RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780233|ref|YP_003064646.1| GTP-binding protein [Candidatus Liberibacter asiaticus str. psy62] (624 letters) >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 = 943 bits (2439), Expect = 0.0 Identities = 368/596 (61%), Positives = 455/596 (76%), Gaps = 3/596 (0%) Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIV 78 IRNIAIIAHVDHGKTTLVD LLKQSG FR N+ V+ERVMD NDLE+ERGITILAK T+I Sbjct: 1 IRNIAIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDLERERGITILAKNTAIR 60 Query: 79 WNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPI 138 +N +INIVDTPGHADFGGEVER+L MV+ V++LVDA+EGPMPQT+FV+ KAL++GL+PI Sbjct: 61 YNGTKINIVDTPGHADFGGEVERVLGMVDGVLLLVDASEGPMPQTRFVLKKALELGLKPI 120 Query: 139 VVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSRDQGM 198 VV+NK+DR AR DEV++EVFDLF+ L A D QLDFPI+Y SGR GW S D D M Sbjct: 121 VVINKIDRPSARPDEVVDEVFDLFAELGADDEQLDFPIVYASGRAGWASLDLDDPSDN-M 179 Query: 199 VPLLNLIVDHVPPPVIS-EGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPD 257 PL + IV HVP P + +M+ T L+ D +LGRI GR+H GT+K Q + + D Sbjct: 180 APLFDAIVRHVPAPKGDLDEPLQMLVTNLDYDEYLGRIAIGRVHRGTVKKGQQVALMKRD 239 Query: 258 GALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVKATVADTFCDPSIDEPLKAQPI 317 G + GR+SK+L F G++R IDEA AGDIV++AGL + +T DP + E L + Sbjct: 240 GTIEN-GRISKLLGFEGLERVEIDEAGAGDIVAVAGLEDINIGETIADPEVPEALPTITV 298 Query: 318 DPPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEGNIALKIEESSSKDAFFVSGRG 377 D PT++MTF VNDSPLAG EG KVTSR IRDRL +E E N+AL++E++ S D F VSGRG Sbjct: 299 DEPTLSMTFSVNDSPLAGKEGKKVTSRHIRDRLMRELETNVALRVEDTESADKFEVSGRG 358 Query: 378 ELQLAVLIETMRREGFELAVSRPRVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTLH 437 EL L++LIETMRREGFEL V RP+V+ K+ LEPIEE+ IDV EEH GAV++K+ Sbjct: 359 ELHLSILIETMRREGFELQVGRPQVIYKEIDGKKLEPIEELTIDVPEEHVGAVIEKLGKR 418 Query: 438 KSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMTDTRGTAIMNRLFHSYQPHKGEIGGR 497 K EM+++ PSG GR RL F P+RGLIG++++ +TDTRGT IMN +F Y+P KGEI R Sbjct: 419 KGEMVDMEPSGNGRTRLEFKIPSRGLIGFRTEFLTDTRGTGIMNHVFDEYEPWKGEIETR 478 Query: 498 SNGVLLSNEEGKVVAYALFNLEDRGSMIVEPGDKVYQGMIVGIHTRENDLDVNVLKGKKL 557 NG L+S E+G AYAL+NL++RG M V PG +VY+GMI+G H+RENDLDVN K KKL Sbjct: 479 RNGSLVSMEDGTATAYALWNLQERGVMFVSPGTEVYEGMIIGEHSRENDLDVNPCKAKKL 538 Query: 558 TNMRASGKDEAVKLVPAVKMTLEQALSWIQNDELVEVTPKSIRLRKMYLDPNERKR 613 TN+R+SGKDEAVKL P K++LEQAL +I++DELVEVTPKSIRLRK LDPNERKR Sbjct: 539 TNVRSSGKDEAVKLTPPRKLSLEQALEYIEDDELVEVTPKSIRLRKRVLDPNERKR 594 >gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional. Length = 607 Score = 628 bits (1620), Expect = e-180 Identities = 336/606 (55%), Positives = 426/606 (70%), Gaps = 6/606 (0%) Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIV 78 +RNIAIIAHVDHGKTTLVD+LL+QSG F ERVMD NDLEKERGITILAK T+I Sbjct: 5 LRNIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNTAIK 64 Query: 79 WNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPI 138 WND RINIVDTPGHADFGGEVER++ MV+SV+++VDA +GPMPQT+FV KA GL+PI Sbjct: 65 WNDYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDAFDGPMPQTRFVTKKAFAYGLKPI 124 Query: 139 VVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMS-DSSDGSRDQG 197 VV+NKVDR AR D V+++VFDLF LDATD QLDFPI+Y S G D D + D Sbjct: 125 VVINKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNGIAGLDHEDMAED-- 182 Query: 198 MVPLLNLIVDHVPPPVIS-EGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSP 256 M PL IVDHVP P + +G F+M + L+ + ++G I GRI G +K NQ + + Sbjct: 183 MTPLYQAIVDHVPAPDVDLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQVTIIDS 242 Query: 257 DGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVKATVADTFCDPSIDEPLKAQP 316 +G +V K+L G++R D A AGDIV+I GL + ++DT CD E L A Sbjct: 243 EGK-TRNAKVGKVLGHLGLERIETDLAEAGDIVAITGLGELNISDTVCDTQNVEALPALS 301 Query: 317 IDPPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEGNIALKIEESSSKDAFFVSGR 376 +D PTV+M F VN SP G EG VTSR I DRL KE N+AL++EE+ DAF VSGR Sbjct: 302 VDEPTVSMFFCVNTSPFCGKEGKFVTSRQILDRLNKELVHNVALRVEETEDADAFRVSGR 361 Query: 377 GELQLAVLIETMRREGFELAVSRPRVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTL 436 GEL L+VLIE MRREGFELAVSRP+V+ ++ EP E V +DV+E+H G+V+Q + Sbjct: 362 GELHLSVLIENMRREGFELAVSRPKVIFREIDGRKQEPYENVTLDVEEQHQGSVMQALGE 421 Query: 437 HKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQLMTDTRGTAIMNRLFHSYQPHK-GEIG 495 K ++ + P G GRVRL ++ P+RGLIG++S+ MT T GT ++ F Y + GE+G Sbjct: 422 RKGDLKNMNPDGKGRVRLDYVIPSRGLIGFRSEFMTMTSGTGLLYSTFSHYDDVRPGEVG 481 Query: 496 GRSNGVLLSNEEGKVVAYALFNLEDRGSMIVEPGDKVYQGMIVGIHTRENDLDVNVLKGK 555 R NGVL+SN +GK VA+ALF L+DRG + + G +VY+G I+GIH+R NDL VN L GK Sbjct: 482 QRQNGVLISNGQGKAVAFALFGLQDRGKLFLGHGAEVYEGQIIGIHSRSNDLTVNCLTGK 541 Query: 556 KLTNMRASGKDEAVKLVPAVKMTLEQALSWIQNDELVEVTPKSIRLRKMYLDPNERKRKG 615 KLTNMRASG DEAV LVP ++MTLEQAL +I +DELVEVTP SIR+RK +L N+R+R Sbjct: 542 KLTNMRASGTDEAVVLVPPIRMTLEQALEFIDDDELVEVTPTSIRIRKRHLTENDRRRAN 601 Query: 616 KSVNLE 621 ++ + Sbjct: 602 RAPKDD 607 >gnl|CDD|181029 PRK07560, PRK07560, elongation factor EF-2; Reviewed. Length = 731 Score = 187 bits (477), Expect = 8e-48 Identities = 145/508 (28%), Positives = 227/508 (44%), Gaps = 130/508 (25%) Query: 18 QIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSI 77 QIRNI IIAH+DHGKTTL D LL +G+ + + +D ++ E+ RGITI A S+ Sbjct: 19 QIRNIGIIAHIDHGKTTLSDNLLAGAGMISEELAGEQLALDFDEEEQARGITIKAANVSM 78 Query: 78 VW----NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKI 133 V + IN++DTPGH DFGG+V R + V+ +V+VDA EG MPQT+ V+ +AL+ Sbjct: 79 VHEYEGKEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDAVEGVMPQTETVLRQALRE 138 Query: 134 GLRPIVVVNKVDR-----------SDARADEVINEVFDLFSA-----------LDATDAQ 171 ++P++ +NKVDR R ++I +V L +D D Sbjct: 139 RVKPVLFINKVDRLIKELKLTPQEMQQRLLKIIKDVNKLIKGMAPEEFKEKWKVDVEDGT 198 Query: 172 LDFPILYGSGRFGW-------------MSDSSDGSRDQGM------VPL----LNLIVDH 208 + F GS + W D D PL L+++V H Sbjct: 199 VAF----GSALYNWAISVPMMQKTGIKFKDIIDYYEKGKQKELAEKAPLHEVVLDMVVKH 254 Query: 209 VPPPVISE--------------------------GEFKMIGTILEKDPFLGRIVTGRIHS 242 +P P+ ++ G M+ T + DP G + TGR+ S Sbjct: 255 LPNPIEAQKYRIPKIWKGDLNSEVGKAMLNCDPNGPLVMMVTDIIVDPHAGEVATGRVFS 314 Query: 243 GTIKSNQNIKALSPDGALVEVGRVSKILA---FRGIDRQPIDEAHAGDIVSIAGLVKATV 299 GT++ Q + LV + +++ + G +R+ ++E AG+I ++ GL A Sbjct: 315 GTLRKGQEVY-------LVGAKKKNRVQQVGIYMGPEREEVEEIPAGNIAAVTGLKDARA 367 Query: 300 ADTFCDPSIDEPLKA-QPIDPPTVTMTF---GVNDSPLAGTEGDKVTSRMI---RDRLFK 352 +T P ++ + I P VT+ D P ++I R L K Sbjct: 368 GETVVSVEDMTPFESLKHISEPVVTVAIEAKNPKDLP-----------KLIEVLRQ-LAK 