DD K R +LADKYE+D +ARKIW FGP+ G
Sbjct: 577 HNRLYMKAEPLTEELAEAIEEGKVGPEDDPKERANFLADKYEWDKNDARKIWCFGPENKG 636
Query: 556 PNLLIDCTKGVQYLNEIKDSVVAGFQWAAKEGVLSEENLRGVRFNIHDVTLHADAIHRGG 615
PN+L+D TKGVQY+NEIKDS V+ FQWA KEGVL +EN+RG+RFNI DVTLHADAIHRG
Sbjct: 637 PNVLVDVTKGVQYMNEIKDSCVSAFQWATKEGVLCDENMRGIRFNILDVTLHADAIHRGA 696
Query: 616 GQIIPTTRRVLYASLLTACPRLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAG 675
GQIIPT RRV YA LTA PRL+EP++L +I PE A+GGIY VLNRRRG V E Q G
Sbjct: 697 GQIIPTARRVFYACELTASPRLLEPMFLVDITAPEDAMGGIYSVLNRRRGVVIGEEQRPG 756
Query: 676 TPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQVLPGDPTDPGSKPYNVVQET 735
TP+ +KAYLPV ESFGFTA LR+ T GQAFPQCVFDHWQV+PGDP +PGSK +V
Sbjct: 757 TPLSNIKAYLPVAESFGFTAALRAATSGQAFPQCVFDHWQVVPGDPLEPGSKANEIVLSI 816
Query: 736 RKRKGLKEGLPDLQSYLDKL 755
RKRKGLK +PDL +YLDKL
Sbjct: 817 RKRKGLKPEIPDLDNYLDKL 836
Score = 363 bits (933), Expect = e-113
Identities = 139/200 (69%), Positives = 162/200 (81%), Gaps = 12/200 (6%)
Query: 1 MMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIK 60
+MD IRNMSVIAHVDHGKSTLTDSLV KAGII+ AG+ RFTDTR DEQER ITIK
Sbjct: 12 IMDNPDQIRNMSVIAHVDHGKSTLTDSLVCKAGIISSKNAGDARFTDTRADEQERGITIK 71
Query: 61 STAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALV 120
ST IS+Y+E D +D +++ FLINLIDSPGHVDFSSEVTAALRVTDGALV
Sbjct: 72 STGISLYYEHDLED----------GDDKQPFLINLIDSPGHVDFSSEVTAALRVTDGALV 121
Query: 121 VVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNV 180
VVDCV GVCVQTETVLRQA+ ERI+PVLF+NK+DRA+LELQLD E++YQ F + +ENVNV
Sbjct: 122 VVDCVEGVCVQTETVLRQALQERIRPVLFINKVDRAILELQLDPEEIYQNFVKTIENVNV 181
Query: 181 IIATYSDDSGPMGEVRVFDS 200
IIATY+D+ MG+V+V+
Sbjct: 182 IIATYNDEL--MGDVQVYPE 199
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 1010 bits (2612), Expect = 0.0
Identities = 368/563 (65%), Positives = 451/563 (80%), Gaps = 3/563 (0%)
Query: 196 RVFDSIMNYKKEEAESLLSKLGIELKPEDKEKDGKALLKVVMRTWLPAGEALLQMIAIHL 255
++ ++ MN +K++ +L KLG+ LK ++KE GKAL+K VM+TWLPA +ALL+MI HL
Sbjct: 281 QIINTCMNDQKDKLWPMLEKLGVTLKSDEKELMGKALMKRVMQTWLPASDALLEMIIFHL 340
Query: 256 PSPVVAQKYRMEMLYEGPHDDEAAIGIKNCDPNAPLMMYVSKMVPTSDKGRFYAFGRVFS 315
PSP AQ+YR+E LYEGP DD+ A I+NCDPN PLM+YVSKM+P SDKGRF+AFGRVFS
Sbjct: 341 PSPAKAQRYRVENLYEGPLDDKYATAIRNCDPNGPLMLYVSKMIPASDKGRFFAFGRVFS 400
Query: 316 GKVATGQKARIMGPNYIPGKKEDLYEKAIQRTILMMGRYVEAIEDVPSGNICGLVGVDQF 375
G VATG K RIMGPNY+PG+K+DLY K++QRT++ MG+ E++EDVP GN +VG+DQF
Sbjct: 401 GTVATGMKVRIMGPNYVPGEKKDLYVKSVQRTVIWMGKKQESVEDVPCGNTVAMVGLDQF 460
Query: 376 LVKTGTITTFK--DAHNLRVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLSKSDPMVQC 433
+ K T+T K DAH ++ MKFSVSPVVRVAV+ KN +DLPKLVEGLKRL+KSDPMVQC
Sbjct: 461 ITKNATLTNEKEVDAHPIKAMKFSVSPVVRVAVQCKNASDLPKLVEGLKRLAKSDPMVQC 520
Query: 434 IIEESGEHIVAGAGELHLEICLKDLEEDH-ACIPIKKSDPVVSYRETVSEESDQVCLSKS 492
IEESGEHI+AGAGELHLEICLKDL++D IK SDPVVS+RETV E+S + +SKS
Sbjct: 521 TIEESGEHIIAGAGELHLEICLKDLQDDFMGGAEIKVSDPVVSFRETVLEKSCRTVMSKS 580
Query: 493 PNKHNRLFMKAAPLPDGLPEDIDKGEVNPRDDFKIRGRYLADKYEFDVTEARKIWSFGPD 552
PNKHNRL+M+A PL +GL E ID G + PRDD KIR + LA+++ +D A+KIW FGP+
Sbjct: 581 PNKHNRLYMEARPLEEGLAEAIDDGRIGPRDDPKIRSKILAEEFGWDKDLAKKIWCFGPE 640
Query: 553 GTGPNLLIDCTKGVQYLNEIKDSVVAGFQWAAKEGVLSEENLRGVRFNIHDVTLHADAIH 612
TGPN+++D KGVQYLNEIKDSVVAGFQWA KEG L+EEN+RG+ F + DV LHADAIH
Sbjct: 641 TTGPNMVVDMCKGVQYLNEIKDSVVAGFQWATKEGALAEENMRGICFEVCDVVLHADAIH 700
Query: 613 RGGGQIIPTTRRVLYASLLTACPRLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQ 672
RGGGQIIPT RRV+YAS LTA PRL+EPVYL EIQ PE A+GGIY VLN++RGHVFEEMQ
Sbjct: 701 RGGGQIIPTARRVIYASQLTAKPRLLEPVYLVEIQAPEQALGGIYSVLNQKRGHVFEEMQ 760
Query: 673 VAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQVLPGDPTDPGSKPYNVV 732
GTP++ +KAYLPV ESFGF+ LR+ T GQAFPQCVFDHW ++ DP + GS+ +V
Sbjct: 761 RPGTPLYNIKAYLPVIESFGFSGTLRAATSGQAFPQCVFDHWDMMSSDPLEAGSQAAQLV 820
Query: 733 QETRKRKGLKEGLPDLQSYLDKL 755
+ RKRKGLKE +P L Y DKL
Sbjct: 821 ADIRKRKGLKEQMPPLSEYEDKL 843
Score = 349 bits (896), Expect = e-108
Identities = 133/197 (67%), Positives = 157/197 (79%), Gaps = 6/197 (3%)
Query: 1 MMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIK 60
+MDKK NIRNMSVIAHVDHGKSTLTDSLV+ AGIIA AG+ R TDTR DE ER ITIK
Sbjct: 12 IMDKKHNIRNMSVIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRMTDTRADEAERGITIK 71
Query: 61 STAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALV 120
ST IS+Y+E+ D+ + ++ +LINLIDSPGHVDFSSEVTAALR+TDGALV
Sbjct: 72 STGISLYYEMTDESLKDFKG----ERDGNEYLINLIDSPGHVDFSSEVTAALRITDGALV 127
Query: 121 VVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNV 180
VVDC+ GVCVQTETVLRQA+ ERI+PVL +NKMDR LELQ+D E+ YQTF R++EN NV
Sbjct: 128 VVDCIEGVCVQTETVLRQALGERIRPVLTVNKMDRCFLELQVDGEEAYQTFSRVIENANV 187
Query: 181 IIATYSDDSGPMGEVRV 197
I+ATY D +G+V+V
Sbjct: 188 IMATYEDPL--LGDVQV 202
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 637 bits (1646), Expect = 0.0
Identities = 290/784 (36%), Positives = 441/784 (56%), Gaps = 98/784 (12%)
Query: 2 MDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKS 61
M + IRN+ +IAH+DHGK+TL+D+L++ AG+I+ AGE D ++EQ R ITIK+
Sbjct: 14 MKNPEQIRNIGIIAHIDHGKTTLSDNLLAGAGMISEELAGEQLALDFDEEEQARGITIKA 73
Query: 62 TAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVV 121
+SM E + K+ +LINLID+PGHVDF +VT A+R DGA+VV
Sbjct: 74 ANVSMVHEYEGKE----------------YLINLIDTPGHVDFGGDVTRAMRAVDGAIVV 117
Query: 122 VDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNVI 181
VD V GV QTETVLRQA+ ER+KPVLF+NK+DR + EL+L +++ Q +I+++VN +
Sbjct: 118 VDAVEGVMPQTETVLRQALRERVKPVLFINKVDRLIKELKLTPQEMQQRLLKIIKDVNKL 177
Query: 182 IATYSDD--------------------------SGP-MGEVRV-FDSIMNYKKEEAESLL 213
I + + S P M + + F I++Y ++ + L
Sbjct: 178 IKGMAPEEFKEKWKVDVEDGTVAFGSALYNWAISVPMMQKTGIKFKDIIDYYEKGKQKEL 237
Query: 214 SKLGIELKPEDKEKDGKALLKVVMRTWLPAGEALLQMIAIHLPSPVVAQKYRMEMLYEGP 273
++ KA P E +L M+ HLP+P+ AQKYR+ +++G
Sbjct: 238 AE--------------KA----------PLHEVVLDMVVKHLPNPIEAQKYRIPKIWKGD 273
Query: 274 HDDEAAIGIKNCDPNAPLMMYVSKMVPTSDKGRFYAFGRVFSGKVATGQKARIMGPNYIP 333
+ E + NCDPN PL+M V+ ++ G A GRVFSG + GQ+ ++G
Sbjct: 274 LNSEVGKAMLNCDPNGPLVMMVTDIIVDPHAG-EVATGRVFSGTLRKGQEVYLVG---AK 329
Query: 334 GKKEDLYEKAIQRTILMMGRYVEAIEDVPSGNICGLVGVDQFLVKTGTITTFKDAHNLRV 393
K +Q+ + MG E +E++P+GNI + G+ T+ + +D
Sbjct: 330 KKNR------VQQVGIYMGPEREEVEEIPAGNIAAVTGLKDARAGE-TVVSVEDMTPFES 382
Query: 394 MKFSVSPVVRVAVEPKNPADLPKLVEGLKRLSKSDPMVQCII-EESGEHIVAGAGELHLE 452
+K PVV VA+E KNP DLPKL+E L++L+K DP + I EE+GEH+++G GELHLE
Sbjct: 383 LKHISEPVVTVAIEAKNPKDLPKLIEVLRQLAKEDPTLVVKINEETGEHLLSGMGELHLE 442
Query: 453 ICLKDLEEDHACIPIKKSDPVVSYRETVSEESDQVCLSKSPNKHNRLFMKAAPLPDGLPE 512
+ ++ D+ I + S+P+V YRETV +S QV KSPNKHNR ++ PL + + E
Sbjct: 443 VITYRIKRDYG-IEVVTSEPIVVYRETVRGKS-QVVEGKSPNKHNRFYISVEPLEEEVIE 500
Query: 513 DIDKGEVNPRDDFKIRGRYLADKYE---FDVTEARKIWSFGPDGTGPNLLIDCTKGVQYL 569
I +GE++ D K + L +K D EA+++W+ N+ ID TKG+QYL
Sbjct: 501 AIKEGEISEDMDKKEA-KILREKLIEAGMDKDEAKRVWAI----YNGNVFIDMTKGIQYL 555
Query: 570 NEIKDSVVAGFQWAAKEGVLSEENLRGVRFNIHDVTLHADAIHRGGGQIIPTTRRVLYAS 629
NE+ + ++ GF+ A KEG L+ E +RGV+ +HD LH DAIHRG Q+IP R ++A+
Sbjct: 556 NEVMELIIEGFREAMKEGPLAAEPVRGVKVRLHDAKLHEDAIHRGPAQVIPAVRNAIFAA 615
Query: 630 LLTACPRLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNE 689
+LTA P L+EP+ +I P+ +G + + RRG + +M+ G M +++A PV E
Sbjct: 616 MLTAKPTLLEPIQKVDINVPQDYMGAVTREIQGRRGKIL-DMEQEGD-MAIIEAEAPVAE 673
Query: 690 SFGFTADLRSNTGGQAFPQCVFDHWQVLPGDPTDPGSKPYNVVQETRKRKGLKEGLPDLQ 749
FGF ++RS T G+A F ++ +P ++V++ R+RKGLK LP +
Sbjct: 674 MFGFAGEIRSATEGRALWSTEFAGFEPVPDSLQL------DIVRQIRERKGLKPELPKPE 727
Query: 750 SYLD 753
+L
Sbjct: 728 DFLS 731
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 584 bits (1508), Expect = 0.0
Identities = 236/789 (29%), Positives = 343/789 (43%), Gaps = 148/789 (18%)
Query: 4 KKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETR----FTDTRKDEQERCITI 59
+ IRN+ ++AH+D GK+TLT+ ++ GII+ K GE D + EQER ITI
Sbjct: 6 PLERIRNIGIVAHIDAGKTTLTERILFYTGIIS--KIGEVHDGAATMDWMEQEQERGITI 63
Query: 60 KSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGAL 119
S A +++++ D + INLID+PGHVDF+ EV +LRV DGA+
Sbjct: 64 TSAATTLFWKGD-------------------YRINLIDTPGHVDFTIEVERSLRVLDGAV 104
Query: 120 VVVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVN 179
VVVD V GV QTETV RQA + +LF+NKMDR + L E L + V
Sbjct: 105 VVVDAVEGVEPQTETVWRQADKYGVPRILFVNKMDRLGADFYLVVEQLKERLGANPVPVQ 164
Query: 180 VIIATYSDDSGP-----MGEVRVFDSIMNY--------KKEEAESLLSKL---------- 216
+ I + G M V F Y KE AE KL
Sbjct: 165 LPIGAEEEFEGVIDLVEMKAVA-FGDGAKYEWIEIPADLKEIAEEAREKLLEALAEFDEE 223
Query: 217 -------GIELKPED----------KEKDGKALLKVVMRTWLPAGEALLQMIAIHLPSPV 259
G E E+ K L + + LL + +LPSP+
Sbjct: 224 LMEKYLEGEEPTEEEIKKALRKGTIAGKIVPVLCGSAFKN--KGVQPLLDAVVDYLPSPL 281
Query: 260 VAQKYRMEMLYEGPHDDEAAIGIKN-CDPNAPLMMYVSKMVPTSDKGRFYAFGRVFSGKV 318
+G DDE + PL V K++ G+ F RV+SG +
Sbjct: 282 DVP------PIKGDLDDEIEKAVLRKASDEGPLSALVFKIMTDPFVGKLT-FVRVYSGTL 334
Query: 319 ATGQKARIMGPNYIPGKKEDLYEKAIQRTILMMGRYVEAIEDVPSGNICGLVGVDQFLVK 378
+G + N GKKE + R +LM G E +++VP+G+I LVG+
Sbjct: 335 KSGSEVL----NSTKGKKE-----RVGRLLLMHGNEREEVDEVPAGDIVALVGLKD--AT 383
Query: 379 TG-TITTFKDAHNLRVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLSKSDPMVQC-IIE 436
TG T+ L M+F PV+ VAVEPK AD KL E L +L++ DP + E
Sbjct: 384 TGDTLCDENKPVILESMEFP-EPVISVAVEPKTKADQEKLSEALNKLAEEDPTFRVETDE 442
Query: 437 ESGEHIVAGAGELHLEICLKDLEEDHACIPIKKSDPVVSYRETVSEESDQV----CLSKS 492
E+GE I++G GELHLEI + D + + ++ P V+YRET+ ++S+ S
Sbjct: 443 ETGETIISGMGELHLEIIV-DRLKREFGVEVEVGKPQVAYRETIRKKSEVEGKHKKQSGG 501
Query: 493 PNKHNRLFMKAAPLPDGLPEDIDKGEVNPRDDFKIRGRYLADKYEFDVTEARKIWSFGPD 552
P ++ ++++ PL DG G DK V P
Sbjct: 502 PGQYGHVYIEIEPLEDGS------------------GFEFVDKIVGGV---------VPK 534
Query: 553 GTGPNLLIDCTKGVQYLNEIKDSVVAGFQWAAKEGVLSEENLRGVRFNIHDVTLHADAIH 612
+Y+ ++ GF+ A K G L+ + V+ + D + H
Sbjct: 535 --------------EYIPAVEK----GFREALKSGPLAGYPVVDVKVTLLDGSYHEVD-- 574
Query: 613 RGGGQIIPTTRRVLYASLLTACPRLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQ 672
++L A P L+EP+ EI PE +G + G LN RRG + Q
Sbjct: 575 SSEMAFKIAASLAFKEAMLKAKPVLLEPIMKVEITTPEEYMGDVIGDLNSRRGQILGMEQ 634
Query: 673 VAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQVLPGDPTDPGSKPYNVV 732
G + V+KA +P+ E FG+ DLRS T G+A FDH++ +P + ++
Sbjct: 635 RPGGGLDVIKAEVPLAEMFGYATDLRSATQGRASFSMEFDHYEEVPSSVAEE------II 688
Query: 733 QETRKRKGL 741
+ RKRKGL
Sbjct: 689 AKRRKRKGL 697
>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 = 475 bits (1223), Expect = e-158
Identities = 273/755 (36%), Positives = 417/755 (55%), Gaps = 61/755 (8%)
Query: 1 MMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIK 60
+M K K IRN+ ++AH+DHGK+TL+D+L++ AG+I+ AG+ + D + EQER ITI
Sbjct: 12 LMWKPKFIRNIGIVAHIDHGKTTLSDNLLAGAGMISEELAGQQLYLDFDEQEQERGITIN 71
Query: 61 STAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALV 120
+ +SM E + + +LINLID+PGHVDF +VT A+R DGA+V
Sbjct: 72 AANVSMVHEYEGNE----------------YLINLIDTPGHVDFGGDVTRAMRAVDGAIV 115
Query: 121 VVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNV 180
VV V GV QTETVLRQA+ E +KPVLF+NK+DR + EL+L ++L + F +I+ VN
Sbjct: 116 VVCAVEGVMPQTETVLRQALKENVKPVLFINKVDRLINELKLTPQELQERFIKIITEVNK 175
Query: 181 II-ATYSDDSGPMGEVRVFDSIMNYKKEEAESLLS-----KLGIELK------PEDKEKD 228
+I A ++ +VRV D + + +S K GI K EDK+K+
Sbjct: 176 LIKAMAPEEFRDKWKVRVEDGSVAFGSAYYNWAISVPSMKKTGIGFKDIYKYCKEDKQKE 235
Query: 229 GKALLKVVMRTWLPAGEALLQMIAIHLPSPVVAQKYRMEMLYEGPHDDEAAIGIKNCDPN 288
L K P + +L M+ HLPSP+ AQKYR+ ++++G + E + NCDP
Sbjct: 236 ---LAKKS-----PLHQVVLDMVIRHLPSPIEAQKYRIPVIWKGDLNSEVGKAMLNCDPK 287
Query: 289 APLMMYVSKMVPTSDKGRFYAFGRVFSGKVATGQKARIMGPNYIPGKKEDLYEKAIQRTI 348
PL + ++K+V G A GR++SG + G + YI +K + IQ+
Sbjct: 288 GPLALMITKIVVDKHAGEV-AVGRLYSGTIRPGMEV------YIVDRKA---KARIQQVG 337
Query: 349 LMMGRYVEAIEDVPSGNICGLVGVDQFLVKTGTITTFKDAHNLRVMKFSVSPVVRVAVEP 408
+ MG ++++P+GNI ++G+ + TT ++ +K PVV VA+E
Sbjct: 338 VYMGPERVEVDEIPAGNIVAVIGLKDAVAGETICTTVENITPFESIKHISEPVVTVAIEA 397
Query: 409 KNPADLPKLVEGLKRLSKSDPMVQCII-EESGEHIVAGAGELHLEICLKDLEEDHACIPI 467
KN DLPKL+E L++++K DP V I EE+GEH+++G GELHLEI ++ + ED+ + +
Sbjct: 398 KNTKDLPKLIEVLRQVAKEDPTVHVEINEETGEHLISGMGELHLEIIVEKIREDYG-LDV 456
Query: 468 KKSDPVVSYRETVSEESDQVCLSKSPNKHNRLFMKAAPLPDGLPEDIDKGEVNPRDDFKI 527
+ S P+V YRETV+ S V KSPNKHNR ++ PL + + + +G++ K
Sbjct: 457 ETSPPIVVYRETVTGTSP-VVEGKSPNKHNRFYIVVEPLEESVIQAFKEGKIVDMKMKKK 515
Query: 528 RGRYLADKYEFDVTEARKIWSFGPDGTGPNLLIDCTKGVQYLNEIKDSVVAGFQWAAKEG 587
R L + D EA ++ + NL I+ T+G+QYL+E K+ ++ GF+ A + G
Sbjct: 516 ERRRLLIEAGMDSEEAARVEEYYEG----NLFINMTRGIQYLDETKELILEGFREAMRNG 571
Query: 588 VLSEENLRGVRFNIHDVTLHADAIHRGGGQIIPTTRRVLYASLLTACPRLMEPVYLCEIQ 647
++ E GV+ + D LH DA+HRG Q+IP R ++A+++ A P L+EP I
Sbjct: 572 PIAREKCMGVKVKLMDAKLHEDAVHRGPAQVIPAVRSGIFAAMMQAKPVLLEPYQKVFIN 631
Query: 648 CPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFP 707
P+ +G + RRG + EM+ G M + A PV E FGF +R T G+
Sbjct: 632 VPQDMMGAATREIQNRRGQIL-EMKQEGD-MVTIIAKAPVAEMFGFAGAIRGATSGRCLW 689
Query: 708 QCVFDHWQVLPGDPTDPGSKPYNVVQETRKRKGLK 742
++++P + V E RKRKGLK
Sbjct: 690 STEHAGFELVPQNLQQ------EFVMEVRKRKGLK 718
>gnl|CDD|238839 cd01681, aeEF2_snRNP_like_IV, This family represents domain IV of
archaeal and eukaryotic elongation factor 2 (aeEF-2) and
of an evolutionarily conserved U5 snRNP-specific
protein. U5 snRNP is a GTP-binding factor closely
related to the ribosomal translocase EF-2. 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 of the small subunit
of ribosome and the mRNA is shifted one codon relative
to the ribosome. It has been shown that EF-2_IV domain
mimics the shape of anticodon arm of the tRNA in the
structurally homologous ternary complex of Phe-tRNA,
EF-1 (another transcriptional elongation factor) and GTP
analog. The tip portion of this domain is found in a
position that overlaps the anticodon arm of the A-site
tRNA, implying that EF-2 displaces the A-site tRNA to
the P-site by physical interaction with the anticodon
arm.
