RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780321|ref|YP_003064734.1| GTP-binding protein LepA
[Candidatus Liberibacter asiaticus str. psy62]
(606 letters)
>gnl|CDD|180078 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 1206 bits (3122), Expect = 0.0
Identities = 377/601 (62%), Positives = 482/601 (80%), Gaps = 2/601 (0%)
Query: 6 TPLSRIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQT 65
+ IRNFSI+AHIDHGKSTLADR I+ L+EREM +QVLD+MD+ERERGITIKAQ
Sbjct: 2 MDMKNIRNFSIIAHIDHGKSTLADRLIELTGTLSEREMKAQVLDSMDLERERGITIKAQA 61
Query: 66 VRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQ 125
VRLNY + D + Y LNLIDTPGHVDF+YEVSRSL+ACEG+LLVVDA+QGVEAQTLANVY
Sbjct: 62 VRLNYKAKDGETYILNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYL 121
Query: 126 AIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQ 185
A++N+ EII VLNK DLP+ADP+RVK++IE+ IGI DA+LVSAKTG GI +LE IV+
Sbjct: 122 ALENDLEIIPVLNKIDLPAADPERVKQEIEDVIGIDASDAVLVSAKTGIGIEEVLEAIVE 181
Query: 186 QLPSPTSPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVER 245
++P P +APLKAL+ DSWY++Y GV+VLVR+++G L KG I++M T +Y+V+
Sbjct: 182 RIPPPKGDP--DAPLKALIFDSWYDNYRGVVVLVRVVDGTLKKGDKIKMMSTGKEYEVDE 239
Query: 246 IGILTPKMIDIEALYPGEIGVMIASIKEVSHTRVGDTITDDSSPTTSALPGFKPIQPVVF 305
+G+ TPKM+ ++ L GE+G +IA IK+V RVGDTIT +P LPGFK ++P+VF
Sbjct: 240 VGVFTPKMVPVDELSAGEVGYIIAGIKDVRDARVGDTITLAKNPAEEPLPGFKEVKPMVF 299
Query: 306 CGLFPVDATQFENLRTAINKLRLNDASFSFELENSTALGFGFRCGFLGLLHLEIIQERLE 365
GL+PVD+ +E+LR A+ KL+LNDAS ++E E S ALGFGFRCGFLGLLH+EIIQERLE
Sbjct: 300 AGLYPVDSDDYEDLRDALEKLQLNDASLTYEPETSQALGFGFRCGFLGLLHMEIIQERLE 359
Query: 366 REFSLNLIGTSPSVVYELYMHDGSMQKLSNPIDMPEVTKIAELREPWIQVTIITPNEYLG 425
REF L+LI T+PSVVYE+ + DG + ++ NP +P+ KI E+ EP ++ TII P EY+G
Sbjct: 360 REFDLDLITTAPSVVYEVTLTDGEVIEVDNPSKLPDPGKIEEIEEPIVKATIIVPQEYVG 419
Query: 426 SILKLCQERRGIQIDMSHLDNRAMIVYELPLNEVIFDFYDRLKSVSKGYASFDYNVIDYR 485
++++LCQE+RG+Q DM +L NR + YELPL E++FDF+DRLKSVS+GYAS DY I YR
Sbjct: 420 AVMELCQEKRGVQKDMEYLGNRVELTYELPLAEIVFDFFDRLKSVSRGYASLDYEFIGYR 479
Query: 486 DSDLVKLTILVNNETIDALSILVHRSVSEKRGRGICEKLKNLIPQQMFQIAIQAAIGGRI 545
+SDLVKL IL+N E +DALS +VHR + +RGR + EKLK LIP+Q F+I IQAAIG +I
Sbjct: 480 ESDLVKLDILINGEPVDALSFIVHRDKAYERGRALVEKLKELIPRQQFEIPIQAAIGSKI 539
Query: 546 IARETVKARRKDVTAKCYGGDITRKRKLLEKQKEGKKRMRRFGRVDIPQSAFISILKTDN 605
IARET+KA RKDV AKCYGGDI+RKRKLLEKQKEGKKRM++ G V+IPQ AF+++LK D+
Sbjct: 540 IARETIKALRKDVLAKCYGGDISRKRKLLEKQKEGKKRMKQIGNVEIPQEAFLAVLKVDD 599
Query: 606 E 606
+
Sbjct: 600 D 600
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast) originated
within the bacterial LepA family. The function is
unknown.
Length = 595
Score = 985 bits (2548), Expect = 0.0
Identities = 371/598 (62%), Positives = 478/598 (79%), Gaps = 5/598 (0%)
Query: 9 SRIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRL 68
IRNFSI+AHIDHGKSTLADR +++ ++EREM QVLD+MD+ERERGITIKAQ VRL
Sbjct: 1 KNIRNFSIIAHIDHGKSTLADRLLEYTGAISEREMREQVLDSMDLERERGITIKAQAVRL 60
Query: 69 NYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAID 128
NY + D + Y LNLIDTPGHVDF+YEVSRSL+ACEG+LL+VDA QG+EAQTLANVY A++
Sbjct: 61 NYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQTLANVYLALE 120
Query: 129 NNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQLP 188
N+ EII V+NK DLPSADP+RVKK+IEE IG+ +A+L SAKTG GI +LE IV+++P
Sbjct: 121 NDLEIIPVINKIDLPSADPERVKKEIEEVIGLDASEAILASAKTGIGIEEILEAIVKRVP 180
Query: 189 SPT-SPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIG 247
P P+ APLKAL+ DS Y++Y GV+ LVR+ G + G IR M T +Y+V+ +G
Sbjct: 181 PPKGDPD---APLKALIFDSHYDNYRGVVALVRVFEGTIKPGDKIRFMSTGKEYEVDEVG 237
Query: 248 ILTPKMIDIEALYPGEIGVMIASIKEVSHTRVGDTITDDSSPTTSALPGFKPIQPVVFCG 307
+ TPK+ + L GE+G +IA IK+VS RVGDTIT +P LPGFK ++P+VF G
Sbjct: 238 VFTPKLTKTDELSAGEVGYIIAGIKDVSDVRVGDTITHVKNPAKEPLPGFKEVKPMVFAG 297
Query: 308 LFPVDATQFENLRTAINKLRLNDASFSFELENSTALGFGFRCGFLGLLHLEIIQERLERE 367
L+P+D +E+LR A+ KL+LNDAS ++E E+S ALGFGFRCGFLGLLH+EIIQERLERE
Sbjct: 298 LYPIDTEDYEDLRDALEKLKLNDASLTYEPESSPALGFGFRCGFLGLLHMEIIQERLERE 357
Query: 368 FSLNLIGTSPSVVYELYMHDGSMQKLSNPIDMPEVTKIAELREPWIQVTIITPNEYLGSI 427
F+L+LI T+PSV+Y +Y+ +G + ++ NP D+P+ KI + EP+++ TIITP EYLG I
Sbjct: 358 FNLDLITTAPSVIYRVYLTNGEVIEVDNPSDLPDPGKIEHVEEPYVKATIITPTEYLGPI 417
Query: 428 LKLCQERRGIQIDMSHLD-NRAMIVYELPLNEVIFDFYDRLKSVSKGYASFDYNVIDYRD 486
+ LCQE+RG+Q +M +LD NR ++YE+PL E+++DF+D+LKS+S+GYASFDY +I YR
Sbjct: 418 MTLCQEKRGVQTNMEYLDPNRVELIYEMPLAEIVYDFFDKLKSISRGYASFDYELIGYRP 477
Query: 487 SDLVKLTILVNNETIDALSILVHRSVSEKRGRGICEKLKNLIPQQMFQIAIQAAIGGRII 546
SDLVKL IL+N E +DALS +VHR + RGR ICEKLK LIP+Q F+I IQAAIGG+II
Sbjct: 478 SDLVKLDILINGEPVDALSFIVHRDKAYSRGREICEKLKELIPRQQFEIPIQAAIGGKII 537
Query: 547 ARETVKARRKDVTAKCYGGDITRKRKLLEKQKEGKKRMRRFGRVDIPQSAFISILKTD 604
ARET+KA RKDVTAKCYGGDITRKRKLLEKQKEGKKRM++ G+V++PQ AF+++LK D
Sbjct: 538 ARETIKALRKDVTAKCYGGDITRKRKLLEKQKEGKKRMKQIGKVEVPQEAFLAVLKVD 595
>gnl|CDD|148181 pfam06421, LepA_C, GTP-binding protein LepA C-terminus. This
family consists of the C-terminal region of several pro-
and eukaryotic GTP-binding LepA proteins.
Length = 108
Score = 200 bits (511), Expect = 8e-52
Identities = 70/108 (64%), Positives = 89/108 (82%)
Query: 496 VNNETIDALSILVHRSVSEKRGRGICEKLKNLIPQQMFQIAIQAAIGGRIIARETVKARR 555
+N + +DALS +VHR + RGR + EKLK LIP+Q F+I IQAAIG +IIARET+KA R
Sbjct: 1 INGKPVDALSFIVHRDKAYNRGRELVEKLKELIPRQQFEIPIQAAIGSKIIARETIKALR 60
Query: 556 KDVTAKCYGGDITRKRKLLEKQKEGKKRMRRFGRVDIPQSAFISILKT 603
K+V AKCYGGDI+RK+KLLEKQKEGKKRM++ G V+IPQ AF+++LK
Sbjct: 61 KNVLAKCYGGDISRKKKLLEKQKEGKKRMKQVGNVEIPQEAFLAVLKL 108
>gnl|CDD|162336 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions. Mutants
show altered regulation of some pathways, but the
precise function is unknown.