415 Query: 353 EAEGNIALKIEESSSKDAFFVSGRGELQLAVLIETMRRE-GFELAVSRPRVV----IKK- 406 E + + +KI E + + +SG GEL L V+ ++R+ G E+ S P VV ++ Sbjct: 416 E-DPTLVVKINEETGE--HLLSGMGELHLEVITYRIKRDYGIEVVTSEPIVVYRETVRGK 472 Query: 407 ----EGDS---------LLEPIEEVVID 421 EG S +EP+EE VI+ Sbjct: 473 SQVVEGKSPNKHNRFYISVEPLEEEVIE 500 Score = 36.4 bits (85), Expect = 0.022 Identities = 19/82 (23%), Positives = 46/82 (56%), Gaps = 1/82 (1%) Query: 408 GDSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQ 467 +LLEPI++V I+V +++ GAV +++ + +++++ G + +P + G+ Sbjct: 620 KPTLLEPIQKVDINVPQDYMGAVTREIQGRRGKILDMEQEGD-MAIIEAEAPVAEMFGFA 678 Query: 468 SQLMTDTRGTAIMNRLFHSYQP 489 ++ + T G A+ + F ++P Sbjct: 679 GEIRSATEGRALWSTEFAGFEP 700 >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 = 180 bits (459), Expect = 8e-46 Identities = 143/521 (27%), Positives = 238/521 (45%), Gaps = 108/521 (20%) Query: 16 YMQIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVT 75 IRNI I+AH+DHGKTTL D LL +G+ + + +D ++ E+ERGITI A Sbjct: 16 PKFIRNIGIVAHIDHGKTTLSDNLLAGAGMISEELAGQQLYLDFDEQEQERGITINAANV 75 Query: 76 SIVW----NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKAL 131 S+V N+ IN++DTPGH DFGG+V R + V+ +V+V A EG MPQT+ V+ +AL Sbjct: 76 SMVHEYEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCAVEGVMPQTETVLRQAL 135 Query: 132 KIGLRPIVVVNKVDR-----------SDARADEVINEVFDLFSALDATDAQ-------LD 173 K ++P++ +NKVDR R ++I EV L A+ + + D Sbjct: 136 KENVKPVLFINKVDRLINELKLTPQELQERFIKIITEVNKLIKAMAPEEFRDKWKVRVED 195 Query: 174 FPILYGSGRFGW------MSDSSDGSRD-------------QGMVPL----LNLIVDHVP 210 + +GS + W M + G +D PL L++++ H+P Sbjct: 196 GSVAFGSAYYNWAISVPSMKKTGIGFKDIYKYCKEDKQKELAKKSPLHQVVLDMVIRHLP 255 Query: 211 PPVIS--------------------------EGEFKMIGTILEKDPFLGRIVTGRIHSGT 244 P+ + +G ++ T + D G + GR++SGT Sbjct: 256 SPIEAQKYRIPVIWKGDLNSEVGKAMLNCDPKGPLALMITKIVVDKHAGEVAVGRLYSGT 315 Query: 245 IKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVKATVADTFC 304 I+ + + R+ ++ + G +R +DE AG+IV++ GL A +T C Sbjct: 316 IRPGMEVYIVDRKAK----ARIQQVGVYMGPERVEVDEIPAGNIVAVIGLKDAVAGETIC 371 Query: 305 DP-SIDEPLKA-QPIDPPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEGNIALKI 362 P ++ + I P VT+ ++ K ++I + L + A+ + + + Sbjct: 372 TTVENITPFESIKHISEPVVTVAIEAKNT--------KDLPKLI-EVLRQVAKEDPTVHV 422 Query: 363 EESSSKDAFFVSGRGELQLAVLIETMRRE-GFELAVSRPRVVIKK---------EGDS-- 410 E + +SG GEL L +++E +R + G ++ S P VV ++ EG S Sbjct: 423 EINEETGEHLISGMGELHLEIIVEKIREDYGLDVETSPPIVVYRETVTGTSPVVEGKSPN 482 Query: 411 -------LLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIEL 444 ++EP+EE VI +E + M + K E L Sbjct: 483 KHNRFYIVVEPLEESVIQAFKE---GKIVDMKMKKKERRRL 520 Score = 30.3 bits (68), Expect = 1.7 Identities = 16/78 (20%), Positives = 40/78 (51%), Gaps = 1/78 (1%) Query: 411 LLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQL 470 LLEP ++V I+V ++ GA +++ + +++E++ G V ++ +P + G+ + Sbjct: 621 LLEPYQKVFINVPQDMMGAATREIQNRRGQILEMKQEGD-MVTIIAKAPVAEMFGFAGAI 679 Query: 471 MTDTRGTAIMNRLFHSYQ 488 T G + + ++ Sbjct: 680 RGATSGRCLWSTEHAGFE 697 >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 = 160 bits (406), Expect = 1e-39 Identities = 143/512 (27%), Positives = 218/512 (42%), Gaps = 76/512 (14%) Query: 18 QIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSI 77 IRN +IIAH+DHGK+TL D LL+ +G + + + E+V+D DLE+ERGITI A+ + Sbjct: 2 NIRNFSIIAHIDHGKSTLADRLLEYTGAISERE-MREQVLDSMDLERERGITIKAQAVRL 60 Query: 78 VW-----NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALK 132 + +N++DTPGH DF EV R L E ++LVDAA+G QT V AL+ Sbjct: 61 NYKAKDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQTLANVYLALE 120 Query: 133 IGLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDG 192 L I V+NK+D A + V E+ ++ LDA++A L S + G Sbjct: 121 NDLEIIPVINKIDLPSADPERVKKEIEEVI-GLDASEAIL------ASAKTG-------- 165 Query: 193 SRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEK--DPFLGRIVTGRIHSGTIKSNQN 250 G+ +L IV VPPP + + + I + D + G + R+ GTIK Sbjct: 166 ---IGIEEILEAIVKRVPPP-KGDPDAPLKALIFDSHYDNYRGVVALVRVFEGTIKPGDK 221 Query: 251 IKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAGLVK----ATVADTF--C 304 I+ +S G EV V DE AG++ I +K V DT Sbjct: 222 IRFMS-TGKEYEVDEV----GVFTPKLTKTDELSAGEVGYIIAGIKDVSDVRVGDTITHV 276 Query: 305 DPSIDEPLKA-QPIDPPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKEAEGNIALKIE 363 EPL + + P M F + L + + +RD L K + +L E Sbjct: 277 KNPAKEPLPGFKEVKP----MVF----AGLYPIDTEDYED--LRDALEKLKLNDASLTYE 326 Query: 364 ESSSKD---AFFVSGRGELQLAVLIETMRREGFELAV--SRPRV---VIKKEG------- 408 SS F G L + ++ E + RE F L + + P V V G Sbjct: 327 PESSPALGFGFRCGFLGLLHMEIIQERLERE-FNLDLITTAPSVIYRVYLTNGEVIEVDN 385 Query: 409 ----------DSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLS 458 + + EP + I E+ G ++ + + RV L++ Sbjct: 386 PSDLPDPGKIEHVEEPYVKATIITPTEYLGPIMTLCQEKRGVQTNMEYLDPNRVELIYEM 445 Query: 459 P-TRGLIGYQSQLMTDTRGTAIMNRLFHSYQP 489 P + + +L + +RG A + Y+P Sbjct: 446 PLAEIVYDFFDKLKSISRGYASFDYELIGYRP 477 >gnl|CDD|180078 PRK05433, PRK05433, GTP-binding protein LepA; Provisional. Length = 600 Score = 146 bits (371), Expect = 2e-35 Identities = 108/331 (32%), Positives = 153/331 (46%), Gaps = 74/331 (22%) Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER-----VMDCNDLEKERGITILAK 73 IRN +IIAH+DHGK+TL D L++ +G +SER V+D DLE+ERGITI A+ Sbjct: 7 IRNFSIIAHIDHGKSTLADRLIELTGT------LSEREMKAQVLDSMDLERERGITIKAQ 60 Query: 74 VTSIVW-----NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVG 128 + + +N++DTPGH DF EV R L E +++VDA++G QT V Sbjct: 61 AVRLNYKAKDGETYILNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVY 120 Query: 129 KALKIGLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSD 188 AL+ L I V+NK+D A + V E+ D+ +DA+DA L S + G Sbjct: 121 LALENDLEIIPVLNKIDLPAADPERVKQEIEDVI-GIDASDAVL------VSAKTG---- 169 Query: 189 SSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEK----------DPFLGRIVTG 238 G+ +L IV+ +PPP G D + G +V Sbjct: 170 -------IGIEEVLEAIVERIPPPK---------GDPDAPLKALIFDSWYDNYRGVVVLV 213 Query: 239 RIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGI---DRQPIDEAHAGD----IVSI 291 R+ GT+K IK +S G EV V G+ P+DE AG+ I I Sbjct: 214 RVVDGTLKKGDKIKMMS-TGKEYEVDEV-------GVFTPKMVPVDELSAGEVGYIIAGI 265 Query: 292 AGLVKATVADTFCDPS--IDEPL----KAQP 316 + A V DT +EPL + +P Sbjct: 266 KDVRDARVGDTITLAKNPAEEPLPGFKEVKP 296 >gnl|CDD|183990 PRK13351, PRK13351, elongation factor G; Reviewed. Length = 687 Score = 133 bits (337), Expect = 1e-31 Identities = 64/150 (42%), Positives = 93/150 (62%), Gaps = 2/150 (1%) Query: 