Length = 177
Score = 311 bits (799), Expect = e-102
Identities = 119/177 (67%), Positives = 138/177 (77%), Gaps = 4/177 (2%)
Query: 471 DPVVSYRETVSEESDQVCLSKSPNKHNRLFMKAAPLPDGLPEDIDKGEVNPRDDFKIRGR 530
DPVVS+RETV E S CL+KSPNKHNRL+M+A PLP+ L EDI+KG++ +DD K R R
Sbjct: 1 DPVVSFRETVVETSSGTCLAKSPNKHNRLYMRAEPLPEELIEDIEKGKITLKDDKKKRAR 60
Query: 531 YLADKYEFDVTEARKIWSFGPDGTGPNLLIDCTKGVQY----LNEIKDSVVAGFQWAAKE 586
L DKY +D ARKIW+FGPD TGPN+L+D TKGVQY LNEIKDS+VAGFQWA KE
Sbjct: 61 ILLDKYGWDKLAARKIWAFGPDRTGPNILVDDTKGVQYDKSLLNEIKDSIVAGFQWATKE 120
Query: 587 GVLSEENLRGVRFNIHDVTLHADAIHRGGGQIIPTTRRVLYASLLTACPRLMEPVYL 643
G L EE +RGV+F + D TLHADAIHRGGGQIIP RR YA+ L A PRLMEP+YL
Sbjct: 121 GPLCEEPMRGVKFKLEDATLHADAIHRGGGQIIPAARRACYAAFLLASPRLMEPMYL 177
>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 = 310 bits (797), Expect = e-101
Identities = 116/195 (59%), Positives = 144/195 (73%), Gaps = 12/195 (6%)
Query: 9 RNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYF 68
RN+ +IAHVDHGK+TL+DSL++ AGII+ AG+ R+ DTR+DEQER ITIKS+AIS+YF
Sbjct: 1 RNICIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYLDTREDEQERGITIKSSAISLYF 60
Query: 69 ELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGV 128
E +++ M + +LINLIDSPGHVDFSSEVTAALR+TDGALVVVD V GV
Sbjct: 61 EYEEEKM-----------DGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDAVEGV 109
Query: 129 CVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNVIIATYSDD 188
CVQTETVLRQA+ ER+KPVL +NK+DR +LEL+L E+ YQ RIVE+VN II TY+ +
Sbjct: 110 CVQTETVLRQALEERVKPVLVINKIDRLILELKLSPEEAYQRLLRIVEDVNAIIETYAPE 169
Query: 189 SGPMGEVRVFDSIMN 203
E F
Sbjct: 170 E-FKQEKWKFSPQKG 183
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 241 bits (617), Expect = 1e-69
Identities = 215/804 (26%), Positives = 322/804 (40%), Gaps = 193/804 (24%)
Query: 6 KNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGE----TRFTDTRKDEQERCITIKS 61
IRN+ ++AH+D GK+TLT+ ++ G I K GE T TD EQER ITI+S
Sbjct: 6 MQIRNIGILAHIDAGKTTLTERILFYTGKIH--KMGEVEDGTTVTDWMPQEQERGITIES 63
Query: 62 TAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVV 121
A S + INLID+PGH+DF+ EV +LRV DGA+VV
Sbjct: 64 AATSCDW--------------------DNHRINLIDTPGHIDFTGEVERSLRVLDGAVVV 103
Query: 122 VDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDR------ALLE------------LQLD 163
D V+GV QTETV RQA I ++F+NKMDR +LE LQL
Sbjct: 104 FDAVTGVQPQTETVWRQADRYGIPRLIFINKMDRVGADLFKVLEDIEERFGKRPLPLQLP 163
Query: 164 AEDLYQTFQRIVENVNVIIATYSDDSGPMGEVRVFDSIMNYKKEEAESLLSKL------- 216
F+ +V+ + +S+ G G I EE E KL
Sbjct: 164 IGSEDG-FEGVVDLITEPELHFSEGDG--GSTVEEGPIPEELLEEVEEAREKLIEALAEF 220
Query: 217 ----------GIELKPEDKEKDGKALLK------VVMRTWLP-AG-EALLQMIAIHLPSP 258
G EL E + + V+ + L G E LL + +LPSP
Sbjct: 221 DDELLELYLEGEELSAEQLRAPLREGTRSGHLVPVLFGSALKNIGIEPLLDAVVDYLPSP 280
Query: 259 VVAQKYRMEMLYEGPHDDEAAIGIKNCDPNAPLMMYVSKMVPTSDKGRFYAFGRVFSGKV 318
+ R G D+ + + + DP PL+ V K+ G+ RV+SG +
Sbjct: 281 LEVPPPR------GSKDNGKPVKV-DPDPEKPLLALVFKVQYDPYAGKLTYL-RVYSGTL 332
Query: 319 ATGQKARIMGPNYIPGKKEDLYEKAIQRTILMMGRYVEAIEDVPSGNICGLVGVDQFLVK 378
G + G K EK + R + G E ++ +G+I + G+ + ++
Sbjct: 333 RAGSQLYNGT-----GGKR---EK-VGRLFRLQGNKREEVDRAKAGDIVAVAGLKE--LE 381
Query: 379 TGTITTFKDAHN---LRVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLSKSDPMVQC-I 434
TG T D+ + L ++ F PVV +AVEP+ D KL E L++L DP ++
Sbjct: 382 TG--DTLHDSADPVLLELLTF-PEPVVSLAVEPERRGDEQKLAEALEKLVWEDPSLRVEE 438
Query: 435 IEESGEHIVAGAGELHLEICLKDLEEDHACIPIKKSDPVVSYRETVSEESDQVCLSKSPN 494
EE+G+ I++G GELHLE+ L+ L + + + P V+YRET+ + ++ V
Sbjct: 439 DEETGQTILSGMGELHLEVALERLRREFK-LEVNTGKPQVAYRETIRKMAEGVYR----- 492
Query: 495 KHNRLF----------MKAAPLPDGLPEDIDKGEVNPRDDFKIRGRYLADKYEFDVTEAR 544
H + F ++ PL G A
Sbjct: 493 -HKKQFGGKGQFGEVHLRVEPLERG-----------------------AGFIFVSKVVGG 528
Query: 545 KIWSFGPDGTGPNLLIDC-TKGVQYLNEIKDSVVAGFQWAAKEGVLSEENLRGVRFNIHD 603
I P LI KG I++++ +G L+ + +R + D
Sbjct: 529 AI---------PEELIPAVEKG------IREALASGP--------LAGYPVTDLRVTVLD 565
Query: 604 VTLH---------ADAIHRGGGQIIPTTRRVLYASLLTACPRLMEPVYLCEIQCPEVAVG 654
H A + + VL +EP+ EI P VG
Sbjct: 566 GKYHPVDSSESAFKAAARKAFLEAFRKANPVL-----------LEPIMELEITVPTEHVG 614
Query: 655 GIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHW 714
+ G L++RRG + E + G +VKA P+ E FG+ LRS T G+ F H+
Sbjct: 615 DVLGDLSQRRGRI-EGTEPRGDGEVLVKAEAPLAELFGYATRLRSMTKGRGSFTMEFSHF 673
Query: 715 QVLPGDPTDPGSKPYNVVQETRKR 738
P V ++ +
Sbjct: 674 DP----------VPPAVQKKVGSK 687
>gnl|CDD|238840 cd01683, EF2_IV_snRNP, EF-2_domain IV_snRNP domain is a part of
116kD U5-specific protein of the U5 small nucleoprotein
(snRNP) particle, essential component of the
spliceosome. The protein is structurally closely related
to the eukaryotic translational elongation factor EF2.
This domain has been also identified in 114kD
U5-specific protein of Saccharomyces cerevisiae and may
play an important role either in splicing process itself
or the recycling of spliceosomal snRNP.