Length = 594
Score = 200 bits (511), Expect = 8e-52
Identities = 136/482 (28%), Positives = 230/482 (47%), Gaps = 79/482 (16%)
Query: 11 IRNFSIVAHIDHGKSTLADRFIQHCRGLTERE-MSSQVLDNMDIERERGITIKAQTVRLN 69
IRN +I+AH+DHGK+TL D ++ E ++ +V+D+ D+ERERGITI A+ +
Sbjct: 1 IRNIAIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDLERERGITILAKNTAIR 60
Query: 70 YTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDN 129
Y ++N++DTPGH DF EV R L +G LL+VDA++G QT + +A++
Sbjct: 61 Y-----NGTKINIVDTPGHADFGGEVERVLGMVDGVLLLVDASEGPMPQTRFVLKKALEL 115
Query: 130 NHEIITVLNKADLPSADPDRVKKQIEE---TIGISTEDAL-----LVSAKTG-------- 173
+ I V+NK D PSA PD V ++ + +G + ++ L S + G
Sbjct: 116 GLKPIVVINKIDRPSARPDEVVDEVFDLFAELG-ADDEQLDFPIVYASGRAGWASLDLDD 174
Query: 174 --EGIPLLLERIVQQLPSPTSPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQS 231
+ + L + IV+ +P+P + PL+ L+ + Y+ YLG + + R+ G + KGQ
Sbjct: 175 PSDNMAPLFDAIVRHVPAPKGDL--DEPLQMLVTNLDYDEYLGRIAIGRVHRGTVKKGQQ 232
Query: 232 IRLMGTNAKYQVERIGILTPKM----IDIEALYPGEIGVMIASIKEVSHTRVGDTITDDS 287
+ LM + + RI L ++I+ G+I V +A +++++ +G+TI D
Sbjct: 233 VALMKRDGTIENGRISKLLGFEGLERVEIDEAGAGDI-VAVAGLEDIN---IGETIADPE 288
Query: 288 SPTTSALPGFKPIQPVVFCGLFPVDATQF---ENLRTAINKL--RLNDASFSFELENSTA 342
P ALP + F V+ + E + + RL ELE + A
Sbjct: 289 VPE--ALP-TITVDEPTLSMTFSVNDSPLAGKEGKKVTSRHIRDRLMR-----ELETNVA 340
Query: 343 LGF-------GFRCGFLGLLHLEIIQERLERE-FSLNLIGTSPSVVYELYMHDGSMQKLS 394
L F G LHL I+ E + RE F L + P V+Y+
Sbjct: 341 LRVEDTESADKFEVSGRGELHLSILIETMRREGFELQV--GRPQVIYK------------ 386
Query: 395 NPIDMPEVTKIAELREPWIQVTIITPNEYLGSILKLCQERRGIQIDM-SHLDNRAMIVYE 453
+ EP ++TI P E++G++++ +R+G +DM + R + ++
Sbjct: 387 --------EIDGKKLEPIEELTIDVPEEHVGAVIEKLGKRKGEMVDMEPSGNGRTRLEFK 438
Query: 454 LP 455
+P
Sbjct: 439 IP 440
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 153 bits (387), Expect = 1e-37
Identities = 144/512 (28%), Positives = 236/512 (46%), Gaps = 82/512 (16%)
Query: 8 LSRIRNFSIVAHIDHGKSTLADRFIQHCRGLTER-EMSSQVLDNMDIERERGITIKAQTV 66
+ ++RN +I+AH+DHGK+TL D+ +Q R E +V+D+ D+E+ERGITI A+
Sbjct: 2 IEKLRNIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNT 61
Query: 67 RLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQA 126
+ + DY++N++DTPGH DF EV R +S + LLVVDA G QT +A
Sbjct: 62 AIKWN-----DYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKA 116
Query: 127 IDNNHEIITVLNKADLPSADPDRVKKQIEET-IGISTEDALL------VSAKTG------ 173
+ I V+NK D P A PD V Q+ + + + D L SA G
Sbjct: 117 FAYGLKPIVVINKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNGIAGLDH 176
Query: 174 ----EGIPLLLERIVQQLPSPTSPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKG 229
E + L + IV +P+P + P + + YNSY+GV+ + RI G++
Sbjct: 177 EDMAEDMTPLYQAIVDHVPAPDV--DLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPN 234
Query: 230 QSIRLMGTNAKYQVERIG-ILTP---KMIDIEALYPGEIGVMIASIKEVSHTRVGDTITD 285
Q + ++ + K + ++G +L + I+ + G+I V I + E++ + DT+ D
Sbjct: 235 QQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEAGDI-VAITGLGELN---ISDTVCD 290
Query: 286 DSSPTTSALPGFKPIQPVV----------FCGLFPVDATQFENLRTAINKLRLNDASFSF 335
+ ALP +P V FCG T + L +L N A
Sbjct: 291 TQN--VEALPALSVDEPTVSMFFCVNTSPFCGKEGKFVTSRQILDRLNKELVHNVALRVE 348
Query: 336 ELENSTALGFGFRCGFLGLLHLEIIQERLEREFSLNLIGTSPSVVYELYMHDGSMQKLSN 395
E E++ A FR G LHL ++ E + RE L + P V++ DG Q
Sbjct: 349 ETEDADA----FRVSGRGELHLSVLIENMRRE-GFELAVSRPKVIFREI--DGRKQ---- 397
Query: 396 PIDMPEVTKIAELREPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLD----NRAMIV 451
EP+ VT+ ++ GS+++ ER+G D+ +++ R +
Sbjct: 398 --------------EPYENVTLDVEEQHQGSVMQALGERKG---DLKNMNPDGKGRVRLD 440
Query: 452 YELPLNEVIFDFYDRLKSVSKG----YASFDY 479
Y +P +I F +++ G Y++F +
Sbjct: 441 YVIPSRGLI-GFRSEFMTMTSGTGLLYSTFSH 471
>gnl|CDD|183990 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 128 bits (325), Expect = 3e-30
Identities = 67/159 (42%), Positives = 90/159 (56%), Gaps = 12/159 (7%)
Query: 7 PLSRIRNFSIVAHIDHGKSTLADRFI-----QHCRGLTEREMSSQVLDNMDIERERGITI 61
PL +IRN I+AHID GK+TL +R + H G E + V D M E+ERGITI
Sbjct: 4 PLMQIRNIGILAHIDAGKTTLTERILFYTGKIHKMGEVED--GTTVTDWMPQEQERGITI 61
Query: 62 KAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLA 121
++ TS D ++++NLIDTPGH+DFT EV RSL +G+++V DA GV+ QT
Sbjct: 62 ES-----AATSCDWDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTGVQPQTET 116
Query: 122 NVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGI 160
QA + +NK D AD +V + IEE G
Sbjct: 117 VWRQADRYGIPRLIFINKMDRVGADLFKVLEDIEERFGK 155
Score = 86.5 bits (215), Expect = 2e-17
Identities = 69/236 (29%), Positives = 96/236 (40%), Gaps = 32/236 (13%)
Query: 166 LLVSAKTGEGIPLLLERIVQQLPSPT---SPEG-------------ANAPLKALLIDSWY 209
L SA GI LL+ +V LPSP P G PL AL+ Y
Sbjct: 256 LFGSALKNIGIEPLLDAVVDYLPSPLEVPPPRGSKDNGKPVKVDPDPEKPLLALVFKVQY 315
Query: 210 NSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGIL-TPKMIDIEALYPGEIGVMI 268
+ Y G + +R+ +G L G + + +V R+ L K +++ G+I +
Sbjct: 316 DPYAGKLTYLRVYSGTLRAGSQLYNGTGGKREKVGRLFRLQGNKREEVDRAKAGDIVA-V 374
Query: 269 ASIKEVSHTRVGDTITDDSSPTTSALPGFKPIQPVVFCGLFPVDATQFENLRTAINKLRL 328
A +KE GDT+ D + P L +PVV + P + L A+ KL
Sbjct: 375 AGLKE---LETGDTLHDSADPVL--LELLTFPEPVVSLAVEPERRGDEQKLAEALEKLVW 429
Query: 329 NDASFSFEL---ENSTALGFGFRCGFLGLLHLEIIQERLEREFSLNLIGTSPSVVY 381
D S E T L G +G LHLE+ ERL REF L + P V Y
Sbjct: 430 EDPSLRVEEDEETGQTIL-SG-----MGELHLEVALERLRREFKLEVNTGKPQVAY 479
Score = 49.6 bits (119), Expect = 2e-06
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 407 ELREPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDNRAMIVY-ELPLNEVIFDFYD 465
L EP +++ I P E++G +L +RRG + ++V E PL E+ F +
Sbjct: 596 VLLEPIMELEITVPTEHVGDVLGDLSQRRGRIEGTEPRGDGEVLVKAEAPLAEL-FGYAT 654
Query: 466 RLKSVSKGYASF 477
RL+S++KG SF
Sbjct: 655 RLRSMTKGRGSF 666
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G.
Length = 689
Score = 127 bits (321), Expect = 7e-30
Identities = 63/160 (39%), Positives = 92/160 (57%), Gaps = 12/160 (7%)
Query: 6 TPLSRIRNFSIVAHIDHGKSTLADRFIQHC---RGLTEREMSSQVLDNMDIERERGITIK 62
T L+R RN I AHID GK+T +R + + + E + +D M+ E+ERGITI
Sbjct: 5 TDLNRFRNIGISAHIDAGKTTTTERILFYTGRIHKIGEVHDGAATMDWMEQEKERGITIT 64
Query: 63 AQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLAN 122
+ T+ K +++N+IDTPGHVDFT EV RSL +G++ V+DA GV+ Q+
Sbjct: 65 SAA-----TTVFWKGHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSETV 119
Query: 123 VYQAIDNNHEI--ITVLNKADLPSADPDRVKKQIEETIGI 160
QA N +E+ I +NK D A+ RV QI++ +G
Sbjct: 120 WRQA--NRYEVPRIAFVNKMDKTGANFLRVVNQIKQRLGA 157
Score = 70.2 bits (172), Expect = 2e-12
Identities = 58/234 (24%), Positives = 97/234 (41%), Gaps = 33/234 (14%)
Query: 169 SAKTGEGIPLLLERIVQQLPSPTSPEGANA-----------------PLKALLIDSWYNS 211
SA +G+ LLL+ +V LPSPT P AL +
Sbjct: 260 SAFKNKGVQLLLDAVVDYLPSPTDVPAIKGIDPDTEKEIERKASDDEPFSALAFKVATDP 319
Query: 212 YLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERI-GILTPKMIDIEALYPGEIGVMIAS 270
++G + VR+ +G L G ++ N K +V R+ + +I+ + G+I I
Sbjct: 320 FVGQLTFVRVYSGVLKSGSYVKNSRKNKKERVGRLVKMHANNREEIKEVRAGDICAAIG- 378
Query: 271 IKEVSHTRVGDTITDDSSPTTSALPGFKPIQPVVFCGLFPVDATQFENLRTAINKLRLND 330
+K+ + GDT+ D L + +PV+ + P E + A+ KL D
Sbjct: 379 LKDTT---TGDTLCDPKIDVI--LERMEFPEPVISLAVEPKTKADQEKMGIALGKLAEED 433
Query: 331 ASF---SFELENSTALGFGFRCGFLGLLHLEIIQERLEREFSLNLIGTSPSVVY 381
+F + T + +G LHL+II +R++REF + +P V Y
Sbjct: 434 PTFRTFTDPETGQTIIAG------MGELHLDIIVDRMKREFKVEANVGAPQVAY 481
Score = 46.7 bits (111), Expect = 2e-05
Identities = 38/129 (29%), Positives = 59/129 (45%), Gaps = 16/129 (12%)
Query: 360 IQERLEREFSLNLIGTSPSVVYELYMHDGSMQ---------KLSNPIDMPEVTKIAE--L 408
+QE +E L G P V + + DGS KL+ + E K A L
Sbjct: 543 LQEAMESG---PLAGY-PVVDIKATLFDGSYHDVDSSEMAFKLAASLAFKEAGKKANPVL 598
Query: 409 REPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDNRAMIVYELPLNEVIFDFYDRLK 468
EP ++V + P EY+G ++ RRGI M N I E+PL+E +F + L+
Sbjct: 599 LEPIMKVEVEVPEEYMGDVMGDLSSRRGIIEGMEARGNVQKIKAEVPLSE-MFGYATDLR 657
Query: 469 SVSKGYASF 477
S ++G ++
Sbjct: 658 SFTQGRGTY 666
>gnl|CDD|181029 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 122 bits (309), Expect = 2e-28
Identities = 57/134 (42%), Positives = 86/134 (64%), Gaps = 4/134 (2%)
Query: 10 RIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQ--VLDNMDIERERGITIKAQTVR 67
+IRN I+AHIDHGK+TL+D + G+ E++ + LD + E+ RGITIKA V
Sbjct: 19 QIRNIGIIAHIDHGKTTLSDNLLAGA-GMISEELAGEQLALDFDEEEQARGITIKAANVS 77
Query: 68 LNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAI 127
+ + K+Y +NLIDTPGHVDF +V+R++ A +G+++VVDA +GV QT + QA+
Sbjct: 78 M-VHEYEGKEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQTETVLRQAL 136
Query: 128 DNNHEIITVLNKAD 141
+ + +NK D
Sbjct: 137 RERVKPVLFINKVD 150
Score = 49.5 bits (119), Expect = 3e-06
Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 408 LREPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDNRAMIVYELPLNEVIFDFYDRL 467
L EP +V I P +Y+G++ + Q RRG +DM + A+I E P+ E +F F +
Sbjct: 623 LLEPIQKVDINVPQDYMGAVTREIQGRRGKILDMEQEGDMAIIEAEAPVAE-MFGFAGEI 681
Query: 468 KSVSKGYASF 477
+S ++G A +
Sbjct: 682 RSATEGRALW 691
Score = 45.2 bits (108), Expect = 5e-05
Identities = 42/169 (24%), Positives = 81/169 (47%), Gaps = 21/169 (12%)
Query: 220 RIINGQLTKGQSIRLMGTNAKYQVERIGI-LTPKMIDIEALYPGEIGVMIASIKEVSHTR 278
R+ +G L KGQ + L+G K +V+++GI + P+ ++E + G I + +K+ R
Sbjct: 311 RVFSGTLRKGQEVYLVGAKKKNRVQQVGIYMGPEREEVEEIPAGNI-AAVTGLKDA---R 366
Query: 279 VGDTITDDSSPTTSALPGFKPIQ----PVVFCGLFPVDATQFENLRTAINKLRLNDASFS 334
G+T+ + F+ ++ PVV + + L + +L D +
Sbjct: 367 AGETVVSVED-----MTPFESLKHISEPVVTVAIEAKNPKDLPKLIEVLRQLAKEDPTLV 421
Query: 335 FELENSTA--LGFGFRCGFLGLLHLEIIQERLEREFSLNLIGTSPSVVY 381
++ T L G +G LHLE+I R++R++ + ++ + P VVY
Sbjct: 422 VKINEETGEHLLSG-----MGELHLEVITYRIKRDYGIEVVTSEPIVVY 465
>gnl|CDD|183712 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 118 bits (298), Expect = 4e-27
Identities = 61/162 (37%), Positives = 93/162 (57%), Gaps = 16/162 (9%)
Query: 6 TPLSRIRNFSIVAHIDHGKSTLADRFIQHCRGLTER-----EMSSQVLDNMDIERERGIT 60
PL + RN I+AHID GK+T +R + + G + + + ++ +D M+ E+ERGIT
Sbjct: 3 FPLEKTRNIGIMAHIDAGKTTTTERILYYT-GKSHKIGEVHDGAAT-MDWMEQEQERGIT 60
Query: 61 IKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTL 120
