RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780233|ref|YP_003064646.1| GTP-binding protein
[Candidatus Liberibacter asiaticus str. psy62]
(624 letters)
>gnl|CDD|31410 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 944 bits (2443), Expect = 0.0
Identities = 377/602 (62%), Positives = 454/602 (75%), Gaps = 3/602 (0%)
Query: 17 MQIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTS 76
IRNIAIIAHVDHGKTTLVD LLKQSG FR+ + V+ERVMD NDLEKERGITILAK T+
Sbjct: 3 EDIRNIAIIAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGITILAKNTA 62
Query: 77 IVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLR 136
+ +N RINIVDTPGHADFGGEVER+L MV+ V++LVDA+EGPMPQT+FV+ KAL +GL+
Sbjct: 63 VNYNGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALALGLK 122
Query: 137 PIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSRDQ 196
PIVV+NK+DR DAR DEV++EVFDLF L ATD QLDFPI+Y S R G S + D
Sbjct: 123 PIVVINKIDRPDARPDEVVDEVFDLFVELGATDEQLDFPIVYASARNGTASLDPEDEADD 182
Query: 197 GMVPLLNLIVDHVPPPVI-SEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALS 255
M PL I+DHVP P + +M T L+ + ++GRI GRI GT+K NQ + +
Sbjct: 183 -MAPLFETILDHVPAPKGDLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALIK 241
Query: 256 PDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVKATVADTFCDPSIDEPLKAQ 315
DG E GR++K+L F G++R I+EA AGDIV+IAGL + DT CDP E L A
Sbjct: 242 SDGT-TENGRITKLLGFLGLERIEIEEAEAGDIVAIAGLEDINIGDTICDPDNPEALPAL 300
Query: 316 PIDPPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEGNIALKIEESSSKDAFFVSG 375
+D PT++MTF VNDSP AG EG VTSR IRDRL KE E N+AL++EE+ S DAF VSG
Sbjct: 301 SVDEPTLSMTFSVNDSPFAGKEGKFVTSRQIRDRLNKELETNVALRVEETESPDAFEVSG 360
Query: 376 RGELQLAVLIETMRREGFELAVSRPRVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMT 435
RGEL L++LIE MRREGFEL VSRP V+IK+ EP EEV IDV EEH GAV++K+
Sbjct: 361 RGELHLSILIENMRREGFELQVSRPEVIIKEIDGVKCEPFEEVTIDVPEEHQGAVIEKLG 420
Query: 436 LHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMTDTRGTAIMNRLFHSYQPHKGEIG 495
K EM ++ P G GRVRL F+ P RGLIG++++ +T TRGT IMN F Y+P KGEIG
Sbjct: 421 ERKGEMKDMAPDGKGRVRLEFVIPARGLIGFRTEFLTMTRGTGIMNHSFDHYRPVKGEIG 480
Query: 496 GRSNGVLLSNEEGKVVAYALFNLEDRGSMIVEPGDKVYQGMIVGIHTRENDLDVNVLKGK 555
GR NGVL+SNE GK VAYALFNL+DRG + +EPG KVY+GMI+G H+R+NDL VNVLKGK
Sbjct: 481 GRHNGVLISNETGKAVAYALFNLQDRGKLFIEPGTKVYEGMIIGEHSRDNDLTVNVLKGK 540
Query: 556 KLTNMRASGKDEAVKLVPAVKMTLEQALSWIQNDELVEVTPKSIRLRKMYLDPNERKRKG 615
KLTNMRASGKDEAV L P ++MTLE+AL +I +DELVEVTP+SIRLRK L+ NERKR
Sbjct: 541 KLTNMRASGKDEAVTLTPPIRMTLERALEFIADDELVEVTPESIRLRKKILNENERKRAE 600
Query: 616 KS 617
K
Sbjct: 601 KR 602
>gnl|CDD|35683 KOG0462, KOG0462, KOG0462, Elongation factor-type GTP-binding
protein [Translation, ribosomal structure and
biogenesis].
Length = 650
Score = 415 bits (1069), Expect = e-116
Identities = 171/612 (27%), Positives = 264/612 (43%), Gaps = 57/612 (9%)
Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIV 78
IRN +IIAHVDHGK+TL D LL+ +G DN E+V+D +E+ERGITI A+ SI
Sbjct: 60 IRNFSIIAHVDHGKSTLADRLLELTG-TIDNNIGQEQVLDKLQVERERGITIKAQTASIF 118
Query: 79 WNDVR---INIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGL 135
+ D + +N++DTPGH DF GEV R L + +++VDA++G QT A + GL
Sbjct: 119 YKDGQSYLLNLIDTPGHVDFSGEVSRSLAACDGALLVVDASQGVQAQTVANFYLAFEAGL 178
Query: 136 RPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSRD 195
I V+NK+D A + V N++F+LF A ++Y S + G
Sbjct: 179 AIIPVLNKIDLPSADPERVENQLFELFDIPPA-------EVIYVSAKTGL---------- 221
Query: 196 QGMVPLLNLIVDHVPPP-VISEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKAL 254
+ LL I+ VPPP I + +M+ E D + G I R+ G ++ +++
Sbjct: 222 -NVEELLEAIIRRVPPPKGIRDAPLRMLIFDSEYDEYRGVIALVRVVDGVVRKGDKVQSA 280
Query: 255 SPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVK-ATVADTFCDPSIDEPLK 313
+ G EV +V ++ +D G I+ VK A + DT S+ + ++
Sbjct: 281 A-TGKSYEV-KVVGVMRPEMTPVVELDAGQVGYIICNMRNVKEAQIGDTIAHKSVTKAVE 338
Query: 314 AQPIDPPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEGNIALKIEESSSKDAFFV 373
P PT M F V PL G+ D T R +RL E +K + + +
Sbjct: 339 TLPGFEPTKPMVF-VGLFPLDGS--DYETLRDAIERLVLNDESVTVIKESSGALGQGWRL 395
Query: 374 SGRGELQLAVLIETMRRE-GFELAVSRPRVVIKKE--------------------GDSLL 412
G L + V IE + RE G EL V+ P V + L
Sbjct: 396 GFLGLLHMEVFIERLEREYGAELIVTPPTVPYRVVYSNGDEILISNPALFPDPSDVKEFL 455
Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIG-YQSQLM 471
EP E I +E+ GAV++ + + E ++ RV L + P R L+G + +L
Sbjct: 456 EPYVEATIITPDEYVGAVIELCSERRGEQKDMTYIDGNRVMLKYQLPLRELVGDFFDRLK 515
Query: 472 TDTRGTAIMNRLFHSYQPHKGEIGGRSNGVLLSNEEGKVVAYALFNLEDRGSMIVEPGDK 531
+ T G A + YQ ++ + +G L E RG V+
Sbjct: 516 SLTSGYASFDYEDAGYQA--SDLVKLDILLNGKMVDGLSTIVHLSKAESRGREFVQKLKD 573
Query: 532 VYQGMIVGIHTRENDLDVNVLKGKKLTNMRASGKDEAVKLVPAVKMTLEQALSWIQNDEL 591
+ I +H + N+ + + A KD KL L++ L +
Sbjct: 574 LIPRQIFEVHIQACIGSKNIARET----ISAYRKDVLAKLYGGDVTRLKKLLKKQAEGKK 629
Query: 592 VEVTPKSIRLRK 603
T +IR+ K
Sbjct: 630 RMKTVGNIRIPK 641
>gnl|CDD|133291 cd01891, TypA_BipA, TypA (tyrosine phosphorylated protein A)/BipA
subfamily. 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 = 371 bits (956), Expect = e-103
Identities = 129/194 (66%), Positives = 161/194 (82%), Gaps = 1/194 (0%)
Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIV 78
IRNIAIIAHVDHGKTTLVD LLKQSG FR+N+ V ERVMD NDLE+ERGITILAK T++
Sbjct: 2 IRNIAIIAHVDHGKTTLVDALLKQSGTFRENEEVEERVMDSNDLERERGITILAKNTAVT 61
Query: 79 WNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPI 138
+ D +INIVDTPGHADFGGEVER+L MV+ V++LVDA+EGPMPQT+FV+ KAL++GL+PI
Sbjct: 62 YKDTKINIVDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALELGLKPI 121
Query: 139 VVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSRDQGM 198
VV+NK+DR DAR +EV++EVFDLF L AT+ QLDFP+LY S + GW S + + + +
Sbjct: 122 VVINKIDRPDARPEEVVDEVFDLFIELGATEEQLDFPVLYASAKNGWASLNLEDPSED-L 180
Query: 199 VPLLNLIVDHVPPP 212
PL + I++HVP P
Sbjct: 181 EPLFDTIIEHVPAP 194
>gnl|CDD|143801 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 = 185
Score = 201 bits (514), Expect = 4e-52
Identities = 72/197 (36%), Positives = 97/197 (49%), Gaps = 14/197 (7%)
Query: 17 MQIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVS-ERVMDCNDLEKERGITILAKVT 75
+ RNI II HVDHGKTTL D LL +G V E +D E+ERGITI
Sbjct: 1 KRHRNIGIIGHVDHGKTTLTDALLYVTGAIDKRGEVKQEGELDRLKEERERGITIKIAAV 60
Query: 76 SIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGL 135
S INI+DTPGH DF E+ R + +++VDA EG MPQT+ + A ++G+
Sbjct: 61 SFETKKRHINIIDTPGHVDFTKEMIRGAAQADGAILVVDAVEGVMPQTREHLLLAKQLGV 120
Query: 136 RPIVVVNKVDR-SDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSR 194
IV +NK+DR DA DEV+ E+ P++ GS G
Sbjct: 121 PIIVFINKMDRVDDAELDEVVEEISREL-LEKYGFGGETIPVIPGSALTGE--------- 170
Query: 195 DQGMVPLLNLIVDHVPP 211
G+ LL + ++P
Sbjct: 171 --GIDTLLEALDLYLPS 185
>gnl|CDD|133257 cd00881, GTP_translation_factor, GTP translation factor family.
This family consists primarily of translation
initiation, elongation, and release factors, which play
specific roles in protein translation. In addition, the
family includes Snu114p, a component of the U5 small
nuclear riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 189
Score = 187 bits (477), Expect = 8e-48
Identities = 77/200 (38%), Positives = 108/200 (54%), Gaps = 19/200 (9%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80
N+ I HVDHGKTTL + LL +G + V E +D E+ERGITI + V + W
Sbjct: 1 NVGIAGHVDHGKTTLTERLLYVTGDIERDGTVEETFLDVLKEERERGITIKSGVATFEWP 60
Query: 81 DVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIVV 140
D R+N +DTPGH DF EV R L + + +++VDA EG PQT+ + A + GL IV
Sbjct: 61 DRRVNFIDTPGHEDFSSEVIRGLSVSDGAILVVDANEGVQPQTREHLRIAREGGLPIIVA 120
Query: 141 VNKVDR-SDARADEVINEVFDLFSAL-------DATDAQLDFPILYGSGRFGWMSDSSDG 192
+NK+DR + +EV+ E+ +L + + T L PI+ GS G
Sbjct: 121 INKIDRVGEEDLEEVLREIKELLGLIGFISTKEEGTRNGLLVPIVPGSALTGI------- 173
Query: 193 SRDQGMVPLLNLIVDHVPPP 212
G+ LL IV+H+PPP
Sbjct: 174 ----GVEELLEAIVEHLPPP 189
>gnl|CDD|30829 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 179 bits (456), Expect = 2e-45
Identities = 145/510 (28%), Positives = 226/510 (44%), Gaps = 72/510 (14%)
Query: 18 QIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSI 77
IRN +IIAH+DHGK+TL D LL+ +G + + +V+D D+E+ERGITI A+ +
Sbjct: 8 NIRNFSIIAHIDHGKSTLADRLLELTGGLSEREM-RAQVLDSMDIERERGITIKAQAVRL 66
Query: 78 VW-----NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALK 132
+ +N++DTPGH DF EV R L E +++VDA++G QT V AL+
Sbjct: 67 NYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYLALE 126
Query: 133 IGLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDG 192
L I V+NK+D A + V E+ D+ +DA+DA L S + G
Sbjct: 127 NNLEIIPVLNKIDLPAADPERVKQEIEDII-GIDASDAVL------VSAKTG-------- 171
Query: 193 SRDQGMVPLLNLIVDHVPPPVIS-EGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNI 251
G+ +L IV+ +PPP + K + D +LG +V RI GT+K I
Sbjct: 172 ---IGIEDVLEAIVEKIPPPKGDPDAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKGDKI 228
Query: 252 KALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVK----ATVADTF--CD 305
+ +S G EV V +DE AG++ I +K A V DT
Sbjct: 229 RMMS-TGKEYEVDEV----GIFTPKMVKVDELKAGEVGYIIAGIKDVRDARVGDTITLAS 283
Query: 306 PSIDEPLKA-QPIDPPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEGNIALKIE- 363
EPL + + P M F + L + D +RD L K + +L E
Sbjct: 284 NPATEPLPGFKEVKP----MVF----AGLYPVDSDDY--EDLRDALEKLQLNDASLTYEP 333
Query: 364 ESSSKDAF-FVSG-RGELQLAVLIETMRRE-GFELAVSRPRV---VIKKEG--------- 408
E+S F F G G L + ++ E + RE +L + P V V +G
Sbjct: 334 ETSQALGFGFRCGFLGLLHMEIIQERLEREFDLDLITTAPSVVYKVELTDGEEIEVDNPS 393
Query: 409 --------DSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPT 460
+ + EP + I +E+ G V++ + I++ RV L + P
Sbjct: 394 DLPDPNKIEEIEEPYVKATIITPQEYLGNVMELCQEKRGIQIDMEYLDQNRVMLTYELPL 453
Query: 461 RGLI-GYQSQLMTDTRGTAIMNRLFHSYQP 489
++ + +L + ++G A + F Y+
Sbjct: 454 AEIVFDFFDKLKSISKGYASFDYEFIGYRE 483
>gnl|CDD|133285 cd01885, EF2, EF2 (for 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 = 222
Score = 150 bits (381), Expect = 1e-36
Identities = 75/227 (33%), Positives = 112/227 (49%), Gaps = 39/227 (17%)
Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSI-- 77
RNI IIAHVDHGKTTL D LL +G+ + R MD + E+ERGIT+ K ++I
Sbjct: 1 RNICIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYMDSREDEQERGITM--KSSAISL 58
Query: 78 ----------VWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVV 127
N+ IN++D+PGH DF EV L + + +V+VDA EG QT+ V+
Sbjct: 59 YFEYEEEDKADGNEYLINLIDSPGHVDFSSEVTAALRLCDGALVVVDAVEGVCVQTETVL 118
Query: 128 GKALKIGLRPIVVVNKVDR---------SDA--RADEVINEVFDLFSAL--------DAT 168
+ALK ++P++V+NK+DR +A R +I +V + D
Sbjct: 119 RQALKERVKPVLVINKIDRLILELKLSPEEAYQRLARIIEQVNAIIGTYADEEFKEKDDE 178
Query: 169 DAQLDFP---ILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPP 212
+ +GS GW +R + +L ++V H+P P
Sbjct: 179 KWYFSPQKGNVAFGSALHGWGFTIIKFAR---IYAVLEMVVKHLPSP 222