17 MQIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSE--RVMDCNDLEKERGITILAKV 74 MQIRNI I+AH+D GKTTL + +L +G V + V D E+ERGITI + Sbjct: 6 MQIRNIGILAHIDAGKTTLTERILFYTGKIHKMGEVEDGTTVTDWMPQEQERGITIESAA 65 Query: 75 TSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIG 134 TS W++ RIN++DTPGH DF GEVER L +++ VV+ DA G PQT+ V +A + G Sbjct: 66 TSCDWDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAVTGVQPQTETVWRQADRYG 125 Query: 135 LRPIVVVNKVDRSDARADEVINEVFDLFSA 164 + ++ +NK+DR A +V+ ++ + F Sbjct: 126 IPRLIFINKMDRVGADLFKVLEDIEERFGK 155 Score = 83.8 bits (208), Expect = 1e-16 Identities = 64/250 (25%), Positives = 111/250 (44%), Gaps = 44/250 (17%) Query: 174 FPILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDH------VPPPVISEGEFKMI----- 222 P+L+GS ++ G+ PLL+ +VD+ VPPP S+ K + Sbjct: 253 VPVLFGSAL-----------KNIGIEPLLDAVVDYLPSPLEVPPPRGSKDNGKPVKVDPD 301 Query: 223 --GTIL------EKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRG 274 +L + DP+ G++ R++SGT+++ L +V ++ +G Sbjct: 302 PEKPLLALVFKVQYDPYAGKLTYLRVYSGTLRAG---SQLYNGTGGKRE-KVGRLFRLQG 357 Query: 275 IDRQPIDEAHAGDIVSIAGLVKATVADTFCDPSIDEPLKAQPIDPPTVTMTFGVNDSPLA 334 R+ +D A AGDIV++AGL + DT D +P+ + + P + P Sbjct: 358 NKREEVDRAKAGDIVAVAGLKELETGDTLHDS--ADPVLLELLTFP--EPVVSLAVEPER 413 Query: 335 GTEGDKVTSRMIRDRLFKEAEGNIALKIEESSSKDAFFVSGRGELQLAVLIETMRRE-GF 393 + K+ + ++L E L++EE +SG GEL L V +E +RRE Sbjct: 414 RGDEQKLAEAL--EKLVWEDPS---LRVEEDEETGQTILSGMGELHLEVALERLRREFKL 468 Query: 394 ELAVSRPRVV 403 E+ +P+V Sbjct: 469 EVNTGKPQVA 478 Score = 38.0 bits (89), Expect = 0.008 Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 2/79 (2%) Query: 404 IKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGL 463 +K LLEPI E+ I V EH G V+ ++ + + P G G V + +P L Sbjct: 590 FRKANPVLLEPIMELEITVPTEHVGDVLGDLSQRRGRIEGTEPRGDGEVLVKAEAPLAEL 649 Query: 464 IGYQSQL--MTDTRGTAIM 480 GY ++L MT RG+ M Sbjct: 650 FGYATRLRSMTKGRGSFTM 668 >gnl|CDD|185604 PTZ00416, PTZ00416, elongation factor 2; Provisional. Length = 836 Score = 124 bits (314), Expect = 6e-29 Identities = 67/198 (33%), Positives = 100/198 (50%), Gaps = 33/198 (16%) Query: 18 QIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSI 77 QIRN+++IAHVDHGK+TL D L+ ++G+ R D E+ERGITI K T I Sbjct: 18 QIRNMSVIAHVDHGKSTLTDSLVCKAGIISSKNAGDARFTDTRADEQERGITI--KSTGI 75 Query: 78 ------------VWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKF 125 IN++D+PGH DF EV L + + +V+VD EG QT+ Sbjct: 76 SLYYEHDLEDGDDKQPFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVEGVCVQTET 135 Query: 126 VVGKALKIGLRPIVVVNKVDR--------------SDARADEVINEVFDLFSALDATDAQ 171 V+ +AL+ +RP++ +NKVDR + + E +N + ++ D Q Sbjct: 136 VLRQALQERIRPVLFINKVDRAILELQLDPEEIYQNFVKTIENVNVIIATYNDELMGDVQ 195 Query: 172 LDFP----ILYGSGRFGW 185 + P + +GSG GW Sbjct: 196 VY-PEKGTVAFGSGLQGW 212 >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 = 119 bits (299), Expect = 3e-27 Identities = 62/163 (38%), Positives = 89/163 (54%), Gaps = 5/163 (3%) Query: 16 YMQIRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRV--SERVMDCNDLEKERGITILAK 73 + RNI I AH+D GKTT + +L +G V MD + EKERGITI + Sbjct: 7 LNRFRNIGISAHIDAGKTTTTERILFYTGRIHKIGEVHDGAATMDWMEQEKERGITITSA 66 Query: 74 VTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKI 133 T++ W RINI+DTPGH DF EVER L +++ V ++DA G PQ++ V +A + Sbjct: 67 ATTVFWKGHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSETVWRQANRY 126 Query: 134 GLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPI 176 + I VNK+D++ A V+N+ + L A + PI Sbjct: 127 EVPRIAFVNKMDKTGANFLRVVNQ---IKQRLGANAVPIQLPI 166 Score = 79.5 bits (196), Expect = 3e-15 Identities = 58/230 (25%), Positives = 97/230 (42%), Gaps = 34/230 (14%) Query: 194 RDQGMVPLLNLIVDHVPPPV--------------------ISEGEFKMIGTILEKDPFLG 233 +++G+ LL+ +VD++P P + F + + DPF+G Sbjct: 263 KNKGVQLLLDAVVDYLPSPTDVPAIKGIDPDTEKEIERKASDDEPFSALAFKVATDPFVG 322 Query: 234 RIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSIAG 293 ++ R++SG +KS +K + RV +++ +R+ I E AGDI + G Sbjct: 323 QLTFVRVYSGVLKSGSYVKNSRKNKKE----RVGRLVKMHANNREEIKEVRAGDICAAIG 378 Query: 294 LVKATVADTFCDPSIDEPLKAQPIDPPTVTMTFGVNDSPLAGTEGDKVTSRMIRDRLFKE 353 L T DT CDP ID L+ P ++ LA K + L K Sbjct: 379 LKDTTTGDTLCDPKIDVILERMEFPEPVIS---------LAVEPKTKADQEKMGIALGKL 429 Query: 354 AEGNIALKIEESSSKDAFFVSGRGELQLAVLIETMRRE-GFELAVSRPRV 402 AE + + ++G GEL L ++++ M+RE E V P+V Sbjct: 430 AEEDPTFRTFTDPETGQTIIAGMGELHLDIIVDRMKREFKVEANVGAPQV 479 Score = 27.9 bits (62), Expect = 8.1 Identities = 27/96 (28%), Positives = 46/96 (47%), Gaps = 2/96 (2%) Query: 393 FELAVSRP-RVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGR 451 F+LA S + KK LLEPI +V ++V EE+ G V+ ++ + +IE + Sbjct: 579 FKLAASLAFKEAGKKANPVLLEPIMKVEVEVPEEYMGDVMGDLSSRRG-IIEGMEARGNV 637 Query: 452 VRLVFLSPTRGLIGYQSQLMTDTRGTAIMNRLFHSY 487 ++ P + GY + L + T+G + F Y Sbjct: 638 QKIKAEVPLSEMFGYATDLRSFTQGRGTYSMEFLHY 673 >gnl|CDD|183713 PRK12740, PRK12740, elongation factor G; Reviewed. Length = 668 Score = 119 bits (300), Expect = 3e-27 Identities = 55/142 (38%), Positives = 81/142 (57%), Gaps = 2/142 (1%) Query: 25 IAHVDHGKTTLVDELLKQSGVFRDNQRVSE--RVMDCNDLEKERGITILAKVTSIVWNDV 82 + H GKTTL + +L +G V + MD E+ERGI+I + T+ W Sbjct: 1 VGHSGAGKTTLTEAILFYTGAIHRIGEVEDGTTTMDFMPEERERGISITSAATTCEWKGH 60 Query: 83 RINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIVVVN 142 +IN++DTPGH DF GEVER L +++ VV+V A G PQT+ V +A K G+ I+ VN Sbjct: 61 KINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTETVWRQAEKYGVPRIIFVN 120 Query: 143 KVDRSDARADEVINEVFDLFSA 164 K+DR+ A V+ ++ + A Sbjct: 121 KMDRAGADFFRVLAQLQEKLGA 142 Score = 91.3 bits (228), Expect = 6e-19 Identities = 64/249 (25%), Positives = 113/249 (45%), Gaps = 43/249 (17%) Query: 174 FPILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPV-------ISEGEFKMIGTIL 226 P+ GS +++G+ LL+ +VD++P P+ E + Sbjct: 237 VPVFCGSAL-----------KNKGVQRLLDAVVDYLPSPLEVPPVDGEDGEEGAELAPDP 285 Query: 227 EK-----------DPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGI 275 + DPF+G++ R++SGT+K + + E RV ++ G Sbjct: 286 DGPLVALVFKTMDDPFVGKLSLVRVYSGTLKKGDTL--YNSGTGKKE--RVGRLYRMHGK 341 Query: 276 DRQPIDEAHAGDIVSIAGLVKATVADTFCDPSIDEPLKAQPIDPPTVTMTFGVNDSPLAG 335 R+ +DEA AGDIV++A L A DT CD +P+ +P++ P ++ + P Sbjct: 342 QREEVDEAVAGDIVAVAKLKDAATGDTLCDK--GDPILLEPMEFPEPVISLAI--EPKDK 397 Query: 336 TEGDKVTSRMIRDRLFKEAEGNIALKIEESSSKDAFFVSGRGELQLAVLIETMRRE-GFE 394 + +K++ + +L AE + L++E +SG GEL L V +E ++RE G E Sbjct: 398 GDEEKLSEAL--GKL---AEEDPTLRVERDEETGQTILSGMGELHLDVALERLKREYGVE 452 Query: 395 LAVSRPRVV 403 + P+V