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)