I + T+ K +++N+IDTPGHVDFT EV RSL +G++ V DA GVE Q+
Sbjct: 61 ITSAA-----TTCFWKGHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQSE 115
Query: 121 ANVYQAIDNNHEI--ITVLNKADLPSADPDRVKKQIEETIGI 160
QA + + + I +NK D AD R +QI++ +G
Sbjct: 116 TVWRQA--DKYGVPRIVFVNKMDRIGADFFRSVEQIKDRLGA 155
Score = 53.3 bits (129), Expect = 2e-07
Identities = 62/231 (26%), Positives = 103/231 (44%), Gaps = 39/231 (16%)
Query: 175 GIPLLLERIVQQLPSP--------TSPEGA---------NAPLKALLIDSWYNSYLGVMV 217
G+ LL+ +V LPSP +P+ + P AL + ++G +
Sbjct: 265 GVQPLLDAVVDYLPSPLDVPAIKGINPDTEEEIERPASDDEPFAALAFKIMTDPFVGRLT 324
Query: 218 LVRIINGQLTKGQSIRLMGTNAKYQVERIG-ILTPKM-----IDIEALYPGEIGVMIASI 271
R+ +G L G + K ERIG +L +M +I+ +Y G+I + +
Sbjct: 325 FFRVYSGVLESGSYVLNTTKGKK---ERIGRLL--QMHANKREEIKEVYAGDIAAAVG-L 378
Query: 272 KEVSHTRVGDTITDDSSPTTSALPGFKPIQPVVFCGLFPVDATQFENLRTAINKLRLNDA 331
K+ T GDT+ D+ +P L + +PV+ + P + + A+ KL D
Sbjct: 379 KD---TTTGDTLCDEKAPII--LESMEFPEPVISLAVEPKTKADQDKMGLALQKLAEEDP 433
Query: 332 SFSFELENSTALGFGFRCGFLGLLHLEIIQERLEREFSLNL-IGTSPSVVY 381
+F E + T G G +G LHL+II +R++REF + +G P V Y
Sbjct: 434 TFRVETDEET--GQTIISG-MGELHLDIIVDRMKREFKVEANVGA-PQVAY 480
Score = 42.5 bits (101), Expect = 3e-04
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 408 LREPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDNRAMIVYELPLNEVIFDFYDRL 467
+ EP ++V ++TP EY+G ++ RRG M ++ +PL+E +F + L
Sbjct: 598 ILEPIMKVEVVTPEEYMGDVIGDLNRRRGQIQGMEARGGAQIVKAFVPLSE-MFGYATDL 656
Query: 468 KSVSKGYASF 477
+S ++G A+F
Sbjct: 657 RSATQGRATF 666
>gnl|CDD|183713 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 117 bits (297), Expect = 7e-27
Identities = 59/150 (39%), Positives = 80/150 (53%), Gaps = 14/150 (9%)
Query: 17 VAHIDHGKSTLADRFIQHCRGLTER----EMSSQVLDNMDIERERGITIKAQTVRLNYTS 72
V H GK+TL + I G R E + +D M ERERGI+I T+
Sbjct: 1 VGHSGAGKTTLTEA-ILFYTGAIHRIGEVEDGTTTMDFMPEERERGISI-----TSAATT 54
Query: 73 TDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHE 132
+ K +++NLIDTPGHVDFT EV R+L +G+++VV A GVE QT QA +
Sbjct: 55 CEWKGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTETVWRQA--EKYG 112
Query: 133 I--ITVLNKADLPSADPDRVKKQIEETIGI 160
+ I +NK D AD RV Q++E +G
Sbjct: 113 VPRIIFVNKMDRAGADFFRVLAQLQEKLGA 142
Score = 100 bits (252), Expect = 1e-21
Identities = 64/238 (26%), Positives = 103/238 (43%), Gaps = 37/238 (15%)
Query: 166 LLVSAKTGEGIPLLLERIVQQLPSPTSPEG---------------ANAPLKALLIDSWYN 210
SA +G+ LL+ +V LPSP + PL AL+ + +
Sbjct: 240 FCGSALKNKGVQRLLDAVVDYLPSPLEVPPVDGEDGEEGAELAPDPDGPLVALVFKTMDD 299
Query: 211 SYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIG-ILTP---KMIDIEALYPGEIGV 266
++G + LVR+ +G L KG ++ GT K ER+G + + +++ G+I V
Sbjct: 300 PFVGKLSLVRVYSGTLKKGDTLYNSGTGKK---ERVGRLYRMHGKQREEVDEAVAGDI-V 355
Query: 267 MIASIKEVSHTRVGDTITDDSSPTTSALPGFKPIQPVVFCGLFPVDATQFENLRTAINKL 326
+A +K GDT+ D P L + +PV+ + P D E L A+ KL
Sbjct: 356 AVAKLK---DAATGDTLCDKGDPIL--LEPMEFPEPVISLAIEPKDKGDEEKLSEALGKL 410
Query: 327 RLNDASFSFELENSTA---LGFGFRCGFLGLLHLEIIQERLEREFSLNLIGTSPSVVY 381
D + E + T L +G LHL++ ERL+RE+ + + P V Y
Sbjct: 411 AEEDPTLRVERDEETGQTIL----SG--MGELHLDVALERLKREYGVEVETGPPQVPY 462
Score = 46.3 bits (111), Expect = 2e-05
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 410 EPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDNRAMIVYELPLNEVIFDFYDRLKS 469
EP ++V + P E++G ++ RRG + M ++ E+PL E +F + L+S
Sbjct: 582 EPIMKVEVSVPEEFVGDVIGDLSSRRGRILGMESRGGGDVVRAEVPLAE-MFGYATDLRS 640
Query: 470 VSKGYASF 477
+++G SF
Sbjct: 641 LTQGRGSF 648
>gnl|CDD|178789 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 116 bits (294), Expect = 2e-26
Identities = 67/161 (41%), Positives = 94/161 (58%), Gaps = 16/161 (9%)
Query: 6 TPLSRIRNFSIVAHIDHGKSTLADRF-----IQHCRGLTEREMSSQVLDNMDIERERGIT 60
TPL R RN I+AHID GK+T +R + H G E + +D M+ E+ERGIT
Sbjct: 5 TPLERYRNIGIMAHIDAGKTTTTERILFYTGVNHKIG--EVHDGAATMDWMEQEQERGIT 62
Query: 61 IKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTL 120
I + T+ KD+++N+IDTPGHVDFT EV RSL +G++ V DA GVE Q+
Sbjct: 63 ITSAA-----TTCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVGGVEPQSE 117
Query: 121 ANVYQAIDNNHEI--ITVLNKADLPSADPDRVKKQIEETIG 159
QA + +++ I +NK D AD RV +QI++ +G
Sbjct: 118 TVWRQA--DKYKVPRIAFVNKMDRTGADFYRVVEQIKDRLG 156
Score = 50.1 bits (121), Expect = 2e-06
Identities = 65/234 (27%), Positives = 103/234 (44%), Gaps = 58/234 (24%)
Query: 169 SAKTGEGIPLLLERIVQQLPSP--------TSPEGA----------NAPLKALLIDSWYN 210
SA +G+ LL+ +V LPSP P+G + P AL +
Sbjct: 261 SAFKNKGVQPLLDAVVDYLPSPLDVPAIKGILPDGEEEEVERKASDDEPFSALAFKIMTD 320
Query: 211 SYLGVMVLVRIINGQLTKGQSIRLMGTNA-KYQVERIG-ILTPKM-----IDIEALYPGE 263
++G + R+ +G L G + N+ K + ERIG IL +M +I+ + G+
Sbjct: 321 PFVGKLTFFRVYSGVLESGSYV----LNSTKGKKERIGRIL--QMHANKREEIKEVRAGD 374
Query: 264 IGVMIASIKEVSHTRVGDTITDDSSPTTSAL-----PGFKPIQPVVFCGLFP-VDATQFE 317
I + +K+ T GDT+ D+ +P L P +PV+ + P A Q E
Sbjct: 375 IAAAVG-LKD---TTTGDTLCDEKNPII--LESMEFP-----EPVISVAVEPKTKADQ-E 422
Query: 318 NLRTAINKLRLNDASFSFELE---NSTALGFGFRCGFLGLLHLEIIQERLEREF 368
+ A+ KL D SF + T + G +G LHL+II +R++REF
Sbjct: 423 KMGIALQKLAEEDPSFRVSTDEETGQTIIA-G-----MGELHLDIIVDRMKREF 470
Score = 35.5 bits (83), Expect = 0.040
Identities = 25/71 (35%), Positives = 44/71 (61%), Gaps = 3/71 (4%)
Query: 408 LREPWIQVTIITPNEYLGSILKLCQERRGIQID-MSHLDNRAMIVYELPLNEVIFDFYDR 466
L EP ++V ++TP EY+G ++ RRG QI+ M +I E+PL+E +F +
Sbjct: 601 LLEPIMKVEVVTPEEYMGDVIGDLNSRRG-QIEGMEDRGGAKVIRAEVPLSE-MFGYATD 658
Query: 467 LKSVSKGYASF 477
L+S+++G A++
Sbjct: 659 LRSMTQGRATY 669
>gnl|CDD|185604 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 112 bits (281), Expect = 3e-25
Identities = 53/138 (38%), Positives = 81/138 (58%), Gaps = 6/138 (4%)
Query: 10 RIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREM-SSQVLDNMDIERERGITIKAQTVRL 68
+IRN S++AH+DHGKSTL D + ++ + ++ D E+ERGITIK+ + L
Sbjct: 18 QIRNMSVIAHVDHGKSTLTDSLVCKAGIISSKNAGDARFTDTRADEQERGITIKSTGISL 77
Query: 69 NYTST-----DAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANV 123
Y D + + +NLID+PGHVDF+ EV+ +L +G+L+VVD +GV QT +
Sbjct: 78 YYEHDLEDGDDKQPFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVEGVCVQTETVL 137
Query: 124 YQAIDNNHEIITVLNKAD 141
QA+ + +NK D
Sbjct: 138 RQALQERIRPVLFINKVD 155
Score = 32.7 bits (75), Expect = 0.29
Identities = 27/115 (23%), Positives = 48/115 (41%), Gaps = 17/115 (14%)
Query: 380 VYELYMHDGSMQKLSNPIDMP---------EVTKIAELREPWIQVTIITPNEYLGSILKL 430
+ ++ +H ++ + + I +P E+T L EP V I P + +G I +
Sbjct: 682 ILDVTLHADAIHRGAGQI-IPTARRVFYACELTASPRLLEPMFLVDITAPEDAMGGIYSV 740
Query: 431 CQERRGIQIDMSHLDNRAMIVYE--LPLNEVIFDFYDRLKSVSKGYA----SFDY 479
RRG+ I + + LP+ E F F L++ + G A FD+
Sbjct: 741 LNRRRGVVIGEEQRPGTPLSNIKAYLPVAES-FGFTAALRAATSGQAFPQCVFDH 794
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. This model
represents archaeal elongation factor 2, a protein more
similar to eukaryotic EF-2 than to bacterial EF-G, both
in sequence similarity and in sharing with eukaryotes
the property of having a diphthamide (modified His)
residue at a conserved position. The diphthamide can be
ADP-ribosylated by diphtheria toxin in the presence of
NAD.
Length = 720
Score = 110 bits (277), Expect = 1e-24
Identities = 58/134 (43%), Positives = 85/134 (63%), Gaps = 4/134 (2%)
Query: 10 RIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQ--VLDNMDIERERGITIKAQTVR 67
IRN IVAHIDHGK+TL+D + G+ E++ Q LD + E+ERGITI A V
Sbjct: 18 FIRNIGIVAHIDHGKTTLSDNLLAGA-GMISEELAGQQLYLDFDEQEQERGITINAANVS 76
Query: 68 LNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAI 127
+ + + +Y +NLIDTPGHVDF +V+R++ A +G+++VV A +GV QT + QA+
Sbjct: 77 MVHE-YEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCAVEGVMPQTETVLRQAL 135
Query: 128 DNNHEIITVLNKAD 141
N + + +NK D
Sbjct: 136 KENVKPVLFINKVD 149
Score = 51.8 bits (124), Expect = 5e-07
Identities = 49/232 (21%), Positives = 102/232 (43%), Gaps = 39/232 (16%)
Query: 178 LLLERIVQQLPSP----------------TSPEGA-------NAPLKALLIDSWYNSYLG 214
++L+ +++ LPSP S G PL ++ + + G
Sbjct: 245 VVLDMVIRHLPSPIEAQKYRIPVIWKGDLNSEVGKAMLNCDPKGPLALMITKIVVDKHAG 304
Query: 215 VMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGI-LTPKMIDIEALYPGEIGVMIASIKE 273
+ + R+ +G + G + ++ AK +++++G+ + P+ ++++ + G I V + +K+
Sbjct: 305 EVAVGRLYSGTIRPGMEVYIVDRKAKARIQQVGVYMGPERVEVDEIPAGNI-VAVIGLKD 363
Query: 274 VSHTRVGDTITDDSSPTTSALPGFKPI----QPVVFCGLFPVDATQFENLRTAINKLRLN 329
G+TI T + F+ I +PVV + + L + ++
Sbjct: 364 AV---AGETICT----TVENITPFESIKHISEPVVTVAIEAKNTKDLPKLIEVLRQVAKE 416
Query: 330 DASFSFELENSTALGFGFRCGFLGLLHLEIIQERLEREFSLNLIGTSPSVVY 381
D + E+ T G G +G LHLEII E++ ++ L++ + P VVY
Sbjct: 417 DPTVHVEINEET--GEHLISG-MGELHLEIIVEKIREDYGLDVETSPPIVVY 465
Score = 38.3 bits (89), Expect = 0.006
Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 408 LREPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDNRAMIVYELPLNEVIFDFYDRL 467
L EP+ +V I P + +G+ + Q RRG ++M + I+ + P+ E +F F +
Sbjct: 621 LLEPYQKVFINVPQDMMGAATREIQNRRGQILEMKQEGDMVTIIAKAPVAE-MFGFAGAI 679
Query: 468 KSVSKGYA 475
+ + G
Sbjct: 680 RGATSGRC 687
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 108 bits (272), Expect = 4e-24
Identities = 61/154 (39%), Positives = 85/154 (55%), Gaps = 18/154 (11%)
Query: 1 MQKKPTPLSRIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQV--LDNMDIERERG 58
M KK IRN S++AH+DHGKSTL D + G+ +E++ V D E ERG
Sbjct: 13 MDKK----HNIRNMSVIAHVDHGKSTLTDSLVAAA-GIIAQEVAGDVRMTDTRADEAERG 67
Query: 59 ITIKAQTVRLNYTSTDA-----------KDYQLNLIDTPGHVDFTYEVSRSLSACEGSLL 107
ITIK+ + L Y TD +Y +NLID+PGHVDF+ EV+ +L +G+L+
Sbjct: 68 ITIKSTGISLYYEMTDESLKDFKGERDGNEYLINLIDSPGHVDFSSEVTAALRITDGALV 127
Query: 108 VVDATQGVEAQTLANVYQAIDNNHEIITVLNKAD 141
VVD +GV QT + QA+ + +NK D
Sbjct: 128 VVDCIEGVCVQTETVLRQALGERIRPVLTVNKMD 161
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation
releasing factor, RF-3 (prfC) was originally described
as stop codon-independent, in contrast to peptide chain
release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and
RF-2 are closely related to each other, while RF-3 is
similar to elongation factors EF-Tu and EF-G; RF-1 is
active at UAA and UAG and RF-2 is active at UAA and UGA.