Sbjct: 453 VETGPPQVP 461 Score = 34.7 bits (81), Expect = 0.068 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 1/79 (1%) Query: 411 LLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQL 470 LLEPI +V + V EE G V+ ++ + ++ + G G + P + GY + L Sbjct: 580 LLEPIMKVEVSVPEEFVGDVIGDLSSRRGRILGMESRGGG-DVVRAEVPLAEMFGYATDL 638 Query: 471 MTDTRGTAIMNRLFHSYQP 489 + T+G + F Y+ Sbjct: 639 RSLTQGRGSFSMEFSHYEE 657 >gnl|CDD|183712 PRK12739, PRK12739, elongation factor G; Reviewed. Length = 691 Score = 114 bits (288), Expect = 7e-26 Identities = 64/163 (39%), Positives = 90/163 (55%), Gaps = 11/163 (6%) Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSE-----RVMDCNDLEKERGITILAK 73 RNI I+AH+D GKTT + +L +G + ++ E MD + E+ERGITI + Sbjct: 8 TRNIGIMAHIDAGKTTTTERILYYTGK---SHKIGEVHDGAATMDWMEQEQERGITITSA 64 Query: 74 VTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKI 133 T+ W RINI+DTPGH DF EVER L +++ V + DA G PQ++ V +A K Sbjct: 65 ATTCFWKGHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVSGVEPQSETVWRQADKY 124 Query: 134 GLRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPI 176 G+ IV VNK+DR A + ++ D L A + PI Sbjct: 125 GVPRIVFVNKMDRIGADFFRSVEQIKDR---LGANAVPIQLPI 164 Score = 65.2 bits (160), Expect = 4e-11 Identities = 70/274 (25%), Positives = 112/274 (40%), Gaps = 93/274 (33%) Query: 174 FPILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPV----------ISEGE----- 218 FP+L GS F +++G+ PLL+ +VD++P P+ +E E Sbjct: 253 FPVLCGSA-F----------KNKGVQPLLDAVVDYLPSPLDVPAIKGINPDTEEEIERPA 301 Query: 219 ----------FKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSK 268 FK I T DPF+GR+ R++SG ++S + + + R+ + Sbjct: 302 SDDEPFAALAFK-IMT----DPFVGRLTFFRVYSGVLESGSYVLNTTKG----KKERIGR 352 Query: 269 ILAFRGIDRQPIDEAHAGDIVSIAGLVKATVADTFCDP-------SID--EPLKAQPIDP 319 +L R+ I E +AGDI + GL T DT CD S++ EP+ + ++P Sbjct: 353 LLQMHANKREEIKEVYAGDIAAAVGLKDTTTGDTLCDEKAPIILESMEFPEPVISLAVEP 412 Query: 320 PTVT----MTFGVNDSPLAG------TEGDKVTSRMIRDRLFKEAEGNIALKIEESSSKD 369 T M + LA E D+ T + I Sbjct: 413 KTKADQDKMGLAL--QKLAEEDPTFRVETDEETGQTI----------------------- 447 Query: 370 AFFVSGRGELQLAVLIETMRRE-GFELAVSRPRV 402 +SG GEL L ++++ M+RE E V P+V Sbjct: 448 ---ISGMGELHLDIIVDRMKREFKVEANVGAPQV 478 Score = 32.9 bits (76), Expect = 0.24 Identities = 28/102 (27%), Positives = 46/102 (45%), Gaps = 10/102 (9%) Query: 393 FELAVSRP-RVVIKKEGDSLLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGR 451 F++A S + KK G +LEPI +V + EE+ G V+ + + ++ + G + Sbjct: 579 FKIAASMALKEAAKKAGPVILEPIMKVEVVTPEEYMGDVIGDLNRRRGQIQGMEARGGAQ 638 Query: 452 V--RLVFLSPTRGLIGYQSQL--MTDTRGTAIMNRLFHSYQP 489 + V LS + GY + L T R T M F Y+ Sbjct: 639 IVKAFVPLSE---MFGYATDLRSATQGRATFSME--FDHYEE 675 >gnl|CDD|178789 PRK00007, PRK00007, elongation factor G; Reviewed. Length = 693 Score = 110 bits (278), Expect = 1e-24 Identities = 60/135 (44%), Positives = 82/135 (60%), Gaps = 8/135 (5%) Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSE-----RVMDCNDLEKERGITILAKV 74 RNI I+AH+D GKTT + +L +GV N ++ E MD + E+ERGITI + Sbjct: 11 RNIGIMAHIDAGKTTTTERILFYTGV---NHKIGEVHDGAATMDWMEQEQERGITITSAA 67 Query: 75 TSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIG 134 T+ W D RINI+DTPGH DF EVER L +++ V + DA G PQ++ V +A K Sbjct: 68 TTCFWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVGGVEPQSETVWRQADKYK 127 Query: 135 LRPIVVVNKVDRSDA 149 + I VNK+DR+ A Sbjct: 128 VPRIAFVNKMDRTGA 142 Score = 58.2 bits (142), Expect = 7e-09 Identities = 28/87 (32%), Positives = 40/87 (45%), Gaps = 20/87 (22%) Query: 229 DPFLGRIVTGRIHSGTIKSNQNIKALSPDGALV--------EVGRVSKILAFRGIDRQPI 280 DPF+G++ R++SG ++S G+ V E R+ +IL R+ I Sbjct: 320 DPFVGKLTFFRVYSGVLES----------GSYVLNSTKGKKE--RIGRILQMHANKREEI 367 Query: 281 DEAHAGDIVSIAGLVKATVADTFCDPS 307 E AGDI + GL T DT CD Sbjct: 368 KEVRAGDIAAAVGLKDTTTGDTLCDEK 394 Score = 28.6 bits (65), Expect = 5.6 Identities = 12/30 (40%), Positives = 20/30 (66%), Gaps = 1/30 (3%) Query: 374 SGRGELQLAVLIETMRRE-GFELAVSRPRV 402 +G GEL L ++++ M+RE E V +P+V Sbjct: 452 AGMGELHLDIIVDRMKREFKVEANVGKPQV 481 >gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit; Provisional. Length = 843 Score = 107 bits (270), Expect = 7e-24 Identities = 57/146 (39%), Positives = 80/146 (54%), Gaps = 20/146 (13%) Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIV 78 IRN+++IAHVDHGK+TL D L+ +G+ R+ D E ERGITI K T I Sbjct: 19 IRNMSVIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRMTDTRADEAERGITI--KSTGIS 76 Query: 79 W------------------NDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPM 120 N+ IN++D+PGH DF EV L + + +V+VD EG Sbjct: 77 LYYEMTDESLKDFKGERDGNEYLINLIDSPGHVDFSSEVTAALRITDGALVVVDCIEGVC 136 Query: 121 PQTKFVVGKALKIGLRPIVVVNKVDR 146 QT+ V+ +AL +RP++ VNK+DR Sbjct: 137 VQTETVLRQALGERIRPVLTVNKMDR 162 >gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional. Length = 526 Score = 90.2 bits (225), Expect = 1e-18 Identities = 55/149 (36%), Positives = 84/149 (56%), Gaps = 14/149 (9%) Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER------VMDCNDLEKERGITILAK 73 R AII+H D GKTTL ++LL G ++ V R D ++EK+RGI++ + Sbjct: 11 RTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGRHATSDWMEMEKQRGISVTSS 70 Query: 74 VTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTK--FVVGKAL 131 V + D IN++DTPGH DF + R L V+S ++++DAA+G PQT+ V + Sbjct: 71 VMQFPYRDCLINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKGVEPQTRKLMEVCRLR 130 Query: 132 KIGLRPIVV-VNKVDRSDARAD-EVINEV 158 PI +NK+DR D R E+++E+ Sbjct: 131 DT---PIFTFINKLDR-DGREPLELLDEI 155 >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 = 86.9 bits (215), Expect = 2e-17 Identities = 80/306 (26%), Positives = 121/306 (39%), Gaps = 60/306 (19%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 IA HVDHGKTTL+ L +G+ R+ E EK+RG+TI Sbjct: 2 IIATAGHVDHGKTTLLKAL---TGI--AADRLPE--------EKKRGMTIDLGFAYFPLP 48 Query: 81 DVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTK--FVVGKALKIGLRPI 138 D R+ +D PGH F +++ +++VDA EG M QT V L I I Sbjct: 49 DYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLAVLDLLGIPHT-I 107 Query: 139 VVVNKVDRSD-ARADEVINEVFD-LFSALDATDAQLDFPILYGSGR--------FGWMSD 188 VV+ K DR + + L S + +A++ F +G+ + + Sbjct: 108 VVITKADRVNEEEIKRTEMFMKQILNSYIFLKNAKI-FKTSAKTGQGIGELKKELKNLLE 166 Query: 189 SSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSN 248 S D R Q L + +D FK+ G G +VTG SG +K Sbjct: 167 SLDIKRIQKP---LRMAIDRA---------FKVKGA--------GTVVTGTAFSGEVKVG 206 Query: 249 QNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVS--IAGLVKATVADTFCDP 306 