>gnl|CDD|30828 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 145 bits (367), Expect = 4e-35
Identities = 64/156 (41%), Positives = 92/156 (58%), Gaps = 3/156 (1%)
Query: 12 GRLGYMQIRNIAIIAHVDHGKTTLVDELLKQSGVFRD--NQRVSERVMDCNDLEKERGIT 69
+ +IRNI I+AH+D GKTTL + +L +G+ MD + E+ERGIT
Sbjct: 3 RLMPLERIRNIGIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQERGIT 62
Query: 70 ILAKVTSIVWND-VRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVG 128
I + T++ W RIN++DTPGH DF EVER L +++ VV+VDA EG PQT+ V
Sbjct: 63 ITSAATTLFWKGDYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAVEGVEPQTETVWR 122
Query: 129 KALKIGLRPIVVVNKVDRSDARADEVINEVFDLFSA 164
+A K G+ I+ VNK+DR A V+ ++ + A
Sbjct: 123 QADKYGVPRILFVNKMDRLGADFYLVVEQLKERLGA 158
Score = 96.8 bits (241), Expect = 2e-20
Identities = 71/309 (22%), Positives = 132/309 (42%), Gaps = 61/309 (19%)
Query: 129 KALKIGLRPIVVVNKVDRSDARADEVINE----VFDLFSAL-DATDAQLDFPILYGSGRF 183
K + R ++ + + ++ + ++ AL T A P+L GS
Sbjct: 203 KEIAEEAREKLLEALAEFDEELMEKYLEGEEPTEEEIKKALRKGTIAGKIVPVLCGSA-- 260
Query: 184 GWMSDSSDGSRDQGMVPLLNLIVDHVPPPV---------------------ISEGEFKMI 222
+++G+ PLL+ +VD++P P+ EG +
Sbjct: 261 ---------FKNKGVQPLLDAVVDYLPSPLDVPPIKGDLDDEIEKAVLRKASDEGPLSAL 311
Query: 223 GTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDE 282
+ DPF+G++ R++SGT+KS + + + RV ++L G +R+ +DE
Sbjct: 312 VFKIMTDPFVGKLTFVRVYSGTLKSGSEVLNSTKG----KKERVGRLLLMHGNEREEVDE 367
Query: 283 AHAGDIVSIAGLVKATVADTFCDPSIDEPLKAQPIDPPTVTMTFGVNDSPLAGTEGDKVT 342
AGDIV++ GL AT DT CD + L++ P +++ P + +K+
Sbjct: 368 VPAGDIVALVGLKDATTGDTLCDENKPVILESMEFPEPVISVAV----EPKTKADQEKL- 422
Query: 343 SRMIRDRLFKEAEGNIA-----LKIEESSSKDAFFVSGRGELQLAVLIETMRRE-GFELA 396
EA +A ++E +SG GEL L ++++ ++RE G E+
Sbjct: 423 ---------SEALNKLAEEDPTFRVETDEETGETIISGMGELHLEIIVDRLKREFGVEVE 473
Query: 397 VSRPRVVIK 405
V +P+V +
Sbjct: 474 VGKPQVAYR 482
Score = 39.4 bits (92), Expect = 0.003
Identities = 26/99 (26%), Positives = 46/99 (46%), Gaps = 2/99 (2%)
Query: 393 FELAVSRP-RVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRP-SGTG 450
F++A S + + K LLEPI +V I EE+ G V+ + + +++ + G G
Sbjct: 580 FKIAASLAFKEAMLKAKPVLLEPIMKVEITTPEEYMGDVIGDLNSRRGQILGMEQRPGGG 639
Query: 451 RVRLVFLSPTRGLIGYQSQLMTDTRGTAIMNRLFHSYQP 489
+ P + GY + L + T+G A + F Y+
Sbjct: 640 LDVIKAEVPLAEMFGYATDLRSATQGRASFSMEFDHYEE 678
>gnl|CDD|133368 cd04168, TetM_like, Tet(M)-like subfamily. 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 = 140 bits (354), Expect = 1e-33
Identities = 59/147 (40%), Positives = 91/147 (61%), Gaps = 4/147 (2%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER--VMDCNDLEKERGITILAKVTSIV 78
NI I+AHVD GKTTL + LL SG R V + D +LE++RGITI + V S
Sbjct: 1 NIGILAHVDAGKTTLTESLLYTSGAIRKLGSVDKGTTRTDTMELERQRGITIFSAVASFQ 60
Query: 79 WNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKI-GLRP 137
W D ++N++DTPGH DF EVER L +++ ++++ A EG QT+ ++ + L+ +
Sbjct: 61 WEDTKVNLIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTR-ILWRLLRKLNIPT 119
Query: 138 IVVVNKVDRSDARADEVINEVFDLFSA 164
I+ VNK+DR+ A ++V E+ + S+
Sbjct: 120 IIFVNKIDRAGADLEKVYQEIKEKLSS 146
>gnl|CDD|133290 cd01890, LepA, LepA subfamily. LepA belongs to the GTPase family
of and exhibits significant homology to the translation
factors EF-G and EF-Tu, indicating its possible
involvement in translation and association with the
ribosome. LepA is ubiquitous in bacteria and eukaryota
(e.g. yeast GUF1p), but is missing from archaea. This
pattern of phyletic distribution suggests that LepA
evolved through a duplication of the EF-G gene in
bacteria, followed by early transfer into the eukaryotic
lineage, most likely from the promitochondrial
endosymbiont. Yeast GUF1p is not essential and mutant
cells did not reveal any marked phenotype.
Length = 179
Score = 138 bits (349), Expect = 6e-33
Identities = 73/198 (36%), Positives = 106/198 (53%), Gaps = 24/198 (12%)
Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVW 79
RN +IIAH+DHGK+TL D LL+ +G + E+V+D DLE+ERGITI A+ + +
Sbjct: 1 RNFSIIAHIDHGKSTLADRLLELTGTVSKREM-KEQVLDSMDLERERGITIKAQTVRLNY 59
Query: 80 -----NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIG 134
+ +N++DTPGH DF EV R L E ++LVDA +G QT AL+
Sbjct: 60 KAKDGQEYLLNLIDTPGHVDFSYEVSRSLAACEGALLLVDATQGVEAQTLANFYLALENN 119
Query: 135 LRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSR 194
L I V+NK+D A + V ++ D+ LD ++A + S + G
Sbjct: 120 LEIIPVINKIDLPSADPERVKQQIEDVLG-LDPSEA------ILVSAKTG---------- 162
Query: 195 DQGMVPLLNLIVDHVPPP 212
G+ LL IV+ +PPP
Sbjct: 163 -LGVEDLLEAIVERIPPP 179
>gnl|CDD|133286 cd01886, EF-G, Elongation factor G (EF-G) subfamily. 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-29
Identities = 59/140 (42%), Positives = 81/140 (57%), Gaps = 2/140 (1%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER--VMDCNDLEKERGITILAKVTSIV 78
NI IIAH+D GKTT + +L +G V MD + E+ERGITI + T+
Sbjct: 1 NIGIIAHIDAGKTTTTERILYYTGRIHKIGEVHGGGATMDFMEQERERGITIQSAATTCF 60
Query: 79 WNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPI 138
W D RINI+DTPGH DF EVER L +++ V + DA G PQT+ V +A + + I
Sbjct: 61 WKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQADRYNVPRI 120
Query: 139 VVVNKVDRSDARADEVINEV 158
VNK+DR+ A V+ ++
Sbjct: 121 AFVNKMDRTGADFFRVVEQI 140
>gnl|CDD|35686 KOG0465, KOG0465, KOG0465, Mitochondrial elongation factor
[Translation, ribosomal structure and biogenesis].
Length = 721
Score = 125 bits (315), Expect = 4e-29
Identities = 62/161 (38%), Positives = 90/161 (55%), Gaps = 5/161 (3%)
Query: 18 QIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER--VMDCNDLEKERGITILAKVT 75
+IRNI I AH+D GKTTL + +L +G + V MD +LE++RGITI + T
Sbjct: 38 KIRNIGISAHIDAGKTTLTERMLYYTGRIKHIGEVRGGGATMDSMELERQRGITIQSAAT 97
Query: 76 SIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGL 135
W D RINI+DTPGH DF EVER L +++ V+++DA G QT+ V + + +
Sbjct: 98 YFTWRDYRINIIDTPGHVDFTFEVERALRVLDGAVLVLDAVAGVESQTETVWRQMKRYNV 157
Query: 136 RPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPI 176
I +NK+DR A +N + + L+ A + PI
Sbjct: 158 PRICFINKMDRMGASPFRTLN---QIRTKLNHKPAVVQIPI 195
Score = 63.4 bits (154), Expect = 2e-10
Identities = 70/287 (24%), Positives = 122/287 (42%), Gaps = 58/287 (20%)
Query: 149 ARADEVINEVF---------DLFSAL-DATDAQLDFPILYGSGRFGWMSDSSDGSRDQGM 198
A DE + E+F L +A+ AT + P+L GS +++G+
Sbjct: 248 ADVDETLAEMFLEEEEPSAQQLKAAIRRATIKRSFVPVLCGSAL-----------KNKGV 296
Query: 199 VPLLNLIVDHVPPPV---------ISEGEFKMIGTI-LEKDPFLG---RIVTG------- 238
PLL+ +VD++P P + + K+ + +KDPF+ ++ G
Sbjct: 297 QPLLDAVVDYLPSPSEVENYALNKETNSKEKVTLSPSRDKDPFVALAFKLEEGRFGQLTY 356
Query: 239 -RIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVKA 297
R++ GT+ I G V VGR+ ++ A D + ++E AGDI ++ G+ A
Sbjct: 357 VRVYQGTLSKGDTIYN-VRTGKKVRVGRLVRMHA---NDMEDVNEVLAGDICALFGIDCA 412
Query: 298 TVADTFCDPSIDEPLKAQPID-PPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEG 356
+ DTF D + L + I P V V P+ + D + + R KE
Sbjct: 413 S-GDTFTDKQ-NLALSMESIHIPEPV---ISVAIKPVNKKDADNFSKALN--RFTKE--- 462
Query: 357 NIALKIEESSSKDAFFVSGRGELQLAVLIETMRRE-GFELAVSRPRV 402
+ ++ +SG GEL L + +E + RE + + +P+V
Sbjct: 463 DPTFRVSLDPEMKQTVISGMGELHLEIYVERLVREYKVDAELGKPQV 509
Score = 34.5 bits (79), Expect = 0.086
Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 1/89 (1%)
Query: 401 RVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPT 460
R K+ +LEPI V + EE G V+ + K+++ + S + + P
Sbjct: 621 REAFKRAPPRILEPIMNVEVTTPEEFQGTVIGDLNKRKAQITGIDSSEDYKT-IKAEVPL 679
Query: 461 RGLIGYQSQLMTDTRGTAIMNRLFHSYQP 489
+ GY S+L + T+G + Y P
Sbjct: 680 NEMFGYSSELRSLTQGKGEFTMEYSRYSP 708
>gnl|CDD|58063 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 = 122 bits (307), Expect = 3e-28
Identities = 45/79 (56%), Positives = 61/79 (77%)
Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMT 472
EPIEE+ IDV EE+SGAV++K+ K EM+++ P G GR RL F P+RGLIG++S+ +T
Sbjct: 1 EPIEELTIDVPEEYSGAVIEKLGKRKGEMVDMEPDGNGRTRLEFKIPSRGLIGFRSEFLT 60
Query: 473 DTRGTAIMNRLFHSYQPHK 491
DTRGT IMN +F Y+P+K
Sbjct: 61 DTRGTGIMNHVFDGYEPYK 79
>gnl|CDD|35688 KOG0467, KOG0467, KOG0467, Translation elongation factor 2/ribosome
biogenesis protein RIA1 and related proteins
[Translation, ribosomal structure and biogenesis].
Length = 887
Score = 120 bits (301), Expect = 2e-27
Identities = 55/128 (42%), Positives = 79/128 (61%)
Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIV 78
IRNI ++AHVDHGKT+L D L+ +GV R +D + E+ RGIT+ + S++
Sbjct: 9 IRNICLVAHVDHGKTSLADSLVASNGVISSRLAGKIRFLDTREDEQTRGITMKSSAISLL 68
Query: 79 WNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPI 138
D IN++D+PGH DF EV + + +VLVD EG QT V+ +A GL+PI
Sbjct: 69 HKDYLINLIDSPGHVDFSSEVSSASRLSDGALVLVDVVEGVCSQTYAVLRQAWIEGLKPI 128
Query: 139 VVVNKVDR 146
+V+NK+DR
Sbjct: 129 LVINKIDR 136
Score = 41.9 bits (98), Expect = 5e-04
Identities = 60/267 (22%), Positives = 101/267 (37%), Gaps = 29/267 (10%)
Query: 220 KMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPD---GALVEVGRVSKILAFRGID 276
KM+ T L+ P + RI SGT++ Q + L PD + V + F G +
Sbjct: 366 KMLATPLKYLPQSRLLAFARIFSGTLRVGQVVYVLGPDPLSPEHITECTVESLYLFMGQE 425
Query: 277 RQPIDEAHAGDIVSIAGLVKATVADTFCDPSIDEPLKAQPIDPPTVTMTFGVNDSPLAGT 336
P+DE +G++V+I G + T C P +T V P
Sbjct: 426 LVPLDEVPSGNVVAIGGAGIVLKSATLCSKVPCGPNLVVNF---QITPIVRVAIEPDDPD 482
Query: 337 EGDKVTSRMIRDRLFKEAEGNIALKIEESSSKDAFFVSGRGELQLAVLIETMRR-EGFEL 395
E DK+ + +L +A+ + +++EE+ + GE+ L ++ ++ E+
Sbjct: 483 EMDKLVEGL---KLLNQADPFVKIRVEENGE---HVLVTAGEVHLERCLKDLKEFAKIEI 536
Query: 396 AVSRPRVVIKKEGDSLLEPIEEVVI---DVDEEHSGAVVQKMTLHKSEMIELRPSGTGRV 452
+VS P L P E +I D+ S K I+LR
Sbjct: 537 SVSEP-----------LVPFRETIIEDSDLLANLSIGQETKCLPRGQLKIKLRVVPLSGA 585
Query: 453 RLVFLSPTRGLIGYQSQLMTDTRGTAI 479
+ L LI + L ++R I
Sbjct: 586 VVDLLDKNSSLIS--NILRGESRQVPI 610
>gnl|CDD|133367 cd04167, Snu114p, 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 = 119 bits (300), Expect = 2e-27
Identities = 67/217 (30%), Positives = 112/217 (51%), Gaps = 28/217 (12%)
Query: 20 RNIAIIAHVDHGKTTLVDELLKQS---GVFRDNQRVSERVMDCNDLEKERGITILAKVTS 76
RN+AI H+ HGKT+L+D L++Q+ + R D E+ERGI+I + S
Sbjct: 1 RNVAIAGHLHHGKTSLLDMLIEQTHDLTPSGKDGWKPLRYTDIRKDEQERGISIKSSPIS 60
Query: 77 IVWNDVR-----INIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKAL 131
+V D + NI+DTPGH +F EV L + + VV++VD EG T+ ++ A+
Sbjct: 61 LVLPDSKGKSYLFNIIDTPGHVNFMDEVAAALRLSDGVVLVVDVVEGVTSNTERLIRHAI 120
Query: 132 KIGLRPIVVVNKVDR---------SDA--RADEVINEVFDLFSALDATDAQLDFP----I 176
GL ++V+NK+DR +DA + +I+EV ++ ++ T + L P +
Sbjct: 121 LEGLPIVLVINKIDRLILELKLPPNDAYFKLRHIIDEVNNIIASFSTTLSFLFSPENGNV 180
Query: 177 LYGSGRFGWM-SDSSDGSRDQGMVPLLNLIVDHVPPP 212
+ S +FG+ + S L++ IV ++P P
Sbjct: 181 CFASSKFGFCFTLESFAK----KYGLVDSIVSNIPSP 213
>gnl|CDD|35690 KOG0469, KOG0469, KOG0469, Elongation factor 2 [Translation,
ribosomal structure and biogenesis].