More recently, RF-3 was shown to be active primarily at
UGA stop codons in E. coli. All bacteria and organelles
have RF-1. The Mycoplasmas and organelles, which
translate UGA as Trp rather than as a stop codon, lack
RF-2. RF-3, in contrast, seems to be rare among bacteria
and is found so far only in Escherichia coli and some
other gamma subdivision Proteobacteria, in Synechocystis
PCC6803, and in Staphylococcus aureus.
Length = 527
Score = 96.5 bits (240), Expect = 2e-20
Identities = 49/164 (29%), Positives = 87/164 (53%), Gaps = 16/164 (9%)
Query: 8 LSRIRNFSIVAHIDHGKSTLADRFIQHCRGLTE-------REMSSQVLDNMDIERERGIT 60
+ + R F+I++H D GK+T+ ++ + + + D M++E++RGI+
Sbjct: 8 VDKRRTFAIISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGIS 67
Query: 61 IKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQT- 119
I ++ Y +D +NL+DTPGH DF+ + R+L+A + L+V+DA +GVE +T
Sbjct: 68 ITTSVMQFPY-----RDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTR 122
Query: 120 -LANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGIST 162
L V + D I T +NK D DP + ++E + I+
Sbjct: 123 KLMEVTRLRDT--PIFTFMNKLDRDIRDPLELLDEVENELKINC 164
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes.
Length = 581
Score = 94.9 bits (236), Expect = 6e-20
Identities = 64/242 (26%), Positives = 104/242 (42%), Gaps = 28/242 (11%)
Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTS 72
+ H+DHGK+TL + LT D + E++RG+TI L +
Sbjct: 2 IIATAGHVDHGKTTLL-------KALTGIAA-----DRLPEEKKRGMTID-----LGFAY 44
Query: 73 TDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQA-IDNNH 131
DY+L ID PGH F + +LLVVDA +GV QT ++ +
Sbjct: 45 FPLPDYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIP 104
Query: 132 EIITVLNKAD-LPSADPDRVKKQI----EETIGISTEDALLVSAKTGEGIPLLLERIVQQ 186
I V+ KAD + + R + + I + SAKTG+GI L + + +
Sbjct: 105 HTIVVITKADRVNEEEIKRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKEL-KN 163
Query: 187 LPSPTSPEGANAPLKALLIDSWYNSYLGVMVLVR--IINGQLTKGQSIRLMGTNAKYQVE 244
L + PL+ + ID + G +V +G++ G ++RL+ N + +V+
Sbjct: 164 LLESLDIKRIQKPLR-MAIDRAF-KVKGAGTVVTGTAFSGEVKVGDNLRLLPINHEVRVK 221
Query: 245 RI 246
I
Sbjct: 222 AI 223
>gnl|CDD|183433 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 91.5 bits (228), Expect = 5e-19
Identities = 76/288 (26%), Positives = 123/288 (42%), Gaps = 58/288 (20%)
Query: 1 MQKKPTPLSRIRNFSIVAHIDHGKSTLADRFI-------QHCRGLTEREMSSQ------- 46
++KP N +++ H+DHGKSTL R + +H E +
Sbjct: 1 AKEKP-----HLNLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKF 55
Query: 47 --VLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEG 104
V+D + ERERG+TI L + + Y ++D PGH DF + S +
Sbjct: 56 AWVMDRLKEERERGVTID-----LAHKKFETDKYYFTIVDCPGHRDFVKNMITGASQADA 110
Query: 105 SLLVVDA--TQGVEAQTLANVYQA----IDNNHEIITVLNKADLPSADPDR---VKKQIE 155
++LVV A GV QT +V+ A I+ ++I +NK D + D R VK+++
Sbjct: 111 AVLVVAADDAGGVMPQTREHVFLARTLGIN---QLIVAINKMDAVNYDEKRYEEVKEEVS 167
Query: 156 E---TIGISTEDALL--VSAKTGEGI------------PLLLERIVQQLPSPTSPEGANA 198
+ +G +D VSA G+ + P LLE + L P P +
Sbjct: 168 KLLKMVGYKPDDIPFIPVSAFEGDNVVKKSENMPWYNGPTLLEAL-DNLKPPEKP--TDK 224
Query: 199 PLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERI 246
PL+ + D + S +G + + R+ G L G + M +V+ I
Sbjct: 225 PLRIPIQDVYSISGVGTVPVGRVETGVLKVGDKVVFMPAGVVGEVKSI 272
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 89.0 bits (222), Expect = 3e-18
Identities = 59/174 (33%), Positives = 94/174 (54%), Gaps = 38/174 (21%)
Query: 9 SRIRNFSIVAHIDHGKSTLADRF------IQHC-----RGLTEREMSSQVLDNMDIERER 57
++ R F+I++H D GK+TL ++ IQ R + R +S D M++E++R
Sbjct: 8 AKRRTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRK-SGRHATS---DWMEMEKQR 63
Query: 58 GITIKAQTVRLNYTST----DAKDYQLNLIDTPGHVDF---TYEVSRSLSACEGSLLVVD 110
GI++ TS+ +D +NL+DTPGH DF TY R+L+A + +L+V+D
Sbjct: 64 GISV---------TSSVMQFPYRDCLINLLDTPGHEDFSEDTY---RTLTAVDSALMVID 111
Query: 111 ATQGVEAQT--LANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGIST 162
A +GVE QT L V + + I T +NK D +P + +IEE +GI+
Sbjct: 112 AAKGVEPQTRKLMEVCRL--RDTPIFTFINKLDRDGREPLELLDEIEEVLGIAC 163
>gnl|CDD|161900 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU.
Length = 587
Score = 88.3 bits (219), Expect = 6e-18
Identities = 70/226 (30%), Positives = 105/226 (46%), Gaps = 30/226 (13%)
Query: 15 SIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGIT--IKAQTVRLNYTS 72
+I+ H+DHGK++L D I+ + + + E GIT I A V
Sbjct: 91 TIMGHVDHGKTSLLD-SIRKTK-VAQGEAG-------------GITQHIGAYHVENE--- 132
Query: 73 TDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHE 132
D K + +DTPGH FT +R + +LVV A GV QT+ + A N
Sbjct: 133 -DGK--MITFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVP 189
Query: 133 IITVLNKADLPSADPDRVKKQIEETIGISTED------ALLVSAKTGEGIPLLLERIVQQ 186
II +NK D P A+PDRVK+++ E G+ ED + VSA TG+GI LL+ I+ Q
Sbjct: 190 IIVAINKIDKPEANPDRVKQELSE-YGLVPEDWGGDTIFVPVSALTGDGIDELLDMILLQ 248
Query: 187 LPSPTSPEGANAPLKALLIDSWYNSYLGVMVLVRIINGQLTKGQSI 232
N ++I++ + G + V + +G L G +
Sbjct: 249 SEVEELKANPNGQASGVVIEAQLDKGRGPVATVLVQSGTLRVGDIV 294
>gnl|CDD|129574 TIGR00483, EF-1_alpha, translation elongation factor EF-1 alpha.
This model represents the counterpart of bacterial EF-Tu
for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1
alpha). The trusted cutoff is set fairly high so that
incomplete sequences will score between suggested and
trusted cutoff levels.
Length = 426
Score = 77.6 bits (191), Expect = 8e-15
Identities = 75/324 (23%), Positives = 131/324 (40%), Gaps = 57/324 (17%)
Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQ----------------VLDNMDIERE 56
N + + H+DHGKST + C + E+ + V+D + ERE
Sbjct: 9 NVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVMDRLKEERE 68
Query: 57 RGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVV---DATQ 113
RG+TI + + + Y++ ++D PGH DF + S + ++LVV D
Sbjct: 69 RGVTID-----VAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEF 123
Query: 114 GVEAQTLANVYQAID-NNHEIITVLNKADLPSADPDRVKKQIEETIGI--------STED 164
V+ QT + + A +++I +NK D + D + + +E + T
Sbjct: 124 EVQPQTREHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTVP 183
Query: 165 ALLVSAKTGEGI------------PLLLERIVQQLPSPTSPEGANAPLKALLIDSWYNSY 212
+ +SA G+ + LLE + L P P + PL+ + D + +
Sbjct: 184 FIPISAWNGDNVIKKSENTPWYKGKTLLEAL-DALEPPEKP--TDKPLRIPIQDVYSITG 240
Query: 213 LGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTPKMIDIEALYPGE-IG--VMIA 269
+G + + R+ G L G + +V+ I + + IE PG+ IG V
Sbjct: 241 VGTVPVGRVETGVLKPGDKVVFEPAGVSGEVKSIEMHHEQ---IEQAEPGDNIGFNVRGV 297
Query: 270 SIKEVSHTRVGDTITDDSSPTTSA 293
S K++ R GD +P A
Sbjct: 298 SKKDI---RRGDVCGHPDNPPKVA 318
>gnl|CDD|180006 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 787
Score = 73.4 bits (181), Expect = 1e-13
Identities = 64/179 (35%), Positives = 85/179 (47%), Gaps = 43/179 (24%)
Query: 19 HIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGIT--IKAQTVRLNYTSTDAK 76
H+DHGK++L D I+ + E GIT I A V N
Sbjct: 298 HVDHGKTSLLDA-IRKTN-VAAGEAG-------------GITQHIGAYQVETN------- 335
Query: 77 DYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNH----- 131
++ +DTPGH FT +R + +LVV A GV QT+ +AI NH
Sbjct: 336 GGKITFLDTPGHEAFTAMRARGAQVTDIVVLVVAADDGVMPQTI----EAI--NHAKAAG 389
Query: 132 -EIITVLNKADLPSADPDRVKKQIEETIGISTED------ALLVSAKTGEGIPLLLERI 183
II +NK D P A+PDRVK+++ E G+ E+ + VSAKTGEGI LLE I
Sbjct: 390 VPIIVAINKIDKPGANPDRVKQELSE-YGLVPEEWGGDTIFVPVSAKTGEGIDELLEAI 447
>gnl|CDD|161778 TIGR00231, small_GTP, small GTP-binding protein domain. This model
recognizes a large number of small GTP-binding proteins
and related domains in larger proteins. Note that the
alpha chains of heterotrimeric G proteins are larger
proteins in which the NKXD motif is separated from the
GxxxxGK[ST] motif (P-loop) by a long insert and are not
easily detected by this model.
Length = 161
Score = 67.8 bits (166), Expect = 8e-12
Identities = 44/176 (25%), Positives = 66/176 (37%), Gaps = 44/176 (25%)
Query: 16 IVAHIDHGKSTLADRFIQHCRGLTEREMSSQ----VLDNMDIERERGITIKAQTVRLNYT 71
IV + GKSTL +R + + + + E G T K
Sbjct: 6 IVGDPNVGKSTLLNRLLG-----NKFITEYKPGTTRNYVTTVIEEDGKTYK--------- 51
Query: 72 STDAKDYQLNLIDTPGHVDF-------TYEVSRSLSACEGSLLVVDATQGVEAQTLANVY 124
NL+DT G D+ V SL + +LV+D + +E QT
Sbjct: 52 --------FNLLDTAGQEDYRAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQT----K 99
Query: 125 QAI---DNNHEIITVLNKADLPSADPD-RVKKQIEETIGISTEDALLVSAKTGEGI 176
+ I ++N II V NK DL A V + + E + +SA+TG+ I
Sbjct: 100 EIIHHAESNVPIILVGNKIDLRDAKLKTHVAFLFAKL---NGEPIIPLSAETGKNI 152
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 67.1 bits (164), Expect = 1e-11
Identities = 40/123 (32%), Positives = 55/123 (44%), Gaps = 31/123 (25%)
Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTER----------EMSSQ------VLDNMDIERE 56
N ++ H+D GKST I C G+ +R EM VLD + ERE
Sbjct: 9 NLVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERE 68
Query: 57 RGITI-----KAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDA 111
RGITI K +T + +T +ID PGH DF + S + ++LVV +
Sbjct: 69 RGITIDIALWKFETPKYYFT----------IIDAPGHRDFIKNMITGTSQADVAILVVAS 118
Query: 112 TQG 114
T G
Sbjct: 119 TAG 121
>gnl|CDD|131089 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
Homologous to this E.coli activation pathway are nodPQH
gene products found among members of the Rhizobiaceae
family. These gene products have been shown to exhibit
ATP sulfurase and APS kinase activity, yet are involved
in Nod factor sulfation, and sulfation of other
macromolecules. With members of the Rhizobiaceae family,
nodQ often appears as a fusion of cysN (large subunit of
ATP sulfurase) and cysC (APS kinase).