Length = 178
Score = 213 bits (544), Expect = 6e-65
Identities = 86/177 (48%), Positives = 115/177 (64%), Gaps = 4/177 (2%)
Query: 471 DPVVSYRETVSEESDQVCLSKSPNKHNRLFMKAAPLPDGLPEDIDKGEVNPRDDFKIRGR 530
DPVV++ ETV E S C +++PNK N++ M A PL GL EDI+ G++ + K G+
Sbjct: 1 DPVVTFCETVVETSSAKCFAETPNKKNKITMIAEPLDKGLAEDIENGQLKLSWNRKKLGK 60
Query: 531 YLADKYEFDVTEARKIWSFGPDGTGPNLLIDCT----KGVQYLNEIKDSVVAGFQWAAKE 586
+L KY +D AR IW+FGPD GPN+LID T LN +K+S+V GFQWA +E
Sbjct: 61 FLRTKYGWDALAARSIWAFGPDTKGPNVLIDDTLPEEVDKNLLNSVKESIVQGFQWAVRE 120
Query: 587 GVLSEENLRGVRFNIHDVTLHADAIHRGGGQIIPTTRRVLYASLLTACPRLMEPVYL 643
G L EE +R V+F + D + ++ I RGGGQIIPT RR Y++ L A PRLMEP+Y
Sbjct: 121 GPLCEEPIRNVKFKLLDADIASEPIDRGGGQIIPTARRACYSAFLLATPRLMEPIYE 177
>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 = 225 bits (575), Expect = 8e-64
Identities = 205/791 (25%), Positives = 326/791 (41%), Gaps = 165/791 (20%)
Query: 6 KNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETR----FTDTRKDEQERCITIKS 61
RN+ + AH+D GK+T T+ ++ G I K GE D + E+ER ITI S
Sbjct: 8 NRFRNIGISAHIDAGKTTTTERILFYTGRIH--KIGEVHDGAATMDWMEQEKERGITITS 65
Query: 62 TAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVV 121
A ++++ KG IN+ID+PGHVDF+ EV +LRV DGA+ V
Sbjct: 66 AATTVFW--------------------KGHRINIIDTPGHVDFTVEVERSLRVLDGAVAV 105
Query: 122 VDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRA--------------------LLELQ 161
+D V GV Q+ETV RQA + + F+NKMD+ ++L
Sbjct: 106 LDAVGGVQPQSETVWRQANRYEVPRIAFVNKMDKTGANFLRVVNQIKQRLGANAVPIQLP 165
Query: 162 LDAEDLYQTFQRIVENVNVIIATYSDDSGPMGEVRVFDSIMNYKKEEAESLLSKLGIELK 221
+ AED F +++ V + ++ D G + I + E+A+ L L +
Sbjct: 166 IGAED---NFIGVIDLVEMKAYFFNGD---KGTKAIEKEIPSDLLEQAKELRENLVEAVA 219
Query: 222 PEDKE-----KDGKAL----LKVVMRTWLPAGE----------------ALLQMIAIHLP 256
D+E +G+ L +K +R + E LL + +LP
Sbjct: 220 EFDEELMEKYLEGEELTIEEIKNAIRKGVLNCEFFPVLCGSAFKNKGVQLLLDAVVDYLP 279
Query: 257 SPV-VAQKYRMEMLYEGPHDDEAAIGIKNCDPNAPLMMYVSKMVPTSDKGRFYAFGRVFS 315
SP V ++ D E I K D + P K+ G+ F RV+S
Sbjct: 280 SPTDVPAIKGIDP------DTEKEIERKASD-DEPFSALAFKVATDPFVGQL-TFVRVYS 331
Query: 316 GKVATGQKARIMGPNYIPGKKEDLYEKAIQRTILMMGRYVEAIEDVPSGNICGLVGVDQF 375
G + +G + N KKE + R + M E I++V +G+IC +G+
Sbjct: 332 GVLKSGSYVK----NSRKNKKE-----RVGRLVKMHANNREEIKEVRAGDICAAIGLKD- 381
Query: 376 LVKTG-TITTFKDAHNLRVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLSKSDPMVQCI 434
TG T+ K L M+F PV+ +AVEPK AD K+ L +L++ DP +
Sbjct: 382 -TTTGDTLCDPKIDVILERMEFP-EPVISLAVEPKTKADQEKMGIALGKLAEEDPTFRTF 439
Query: 435 I-EESGEHIVAGAGELHLEICLKDLEEDHACIPIKKSDPVVSYRET----VSEESDQVCL 489
E+G+ I+AG GELHL+I + ++ + + P V+YRET V E
Sbjct: 440 TDPETGQTIIAGMGELHLDIIVDRMKREFK-VEANVGAPQVAYRETIRSKVEVEGKHAKQ 498
Query: 490 SKSPNKHNRLFMKAAPLPDGLPEDIDKGEVNPRDDFKIRGRYLADKYEFDVTEARKIWSF 549
S ++ + ++ PL YEF
Sbjct: 499 SGGRGQYGHVKIRFEPLEPK-------------------------GYEF----------- 522
Query: 550 GPDGTGPNLLIDCTKGVQYLNEIKDSVVAGFQWAAKEGVLSEENLRGVRFNIHDVTLHAD 609
++ KG E +V G Q A + G L+ + ++ + D + H
Sbjct: 523 ----------VNEIKGGVIPREYIPAVDKGLQEAMESGPLAGYPVVDIKATLFDGSYHDV 572
Query: 610 AIHRGGGQIIPTTRRVLYASLLTACPRLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFE 669
++ + + A P L+EP+ E++ PE +G + G L+ RRG +
Sbjct: 573 DSSEMAFKLAASL--AFKEAGKKANPVLLEPIMKVEVEVPEEYMGDVMGDLSSRRGII-- 628
Query: 670 EMQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQVLPGDPTDPGSKPY 729
E A + +KA +P++E FG+ DLRS T G+ F H+ G P
Sbjct: 629 EGMEARGNVQKIKAEVPLSEMFGYATDLRSFTQGRGTYSMEFLHY----------GEVPS 678
Query: 730 NVVQETRKRKG 740
+V E +++
Sbjct: 679 SVANEIIEKRK 689
>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 = 191 bits (488), Expect = 9e-57
Identities = 64/167 (38%), Positives = 88/167 (52%), Gaps = 21/167 (12%)
Query: 6 KNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAIS 65
K RN+ +I HVDHGK+TLTD+L+ G I+ A R D K+E+ER ITIK A+S
Sbjct: 1 KRHRNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVS 60
Query: 66 MYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCV 125
K LIN+ID+PGHVDF+ E+ DGA++VVD V
Sbjct: 61 FE--------------------TKKRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAV 100
Query: 126 SGVCVQTETVLRQAIAERIKPVLFMNKMDRAL-LELQLDAEDLYQTF 171
GV QT L A + ++F+NK+DR EL+ E++ +
Sbjct: 101 EGVMPQTREHLLLAKTLGVPIIVFINKIDRVDDAELEEVVEEISREL 147
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 189 bits (484), Expect = 2e-51
Identities = 158/528 (29%), Positives = 245/528 (46%), Gaps = 111/528 (21%)
Query: 14 IAHVDHGKSTLTDSLVSKAGII--AGAKAGETRFTDTRKDEQERCITIKSTAISMYFELD 71
+ H GK+TLT++++ G I G T D +E+ER I+I S A + +
Sbjct: 1 VGHSGAGKTTLTEAILFYTGAIHRIGEVEDGTTTMDFMPEERERGISITSAATTCEW--- 57
Query: 72 DKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQ 131
KG INLID+PGHVDF+ EV ALRV DGA+VVV V GV Q
Sbjct: 58 -----------------KGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQ 100
Query: 132 TETVLRQAIAERIKPVLFMNKMDRA--------------------LLELQLDAEDLYQTF 171
TETV RQA + ++F+NKMDRA L+L + D F
Sbjct: 101 TETVWRQAEKYGVPRIIFVNKMDRAGADFFRVLAQLQEKLGAPVVPLQLPIGEGD---DF 157
Query: 172 QRIVENVNVII--ATYSDDSGPMGEVRV----FDSIMNYKKE--EA-----ESLLSKL-- 216
+ V+++ A D+ GP E+ + D ++E EA + L+ K
Sbjct: 158 TGV---VDLLSMKAYRYDEGGPSEEIEIPAELLDRAEEAREELLEALAEFDDELMEKYLE 214
Query: 217 GIELKPEDKEKDG--KALLKVVMRTWLP--AGEA--------LLQMIAIHLPSPVVAQKY 264
G EL E++ K G KA L +P G A LL + +LPSP
Sbjct: 215 GEEL-SEEEIKAGLRKATLA---GEIVPVFCGSALKNKGVQRLLDAVVDYLPSP------ 264
Query: 265 RMEMLYEGPHDDEAAIGIKNCDPNAPLMMYVSKMVPTSDKGRFYAFGRVFSGKVATGQKA 324
+E+ D E + DP+ PL+ V K + G+ + RV+SG + G
Sbjct: 265 -LEVPPVDGEDGEEGAELA-PDPDGPLVALVFKTMDDPFVGK-LSLVRVYSGTLKKGDTL 321
Query: 325 RIMGPNYIPGKKEDLYEK--AIQRTILMMGRYVEAIEDVPSGNICGLVGVDQFLVKTG-T 381
Y G + E+ + R M G+ E +++ +G+I + + TG T
Sbjct: 322 ------YNSGTGKK--ERVGRLYR---MHGKQREEVDEAVAGDIVAVAKLKD--AATGDT 368
Query: 382 ITTFKDAHNLRVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLSKSDPMVQCIIE---ES 438
+ D L M+F PV+ +A+EPK+ D KL E L +L++ DP ++ +E E+
Sbjct: 369 LCDKGDPILLEPMEFPE-PVISLAIEPKDKGDEEKLSEALGKLAEEDPTLR--VERDEET 425
Query: 439 GEHIVAGAGELHLEICLKDLEEDHACIPIKKSDPVVSYRETVSEESDQ 486
G+ I++G GELHL++ L+ L+ ++ + ++ P V YRET+ ++++
Sbjct: 426 GQTILSGMGELHLDVALERLKREYG-VEVETGPPQVPYRETIRKKAEG 472
Score = 72.9 bits (180), Expect = 3e-13
Identities = 46/154 (29%), Positives = 75/154 (48%), Gaps = 14/154 (9%)
Query: 575 SVVAGFQWAAKEGVLSEENLRGVRFNIHDVTLHA-D----AIHRGGGQIIPTTRRVLYAS 629
+V G + A ++GVL+ + V+ + D + H+ D A R +
Sbjct: 520 AVEKGVREALEKGVLAGYPVVDVKVTLTDGSYHSVDSSEMAFKIAA-------RLAFREA 572
Query: 630 LLTACPRLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNE 689
L A P L+EP+ E+ PE VG + G L+ RRG + M+ + VV+A +P+ E
Sbjct: 573 LPKAKPVLLEPIMKVEVSVPEEFVGDVIGDLSSRRGRI-LGME-SRGGGDVVRAEVPLAE 630
Query: 690 SFGFTADLRSNTGGQAFPQCVFDHWQVLPGDPTD 723
FG+ DLRS T G+ F H++ +PG+ +
Sbjct: 631 MFGYATDLRSLTQGRGSFSMEFSHYEEVPGNVAE 664
>gnl|CDD|239763 cd04096, eEF2_snRNP_like_C, eEF2_snRNP_like_C: this family
represents a C-terminal domain of eukaryotic elongation
factor 2 (eEF-2) and a homologous domain of the
spliceosomal human 116kD U5 small nuclear
ribonucleoprotein (snRNP) protein (U5-116 kD) and, its
yeast counterpart Snu114p. 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 = 80
Score = 166 bits (423), Expect = 5e-49
Identities = 52/80 (65%), Positives = 62/80 (77%)
Query: 639 EPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFGFTADLR 698
EP+YL EIQCPE A+G +Y VL++RRGHV E GTP+F +KAYLPV ESFGF DLR
Sbjct: 1 EPIYLVEIQCPEDALGKVYSVLSKRRGHVLSEEPKEGTPLFEIKAYLPVIESFGFETDLR 60
Query: 699 SNTGGQAFPQCVFDHWQVLP 718
S T GQAFPQ VF HW+++P
Sbjct: 61 SATSGQAFPQLVFSHWEIVP 80
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 180 bits (459), Expect = 7e-48
Identities = 161/537 (29%), Positives = 245/537 (45%), Gaps = 108/537 (20%)
Query: 6 KNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETR----FTDTRKDEQERCITIKS 61
+ RN+ ++AH+D GK+T T+ ++ G K GE D + EQER ITI S
Sbjct: 6 EKTRNIGIMAHIDAGKTTTTERILYYTGKSH--KIGEVHDGAATMDWMEQEQERGITITS 63
Query: 62 TAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVV 121
A T KG IN+ID+PGHVDF+ EV +LRV DGA+ V
Sbjct: 64 AA--------------------TTCFWKGHRINIIDTPGHVDFTIEVERSLRVLDGAVAV 103
Query: 122 VDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRA--------------------LLELQ 161
D VSGV Q+ETV RQA + ++F+NKMDR ++L
Sbjct: 104 FDAVSGVEPQSETVWRQADKYGVPRIVFVNKMDRIGADFFRSVEQIKDRLGANAVPIQLP 163
Query: 162 LDAEDLYQTFQRIVENVNVIIATYSDDSGPMGEVRVFDSIMNYKKEEAESLLSKLGIEL- 220
+ AED F+ +++ + + + D++ +G + I KE+AE KL IE
Sbjct: 164 IGAED---DFKGVIDLIKMKAIIWDDET--LGAKYEEEDIPADLKEKAEEYREKL-IEAV 217
Query: 221 -------------KPEDKEKDGKALLK--VVMRTWLP--AGEA--------LLQMIAIHL 255
E E++ KA ++ + + P G A LL + +L
Sbjct: 218 AEVDEELMEKYLEGEEITEEEIKAAIRKATINMEFFPVLCGSAFKNKGVQPLLDAVVDYL 277
Query: 256 PSPV-VAQKYRMEMLYEGPH-DDEAAIGIKNCDPNAPLMMYVSKMVPTSDK--GRFYAFG 311
PSP+ V +G + D E I + P K++ +D GR F
Sbjct: 278 PSPLDVPA-------IKGINPDTEEEIERP-ASDDEPFAALAFKIM--TDPFVGRL-TFF 326
Query: 312 RVFSGKVATGQKARIMGPNYIPGKKEDLYEKAIQRTILMMGRYVEAIEDVPSGNICGLVG 371
RV+SG + +G N GKKE I R + M E I++V +G+I VG
Sbjct: 327 RVYSGVLESGSYVL----NTTKGKKE-----RIGRLLQMHANKREEIKEVYAGDIAAAVG 377
Query: 372 VDQFLVKTG-TITTFKDAHNLRVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLSKSDPM 430
+ TG T+ K L M+F PV+ +AVEPK AD K+ L++L++ DP
Sbjct: 378 LKD--TTTGDTLCDEKAPIILESMEFPE-PVISLAVEPKTKADQDKMGLALQKLAEEDPT 434
Query: 431 VQCII-EESGEHIVAGAGELHLEICLKDLEEDHACIPIKKSDPVVSYRETVSEESDQ 486
+ EE+G+ I++G GELHL+I + ++ + + P V+YRET+++ +
Sbjct: 435 FRVETDEETGQTIISGMGELHLDIIVDRMKREFK-VEANVGAPQVAYRETITKSVEA 490
Score = 68.3 bits (168), Expect = 8e-12
Identities = 51/169 (30%), Positives = 82/169 (48%), Gaps = 23/169 (13%)
Query: 564 KGVQYLNEIKD---------SVVAGFQWAAKEGVLSEENLRGVRFNI-----HDVTLHAD 609
KG +++N+I +V G + A K GVL+ + V+ + HDV
Sbjct: 518 KGFEFVNKIVGGVIPKEYIPAVEKGLEEAMKNGVLAGYPMVDVKATLYDGSYHDVDSSEL 577
Query: 610 AIHRGGGQIIPTTRRVLYASLLTACPRLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFE 669
A + + A P ++EP+ E+ PE +G + G LNRRRG + +
Sbjct: 578 AFKIAASMALKEAAK-------KAGPVILEPIMKVEVVTPEEYMGDVIGDLNRRRGQI-Q 629
Query: 670 EMQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQVLP 718
M+ G +VKA++P++E FG+ DLRS T G+A FDH++ +P
Sbjct: 630 GMEARG-GAQIVKAFVPLSEMFGYATDLRSATQGRATFSMEFDHYEEVP 677
>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 = 167 bits (424), Expect = 7e-48
Identities = 63/182 (34%), Positives = 86/182 (47%), Gaps = 26/182 (14%)
Query: 10 NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYFE 69
N+ VI HVDHGK+TLT SL+ + G I + F DT K+E+ER ITIK+ + +
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEW- 59
Query: 70 LDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVC 129
IN ID+PGH DFS E L DGAL+VVD GV
Sbjct: 60 -------------------PKRRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGVE 100
Query: 130 VQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNVIIATYSDDS 189
QT L A+A + ++ +NK+DR ED + + I E + +I T+
Sbjct: 101 PQTREHLNIALAGGLPIIVAVNKIDRV------GEEDFDEVLREIKELLKLIGFTFLKGK 154
Query: 190 GP 191
Sbjct: 155 DV 156
>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 = 163 bits (416), Expect = 2e-46
Identities = 76/186 (40%), Positives = 109/186 (58%), Gaps = 18/186 (9%)
Query: 9 RNMSVIAHVDHGKSTLTDSLV--SKAGIIAGAKAGE-TRFTDTRKDEQERCITIKSTAIS 65
RN+ + H+ HGK++L D L+ + + + R+TDTRKDEQER I+IKS IS
Sbjct: 1 RNVCIAGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPLRYTDTRKDEQERGISIKSNPIS 60
Query: 66 MYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCV 125
+ E D K K +LIN+ID+PGHV+F EV AALR+ DG ++VVD V
Sbjct: 61 LVLE-DSKG--------------KSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDVV 105
Query: 126 SGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNVIIATY 185
G+ TE ++R AI E + VL +NK+DR +LEL+L D Y + ++ +N IA++
Sbjct: 106 EGLTSVTERLIRHAIQEGLPMVLVINKIDRLILELKLPPTDAYYKLRHTIDEINNYIASF 165
Query: 186 SDDSGP 191
S G
Sbjct: 166 STTEGF 171
>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 = 156 bits (398), Expect = 2e-45
Identities = 57/94 (60%), Positives = 72/94 (76%), Gaps = 2/94 (2%)
Query: 291 LMMYVSKMVPTSDKGRFYAFGRVFSGKVATGQKARIMGPNYIPGKKEDLYEKAIQRTILM 350
L+MYV+KMVPT DKG F AFGRVFSG + GQK R++GPNY P +EDL +K IQR LM
Sbjct: 1 LVMYVTKMVPTPDKGGFIAFGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLM 60
Query: 351 MGRYVEAIEDVPSGNICGLVGVDQFLVKTGTITT 384
MGRY E +++VP+GNI +VG+DQ +K+GT T
Sbjct: 61 MGRYREPVDEVPAGNIVLIVGLDQ--LKSGTTAT 92
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 161 bits (410), Expect = 1e-41
Identities = 164/546 (30%), Positives = 248/546 (45%), Gaps = 125/546 (22%)
Query: 6 KNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETR----FTDTRKDEQERCITIKS 61
+ RN+ ++AH+D GK+T T+ ++ G+ K GE D + EQER ITI S
Sbjct: 8 ERYRNIGIMAHIDAGKTTTTERILFYTGVNH--KIGEVHDGAATMDWMEQEQERGITITS 65
Query: 62 TAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVV 121
A + ++ K IN+ID+PGHVDF+ EV +LRV DGA+ V
Sbjct: 66 AATTCFW--------------------KDHRINIIDTPGHVDFTIEVERSLRVLDGAVAV 105
Query: 122 VDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDR--------------------ALLELQ 161
D V GV Q+ETV RQA ++ + F+NKMDR ++L
Sbjct: 106 FDAVGGVEPQSETVWRQADKYKVPRIAFVNKMDRTGADFYRVVEQIKDRLGANPVPIQLP 165
Query: 162 LDAEDLYQTFQRIVENVNVIIATYSDDSGPMGEVRVFDSIMNYKKEEAESLLSKLGIELK 221
+ AED F+ +V+ V + +++ +G ++ I K++AE KL IE
Sbjct: 166 IGAED---DFKGVVDLVKMKAIIWNEAD--LGATFEYEEIPADLKDKAEEYREKL-IEAA 219
Query: 222 PE------DKEKDGKAL----LKVVMRTWLPAGE----------------ALLQMIAIHL 255
E +K +G+ L +K +R A E LL + +L
Sbjct: 220 AEADEELMEKYLEGEELTEEEIKAALRKATIANEIVPVLCGSAFKNKGVQPLLDAVVDYL 279
Query: 256 PSP--VVAQKYRMEMLYEG--PHDDEAAIGIKNCDPNAPLMMYVSKMVPTSDK--GRFYA 309
PSP V A +G P +E + K + P K++ +D G+
Sbjct: 280 PSPLDVPA--------IKGILPDGEEEEVERKA-SDDEPFSALAFKIM--TDPFVGKL-T 327
Query: 310 FGRVFSGKVATGQKARIMGPNYIPGKKEDLYEKAIQRTILMMGRYVEAIEDVPSGNICGL 369
F RV+SG + +G N GKKE I R + M E I++V +G+I
Sbjct: 328 FFRVYSGVLESGSYVL----NSTKGKKE-----RIGRILQMHANKREEIKEVRAGDIAAA 378
Query: 370 VGVDQFLVKTGTITTFKDAHN---LRVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLSK 426
VG L T T T D N L M+F PV+ VAVEPK AD K+ L++L++
Sbjct: 379 VG----LKDTTTGDTLCDEKNPIILESMEFP-EPVISVAVEPKTKADQEKMGIALQKLAE 433
Query: 427 SDPMVQ-CIIEESGEHIVAGAGELHLEICLKDLEEDHACIPIKKSD-----PVVSYRETV 480
DP + EE+G+ I+AG GELHL+I + ++ + K + P V+YRET+
Sbjct: 434 EDPSFRVSTDEETGQTIIAGMGELHLDIIVDRMKREF------KVEANVGKPQVAYRETI 487
Query: 481 SEESDQ 486
++ +
Sbjct: 488 RKKVEV 493
Score = 61.3 bits (150), Expect = 1e-09
Identities = 35/86 (40%), Positives = 52/86 (60%), Gaps = 2/86 (2%)
Query: 633 ACPRLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFG 692
A P L+EP+ E+ PE +G + G LN RRG + E M+ G V++A +P++E FG
Sbjct: 597 ANPVLLEPIMKVEVVTPEEYMGDVIGDLNSRRGQI-EGMEDRGGAK-VIRAEVPLSEMFG 654
Query: 693 FTADLRSNTGGQAFPQCVFDHWQVLP 718
+ DLRS T G+A FDH++ +P
Sbjct: 655 YATDLRSMTQGRATYSMEFDHYEEVP 680
>gnl|CDD|202760 pfam03764, EFG_IV, Elongation factor G, domain IV. This domain is
found in elongation factor G, elongation factor 2 and
some tetracycline resistance proteins and adopts a
ribosomal protein S5 domain 2-like fold.