Length = 842
Score = 107 bits (268), Expect = 1e-23
Identities = 64/201 (31%), Positives = 102/201 (50%), Gaps = 35/201 (17%)
Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIV 78
IRN+++IAHVDHGK+TL D L++++G+ + R D E+ERGITI + S+
Sbjct: 19 IRNMSVIAHVDHGKSTLTDSLVQKAGIISAAKAGETRFTDTRKDEQERGITIKSTAISLF 78
Query: 79 W----------------NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQ 122
+ N IN++D+PGH DF EV L + + +V+VD G Q
Sbjct: 79 FEMSDDDLKFIKQEGDGNGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQ 138
Query: 123 TKFVVGKALKIGLRPIVVVNKVDRSD--------------ARADEVINEVFDLFSALDAT 168
T+ V+ +A+ ++P++V+NK+DR+ R E +N + +
Sbjct: 139 TETVLRQAIAERIKPVLVMNKMDRALLELQLSQEELYQTFQRIVENVNVIISTYGDGPMG 198
Query: 169 DAQLDFP----ILYGSGRFGW 185
D Q+D P + +GSG GW
Sbjct: 199 DVQVD-PEKGTVGFGSGLHGW 218
Score = 28.8 bits (64), Expect = 4.2
Identities = 23/112 (20%), Positives = 41/112 (36%), Gaps = 11/112 (9%)
Query: 384 LIETMRREGFELAV-SRPRVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMI 442
+I T RR + + + P L EP+ V I E+ G + + + +
Sbjct: 705 IIPTARRVLYASVLTAGPI---------LQEPVYLVEIQCPEQAVGGIYGVLNRKRGHVF 755
Query: 443 ELRP-SGTGRVRLVFLSPTRGLIGYQSQLMTDTRGTAIMNRLFHSYQPHKGE 493
E GT + P G+ + L ++T G A +F + G+
Sbjct: 756 EEEQVPGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQMVFDHWSILPGD 807
Score = 27.6 bits (61), Expect = 9.8
Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 9/75 (12%)
Query: 238 GRIHSGTIKSNQNIKALSPD-----GALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIA 292
GR+ SG + + ++ P+ + + + + + G +PI++ AG+I+ +
Sbjct: 398 GRVFSGKVFTGLKVRIQGPNYVPGKKEDLYIKAIQRTVLMMGRFVEPIEDCPAGNIIGLV 457
Query: 293 G----LVKATVADTF 303
G LVK T
Sbjct: 458 GVDQFLVKTGTITTS 472
>gnl|CDD|35685 KOG0464, KOG0464, KOG0464, Elongation factor G [Translation,
ribosomal structure and biogenesis].
Length = 753
Score = 107 bits (267), Expect = 1e-23
Identities = 54/143 (37%), Positives = 80/143 (55%), Gaps = 2/143 (1%)
Query: 18 QIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSE--RVMDCNDLEKERGITILAKVT 75
+IRNI IIAH+D GKTT + +L +G V + V D +E+ERGITI +
Sbjct: 36 KIRNIGIIAHIDAGKTTTTERILYLAGAIHSAGDVDDGDTVTDFLAIERERGITIQSAAV 95
Query: 76 SIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGL 135
+ W RIN++DTPGH DF EVER L +++ V + DA+ G QT V +A K +
Sbjct: 96 NFDWKGHRINLIDTPGHVDFRLEVERCLRVLDGAVAVFDASAGVEAQTLTVWRQADKFKI 155
Query: 136 RPIVVVNKVDRSDARADEVINEV 158
+NK+D+ A + ++ +
Sbjct: 156 PAHCFINKMDKLAANFENAVDSI 178
Score = 35.1 bits (80), Expect = 0.052
Identities = 44/176 (25%), Positives = 72/176 (40%), Gaps = 33/176 (18%)
Query: 145 DRSDARADEVINEVFDLFSALDA----------TDAQLDFPILYGSGRFGWMSDSSDGSR 194
D AD+ ++E + F +DA T AQ PIL GS +
Sbjct: 254 DLDADFADKFLDEFDENFDKIDAEELKSAIHELTCAQKAAPILCGSA-----------IK 302
Query: 195 DQGMVPLLNLIVDHVPPPVISEGEFKM--------IGTILEKDPFLGRIVTGRIHSGTIK 246
++G+ PLL+ + ++P P EF + + D G + RI+SG+I
Sbjct: 303 NKGIQPLLDAVTMYLPSPEERNYEFLQWYKDDLCALAFKVLHDKQRGPLSFMRIYSGSIH 362
Query: 247 SNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVKATVADT 302
+N I ++ G E + K+ + + I++ AG+I AGL DT
Sbjct: 363 NNLAIFNIN--GMCSE--GILKLFLPFADEHREIEQLSAGNIALTAGLKHTATGDT 414
>gnl|CDD|133369 cd04169, RF3, RF3 subfamily. 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 = 267
Score = 106 bits (266), Expect = 3e-23
Identities = 59/152 (38%), Positives = 85/152 (55%), Gaps = 18/152 (11%)
Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER------VMDCNDLEKERGITILAK 73
R AII+H D GKTTL ++LL G R+ V R D ++EK+RGI++ +
Sbjct: 3 RTFAIISHPDAGKTTLTEKLLLFGGAIREAGAVKARKSRKHATSDWMEIEKQRGISVTSS 62
Query: 74 VTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTK--FVVGKAL 131
V + D IN++DTPGH DF + R L V+S V+++DAA+G PQT+ F V +
Sbjct: 63 VMQFEYRDCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLR 122
Query: 132 KIGLRPIV-VVNKVDRSDARA-----DEVINE 157
I PI+ +NK+DR + R DE+ E
Sbjct: 123 GI---PIITFINKLDR-EGRDPLELLDEIEEE 150
>gnl|CDD|58082 cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also called
TypA) having homology to domain II of the elongation
factors (EFs) EF-G and EF-Tu. BipA is a highly
conserved protein with global regulatory properties in
Escherichia coli. BipA is phosphorylated on a tyrosine
residue under some cellular conditions. Mutants show
altered regulation of some pathways. BipA functions as a
translation factor that is required specifically for the
expression of the transcriptional modulator Fis. BipA
binds to ribosomes at a site that coincides with that of
EF-G and has a GTPase activity that is sensitive to high
GDP:GTP ratios and, is stimulated by 70S ribosomes
programmed with mRNA and aminoacylated tRNAs. The growth
rate-dependent induction of BipA allows the efficient
expression of Fis, thereby modulating a range of
downstream processes, including DNA metabolism and type
III secretion..
Length = 86
Score = 105 bits (263), Expect = 5e-23
Identities = 36/87 (41%), Positives = 55/87 (63%), Gaps = 1/87 (1%)
Query: 219 FKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQ 278
+M+ T L+ D ++GRI GRI GT+K Q + + DG +E +++K+ F G+ R
Sbjct: 1 LQMLVTTLDYDDYVGRIAIGRIFRGTVKVGQQVAVVKRDGK-IEKAKITKLFGFEGLKRV 59
Query: 279 PIDEAHAGDIVSIAGLVKATVADTFCD 305
++EA AGDIV+IAG+ T+ DT CD
Sbjct: 60 EVEEAEAGDIVAIAGIEDITIGDTICD 86
>gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily.
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 = 104 bits (262), Expect = 7e-23
Identities = 47/146 (32%), Positives = 76/146 (52%), Gaps = 2/146 (1%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSE--RVMDCNDLEKERGITILAKVTSIV 78
NIA++ H GKTTL + LL +G V + V D + E +R ++I V +
Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGAIDRLGSVEDGTTVSDYDPEEIKRKMSISTSVAPLE 60
Query: 79 WNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPI 138
W +IN++DTPG+ADF GE L ++ +V+V A G T+ + A + G+ I
Sbjct: 61 WKGHKINLIDTPGYADFVGETRAALRAADAALVVVSAQSGVEVGTEKLWEFADEAGIPRI 120
Query: 139 VVVNKVDRSDARADEVINEVFDLFSA 164
+ +NK+DR A D+ + + + F
Sbjct: 121 IFINKMDRERADFDKTLAALQEAFGR 146
>gnl|CDD|33865 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 102 bits (255), Expect = 4e-22
Identities = 55/148 (37%), Positives = 83/148 (56%), Gaps = 12/148 (8%)
Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER------VMDCNDLEKERGITILAK 73
R AII+H D GKTTL ++LL G ++ V R D ++EK+RGI++ +
Sbjct: 13 RTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGKHAKSDWMEIEKQRGISVTSS 72
Query: 74 VTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTK--FVVGKAL 131
V + D +N++DTPGH DF + R L V+S V+++DAA+G PQT F V +
Sbjct: 73 VMQFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGIEPQTLKLFEVCRLR 132
Query: 132 KIGLRPIV-VVNKVDRSDARADEVINEV 158
I PI +NK+DR E+++E+
Sbjct: 133 DI---PIFTFINKLDREGRDPLELLDEI 157
Score = 38.3 bits (89), Expect = 0.006
Identities = 36/137 (26%), Positives = 55/137 (40%), Gaps = 26/137 (18%)
Query: 197 GMVPLLNLIVDHVPPP--------VISEGEFKMIGTILE----KDP-FLGRIVTGRIHSG 243
G+ L+ +VD P P + E K G + + DP RI R+ SG
Sbjct: 263 GVDHFLDALVDWAPSPRARQADTREVEPTEDKFSGFVFKIQANMDPKHRDRIAFMRVCSG 322
Query: 244 TIKSNQNIKALSPDGALVEVGR---VSKILAFRGIDRQPIDEAHAGDIVSIAGLVKATVA 300
+ + V G+ +S L F DR+ ++EA+AGDI+ + +
Sbjct: 323 KFERGMKVT-------HVRTGKDVKLSDALTFMAQDRETVEEAYAGDIIGLHNHGTIQIG 375
Query: 301 DTFCDPSIDEPLKAQPI 317
DTF + E LK I
Sbjct: 376 DTFTE---GEKLKFTGI 389
>gnl|CDD|35689 KOG0468, KOG0468, KOG0468, U5 snRNP-specific protein [Translation,
ribosomal structure and biogenesis].
Length = 971
Score = 100 bits (251), Expect = 1e-21
Identities = 64/188 (34%), Positives = 102/188 (54%), Gaps = 21/188 (11%)
Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGV-FRDNQRVSERVMDCNDLEKERGITILAKVTSI 77
IRN+ ++ H+ HGKT L+D L++Q+ F N R D E+ERG +I + ++
Sbjct: 128 IRNVGLVGHLHHGKTALMDLLVEQTHPDFSKNTEADLRYTDTLFYEQERGCSIKSTPVTL 187
Query: 78 VWNDVR-----INIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALK 132
V +D + +NI+DTPGH +F E L + + VV++VD AEG M T+ ++ A++
Sbjct: 188 VLSDSKGKSYLMNILDTPGHVNFSDETTASLRLSDGVVLVVDVAEGVMLNTERIIKHAIQ 247
Query: 133 IGLRPIVVVNKVDR---------SDA--RADEVINEVFDLFSALDATDAQLDFPIL---- 177
L +VV+NKVDR DA + +I+E+ +L S D + PIL
Sbjct: 248 NRLPIVVVINKVDRLILELKLPPMDAYYKLRHIIDEINNLISTFSKDDNPVVSPILGNVC 307
Query: 178 YGSGRFGW 185
+ SG+ G+
Sbjct: 308 FASGKLGF 315
Score = 40.4 bits (94), Expect = 0.002
Identities = 45/181 (24%), Positives = 74/181 (40%), Gaps = 24/181 (13%)
Query: 236 VTGRIHSGTIKSNQNIKALS-----PDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVS 290
V GR++SG + + Q+++ L D + + V ++ R R P+ A AG V
Sbjct: 491 VFGRVYSGQVVTGQDVRVLGENYSLEDEEDMVICEVGELWVVRARYRIPVSRAPAGLWVL 550
Query: 291 IAGLVKATV-ADTFCDPSIDEPLKAQPIDPPTVTMT---FGVNDSPLAGTEGDKVTSRMI 346
I G+ ++ V T E + I P T V PL +E K+
Sbjct: 551 IEGVDQSIVKTATIKSLEYKEDVY---IFRPLKFNTEPVVKVAVEPLNPSELPKML---- 603
Query: 347 RDRLFKEAEG--NIALKIEESSSKDAFFVSGRGELQLAVLIETMRR--EGFELAVSRPRV 402
D L K + + K+EES + G GEL + ++ +R+ E+ V+ P V
Sbjct: 604 -DGLRKINKSYPLVITKVEESGEH---VILGTGELYMDCVLYDLRKSYSEIEIKVADPVV 659
Query: 403 V 403
Sbjct: 660 R 660
Score = 28.5 bits (63), Expect = 5.8
Identities = 23/113 (20%), Positives = 45/113 (39%), Gaps = 11/113 (9%)
Query: 383 VLIETMRREGFE-LAVSRPRVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEM 441
+I T RR + ++ PR L+EP+ V I + AV ++ + +
Sbjct: 806 QIIPTARRVAYSAFLMATPR---------LMEPVYLVEITAPADCVPAVYTVLSRRRGHV 856
Query: 442 IELRP-SGTGRVRLVFLSPTRGLIGYQSQLMTDTRGTAIMNRLFHSYQPHKGE 493
+ P G+ + P G+++ L T+G A +F ++ G+
Sbjct: 857 TQDIPVPGSPLYTVKAYLPVIESFGFETDLRVHTQGQAFCLSVFDHWRIVPGD 909
>gnl|CDD|34853 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 97.6 bits (243), Expect = 9e-21
Identities = 83/339 (24%), Positives = 132/339 (38%), Gaps = 55/339 (16%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER-----------------VMDCNDLE 63
N+ I HVD GK+TLV LL G ++R E+ V+D E
Sbjct: 9 NLVFIGHVDAGKSTLVGRLLYDLGEI--DKRTMEKLEKEAKELGKESFKFAWVLDKTKEE 66
Query: 64 KERGITILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEG----- 118
+ERG+TI + + I+D PGH DF + + V++VDA +G
Sbjct: 67 RERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEFEAG 126
Query: 119 --PMPQTKFVVGKALKIGLRPIVV-VNKVDR---SDARADEVINEVFDLFSALDATDAQL 172
QT+ A +G++ ++V VNK+D + R +E+++EV L + +
Sbjct: 127 FGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLKMVGYNPKDV 186
Query: 173 DF-PI--LYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKD 229
F PI G ++ S+ LL + PP + ++ I +
Sbjct: 187 PFIPISGFKGDN----LTKKSENMPWYKGPTLLEALDQLEPPERPLDKPLRL--PIQDVY 240
Query: 230 PFLGR--IVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGD 287
G + GR+ SG IK Q + P G + EV + + + I +A GD
Sbjct: 241 SISGIGTVPVGRVESGVIKPGQKVT-FMPAGVVGEVKSIE-------MHHEEISQAEPGD 292
Query: 288 IVSIAGLVKATVADTFCDPSIDEPLKAQPIDPPTVTMTF 326
V G V + +PPTV+ F
Sbjct: 293 NV---GFNVRGVEKNDIRRGD---VIGHSDNPPTVSPEF 325
>gnl|CDD|30399 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 91.8 bits (228), Expect = 4e-19
Identities = 77/291 (26%), Positives = 123/291 (42%), Gaps = 47/291 (16%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDL---EKERGITILAKVTSI 77
N+ I HVDHGKTTL + + V + D D EK RGITI
Sbjct: 14 NVGTIGHVDHGKTTLTAAI---TTVLAKKGGAEAKAYDQIDNAPEEKARGITINTAHVEY 70
Query: 78 VWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRP 137
+ VD PGHAD+ + ++ +++V A +GPMPQT+ + A ++G+
Sbjct: 71 ETANRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVGVPY 130
Query: 138 IVV-VNKVDRSDAR--ADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSR 194
IVV +NKVD D + V EV +L S D PI+ GS + +
Sbjct: 131 IVVFLNKVDMVDDEELLELVEMEVRELLSEYGFPGD--DTPIIRGSA-LKALEGDAKW-- 185
Query: 195 DQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKDPFL------------GRIVTGRIHS 242
+ + L++ + ++P P PFL G +VTGR+
Sbjct: 186 EAKIEELMDAVDSYIPTPERD-----------IDKPFLMPVEDVFSISGRGTVVTGRVER 234
Query: 243 GTIKSNQNIKALSPDGALVEVGRVSKILAFRGID--RQPIDEAHAGDIVSI 291
G +K + ++ + + ++ G++ R+ +DE AGD V +
Sbjct: 235 GILKVGEEVEIVG--------IKETQKTTVTGVEMFRKLLDEGQAGDNVGV 277
>gnl|CDD|144322 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 = 90.7 bits (226), Expect = 1e-18
Identities = 29/84 (34%), Positives = 47/84 (55%)
Query: 411 LLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQL 470
LLEPI +V I V EE+ G V+ + + E++++ P G GRV + P L G+ ++L
Sbjct: 2 LLEPIMKVEITVPEEYLGDVIGDLNKRRGEILDMEPIGGGRVVIEAEVPLAELFGFSTEL 61
Query: 471 MTDTRGTAIMNRLFHSYQPHKGEI 494
+ T+G + F Y+P G+I
Sbjct: 62 RSLTQGRGSFSMEFSGYEPVPGDI 85
>gnl|CDD|35681 KOG0460, KOG0460, KOG0460, Mitochondrial translation elongation
factor Tu [Translation, ribosomal structure and
biogenesis].