Length = 406
Score = 61.2 bits (149), Expect = 8e-10
Identities = 52/183 (28%), Positives = 86/183 (46%), Gaps = 32/183 (17%)
Query: 20 IDHGKSTLADRFIQHCRGLTEREMSSQ------------------VLDNMDIERERGITI 61
+D GKSTL R + + + E ++++ ++D + ERE+GITI
Sbjct: 9 VDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQGGEIDLALLVDGLQAEREQGITI 68
Query: 62 KAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLA 121
V Y STD + + + DTPGH +T ++ S + ++L+VDA +GV QT
Sbjct: 69 D---VAYRYFSTDKRKFIV--ADTPGHEQYTRNMATGASTADLAVLLVDARKGVLEQTRR 123
Query: 122 NVYQA--IDNNHEIITVLNKADLPSADP---DRVKK---QIEETIGISTEDALLVSAKTG 173
+ Y A + H ++ V NK DL D + +KK E +G + +SA G
Sbjct: 124 HSYIASLLGIRHVVLAV-NKMDLVDYDEEVFENIKKDYLAFAEQLGFRDVTFIPLSALKG 182
Query: 174 EGI 176
+ +
Sbjct: 183 DNV 185
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 59.3 bits (143), Expect = 3e-09
Identities = 78/325 (24%), Positives = 130/325 (40%), Gaps = 60/325 (18%)
Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTER----------EMSSQ------VLDNMDIERE 56
N ++ H+D GKST I G+ +R EM+ + VLD + ERE
Sbjct: 9 NIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFEKEAAEMNKRSFKYAWVLDKLKAERE 68
Query: 57 RGITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQG-- 114
RGITI + T Y +ID PGH DF + S + ++L++D+T G
Sbjct: 69 RGITIDIALWKFETTK-----YYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGGF 123
Query: 115 -----VEAQTLANVYQAID-NNHEIITVLNKADLPS-----ADPDRVKKQIE---ETIGI 160
+ QT + A ++I NK D + A D + K++ + +G
Sbjct: 124 EAGISKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGY 183
Query: 161 STEDALLVSAKTGEGI--------------PLLLERIVQQLPSPTSPEGANAPLKALLID 206
+ + V EG P LLE + Q+ P P ++ PL+ L D
Sbjct: 184 NPDKIPFVPISGFEGDNMIERSTNLDWYKGPTLLEAL-DQINEPKRP--SDKPLRLPLQD 240
Query: 207 SWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTPKMIDIEALYPGE--- 263
+ +G + + R+ G + G + T +V+ + + + EAL PG+
Sbjct: 241 VYKIGGIGTVPVGRVETGVIKPGMVVTFGPTGLTTEVKSVEMHHESL--QEAL-PGDNVG 297
Query: 264 IGVMIASIKEVSHTRVGDTITDDSS 288
V ++K++ V DD +
Sbjct: 298 FNVKNVAVKDLKRGYVASNSKDDPA 322
>gnl|CDD|178858 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 58.1 bits (142), Expect = 7e-09
Identities = 49/178 (27%), Positives = 76/178 (42%), Gaps = 36/178 (20%)
Query: 23 GKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNL 82
GKS+L + + ER + S DI G T + + L
Sbjct: 185 GKSSLINALLG-----EERVIVS------DIA---GTTRDSIDTPFER-----DGQKYTL 225
Query: 83 IDTPG-----HVDFT---YEVSRSLSACEGS---LLVVDATQGVEAQ--TLANVYQAIDN 129
IDT G V Y V R+L A E + LLV+DAT+G+ Q +A A++
Sbjct: 226 IDTAGIRRKGKVTEGVEKYSVIRTLKAIERADVVLLVIDATEGITEQDLRIAG--LALEA 283
Query: 130 NHEIITVLNKADLPSADP-DRVKKQIEETIG-ISTEDALLVSAKTGEGIPLLLERIVQ 185
++ V+NK DL + KK++ + + + +SA TG+G+ LLE I +
Sbjct: 284 GRALVIVVNKWDLVDEKTMEEFKKELRRRLPFLDYAPIVFISALTGQGVDKLLEAIDE 341
Score = 40.0 bits (95), Expect = 0.002
Identities = 35/136 (25%), Positives = 59/136 (43%), Gaps = 19/136 (13%)
Query: 77 DYQLNLIDTPGHV----DFTYEVSR-SLSACEGS---LLVVDATQGVEAQ--TLAN-VYQ 125
+ LIDT G F ++ + A E + L VVD G+ +A + +
Sbjct: 48 GREFILIDTGGIEPDDDGFEKQIREQAELAIEEADVILFVVDGRAGLTPADEEIAKILRK 107
Query: 126 AIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQ 185
+ N +I V+NK D P + D E + + +SA+ G GI LL+ I++
Sbjct: 108 S---NKPVILVVNKVDGPDEEAD-----AYEFYSLGLGEPYPISAEHGRGIGDLLDAILE 159
Query: 186 QLPSPTSPEGANAPLK 201
+LP + + P+K
Sbjct: 160 ELPEEEEEDEEDEPIK 175
>gnl|CDD|178854 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 57.8 bits (141), Expect = 7e-09
Identities = 37/143 (25%), Positives = 57/143 (39%), Gaps = 23/143 (16%)
Query: 62 KAQTVRLN----YTSTDAKDYQLNLIDTPG-H----------VDFTYEVSRSLSACEGSL 106
K QT R T D Q+ +DTPG H SL + L
Sbjct: 36 KPQTTRHRIRGIVTE---DDAQIIFVDTPGIHKPKRALNRAMNKA---AWSSLKDVDLVL 89
Query: 107 LVVDATQGVEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVKKQIEE-TIGISTEDA 165
VVDA + + + + +I VLNK DL D + + +EE + + +
Sbjct: 90 FVVDADEKIGPGDEFILEKLKKVKTPVILVLNKIDL-VKDKEELLPLLEELSELMDFAEI 148
Query: 166 LLVSAKTGEGIPLLLERIVQQLP 188
+ +SA G+ + LL+ I + LP
Sbjct: 149 VPISALKGDNVDELLDVIAKYLP 171
>gnl|CDD|163343 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability.
Length = 429
Score = 57.5 bits (140), Expect = 1e-08
Identities = 48/180 (26%), Positives = 77/180 (42%), Gaps = 39/180 (21%)
Query: 23 GKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDYQLNL 82
GKSTL + + ER + S DI G T + + + L
Sbjct: 184 GKSTLVNALLG-----EERVIVS------DIA---GTTRDSIDIPFER-----NGKKYLL 224
Query: 83 IDTPG---------HVDFTYEVSRSLSACEGS---LLVVDATQGVEAQ--TLANVYQAID 128
IDT G V+ Y V R+L A E + LLV+DAT+G+ Q +A ++
Sbjct: 225 IDTAGIRRKGKVTEGVEK-YSVLRTLKAIERADVVLLVLDATEGITEQDLRIAG--LILE 281
Query: 129 NNHEIITVLNKADL--PSADPDRVKKQIEETIG-ISTEDALLVSAKTGEGIPLLLERIVQ 185
++ V+NK DL + KK++ + + + +SA TG+G+ LL+ I +
Sbjct: 282 AGKALVIVVNKWDLVKDEKTREEFKKELRRKLPFLDFAPIVFISALTGQGVDKLLDAIDE 341
Score = 37.0 bits (87), Expect = 0.012
Identities = 32/131 (24%), Positives = 53/131 (40%), Gaps = 21/131 (16%)
Query: 76 KDYQLNLIDTPGHVD----FTYEVSR-SLSACEGS---LLVVDATQGVEA--QTLANVYQ 125
+ LIDT G + ++ + A E + L VVD +G+ + +A +
Sbjct: 45 GGREFILIDTGGIEEDDDGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEEIAKWLR 104
Query: 126 AIDNNHEIITVLNKADLPSADPDRVKKQIEE--TIGISTEDALLVSAKTGEGIPLLLERI 183
+I V NK D D E ++G + + +SA+ G GI LL+ I
Sbjct: 105 KSGKP--VILVANKIDGKKEDAV-----AAEFYSLGF--GEPIPISAEHGRGIGDLLDAI 155
Query: 184 VQQLPSPTSPE 194
++ LP E
Sbjct: 156 LELLPEEEEEE 166
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This alignment
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation.
Length = 394
Score = 57.5 bits (139), Expect = 1e-08
Identities = 42/133 (31%), Positives = 61/133 (45%), Gaps = 9/133 (6%)
Query: 13 NFSIVAHIDHGKSTL--ADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNY 70
N + H+DHGK+TL A + G Q+ DN E+ RGITI V
Sbjct: 14 NIGTIGHVDHGKTTLTAAITTVLAKEGGAAARAYDQI-DNAPEEKARGITINTAHVEY-- 70
Query: 71 TSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAID-N 129
T+ + Y +D PGH D+ + + +G++LVV AT G QT ++ A
Sbjct: 71 -ETENRHYA--HVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMPQTREHILLARQVG 127
Query: 130 NHEIITVLNKADL 142
I+ LNK D+
Sbjct: 128 VPYIVVFLNKCDM 140
>gnl|CDD|179996 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 56.3 bits (137), Expect = 2e-08
Identities = 36/118 (30%), Positives = 54/118 (45%), Gaps = 27/118 (22%)
Query: 80 LNLIDTPG------HVDFTYE---VSRSLSACEGS---LLVVDATQGVEAQTLANVYQAI 127
L LIDT G V E + RS A E + LLV+DA++ + + + + +
Sbjct: 265 LRLIDTAGIRETDDEV----EKIGIERSREAIEEADLVLLVLDASEPLTEEDDE-ILEEL 319
Query: 128 DNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQ 185
+ +I VLNKADL + + + + +SAKTGEGI L E I +
Sbjct: 320 -KDKPVIVVLNKADLTGE---------IDLEEENGKPVIRISAKTGEGIDELREAIKE 367
>gnl|CDD|183709 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 55.7 bits (135), Expect = 3e-08
Identities = 45/140 (32%), Positives = 70/140 (50%), Gaps = 12/140 (8%)
Query: 13 NFSIVAHIDHGKSTL--ADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNY 70
N + H+DHGK+TL A + RGL + + + D E+ERGITI T + Y
Sbjct: 14 NIGTIGHVDHGKTTLTAAITKVLAERGLNQAKDYDSI-DAAPEEKERGITI--NTAHVEY 70
Query: 71 TSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQA--ID 128
T+ + Y +D PGH D+ + + +G++LVV AT G QT ++ A +
Sbjct: 71 -ETEKRHYA--HVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVG 127
Query: 129 NNHEIITVLNKADLPSADPD 148
+ ++ LNK DL D +
Sbjct: 128 VPY-LVVFLNKVDLVD-DEE 145
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 55.1 bits (133), Expect = 5e-08
Identities = 58/188 (30%), Positives = 82/188 (43%), Gaps = 38/188 (20%)
Query: 19 HIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAKDY 78
H+DHGK+TL +Q G+ D + E++RG+TI L Y D
Sbjct: 8 HVDHGKTTL----LQAITGVNA--------DRLPEEKKRGMTID-----LGYAYWPQPDG 50
Query: 79 Q-LNLIDTPGHVDFTYEVSRSLSACEG---SLLVVDATQGVEAQTLANVYQAI---DNNH 131
+ L ID PGH F +S L+ G +LLVV GV AQT ++ AI N
Sbjct: 51 RVLGFIDVPGHEKF---LSNMLAGVGGIDHALLVVACDDGVMAQTREHL--AILQLTGNP 105
Query: 132 EIITVLNKADLPSADPDR---VKKQIEETI---GISTEDALLVSAKTGEGIPLLLERIVQ 185
+ L KAD D R V++Q++ + G + + +A G GI L E +
Sbjct: 106 MLTVALTKADR--VDEARIAEVRRQVKAVLREYGFAEAKLFVTAATEGRGIDALREHL-L 162
Query: 186 QLPSPTSP 193
QLP
Sbjct: 163 QLPEREHA 170
>gnl|CDD|179704 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 54.4 bits (132), Expect = 7e-08
Identities = 66/228 (28%), Positives = 90/228 (39%), Gaps = 88/228 (38%)
Query: 16 IVA---HIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERG-IT--IKAQTVRLN 69
IV H+DHGK+TL D+ RG + V +E G IT I A V ++
Sbjct: 8 IVVVLGHVDHGKTTLLDKI----RG-------TAV-----AAKEAGGITQHIGATEVPID 51
Query: 70 YTSTDAKDYQLNL-----------IDTPGHVDFTYEVSRSLSACEGSL-----LVVDATQ 113
A + L IDTPGH FT +L G+L LVVD +
Sbjct: 52 VIEKIAGPLKKPLPIKLKIPGLLFIDTPGHEAFT-----NLRKRGGALADIAILVVDINE 106
Query: 114 GVEAQTLANVYQAID----NNHEIITVLNKADL-----PSAD----------PDRVKKQI 154
G + QT +AI+ + NK D + D RV++++
Sbjct: 107 GFQPQT----IEAINILKRRKTPFVVAANKIDRIPGWKSTEDAPFLESIEKQSQRVQQEL 162
Query: 155 EETI----------GISTE------D-----ALL-VSAKTGEGIPLLL 180
EE + G S + D A++ VSAKTGEGIP LL
Sbjct: 163 EEKLYELIGQLSELGFSADRFDRVKDFTKTVAIVPVSAKTGEGIPDLL 210
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 53.7 bits (130), Expect = 2e-07
Identities = 45/140 (32%), Positives = 64/140 (45%), Gaps = 23/140 (16%)
Query: 13 NFSIVAHIDHGKSTL--ADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNY 70
N + H+DHGK+TL A + +G E + Q+ DN E+ RGITI T + Y
Sbjct: 14 NVGTIGHVDHGKTTLTAAITKVLAKKGGGEAKAYDQI-DNAPEEKARGITI--NTSHVEY 70
Query: 71 TSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQT-----LA---N 122
T + Y +D PGH D+ + + +G++LVV A G QT LA
Sbjct: 71 -ETANRHYA--HVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVG 127
Query: 123 VYQAIDNNHEIITVLNKADL 142
V I+ LNK D+
Sbjct: 128 V-------PYIVVFLNKCDM 140
>gnl|CDD|163393 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. eIF-2 functions in the early steps of protein
synthesis by forming a ternary complex with GTP and
initiator tRNA.