Length = 120
Score = 144 bits (366), Expect = 1e-40
Identities = 42/121 (34%), Positives = 54/121 (44%), Gaps = 6/121 (4%)
Query: 517 GEVNPR----DDFKIRGRYLADKYEFDVTEARKIWSFGPDGTGPNLLIDCTKGVQYLNEI 572
+V R D K R L + D A+ I P G N +D TKG QY NE
Sbjct: 1 PQVAYRETIGKDVKERAYKLKKQSGGDGQYAKVILRIEPLPGGGNEFVDETKGGQYPNEF 60
Query: 573 KDSVVAGFQWAAKEGVLSEENLRGVRFNIHDVTLHADAIHRGGGQIIPTTRRVLYASLLT 632
K +V GFQ A KEG L+ E +R V+ + D + H + IP RR +LL
Sbjct: 61 KPAVEKGFQEAMKEGPLAGEPVRDVKVTLTDGSYH--EVDSSEAAFIPAARRAFKEALLK 118
Query: 633 A 633
A
Sbjct: 119 A 119
>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 = 133 bits (338), Expect = 4e-36
Identities = 68/195 (34%), Positives = 101/195 (51%), Gaps = 44/195 (22%)
Query: 9 RNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYF 68
RN S+IAH+DHGKSTL D L+ G ++ + + + D+ E+ER ITIK+ A+ +++
Sbjct: 1 RNFSIIAHIDHGKSTLADRLLELTGTVS-EREMKEQVLDSMDLERERGITIKAQAVRLFY 59
Query: 69 ELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGV 128
AK+ + +L+NLID+PGHVDFS EV+ +L +GAL+VVD GV
Sbjct: 60 ---------------KAKDGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQGV 104
Query: 129 CVQTETVLRQAIAER---IKPVLFMNKMD-------RALLELQ----LDAED-------- 166
QT A+ E I PV+ NK+D R E++ LDA +
Sbjct: 105 EAQTLANFYLAL-ENNLEIIPVI--NKIDLPAADPDRVKQEIEDVLGLDASEAILVSAKT 161
Query: 167 ---LYQTFQRIVENV 178
+ + IVE +
Sbjct: 162 GLGVEDLLEAIVERI 176
>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 (321), Expect = 1e-32
Identities = 61/150 (40%), Positives = 82/150 (54%), Gaps = 26/150 (17%)
Query: 10 NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKD----EQERCITIKSTAIS 65
N+ +IAH+D GK+T T+ ++ G I K GE D E+ER ITI+S A +
Sbjct: 1 NIGIIAHIDAGKTTTTERILYYTGRIH--KIGEVHGGGATMDWMEQERERGITIQSAATT 58
Query: 66 MYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCV 125
++ K IN+ID+PGHVDF+ EV +LRV DGA+ V D V
Sbjct: 59 CFW--------------------KDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAV 98
Query: 126 SGVCVQTETVLRQAIAERIKPVLFMNKMDR 155
+GV QTETV RQA + + F+NKMDR
Sbjct: 99 AGVQPQTETVWRQADRYGVPRIAFVNKMDR 128
>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 = 124 bits (314), Expect = 1e-32
Identities = 58/151 (38%), Positives = 83/151 (54%), Gaps = 24/151 (15%)
Query: 7 NIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITI--KSTAI 64
IRN+++IAHVDHGK+TL D+L+ ++G + R D+ E+ER ITI K+TAI
Sbjct: 1 KIRNIAIIAHVDHGKTTLVDALLKQSGTFRENEEVGERVMDSNDLERERGITILAKNTAI 60
Query: 65 SMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDC 124
K IN+ID+PGH DF EV L + DG L++VD
Sbjct: 61 ----------------------TYKDTKINIIDTPGHADFGGEVERVLSMVDGVLLLVDA 98
Query: 125 VSGVCVQTETVLRQAIAERIKPVLFMNKMDR 155
G QT VL++A+ +KP++ +NK+DR
Sbjct: 99 SEGPMPQTRFVLKKALEAGLKPIVVINKIDR 129
>gnl|CDD|239765 cd04098, eEF2_C_snRNP, eEF2_C_snRNP: This family includes a
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 the C-terminal domain 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 = 80
Score = 120 bits (303), Expect = 1e-32
Identities = 47/80 (58%), Positives = 59/80 (73%)
Query: 639 EPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFGFTADLR 698
EP+Y EI CP AV +Y VL+RRRGHV + + GTP++ VKA++PV ESFGF DLR
Sbjct: 1 EPIYEVEITCPADAVSAVYEVLSRRRGHVIYDTPIPGTPLYEVKAFIPVIESFGFETDLR 60
Query: 699 SNTGGQAFPQCVFDHWQVLP 718
+T GQAF Q VFDHWQ++P
Sbjct: 61 VHTQGQAFCQSVFDHWQIVP 80
>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 = 119 bits (300), Expect = 4e-32
Identities = 34/80 (42%), Positives = 47/80 (58%), Gaps = 1/80 (1%)
Query: 639 EPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFGFTADLR 698
EP+ EI PE +G + G L++RRG + M+ GT V+KA LP+ E FGF DLR
Sbjct: 1 EPIMKVEITVPEEYLGAVIGDLSKRRGEI-LGMEPRGTGRVVIKAELPLAEMFGFATDLR 59
Query: 699 SNTGGQAFPQCVFDHWQVLP 718
S T G+A F H++ +P
Sbjct: 60 SLTQGRASFSMEFSHYEPVP 79
>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 = 128 bits (324), Expect = 5e-31
Identities = 99/381 (25%), Positives = 152/381 (39%), Gaps = 112/381 (29%)
Query: 8 IRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITI--KSTAIS 65
IRN+++IAHVDHGK+TL D+L+ ++G +A R D+ E+ER ITI K+TAI
Sbjct: 1 IRNIAIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDLERERGITILAKNTAI- 59
Query: 66 MYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCV 125
Y G IN++D+PGH DF EV L + DG L++VD
Sbjct: 60 RY---------------------NGTKINIVDTPGHADFGGEVERVLGMVDGVLLLVDAS 98
Query: 126 SGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNVIIATY 185
G QT VL++A+ +KP++ +NK+DR A R E V+
Sbjct: 99 EGPMPQTRFVLKKALELGLKPIVVINKIDRP------SA--------RPDEVVD------ 138
Query: 186 SDDSGPMGEVRVFDSIMNYKKEEAESL----LSKLGIE----LKPEDKEKDGKALLKVVM 237
VFD ++ E L + G L +D + L ++
Sbjct: 139 ----------EVFDLFAELGADD-EQLDFPIVYASGRAGWASLDLDDPSDNMAPLFDAIV 187
Query: 238 RTWLPAGEALLQMIAIHLPSPVVAQKYRMEMLYEGPHDDEAAIGIKNCDPNAPLMMYVSK 297
R H+P+P D + L M V+
Sbjct: 188 R---------------HVPAPKG--------------DLDEP-----------LQMLVTN 207
Query: 298 MVPTSDKGRFYAFGRVFSGKVATGQKARIMGPNYIPGKKEDLYEKA-IQRTILMMGRYVE 356
+ GR A GRV G V GQ+ +M K++ E I + + G
Sbjct: 208 LDYDEYLGRI-AIGRVHRGTVKKGQQVALM-------KRDGTIENGRISKLLGFEGLERV 259
Query: 357 AIEDVPSGNICGLVGVDQFLV 377
I++ +G+I + G++ +
Sbjct: 260 EIDEAGAGDIVAVAGLEDINI 280
Score = 35.7 bits (83), Expect = 0.088
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 637 LMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFGFTAD 696
+EP+ I PE VG + L +R+G + +M+ +G ++ +P GF +
Sbjct: 392 KLEPIEELTIDVPEEHVGAVIEKLGKRKGEMV-DMEPSGNGRTRLEFKIPSRGLIGFRTE 450
Query: 697 LRSNTGGQAFPQCVFDHWQVLPGD 720
++T G VFD ++ G+
Sbjct: 451 FLTDTRGTGIMNHVFDEYEPWKGE 474
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 125 bits (315), Expect = 8e-30
Identities = 93/342 (27%), Positives = 140/342 (40%), Gaps = 118/342 (34%)
Query: 6 KNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITI--KSTA 63
++IRN+++IAHVDHGK+TL D+L+ ++G + R D+ E+ER ITI K+TA
Sbjct: 3 EDIRNIAIIAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGITILAKNTA 62
Query: 64 ISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVD 123
+ N G IN++D+PGH DF EV L + DG L++VD
Sbjct: 63 V----------------------NYNGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVD 100
Query: 124 CVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNVIIA 183
G QT VL++A+A +KP++ +NK+DR R E V+
Sbjct: 101 ASEGPMPQTRFVLKKALALGLKPIVVINKIDRP--------------DARPDEVVD---- 142
Query: 184 TYSDDSGPMGEVRVFDSIMNYKKEEAESLLSKLGIELKPEDKE----------KDGKALL 233
VFD L +EL D++ ++G A L
Sbjct: 143 ------------EVFD----------------LFVELGATDEQLDFPIVYASARNGTASL 174
Query: 234 KVVMRTWLPAGEA-----LLQMIAIHLPSPVVAQKYRMEMLYEGPHDDEAAIGIKNCDPN 288
P EA L + I H+P+P D +
Sbjct: 175 D-------PEDEADDMAPLFETILDHVPAPKG-------------------------DLD 202
Query: 289 APLMMYVSKMVPTSDKGRFYAFGRVFSGKVATGQKARIMGPN 330
PL M V+++ S GR GR+F G V Q+ ++ +
Sbjct: 203 EPLQMQVTQLDYNSYVGRI-GIGRIFRGTVKPNQQVALIKSD 243
Score = 32.2 bits (74), Expect = 1.1
Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 1/85 (1%)
Query: 636 RLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFGFTA 695
EP I PE G + L R+G + ++M G ++ +P GF
Sbjct: 395 VKCEPFEEVTIDVPEEHQGAVIEKLGERKGEM-KDMAPDGKGRVRLEFVIPARGLIGFRT 453
Query: 696 DLRSNTGGQAFPQCVFDHWQVLPGD 720
+ + T G FDH++ + G+
Sbjct: 454 EFLTMTRGTGIMNHSFDHYRPVKGE 478
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 123 bits (312), Expect = 2e-29
Identities = 69/179 (38%), Positives = 99/179 (55%), Gaps = 33/179 (18%)
Query: 2 MDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKS 61
M KNIRN S+IAH+DHGKSTL D L+ G ++ + + + D+ E+ER ITIK+
Sbjct: 1 MMDMKNIRNFSIIAHIDHGKSTLADRLIELTGTLS-EREMKAQVLDSMDLERERGITIKA 59
Query: 62 TAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVV 121
A+ + + AK+ + +++NLID+PGHVDFS EV+ +L +GAL+V
Sbjct: 60 QAVRLNY---------------KAKDGETYILNLIDTPGHVDFSYEVSRSLAACEGALLV 104
Query: 122 VDCVSGVCVQTETVLRQAIAER---IKPVLFMNKMD-------RALLELQ----LDAED 166
VD GV QT + A+ E I PVL NK+D R E++ +DA D
Sbjct: 105 VDASQGVEAQTLANVYLAL-ENDLEIIPVL--NKIDLPAADPERVKQEIEDVIGIDASD 160
>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 = 115 bits (291), Expect = 5e-29
Identities = 67/194 (34%), Positives = 102/194 (52%), Gaps = 36/194 (18%)
Query: 10 NMSVIAHVDHGKSTLTDSLVSKAGIIA--GAKAGETRFTDTRKDEQERCITIKSTAISMY 67
N+ ++AHVD GK+TLT+SL+ +G I G+ T TD+ + E++R ITI S S
Sbjct: 1 NIGILAHVDAGKTTLTESLLYTSGAIRELGSVDKGTTRTDSMELERQRGITIFSAVAS-- 58
Query: 68 FELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSG 127
F+ +D +N+ID+PGH+DF +EV +L V DGA++V+ V G
Sbjct: 59 FQWEDTK------------------VNIIDTPGHMDFIAEVERSLSVLDGAILVISAVEG 100
Query: 128 VCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNVIIATYSD 187
V QT + R I ++F+NK+DRA DL + +Q I E + S
Sbjct: 101 VQAQTRILFRLLRKLNIPTIIFVNKIDRA-------GADLEKVYQEIKEKL-------SP 146
Query: 188 DSGPMGEVRVFDSI 201
D PM +V ++ +I
Sbjct: 147 DIVPMQKVGLYPNI 160
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 122 bits (308), Expect = 5e-29
Identities = 67/179 (37%), Positives = 97/179 (54%), Gaps = 31/179 (17%)
Query: 1 MMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIK 60
+KNIRN S+IAH+DHGKSTL D L+ G ++ + + D+ E+ER ITIK
Sbjct: 2 TFTPQKNIRNFSIIAHIDHGKSTLADRLLELTGGLS-EREMRAQVLDSMDIERERGITIK 60
Query: 61 STAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALV 120
+ A+ + + AK+ + +++NLID+PGHVDFS EV+ +L +GAL+
Sbjct: 61 AQAVRLNY---------------KAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALL 105
Query: 121 VVDCVSGVCVQTETVLRQAIAE--RIKPVLFMNKMD-------RALLELQ----LDAED 166
VVD GV QT + A+ I PVL NK+D R E++ +DA D
Sbjct: 106 VVDASQGVEAQTLANVYLALENNLEIIPVL--NKIDLPAADPERVKQEIEDIIGIDASD 162
Score = 31.4 bits (72), Expect = 2.2
Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 2/68 (2%)
Query: 639 EPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNE-SFGFTADL 697
EP I P+ +G + + +RG + +M+ ++ LP+ E F F L
Sbjct: 406 EPYVKATIITPQEYLGNVMELCQEKRG-IQIDMEYLDQNRVMLTYELPLAEIVFDFFDKL 464
Query: 698 RSNTGGQA 705
+S + G A
Sbjct: 465 KSISKGYA 472
>gnl|CDD|214887 smart00889, EFG_IV, Elongation factor G, domain IV. Translation
elongation factors are responsible for two main
processes during protein synthesis on the ribosome. EF1A
(or EF-Tu) is responsible for the selection and binding
of the cognate aminoacyl-tRNA to the A-site (acceptor
site) of the ribosome. EF2 (or EF-G) is responsible for
the translocation of the peptidyl-tRNA from the A-site
to the P-site (peptidyl-tRNA site) of the ribosome,
thereby freeing the A-site for the next aminoacyl-tRNA
to bind. Elongation factors are responsible for
achieving accuracy of translation and both EF1A and EF2
are remarkably conserved throughout evolution.
Elongation factor EF2 (EF-G) is a G-protein. It brings
about the translocation of peptidyl-tRNA and mRNA
through a ratchet-like mechanism: the binding of GTP-EF2
to the ribosome causes a counter-clockwise rotation in
the small ribosomal subunit; the hydrolysis of GTP to
GDP by EF2 and the subsequent release of EF2 causes a
clockwise rotation of the small subunit back to the
starting position. This twisting action destabilises
tRNA-ribosome interactions, freeing the tRNA to
translocate along the ribosome upon GTP-hydrolysis by
EF2. EF2 binding also affects the entry and exit channel
openings for the mRNA, widening it when bound to enable
the mRNA to translocate along the ribosome. EF2 has five
domains. This entry represents domain IV found in EF2
(or EF-G) of both prokaryotes and eukaryotes. The
EF2-GTP-ribosome complex undergoes extensive structural
rearrangement for tRNA-mRNA movement to occur. Domain
IV, which extends from the 'body' of the EF2 molecule
much like a lever arm, appears to be essential for the
structural transition to take place.