Length = 449
Score = 81.1 bits (200), Expect = 8e-16
Identities = 77/276 (27%), Positives = 125/276 (45%), Gaps = 23/276 (8%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80
N+ I HVDHGKTTL + K + +D EK RGITI A
Sbjct: 56 NVGTIGHVDHGKTTLTAAITKILAEKGGAKFKKYDEIDKAPEEKARGITINAAHVEYETA 115
Query: 81 DVRINIVDTPGHADFGGEVERILC---MVESVVVLVDAAEGPMPQTKFVVGKALKIGLRP 137
D PGHAD+ ++ ++ ++ +++V A +GPMPQT+ + A ++G++
Sbjct: 116 KRHYAHTDCPGHADY---IKNMITGAAQMDGAILVVAATDGPMPQTREHLLLARQVGVKH 172
Query: 138 IVV-VNKVDR-SDARADEVIN-EVFDLFS--ALDATDAQLDFPILYGSGRFGWMSDSSDG 192
IVV +NKVD D E++ E+ +L S D + P++ GS +
Sbjct: 173 IVVFINKVDLVDDPEMLELVEMEIRELLSEFGFDGDNT----PVIRGSALCALEGRQPEI 228
Query: 193 SRDQGMVPLLNLIVDHVPPPV-ISEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNI 251
+ + LL+ + ++P P + F + + P G +VTGR+ G +K +
Sbjct: 229 GL-EAIEKLLDAVDSYIPTPERDLDKPFLLPIEDVFSIPGRGTVVTGRLERGVLKKGDEV 287
Query: 252 KALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGD 287
+ + + L V+ I FR +DEA AGD
Sbjct: 288 EIVGHNKTLKTT--VTGIEMFRKS----LDEAQAGD 317
>gnl|CDD|58061 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 = 76.4 bits (188), Expect = 2e-14
Identities = 27/77 (35%), Positives = 44/77 (57%)
Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMT 472
EPI +V I V EE+ GAV+ ++ + E++ + P GTGRV + P + G+ + L +
Sbjct: 1 EPIMKVEITVPEEYLGAVIGDLSKRRGEILGMEPRGTGRVVIKAELPLAEMFGFATDLRS 60
Query: 473 DTRGTAIMNRLFHSYQP 489
T+G A + F Y+P
Sbjct: 61 LTQGRASFSMEFSHYEP 77
>gnl|CDD|133283 cd01883, EF1_alpha, Eukaryotic elongation factor 1 (EF1) alpha
subfamily. 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 = 76.4 bits (189), Expect = 2e-14
Identities = 52/179 (29%), Positives = 77/179 (43%), Gaps = 54/179 (30%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER-----------------VMDCNDLE 63
N+ +I HVD GK+T LL G ++R E+ V+D E
Sbjct: 1 NLVVIGHVDAGKSTTTGHLLYLLGGV--DKRTIEKYEKEAKEMGKGSFKYAWVLDTLKEE 58
Query: 64 KERGITI---LAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESV------VVLVD 114
+ERG+TI LAK + R I+D PGH DF + M+ V++VD
Sbjct: 59 RERGVTIDVGLAKFET---EKYRFTILDAPGHRDF------VPNMITGASQADVAVLVVD 109
Query: 115 AAEG-------PMPQTK---FVVGKALKIGLRPIVVVNKVDR-----SDARADEVINEV 158
A +G QT+ + + L + + IV VNK+D S+ R DE+ E+
Sbjct: 110 ARKGEFEAGFEKGGQTREHALLA-RTLGVK-QLIVAVNKMDDVTVNWSEERYDEIKKEL 166
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 74.2 bits (183), Expect = 1e-13
Identities = 87/306 (28%), Positives = 130/306 (42%), Gaps = 67/306 (21%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80
NI I HVDHGKTTL + + +D EK RGITI
Sbjct: 14 NIGTIGHVDHGKTTLTAAITMTLAAKGGAKAKKYDEIDSAPEEKARGITINTAHVEYETE 73
Query: 81 DVRINIVDTPGHADFGGEVERILCM------VESVVVLVDAAEGPMPQTKFVVGKALKIG 134
+ VD PGHAD+ + M ++ +++V AA+GPMPQTK + A ++G
Sbjct: 74 NRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVG 127
Query: 135 LRPIVV-VNKVDRSDARADEVIN----EVFDLFSALD-ATDAQLDFPILYGSGRFGWMSD 188
+ IVV +NK D+ D +E++ EV +L S D D D PI+ GS +
Sbjct: 128 VPNIVVFLNKEDQVD--DEELLELVELEVRELLSKYDFPGD---DIPIVSGSALLALEAL 182
Query: 189 SSDGSRDQGMVP-------LLNLIVDHVPPPVISEGEFKMIGTILEKD-PFL-------- 232
+ + +G L++ + ++P P + D PFL
Sbjct: 183 TENPKIKRGENKWVDKIYNLMDAVDSYIPTPE------------RDTDKPFLMAIEDVFS 230
Query: 233 ----GRIVTGRIHSGTIKSNQNIKALSPDGALVEVG-RVSKILAFRGID--RQPIDEAHA 285
G + TGRI GT+K ++ VG R +K G++ ++ +DE A
Sbjct: 231 ITGRGTVATGRIERGTVKVGDTVEI---------VGLRETKTTTVTGLEMFQKTLDEGLA 281
Query: 286 GDIVSI 291
GD V I
Sbjct: 282 GDNVGI 287
>gnl|CDD|133371 cd04171, SelB, SelB subfamily. 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 = 164
Score = 73.0 bits (180), Expect = 2e-13
Identities = 51/154 (33%), Positives = 74/154 (48%), Gaps = 30/154 (19%)
Query: 27 HVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITI-LAKVTSIVWNDVRIN 85
H+DHGKTTL+ L +G+ + R+ E EK+RGITI L + + R+
Sbjct: 8 HIDHGKTTLIKAL---TGI--ETDRLPE--------EKKRGITIDLGFAYLDLPSGKRLG 54
Query: 86 IVDTPGHADFGGEVERILCMVESV-----VVLVDAA-EGPMPQTK--FVVGKALKIGLRP 137
+D PGH F I M+ V+LV AA EG MPQT+ + + L I R
Sbjct: 55 FIDVPGHEKF------IKNMLAGAGGIDLVLLVVAADEGIMPQTREHLEILELLGIK-RG 107
Query: 138 IVVVNKVDR-SDARADEVINEVFDLFSALDATDA 170
+VV+ K D + + V E+ +L + DA
Sbjct: 108 LVVLTKADLVDEDWLELVEEEIRELLAGTFLADA 141
>gnl|CDD|133287 cd01887, IF2_eIF5B, IF2/eIF5B (initiation factors 2/ eukaryotic
initiation factor 5B) subfamily. 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 = 168
Score = 71.8 bits (177), Expect = 6e-13
Identities = 46/147 (31%), Positives = 68/147 (46%), Gaps = 33/147 (22%)
Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKE-RGIT--ILA-KVTSI 77
+ ++ HVDHGKTTL+D++ K N E GIT I A +V +
Sbjct: 3 VTVMGHVDHGKTTLLDKIRK-----------------TNVAAGEAGGITQHIGAFEVPAE 45
Query: 78 VWNDVRINIVDTPGHADF------GGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKAL 131
V I +DTPGH F G + I +++V A +G MPQT + A
Sbjct: 46 VLKIPGITFIDTPGHEAFTNMRARGASLTDI------AILVVAADDGVMPQTIEAIKLAK 99
Query: 132 KIGLRPIVVVNKVDRSDARADEVINEV 158
+ IV +NK+D+ +A + V NE+
Sbjct: 100 AANVPFIVALNKIDKPNANPERVKNEL 126
>gnl|CDD|32720 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 70.7 bits (173), Expect = 1e-12
Identities = 78/327 (23%), Positives = 129/327 (39%), Gaps = 46/327 (14%)
Query: 27 HVDHGKTTLVDELLKQSGVFRDNQ-----RVSER------------VMDCNDLEKERGIT 69
VD GK+TL+ LL + ++Q R S+R ++D + E+E+GIT
Sbjct: 14 SVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDGLEAEREQGIT 73
Query: 70 ILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGK 129
I + I DTPGH + + + ++LVDA +G + QT+
Sbjct: 74 IDVAYRYFSTEKRKFIIADTPGHEQYTRNMATGASTADLAILLVDARKGVLEQTRRHSFI 133
Query: 130 ALKIGLRPIVV-VNK---VDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFG- 184
A +G+R +VV VNK VD S+ + ++ + + L D + PI S G
Sbjct: 134 ASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAAQLGLKDVRF-IPI---SALLGD 189
Query: 185 WMSDSSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKDPFLGRIVTGRIHSGT 244
+ S+ LL ++ S F+ + + R G I SG+
Sbjct: 190 NVVSKSENMPWYKGPTLLEILETVEIADDRSAKAFRFPVQYVNRPNLDFRGYAGTIASGS 249
Query: 245 IKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSI--AGLVKATVADT 302
+K + L P G + RV +I+ F G + +A AG+ V++ A + + D
Sbjct: 250 VKVGDEVVVL-PSG---KTSRVKRIVTFDG----ELAQASAGEAVTLVLADEIDISRGDL 301
Query: 303 FCDPSIDEPLKAQPIDPPTVTMTFGVN 329
PP V F +
Sbjct: 302 IVAAD----------APPAVADAFDAD 318
>gnl|CDD|33087 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 70.0 bits (171), Expect = 2e-12
Identities = 77/276 (27%), Positives = 116/276 (42%), Gaps = 44/276 (15%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80
I H+DHGKTTL+ L +G D R+ E EK+RGITI
Sbjct: 2 IIGTAGHIDHGKTTLLKAL---TGGVTD--RLPE--------EKKRGITIDLGFYYRKLE 48
Query: 81 DVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTK--FVVGKALKIGLRPI 138
D + +D PGH DF + L ++ +++V A EG M QT ++ L I I
Sbjct: 49 DGVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADEGLMAQTGEHLLILDLLGI-KNGI 107
Query: 139 VVVNKVDRSD-ARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSRDQG 197
+V+ K DR D AR ++ I ++ S +A F +G +G
Sbjct: 108 IVLTKADRVDEARIEQKIKQILADLSLANAK----IFKTSAKTG--------------RG 149
Query: 198 MVPLLNLIVDHVPPPVI-SEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSP 256
+ L N ++D + + F++ +G +VTG + SG +K + LSP
Sbjct: 150 IEELKNELIDLLEEIERDEQKPFRIAIDRAFTVKGVGTVVTGTVLSGEVKVGDKLY-LSP 208
Query: 257 DGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIA 292
V RV I A ++EA AG V +A
Sbjct: 209 INKEV---RVRSIQAH----DVDVEEAKAGQRVGLA 237
>gnl|CDD|35679 KOG0458, KOG0458, KOG0458, Elongation factor 1 alpha [Translation,
ribosomal structure and biogenesis].
Length = 603
Score = 67.3 bits (164), Expect = 1e-11
Identities = 75/304 (24%), Positives = 128/304 (42%), Gaps = 43/304 (14%)
Query: 21 NIAIIAHVDHGKTTLVDELLK-----QSGVFRDNQRVSER----------VMDCNDLEKE 65
N+ ++ HVD GK+TL+ LL S +R S+ ++D E+E
Sbjct: 179 NLVVLGHVDAGKSTLMGHLLYDLGEISSRSMHKLERESKNLGKSSFAYAWILDETKEERE 238
Query: 66 RGITILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEG------- 118
RG+T+ K T + ++D PGH DF + + V++VDA+ G
Sbjct: 239 RGVTMDVKTTWFESKSKIVTLIDAPGHKDFIPNMISGASQADVAVLVVDASTGEFESGFD 298
Query: 119 PMPQTKFVVGKALKIGLRP-IVVVNKVDR---SDARADEVINEVFD-LFSALDATDAQLD 173
P QT+ +G+ IV +NK+D S R +E+ N++ L + ++ +
Sbjct: 299 PGGQTREHALLLRSLGISQLIVAINKMDLVSWSQDRFEEIKNKLSSFLKESCGFKESSVK 358
Query: 174 F-PI--LYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILE--K 228
F PI L G ++ +G LL+ I P + ++ TI +
Sbjct: 359 FIPISGLSGENLIKIEQENELSQWYKGPT-LLSQIDSFKIPERPIDKPLRL--TISDIYP 415
Query: 229 DPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDI 288
P G ++G+I SG I+ Q + ++ E V + + + +P A AGD
Sbjct: 416 LPSSGVSISGKIESGYIQPGQKLYIMTS----REDATVKGLTS----NDEPKTWAVAGDN 467
Query: 289 VSIA 292
VS+
Sbjct: 468 VSLK 471
>gnl|CDD|30878 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 66.0 bits (161), Expect = 3e-11
Identities = 74/305 (24%), Positives = 120/305 (39%), Gaps = 74/305 (24%)
Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGIT--ILA-KVTSIV 78
+ I+ HVDHGKTTL+D++ K + + GIT I A +V V
Sbjct: 8 VTIMGHVDHGKTTLLDKIRKTNVAAGE----------------AGGITQHIGAYQVPLDV 51
Query: 79 WNDVRINIVDTPGHADF------GGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALK 132
I +DTPGH F G V I +++V A +G MPQT + A
Sbjct: 52 IKIPGITFIDTPGHEAFTAMRARGASVTDI------AILVVAADDGVMPQTIEAINHAKA 105
Query: 133 IGLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDG 192
G+ +V +NK+D+ +A D+V E+ + L + D + S + G
Sbjct: 106 AGVPIVVAINKIDKPEANPDKVKQELQEY--GLVPEEWGGDVIFVPVSAKTG-------- 155
Query: 193 SRDQGMVPLLNLIVDHVPPPVISEGEFKM--------IGTILE--KDPFLGRIVTGRIHS 242
+G+ LL LI ++ ++ GT++E D LG + T +
Sbjct: 156 ---EGIDELLELI-------LLLAEVLELKANPEGPARGTVIEVKLDKGLGPVATVIVQD 205
Query: 243 GTIK---------SNQNIKALSPD-GALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIA 292
GT+K ++ + D G ++ SK + G+ P A + +
Sbjct: 206 GTLKKGDIIVAGGEYGRVRTMVDDLGKPIKEAGPSKPVEILGLSEVP---AAGDVFIVVK 262
Query: 293 GLVKA 297
KA
Sbjct: 263 DEKKA 267
>gnl|CDD|36360 KOG1145, KOG1145, KOG1145, Mitochondrial translation initiation
factor 2 (IF-2; GTPase) [Translation, ribosomal
structure and biogenesis].