Length = 406
Score = 53.1 bits (128), Expect = 2e-07
Identities = 51/215 (23%), Positives = 86/215 (40%), Gaps = 43/215 (20%)
Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIK---AQTV--- 66
N +V H+DHGK+TL + ++ D E +RGI+I+ A
Sbjct: 6 NIGMVGHVDHGKTTLT------------KALTGVWTDTHSEELKRGISIRLGYADAEIYK 53
Query: 67 ------RLNYTSTDAKDY---------QLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDA 111
YT+ +++ +D PGH + + +G+LLV+ A
Sbjct: 54 CPECDGPECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALLVIAA 113
Query: 112 TQGV-EAQTLANVYQA-IDNNHEIITVLNKADLPSADPDRVKK---QIEETI-GISTEDA 165
+ + QT ++ I I+ V NK DL ++ + +I+E + G E+A
Sbjct: 114 NEPCPQPQTKEHLMALEIIGIKNIVIVQNKIDL--VSKEKALENYEEIKEFVKGTVAENA 171
Query: 166 LL--VSAKTGEGIPLLLERIVQQLPSPTSPEGANA 198
+ VSA I LLE I + +P+P
Sbjct: 172 PIIPVSALHNANIDALLEAIEKFIPTPERDLDKPP 206
>gnl|CDD|178823 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 53.3 bits (129), Expect = 2e-07
Identities = 44/135 (32%), Positives = 63/135 (46%), Gaps = 25/135 (18%)
Query: 19 HIDHGKSTL--ADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNYTSTDAK 76
H+DHGK+TL A + +G E + Q+ D E+ RGITI T + Y T+ +
Sbjct: 20 HVDHGKTTLTAAITKVLAKKGGAEAKAYDQI-DKAPEEKARGITI--NTAHVEY-ETEKR 75
Query: 77 DYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQT-----LA---NV-YQAI 127
Y +D PGH D+ + + +G++LVV A G QT LA V Y
Sbjct: 76 HYA--HVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPY--- 130
Query: 128 DNNHEIITVLNKADL 142
I+ LNK D+
Sbjct: 131 -----IVVFLNKCDM 140
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end;
this model does not correctly align the sequences from
Methanococcus jannaschii and Pyrococcus horikoshii in
this region.
Length = 590
Score = 51.0 bits (122), Expect = 9e-07
Identities = 67/291 (23%), Positives = 116/291 (39%), Gaps = 62/291 (21%)
Query: 15 SIVAHIDHGKSTLADRFIQHCR-------GLTEREMSSQVLDNMD-IERERGITIKAQTV 66
S++ H+DHGK+TL D+ I+ G+T+ ++++ MD IE G +K +
Sbjct: 8 SVLGHVDHGKTTLLDK-IRGSAVAKREAGGITQHIGATEI--PMDVIEGICGDLLKKFKI 64
Query: 67 RLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTL------ 120
RL L IDTPGH FT R + + ++L+VD +G + QT
Sbjct: 65 RLKIPG-------LLFIDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQEALNIL 117
Query: 121 ----------ANVYQAID--NNHE---IITVLNKADLPSADPDRVKKQIEETIGI----- 160
AN I +HE + +K ++ + ++ +
Sbjct: 118 RMYKTPFVVAANKIDRIPGWRSHEGRPFMESFSKQEIQVQ--QNLDTKVYNLVIKLHEEG 175
Query: 161 -------------STEDALLVSAKTGEGIPLLLERIV---QQLPSPTSPEGANAPLKALL 204
T + +SA TGEGIP LL + QQ P + +
Sbjct: 176 FEAERFDRVTDFTKTVAIIPISAITGEGIPELLTMLAGLAQQYLEEQLKLEEEGPARGTI 235
Query: 205 IDSWYNSYLGVMVLVRIINGQLTKGQSIRLMGTNAKYQVERIGILTPKMID 255
++ + LG+ + I +G L KG +I + G++ +L P+ ++
Sbjct: 236 LEVKEETGLGMTIDAVIYDGILRKGDTIAMAGSDDVIVTRVRALLKPRPLE 286
>gnl|CDD|163162 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like).
Length = 351
Score = 50.9 bits (123), Expect = 9e-07
Identities = 30/84 (35%), Positives = 42/84 (50%), Gaps = 11/84 (13%)
Query: 108 VVDAT-QGVEAQ--TLANVYQAIDNNH-EIITVLNKADLPSADPDRVKKQIEETIGISTE 163
VVDA+ E Q + V + + + V NK DL D R+ E +
Sbjct: 275 VVDASDPDREEQIEAVEKVLEELGAEDIPQLLVYNKIDL--LDEPRI-----ERLEEGYP 327
Query: 164 DALLVSAKTGEGIPLLLERIVQQL 187
+A+ VSAKTGEG+ LLLE I ++L
Sbjct: 328 EAVFVSAKTGEGLDLLLEAIAERL 351
>gnl|CDD|179943 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 49.1 bits (118), Expect = 3e-06
Identities = 37/119 (31%), Positives = 61/119 (51%), Gaps = 25/119 (21%)
Query: 20 IDHGKSTLADRFIQHCRGLTEREMSS------------------QVLDNMDIERERGITI 61
+D GKSTL R + + + E +++S ++D + ERE+GITI
Sbjct: 36 VDDGKSTLIGRLLHDTKQIYEDQLASLHNDSKRHGTQGEKLDLALLVDGLQAEREQGITI 95
Query: 62 KAQTVRLNYTSTDAKDYQLNLI-DTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQT 119
V Y ST+ + + +I DTPGH +T ++ S C+ ++L++DA +GV QT
Sbjct: 96 D---VAYRYFSTEKRKF---IIADTPGHEQYTRNMATGASTCDLAILLIDARKGVLDQT 148
>gnl|CDD|129071 smart00838, EFG_C, Elongation factor G C-terminus. This domain
includes the carboxyl terminal regions of Elongation
factor G, elongation factor 2 and some tetracycline
resistance proteins and adopt a ferredoxin-like fold.
Length = 85
Score = 49.0 bits (118), Expect = 4e-06
Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 408 LREPWIQVTIITPNEYLGSILKLCQERRGIQIDMSHLDNRAMIVYELPLNEVIFDFYDRL 467
L EP ++V + P EY+G ++ RRG M +I ++PL+E +F + L
Sbjct: 1 LLEPIMKVEVTVPEEYMGDVIGDLNSRRGKIEGMEQRGGAQVIKAKVPLSE-MFGYATDL 59
Query: 468 KSVSKGYASF 477
+S ++G A++
Sbjct: 60 RSATQGRATW 69
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 48.0 bits (115), Expect = 7e-06
Identities = 35/120 (29%), Positives = 58/120 (48%), Gaps = 27/120 (22%)
Query: 20 IDHGKSTLADRFIQHCRGLTE----------REMSSQ--------VLDNMDIERERGITI 61
+D GKSTL R + + + E +++ +Q ++D + ERE+GITI
Sbjct: 33 VDDGKSTLIGRLLYDSKMIFEDQLAALERDSKKVGTQGDEIDLALLVDGLAAEREQGITI 92
Query: 62 KAQTVRLNYTSTDAKDYQLNLI--DTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQT 119
V Y +T + + I DTPGH +T + S + ++++VDA +GV QT
Sbjct: 93 D---VAYRYFATPKRKF----IVADTPGHEQYTRNMVTGASTADLAIILVDARKGVLTQT 145
>gnl|CDD|178672 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 47.7 bits (113), Expect = 8e-06
Identities = 38/133 (28%), Positives = 58/133 (43%), Gaps = 11/133 (8%)
Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDI---ERERGITIKAQTVRLN 69
N + H+DHGK+TL + + + D +D ER RGITI TV
Sbjct: 83 NIGTIGHVDHGKTTLTAALTMALASMGGS--APKKYDEIDAAPEERARGITINTATVEY- 139
Query: 70 YTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAID- 128
T+ + Y +D PGH D+ + + +G++LVV G QT ++ A
Sbjct: 140 --ETENRHYAH--VDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQV 195
Query: 129 NNHEIITVLNKAD 141
++ LNK D
Sbjct: 196 GVPNMVVFLNKQD 208
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 47.1 bits (112), Expect = 1e-05
Identities = 34/111 (30%), Positives = 48/111 (43%), Gaps = 12/111 (10%)
Query: 13 NFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQV----LDNMDIERERGITIKAQTVRL 68
N + H+DHGK+TL + L E + V +D E+ RGITI V
Sbjct: 63 NVGTIGHVDHGKTTLTAAIT---KVLAEEGKAKAVAFDEIDKAPEEKARGITIATAHVEY 119
Query: 69 NYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQT 119
T + Y +D PGH D+ + + +G +LVV A G QT
Sbjct: 120 ---ETAKRHYAH--VDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQT 165
>gnl|CDD|179703 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 46.0 bits (110), Expect = 3e-05
Identities = 60/231 (25%), Positives = 89/231 (38%), Gaps = 70/231 (30%)
Query: 1 MQKKPTPLSRIRNFSIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGIT 60
M +K P N +V H+DHGK+TL + ++ D E +RGIT
Sbjct: 2 MWEKVQPEV---NIGMVGHVDHGKTTLV------------QALTGVWTDRHSEELKRGIT 46
Query: 61 IKAQTVRLNYTSTD-AKDYQLN-------------------------LIDTPGHVDFTYE 94
I RL Y K +D PGH E
Sbjct: 47 I-----RLGYADATIRKCPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGH-----E 96
Query: 95 V--SRSLSAC---EGSLLVVDATQGV-EAQT---LANVYQAIDNNHEIITVLNKADLPSA 145
+ LS +G++LV+ A + + QT L I + I+ V NK DL
Sbjct: 97 TLMATMLSGAALMDGAILVIAANEPCPQPQTKEHLM-ALDIIGIKN-IVIVQNKIDL--V 152
Query: 146 DPDRVKK---QIEETI-GISTEDALL--VSAKTGEGIPLLLERIVQQLPSP 190
+R + QI+E + G E+A + VSA I L+E I +++P+P
Sbjct: 153 SKERALENYEQIKEFVKGTVAENAPIIPVSALHKVNIDALIEAIEEEIPTP 203
>gnl|CDD|183417 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 42.8 bits (102), Expect = 2e-04
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 134 ITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQLPSPTSP 193
I VLNK DL + +R +K+ + L+SA TGEG+ LL + + L
Sbjct: 275 ILVLNKIDLLDEEEER-EKRAALELAALGGPVFLISAVTGEGLDELLRALWELLEEARRE 333
Query: 194 E 194
E
Sbjct: 334 E 334
>gnl|CDD|179035 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 42.4 bits (101), Expect = 3e-04
Identities = 14/68 (20%), Positives = 31/68 (45%), Gaps = 2/68 (2%)
Query: 122 NVYQAIDNNH-EIITVLNKAD-LPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLL 179
+ + + ++ VL KAD L + + K++ + + ++ +L S+ +GI L
Sbjct: 126 QMIEWLKEYGIPVLIVLTKADKLKKGERKKQLKKVRKALKFGDDEVILFSSLKKQGIDEL 185
Query: 180 LERIVQQL 187
I + L
Sbjct: 186 RAAIAKWL 193
>gnl|CDD|162989 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal.