N++ L P V RV I A Q ++ A+AG ++ + + ++ Sbjct: 207 DNLR-LLPINHEV---RVKAIQAQ----NQDVEIAYAGQRIALNLMDVEPESLKRGLL-- 256 Query: 307 SIDEPL 312 I P Sbjct: 257 -ILTPE 261 >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 = 83.8 bits (207), Expect = 1e-16 Identities = 48/146 (32%), Positives = 82/146 (56%), Gaps = 8/146 (5%) Query: 20 RNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER------VMDCNDLEKERGITILAK 73 R AII+H D GKTT+ +++L G + V R D ++EK+RGI+I Sbjct: 12 RTFAIISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGISITTS 71 Query: 74 VTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKI 133 V + D +N++DTPGH DF + R L V++ ++++DAA+G +T+ ++ + ++ Sbjct: 72 VMQFPYRDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLM-EVTRL 130 Query: 134 GLRPIVV-VNKVDRSDARADEVINEV 158 PI +NK+DR E+++EV Sbjct: 131 RDTPIFTFMNKLDRDIRDPLELLDEV 156 Score = 31.4 bits (71), Expect = 0.68 Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 3/53 (5%) Query: 265 RVSKILAFRGIDRQPIDEAHAGDIVSIAGLVKATVADTFCDPSIDEPLKAQPI 317 +S L F DR+ ++EA+AGDI+ + + DTF + E +K I Sbjct: 339 VISDALTFMAGDREHVEEAYAGDIIGLHNHGTIQIGDTF---TQGEKIKFTGI 388 >gnl|CDD|183709 PRK12736, PRK12736, elongation factor Tu; Reviewed. Length = 394 Score = 81.5 bits (202), Expect = 5e-16 Identities = 86/307 (28%), Positives = 132/307 (42%), Gaps = 87/307 (28%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 NI I HVDHGKTTL + K NQ +D EKERGITI Sbjct: 14 NIGTIGHVDHGKTTLTAAITKVLAERGLNQAKDYDSIDAAPEEKERGITI---------- 63 Query: 81 DVRINI--------------VDTPGHADFGGEVERILCMV------ESVVVLVDAAEGPM 120 N VD PGHAD+ + M+ + +++V A +GPM Sbjct: 64 ----NTAHVEYETEKRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVAATDGPM 113 Query: 121 PQTKFVVGKALKIGLRPIVV-VNKVDRSDARADEVIN----EVFDLFSALD-ATDAQLDF 174 PQT+ + A ++G+ +VV +NKVD D +E++ EV +L S D D D Sbjct: 114 PQTREHILLARQVGVPYLVVFLNKVDLVD--DEELLELVEMEVRELLSEYDFPGD---DI 168 Query: 175 PILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKDPFL-- 232 P++ GS + D + ++ L++ + +++P P +K PFL Sbjct: 169 PVIRGSAL---KALEGDPKWEDAIMELMDAVDEYIPTPERD----------TDK-PFLMP 214 Query: 233 ----------GRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGID--RQPI 280 G +VTGR+ GT+K ++ +V + K + G++ R+ + Sbjct: 215 VEDVFTITGRGTVVTGRVERGTVKVGDEVE-------IVGIKETQKTVV-TGVEMFRKLL 266 Query: 281 DEAHAGD 287 DE AGD Sbjct: 267 DEGQAGD 273 >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 = 80.2 bits (198), Expect = 2e-15 Identities = 83/297 (27%), Positives = 129/297 (43%), Gaps = 59/297 (19%) Query: 21 NIAIIAHVDHGKTTLVDEL-----LKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVT 75 NI I HVDHGKTTL + + R ++ D EK RGITI Sbjct: 14 NIGTIGHVDHGKTTLTAAITTVLAKEGGAAARAYDQI-----DNAPEEKARGITINTAHV 68 Query: 76 SIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGL 135 + VD PGHAD+ + ++ +++V A +GPMPQT+ + A ++G+ Sbjct: 69 EYETENRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSATDGPMPQTREHILLARQVGV 128 Query: 136 RPIVV-VNKVDRSDARADE-----VINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDS 189 IVV +NK D D DE V EV +L S D D PI+ GS + Sbjct: 129 PYIVVFLNKCDMVD---DEELLELVEMEVRELLSEYDFPGD--DTPIIRGS---ALKALE 180 Query: 190 SDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKDPFL------------GRIVT 237 D + ++ L++ + +++P P +K PFL G +VT Sbjct: 181 GDAEWEAKILELMDAVDEYIPTPE----------RETDK-PFLMPIEDVFSITGRGTVVT 229 Query: 238 GRIHSGTIKSNQNIKALSPDGALVEVG-RVSKILAFRGID--RQPIDEAHAGDIVSI 291 GR+ G +K + ++ VG + ++ G++ R+ +DE AGD V + Sbjct: 230 GRVERGIVKVGEEVEI---------VGLKDTRKTTVTGVEMFRKELDEGRAGDNVGL 277 >gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional. Length = 447 Score = 78.7 bits (194), Expect = 4e-15 Identities = 84/286 (29%), Positives = 131/286 (45%), Gaps = 37/286 (12%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 N+ I HVDHGKTTL + K + V+ +D EK RGITI Sbjct: 63 NVGTIGHVDHGKTTLTAAITKVLAEEGKAKAVAFDEIDKAPEEKARGITIATAHVEYETA 122 Query: 81 DVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIVV 140 VD PGHAD+ + ++ +++V A +GPMPQTK + A ++G+ +VV Sbjct: 123 KRHYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVV 182 Query: 141 -VNKVDRSDARA--DEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSRDQG 197 +NKVD D + V E+ +L S + PI+ GS + ++D Sbjct: 183 FLNKVDVVDDEELLELVEMELRELLSFYKFPGD--EIPIIRGSA-LSALQGTNDEIGKNA 239 Query: 198 MVPLLNLIVDHVPPPVISEGEFKMIGTILEKDPFL------------GRIVTGRIHSGTI 245 ++ L++ + +++P PV +L+K PFL G + TGR+ GTI Sbjct: 240 ILKLMDAVDEYIPEPV----------RVLDK-PFLMPIEDVFSIQGRGTVATGRVEQGTI 288 Query: 246 KSNQNIK--ALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIV 289 K + ++ L P G L V+ + F+ I +D+ AGD V Sbjct: 289 KVGEEVEIVGLRPGGPLKTT--VTGVEMFKKI----LDQGQAGDNV 328 >gnl|CDD|183433 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed. Length = 425 Score = 76.1 bits (188), Expect = 2e-14 Identities = 57/172 (33%), Positives = 78/172 (45%), Gaps = 33/172 (19%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER---------------VMDCNDLEKE 65 N+A+I HVDHGK+TLV LL ++G ++ R VMD E+E Sbjct: 8 NLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDRLKEERE 67 Query: 66 RGITILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVES--------VVVLVDAAE 117 RG+TI + IVD PGH DF + M+ +VV D A Sbjct: 68 RGVTIDLAHKKFETDKYYFTIVDCPGHRDF------VKNMITGASQADAAVLVVAADDAG 121 Query: 118 GPMPQTKFVVGKALKIGLRP-IVVVNKVDRSD---ARADEVINEVFDLFSAL 165 G MPQT+ V A +G+ IV +NK+D + R +EV EV L + Sbjct: 122 GVMPQTREHVFLARTLGINQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMV 173 >gnl|CDD|178823 PRK00049, PRK00049, elongation factor Tu; Reviewed. Length = 396 Score = 74.5 bits (184), Expect = 8e-14 Identities = 76/270 (28%), Positives = 111/270 (41%), Gaps = 77/270 (28%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 N+ I HVDHGKTTL + K + + +D EK RGITI Sbjct: 14 NVGTIGHVDHGKTTLTAAITKVLAKKGGAEAKAYDQIDKAPEEKARGITI---------- 63 Query: 81 DVRINI--------------VDTPGHADFGGEVERILCMV------ESVVVLVDAAEGPM 120 N VD PGHAD+ + M+ + +++V AA+GPM Sbjct: 64 ----NTAHVEYETEKRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSAADGPM 113 Query: 121 PQTKFVVGKALKIGLRPIVV-VNKVDRSDARADE-----VINEVFDLFSALDATDAQLDF 174 PQT+ + A ++G+ IVV +NK D D DE V EV +L S D D Sbjct: 114 PQTREHILLARQVGVPYIVVFLNKCDMVD---DEELLELVEMEVRELLSKYDFPGD--DT 168 Query: 175 PILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKD-PFL- 232 PI+ GS + D ++ ++ L++ + ++P P D PFL Sbjct: 169 PIIRGSA-LKALEGDDDEEWEKKILELMDAVDSYIPTPE------------RAIDKPFLM 215 Query: 233 -----------GRIVTGRIHSGTIKSNQNI 251 G +VTGR+ G IK + + Sbjct: 216 