Length = 683
Score = 65.4 bits (159), Expect = 5e-11
Identities = 45/139 (32%), Positives = 67/139 (48%), Gaps = 19/139 (13%)
Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGIT--ILAKVTSIVW 79
+ I+ HVDHGKTTL+D L K S + GIT I A ++
Sbjct: 156 VTIMGHVDHGKTTLLDALRKSSVAAGEAG----------------GITQHIGAFTVTLP- 198
Query: 80 NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIV 139
+ I +DTPGHA F R + + VV++V A +G MPQT + A + +V
Sbjct: 199 SGKSITFLDTPGHAAFSAMRARGANVTDIVVLVVAADDGVMPQTLEAIKHAKSANVPIVV 258
Query: 140 VVNKVDRSDARADEVINEV 158
+NK+D+ A ++V E+
Sbjct: 259 AINKIDKPGANPEKVKREL 277
>gnl|CDD|133284 cd01884, EF_Tu, 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 = 63.7 bits (156), Expect = 1e-10
Identities = 65/228 (28%), Positives = 94/228 (41%), Gaps = 72/228 (31%)
Query: 21 NIAIIAHVDHGKTTLVDEL-----LKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVT 75
N+ I HVDHGKTTL + K F+ + D EK RGITI
Sbjct: 4 NVGTIGHVDHGKTTLTAAITKVLAKKGGAKFKKYDEI-----DKAPEEKARGITI----- 53
Query: 76 SIVWNDVRINI--------------VDTPGHADFGGEVERILCMV------ESVVVLVDA 115
N VD PGHAD+ I M+ + +++V A
Sbjct: 54 ---------NTAHVEYETANRHYAHVDCPGHADY------IKNMITGAAQMDGAILVVSA 98
Query: 116 AEGPMPQTKFVVGKALKIGLRPIVV-VNKVDRSDARADE-----VINEVFDLFSA--LDA 167
+GPMPQT+ + A ++G+ IVV +NK D D DE V EV +L S D
Sbjct: 99 TDGPMPQTREHLLLARQVGVPYIVVFLNKADMVD---DEELLELVEMEVRELLSKYGFDG 155
Query: 168 TDAQLDFPILYGSGRFGWMSDSSDGSRDQGMVPLLNLI--VD-HVPPP 212
+ PI+ GS + ++ + +L L+ +D ++P P
Sbjct: 156 DNT----PIVRGSA-LKALEGDDP---NKWVKKILELLDALDSYIPTP 195
>gnl|CDD|133289 cd01889, SelB_euk, SelB subfamily. 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 = 63.5 bits (155), Expect = 1e-10
Identities = 42/144 (29%), Positives = 71/144 (49%), Gaps = 33/144 (22%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITI---------- 70
N+ ++ HVD GKT+L L ++ S D N +ERGIT+
Sbjct: 2 NVGVLGHVDSGKTSLAKAL---------SEIASTAAFDKNPQSQERGITLDLGFSSFYVD 52
Query: 71 ----LAKVTSIVWNDVRINIVDTPGHADFGGEVERILC---MVESVVVLVDAAEGPMPQT 123
L ++ + +++I +VD PGHA + I+ +++ ++++VDA +G QT
Sbjct: 53 KPKHLRELINPGEENLQITLVDCPGHASL---IRTIIGGAQIIDLMLLVVDATKGIQTQT 109
Query: 124 K--FVVGKALKIGLRPIVVVNKVD 145
V+G+ L L IVV+NK+D
Sbjct: 110 AECLVIGEILCKKL--IVVLNKID 131
>gnl|CDD|58095 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 = 61.6 bits (150), Expect = 6e-10
Identities = 26/77 (33%), Positives = 44/77 (57%), Gaps = 4/77 (5%)
Query: 229 DPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDI 288
DPF+G++ R++SGT+K+ + + + RV ++L G ++ ++EA AGDI
Sbjct: 11 DPFVGKLSFVRVYSGTLKAGSTLYNSTKG----KKERVGRLLRMHGKKQEEVEEAGAGDI 66
Query: 289 VSIAGLVKATVADTFCD 305
++AGL DT CD
Sbjct: 67 GAVAGLKDTATGDTLCD 83
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 61.0 bits (148), Expect = 9e-10
Identities = 40/138 (28%), Positives = 63/138 (45%), Gaps = 22/138 (15%)
Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKER-GIT--ILAKVTSIV 78
+ I+ HVDHGKTTL+D++ K +KE GIT I A
Sbjct: 247 VTILGHVDHGKTTLLDKIRKT-----------------QIAQKEAGGITQKIGAYEVEFE 289
Query: 79 WNDVRINIV--DTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLR 136
+ D IV DTPGH F R + + ++++ A +G PQT + +
Sbjct: 290 YKDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVP 349
Query: 137 PIVVVNKVDRSDARADEV 154
IV +NK+D+++A + +
Sbjct: 350 IIVAINKIDKANANTERI 367
>gnl|CDD|133366 cd04166, CysN_ATPS, 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 = 208
Score = 58.7 bits (143), Expect = 5e-09
Identities = 49/188 (26%), Positives = 79/188 (42%), Gaps = 57/188 (30%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQR---VSER------------VMDCNDLEKE 65
VD GK+TL+ LL S ++Q S+ ++D E+E
Sbjct: 1 RFLTCGSVDDGKSTLIGRLLYDSKSIFEDQLAALESKSCGTGGEPLDLALLVDGLQAERE 60
Query: 66 RGITILAKVTSIVWNDV----------RINIVDTPGHADFGGEVERILCMV------ESV 109
+GITI DV + I DTPGH + MV +
Sbjct: 61 QGITI----------DVAYRYFSTPKRKFIIADTPGHEQYTRN------MVTGASTADLA 104
Query: 110 VVLVDAAEGPMPQTK---FVVGKALKIGLRPIVV-VNK---VDRSDARADEVINEVFDLF 162
++LVDA +G + QT+ +++ +L +G+R +VV VNK VD S+ +E++ +
Sbjct: 105 ILLVDARKGVLEQTRRHSYIL--SL-LGIRHVVVAVNKMDLVDYSEEVFEEIVADYLAFA 161
Query: 163 SALDATDA 170
+ L D
Sbjct: 162 AKLGIEDI 169
>gnl|CDD|35680 KOG0459, KOG0459, KOG0459, Polypeptide release factor 3
[Translation, ribosomal structure and biogenesis].
Length = 501
Score = 57.3 bits (138), Expect = 1e-08
Identities = 69/302 (22%), Positives = 117/302 (38%), Gaps = 43/302 (14%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQR-VSER--------------VMDCNDLEKE 65
N I HVD GK+T+ +L +G+ ER +D N E++
Sbjct: 81 NAVFIGHVDAGKSTIGGNILFLTGMVDKRTLEKYEREAKEKNRESWYLSWALDTNGEERD 140
Query: 66 RGITILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPM----- 120
+G T+ + R I+D PGH F + + V+++ A +G
Sbjct: 141 KGKTVEVGRAYFETENKRFTILDAPGHKSFVPNMIGGASQADLAVLVISARKGEFETGFE 200
Query: 121 --PQTK--FVVGKALKIGLRPIVVVNKVDR-----SDARADEVINEVFDLFSALDATDAQ 171
QT+ ++ K + IV++NK+D S+ R +E E F + +
Sbjct: 201 KGGQTREHAMLAKTAGVK-HLIVLINKMDDPTVNWSNERYEE-CKEKLQPFLRKLGFNPK 258
Query: 172 LDFPILYGSGRFG-WMSDSSDGSRDQGMVPLLNLIVDHVP-PPVISEGEFKMIGTILEKD 229
D + SG G + D +D P+ +D +P I G + + K
Sbjct: 259 PDKHFVPVSGLTGANVKDRTDSVCPWYKGPIFLEYLDELPHLERILNGPIRC--PVANKY 316
Query: 230 PFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIV 289
+G +V G++ SG+IK Q + + P+ VE V I + D D G+ V
Sbjct: 317 KDMGTVVGGKVESGSIKKGQQLVVM-PNKTNVE---VLGIYS----DDVETDRVAPGENV 368
Query: 290 SI 291
+
Sbjct: 369 KL 370
>gnl|CDD|35682 KOG0461, KOG0461, KOG0461, Selenocysteine-specific elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 522
Score = 56.2 bits (135), Expect = 3e-08
Identities = 66/284 (23%), Positives = 115/284 (40%), Gaps = 38/284 (13%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITI---------L 71
N+ I+ HVD GKTTL L + S D + ERGIT+ L
Sbjct: 9 NLGILGHVDSGKTTLARALSELG---------STAAFDKHPQSTERGITLDLGFSTMTVL 59
Query: 72 AKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKAL 131
+ ++ +VD PGHA + +++ +++++D +G QT +
Sbjct: 60 SPARLPQGEQLQFTLVDCPGHASLIRTIIGGAQIIDLMILVIDVQKGKQTQTAECLIIGE 119
Query: 132 KIGLRPIVVVNKVD--RSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDS 189
+ + +VV+NK+D + RA ++ + L++T + PI+ S +
Sbjct: 120 LLCKKLVVVINKIDVLPENQRASKIEKSAKKVRKTLESTGFDGNSPIVEVS--------A 171
Query: 190 SDGSRDQGMVPLLNLIVDH--VPPPVISEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKS 247
+DG + M+ L ++ P EG F M G ++TG + G ++
Sbjct: 172 ADGYFKEEMIQELKEALESRIFEPKRDEEGPFLMAVDHCFAIKGQGTVLTGTVLRGVLRL 231
Query: 248 NQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSI 291
N I+ AL E +V + F +Q + A AGD
Sbjct: 232 NTEIEF----PALNEKRKVKSLQMF----KQRVTSAAAGDRAGF 267
>gnl|CDD|145992 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 = 54.6 bits (132), Expect = 9e-08
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 233 GRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIA 292
G + TGR+ SGT+K + + GRV+ + F G R+ + A+AG I++
Sbjct: 1 GTVATGRVESGTLKKGDKVVIGP--NGTGKKGRVTSLEMFHGDLREAVAGANAGIILAGI 58
Query: 293 GLVKATVADTFC 304
GL DT
Sbjct: 59 GLKDIKRGDTLT 70
>gnl|CDD|34854 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 53.3 bits (128), Expect = 2e-07
Identities = 75/334 (22%), Positives = 131/334 (39%), Gaps = 87/334 (26%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80
NI ++ HVDHGKTTL L SGV+ D R SE E +RGITI
Sbjct: 12 NIGMVGHVDHGKTTLTKAL---SGVWTD--RHSE--------ELKRGITIKLGYADAKIY 58
Query: 81 DV--------------------------RINIVDTPGHADFGGEVERILCMVESVVVLVD 114
R++ VD PGH + +++ ++++
Sbjct: 59 KCPECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGAALMDGALLVIA 118
Query: 115 AAEG-PMPQTKFVVGKALKIGLRPIVVV-NKVDR-SDARADEVINEVFDLFSALDATDAQ 171
A E P PQT+ + IG++ I++V NK+D S RA E ++ + A +A
Sbjct: 119 ANEPCPQPQTREHLMALEIIGIKNIIIVQNKIDLVSRERALENYEQIKEFVKGTVAENA- 177
Query: 172 LDFPILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPVISEGE-FKMI-------- 222
PI+ S + D+ L+ I ++P P + +M
Sbjct: 178 ---PIIPISAQHKANIDA-----------LIEAIEKYIPTPERDLDKPPRMYVARSFDVN 223
Query: 223 --GTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRV------SKILAFRG 274
GT + G ++ G + G ++ I+ + P + + G+ ++I++ +
Sbjct: 224 KPGT--PPEELKGGVIGGSLVQGVLRVGDEIE-IRPGIVVEKGGKTVWEPITTEIVSLQA 280
Query: 275 IDRQPIDEAHAGDIVSIAGLVKATVADTFCDPSI 308
+ ++EA G +V + T DP++
Sbjct: 281 -GGEDVEEARPGGLVGVG---------TKLDPTL 304
>gnl|CDD|133288 cd01888, eIF2_gamma, eIF2-gamma (gamma subunit of initiation factor
2). 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 = 203
Score = 52.6 bits (127), Expect = 3e-07
Identities = 47/171 (27%), Positives = 63/171 (36%), Gaps = 70/171 (40%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITI---------- 70
NI I HV HGK+TLV L SGV+ R E E ER ITI
Sbjct: 2 NIGTIGHVAHGKSTLVKAL---SGVWTV--RFKE--------ELERNITIKLGYANAKIY 48
Query: 71 -----------LAKVTSIVWNDVR------------INIVDTPGHADFGGEVERIL---- 103
+ ++ VD PGH IL
Sbjct: 49 KCPNCGCPRPYCYRSKEDSPECECPGCGGETKLVRHVSFVDCPGH--------EILMATM 100
Query: 104 ----CMVESVVVLVDAAEG-PMPQTK--FVVGKALKI-GLRPIVVV-NKVD 145
+++ ++L+ A E P PQT AL+I GL+ I++V NK+D
Sbjct: 101 LSGAAVMDGALLLIAANEPCPQPQTSEHLA---ALEIMGLKHIIIVQNKID 148
>gnl|CDD|58078 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 = 49.2 bits (117), Expect = 3e-06
Identities = 28/89 (31%), Positives = 41/89 (46%), Gaps = 8/89 (8%)
Query: 219 FKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQ 278
+ + + KD G + TGR+ SGT+K ++ G G+V + F+G
Sbjct: 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGG--GVKGKVKSLKRFKG---- 54
Query: 279 PIDEAHAGDIVSIAGLVK--ATVADTFCD 305
+DEA AGDIV I K + DT D
Sbjct: 55 EVDEAVAGDIVGIVLKDKDDIKIGDTLTD 83
>gnl|CDD|34855 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 48.8 bits (116), Expect = 5e-06
Identities = 76/314 (24%), Positives = 121/314 (38%), Gaps = 56/314 (17%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80
+ + HVDHGK+TLV L+ +G D + +D E ERG++ + ++
Sbjct: 119 LVGVAGHVDHGKSTLVGVLV--TGRLDDGDGATRSYLDVQKHEVERGLSADISLRVYGFD 176
Query: 81 DVR-----------------------INIVDTPGHADFGGEVERILC--MVESVVVLVDA 115
D + ++ VDT GH + R L V+ +++V A
Sbjct: 177 DGKVVRLKNPLDEAEKAAVVKRADKLVSFVDTVGHEPWLRTTIRGLLGQKVDYGLLVVAA 236
Query: 116 AEGPMPQTKFVVGKALKIGLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFP 175
+G TK +G AL + L IVVV K+D D+ V + SAL ++
Sbjct: 237 DDGVTKMTKEHLGIALAMELPVIVVVTKIDMVP---DDRFQGVVEEISALLKRVGRIPLI 293
Query: 176 ILYGSGRFGWMSDSSDGSRDQGMVP-------------LLNLIVDHVPPPVIS--EGEFK 220
+ + + +G+VP LL+ +P EG F
Sbjct: 294 V---KDTDDVVLAAKAMKAGRGVVPIFYTSSVTGEGLDLLDEFFLLLPKRRRWDDEGPFL 350
Query: 221 MIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSP--DGALVEVGRVSKILAFRGIDRQ 278
M + +G +V+G + SG + + L P DG EV V I +
Sbjct: 351 MYIDKIYSVTGVGTVVSGSVKSGILHVGDTV-LLGPFKDGKFREV-VVKSI----EMHHY 404
Query: 279 PIDEAHAGDIVSIA 292
+D A AG I+ IA
Sbjct: 405 RVDSAKAGSIIGIA 418
>gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 48.6 bits (116), Expect = 5e-06
Identities = 41/179 (22%), Positives = 72/179 (40%), Gaps = 37/179 (20%)
Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWND 81
IAII + GK++L++ +L + ERV+ + G T + +
Sbjct: 181 IAIIGRPNVGKSSLINAILGE-----------ERVIVSD----IAGTTRDSIDIEFERDG 225
Query: 82 VRINIVDTPG---HADFGGEVE--------RILCMVESVVVLVDAAEGPMPQTKFVVGKA 130
+ ++DT G VE + + + V++++DA EG Q + G
Sbjct: 226 RKYVLIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDLRIAGLI 285
Query: 131 LKIGLRPIVVVNK---VDRSDARADEVINEVFDLFSALDATDAQLDF-PILYGSGRFGW 185
+ G ++VVNK V+ +A +E + L LDF PI++ S G
Sbjct: 286 EEAGRGIVIVVNKWDLVEEDEATMEEFKKK-------LRRKLPFLDFAPIVFISALTGQ 337
Score = 44.4 bits (105), Expect = 9e-05
Identities = 40/211 (18%), Positives = 73/211 (34%), Gaps = 47/211 (22%)
Query: 17 MQIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTS 76
M +AI+ + GK+TL + L + R+ +D G+T
Sbjct: 1 MSTPVVAIVGRPNVGKSTLFNRLTGR------------RIAIVSDTP---GVTRDRIYGD 45
Query: 77 IVWNDVRINIVDTPGHADFGGE---------VERILCMVESVVVLVDAAEGPMPQTKFVV 127
W ++DT G D + + + ++ +VD EG P + +
Sbjct: 46 AEWLGREFILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVVDGREGITPADEEIA 105
Query: 128 GKALKIGLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMS 187
+ I+VVNK+D A ++ +S G G +S
Sbjct: 106 KILRRSKKPVILVVNKIDNLKAEEL-----AYEFYS--------------LGFGEPVPIS 146
Query: 188 DSSDGSRDQGMVPLLNLIVDHVPPPVISEGE 218
+G+ LL+ +++ +PP E E
Sbjct: 147 ----AEHGRGIGDLLDAVLELLPPDEEEEEE 173
>gnl|CDD|133295 cd01895, EngA2, EngA2 subfamily. This CD represents the second
GTPase domain of EngA and its orthologs, which are
composed of two adjacent GTPase domains. Since the
sequences of the two domains are more similar to each
other than to other GTPases, it is likely that an
ancient gene duplication, rather than a fusion of
evolutionarily distinct GTPases, gave rise to this
family. Although the exact function of these proteins
has not been elucidated, studies have revealed that the
E. coli EngA homolog, Der, and Neisseria gonorrhoeae
EngA are essential for cell viability. A recent report
suggests that E. coli Der functions in ribosome assembly
and stability.