Length = 120
Score = 110 bits (278), Expect = 1e-28
Identities = 28/115 (24%), Positives = 38/115 (33%), Gaps = 5/115 (4%)
Query: 521 PRDDFKIRGRYLADKYEFDVTEARKIWSFGPDGTGPNLLIDCTK--GVQYLNEIKDSVVA 578
K + D AR I P G D T GV E +V
Sbjct: 8 ITKPVKEAEGKHKKQSGGDGQYARVILEVEPLERGSGFEFDDTIVGGVIPK-EYIPAVEK 66
Query: 579 GFQWAAKEGVLSEENLRGVRFNIHDVTLHADAIHRGGGQIIPTTRRVLYASLLTA 633
GF+ A +EG L+ + V+ + D + H P RR +LL A
Sbjct: 67 GFREALEEGPLAGYPVVDVKVTLLDGSYHEV-DSSEMA-FKPAARRAFKEALLKA 119
>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 = 119 bits (301), Expect = 4e-28
Identities = 62/152 (40%), Positives = 90/152 (59%), Gaps = 22/152 (14%)
Query: 6 KNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAIS 65
KNIRN S+IAH+DHGKSTL D L+ G I+ + E + D+ E+ER ITIK+ A+
Sbjct: 1 KNIRNFSIIAHIDHGKSTLADRLLEYTGAISEREMRE-QVLDSMDLERERGITIKAQAVR 59
Query: 66 MYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCV 125
+ + AK+ + +++NLID+PGHVDFS EV+ +L +GAL++VD
Sbjct: 60 LNY---------------KAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAA 104
Query: 126 SGVCVQTETVLRQAIAER---IKPVLFMNKMD 154
G+ QT + A+ E I PV+ NK+D
Sbjct: 105 QGIEAQTLANVYLAL-ENDLEIIPVI--NKID 133
Score = 32.7 bits (75), Expect = 0.88
Identities = 55/207 (26%), Positives = 84/207 (40%), Gaps = 34/207 (16%)
Query: 286 DPNAPLMMYVSKMVPTSDKGRFYAFGRVFSGKVATGQKARIMGPNYIPGKKEDLYE---- 341
DP+APL + + +G A RVF G + G K R M GK+ ++ E
Sbjct: 185 DPDAPLKALIFDSHYDNYRG-VVALVRVFEGTIKPGDKIRFMS----TGKEYEVDEVGVF 239
Query: 342 --KAIQRTIL---MMGRYVEAIEDVPSGNICGLVGVDQFLVKTG-TITTFKDAHNLRVMK 395
K + L +G + I+DV V+ G TIT K+ +
Sbjct: 240 TPKLTKTDELSAGEVGYIIAGIKDVSD-------------VRVGDTITHVKNPAKEPLPG 286
Query: 396 F-SVSPVVRVAVEPKNPADLPKLVEGLKRLSKSDPMVQCIIEES---GEHIVAG-AGELH 450
F V P+V + P + D L + L++L +D + E S G G G LH
Sbjct: 287 FKEVKPMVFAGLYPIDTEDYEDLRDALEKLKLNDASLTYEPESSPALGFGFRCGFLGLLH 346
Query: 451 LEICLKDLEEDHACIPIKKSDPVVSYR 477
+EI + LE + + + + P V YR
Sbjct: 347 MEIIQERLEREFN-LDLITTAPSVIYR 372
>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 = 101 bits (254), Expect = 7e-26
Identities = 32/86 (37%), Positives = 50/86 (58%), Gaps = 1/86 (1%)
Query: 636 RLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFGFTA 695
L+EP+ EI PE +G + G LN+RRG + +M+ G V++A +P+ E FGF+
Sbjct: 1 VLLEPIMKVEITVPEEYLGDVIGDLNQRRGEI-LDMEPDGGGRVVIEAEVPLAELFGFST 59
Query: 696 DLRSNTGGQAFPQCVFDHWQVLPGDP 721
+LRS T G+ F ++ +PGD
Sbjct: 60 ELRSLTQGRGSFSMEFSGYEPVPGDI 85
>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 = 98.4 bits (246), Expect = 9e-25
Identities = 38/94 (40%), Positives = 61/94 (64%)
Query: 291 LMMYVSKMVPTSDKGRFYAFGRVFSGKVATGQKARIMGPNYIPGKKEDLYEKAIQRTILM 350
L+++V+K+ TSD G F+AFGR++SG + GQK +++G NY +ED+ I R ++
Sbjct: 1 LVVHVTKLYSTSDGGSFWAFGRIYSGTIKKGQKVKVLGENYSLDDEEDMTICTIGRLWIL 60
Query: 351 MGRYVEAIEDVPSGNICGLVGVDQFLVKTGTITT 384
GRY + + P+GN + G+D +VKT TIT+
Sbjct: 61 GGRYKIEVNEAPAGNWVLIKGIDSSIVKTATITS 94
>gnl|CDD|197906 smart00838, 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 = 85
Score = 90.6 bits (226), Expect = 4e-22
Identities = 32/87 (36%), Positives = 49/87 (56%), Gaps = 2/87 (2%)
Query: 637 LMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFGFTAD 696
L+EP+ E+ PE +G + G LN RRG + E M+ V+KA +P++E FG+ D
Sbjct: 1 LLEPIMKVEVTVPEEYMGDVIGDLNSRRGKI-EGME-QRGGAQVIKAKVPLSEMFGYATD 58
Query: 697 LRSNTGGQAFPQCVFDHWQVLPGDPTD 723
LRS T G+A F H++ +P +
Sbjct: 59 LRSATQGRATWSMEFSHYEEVPKSIAE 85
>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 = 96.1 bits (240), Expect = 5e-22
Identities = 47/149 (31%), Positives = 75/149 (50%), Gaps = 22/149 (14%)
Query: 10 NMSVIAHVDHGKSTLTDSLVSKAGII--AGAKAGETRFTDTRKDEQERCITIKSTAISMY 67
N++++ H GK+TL ++L+ G I G +D +E++R ++I+++
Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGAIDRLGRVEDGNTVSDYDPEEKKRKMSIETSVAP-- 58
Query: 68 FELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSG 127
E + INLID+PG+ DF E +ALR D AL+VV+ SG
Sbjct: 59 LEWNGHK------------------INLIDTPGYADFVGETLSALRAVDAALIVVEAQSG 100
Query: 128 VCVQTETVLRQAIAERIKPVLFMNKMDRA 156
V V TE V ++ ++F+NKMDRA
Sbjct: 101 VEVGTEKVWEFLDDAKLPRIIFINKMDRA 129
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 98.6 bits (245), Expect = 2e-21
Identities = 54/152 (35%), Positives = 81/152 (53%), Gaps = 24/152 (15%)
Query: 6 KNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITI--KSTA 63
+ +RN+++IAHVDHGK+TL D L+ ++G + R D+ E+ER ITI K+TA
Sbjct: 3 EKLRNIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTA 62
Query: 64 ISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVD 123
I + IN++D+PGH DF EV + + D L+VVD
Sbjct: 63 IKW----------------------NDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVD 100
Query: 124 CVSGVCVQTETVLRQAIAERIKPVLFMNKMDR 155
G QT V ++A A +KP++ +NK+DR
Sbjct: 101 AFDGPMPQTRFVTKKAFAYGLKPIVVINKVDR 132
>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 = 86.1 bits (214), Expect = 1e-18
Identities = 52/153 (33%), Positives = 76/153 (49%), Gaps = 26/153 (16%)
Query: 9 RNMSVIAHVDHGKSTLTDSLVSKAGII--AGA-KA-GETRFT--DTRKDEQERCITIKST 62
R ++I+H D GK+TLT+ L+ G I AGA KA + D + E++R I++ S+
Sbjct: 3 RTFAIISHPDAGKTTLTEKLLLFGGAIQEAGAVKARKSRKHATSDWMEIEKQRGISVTSS 62
Query: 63 AISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVV 122
M FE KG +INL+D+PGH DFS + L D A++V+
Sbjct: 63 V--MQFEY------------------KGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVI 102
Query: 123 DCVSGVCVQTETVLRQAIAERIKPVLFMNKMDR 155
D GV QT + I + F+NK+DR
Sbjct: 103 DAAKGVEPQTRKLFEVCRLRGIPIITFINKLDR 135
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 86.1 bits (214), Expect = 2e-17
Identities = 47/154 (30%), Positives = 73/154 (47%), Gaps = 28/154 (18%)
Query: 9 RNMSVIAHVDHGKSTLTDSLVSKAGII--AGA-KAGETRFTDTRKD----EQERCITIKS 61
R ++I+H D GK+TLT+ L+ G I AG K ++ + D E++R I++ S
Sbjct: 13 RTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSG-KHAKSDWMEIEKQRGISVTS 71
Query: 62 TAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVV 121
+ M F+ D L+NL+D+PGH DFS + L D A++V
Sbjct: 72 SV--MQFDYADC------------------LVNLLDTPGHEDFSEDTYRTLTAVDSAVMV 111
Query: 122 VDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDR 155
+D G+ QT + I F+NK+DR
Sbjct: 112 IDAAKGIEPQTLKLFEVCRLRDIPIFTFINKLDR 145
>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 = 72.2 bits (178), Expect = 1e-15
Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 639 EPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFGFTADLR 698
EP+ E+ PE +G + G L+ RRG + + G V+KA +P+ E FG++ DLR
Sbjct: 1 EPIMKVEVTVPEEYMGDVIGDLSSRRGQI-LGTESRGG-WKVIKAEVPLAEMFGYSTDLR 58
Query: 699 SNTGGQAFPQCVFDHWQVLP 718
S T G+ F H++ +P
Sbjct: 59 SLTQGRGSFTMEFSHYEEVP 78
>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 = 76.5 bits (188), Expect = 2e-14
Identities = 118/506 (23%), Positives = 195/506 (38%), Gaps = 114/506 (22%)
Query: 9 RNMSVIAHVDHGKSTLTDSL------VSKAGIIAGAKAGETRFTDTRKDEQERCITIKST 62
R ++I+H D GK+T+T+ + + AG + G + +D + E++R I+I ++
Sbjct: 12 RTFAIISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGISITTS 71
Query: 63 AISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVV 122
M F D L+NL+D+PGH DFS + L D L+V+
Sbjct: 72 V--MQFPYRDC------------------LVNLLDTPGHEDFSEDTYRTLTAVDNCLMVI 111
Query: 123 DCVSGVCVQTETVLRQAIAERIKPVL-FMNKMD---RALLELQLDAE------------- 165
D GV +T L + R P+ FMNK+D R LEL + E
Sbjct: 112 DAAKGVETRTRK-LMEVTRLRDTPIFTFMNKLDRDIRDPLELLDEVENELKINCAPITWP 170
Query: 166 ----DLYQTFQRIVENVNVIIATYSDDSGPMGEVRVFDSIMNYKKEEAESLL-SKLGIEL 220
L++ ++++ TY SG G ++ + +S + S L +L
Sbjct: 171 IGCGKLFKGVYHLLKD-----ETYLYQSGTGGTIQAVRQVKGLNNPALDSAVGSDLAQQL 225
Query: 221 KPE-------DKEKDGKALLKVVMRTWLPAGEAL--------LQMIAIHLPSPVVAQKYR 265
+ E E D A M T + G AL L + P P Q
Sbjct: 226 RDELELVEGASNEFDLAAFHGGEM-TPVFFGTALGNFGVDHFLDGLLQWAPKPEARQSDT 284
Query: 266 MEMLYEGPHDDEAAIGIK---NCDPNAPLMMYVSKMVPTSDKGRFYAFGRVFSGKVATGQ 322
+ E + + K N DP + R AF RV SGK G
Sbjct: 285 RTV--EPTEEKFSGFVFKIQANMDPK--------------HRDRV-AFMRVVSGKYEKGM 327
Query: 323 KARIMGPNYIPGKKEDLYEKAIQRTILMMGRYVEAIEDVPSGNICGLVGVDQFLVKTGTI 382
K + +D+ I + M E +E+ +G+I G L GTI
Sbjct: 328 KLK------HVRTGKDV---VISDALTFMAGDREHVEEAYAGDIIG-------LHNHGTI 371
Query: 383 TTFKDAHNLRVMKF----SVSPVVRVAVEPKNPADLPKLVEGLKRLSKSDPMVQCI--IE 436
+KF + +P + + K+P +L++GL +LS+ + VQ ++
Sbjct: 372 QIGDTFTQGEKIKFTGIPNFAPELFRRIRLKDPLKQKQLLKGLVQLSE-EGAVQVFRPLD 430
Query: 437 ESGEHIVAGAGELHLEICLKDLEEDH 462
+ + IV G L ++ + L+E++
Sbjct: 431 NN-DLIVGAVGVLQFDVVVYRLKEEY 455
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 75.6 bits (187), Expect = 3e-14
Identities = 55/163 (33%), Positives = 80/163 (49%), Gaps = 46/163 (28%)
Query: 9 RNMSVIAHVDHGKSTLTDSL------VSKAGIIAGAKAGETRF--TDTRKDEQERCITIK 60
R ++I+H D GK+TLT+ L + +AG + G K+G R +D + E++R I++
Sbjct: 11 RTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSG--RHATSDWMEMEKQRGISVT 68
Query: 61 STAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSE----VTAALRVTD 116
S+ M F D LINL+D+PGH DFS + +TA D
Sbjct: 69 SSV--MQFPYRDC------------------LINLLDTPGHEDFSEDTYRTLTAV----D 104
Query: 117 GALVVVDCVSGVCVQTET---VLRQAIAERIKPVL-FMNKMDR 155
AL+V+D GV QT V R R P+ F+NK+DR
Sbjct: 105 SALMVIDAAKGVEPQTRKLMEVCRL----RDTPIFTFINKLDR 143
>gnl|CDD|238838 cd01680, EFG_like_IV, Elongation Factor G-like domain IV. This
family includes the translational elongation factor
termed EF-2 (for Archaea and Eukarya) and EF-G (for
Bacteria), ribosomal protection proteins that mediate
tetracycline resistance and, an evolutionarily conserved
U5 snRNP-specific protein (U5-116kD). In complex with
GTP, EF-G/EF-2 promotes the translocation step of
translation. During translocation the peptidyl-tRNA is
moved from the A site to the P site of the small subunit
of ribosome and the mRNA is shifted one codon relative
to the ribosome. It has been shown that EF-G/EF-2_IV
domain mimics the shape of anticodon arm of the tRNA in
the structurally homologous ternary complex of Petra,
EF-Tu (another transcriptional elongation factor) and
GTP analog. The tip portion of this domain is found in a
position that overlaps the anticodon arm of the A-site
tRNA, implying that EF-G/EF-2 displaces the A-site tRNA
to the P-site by physical interaction with the anticodon
arm.
Length = 116
Score = 66.1 bits (162), Expect = 3e-13
Identities = 23/164 (14%), Positives = 41/164 (25%), Gaps = 55/164 (33%)
Query: 476 YRETVSEESDQVCLSKSPN------KHNRLFMKAAPLPDGLPEDIDKGEVNPRDDFKIRG 529
YRET+ + + + + + ++ PL G
Sbjct: 1 YRETIRKSVE--ATGEFERELGGKPQFGEVTLRVEPLERG-------------------- 38
Query: 530 RYLADKYEFDVTEARKIWSFGPDGTGPNLLIDCTKGVQYLNEIKDSVVAGFQWAAKEGVL 589
++D E+K++V G + A G L
Sbjct: 39 -------------------------SGVRVVDPVDEELLPAELKEAVEEGIRDACASGPL 73
Query: 590 SEENLRGVRFNIHDVTLHADAIHRGGGQIIPTTRRVLYASLLTA 633
+ L VR + DV H R ++ A
Sbjct: 74 TGYPLTDVRVTVLDVPYHEGV--STEAGFRAAAGRAFESAAQKA 115
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 65.0 bits (159), Expect = 5e-11
Identities = 55/171 (32%), Positives = 76/171 (44%), Gaps = 34/171 (19%)
Query: 2 MDKKKNIR-----NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERC 56
M K+K R N+ I HVDHGK+TLT ++ + GA+A D +E+ R
Sbjct: 1 MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKKGGAEAKAYDQIDNAPEEKARG 60
Query: 57 ITIKSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTD 116
ITI +TA Y E ++ +D PGH D+ + D
Sbjct: 61 ITI-NTAHVEY-ETANRHYAH------------------VDCPGHADYVKNMITGAAQMD 100
Query: 117 GALVVVDCVSGVCVQT-ETVL--RQAIAERIKPVLFMNKMD----RALLEL 160
GA++VV G QT E +L RQ I V+F+NK+D LLEL
Sbjct: 101 GAILVVAATDGPMPQTREHILLARQVGVPYI--VVFLNKVDMVDDEELLEL 149
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 64.6 bits (158), Expect = 7e-11
Identities = 54/210 (25%), Positives = 78/210 (37%), Gaps = 50/210 (23%)
Query: 1 MMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGII----------AGAKAGETRF----- 45
M +K ++ N+ I HVD GKSTL L+ G I + G+ F
Sbjct: 1 MASEKPHL-NLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWV 59
Query: 46 TDTRKDEQERCITIKSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFS 105
D K+E+ER +TI FE D + +ID+PGH DF
Sbjct: 60 LDKTKEERERGVTIDVA--HSKFETDK------------------YNFTIIDAPGHRDFV 99
Query: 106 SEVTAALRVTDGALVVVDCVSG-------VCVQTETVLRQAIAERIKPVLF-MNKMDRA- 156
+ D A++VVD G V QT A IK ++ +NKMD
Sbjct: 100 KNMITGASQADVAVLVVDARDGEFEAGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVS 159
Query: 157 -----LLELQLDAEDLYQTFQRIVENVNVI 181
E+ + L + ++V I
Sbjct: 160 WDEERFEEIVSEVSKLLKMVGYNPKDVPFI 189
>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 = 63.4 bits (154), Expect = 3e-10
Identities = 51/207 (24%), Positives = 73/207 (35%), Gaps = 44/207 (21%)
Query: 10 NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYFE 69
++ HVDHGK+TL +L A D +E++R +TI
Sbjct: 2 IIATAGHVDHGKTTLLKALTGIA-------------ADRLPEEKKRGMTI---------- 38
Query: 70 LDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVC 129
D + PD + ID PGH F S A D AL+VVD GV
Sbjct: 39 --DLGFAYFPLPDY--------RLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVM 88