Length = 329
Score = 40.9 bits (97), Expect = 0.001
Identities = 23/92 (25%), Positives = 39/92 (42%), Gaps = 13/92 (14%)
Query: 106 LLVVDATQGVEAQTLANVYQAIDN----------NHEIITVLNKADLPSADPDRVKKQIE 155
L ++D + + + Y+ I N I VLNK DL D + + + ++
Sbjct: 240 LHLIDISPLDGRDPIED-YEIIRNELKKYSPELAEKPRIVVLNKIDLL--DEEELAELLK 296
Query: 156 ETIGISTEDALLVSAKTGEGIPLLLERIVQQL 187
E + +SA TGEG+ LL + + L
Sbjct: 297 ELKKALGKPVFPISALTGEGLDELLYALAELL 328
>gnl|CDD|184332 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 40.6 bits (96), Expect = 0.001
Identities = 23/59 (38%), Positives = 35/59 (59%), Gaps = 5/59 (8%)
Query: 130 NHEIITVLNKAD-LP-SADPDRVKKQIEET---IGISTEDALLVSAKTGEGIPLLLERI 183
N+ ++ V NKAD LP S ++VK + + +G+ D +L+SA+ G GI LLE I
Sbjct: 96 NNPVLLVGNKADLLPKSVKKNKVKNWLRQEAKELGLRPVDVVLISAQKGHGIDELLEAI 154
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 38.8 bits (91), Expect = 0.004
Identities = 35/128 (27%), Positives = 55/128 (42%), Gaps = 24/128 (18%)
Query: 68 LNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSL------SACEGSL--LVVDATQ--GVEA 117
L Y T A ++ N+IDTPG Y +R +A + + LV DAT+ V
Sbjct: 26 LKYKKTQAIEFSDNMIDTPGE----YLENRRFYSALIVTAADADVIALVQDATEPWSVFP 81
Query: 118 QTLANVYQAIDNNHEIITVLNKADLPSADPD--RVKKQIEETIGISTEDALLVSAKTGEG 175
A+++ N +I ++ K DL + + V++ + G VSA T EG
Sbjct: 82 PGFASMF-----NKPVIGIITKIDLAKDEANIEMVEEWLNNA-GAEK--IFEVSAVTNEG 133
Query: 176 IPLLLERI 183
I L +
Sbjct: 134 IDELFAYL 141
>gnl|CDD|183415 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 37.8 bits (89), Expect = 0.009
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 10/60 (16%)
Query: 132 EIITVLNKADLPSADP--DRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQLPS 189
+I+ V NK DLP A+ + K+++ + +SA TG+G+ LL + + L
Sbjct: 277 QIV-VANKMDLPEAEENLEEFKEKLGPKV-------FPISALTGQGLDELLYAVAELLEE 328
>gnl|CDD|184848 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 36.8 bits (85), Expect = 0.017
Identities = 56/223 (25%), Positives = 85/223 (38%), Gaps = 54/223 (24%)
Query: 80 LNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANV-------------YQA 126
L IDTPGH FT R S + ++LVVD +G + QT+ +
Sbjct: 528 LLFIDTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAINILRQYKTPFVVAANK 587
Query: 127 ID--------------------NNH----------EIITVLNKADLPSADPDRVKKQIEE 156
ID + H E+I L + + DRV +
Sbjct: 588 IDLIPGWNISEDEPFLLNFNEQDQHALTELEIKLYELIGKLYELGFDADRFDRV-QDFTR 646
Query: 157 TIGISTEDALLVSAKTGEGIPLLLERIV---QQLPSPTSPEGANAPLKALLIDSWYNSYL 213
T+ I + VSAKTGEGIP LL + Q+ K +++ L
Sbjct: 647 TVAI-----VPVSAKTGEGIPELLMMVAGLAQKYLEERLKLNVEGYAKGTILEVKEEKGL 701
Query: 214 GVMVLVRIINGQLTKGQSIRLMGTNAKYQVERI-GILTPKMID 255
G + I +G L +G +I + G + V ++ +L PK +D
Sbjct: 702 GTTIDAIIYDGTLRRGDTIVVGGPD-DVIVTKVRALLKPKPLD 743
>gnl|CDD|181925 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 34.8 bits (80), Expect = 0.070
Identities = 27/112 (24%), Positives = 47/112 (41%), Gaps = 20/112 (17%)
Query: 99 LSACEGSLLVVDATQGVEAQTLANVYQAIDNNHEIITVLNKADL-PSADPDRVKKQIEET 157
+ E +L + DA+Q + Q L + A+D ++ V NK DL R+++ +
Sbjct: 530 IERSELALFLFDASQPISEQDLKVMSMAVDAGRALVLVFNKWDLMDEFRRQRLERLWKTE 589
Query: 158 IG-ISTEDALLVSAKTGEGIPLLLERIVQQLPSPTSPEGANAPLKALLIDSW 208
++ + +SAKTG +L A A +AL +SW
Sbjct: 590 FDRVTWARRVNLSAKTG--------WHTNRL--------APAMQEAL--ESW 623
>gnl|CDD|161878 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum.
Length = 591
Score = 34.3 bits (79), Expect = 0.085
Identities = 34/138 (24%), Positives = 59/138 (42%), Gaps = 19/138 (13%)
Query: 58 GITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFT-----YEVSRSLSACEGSLL---VV 109
G+T++ + +L + + + ++D PG T EV+R E L VV
Sbjct: 26 GVTVEKKEGKLGF-----QGEDIEIVDLPGIYSLTTFSLEEEVARDYLLNEKPDLVVNVV 80
Query: 110 DATQGVEAQTLANVYQAIDNNHEIITVLNKADLPSADPDRVK-KQIEETIGISTEDALLV 168
DA+ +E L Q ++ +I LN D R+ +++EE +G+ +
Sbjct: 81 DASN-LERN-LYLTLQLLELGIPMILALNLVDEAEKKGIRIDEEKLEERLGVPV---VPT 135
Query: 169 SAKTGEGIPLLLERIVQQ 186
SA G GI L + I +
Sbjct: 136 SATEGRGIERLKDAIRKA 153
>gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 34.4 bits (80), Expect = 0.086
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 129 NNHEIITVLNKADLPSADPD-RVKKQIEETIGISTEDALLVSAKTGEGIPLLLERI 183
N + I VLNK DL + R + IG D L +SAK GEG+ L +
Sbjct: 110 NGIKPIIVLNKIDLLDDLEEARELLALYRAIGY---DVLELSAKEGEGLDELKPLL 162
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 33.2 bits (76), Expect = 0.19
Identities = 33/94 (35%), Positives = 50/94 (53%), Gaps = 17/94 (18%)
Query: 103 EGSLL--VVDAT-----QGVEAQTLANVYQAIDNNHEIIT--VLNKADLPSADPDRVKKQ 153
+ +LL VVDA + +EA + V + ID HEI T V+NK D+ R+ +
Sbjct: 276 QATLLLHVVDAADVRVQENIEA--VNTVLEEIDA-HEIPTLLVMNKIDMLDDFEPRIDRD 332
Query: 154 IEETIGISTEDALLVSAKTGEGIPLLLERIVQQL 187
EE I + +SA+TG GIPLL + + ++L
Sbjct: 333 -EENKPI----RVWLSAQTGAGIPLLFQALTERL 361
>gnl|CDD|183406 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 33.3 bits (77), Expect = 0.20
Identities = 30/103 (29%), Positives = 39/103 (37%), Gaps = 42/103 (40%)
Query: 80 LNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEAQTLANVYQAIDNNHEIITVLNK 139
LN+ID R L ACE T G+E + VLNK
Sbjct: 136 LNIID------------RYLVACE--------TLGIEP----------------LIVLNK 159
Query: 140 ADL-PSADPDRVKKQIE--ETIGISTEDALLVSAKTGEGIPLL 179
DL V +Q++ IG L+VS+ TGEG+ L
Sbjct: 160 IDLLDDEGRAFVNEQLDIYRNIGYRV---LMVSSHTGEGLEEL 199
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme ethanolamine
ammonia lyase. The function of this gene is unknown,
although the presence of an N-terminal GxxGxGK motif
implies a GTP-binding site.
Length = 142
Score = 33.2 bits (76), Expect = 0.22
Identities = 25/95 (26%), Positives = 40/95 (42%), Gaps = 9/95 (9%)
Query: 68 LNYTSTDAKDYQLNLIDTPGHV--DFTYEVSRSLSACEGSL--LVVDATQGVEAQTLANV 123
+ Y T A +Y IDTPG + + ++A + + LV AT
Sbjct: 25 ILYKKTQAVEYNDGAIDTPGEYVENRRLYSALIVTAADADVIALVQSATD--PESRFPPG 82
Query: 124 YQAIDNNHEIITVLNKADLPSADPD--RVKKQIEE 156
+ +I +I ++ K DL AD D R K+ +E
Sbjct: 83 FASI-FVKPVIGLVTKIDLAEADVDIERAKELLET 116
>gnl|CDD|163346 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes.
Length = 179
Score = 32.4 bits (75), Expect = 0.30
Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 126 AIDNNHEIITVLNKAD-LPSADPDRVKKQIEETIGISTEDA--LLVSAKTGEGIP 177
+ ++ VL KAD L ++ ++ K+I++ + +D L S+ GI
Sbjct: 125 LRERGIPVLIVLTKADKLKKSELNKQLKKIKKALKKDADDPSVQLFSSLKKTGID 179
>gnl|CDD|163345 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members.
Length = 276
Score = 32.5 bits (75), Expect = 0.32
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 7/53 (13%)
Query: 133 IITVLNKADLPSADPDRVKKQIE--ETIGISTEDALLVSAKTGEGIPLLLERI 183
+ VLNKADL ADP K+ ++ E GI AL ++AK G+G+ +++
Sbjct: 51 RLIVLNKADL--ADPAVTKQWLKYFEEKGI---KALAINAKKGKGVKKIIKAA 98
>gnl|CDD|184315 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 32.5 bits (75), Expect = 0.36
Identities = 33/129 (25%), Positives = 57/129 (44%), Gaps = 25/129 (19%)
Query: 82 LIDTPGHVD-FTY-----EVSRSLSACEGSLLV--VDATQGVEAQTLANV------YQAI 127
L+DTPG ++ F + ++ LS S++V +DA V A+T ++ ++
Sbjct: 101 LVDTPGQMELFAFRESGRKLVERLSGSSKSVVVFLIDA---VLAKTPSDFVSLLLLALSV 157
Query: 128 DNNHEI--ITVLNKADL-PSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIV 184
+ I VLNKADL + +R+ K +E+ L K +G LL ++
Sbjct: 158 QLRLGLPQIPVLNKADLLSEEELERILKWLED---PEYLLEELKLEKGLQG--LLSLELL 212
Query: 185 QQLPSPTSP 193
+ L P
Sbjct: 213 RALEETGLP 221
>gnl|CDD|182626 PRK10660, tilS, tRNA(Ile)-lysidine synthetase; Provisional.
Length = 436
Score = 31.5 bits (72), Expect = 0.64
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 17 VAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIE-RERGITIKAQTVR 67
H+ HG S AD +++HC + ++ V++ + ++ R GI A+ R
Sbjct: 49 AIHVHHGLSPNADSWVKHCEQVCQQWQVPLVVERVQLDQRGLGIEAAARQAR 100
>gnl|CDD|161885 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer.
Length = 442
Score = 31.3 bits (71), Expect = 0.65
Identities = 27/125 (21%), Positives = 47/125 (37%), Gaps = 19/125 (15%)
Query: 76 KDYQLNLIDTPG---HVDFTYE--VSRSLSACEGS---LLVVDATQGVEAQTLANVYQAI 127
+ L+DT G H DF + +S A + + + V+DA+Q + +
Sbjct: 249 NGILIKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIYVLDASQPLTKDDFLIIDLNK 308
Query: 128 DNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKT---GEGIPLLLERIV 184
+ I VLNK DL +E + ++ +SAK + LL ++I
Sbjct: 309 -SKKPFILVLNKIDL-------KINSLEFFVSSKVLNSSNLSAKQLKIKALVDLLTQKIN 360
Query: 185 QQLPS 189
Sbjct: 361 AFYSK 365
>gnl|CDD|183416 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 31.4 bits (72), Expect = 0.67
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 136 VLNKADLPSADP-DRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERIVQQL 187
V NK DL + + K I E +G L+SA +G G+ L ++ +
Sbjct: 281 VFNKIDLLDEEEAEERAKAIVEALG-WEGPVYLISAASGLGVKELCWDLMTFI 332
>gnl|CDD|132636 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli.
Length = 360
Score = 31.4 bits (72), Expect = 0.75
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 129 NNHEIITVLNKAD-LP-SADPDRVKKQIEETI---GISTEDALLVSAKTGEGIPLLLERI 183
+ ++ V NK D LP S + ++K+ +++ G+ D +LVSAK G GI LL++I
Sbjct: 89 GGNPVLLVGNKIDLLPKSVNLSKIKEWMKKRAKELGLKPVDIILVSAKKGNGIDELLDKI 148
>gnl|CDD|150194 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 31.2 bits (71), Expect = 0.78
Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 21/116 (18%)
Query: 65 TVRLNYTSTDA---------KDYQLNLIDTPGHVDFTYEVSRSL---SACEGSLLVVDAT 112
+VR TS + K L LID PGHV Y++ +L S+ G + VVD+T
Sbjct: 27 SVRKTVTSQEPSAAYKYMNNKGNSLTLIDFPGHVKLRYKLLETLKDSSSLRGLVFVVDST 86
Query: 113 -QGVEAQTLAN-VYQ------AIDNNHEIITVLNKADLPSA-DPDRVKKQIEETIG 159
E A +Y + N +I+ NK ++ +A P ++K+ +E+ I
Sbjct: 87 AFPKEVTDTAEFLYDILSITELLKNGIDILIACNKQEIFTARPPKKIKQALEKEIN 142
>gnl|CDD|179258 PRK01233, glyS, glycyl-tRNA synthetase subunit beta; Validated.