Length = 174
Score = 47.8 bits (115), Expect = 8e-06
Identities = 42/179 (23%), Positives = 73/179 (40%), Gaps = 37/179 (20%)
Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWND 81
IAII + GK++LV+ LL + ERV+ + G T + ++
Sbjct: 5 IAIIGRPNVGKSSLVNALLGE-----------ERVIVSD----IAGTTRDSIDVPFEYDG 49
Query: 82 VRINIVDTPG-----HADFGGE------VERILCMVESVVVLVDAAEGPMPQTKFVVGKA 130
+ ++DT G + G E + + + V++++DA EG Q + G
Sbjct: 50 KKYTLIDTAGIRRKGKVEEGIEKYSVLRTLKAIERADVVLLVIDATEGITEQDLRIAGLI 109
Query: 131 LKIGLRPIVVVNK---VDRSDARADEVINEVFDLFSALDATDAQLDF-PILYGSGRFGW 185
L+ G ++VVNK V++ E E+ LD+ PI++ S G
Sbjct: 110 LEEGKALVIVVNKWDLVEKDSKTMKEFKKEIRRKL-------PFLDYAPIVFISALTGQ 161
>gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function.
Length = 106
Score = 44.6 bits (106), Expect = 8e-05
Identities = 30/121 (24%), Positives = 51/121 (42%), Gaps = 23/121 (19%)
Query: 31 GKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDVRINIVDTP 90
GK+TL++ L + VS+ G T + + +I +VDTP
Sbjct: 1 GKSTLINALTG-----KKRAIVSDYP----------GTTRDPNEGRVELDGKQIILVDTP 45
Query: 91 G-----HADFGGEVERILCMVES---VVVLVDAAEGPMPQTKFVVGKALKIGLRPIVVVN 142
G G R L +E ++ +VDA+EG + ++ L++G I+V+N
Sbjct: 46 GIIEGASKGEGELGNRTLEAIEEADLILHVVDASEGLTEEDLEILDLLLELGKPVILVLN 105
Query: 143 K 143
K
Sbjct: 106 K 106
>gnl|CDD|58091 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 = 44.4 bits (105), Expect = 1e-04
Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 235 IVTGRIHSGTIKSNQNIKALSP-----DGALVEVGRVSKILAFRGIDRQPIDEAHAGDIV 289
I GR+ SGTI+ Q ++ L P D + + ++ G R+P+DE AG+IV
Sbjct: 18 IAFGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYREPVDEVPAGNIV 77
Query: 290 SIAGLVKATVADT 302
I GL + T
Sbjct: 78 LIVGLDQLKSGTT 90
>gnl|CDD|35275 KOG0052, KOG0052, KOG0052, Translation elongation factor EF-1
alpha/Tu [Translation, ribosomal structure and
biogenesis].
Length = 391
Score = 43.8 bits (103), Expect = 1e-04
Identities = 48/166 (28%), Positives = 71/166 (42%), Gaps = 29/166 (17%)
Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER--------------VMDCNDLEKE 65
NI +I HVD GK+T K G+ + E+ V+D E+E
Sbjct: 8 INIVVIGHVDSGKSTTT--GYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERE 65
Query: 66 RGITILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPM----- 120
RGITI + + + I+D PGH DF + + V++V A G
Sbjct: 66 RGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGIS 125
Query: 121 --PQTKFVVGKALKIGLR-PIVVVNKVDR-----SDARADEVINEV 158
QT+ A +G++ IV VNK+D S+AR +E+ EV
Sbjct: 126 KNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARYEEIKKEV 171
>gnl|CDD|32410 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 42.2 bits (99), Expect = 4e-04
Identities = 36/142 (25%), Positives = 56/142 (39%), Gaps = 8/142 (5%)
Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWND 81
I +I V GKTT V L + V + S + +R T+ SI ++
Sbjct: 13 IVVIGPVGAGKTTFVRALSDKPLVITEADASSVS------GKGKRPTTVAMDFGSIELDE 66
Query: 82 V-RINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIVV 140
+++ TPG F E + +VLVD++ + ++ P+VV
Sbjct: 67 DTGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVV 126
Query: 141 -VNKVDRSDARADEVINEVFDL 161
+NK D DA E I E L
Sbjct: 127 AINKQDLFDALPPEKIREALKL 148
>gnl|CDD|58098 cd04091, mtEFG1_II_like, 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 = 81
Score = 41.3 bits (97), Expect = 8e-04
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 226 LEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHA 285
LE+ F G++ RI+ G +K I + + RV +++ + + ++EA A
Sbjct: 8 LEEGRF-GQLTYMRIYQGKLKKGDTIYNVRTGKKV----RVPRLVRMHSNEMEEVEEAGA 62
Query: 286 GDIVSIAGLVKATVADTFCD 305
GDI +I G+ A+ DTF D
Sbjct: 63 GDICAIFGIDCAS-GDTFTD 81
>gnl|CDD|58065 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 = 41.3 bits (97), Expect = 9e-04
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMT 472
EPI +V + V EE+ G V+ ++ + +++ G G + P + GY + L +
Sbjct: 1 EPIMKVEVTVPEEYMGDVIGDLSSRRGQILGTESRG-GWKVIKAEVPLAEMFGYSTDLRS 59
Query: 473 DTRGTAIMNRLFHSYQP 489
T+G F Y+
Sbjct: 60 LTQGRGSFTMEFSHYEE 76
>gnl|CDD|36359 KOG1144, KOG1144, KOG1144, Translation initiation factor 5B
(eIF-5B) [Translation, ribosomal structure and
biogenesis].
Length = 1064
Score = 39.3 bits (91), Expect = 0.003
Identities = 35/131 (26%), Positives = 56/131 (42%), Gaps = 10/131 (7%)
Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMD------CNDLEKERGITILAKVT 75
I+ HVD GKT L+D+ ++ + V + + N EK + + AK
Sbjct: 478 CCILGHVDTGKTKLLDK-IRGTNVQEGEAGGITQQIGATYFPAENIREKTKELKKDAKKR 536
Query: 76 SIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGL 135
V + ++DTPGH F R + + +++VD G PQT +
Sbjct: 537 LKV---PGLLVIDTPGHESFTNLRSRGSSLCDLAILVVDIMHGLEPQTIESINLLRMRKT 593
Query: 136 RPIVVVNKVDR 146
IV +NK+DR
Sbjct: 594 PFIVALNKIDR 604
>gnl|CDD|133294 cd01894, EngA1, EngA1 subfamily. This CD represents the first
GTPase domain of EngA and its orthologs, which are
composed of two adjacent GTPase domains. Since the
sequences of the two domains are more similar to each
other than to other GTPases, it is likely that an
ancient gene duplication, rather than a fusion of
evolutionarily distinct GTPases, gave rise to this
family. Although the exact function of these proteins
has not been elucidated, studies have revealed that the
E. coli EngA homolog, Der, and Neisseria gonorrhoeae
EngA are essential for cell viability. A recent report
suggests that E. coli Der functions in ribosome assembly
and stability.
Length = 157
Score = 39.3 bits (93), Expect = 0.003
Identities = 34/144 (23%), Positives = 49/144 (34%), Gaps = 47/144 (32%)
Query: 31 GKTTLVDELLKQ--------SGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDV 82
GK+TL + L + GV RD R+ W
Sbjct: 9 GKSTLFNRLTGRRDAIVEDTPGVTRD--RIYGEA---------------------EWGGR 45
Query: 83 RINIVDTPGHADFGGEVERILCMV---------ESVVVL--VDAAEGPMPQTKFVVGKAL 131
++DT G + E I + E+ V+L VD EG P + +
Sbjct: 46 EFILIDTGG---IEPDDEGISKEIREQAELAIEEADVILFVVDGREGLTPADEEIAKYLR 102
Query: 132 KIGLRPIVVVNKVD--RSDARADE 153
K I+VVNKVD + + A E
Sbjct: 103 KSKKPVILVVNKVDNIKEEDEAAE 126
>gnl|CDD|133256 cd00880, Era_like, Era (E. coli Ras-like protein)-like. This
family includes several distinct subfamilies (TrmE/ThdF,
FeoB, YihA (EngG), Era, and EngA/YfgK) that generally
show sequence conservation in the region between the
Walker A and B motifs (G1 and G3 box motifs), to the
exclusion of other GTPases. TrmE is ubiquitous in
bacteria and is a widespread mitochondrial protein in
eukaryotes, but is absent from archaea. The yeast member
of TrmE family, MSS1, is involved in mitochondrial
translation; bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the 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 = 163
Score = 38.5 bits (90), Expect = 0.006
Identities = 29/126 (23%), Positives = 51/126 (40%), Gaps = 27/126 (21%)
Query: 31 GKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVW---NDVRINIV 87
GK++L++ LL Q V VS G T VW + ++
Sbjct: 8 GKSSLLNALLGQE-VAI----VSPV----------PGTTT--DPVEYVWELGPLGPVVLI 50
Query: 88 DTPGHADFGG-------EVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIVV 140
DTPG + GG R+L + ++ +VDA + + ++ + G ++V
Sbjct: 51 DTPGIDEAGGLGREREELARRVLERADLILFVVDADLRADEEEEKLLELLRERGKPVLLV 110
Query: 141 VNKVDR 146
+NK+D
Sbjct: 111 LNKIDL 116
>gnl|CDD|133363 cd04163, Era, Era subfamily. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in
eukaryotes. Era contains two domains: the N-terminal
GTPase domain and a C-terminal domain KH domain that is
critical for RNA binding. Both domains are important
for Era function. Era is functionally able to
compensate for deletion of RbfA, a cold-shock adaptation
protein that is required for efficient processing of the
16S rRNA.
Length = 168
Score = 38.2 bits (90), Expect = 0.008
Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 16/89 (17%)
Query: 87 VDTPG-HADFGGEVERILCMVES----------VVVLVDAAEGPMPQTKFVVGKALKIGL 135
VDTPG H + + MV++ V+ +VDA+E +F++ K
Sbjct: 56 VDTPGIHKP---KKKLGERMVKAAWSALKDVDLVLFVVDASEPIGEGDEFILELLKKSKT 112
Query: 136 RPIVVVNKVDR--SDARADEVINEVFDLF 162
I+V+NK+D ++ ++ +L
Sbjct: 113 PVILVLNKIDLVKDKEDLLPLLEKLKELG 141
>gnl|CDD|133258 cd00882, Ras_like_GTPase, 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 regulate
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 = 157
Score = 36.7 bits (85), Expect = 0.017
Identities = 21/137 (15%), Positives = 45/137 (32%), Gaps = 19/137 (13%)
Query: 24 IIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDVR 83
++ GKT+L++ + V E + I +K + V+
Sbjct: 1 VVGDSGVGKTSLLN-------RLLGGEFVPEE-------YETTIIDFYSKTIEVDGKKVK 46
Query: 84 INIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQ-----TKFVVGKALKIGLRPI 138
+ I DT G F + ++++ D + + ++ + I
Sbjct: 47 LQIWDTAGQERFRSLRRLYYRGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPII 106
Query: 139 VVVNKVDRSDARADEVI 155
+V NK+D + R
Sbjct: 107 LVGNKIDLPEERVVSEE 123
>gnl|CDD|58097 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 = 36.7 bits (85), Expect = 0.022
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 11/65 (16%)
Query: 238 GRIHSGTIKSNQNIKALSP--------DGALVEVGRVSKILAFRGIDRQPIDEAHAGDIV 289
GRI+SGTIK Q +K L D + +GR+ G + ++EA AG+ V
Sbjct: 21 GRIYSGTIKKGQKVKVLGENYSLDDEEDMTICTIGRLW---ILGGRYKIEVNEAPAGNWV 77
Query: 290 SIAGL 294
I G+
Sbjct: 78 LIKGI 82
>gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 36.3 bits (84), Expect = 0.027
Identities = 39/135 (28%), Positives = 60/135 (44%), Gaps = 27/135 (20%)
Query: 22 IAIIAHVDHGKTTLVDELLKQ--SGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVW 79
+AII + GK+TL++ L+ Q S V Q R+ RGI
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRI---------RGIVTT-------- 51
Query: 80 NDVRINIVDTPG----HADFG----GEVERILCMVESVVVLVDAAEGPMPQTKFVVGKAL 131
++ +I VDTPG G L V+ ++ +VDA EG P +F++ +
Sbjct: 52 DNAQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLK 111
Query: 132 KIGLRPIVVVNKVDR 146
K I+VVNK+D+
Sbjct: 112 KTKTPVILVVNKIDK 126
>gnl|CDD|58099 cd04092, mtEFG2_II_like, mtEFG2_C: C-terminus of mitochondrial
Elongation factor G2 (mtEFG2)-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. No clear phenotype has been found for mutants in
the yeast homologue of mtEFG2, MEF2. There are two
forms of mtEFG present in mammals (designated mtEFG1s
and mtEFG2s) mtEFG1s are not present in this group..