Query: 130 VQTETVLRQAIAERIKP-VLFMNKMDRALLELQLDAEDLYQTFQR---IVENVNVIIATY 185
QT L I ++ + K DR E E + ++N + +
Sbjct: 89 TQTGEHLAVLDLLGIPHTIVVITKADRVNEEEIKRTEMFMKQILNSYIFLKNAKIFKTSA 148
Query: 186 SDDSGPMGEVRVFDSIMNYKKEEAESL 212
G +GE++ K ESL
Sbjct: 149 KTGQG-IGELK------KELKNLLESL 168
>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 = 60.2 bits (147), Expect = 3e-10
Identities = 40/133 (30%), Positives = 53/133 (39%), Gaps = 35/133 (26%)
Query: 10 NMSVIAHVDHGKSTLTDSLVSKAGII----------AGAKAGETRFT-----DTRKDEQE 54
N+ VI HVD GKSTLT L+ K G + + G+ F D K+E+E
Sbjct: 1 NLVVIGHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKYAWVLDKLKEERE 60
Query: 55 RCITIKSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRV 114
R +TI FE T K +ID+PGH DF +
Sbjct: 61 RGVTIDVG--LAKFE--------------TEKYR----FTIIDAPGHRDFVKNMITGASQ 100
Query: 115 TDGALVVVDCVSG 127
D A++VV G
Sbjct: 101 ADVAVLVVSARKG 113
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 61.6 bits (150), Expect = 7e-10
Identities = 45/146 (30%), Positives = 59/146 (40%), Gaps = 40/146 (27%)
Query: 15 AHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISM-YFELDDK 73
H+DHGK+TL +L TD +E++R ITI + Y +L+D
Sbjct: 7 GHIDHGKTTLLKALTGGV-------------TDRLPEEKKRGITID---LGFYYRKLEDG 50
Query: 74 DMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQT- 132
M FI D PGH DF S + A L D AL+VV G+ QT
Sbjct: 51 VMGFI------------------DVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTG 92
Query: 133 ET--VLRQAIAERIKPVLFMNKMDRA 156
E +L + VL K DR
Sbjct: 93 EHLLILDLLGIKNGIIVL--TKADRV 116
>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 = 57.0 bits (138), Expect = 1e-09
Identities = 32/154 (20%), Positives = 57/154 (37%), Gaps = 41/154 (26%)
Query: 8 IRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMY 67
+ ++ + GKSTL + L+ I K G TR + I
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTR------NYVTTVIEEDG------ 48
Query: 68 FELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSS-------EVTAALRVTDGALV 120
K + NL+D+ G D+ + V ++LRV D ++
Sbjct: 49 ---------------------KTYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVIL 87
Query: 121 VVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMD 154
V+D + QT+ ++ A + + +L NK+D
Sbjct: 88 VLDVEEILEKQTKEIIHHAESG-VPIILVGNKID 120
>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 = 54.6 bits (132), Expect = 2e-09
Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 12/94 (12%)
Query: 291 LMMYVSKMVPTSDKGRFYAFGRVFSGKVATGQKARIMGPNYIPGKKEDLYEKAIQRTILM 350
L V K+ +G A GRV SG + G K R+ K +++
Sbjct: 1 LRALVFKVFKDKGRGT-VATGRVESGTLKKGDKVRVGPGGGG--------VKGKVKSLKR 51
Query: 351 MGRYVEAIEDVPSGNICGLVGVDQFLVKTGTITT 384
+++ +G+I G+V D+ +K G T
Sbjct: 52 FK---GEVDEAVAGDIVGIVLKDKDDIKIGDTLT 82
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 60.0 bits (145), Expect = 2e-09
Identities = 46/168 (27%), Positives = 73/168 (43%), Gaps = 27/168 (16%)
Query: 3 DKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKST 62
++KK N+ I HVDHGK+TLT +L + G+ + D +E+ R ITI +
Sbjct: 76 ERKKPHVNIGTIGHVDHGKTTLTAALTMALASMGGSAPKKYDEIDAAPEERARGITINTA 135
Query: 63 AISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVV 122
+ +E +++ +D PGH D+ + DGA++VV
Sbjct: 136 TVE--YETENRHYAH------------------VDCPGHADYVKNMITGAAQMDGAILVV 175
Query: 123 DCVSGVCVQT-ETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQ 169
G QT E +L V+F+NK D Q+D E+L +
Sbjct: 176 SGADGPMPQTKEHILLAKQVGVPNMVVFLNKQD------QVDDEELLE 217
>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 = 56.6 bits (137), Expect = 5e-09
Identities = 41/147 (27%), Positives = 61/147 (41%), Gaps = 19/147 (12%)
Query: 10 NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYFE 69
N+ ++ HVD GK++L +L A A D QER IT+ S FE
Sbjct: 2 NVGLLGHVDSGKTSLAKALSEIASTAA---------FDKNPQSQERGITLDLGFSS--FE 50
Query: 70 LDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVC 129
+D D + + I L+D PGH + ++ D L+VVD G+
Sbjct: 51 VDKPKH----LEDNENPQIENYQITLVDCPGHASLIRTIIGGAQIIDLMLLVVDAKKGIQ 106
Query: 130 VQTETVLRQAIAE--RIKPVLFMNKMD 154
QT L I E ++ +NK+D
Sbjct: 107 TQTAECL--VIGELLCKPLIVVLNKID 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 = 56.1 bits (136), Expect = 6e-09
Identities = 54/165 (32%), Positives = 73/165 (44%), Gaps = 43/165 (26%)
Query: 10 NMSVIAHVDHGKSTLTDSLVSKAGIIA-GAKAGETRFT-----DTRKDEQERCITIKSTA 63
N+ I HVDHGK+TLT A I AK G + D +E+ R ITI +
Sbjct: 4 NVGTIGHVDHGKTTLT------AAITKVLAKKGGAKAKKYDEIDKAPEEKARGITINTAH 57
Query: 64 ISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDF-SSEVTAALRVTDGALVVV 122
+ Y +TA +D PGH D+ + +T A ++ DGA++VV
Sbjct: 58 VE-Y---------------ETANRHYAH----VDCPGHADYIKNMITGAAQM-DGAILVV 96
Query: 123 DCVSGVCVQT-ETVL--RQAIAERIKPVLFMNKMDRA----LLEL 160
G QT E +L RQ I V+F+NK D LLEL
Sbjct: 97 SATDGPMPQTREHLLLARQVGVPYI--VVFLNKADMVDDEELLEL 139
>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 = 58.3 bits (141), Expect = 7e-09
Identities = 50/173 (28%), Positives = 73/173 (42%), Gaps = 39/173 (22%)
Query: 2 MDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIA----------GAKAGETRFT----- 46
M K+K N++ I HVDHGKST L+ K G I + G+ F
Sbjct: 1 MAKEKEHINVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVM 60
Query: 47 DTRKDEQERCITIKSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSS 106
D K+E+ER +TI D F +T K E + ++D PGH DF
Sbjct: 61 DRLKEERERGVTI-----------DVAHWKF-----ETDKYE----VTIVDCPGHRDFIK 100
Query: 107 EVTAALRVTDGALVVVDCVSG-VCVQTETVLRQAIAERI---KPVLFMNKMDR 155
+ D A++VV G VQ +T +A + + ++ +NKMD
Sbjct: 101 NMITGASQADAAVLVVAVGDGEFEVQPQTREHAFLARTLGINQLIVAINKMDS 153
>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 = 57.9 bits (140), Expect = 8e-09
Identities = 49/165 (29%), Positives = 72/165 (43%), Gaps = 29/165 (17%)
Query: 3 DKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKST 62
++ K N+ I HVDHGK+TLT ++ + GA A D +E+ R ITI +
Sbjct: 7 ERTKPHVNIGTIGHVDHGKTTLTAAITTVLAKEGGAAARAYDQIDNAPEEKARGITINTA 66
Query: 63 AISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVV 122
+ +E +++ +D PGH D+ + DGA++VV
Sbjct: 67 HVE--YETENRHYAH------------------VDCPGHADYVKNMITGAAQMDGAILVV 106
Query: 123 DCVSGVCVQT-ETVL--RQAIAERIKPVLFMNKMDRA----LLEL 160
G QT E +L RQ I V+F+NK D LLEL
Sbjct: 107 SATDGPMPQTREHILLARQVGVPYI--VVFLNKCDMVDDEELLEL 149
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 57.9 bits (141), Expect = 9e-09
Identities = 56/172 (32%), Positives = 78/172 (45%), Gaps = 36/172 (20%)
Query: 2 MDKKKNIR-----NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERC 56
M K+K R N+ I HVDHGK+TLT ++ G +A D +E+ R
Sbjct: 1 MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITKVLAKKGGGEAKAYDQIDNAPEEKARG 60
Query: 57 ITIKSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDF-SSEVTAALRVT 115
ITI +T+ Y +TA +D PGH D+ + +T A ++
Sbjct: 61 ITI-NTSHVEY---------------ETANRHYAH----VDCPGHADYVKNMITGAAQM- 99
Query: 116 DGALVVVDCVSGVCVQT-ETVL--RQAIAERIKPVLFMNKMDRA----LLEL 160
DGA++VV G QT E +L RQ I V+F+NK D LLEL
Sbjct: 100 DGAILVVSAADGPMPQTREHILLARQVGVPYI--VVFLNKCDMVDDEELLEL 149
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 57.9 bits (140), Expect = 1e-08
Identities = 48/158 (30%), Positives = 67/158 (42%), Gaps = 29/158 (18%)
Query: 10 NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYFE 69
N+ I HVDHGK+TLT ++ AKA D +E+ R ITI + +
Sbjct: 63 NVGTIGHVDHGKTTLTAAITKVLAEEGKAKAVAFDEIDKAPEEKARGITIATAHVEY--- 119
Query: 70 LDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVC 129
+TAK +D PGH D+ + DG ++VV G
Sbjct: 120 -------------ETAKRHYAH----VDCPGHADYVKNMITGAAQMDGGILVVSAPDGPM 162
Query: 130 VQT-ETVL--RQAIAERIKPVLFMNKM----DRALLEL 160
QT E +L RQ + V+F+NK+ D LLEL
Sbjct: 163 PQTKEHILLARQVGVPSL--VVFLNKVDVVDDEELLEL 198
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 56.3 bits (136), Expect = 3e-08
Identities = 46/142 (32%), Positives = 62/142 (43%), Gaps = 37/142 (26%)
Query: 2 MDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGII----------AGAKAGETRFT----- 46
M K+K N+ VI HVD GKST T L+ K G I A+ G+ F
Sbjct: 1 MGKEKTHINLVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVL 60
Query: 47 DTRKDEQERCITIKSTAISMY-FELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFS 105
D K E+ER ITI I+++ FE T K + +ID+PGH DF
Sbjct: 61 DKLKAERERGITID---IALWKFE--------------TPK----YYFTIIDAPGHRDFI 99
Query: 106 SEVTAALRVTDGALVVVDCVSG 127
+ D A++VV +G
Sbjct: 100 KNMITGTSQADVAILVVASTAG 121
>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 = 56.3 bits (136), Expect = 4e-08
Identities = 39/144 (27%), Positives = 62/144 (43%), Gaps = 35/144 (24%)
Query: 12 SVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYFELD 71
+++ HVDHGK++L DS+ K + G G T+ I Y
Sbjct: 91 TIMGHVDHGKTSLLDSI-RKTKVAQGEAGGITQ------------------HIGAY---- 127
Query: 72 DKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQ 131
+NE G +I +D+PGH F+S +VTD ++VV GV Q
Sbjct: 128 ------------HVENEDGKMITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQ 175
Query: 132 TETVLRQAIAERIKPVLFMNKMDR 155
T + A A + ++ +NK+D+
Sbjct: 176 TIEAISHAKAANVPIIVAINKIDK 199
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 55.7 bits (135), Expect = 4e-08
Identities = 56/172 (32%), Positives = 80/172 (46%), Gaps = 36/172 (20%)
Query: 2 MDKKKNIR-----NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERC 56
M K+K R N+ I HVDHGK+TLT ++ +A + D +E+ER
Sbjct: 1 MAKEKFDRSKPHVNIGTIGHVDHGKTTLTAAITKVLAERGLNQAKDYDSIDAAPEEKERG 60
Query: 57 ITIKSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDF-SSEVTAALRVT 115
ITI +TA Y +T K +D PGH D+ + +T A ++
Sbjct: 61 ITI-NTAHVEY---------------ETEKRHYAH----VDCPGHADYVKNMITGAAQM- 99
Query: 116 DGALVVVDCVSGVCVQT-ETVL--RQAIAERIKPVLFMNKMDRA----LLEL 160
DGA++VV G QT E +L RQ + V+F+NK+D LLEL
Sbjct: 100 DGAILVVAATDGPMPQTREHILLARQVGVPYL--VVFLNKVDLVDDEELLEL 149
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 55.2 bits (134), Expect = 6e-08
Identities = 60/175 (34%), Positives = 83/175 (47%), Gaps = 42/175 (24%)
Query: 2 MDKKKNIR-----NMSVIAHVDHGKSTLTDSL---VSKAGIIAGAKAGETRFTDTRKDEQ 53
M K+K R N+ I HVDHGK+TLT ++ ++K G GA+A D +E+
Sbjct: 1 MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITKVLAKKG---GAEAKAYDQIDKAPEEK 57
Query: 54 ERCITIKSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDF-SSEVTAAL 112
R ITI +TA Y +T K +D PGH D+ + +T A
Sbjct: 58 ARGITI-NTAHVEY---------------ETEKRHYAH----VDCPGHADYVKNMITGAA 97
Query: 113 RVTDGALVVVDCVSGVCVQT-ETVL--RQAIAERIKPVLFMNKMDRA----LLEL 160
++ DGA++VV G QT E +L RQ I V+F+NK D LLEL
Sbjct: 98 QM-DGAILVVSAADGPMPQTREHILLARQVGVPYI--VVFLNKCDMVDDEELLEL 149
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 54.9 bits (133), Expect = 7e-08
Identities = 42/146 (28%), Positives = 59/146 (40%), Gaps = 35/146 (23%)
Query: 4 KKKNIRNMSVIAHVDHGKSTLTDSLVSKAGII----------AGAKAGETRFT-----DT 48
K+K N++VI HVDHGKSTL L+ + G I + G+ F D
Sbjct: 2 KEKPHLNLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDR 61
Query: 49 RKDEQERCITIKSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEV 108
K+E+ER +TI FE T K + ++D PGH DF +
Sbjct: 62 LKEERERGVTIDLA--HKKFE--------------TDK----YYFTIVDCPGHRDFVKNM 101
Query: 109 TAALRVTDGALVVVDCVSGVCVQTET 134
D A++VV V +T
Sbjct: 102 ITGASQADAAVLVVAADDAGGVMPQT 127
>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 = 51.8 bits (125), Expect = 1e-07
Identities = 41/143 (28%), Positives = 53/143 (37%), Gaps = 35/143 (24%)
Query: 16 HVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIK-STAISMYFELDDKD 74
H+DHGK+TL +L TD +E++R ITI A Y +L D
Sbjct: 7 HIDHGKTTLIKALTGIE-------------TDRLPEEKKRGITIDLGFA---YLDLPDGK 50
Query: 75 MVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTET 134
+ GF ID PGH F + A D L+VV G+ QT
Sbjct: 51 RL-------------GF----IDVPGHEKFVKNMLAGAGGIDAVLLVVAADEGIMPQTRE 93
Query: 135 VLRQAIAERIKPVLF-MNKMDRA 156
L IK L + K D
Sbjct: 94 HLEILELLGIKKGLVVLTKADLV 116
>gnl|CDD|239764 cd04097, mtEFG1_C, mtEFG1_C: C-terminus of mitochondrial Elongation
factor G1 (mtEFG1)-like proteins found in eukaryotes.
Eukaryotic cells harbor 2 protein synthesis systems: one
localized in the cytoplasm, the other in the
mitochondria. Most factors regulating mitochondrial
protein synthesis are encoded by nuclear genes,
translated in the cytoplasm, and then transported to the
mitochondria. The eukaryotic system of elongation factor
(EF) components is more complex than that in
prokaryotes, with both cytoplasmic and mitochondrial
elongation factors and multiple isoforms being expressed
in certain species. Eukaryotic EF-2 operates in the
cytosolic protein synthesis machinery of eukaryotes,
EF-Gs in protein synthesis in bacteria. Eukaryotic
mtEFG1 proteins show significant homology to bacterial
EF-Gs. Mutants in yeast mtEFG1 have impaired
mitochondrial protein synthesis, respiratory defects and
a tendency to lose mitochondrial DNA. There are two
forms of mtEFG present in mammals (designated mtEFG1s
and mtEFG2s) mtEFG2s are not present in this group.