Length = 682
Score = 29.7 bits (68), Expect = 2.1
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 11/73 (15%)
Query: 427 ILKLCQERRGIQIDMSHLDNRAMIVYELPLNEVIFDF-YDRLKSV--SKGYASFDYNVID 483
IL++ E+ G+ +D+ L +A+ +Y + + + DF DRLK++ +G Y+VID
Sbjct: 484 ILRIILEK-GLDLDLDELIEKAVSLYNANVLDDVLDFFLDRLKALLQDEGI---RYDVID 539
Query: 484 ----YRDSDLVKL 492
R DL L
Sbjct: 540 AVLALRPDDLADL 552
>gnl|CDD|181109 PRK07769, PRK07769, long-chain-fatty-acid--CoA ligase; Validated.
Length = 631
Score = 29.7 bits (67), Expect = 2.1
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 244 ERIGILTPKMID-----IEALYPGEIGVMIASIKEVSHTRVGDTITDDSSPTT 291
+R+ IL P+ +D ALY G I V + E H + DD +P+
Sbjct: 80 DRVAILAPQNLDYLIAFFGALYAGRIAVPLFDPAEPGHVGRLHAVLDDCTPSA 132
>gnl|CDD|181957 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 29.8 bits (68), Expect = 2.3
Identities = 21/45 (46%), Positives = 29/45 (64%), Gaps = 7/45 (15%)
Query: 134 ITVLNKADLPSADPDRVKKQIE--ETIGISTEDALLVSAKTGEGI 176
+ +LNK+DL ADP+ KK IE E GI AL ++AK G+G+
Sbjct: 55 LLILNKSDL--ADPEVTKKWIEYFEEQGI---KALAINAKKGQGV 94
>gnl|CDD|132120 TIGR03076, near_not_gcvH, Chlamydial GcvH-like protein upstream
region protein. The H protein (GcvH) of the glycine
cleavage system shuttles the methylamine group of
glycine from the P protein to the T protein. Most
Chlamydia but lack the P and T proteins, and have a
single homolog of GcvH that appears deeply split from
canonical GcvH in molecular phylogenetic trees. The
protein family modeled here is observed so far only in
the Chlamydiae, always as part of a two-gene operon,
upstream of the homolog of GcvH. Its function is
unknown.
Length = 686
Score = 29.5 bits (66), Expect = 2.4
Identities = 27/86 (31%), Positives = 42/86 (48%), Gaps = 15/86 (17%)
Query: 160 ISTEDALLVSAKTGEGIPLLLE--RIVQQLPSPTSPEGANAPLKALLIDSWYNSY-LGVM 216
IS+E+ SA P L + I QQ+ +P SPEG A ++ L + + Y L M
Sbjct: 129 ISSEEVWKSSA------PQLRDALHIFQQIENPVSPEGFAARVRLFLEEKKFPHYVLRQM 182
Query: 217 VLVR------IINGQLTKGQSIRLMG 236
+ R ++G L +G+ +RL G
Sbjct: 183 LEYRRQMFNLPVDGSLAQGKDLRLFG 208
>gnl|CDD|184137 PRK13553, PRK13553, fumarate reductase cytochrome b-556 subunit;
Provisional.
Length = 258
Score = 29.2 bits (66), Expect = 3.2
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 309 FPVDATQFENLRTAINKLRLNDASFSFELENSTALGFGFRCGFLGLLHLEII 360
FP++ Q++ RT + ++ D S F GF FL +HL ++
Sbjct: 99 FPINYRQYQIFRTHKHLMKHGDTSLWF-----IQAFTGFAMFFLASVHLYVM 145
>gnl|CDD|183407 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 29.2 bits (66), Expect = 3.3
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 132 EIITVLNKADLPSADPDRVKKQIEETIGISTEDALLVSAKTGEGIPLLLERI 183
EI+ LNKADL S ++Q ++ + L +S +TG G+ LLE++
Sbjct: 122 EIVLCLNKADLVSPTE---QQQWQDRLQQWGYQPLFISVETGIGLEALLEQL 170
>gnl|CDD|129183 TIGR00073, hypB, hydrogenase accessory protein HypB. HypB is
implicated in insertion of nickel into the large subunit
of NiFe hydrogenases.
Length = 207
Score = 28.9 bits (65), Expect = 3.8
Identities = 21/53 (39%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 136 VLNKADLPSADPDRVKKQIEETIGISTE-DALLVSAKTGEGIPLLLERIVQQL 187
V+NKADL A V+K + I+ E + +L+S KTGEG+ LE + Q+
Sbjct: 154 VINKADLAEAVGFDVEKMKADAKKINPEAEIILMSLKTGEGLDEWLEFLEGQV 206
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein.
Length = 270
Score = 28.9 bits (65), Expect = 4.1
Identities = 41/187 (21%), Positives = 68/187 (36%), Gaps = 39/187 (20%)
Query: 15 SIVAHIDHGKSTLADRFIQHCRGLTEREMSSQVLDNMDIERERGITIKAQTVRLNY---T 71
+I+ + GKSTL ++ +T KAQT R
Sbjct: 4 AILGRPNVGKSTLLNQLHGQKISITSP--------------------KAQTTRNRISGIH 43
Query: 72 STDAKDYQLNLIDTPG-HVD-------FTYEVSRSLSACEGSLLVVDATQGV-EAQTLAN 122
+T A Q+ IDTPG H E ++ + L VVD+ Q + + +
Sbjct: 44 TTGA--SQIIFIDTPGFHEKKHSLNRLMMKEARSAIGGVDLILFVVDSDQWNGDGEFVLT 101
Query: 123 VYQAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALL-VSAKTGEGIPLLLE 181
Q + ++ NK D D++ I++ + ++ +SA TG+ L
Sbjct: 102 KLQNLKR--PVVLTRNKLDN--KFKDKLLPLIDKYAILEDFKDIVPISALTGDNTSFLAA 157
Query: 182 RIVQQLP 188
I LP
Sbjct: 158 FIEVHLP 164
>gnl|CDD|180745 PRK06915, PRK06915, acetylornithine deacetylase; Validated.
Length = 422
Score = 28.5 bits (64), Expect = 4.6
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 7/67 (10%)
Query: 100 SACEGSLLVVDATQGVEAQTLANVYQAIDNNHEI-----ITVLNKADLPSADPDRVKKQI 154
SA E S+ V+D + +E + + + I I + PS+ PD V +
Sbjct: 227 SAIEKSMFVIDHLRKLEEKRNDRITDPLYKGIPIPIPINIGKIEGGSWPSSVPDSVI--L 284
Query: 155 EETIGIS 161
E GI+
Sbjct: 285 EGRCGIA 291
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University).
Length = 470
Score = 28.2 bits (63), Expect = 5.7
Identities = 13/40 (32%), Positives = 25/40 (62%), Gaps = 4/40 (10%)
Query: 548 RETVKARRKDVTAKC---YG-GDITRKRKLLEKQKEGKKR 583
+E+ +A R + ++C Y DI R R+LL ++ +G++R
Sbjct: 312 QESGRAGRDGLPSECHLFYAPADINRLRRLLMEEPDGQQR 351
>gnl|CDD|114586 pfam05868, Rotavirus_VP7, Rotavirus major outer capsid protein VP7.
This family consists of several Rotavirus major outer
capsid protein VP7 sequences. The rotavirus capsid is
composed of three concentric protein layers. Proteins
VP4 and VP7 comprise the outer layer. VP4 forms spikes
and is the viral attachment protein. VP7 is a
glycoprotein and the major constituent of the outer
protein layer.
Length = 249
Score = 28.3 bits (63), Expect = 6.1
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 460 IFDFYDRLKSVSKGYASFDYNVID----YRDSDLVKLTILVNNETIDALSIL 507
IF Y+ + Y S DY+VID DS L I V + T+D + L
Sbjct: 49 IFRDYNSVTLSFFTYKSQDYDVIDIISKDDDSSCTILAIDVADSTMDFNTFL 100
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 28.2 bits (62), Expect = 6.6
Identities = 37/139 (26%), Positives = 57/139 (41%), Gaps = 16/139 (11%)
Query: 58 GITIKAQTVRLNYTSTDAKDYQLNLIDTPGHVDFTYEVSRSLSACEGSLLVVDATQGVEA 117
GI ++T+ L D +L L DT G F + + +++V D T
Sbjct: 14 GIDFLSKTLYL-----DEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSF 68
Query: 118 QTLANVYQAIDNNH--EIITVL--NKADLPSADPDRVKKQIEETIGISTEDALL---VSA 170
+ Q I N ++I L NK DL D K EE + + E + SA
Sbjct: 69 ENTTKWIQDILNERGKDVIIALVGNKTDLG----DLRKVTYEEGMQKAQEYNTMFHETSA 124
Query: 171 KTGEGIPLLLERIVQQLPS 189
K G I +L ++I +LP+
Sbjct: 125 KAGHNIKVLFKKIAAKLPN 143
>gnl|CDD|128471 smart00174, RHO, Rho (Ras homology) subfamily of Ras-like small
GTPases. Members of this subfamily of Ras-like small
GTPases include Cdc42 and Rac, as well as Rho isoforms.
Length = 174
Score = 27.9 bits (63), Expect = 7.1
Identities = 32/135 (23%), Positives = 48/135 (35%), Gaps = 27/135 (20%)
Query: 65 TVRLNYTST---DAKDYQLNLIDTPGHVDFTYEVSRSLSACEGS-LLVVDATQGVEAQTL 120
TV NY++ D K +L L DT G D Y+ R LS + L+ + +
Sbjct: 30 TVFENYSADVEVDGKPVELGLWDTAGQED--YDRLRPLSYPDTDVFLICFSV--DSPASF 85
Query: 121 ANVY-------QAIDNNHEIITVLNKADLPSADPDRVKKQIEETIGISTEDALLV----- 168
NV + N II V K DL + ++ ++ E +
Sbjct: 86 ENVKEKWYPEVKHFCPNTPIILVGTKLDLREDKSTLRELSKQKQEPVTYEQGEALAKRIG 145
Query: 169 -------SAKTGEGI 176
SA T EG+
Sbjct: 146 AVKYLECSALTQEGV 160
>gnl|CDD|128470 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in
fold and function to the bacterial EF-Tu GTPase. p21Ras
couples receptor Tyr kinases and G protein receptors to
protein kinase cascades.
Length = 164
Score = 27.9 bits (63), Expect = 7.5
Identities = 34/134 (25%), Positives = 54/134 (40%), Gaps = 38/134 (28%)
Query: 23 GKSTLADRFIQHCRGLTEREMSSQVLDNMD--IE---RERGITIKAQTVRLNYTSTDAKD 77
GKS L +F+Q +D+ D IE R++ I I D +
Sbjct: 12 GKSALTIQFVQG-----------HFVDDYDPTIEDSYRKQ-IEI------------DGEV 47
Query: 78 YQLNLIDTPGHVDFTYEVSRSLSACEGSLLV--VDATQGVEAQTLANVYQAI-----DNN 130
L+++DT G +F+ + + EG LLV + Q E + + I ++
Sbjct: 48 CLLDILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEE--IKKFREQILRVKDRDD 105
Query: 131 HEIITVLNKADLPS 144
I+ V NK DL S
Sbjct: 106 VPIVLVGNKCDLES 119
>gnl|CDD|149943 pfam09066, B2-adapt-app_C, Beta2-adaptin appendage, C-terminal
sub-domain. Members of this family adopt a structure
consisting of a 5 stranded beta-sheet, flanked by one
alpha helix on the outer side, and by two alpha helices
on the inner side. This domain is required for binding
to clathrin, and its subsequent polymerisation.
Furthermore, a hydrophobic patch present in the domain
also binds to a subset of D-phi-F/W motif-containing
proteins that are bound by the alpha-adaptin appendage
domain (epsin, AP180, eps15).
Length = 113
Score = 28.0 bits (63), Expect = 7.8
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 14/88 (15%)
Query: 107 LVVDATQGVEAQTLANVYQAID--NNHEIITVLNKADLPSADPDRVKKQIEE----TIGI 160
LV D + + +Q++ N+ E+ N L +PD +++ ++ TI
Sbjct: 1 LVEDGK--LTREEFEETWQSLPESNSQELTLQPNAVVL---NPDSIEELLQRNNIYTIAK 55
Query: 161 STEDA---LLVSAKTGEGIPLLLERIVQ 185
ED L SAKT G+ L+E I
Sbjct: 56 GEEDGQKMLYFSAKTTNGVLFLIELIFN 83
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.319 0.136 0.384
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 9,877,661
Number of extensions: 659077
Number of successful extensions: 1572
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1458
Number of HSP's successfully gapped: 116
Length of query: 606
Length of database: 5,994,473
Length adjustment: 99
Effective length of query: 507
Effective length of database: 3,855,281
Effective search space: 1954627467
Effective search space used: 1954627467
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.9 bits)