Length = 83
Score = 36.0 bits (83), Expect = 0.036
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 4/74 (5%)
Query: 229 DPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDI 288
DP G + R++SGT+K + + R+S++L Q I AG+I
Sbjct: 11 DPQRGPLTFVRVYSGTLKRGSALYNTNTGKKE----RISRLLQPFADQYQEIPSLSAGNI 66
Query: 289 VSIAGLVKATVADT 302
I GL + DT
Sbjct: 67 GVITGLKQTRTGDT 80
>gnl|CDD|133259 cd01850, CDC_Septin, CDC/Septin. Septins are a conserved family
of GTP-binding proteins associated with diverse
processes in dividing and non-dividing cells. They
were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of
the cell cortex and exocytosis. In humans, 12 septin
genes generate dozens of polypeptides, many of which
comprise heterooligomeric complexes. Since septin
mutants are commonly defective in cytokinesis and
formation of the neck formation of the neck
filaments/septin rings, septins have been considered to
be the primary constituents of the neck filaments.
Septins belong to the GTPase superfamily for their
conserved GTPase motifs and enzymatic activities.
Length = 276
Score = 35.6 bits (83), Expect = 0.037
Identities = 13/67 (19%), Positives = 27/67 (40%), Gaps = 8/67 (11%)
Query: 31 GKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDVRI--NIVD 88
GK+T ++ L + + + ++ + I + I N V++ ++D
Sbjct: 16 GKSTFINTLFNTK-LIPSDYPPDPA-----EEHIDKTVEIKSSKAEIEENGVKLKLTVID 69
Query: 89 TPGHADF 95
TPG D
Sbjct: 70 TPGFGDN 76
>gnl|CDD|58080 cd03689, RF3_II, RF3_II: this subfamily represents the domain II of
bacterial Release Factor 3 (RF3). Termination of protein
synthesis by the ribosome requires two release factor
(RF) classes. The class II RF3 is a GTPase that removes
class I RFs (RF1 or RF2) from the ribosome after release
of the nascent polypeptide. RF3 in the GDP state binds
to the ribosomal class I RF complex, followed by an
exchange of GDP for GTP and release of the class I RF.
Sequence comparison of class II release factors with
elongation factors shows that prokaryotic RF3 is more
similar to EF-G whereas eukaryotic eRF3 is more similar
to eEF1A, implying that their precise function may
differ..
Length = 85
Score = 35.2 bits (81), Expect = 0.061
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 4/71 (5%)
Query: 234 RIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAG 293
RI R+ SG + +K L + R+S F DR+ +DEA+ GDI+ +
Sbjct: 17 RIAFVRVCSGKFERGMKVK----HVRLGKEVRLSNPQQFFAQDRETVDEAYPGDIIGLVN 72
Query: 294 LVKATVADTFC 304
+ DT
Sbjct: 73 PGNFQIGDTLT 83
>gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 34.5 bits (79), Expect = 0.087
Identities = 34/149 (22%), Positives = 63/149 (42%), Gaps = 37/149 (24%)
Query: 31 GKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDVRINIVDTP 90
GK++L++ L Q + R S K G T L + +D + +VD P
Sbjct: 36 GKSSLINALTNQKNL----ARTS----------KTPGRTQL--INFFEVDD-ELRLVDLP 78
Query: 91 GHADFG------GEVERILCMVES----------VVVLVDAAEGPMPQTKFVVGKALKIG 134
G +G E+ ++E VV+L+DA P + ++ L++G
Sbjct: 79 G---YGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDREMIEFLLELG 135
Query: 135 LRPIVVVNKVDR-SDARADEVINEVFDLF 162
+ IVV+ K D+ + ++ +N+V +
Sbjct: 136 IPVIVVLTKADKLKKSERNKQLNKVAEEL 164
>gnl|CDD|58062 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 = 34.3 bits (79), Expect = 0.090
Identities = 14/78 (17%), Positives = 33/78 (42%), Gaps = 1/78 (1%)
Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLI-GYQSQLM 471
EP + I E+ GA+++ + ++ RV L + P ++ + +L
Sbjct: 1 EPFVKATIITPSEYLGAIMELCQERRGVQKDMEYLDANRVMLTYELPLAEIVYDFFDKLK 60
Query: 472 TDTRGTAIMNRLFHSYQP 489
+ ++G A ++ Y+
Sbjct: 61 SISKGYASLDYELIGYRE 78
>gnl|CDD|58089 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 = 33.9 bits (78), Expect = 0.14
Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 8/60 (13%)
Query: 233 GRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIA 292
G +V+G++ SG+I+ + + P VEV + +D + +D A AG+ V +
Sbjct: 15 GTVVSGKVESGSIQKGDTL-LVMPSKESVEVKSIY-------VDDEEVDYAVAGENVRLK 66
>gnl|CDD|58086 cd03695, CysN_NodQ_II, CysN_NodQ_II: This subfamily represents the
domain II of the large subunit of ATP sulfurylase
(ATPS): CysN or the N-terminal portion of NodQ, found
mainly in proteobacteria and homologous to the domain II
of EF-Tu. Escherichia coli ATPS consists of CysN and a
smaller subunit CysD and CysN. ATPS produces
adenosine-5'-phosphosulfate (APS) from ATP and sulfate,
coupled with GTP hydrolysis. In the subsequent reaction
APS is phosphorylated by an APS kinase (CysC), to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for
use in amino acid (aa) biosynthesis. The Rhizobiaceae
group (alpha-proteobacteria) appears to carry out the
same chemistry for the sufation of a nodulation factor.
In Rhizobium meliloti, a the hererodimeric complex
comprised of NodP and NodQ appears to possess both ATPS
and APS kinase activities. The N and C termini of NodQ
correspond to CysN and CysC, respectively. Other
eubacteria, Archaea, and eukaryotes use a different ATP
sulfurylase, which shows no aa sequence similarity to
CysN or NodQ. CysN and the N-terminal portion of NodQ
show similarity to GTPases involved in translation, in
particular, EF-Tu and EF-1alpha..
Length = 81
Score = 33.1 bits (76), Expect = 0.21
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 234 RIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSI 291
R G I SG+I+ + L P G + RV I F G +DEA AG+ V++
Sbjct: 16 RGYAGTIASGSIRVGDEVVVL-PSG---KTSRVKSIETFDG----ELDEAGAGESVTL 65
>gnl|CDD|58087 cd03696, selB_II, selB_II: this subfamily represents the domain of
elongation factor SelB, homologous to domain II of
EF-Tu. SelB may function by replacing EF-Tu. In
prokaryotes, the incorporation of selenocysteine as the
21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3' or 5' non-coding elements of mRNA have been found as
probable structures for directing selenocysteine
incorporation..
Length = 83
Score = 32.8 bits (75), Expect = 0.28
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 233 GRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIA 292
G +VTG + SG++K ++ L E RV I + ++EA AGD V++
Sbjct: 15 GTVVTGTVLSGSVKVGDKVEILPLG----EETRVRSIQVH----GKDVEEAKAGDRVALN 66
>gnl|CDD|144365 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are
polypeptides of 30-65kDa with three characteristic
GTPase motifs (G-1, G-3 and G-4) that are similar to
those of the Ras family. The G-4 motif is strictly
conserved with a unique septin consensus of AKAD. Most
septins are thought to have at least one coiled-coil
region, which in some cases is necessary for
intermolecular interactions that allow septins to
polymerize to form rod-shaped complexes. In turn, these
are arranged into tandem arrays to form filaments. They
are multifunctional proteins, with roles in
cytokinesis, sporulation, germ cell development,
exocytosis and apoptosis.
Length = 280
Score = 32.3 bits (74), Expect = 0.37
Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 31 GKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDVRIN--IVD 88
GKTTL++ L + ++ + + ++ + I A I + V++N ++D
Sbjct: 16 GKTTLINTLF-LTDLYPERGIPGPS------EKIKKTVEIKATTVEIEEDGVKLNLTVID 68
Query: 89 TPGHADF 95
TPG D
Sbjct: 69 TPGFGDA 75
>gnl|CDD|36233 KOG1015, KOG1015, KOG1015, Transcription regulator XNP/ATRX,
DEAD-box superfamily [Transcription].
Length = 1567
Score = 32.0 bits (72), Expect = 0.44
Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 7/85 (8%)
Query: 376 RGELQLAVLIETMRREGFELAVSRPR---VVIKKEGDSLLEPIE-EVVIDVDEEHSGAVV 431
R E Q A+ E RR+ E R + V+ ++ EPI ++V+D DEE +V
Sbjct: 600 RKETQNALKEEKERRKRIEEERERQKLRNVIEIEDASPTKEPITTKLVLDEDEETKEPLV 659
Query: 432 QKMTLHKSEMIELRPSGTGRVRLVF 456
Q +H+S +I+L+P V+ ++
Sbjct: 660 Q---VHRSLVIKLKPHQVDGVQFMW 681
>gnl|CDD|58066 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 = 31.6 bits (72), Expect = 0.68
Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 1/78 (1%)
Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRP-SGTGRVRLVFLSPTRGLIGYQSQLM 471
EPI V I E+ G V ++ + ++ P GT + P G+++ L
Sbjct: 1 EPIYLVEIQCPEDALGKVYSVLSKRRGHVLSEEPKEGTPLFEIKAYLPVIESFGFETDLR 60
Query: 472 TDTRGTAIMNRLFHSYQP 489
+ T G A +F ++
Sbjct: 61 SATSGQAFPQLVFSHWEI 78
>gnl|CDD|58064 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 = 31.7 bits (72), Expect = 0.69
Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 1/77 (1%)
Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMT 472
EP ++V ++ G + + + E V L P YQS+L +
Sbjct: 1 EPYLRFELEVPQDALGRAMSDLAKMGAT-FEDPQIKGDEVTLEGTIPVATSQDYQSELPS 59
Query: 473 DTRGTAIMNRLFHSYQP 489
T G ++ F Y+P
Sbjct: 60 YTHGEGVLETEFKGYRP 76
>gnl|CDD|146419 pfam03767, Acid_phosphat_B, HAD superfamily, subfamily IIIB (Acid
phosphatase). This family proteins includes acid
phosphatases and a number of vegetative storage
proteins.
Length = 230
Score = 31.2 bits (71), Expect = 0.82
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 371 FFVSGRGELQLAVLIETMRREGFELAVSRPRVVIKKEGDS 410
FFVSGR E A +E +++ GF +++++ + DS
Sbjct: 140 FFVSGRSEDLRAATVENLKKAGFH---GWEKLILRGKKDS 176
>gnl|CDD|35298 KOG0075, KOG0075, KOG0075, GTP-binding ADP-ribosylation factor-like
protein [General function prediction only].
Length = 186
Score = 30.7 bits (69), Expect = 1.2
Identities = 25/103 (24%), Positives = 43/103 (41%), Gaps = 5/103 (4%)
Query: 69 TILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAE-----GPMPQT 123
T+ + + +V I + D G F ER V ++V +VDAA+ +
Sbjct: 52 TVGFNMRKVTKGNVTIKLWDLGGQPRFRSMWERYCRGVSAIVYVVDAADPDKLEASRSEL 111
Query: 124 KFVVGKALKIGLRPIVVVNKVDRSDARADEVINEVFDLFSALD 166
++ K G+ +V+ NK+D A + + E L S D
Sbjct: 112 HDLLDKPSLTGIPLLVLGNKIDLPGALSKIALIERMGLSSITD 154
>gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 30.9 bits (70), Expect = 1.2
Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 76 SIVWNDVRINIVDTPGHADFGGEVERI--------LCMVESVVVLVDAAEGPMPQTKFVV 127
I N + + +VDT G + VERI + + V+ ++DA++ P+ + +
Sbjct: 259 DINLNGIPVRLVDTAGIRETDDVVERIGIERAKKAIEEADLVLFVLDASQ-PLDKEDLAL 317
Query: 128 GKALKIGLRPIVVVNKVD 145
+ L IVV+NK D
Sbjct: 318 IELLPKKKPIIVVLNKAD 335
>gnl|CDD|58093 cd03702, IF2_mtIF2_II, This family represents the domain II of
bacterial Initiation Factor 2 (IF2) and its eukaryotic
mitochondrial homologue mtIF2. IF2, the largest
initiation factor is an essential GTP binding protein.
In E. coli three natural forms of IF2 exist in the cell,
IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is
structurally and functionally related to eukaryotic
mitochondrial mtIF-2..
Length = 95
Score = 30.8 bits (70), Expect = 1.2
Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 11/74 (14%)
Query: 223 GTILEK--DPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPI 280
G ++E D G + T + +GT+K + A + G+V + G + +
Sbjct: 3 GVVIESKLDKGRGPVATVLVQNGTLKVGDVLVAGT------TYGKVRAMFDENG---KRV 53
Query: 281 DEAHAGDIVSIAGL 294
EA V I GL
Sbjct: 54 KEAGPSTPVEILGL 67
>gnl|CDD|58090 cd03699, lepA_II, lepA_II: This subfamily represents the domain II
of LepA, a GTP-binding protein localized in the
cytoplasmic membrane. The N-terminal domain of LepA
shares regions of homology to translation factors. In
terms of interaction with the ribosome, EF-G, EF-Tu and
IF2 have all been demonstrated to interact at
overlapping sites on the ribosome. Chemical protection
studies demonstrate that they all include the
universally conserved alpha-sarcin loop as part of their
binding site. These data indicate that LepA may bind to
this location on the ribosome as well. LepA has never
been observed in archaea, and eukaryl LepA is
organellar. LepA is therefore a true bacterial GTPase,
found only in the bacterial lineage..
Length = 86
Score = 30.4 bits (69), Expect = 1.4
Identities = 26/81 (32%), Positives = 34/81 (41%), Gaps = 9/81 (11%)
Query: 229 DPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDI 288
DP+ G I R+ GT+K I+ +S G EV V I + P DE AG +
Sbjct: 11 DPYRGVIALVRVFDGTLKKGDKIRFMS-TGKEYEVEEVG-IFRP---EMTPTDELSAGQV 65
Query: 289 VSIAGLVK----ATVADTFCD 305
I +K A V DT
Sbjct: 66 GYIIAGIKTVKDARVGDTITL 86
>gnl|CDD|32934 COG3120, COG3120, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 149
Score = 30.4 bits (68), Expect = 1.5
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 562 ASGKDEAVKLVPAVKMTLEQALSWIQ---NDELVEVTPKSIRL-RKMYLDPNERKRKGKS 617
AS +EAV+ + +++ + WI + ELV ++IR RK + + + + KS
Sbjct: 34 ASAAEEAVQQLLSLENEPVKVNEWIDAHMSPELVNKLKQAIRARRKRHFNAEHQHTRKKS 93
Query: 618 VNLEYNV 624
++LEY V
Sbjct: 94 IDLEYAV 100
>gnl|CDD|58067 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 = 29.8 bits (67), Expect = 2.2
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 1/77 (1%)
Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMT 472
EPI +V + E G V+ + K I +G L P + GY ++L +
Sbjct: 1 EPIMKVEVTAPTEFQGNVIGLLNKRKG-TIVDTDTGEDEFTLEAEVPLNDMFGYSTELRS 59
Query: 473 DTRGTAIMNRLFHSYQP 489
T+G + F Y P
Sbjct: 60 MTQGKGEFSMEFSRYAP 76
>gnl|CDD|38742 KOG3534, KOG3534, KOG3534, p53 inducible protein PIR121 [General
function prediction only].