Length = 78
Score = 48.9 bits (117), Expect = 2e-07
Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 639 EPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFGFTADLR 698
EP+ E+ P G + G+LN+R+G + + F ++A +P+N+ FG++ +LR
Sbjct: 1 EPIMKVEVTAPTEFQGNVIGLLNKRKGTIVDTDTGEDE--FTLEAEVPLNDMFGYSTELR 58
Query: 699 SNTGGQA 705
S T G+
Sbjct: 59 SMTQGKG 65
>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 = 50.5 bits (122), Expect = 3e-07
Identities = 40/150 (26%), Positives = 61/150 (40%), Gaps = 48/150 (32%)
Query: 13 VIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCIT--IKSTAISMYFEL 70
V+ HVDHGK+TL D + +A +AG IT I + + +
Sbjct: 5 VMGHVDHGKTTLLDKIRKTN--VAAGEAGG--------------ITQHIGAYQVPI---- 44
Query: 71 DDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALR-----VTDGALVVVDCV 125
+ K I ID+PGH F+ +R VTD A++VV
Sbjct: 45 ----------------DVKIPGITFIDTPGHEAFT-----NMRARGASVTDIAILVVAAD 83
Query: 126 SGVCVQTETVLRQAIAERIKPVLFMNKMDR 155
GV QT + A A + ++ +NK+D+
Sbjct: 84 DGVMPQTIEAINHAKAANVPIIVAINKIDK 113
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 52.7 bits (127), Expect = 4e-07
Identities = 55/169 (32%), Positives = 80/169 (47%), Gaps = 33/169 (19%)
Query: 3 DKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKST 62
++KK N+ I HVDHGK+TLT ++ GAKA + D+ +E+ R ITI T
Sbjct: 7 ERKKPHVNIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARGITIN-T 65
Query: 63 AISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDF-SSEVTAALRVTDGALVV 121
A Y +T +D PGH D+ + +T A ++ DGA++V
Sbjct: 66 AHVEY---------------ETENRHYAH----VDCPGHADYVKNMITGAAQM-DGAILV 105
Query: 122 VDCVSGVCVQT-ETVL--RQAIAERIKPVLFMNKMDRALLELQLDAEDL 167
V G QT E +L +Q I V+F+NK D Q+D E+L
Sbjct: 106 VSAADGPMPQTKEHILLAKQVGVPNI--VVFLNKED------QVDDEEL 146
>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 = 46.5 bits (111), Expect = 8e-07
Identities = 18/71 (25%), Positives = 25/71 (35%), Gaps = 7/71 (9%)
Query: 307 FYAFGRVFSGKVATGQKARIMGPNYIPGKKEDLYEKAIQRTILMMGRYVEAIEDVPSGNI 366
A GRV SG + G K I PN K + + G EA+ +G I
Sbjct: 2 TVATGRVESGTLKKGDKVVIG-PNGTGKKGR------VTSLEMFHGDLREAVAGANAGII 54
Query: 367 CGLVGVDQFLV 377
+G+
Sbjct: 55 LAGIGLKDIKR 65
>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 = 50.8 bits (122), Expect = 1e-06
Identities = 41/154 (26%), Positives = 69/154 (44%), Gaps = 23/154 (14%)
Query: 10 NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIK--STAISMY 67
N+ ++ HVDHGK+TLT +L +TDT +E +R I+I+ +Y
Sbjct: 6 NIGMVGHVDHGKTTLTKALTGV-------------WTDTHSEELKRGISIRLGYADAEIY 52
Query: 68 -FELDDKDMVFITNP---DQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVD 123
D + T P + ++ E ++ +D+PGH + + + + DGAL+V+
Sbjct: 53 KCPECDGPECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALLVIA 112
Query: 124 CVSGVCVQTETVLRQAIAERI---KPVLFMNKMD 154
C Q +T E I V+ NK+D
Sbjct: 113 ANEP-CPQPQTREHLMALEIIGIKNIVIVQNKID 145
>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 = 46.1 bits (110), Expect = 1e-06
Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 2/80 (2%)
Query: 639 EPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNESFGFTADLR 698
EP E++ P+ A+G L + FE+ Q+ G ++ +PV S + ++L
Sbjct: 1 EPYLRFELEVPQDALGRAMSDLAKMGA-TFEDPQIKG-DEVTLEGTIPVATSQDYQSELP 58
Query: 699 SNTGGQAFPQCVFDHWQVLP 718
S T G+ + F ++
Sbjct: 59 SYTHGEGVLETEFKGYRPCH 78
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 49.9 bits (120), Expect = 4e-06
Identities = 50/183 (27%), Positives = 71/183 (38%), Gaps = 57/183 (31%)
Query: 13 VIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYFELDD 72
++ HVDHGK+TL D + + +A +AG IT A LD
Sbjct: 10 IMGHVDHGKTTLLDKI--RKTNVAAGEAGG--------------ITQHIGAY--QVPLDV 51
Query: 73 KDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALR-----VTDGALVVVDCVSG 127
+ IT ID+PGH F+ A+R VTD A++VV G
Sbjct: 52 IKIPGIT---------------FIDTPGHEAFT-----AMRARGASVTDIAILVVAADDG 91
Query: 128 VCVQTETVLRQAIAERIKPVLFMNKMDR----------ALLELQLDAEDLYQTFQRIVEN 177
V QT + A A + V+ +NK+D+ L E L E+ + V
Sbjct: 92 VMPQTIEAINHAKAAGVPIVVAINKIDKPEANPDKVKQELQEYGLVPEE----WGGDVIF 147
Query: 178 VNV 180
V V
Sbjct: 148 VPV 150
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 49.8 bits (119), Expect = 4e-06
Identities = 44/158 (27%), Positives = 71/158 (44%), Gaps = 32/158 (20%)
Query: 12 SVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYFELD 71
+++ HVDHGK+TL D + + IA +AG IT K A + FE
Sbjct: 248 TILGHVDHGKTTLLDKI--RKTQIAQKEAGG--------------ITQKIGAYEVEFEYK 291
Query: 72 DKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQ 131
D +N+K I +D+PGH FSS + VTD A++++ GV Q
Sbjct: 292 D-------------ENQK---IVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQ 335
Query: 132 TETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQ 169
T + A + ++ +NK+D+A + + L +
Sbjct: 336 TIEAINYIQAANVPIIVAINKIDKANANTERIKQQLAK 373
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 48.1 bits (115), Expect = 1e-05
Identities = 36/131 (27%), Positives = 62/131 (47%), Gaps = 22/131 (16%)
Query: 2 MDKKKNIR---NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCIT 58
M K+I+ N+ ++ HVDHGK+TLT +L +G+ +TD +E +R IT
Sbjct: 1 MADPKHIQPEVNIGMVGHVDHGKTTLTKAL---SGV----------WTDRHSEELKRGIT 47
Query: 59 IK---STAISMYFELDDKDMVFITNPDQTAKNEKGFL---INLIDSPGHVDFSSEVTAAL 112
IK + A + + T P + L ++ +D+PGH + + +
Sbjct: 48 IKLGYADAKIYKCPECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGA 107
Query: 113 RVTDGALVVVD 123
+ DGAL+V+
Sbjct: 108 ALMDGALLVIA 118
>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 = 46.5 bits (111), Expect = 1e-05
Identities = 41/160 (25%), Positives = 68/160 (42%), Gaps = 34/160 (21%)
Query: 10 NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIK-STAISMYF 68
N+ I HV HGK+TL KA ++G T K+E +R ITIK A + +
Sbjct: 2 NIGTIGHVAHGKTTLV-----KA--LSGVW------TVRHKEELKRNITIKLGYANAKIY 48
Query: 69 ELDDK------DMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVT-----DG 117
+ + D P + + ++ +D PGH E+ A ++ DG
Sbjct: 49 KCPNCGCPRPYDTPECECPGCGGETKLVRHVSFVDCPGH-----EILMATMLSGAAVMDG 103
Query: 118 ALVVVDCVSGVCVQTETVLRQAIAERIKP---VLFMNKMD 154
AL+++ + C Q +T A E + ++ NK+D
Sbjct: 104 ALLLIA-ANEPCPQPQTSEHLAALEIMGLKHIIILQNKID 142
>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 = 45.1 bits (107), Expect = 2e-05
Identities = 30/150 (20%), Positives = 46/150 (30%), Gaps = 40/150 (26%)
Query: 13 VIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYFELDD 72
V+ GKS+L ++L+ G TR D +
Sbjct: 2 VVGRGGVGKSSLLNALLGGEVGEVSDVPGTTR------DPDVYVKELD------------ 43
Query: 73 KDMVFITNPDQTAKNEKGFLINLIDSPGHVDFS-----SEVTAALRVTDGALVVVDCVSG 127
+ + L+D+PG +F LR D L+VVD
Sbjct: 44 ---------------KGKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDR 88
Query: 128 VCV--QTETVLRQAIAERIKPVLFMNKMDR 155
+LR+ E I +L NK+D
Sbjct: 89 ESEEDAKLLILRRLRKEGIPIILVGNKIDL 118
>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 = 45.3 bits (108), Expect = 3e-05
Identities = 49/182 (26%), Positives = 71/182 (39%), Gaps = 53/182 (29%)
Query: 16 HVDHGKSTLTDSLV--SK-------AGIIAGAKAGETR-------FTDTRKDEQERCITI 59
VD GKSTL L+ SK A + +G D + E+E+ ITI
Sbjct: 7 SVDDGKSTLIGRLLYDSKSIFEDQLAALERSKSSGTQGEKLDLALLVDGLQAEREQGITI 66
Query: 60 KSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSE-VTAALRVTDGA 118
YF + FI + D+PGH ++ VT A D A
Sbjct: 67 DVAYR--YFSTPKRK--FI----------------IADTPGHEQYTRNMVTGAST-ADLA 105
Query: 119 LVVVDCVSGVCVQTETVLRQA-IAE--RIKP-VLFMNKMDRALLELQLDAEDLYQTFQRI 174
+++VD GV QT R + IA I+ V+ +NKMD L++ + F+ I
Sbjct: 106 ILLVDARKGVLEQTR---RHSYIASLLGIRHVVVAVNKMD--LVDYD------EEVFEEI 154
Query: 175 VE 176
Sbjct: 155 KA 156
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 46.4 bits (111), Expect = 4e-05
Identities = 35/136 (25%), Positives = 61/136 (44%), Gaps = 33/136 (24%)
Query: 1 MMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIK 60
M +K + N+ ++ HVDHGK+TL +L G+ +TD +E +R ITI+
Sbjct: 2 MWEKVQPEVNIGMVGHVDHGKTTLVQAL---TGV----------WTDRHSEELKRGITIR 48
Query: 61 ----STAISMYFELDDKD--MVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVT----- 109
I + ++ + P+ ++ E ++ +D+PGH E
Sbjct: 49 LGYADATIRKCPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGH-----ETLMATML 103
Query: 110 --AALRVTDGALVVVD 123
AAL DGA++V+
Sbjct: 104 SGAAL--MDGAILVIA 117
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 44.7 bits (105), Expect = 1e-04
Identities = 44/142 (30%), Positives = 62/142 (43%), Gaps = 37/142 (26%)
Query: 2 MDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGII----------AGAKAGETRFT----- 46
M K+K N+ VI HVD GKST T L+ K G I A+ + F
Sbjct: 1 MGKEKVHINIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFEKEAAEMNKRSFKYAWVL 60
Query: 47 DTRKDEQERCITIKSTAISMY-FELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFS 105
D K E+ER ITI I+++ FE T K + +ID+PGH DF
Sbjct: 61 DKLKAERERGITID---IALWKFE--------------TTK----YYCTVIDAPGHRDFI 99
Query: 106 SEVTAALRVTDGALVVVDCVSG 127
+ D A++++D +G
Sbjct: 100 KNMITGTSQADCAVLIIDSTTG 121
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 44.7 bits (106), Expect = 2e-04
Identities = 38/117 (32%), Positives = 50/117 (42%), Gaps = 32/117 (27%)
Query: 16 HVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYFELDDKDM 75
HVDHGK+TL + I G A D +E++R +TI D
Sbjct: 8 HVDHGKTTLLQA-------ITGVNA------DRLPEEKKRGMTI------------DLGY 42
Query: 76 VFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQT 132
+ PD G ++ ID PGH F S + A + D AL+VV C GV QT
Sbjct: 43 AYWPQPD-------GRVLGFIDVPGHEKFLSNMLAGVGGIDHALLVVACDDGVMAQT 92
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 42.9 bits (102), Expect = 6e-04
Identities = 49/168 (29%), Positives = 71/168 (42%), Gaps = 50/168 (29%)
Query: 5 KKNIRN--MSVIAHVDHGKSTLTD-----SLVSK-AGIIA---GAKAGETRFTDTRKDEQ 53
+K +R + V+ HVDHGK+TL D ++ +K AG I GA T+ D
Sbjct: 1 EKKLRQPIVVVLGHVDHGKTTLLDKIRGTAVAAKEAGGITQHIGA-------TEVPID-- 51
Query: 54 ERCITIKSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALR 113
I+ A + L K + G L ID+PGH F++ LR
Sbjct: 52 ----VIEKIAGPLKKPLPIKLKI------------PGLL--FIDTPGHEAFTN-----LR 88
Query: 114 -----VTDGALVVVDCVSGVCVQTETVLRQAIAERIKP-VLFMNKMDR 155
+ D A++VVD G QT + + R P V+ NK+DR
Sbjct: 89 KRGGALADIAILVVDINEGFQPQTIEAI-NILKRRKTPFVVAANKIDR 135
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 39.4 bits (92), Expect = 0.003
Identities = 40/187 (21%), Positives = 63/187 (33%), Gaps = 37/187 (19%)
Query: 1 MMDKKKNIRNMS--VIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCIT 58
+ + VI V GK+T +L K +I A A +
Sbjct: 1 LTSAANKMIETKIVVIGPVGAGKTTFVRALSDKPLVITEADA---------SSVSGK--G 49
Query: 59 IKSTAISMYF---ELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVT 115
+ T ++M F ELD+ V L +PG F R
Sbjct: 50 KRPTTVAMDFGSIELDEDTGVH-----------------LFGTPGQERFKFMWEILSRGA 92
Query: 116 DGALVVVDCVSGVCVQTETVLRQ-AIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRI 174
GA+V+VD + E ++ I V+ +NK D L L E + + +
Sbjct: 93 VGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVVAINKQD---LFDALPPEKIREALKLE 149
Query: 175 VENVNVI 181
+ +V VI
Sbjct: 150 LLSVPVI 156
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 40.5 bits (95), Expect = 0.003
Identities = 59/265 (22%), Positives = 97/265 (36%), Gaps = 35/265 (13%)
Query: 3 DKKKNIR---NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITI 59
K + + V HVDHGKSTL LV+ G + + D +K E ER
Sbjct: 109 RKTEEAPEHVLVGVAGHVDHGKSTLVGVLVT--GRLDDGDGATRSYLDVQKHEVERG--- 163
Query: 60 KSTAISM-YFELDDKDMVFITNPDQTAK-----NEKGFLINLIDSPGHVDFSSEVTAALR 113
S IS+ + DD +V + NP A+ L++ +D+ GH + LR
Sbjct: 164 LSADISLRVYGFDDGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPW-------LR 216
Query: 114 VT---------DGALVVVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDA 164
T D L+VV GV T+ L A+A + ++ + K+D +
Sbjct: 217 TTIRGLLGQKVDYGLLVVAADDGVTKMTKEHLGIALAMELPVIVVVTKIDMVPDDRFQGV 276
Query: 165 EDLYQTFQRIVENVNVIIATYSDD-----SGPMGEVRVFDSIMNYKKEEAESLLSKLGIE 219
+ + V + +I+ D + G V + E LL + +
Sbjct: 277 VEEISALLKRVGRIPLIVKDTDDVVLAAKAMKAGRGVVPIFYTSSVTGEGLDLLDEFFLL 336
Query: 220 LKPEDKEKDGKALLKVVMRTWLPAG 244
L + D L + + + G
Sbjct: 337 LPKRRRWDDEGPFLMYIDKIYSVTG 361
>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 = 40.2 bits (94), Expect = 0.004
Identities = 44/148 (29%), Positives = 64/148 (43%), Gaps = 24/148 (16%)
Query: 11 MSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCIT--IKSTAISM-Y 67
+SV+ HVDHGK+TL D + A +A +AG IT I +T I M
Sbjct: 7 VSVLGHVDHGKTTLLDKIRGSA--VAKREAGG--------------ITQHIGATEIPMDV 50
Query: 68 FELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSG 127
E D++ G L ID+PGH F++ + D A+++VD G
Sbjct: 51 IEGICGDLLKKFKIRLKIP---GLLF--IDTPGHEAFTNLRKRGGALADLAILIVDINEG 105
Query: 128 VCVQTETVLRQAIAERIKPVLFMNKMDR 155
QT+ L + V+ NK+DR
Sbjct: 106 FKPQTQEALNILRMYKTPFVVAANKIDR 133
>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 = 35.5 bits (83), Expect = 0.009
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 12/77 (15%)
Query: 309 AFGRVFSGKVATGQKARIMGPNYIPGKKEDLYEKAIQRTILMMGRYVEAIEDVPSGNICG 368
+F RV+SG + G Y K + E+ + R + M G+ E +E+ +G+I
Sbjct: 18 SFVRVYSGTLKAGSTL------YNSTKGKK--ER-VGRLLRMHGKKQEEVEEAGAGDIGA 68
Query: 369 LVGVDQFLVKTG-TITT 384
+ G+ TG T+
Sbjct: 69 VAGLKD--TATGDTLCD 83
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 35.3 bits (82), Expect = 0.025
Identities = 31/143 (21%), Positives = 45/143 (31%), Gaps = 46/143 (32%)
Query: 20 GKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYFELDDKDMVFIT 79
GKSTL ++L I G TR
Sbjct: 11 GKSTLINALTGAKVAIVSDYPGTTRDPILGVLG--------------------------- 43
Query: 80 NPDQTAKNEKGFLINLIDSPG---------HVDFSSEVTAALRVTDGALVVVDCVSGVCV 130
G I L+D+PG V+ + A+R D L+VVD G+
Sbjct: 44 ---------LGRQIILVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTE 94
Query: 131 QTETVLRQAIAERIKPVLF-MNK 152
E +L + KP++ +NK
Sbjct: 95 DDEEILEELEKLPKKPIILVLNK 117
>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 = 34.4 bits (80), Expect = 0.025
Identities = 22/101 (21%), Positives = 38/101 (37%), Gaps = 29/101 (28%)
Query: 290 PLMMYVS-KMVPTSDKGRFYAFGRVFSGKVATGQKARIMGPNYIPGKKEDLYEKAIQRTI 348
P + +S K D+G G+V SG + G +M P+ KE + K+I
Sbjct: 1 PFRLPISDKY---KDQGGTVVSGKVESGSIQKGDTLLVM-PS-----KESVEVKSIY--- 48
Query: 349 LMMGRYVEAIEDVPSGN-ICG------LVGVDQFLVKTGTI 382
++D + G L G+D+ + G +
Sbjct: 49 ---------VDDEEVDYAVAGENVRLKLKGIDEEDISPGDV 80
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 36.5 bits (85), Expect = 0.044
Identities = 23/51 (45%), Positives = 27/51 (52%), Gaps = 13/51 (25%)
Query: 10 NMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIK 60
N+ I HV HGKST V KA ++G K RF K E+ R ITIK
Sbjct: 36 NIGTIGHVAHGKST-----VVKA--LSGVKTV--RF----KREKVRNITIK 73
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 36.5 bits (85), Expect = 0.053
Identities = 40/174 (22%), Positives = 64/174 (36%), Gaps = 45/174 (25%)
Query: 2 MDKKKNIRNMSVIAHVDHGKSTL------------TDSL--VSKAGIIAGAKAGETRF-- 45
K +R ++ VD GKSTL D L + + G + +
Sbjct: 1 QQHKSLLRFITC-GSVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLAL 59
Query: 46 -TDTRKDEQERCITIKSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDF 104
D + E+E+ ITI YF + + FI + D+PGH +
Sbjct: 60 LVDGLEAEREQGITIDVAYR--YFSTEKRK--FI----------------IADTPGHEQY 99
Query: 105 SSEVTAALRVTDGALVVVDCVSGVCVQTETVLRQAIAERI----KPVLFMNKMD 154
+ + D A+++VD GV QT R + + V+ +NKMD
Sbjct: 100 TRNMATGASTADLAILLVDARKGVLEQTR---RHSFIASLLGIRHVVVAVNKMD 150
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 34.9 bits (81), Expect = 0.17
Identities = 38/182 (20%), Positives = 68/182 (37%), Gaps = 35/182 (19%)
Query: 3 DKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKST 62
++ I+ +++I + GKS+L ++++ + +I AG TR D
Sbjct: 174 EETDPIK-IAIIGRPNVGKSSLINAILGEERVIVSDIAGTTR------D----------- 215
Query: 63 AISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVT-AALRVTDGALVV 121
+I + FE D + V I D KG + +S T A+ D L+V
Sbjct: 216 SIDIEFERDGRKYVLI---DTAGIRRKGKITE-----SVEKYSVARTLKAIERADVVLLV 267
Query: 122 VDCVSGVCVQTETVLRQAIAERIKPVLFMNKMD--------RALLELQLDAEDLYQTFQR 173
+D G+ Q + V+ +NK D + +L + + F
Sbjct: 268 IDATEGISEQDLRIAGLIEEAGRGIVIVVNKWDLVEEDEATMEEFKKKLRRKLPFLDFAP 327
Query: 174 IV 175
IV
Sbjct: 328 IV 329
>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 = 31.7 bits (73), Expect = 0.18
Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 9/81 (11%)
Query: 639 EPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPM----FVVKAYLPVNESFGFT 694
EP+ I PE G + L +R+G +M+ G F + P GF
Sbjct: 1 EPIEELTIDVPEEYSGAVIEKLGKRKG-EMVDMEPDGNGRTRLEFKI----PSRGLIGFR 55
Query: 695 ADLRSNTGGQAFPQCVFDHWQ 715
++ ++T G VFD ++
Sbjct: 56 SEFLTDTRGTGIMNHVFDGYE 76
>gnl|CDD|233468 TIGR01558, sm_term_P27, phage terminase, small subunit, putative,
P27 family. This model describes a distinct family of
phage (and integrated prophage) putative terminase small
subunit. Members tend to be adjacent to the phage
terminase large subunit gene [Mobile and
extrachromosomal element functions, Prophage functions].