PIEDVFSISGRGTVVTGRVERGIIKVGEEV 245 >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 = 73.2 bits (180), Expect = 2e-13 Identities = 35/160 (21%), Positives = 63/160 (39%), Gaps = 32/160 (20%) Query: 19 IRNIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERV-----MDCNDLEKERGITILAK 73 I I+ + GK+TL++ LL N+ ++E + +E G T Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLG-------NKFITEYKPGTTRNYVTTVIEEDGKTYKF- 52 Query: 74 VTSIVWNDVRINIVDTPGHADF-------GGEVERILCMVESVVVLVDAAEGPMPQTKFV 126 N++DT G D+ VE L + + V++++D E QTK Sbjct: 53 -----------NLLDTAGQEDYRAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTK-E 100 Query: 127 VGKALKIGLRPIVVVNKVDRSDARADEVINEVFDLFSALD 166 + + + I+V NK+D DA+ + +F + Sbjct: 101 IIHHAESNVPIILVGNKIDLRDAKLKTHVAFLFAKLNGEP 140 >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 = 72.6 bits (178), Expect = 3e-13 Identities = 69/292 (23%), Positives = 117/292 (40%), Gaps = 37/292 (12%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQ------RVSER---------VMDCNDLEKE 65 N+A I HVDHGK+T V LL + G + E+ VMD E+E Sbjct: 9 NVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVMDRLKEERE 68 Query: 66 RGITILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGP---MPQ 122 RG+TI + + IVD PGH DF + ++ V++V +G PQ Sbjct: 69 RGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGDGEFEVQPQ 128 Query: 123 TKFVVGKALKIGLRPIVV-VNKVDR---SDARADEVINEVFDLFSALDATDAQLDF-PI- 176 T+ A +G+ ++V +NK+D + + + EV +L + + F PI Sbjct: 129 TREHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTVPFIPIS 188 Query: 177 -LYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKDPFLGRI 235 G + S+ + LL + PP ++ ++ + +G + Sbjct: 189 AWNGDN----VIKKSENTPWYKGKTLLEALDALEPPEKPTDKPLRIPIQDVYSITGVGTV 244 Query: 236 VTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGD 287 GR+ +G +K + P G EV + + + I++A GD Sbjct: 245 PVGRVETGVLKPGDKV-VFEPAGVSGEVKSIE-------MHHEQIEQAEPGD 288 >gnl|CDD|178672 PLN03126, PLN03126, Elongation factor Tu; Provisional. Length = 478 Score = 71.6 bits (175), Expect = 6e-13 Identities = 77/287 (26%), Positives = 128/287 (44%), Gaps = 29/287 (10%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 NI I HVDHGKTTL L + +D E+ RGITI Sbjct: 83 NIGTIGHVDHGKTTLTAALTMALASMGGSAPKKYDEIDAAPEERARGITINTATVEYETE 142 Query: 81 DVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIVV 140 + VD PGHAD+ + ++ +++V A+GPMPQTK + A ++G+ +VV Sbjct: 143 NRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVV 202 Query: 141 -VNKVDRSDARADE-----VINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSR 194 +NK D+ D DE V EV +L S+ + D PI+ GS + + + Sbjct: 203 FLNKQDQVD---DEELLELVELEVRELLSSYEFPGD--DIPIISGSALLALEALMENPNI 257 Query: 195 DQG-------MVPLLNLIVDHVP-PPVISEGEFKMIGTILEKDPFLGRIVTGRIHSGTIK 246 +G + L++ + ++P P ++ F + + G + TGR+ GT+K Sbjct: 258 KRGDNKWVDKIYELMDAVDSYIPIPQRQTDLPFLLAVEDVFSITGRGTVATGRVERGTVK 317 Query: 247 SNQNIKALSPDGALVEVGRVSKILAFRGID--RQPIDEAHAGDIVSI 291 + + + R ++ G++ ++ +DEA AGD V + Sbjct: 318 VGETVDIVGL--------RETRSTTVTGVEMFQKILDEALAGDNVGL 356 >gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed. Length = 396 Score = 71.0 bits (175), Expect = 9e-13 Identities = 88/304 (28%), Positives = 132/304 (43%), Gaps = 71/304 (23%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWN 80 N+ I HVDHGKTTL + K + + +D EK RGITI TS V Sbjct: 14 NVGTIGHVDHGKTTLTAAITKVLAKKGGGEAKAYDQIDNAPEEKARGITI---NTSHVEY 70 Query: 81 DVRIN---IVDTPGHADFGGEVERILCMV------ESVVVLVDAAEGPMPQTKFVVGKAL 131 + VD PGHAD+ + M+ + +++V AA+GPMPQT+ + A Sbjct: 71 ETANRHYAHVDCPGHADY------VKNMITGAAQMDGAILVVSAADGPMPQTREHILLAR 124 Query: 132 KIGLRPIVV-VNKVDRSDARADE-----VINEVFDLFSALD-ATDAQLDFPILYGSGRFG 184 ++G+ IVV +NK D D DE V EV +L S D D D PI+ GS Sbjct: 125 QVGVPYIVVFLNKCDMVD---DEELLELVEMEVRELLSKYDFPGD---DTPIIRGSA-LK 177 Query: 185 WMSDSSDGSRDQGMVPLLNLIVDHVPPPVISEGEFKMIGTILEKD---PFL--------- 232 + D + ++ L++ + ++P P E+ PFL Sbjct: 178 ALEGDDDEEWEAKILELMDAVDSYIPEP--------------ERAIDKPFLMPIEDVFSI 223 Query: 233 ---GRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGID--RQPIDEAHAGD 287 G +VTGR+ G +K ++ +V + K G++ R+ +DE AGD Sbjct: 224 SGRGTVVTGRVERGIVKVGDEVE-------IVGIKETQKTTV-TGVEMFRKLLDEGQAGD 275 Query: 288 IVSI 291 V + Sbjct: 276 NVGV 279 >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 = 63.6 bits (155), Expect = 1e-10 Identities = 45/143 (31%), Positives = 66/143 (46%), Gaps = 29/143 (20%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWND 81 + I+ HVDHGKT+L+D + K +V++ + GIT + D Sbjct: 90 VTIMGHVDHGKTSLLDSIRKT--------KVAQG--------EAGGITQHIGAYHVENED 133 Query: 82 -VRINIVDTPGHADF------GGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIG 134 I +DTPGH F G +V I VV++V A +G MPQT + A Sbjct: 134 GKMITFLDTPGHEAFTSMRARGAKVTDI------VVLVVAADDGVMPQTIEAISHAKAAN 187 Query: 135 LRPIVVVNKVDRSDARADEVINE 157 + IV +NK+D+ +A D V E Sbjct: 188 VPIIVAINKIDKPEANPDRVKQE 210 >gnl|CDD|180006 PRK05306, infB, translation initiation factor IF-2; Validated. Length = 787 Score = 61.1 bits (149), Expect = 8e-10 Identities = 52/149 (34%), Positives = 68/149 (45%), Gaps = 42/149 (28%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKE-RGIT--ILAKVTSIV 78 + I+ HVDHGKT+L+D + K V E GIT I A + Sbjct: 293 VTIMGHVDHGKTSLLDAIRK------------TNVA-----AGEAGGITQHIGA--YQVE 333 Query: 79 WNDVRINIVDTPGHADF------GGEVERILCMVESVVVLVDAA-EGPMPQTKFVV--GK 129 N +I +DTPGH F G +V I VVLV AA +G MPQT + K Sbjct: 334 TNGGKITFLDTPGHEAFTAMRARGAQVTDI-------VVLVVAADDGVMPQTIEAINHAK 386 Query: 130 ALKIGLRPIVV-VNKVDRSDARADEVINE 157 A + PI+V +NK+D+ A D V E Sbjct: 387 AAGV---PIIVAINKIDKPGANPDRVKQE 412 >gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional. Length = 447 Score = 57.8 bits (139), Expect = 7e-09 Identities = 73/300 (24%), Positives = 121/300 (40%), Gaps = 43/300 (14%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSER-----------------VMDCNDLE 63 NI +I HVD GK+T L+ + G ++RV ER V+D E Sbjct: 9 NIVVIGHVDSGKSTTTGHLIYKLGGI--DKRVIERFEKEAAEMNKRSFKYAWVLDKLKAE 66 Query: 64 KERGITILAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMP-- 121 +ERGITI + ++D PGH DF + + V+++D+ G Sbjct: 67 RERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGGFEAG 126 Query: 122 -----QTKFVVGKALKIGLRPIV-VVNKVDR-----SDARADEVINEVFDLFSALDATDA 170 QT+ A +G++ ++ NK+D S AR DE++ EV + Sbjct: 127 ISKDGQTREHALLAFTLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGYNPD 186 Query: 171 QLDFPILYGSGRFGWMSDSSDGSRDQGMVPLLNLIVDHV-PPPVISEGEFKMIGTILEKD 229 ++ F + G + S++ +G P L +D + P S+ ++ + K Sbjct: 187 KIPFVPISGFEGDNMIERSTNLDWYKG--PTLLEALDQINEPKRPSDKPLRLPLQDVYKI 