Length = 1253
Score = 30.0 bits (67), Expect = 2.2
Identities = 15/53 (28%), Positives = 25/53 (47%)
Query: 561 RASGKDEAVKLVPAVKMTLEQALSWIQNDELVEVTPKSIRLRKMYLDPNERKR 613
+A GKDE +K +P KM I N+++ + K ++ + P E R
Sbjct: 1183 KADGKDEIIKGIPLKKMVERIRRFQILNNQIFIILNKYLKSGEGEGSPVEHVR 1235
>gnl|CDD|58096 cd04089, eRF3_II, eRF3_II: domain II of the eukaryotic class II
release factor (eRF3). In eukaryotes, translation
termination is mediated by two interacting release
factors, eRF1 and eRF3, which act as class I and II
factors, respectively. eRF1 functions as an omnipotent
release factor, decoding all three stop codons and
triggering the release of the nascent peptide catalyzed
by the ribsome. eRF3 is a GTPase, which enhances the
termination efficiency by stimulating the eRF1 activity
in a GTP-dependent manner. Sequence comparison of class
II release factors with elongation factors shows that
eRF3 is more similar to eEF1alpha whereas prokaryote RF3
is more similar to EF-G, implying that their precise
function may differ. Only eukaryote RF3s are found in
this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a
translation termination factor which is divided into
three regions N, M and a C-terminal eEF1a-like region
essential for translation termination. Sup35NM is a
non-pathogenic prion-like protein with the property of
aggregating into polymer-like fibrils..
Length = 82
Score = 29.7 bits (67), Expect = 2.7
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 8/68 (11%)
Query: 225 ILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAH 284
I++K +G +V G++ SGTIK + + P+ VEV + + + A
Sbjct: 6 IIDKYKDMGTVVLGKVESGTIKKGDKL-LVMPNKTQVEVLSIY-------NEDVEVRYAR 57
Query: 285 AGDIVSIA 292
G+ V +
Sbjct: 58 PGENVRLR 65
>gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 29.4 bits (66), Expect = 3.1
Identities = 32/137 (23%), Positives = 61/137 (44%), Gaps = 26/137 (18%)
Query: 17 MQIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTS 76
M+ +A++ + + GKTTL + L +G NQ+V G+T+ K
Sbjct: 1 MKKLTVALVGNPNVGKTTLFNAL---TGA---NQKVGNWP----------GVTVEKKEGK 44
Query: 77 IVWNDVRINIVDTPGHADFGG--EVERILC------MVESVVVLVDAAEGPMPQTKFVVG 128
+ + I IVD PG E E++ + +V +VDA + + ++
Sbjct: 45 LKYKGHEIEIVDLPGTYSLTAYSEDEKVARDFLLEGKPDLIVNVVDATN--LERNLYLTL 102
Query: 129 KALKIGLRPIVVVNKVD 145
+ L++G+ I+ +N +D
Sbjct: 103 QLLELGIPMILALNMID 119
>gnl|CDD|144080 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 29.1 bits (66), Expect = 3.5
Identities = 28/142 (19%), Positives = 46/142 (32%), Gaps = 23/142 (16%)
Query: 20 RNIAII-------AHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILA 72
R ++ A K D L K F D + E + D D G I +
Sbjct: 33 RRPLVLRLGEEPGAIPGAVKVEYKDGLKK----FEDFSELREEIEDETDKISGTGKGISS 88
Query: 73 KVTSI---VWNDVRINIVDTPG-----HADFGGEVERILCMVESVVVLVDAAEGPMPQT- 123
+ + + +VDTPG D E + +++ V A + +
Sbjct: 89 EPIILEILSPLVPGLTLVDTPGLDSVAVGDQ-DLTEEYIKP-ADIILAVVDANHDLSTSE 146
Query: 124 -KFVVGKALKIGLRPIVVVNKV 144
F+ + G R I V+ K
Sbjct: 147 ALFLAREVDPNGKRTIGVLTKD 168
>gnl|CDD|37866 KOG2655, KOG2655, KOG2655, Septin family protein (P-loop GTPase)
[Cell cycle control, cell division, chromosome
partitioning, Nuclear structure, Intracellular
trafficking, secretion, and vesicular transport].
Length = 366
Score = 28.8 bits (64), Expect = 4.7
Identities = 14/67 (20%), Positives = 24/67 (35%), Gaps = 9/67 (13%)
Query: 31 GKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDV--RINIVD 88
GK+T ++ L R + + + I + I N V + ++D
Sbjct: 33 GKSTFINSLFLTD-------LSGNREVPGASERIKETVEIESTKVEIEENGVKLNLTVID 85
Query: 89 TPGHADF 95
TPG D
Sbjct: 86 TPGFGDA 92
>gnl|CDD|35687 KOG0466, KOG0466, KOG0466, Translation initiation factor 2, gamma
subunit (eIF-2gamma; GTPase) [Translation, ribosomal
structure and biogenesis].
Length = 466
Score = 28.8 bits (64), Expect = 4.9
Identities = 61/271 (22%), Positives = 104/271 (38%), Gaps = 57/271 (21%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGV----FRDN-QR--------VSERVMDCNDLE---- 63
NI I HV HGK+T+V + SGV F++ +R + ++ C+D +
Sbjct: 40 NIGTIGHVAHGKSTVVKAI---SGVHTVRFKNELERNITIKLGYANAKIYKCDDPKCPRP 96
Query: 64 ---------KERGITILAKVTSIVWNDVR-INIVDTPGHADFGGEVERILCMVESVVVLV 113
KE VR ++ VD PGH + ++++ ++L+
Sbjct: 97 GCYRSFGSSKEDRPPCDRPGCEGKMKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLI 156
Query: 114 DAAEG-PMPQTKFVVGKALKIGLRPIVVV-NKVDR-SDARADEVINEVFDLFSALDATDA 170
E P PQT + + L+ I+++ NK+D +++A E ++ A A
Sbjct: 157 AGNESCPQPQTSEHLAAVEIMKLKHIIILQNKIDLIKESQALEQHEQIQKFIQGTVAEGA 216
Query: 171 QLDFPILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPV---ISEGEFKMIGTI-- 225
PI+ S + + D + IV +P PV S +I +
Sbjct: 217 ----PIIPISAQLKYNIDV-----------VCEYIVKKIPVPVRDFTSPPRLIVIRSFDV 261
Query: 226 ----LEKDPFLGRIVTGRIHSGTIKSNQNIK 252
E D G + G I G +K Q I+
Sbjct: 262 NKPGSEVDDLKGGVAGGSILKGVLKVGQEIE 292
>gnl|CDD|57926 cd01855, YqeH, YqeH. YqeH is an essential GTP-binding protein.
Depletion of YqeH induces an excess initiation of DNA
replication, suggesting that it negatively controls
initiation of chromosome replication. The YqeH subfamily
is common in eukaryotes and sporadically present in
bacteria with probable acquisition by plants from
chloroplasts. Proteins of the YqeH family contain all
sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases..
Length = 190
Score = 28.7 bits (64), Expect = 4.9
Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 4/64 (6%)
Query: 83 RINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRP-IVVV 141
+I+ V+ P + I VV +VD + P + L G P I+V
Sbjct: 12 KIDPVEIPDEDFILNLLSSISPKKALVVHVVDIFDFPG---SLIPRLRLFGGNNPVILVG 68
Query: 142 NKVD 145
NK+D
Sbjct: 69 NKID 72
>gnl|CDD|144639 pfam01120, Alpha_L_fucos, Alpha-L-fucosidase.
Length = 344
Score = 28.8 bits (65), Expect = 5.1
Identities = 7/16 (43%), Positives = 8/16 (50%)
Query: 85 NIVDTPGHADFGGEVE 100
N VDT D GE+
Sbjct: 130 NSVDTGPKRDIVGELA 145
>gnl|CDD|36760 KOG1547, KOG1547, KOG1547, Septin CDC10 and related P-loop GTPases
[Cell cycle control, cell division, chromosome
partitioning, Signal transduction mechanisms,
Cytoskeleton].
Length = 336
Score = 28.4 bits (63), Expect = 5.4
Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 11/78 (14%)
Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80
NI ++ GK+TL++ L K VS+ N E T + +T ++
Sbjct: 48 NIMVVGQSGLGKSTLINTLFKS--------HVSDSSSSDNSAEPIPKTTEIKSITHVIEE 99
Query: 81 D---VRINIVDTPGHADF 95
+++ ++DTPG D
Sbjct: 100 KGVKLKLTVIDTPGFGDQ 117
>gnl|CDD|143612 cd07304, Chorismate_synthase, Chorismase synthase, the enzyme
catalyzing the final step of the shikimate pathway.
Chorismate synthase (CS;
5-enolpyruvylshikimate-3-phosphate phospholyase;
1-carboxyvinyl-3-phosphoshikimate phosphate-lyase; E.C.
4.2.3.5) catalyzes the seventh and final step in the
shikimate pathway: the conversion of 5-
enolpyruvylshikimate-3-phosphate (EPSP) to chorismate, a
precursor for the biosynthesis of aromatic compounds.
This process has an absolute requirement for reduced FMN
as a co-factor which is thought to facilitate cleavage
of C-O bonds by transiently donating an electron to the
substrate, having no overall change its redox state.
Depending on the capacity of these enzymes to regenerate
the reduced form of FMN, chorismate synthases are
divided into two classes: Enzymes, mostly from plants
and eubacteria, that sequester CS from the cellular
environment, are monofunctiona,l while those that can
generate reduced FMN at the expense of NADPH, such as
found in fungi and the ciliated protozoan Euglena
gracilis, are bifunctional, having an additional
NADPH:FMN oxidoreductase activity. Recently,
bifunctionality of the Mycobacterium tuberculosis enzyme
(MtCS) was determined by measurements of both chorismate
synthase and NADH:FMN oxidoreductase activities. Since
shikimate pathway enzymes are present in bacteria, fungi
and apicomplexan parasites (such as Toxoplasma gondii,
Plasmodium falciparum, and Cryptosporidium parvum) but
absent in mammals, they are potentially attractive
targets for the development of new therapy against
infectious diseases such as tuberculosis (TB).
Length = 344
Score = 28.2 bits (64), Expect = 6.6
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 7/40 (17%)
Query: 67 GITILAKVTSIVWN-DVR----INIVDT--PGHADFGGEV 99
G T + ++ N D R + PGHAD+ G +
Sbjct: 65 GKTTGTPIALLIRNKDQRSWDYSMLKTLPRPGHADYTGFL 104
>gnl|CDD|58068 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 = 28.2 bits (63), Expect = 6.6
Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 1/78 (1%)
Query: 413 EPIEEVVIDVDEEHSGAVVQKMTLHKSEMI-ELRPSGTGRVRLVFLSPTRGLIGYQSQLM 471
EPI EV I + AV + ++ + +I + GT + P G+++ L
Sbjct: 1 EPIYEVEITCPADAVSAVYEVLSRRRGHVIYDTPIPGTPLYEVKAFIPVIESFGFETDLR 60
Query: 472 TDTRGTAIMNRLFHSYQP 489
T+G A +F +Q
Sbjct: 61 VHTQGQAFCQSVFDHWQI 78
>gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 28.0 bits (62), Expect = 7.2
Identities = 32/128 (25%), Positives = 49/128 (38%), Gaps = 28/128 (21%)
Query: 86 IVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPI---VVVN 142
IV+T G EV+ I M ++ +V++ G Q +K G+ I +V+N
Sbjct: 148 IVETVGVGQ--SEVD-IANMADTFLVVMIPGAGDDLQ-------GIKAGIMEIADIIVIN 197
Query: 143 KVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSD--SSDGSRDQGMVP 200
K DR A +L SALD GW ++ +G+
Sbjct: 198 KADRKGAEK-----AARELRSALDLLREVWREN--------GWRPPVVTTSALEGEGIDE 244
Query: 201 LLNLIVDH 208
L + I DH
Sbjct: 245 LWDAIEDH 252
>gnl|CDD|58085 cd03694, GTPBP_II, Domain II of the GP-1 family of GTPase. This
group includes proteins similar to GTPBP1 and GTPBP2.
GTPB1 is structurally, related to elongation factor 1
alpha, a key component of protein biosynthesis
machinery. Immunohistochemical analyses on mouse tissues
revealed that GTPBP1 is expressed in some neurons and
smooth muscle cells of various organs as well as
macrophages. Immunofluorescence analyses revealed that
GTPBP1 is localized exclusively in cytoplasm and shows a
diffuse granular network forming a gradient from the
nucleus to the periphery of the cells in smooth muscle
cell lines and macrophages. No significant difference
was observed in the immune response to protein antigen
between mutant mice and wild-type mice, suggesting
normal function of antigen-presenting cells of the
mutant mice. The absence of an eminent phenotype in
GTPBP1-deficient mice may be due to functional
compensation by GTPBP2, which is similar to GTPBP1 in
structure and tissue distribution..
Length = 87
Score = 28.2 bits (63), Expect = 7.4
Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 10/66 (15%)
Query: 230 PFLGRIVTGRIHSGTIKSNQNIK-ALSPDGALVEVGRVSKILAFRGI--DRQPIDEAHAG 286
P +G +V G + G I+ + DG+ V + I +R P+ AG
Sbjct: 12 PGVGTVVGGTVSKGVIRLGDTLLLGPDQDGSFRPV-------TVKSIHRNRSPVRVVRAG 64
Query: 287 DIVSIA 292
S+A
Sbjct: 65 QSASLA 70
>gnl|CDD|173942 cd08183, Fe-ADH2, Iron-containing alcohol dehydrogenases-like.
Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol
dehydrogenase catalyzes the reduction of acetaldehyde to
alcohol with NADP as cofactor. Its activity requires
iron ions. The protein structure represents a
dehydroquinate synthase-like fold and is a member of the
iron-activated alcohol dehydrogenase-like family. They
are distinct from other alcohol dehydrogenases which
contains different protein domain. Proteins of this
family have not been characterized. Their specific
function is unknown. They are mainly found in bacteria.
Length = 374
Score = 27.9 bits (63), Expect = 9.1
Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 370 AFFVSGRGELQLAVLIETMRREGFELAVSRPRVVIKKEGDSLLEPIEEVVIDVDEEHSGA 429
V+G L+ A LIE +R G E+ VV+ E +E ++ V +
Sbjct: 25 VLLVTGASSLRAAWLIEALRAAGIEVTH----VVVAGEPS--VELVDAAVAEARNAGCDV 78
Query: 430 VV 431
V+
Sbjct: 79 VI 80
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.318 0.138 0.390
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 7,411,369
Number of extensions: 404739
Number of successful extensions: 1197
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1061
Number of HSP's successfully gapped: 130
Length of query: 624
Length of database: 6,263,737
Length adjustment: 100
Effective length of query: 524
Effective length of database: 4,102,837
Effective search space: 2149886588
Effective search space used: 2149886588
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.8 bits)