Length = 116
Score = 31.6 bits (72), Expect = 0.41
Identities = 22/99 (22%), Positives = 37/99 (37%), Gaps = 12/99 (12%)
Query: 142 ERIKPVL----FMNKMDRALLELQLDAEDLYQTFQRIVENVNVIIATYSDD--SGPMGEV 195
+R+ P L + +DR L +A D Y+ +E + + P V
Sbjct: 15 KRVAPELKGSGILTNLDRDALLRYCEAYDRYREATDDLEATGITATVEDGSPKANPALTV 74
Query: 196 RVFDSIMNYKKEEAE-----SLLSKLGIELKPEDKEKDG 229
V D+ + + S S+L I + EDK+ D
Sbjct: 75 -VEDAFKQLRSIGSALGLTPSSRSRLVINVAKEDKKADP 112
>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 = 31.6 bits (73), Expect = 0.87
Identities = 34/144 (23%), Positives = 56/144 (38%), Gaps = 42/144 (29%)
Query: 20 GKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMYFELDDKDMVFIT 79
GKS+L ++L+ + +I AG TR D +I + FE D + I
Sbjct: 14 GKSSLLNALLGEERVIVSDIAGTTR------D-----------SIDVPFEYDGQKYTLI- 55
Query: 80 NPDQTA------KNEKGFLINLIDSPGHVDFSSEVTA--ALRVTDGALVVVDCVSGVCVQ 131
D TA K +G ++ S + A+ D L+V+D G+ Q
Sbjct: 56 --D-TAGIRKKGKVTEG-----------IEKYSVLRTLKAIERADVVLLVLDASEGITEQ 101
Query: 132 TETVLRQAIAERIKPVLF-MNKMD 154
+ + E K ++ +NK D
Sbjct: 102 DLRIAGLIL-EEGKALIIVVNKWD 124
>gnl|CDD|227512 COG5185, HEC1, Protein involved in chromosome segregation,
interacts with SMC proteins [Cell division and
chromosome partitioning].
Length = 622
Score = 32.6 bits (74), Expect = 0.90
Identities = 28/133 (21%), Positives = 55/133 (41%), Gaps = 6/133 (4%)
Query: 140 IAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNVIIATYSDDSGPMG-EVRVF 198
I E IK + +++ + E E+ T + ++N+ I + + E+
Sbjct: 456 INESIKK--SILELNDEIQERIKTEENKSITLEEDIKNLKHDINELTQILEKLELELSEA 513
Query: 199 DSIMNYKKEEAESLLSKLGIELKPEDKEKDGKALLKVVMRTWLPAGEALLQMIAIHLPSP 258
+S KEE E L IE++ +KE + L ++ +T + E L+Q I L
Sbjct: 514 NSKFELSKEENERELVAQRIEIEKLEKELND---LNLLSKTSILDAEQLVQSTEIKLDEL 570
Query: 259 VVAQKYRMEMLYE 271
V + +++
Sbjct: 571 KVDLNRKRYKIHK 583
>gnl|CDD|237738 PRK14508, PRK14508, 4-alpha-glucanotransferase; Provisional.
Length = 497
Score = 32.1 bits (74), Expect = 1.3
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 711 FDHWQVLPGDPTDPGSKPYN 730
+WQ+LP PT G PY
Sbjct: 41 QSYWQILPLGPTGYGDSPYQ 60
>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 = 29.4 bits (67), Expect = 1.4
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 2/68 (2%)
Query: 639 EPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEEMQVAGTPMFVVKAYLPVNE-SFGFTADL 697
EP I P +G I + RRG V ++M+ ++ LP+ E + F L
Sbjct: 1 EPFVKATIITPSEYLGAIMELCQERRG-VQKDMEYLDANRVMLTYELPLAEIVYDFFDKL 59
Query: 698 RSNTGGQA 705
+S + G A
Sbjct: 60 KSISKGYA 67
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 31.7 bits (73), Expect = 1.6
Identities = 43/167 (25%), Positives = 64/167 (38%), Gaps = 58/167 (34%)
Query: 16 HVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIKSTAISMY-FELDDKD 74
HVDHGK++L D++ K + AG G IT I Y E +
Sbjct: 257 HVDHGKTSLLDAI-RKTNVAAGEAGG---------------IT---QHIGAYQVETNGGK 297
Query: 75 MVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALR-----VTDGALVVVDCVSGVC 129
+ F +D+PGH F+ A+R VTD ++VV GV
Sbjct: 298 ITF------------------LDTPGHEAFT-----AMRARGAQVTDIVVLVVAADDGVM 334
Query: 130 VQTETVLRQAIAERIKPVLFMNKMD----------RALLELQLDAED 166
QT + A A + ++ +NK+D + L E L E+
Sbjct: 335 PQTIEAINHAKAAGVPIIVAINKIDKPGANPDRVKQELSEYGLVPEE 381
>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 = 31.2 bits (71), Expect = 1.9
Identities = 43/156 (27%), Positives = 59/156 (37%), Gaps = 38/156 (24%)
Query: 17 VDHGKSTLTDSLVSKAGII--------------AGAKAGETRFT---DTRKDEQERCITI 59
VD GKSTL L+ I G + GE D + E+E+ ITI
Sbjct: 9 VDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQGGEIDLALLVDGLQAEREQGITI 68
Query: 60 KSTAISMYFELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSSEVTAALRVTDGAL 119
YF D + FI + D+PGH ++ + D A+
Sbjct: 69 D--VAYRYFSTDKRK--FI----------------VADTPGHEQYTRNMATGASTADLAV 108
Query: 120 VVVDCVSGVCVQTETVLRQAIAERIKP-VLFMNKMD 154
++VD GV QT A I+ VL +NKMD
Sbjct: 109 LLVDARKGVLEQTRRHSYIASLLGIRHVVLAVNKMD 144
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 31.8 bits (72), Expect = 1.9
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 1 MMDKKKNIRN--MSVIAHVDHGKSTLTDSLV 29
K+K +R ++V+ HVDHGK L + V
Sbjct: 1 KDKKEKRLRCPIVAVLGHVDHGKCLLPEEKV 31
Score = 29.9 bits (67), Expect = 6.6
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 96 IDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTE---TVLRQAIAERIKPVLFMNK 152
ID+PGH F+S + D A++VVD G QT +LRQ + V+ NK
Sbjct: 531 IDTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQY---KTPFVVAANK 587
Query: 153 MDR 155
+D
Sbjct: 588 IDL 590
>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 = 30.3 bits (69), Expect = 2.1
Identities = 18/70 (25%), Positives = 26/70 (37%), Gaps = 8/70 (11%)
Query: 93 INLIDSPGHVD-------FSSEVTAALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIK 145
+ LID+PG + E D L+VVD V+ E L
Sbjct: 48 VVLIDTPGLDEEGGLGRERVEEARQVADRADLVLLVVDS-DLTPVEEEAKLGLLRERGKP 106
Query: 146 PVLFMNKMDR 155
+L +NK+D
Sbjct: 107 VLLVLNKIDL 116
>gnl|CDD|201900 pfam01642, MM_CoA_mutase, Methylmalonyl-CoA mutase. The enzyme
methylmalonyl-CoA mutase is a member of a class of
enzymes that uses coenzyme B12 (adenosylcobalamin) as a
cofactor. The enzyme induces the formation of an
adenosyl radical from the cofactor. This radical then
initiates a free-radical rearrangement of its substrate,
succinyl-CoA, to methylmalonyl-CoA.
Length = 517
Score = 31.2 bits (71), Expect = 2.2
Identities = 13/75 (17%), Positives = 31/75 (41%), Gaps = 5/75 (6%)
Query: 437 ESGEHIVAGAGELHL--EICLKDLEEDHACIPIKKSDPVVSYRETVSEESDQVCLSKS-- 492
+SG ++ G + L E ++ L D+ + +++ + + RE +E+ + L
Sbjct: 421 DSGREVIVGVNKYPLLTEDPVEVLPVDNPGVRVEQIRRLNAIREARDDEAVRAALEALGA 480
Query: 493 -PNKHNRLFMKAAPL 506
+ + PL
Sbjct: 481 AARVGDGNLLALGPL 495
>gnl|CDD|184057 PRK13447, PRK13447, F0F1 ATP synthase subunit epsilon; Provisional.
Length = 136
Score = 30.0 bits (68), Expect = 2.4
Identities = 19/70 (27%), Positives = 27/70 (38%), Gaps = 24/70 (34%)
Query: 99 PGHVDFSSEVTAA--------------------LRVTDGALVVVDCVSGVC----VQTET 134
PGH DF + + A+ LRVT GA V + C V + E
Sbjct: 34 PGHADFLTVLRASVVRWRRADGATHYCAVRGGVLRVTGGARVEIACREAVLGEDLARLEA 93
Query: 135 VLRQAIAERI 144
V+R A ++
Sbjct: 94 VVRAVRAAQL 103
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 30.6 bits (70), Expect = 3.3
Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 141 AERIKPVLFMNKMDRALLELQLDAEDLYQTFQRI 174
A IKP++ +NK+D LL+ +A +L ++ I
Sbjct: 109 ANGIKPIIVLNKID--LLDDLEEARELLALYRAI 140
>gnl|CDD|218187 pfam04637, Herpes_pp85, Herpesvirus phosphoprotein 85 (HHV6-7
U14/HCMV UL25). This family includes UL25 proteins from
HCMV, as well as U14 proteins from HHV 6 and HHV7. These
85 kD phosphoproteins appear to act as structural
antigens, but their precise function is otherwise
unknown.
Length = 502
Score = 30.8 bits (70), Expect = 3.3
Identities = 8/47 (17%), Positives = 15/47 (31%), Gaps = 6/47 (12%)
Query: 624 RVLYASLLTACPRLMEPVYLCEIQCPE------VAVGGIYGVLNRRR 664
R L ++ L E +Y Q PE + +++
Sbjct: 240 RALRKWIVLQLNSLCEDLYFAYTQVPETRETFLDLAREVANMISSNS 286
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 30.0 bits (68), Expect = 3.3
Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 15/81 (18%)
Query: 86 KNEKGFLINLIDSPGHVDFSSEVTAALRVTDGALV-VVDCVSGVCVQTE---------TV 135
+ KG + L+D PGH ++ L+ + A+V VVD + Q +
Sbjct: 42 NSSKGKKLTLVDVPGHEKLRDKLLEYLKASLKAIVFVVDSAT---FQKNIRDVAEFLYDI 98
Query: 136 L--RQAIAERIKPVLFMNKMD 154
L + I +I ++ NK D
Sbjct: 99 LTDLEKIKNKIPILIACNKQD 119
>gnl|CDD|214999 smart01055, Cadherin_pro, Cadherin prodomain like. Cadherins are a
family of proteins that mediate calcium dependent
cell-cell adhesion. They are activated through cleavage
of a prosequence in the late Golgi. This domain
corresponds to the folded region of the prosequence, and
is termed the prodomain. The prodomain shows structural
resemblance to the cadherin domain, but lacks all the
features known to be important for cadherin-cadherin
interactions.
Length = 87
Score = 28.4 bits (64), Expect = 3.8
Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 11/78 (14%)
Query: 34 IIAGAKAGETRFTDTRKDEQERCITIKSTAI---SMYFELDDKDMVFITNPDQTAKNEKG 90
+ AG G F + C+ F + + V+ T P + +K
Sbjct: 18 LEAGQPLGRVNFEE--------CLGSARLQFESSDPDFRVLEDGTVYATRPVSLSSEKKS 69
Query: 91 FLINLIDSPGHVDFSSEV 108
F + DS G +V
Sbjct: 70 FTVLAWDSQGQEKKEIKV 87
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 29.9 bits (67), Expect = 3.8
Identities = 32/199 (16%), Positives = 64/199 (32%), Gaps = 24/199 (12%)
Query: 60 KSTAISMYF--ELDDKDMVFITNPDQTA---KNEKGFLINLIDSPGHVDFSSEVTAALRV 114
K+T ++ E + I N D + + L D+ G ++ S R
Sbjct: 18 KTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYRG 77
Query: 115 TDGALVVVDC----VSGVCVQTE-TVLRQAIAERIKPVLFMNKMD-----------RALL 158
+G L+V D S + LR+ + + +L NK+D L
Sbjct: 78 ANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFDEQSSSEEILNQL 137
Query: 159 ELQLDAEDLYQTFQRIVENVNVIIATYSDDSGPMGEVRVFDSIMN--YKKEEAESLLSKL 216
++ L ++ T + +F ++ ++ E L ++L
Sbjct: 138 NREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKELLRKLLEEIEKLVLKNEL 197
Query: 217 GIELKPEDKEKDGKALLKV 235
+L + + AL
Sbjct: 198 R-QLDRLNNPIEQAALASF 215
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 29.7 bits (67), Expect = 4.2
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 86 KNEKGFLINLIDSPGHVDFSSEVTAALRVTDGA---LVVVD 123
KGF LID PGHV ++ ++ + + VVD
Sbjct: 44 MLHKGFSFTLIDFPGHVKLRQKLLETIKDSSSLRGIVFVVD 84
>gnl|CDD|218745 pfam05783, DLIC, Dynein light intermediate chain (DLIC). This
family consists of several eukaryotic dynein light
intermediate chain proteins. The light intermediate
chains (LICs) of cytoplasmic dynein consist of multiple
isoforms, which undergo post-translational modification
to produce a large number of species. DLIC1 is known to
be involved in assembly, organisation, and function of
centrosomes and mitotic spindles when bound to
pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2
that may play a role in maintaining Golgi organisation
by binding cytoplasmic dynein 2 to its Golgi-associated
cargo.
Length = 490
Score = 29.8 bits (67), Expect = 5.4
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 718 PGDPTDPGSKPY--NVVQETRKRKGLKEGLPDLQSYLDKL 755
PG P GS Q T K+ G K L D+Q+ LD++
Sbjct: 435 PGSPGGGGSPAGTGTNTQGTAKKSGQKPVLTDVQAELDRM 474
>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 = 29.8 bits (68), Expect = 5.4
Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 11/85 (12%)
Query: 95 LIDSPGHVDFSSE-----VTAALRV---TDGALVVVDCVSGVCVQTETVLRQAIAERIKP 146
LID+ G +D E V V TD AL+VVD G ++ + +I
Sbjct: 59 LIDTAG-LDDEGELGELRVEKTREVLDKTDLALLVVDAGVGPGEYELELIEELKERKIPY 117
Query: 147 VLFMNKMDRALLELQLDAEDLYQTF 171
++ +NK+D L E + E L + F
Sbjct: 118 IVVINKID--LGEESAELEKLEKKF 140
>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 = 29.1 bits (66), Expect = 6.3
Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 17/96 (17%)
Query: 93 INLIDSPG---HVDFSSEVT-AALRVTDGALVVVDCVSGVCVQTET---VLRQAIAERIK 145
+ L+D+PG ++ +E+T + L D + V+ TE+ L++ + K
Sbjct: 48 VVLVDTPGLNSTIEHHTEITESFLPRADAVIFVLSADQ---PLTESEREFLKEILKWSGK 104
Query: 146 PVLF-MNKMDRALLELQLDAEDLYQTFQRIVENVNV 180
+ F +NK+D L E+L + + E + V
Sbjct: 105 KIFFVLNKID------LLSEEELEEVLEYSREELGV 134
>gnl|CDD|173854 cd08489, PBP2_NikA, The substrate-binding component of an ABC-type
nickel import system contains the type 2 periplasmic
binding fold. This family represents the periplasmic
substrate-binding domain of nickel transport system,
which functions in the import of nickel and in the
control of chemotactic response away from nickel. The
ATP-binding cassette (ABC) type nickel transport system
is comprised of five subunits NikABCDE: the two
pore-forming integral inner membrane proteins NikB and
NikC; the two inner membrane-associated proteins with
ATPase activity NikD and NikE; and the periplasmic
nickel binding NikA, the initial nickel receptor. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA. The DppA binds dipeptides and some
tripeptides and is involved in chemotaxis toward
dipeptides, whereas the OppA binds peptides of a wide
range of lengths (2-35 amino acid residues) and plays a
role in recycling of cell wall peptides, which precludes
any involvement in chemotaxis. Most of other periplasmic
binding proteins are comprised of only two globular
subdomains corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 488
Score = 29.5 bits (67), Expect = 6.7
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 204 YKKEEAESLLSKLGIELKPEDK--EKDGKAL 232
Y E+A +LL + G L D EKDGK L
Sbjct: 304 YDPEKANALLDEAGWTLNEGDGIREKDGKPL 334
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 29.4 bits (66), Expect = 8.0
Identities = 26/104 (25%), Positives = 38/104 (36%), Gaps = 15/104 (14%)
Query: 69 ELDDKDMVFITNPDQTAKNEKGFLINLIDSPGHVDFSS-EVTAALRVTDGALVVVDCVSG 127
E+D +D +FI + K G +SS AA+ ++ AL + D
Sbjct: 494 EIDGEDWLFIDTAGIKRRQHK--------LTGAEYYSSLRTQAAIERSELALFLFDASQP 545
Query: 128 VCVQTETVLRQAIAERIKPVLFMNKMD------RALLELQLDAE 165
+ Q V+ A+ VL NK D R LE E
Sbjct: 546 ISEQDLKVMSMAVDAGRALVLVFNKWDLMDEFRRQRLERLWKTE 589
>gnl|CDD|240282 PTZ00126, PTZ00126, tyrosyl-tRNA synthetase; Provisional.
Length = 383
Score = 29.3 bits (66), Expect = 8.4
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 414 LPKLVEGLKRLSKSDPMVQCIIEESGEHI 442
LP L+EG +++SKSDP +E+S E +
Sbjct: 248 LPGLLEGQEKMSKSDPNSAIFMEDSEEDV 276
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
0.318 0.137 0.400
Gapped
Lambda K H
0.267 0.0746 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 39,357,692
Number of extensions: 4000812
Number of successful extensions: 3798
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3623
Number of HSP's successfully gapped: 157
Length of query: 755
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 651
Effective length of database: 6,324,786
Effective search space: 4117435686
Effective search space used: 4117435686
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 (21.7 bits)
S2: 63 (28.0 bits)