244 Query: 230 PFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIV 289 +G + GR+ +G IK + P G EV V + + + EA GD V Sbjct: 245 GGIGTVPVGRVETGVIKPGM-VVTFGPTGLTTEVKSVE-------MHHESLQEALPGDNV 296 >gnl|CDD|179703 PRK04000, PRK04000, translation initiation factor IF-2 subunit gamma; Validated. Length = 411 Score = 57.6 bits (140), Expect = 1e-08 Identities = 51/164 (31%), Positives = 70/164 (42%), Gaps = 63/164 (38%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITI---------- 70 NI ++ HVDHGKTTLV L +GV+ D R SE E +RGITI Sbjct: 11 NIGMVGHVDHGKTTLVQAL---TGVWTD--RHSE--------ELKRGITIRLGYADATIR 57 Query: 71 --------LAKVTSIVWNDV--------RINIVDTPGHADFGGEVERILCM--------V 106 A T + R++ VD PGH L + Sbjct: 58 KCPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGH--------ETLMATMLSGAALM 109 Query: 107 ESVVVLVDAAEG-PMPQTK--FVVGKALKI-GLRPIVVV-NKVD 145 + ++++ A E P PQTK + AL I G++ IV+V NK+D Sbjct: 110 DGAILVIAANEPCPQPQTKEHLM---ALDIIGIKNIVIVQNKID 150 >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 = 55.1 bits (133), Expect = 5e-08 Identities = 46/154 (29%), Positives = 71/154 (46%), Gaps = 43/154 (27%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITI-LAKVTSIVW 79 NI ++ HVDHGKTTL L +GV+ D SE E +RGI+I L + ++ Sbjct: 6 NIGMVGHVDHGKTTLTKAL---TGVWTD--THSE--------ELKRGISIRLGYADAEIY 52 Query: 80 NDV-------------------------RINIVDTPGHADFGGEVERILCMVESVVVLVD 114 R++ VD PGH + +++ ++++ Sbjct: 53 KCPECDGPECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALLVIA 112 Query: 115 AAEG-PMPQTKFVVGKALKI-GLRPIVVV-NKVD 145 A E P PQTK + AL+I G++ IV+V NK+D Sbjct: 113 ANEPCPQPQTKEHL-MALEIIGIKNIVIVQNKID 145 >gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation factor; Provisional. Length = 614 Score = 53.5 bits (129), Expect = 2e-07 Identities = 52/177 (29%), Positives = 76/177 (42%), Gaps = 43/177 (24%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWND 81 IA HVDHGKTTL+ + +GV + R+ E EK+RG+TI D Sbjct: 3 IATAGHVDHGKTTLLQAI---TGV--NADRLPE--------EKKRGMTIDLGYAYWPQPD 49 Query: 82 VR-INIVDTPGHADF--------GGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALK 132 R + +D PGH F GG ++ +++V +G M QT+ + L Sbjct: 50 GRVLGFIDVPGHEKFLSNMLAGVGG--------IDHALLVVACDDGVMAQTR----EHLA 97 Query: 133 IGLRPI------VVVNKVDR-SDARADEVINEVFDLFSALDATDAQLDFPILYGSGR 182 I L+ V + K DR +AR EV +V + +A+L F GR Sbjct: 98 I-LQLTGNPMLTVALTKADRVDEARIAEVRRQVKAVLREYGFAEAKL-FVTAATEGR 152 >gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional. Length = 446 Score = 51.7 bits (124), Expect = 6e-07 Identities = 73/291 (25%), Positives = 113/291 (38%), Gaps = 64/291 (21%) Query: 21 NIAIIAHVDHGKTTLVDELL-KQSGVFRDNQRVSER-----------------VMDCNDL 62 N+ +I HVD GK+T L+ K G+ ++R E+ V+D Sbjct: 9 NLVVIGHVDSGKSTTTGHLIYKCGGI---DKRTIEKFEKEAAEMGKGSFKYAWVLDKLKA 65 Query: 63 EKERGITILAKVTSIVWNDVRINIVDTPGHADF-------GGEVERILCMVESVVVLVDA 115 E+ERGITI + I+D PGH DF + + + +V S +A Sbjct: 66 ERERGITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVASTAGEFEA 125 Query: 116 AEGPMPQTKFVVGKALKIGLRPIVV-VNKVDR-----SDARADEVINEVFDLFSALDATD 169 QT+ A +G++ ++V +NK+D S R DE+ EV + Sbjct: 126 GISKDGQTREHALLAFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYNP 185 Query: 170 AQLDF-PILYGSGRFGWMSDSSDGSRDQGMV----PLLNLIVDHVPPPVIS--------- 215 ++ F PI GW D+ D M P L +D + PP Sbjct: 186 EKVPFIPI------SGWQGDNMIEKSDN-MPWYKGPTLLEALDTLEPPKRPVDKPLRLPL 238 Query: 216 EGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRV 266 + +K IG I G + GR+ +G +K + +P G EV V Sbjct: 239 QDVYK-IGGI-------GTVPVGRVETGILKPGMVVT-FAPSGVTTEVKSV 280 >gnl|CDD|179704 PRK04004, PRK04004, translation initiation factor IF-2; Validated. Length = 586 Score = 51.3 bits (124), Expect = 6e-07 Identities = 43/162 (26%), Positives = 68/162 (41%), Gaps = 60/162 (37%) Query: 17 MQIRN--IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERG-IT---- 69 ++R + ++ HVDHGKTTL+D++ + KE G IT Sbjct: 2 KKLRQPIVVVLGHVDHGKTTLLDKIRGTAVA-----------------AKEAGGITQHIG 44 Query: 70 -------ILAKVTSIVWNDVRINI-------VDTPGHADF------GGEVERILCMVESV 109 ++ K+ + + I + +DTPGH F GG + I Sbjct: 45 ATEVPIDVIEKIAGPLKKPLPIKLKIPGLLFIDTPGHEAFTNLRKRGGALADI------A 98 Query: 110 VVLVDAAEGPMPQTKFVVGKALKIGLR----P-IVVVNKVDR 146 +++VD EG PQT +A+ I L+ P +V NK+DR Sbjct: 99 ILVVDINEGFQPQTI----EAINI-LKRRKTPFVVAANKIDR 135 Score = 31.3 bits (72), Expect = 0.76 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 10/59 (16%) Query: 235 IVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQ-PIDEAHAGDIVSIA 292 IV + GTIK + + DG VG + +I D+ + EA AG V+I+ Sbjct: 484 IVGVEVLGGTIKPGVPL--IKEDGK--RVGTIKQIQ-----DQGENVKEAKAGMEVAIS 533 >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 = 72/316 (22%), Positives = 128/316 (40%), Gaps = 57/316 (18%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWND 81 ++++ HVDHGKTTL+D++ + R+ +++ + E + ++ + + Sbjct: 7 VSVLGHVDHGKTTLLDKIRGSAVAKREAGGITQHIG-----ATEIPMDVIEGICGDLLKK 61 Query: 82 VRINI-------VDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIG 134 +I + +DTPGH F +R + + +++VD EG PQT+ +AL I Sbjct: 62 FKIRLKIPGLLFIDTPGHEAFTNLRKRGGALADLAILIVDINEGFKPQTQ----EALNI- 116 Query: 135 LRP-----IVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILY----------- 178 LR +V NK+DR + FS + Q +Y Sbjct: 117 LRMYKTPFVVAANKIDRIPGWRSHEGRPFMESFSKQEIQVQQNLDTKVYNLVIKLHEEGF 176 Query: 179 GSGRFGWMSDSS--------DGSRDQGMVPLLNLIV----DHVPPPVISEGEFKMIGTIL 226 + RF ++D + +G+ LL ++ ++ + E E GTIL Sbjct: 177 EAERFDRVTDFTKTVAIIPISAITGEGIPELLTMLAGLAQQYLEEQLKLEEEGPARGTIL 236 Query: 227 E--KDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDR------- 277 E ++ LG + I+ G ++ I D +V RV +L R ++ Sbjct: 237 EVKEETGLGMTIDAVIYDGILRKGDTIAMAGSDDVIVT--RVRALLKPRPLEEMRESRKK 294 Query: 278 -QPIDEAHAGDIVSIA 292 Q +DE A V IA Sbjct: 295 FQKVDEVVAAAGVKIA 310 >gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional. Length = 632 Score = 45.7 bits (109), Expect = 4e-05 Identities = 54/184 (29%), Positives = 79/184 (42%), Gaps = 59/184 (32%) Query: 28 VDHGKTTLVDELLKQSG-VFRDN----QRVSERVMDCND------------LEKERGITI 70 VD GK+TL+ LL S +F D +R S++V D E+E+GITI Sbjct: 33 VDDGKSTLIGRLLYDSKMIFEDQLAALERDSKKVGTQGDEIDLALLVDGLAAEREQGITI 92 Query: 71 LAKVTSIVWNDV---------RINIV-DTPGHADFGGEVERILCMV------ESVVVLVD 114 DV R IV DTPGH + MV + ++LVD Sbjct: 93 ----------DVAYRYFATPKRKFIVADTPGHEQYTRN------MVTGASTADLAIILVD 136 Query: 115 AAEGPMPQTK---FVVGKALKIGLRPIVV-VNK---VDRSDARADEVINEVFDLFSALDA 167 A +G + QT+ F+ +L +G+R +V+ VNK VD DE++ + + L Sbjct: 137 ARKGVLTQTRRHSFIA--SL-LGIRHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGL 193 Query: 168 TDAQ 171 D Sbjct: 194 HDVT 197 >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 = 45.4 bits (108), Expect = 4e-05 Identities = 72/294 (24%), Positives = 119/294 (40%), Gaps = 50/294 (17%) Query: 28 VDHGKTTLVDELLKQSGVFRDNQ-----RVSER------------VMDCNDLEKERGITI 70 VD GK+TL+ LL + ++Q R S++ ++D E+E+GITI Sbjct: 9 VDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQGGEIDLALLVDGLQAEREQGITI 68 Query: 71 LAKVTSIVWNDVRINIVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKA 130 + + + DTPGH + + + V+LVDA +G + QT+ A Sbjct: 69 DVAYRYFSTDKRKFIVADTPGHEQYTRNMATGASTADLAVLLVDARKGVLEQTRRHSYIA 128 Query: 131 LKIGLRPIVV-VNKVDRS--DARADEVINEVFDLFS-ALDATDAQLDFPI--LYG----- 179 +G+R +V+ VNK+D D E I + + F+ L D P+ L G Sbjct: 129 SLLGIRHVVLAVNKMDLVDYDEEVFENIKKDYLAFAEQLGFRDVTF-IPLSALKGDNVVS 187 Query: 180 -SGRFGWMSDSSDGSRDQGMVPLLNLIVDHVP-PPVISEGEFKMIGTILEKDPFLGRIVT 237 S W S P L I++ V + + + + R Sbjct: 188 RSESMPWYSG-----------PTLLEILETVEVERDAQDLPLRFPVQYVNRPNLDFRGYA 236 Query: 238 GRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGIDRQPIDEAHAGDIVSI 291 G I SG++ + L P G RV++I+ F G +++A AG V++ Sbjct: 237 GTIASGSVHVGDEVVVL-PSG---RSSRVARIVTFDG----DLEQARAGQAVTL 282 >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 = 42.0 bits (100), Expect = 4e-04 Identities = 45/204 (22%), Positives = 70/204 (34%), Gaps = 62/204 (30%) Query: 31 GKTTLVDELLK--------QSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWNDV 82 GK+TL + L GV RD R W Sbjct: 11 GKSTLFNRLTGKRDAIVSDTPGVTRD--RKYGDA---------------------EWGGR 47 Query: 83 RINIVDTPGHAD----FGGEVER--ILCMVESVVVL--VDAAEGPMPQTKFVVGKALKIG 134 ++DT G + ++ + + E+ V+L VD EG P+ + + K G Sbjct: 48 EFILIDTGGIEEDDDGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEEIAKWLRKSG 107 Query: 135 LRPIVVVNKVDRSDARADEVINEVFDLFSALDATDAQLDFPILYGSGRFGWMSDSSDGSR 194 I+V NK+D + D V E F +L + PI S G Sbjct: 108 KPVILVANKID--GKKEDAVAAE----FYSLGFGEP---IPI---SAEHG---------- 145 Query: 195 DQGMVPLLNLIVDHVPPPVISEGE 218 +G+ LL+ I++ +P E E Sbjct: 146 -RGIGDLLDAILELLPEEEEEEEE 168 Score = 41.3 bits (98), Expect = 7e-04 Identities = 46/178 (25%), Positives = 72/178 (40%), Gaps = 36/178 (20%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWND 81 IAII + GK+TLV+ LL + ERV+ + G T + N Sbjct: 175 IAIIGRPNVGKSTLVNALLGE-----------ERVIVSD----IAGTTRDSIDIPFERNG 219 Query: 82 VRINIVDTPG-----HADFGGE------VERILCMVESVVVLVDAAEGPMPQTKFVVGKA 130 + ++DT G G E + + + V++++DA EG Q + G Sbjct: 220 KKYLLIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEGITEQDLRIAGLI 279 Query: 131 LKIGLRPIVVVNKVD--RSDARADEVINEVFDLFSALDATDAQLDF-PILYGSGRFGW 185 L+ G ++VVNK D + + +E E L LDF PI++ S G Sbjct: 280 LEAGKALVIVVNKWDLVKDEKTREEFKKE-------LRRKLPFLDFAPIVFISALTGQ 330 >gnl|CDD|179943 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional. Length = 474 Score = 40.3 bits (95), Expect = 0.001 Identities = 81/325 (24%), Positives = 126/325 (38%), Gaps = 111/325 (34%) Query: 28 VDHGKTTLVDELL---KQ------SGVFRDNQRVS---ERVMDCNDL---------EKER 66 VD GK+TL+ LL KQ + + D++R E++ DL E+E+ Sbjct: 36 VDDGKSTLIGRLLHDTKQIYEDQLASLHNDSKRHGTQGEKL----DLALLVDGLQAEREQ 91 Query: 67 GITILAKVTSIVWNDV----------RINIVDTPGHADF------GGEVERILCMVESVV 110 GITI DV + I DTPGH + G C + + Sbjct: 92 GITI----------DVAYRYFSTEKRKFIIADTPGHEQYTRNMATGAST----C--DLAI 135 Query: 111 VLVDAAEGPMPQTK---FVVGKALKIGLRPIVV-VNK---VDRSDARADEVINEVFDLFS 163 +L+DA +G + QT+ F+ A +G++ +VV VNK VD S+ + + + Sbjct: 136 LLIDARKGVLDQTRRHSFI---ATLLGIKHLVVAVNKMDLVDYSEEVFERIREDYLTFAE 192 Query: 164 ALDATDAQLDF-PI--LYG------SGRFGWMSDSS--------DGSRDQGMVPLLNLIV 206 L + + F P+ L G S W S + D R P V Sbjct: 193 QLP-GNLDIRFVPLSALEGDNVVSQSESMPWYSGPTLLEVLETVDIQRVVDAQP-FRFPV 250 Query: 207 DHVPPPVISEGEFKMIGTILEKDPFLGRIVTGRIHSGTIKSNQNIKALSPDGALVEVGRV 266 +V P + F G G + SG +K +K L P G V Sbjct: 251 QYVNRPNLD---------------FRG--YAGTLASGVVKVGDRVKVL-PSGK---ESNV 289 Query: 267 SKILAFRGIDRQPIDEAHAGDIVSI 291 ++I+ F G D + EA AG+ +++ Sbjct: 290 ARIVTFDG-DLE---EAFAGEAITL 310 >gnl|CDD|178858 PRK00093, PRK00093, GTP-binding protein Der; Reviewed. Length = 435 Score = 38.5 bits (91), Expect = 0.005 Identities = 48/170 (28%), Positives = 73/170 (42%), Gaps = 35/170 (20%) Query: 22 IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITILAKVTSIVWND 81 IAII + GK++L++ LL + ERV+ + G T + T + Sbjct: 176 IAIIGRPNVGKSSLINALLGE-----------ERVIVSD----IAGTTRDSIDTPFERDG 220 Query: 82 VRINIVDTPG-----HADFGGE---VERILCMVES--VVVLV-DAAEGPMPQTKFVVGKA 130 + ++DT G G E V R L +E VV+LV DA EG Q + G A Sbjct: 221 QKYTLIDTAGIRRKGKVTEGVEKYSVIRTLKAIERADVVLLVIDATEGITEQDLRIAGLA 280 Query: 131 LKIGLRPIVVVNKVD-RSDARADEVINEVFDLFSALDATDAQLDF-PILY 178 L+ G ++VVNK D + +E E+ LD+ PI++ Sbjct: 281 LEAGRALVIVVNKWDLVDEKTMEEFKKELRRRL-------PFLDYAPIVF 323 Score = 37.0 bits (87), Expect = 0.016 Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 8/82 (9%) Query: 79 WNDVRINIVDTPG----HADFGGEVER--ILCMVESVVVL--VDAAEGPMPQTKFVVGKA 130 W ++DT G F ++ L + E+ V+L VD G P + + Sbjct: 46 WLGREFILIDTGGIEPDDDGFEKQIREQAELAIEEADVILFVVDGRAGLTPADEEIAKIL 105 Query: 131 LKIGLRPIVVVNKVDRSDARAD 152 K I+VVNKVD D AD Sbjct: 106 RKSNKPVILVVNKVDGPDEEAD 127 >gnl|CDD|178854 PRK00089, era, GTPase Era; Reviewed. Length = 292 Score = 37.7 bits (89), Expect = 0.009 Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 20/91 (21%) Query: 87 VDTPG-HADFGGEVERIL--CMVES----------VVVLVDAAEGPMPQTKFVVGKALKI 133 VDTPG H +R L M ++ V+ +VDA E P +F++ K K+ Sbjct: 58 VDTPGIHKP-----KRALNRAMNKAAWSSLKDVDLVLFVVDADEKIGPGDEFILEKLKKV 112 Query: 134 GLRPIVVVNKVDRSDARAD--EVINEVFDLF 162 I+V+NK+D + + ++ E+ +L Sbjct: 113 KTPVILVLNKIDLVKDKEELLPLLEELSELM 143 >gnl|CDD|185557 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2 gamma subunit; Provisional. Length = 460 Score = 35.7 bits (83), Expect = 0.033 Identities = 21/54 (38%), Positives = 24/54 (44%), Gaps = 21/54 (38%) Query: 21 NIAIIAHVDHGKTTLVDELLKQSGV----FRDNQRVSERVMDCNDLEKERGITI 70 NI I HV HGK+T+V L SGV F+ EK R ITI Sbjct: 36 NIGTIGHVAHGKSTVVKAL---SGVKTVRFKR--------------EKVRNITI 72 >gnl|CDD|181925 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der; Reviewed. Length = 712 Score = 34.4 bits (79), Expect = 0.095 Identities = 33/153 (21%), Positives = 66/153 (43%), Gaps = 29/153 (18%) Query: 5 DGLFFIYGRLGYMQ--IRNIAIIAHVDHGKTTLVDELL-KQSGVFRDNQRVSERVMDCND 61 +G F+ G + +AI+ + GK+TLV+ +L ++ V D V+ Sbjct: 259 EGSGFVAGDEKAGPKAVGVVAIVGRPNVGKSTLVNRILGRREAVVEDTPGVT-------- 310 Query: 62 LEKERGITILAKVTSIVWNDVRINIVDTPG--------HADFGGEVERILCMVESVVVLV 113 ++R ++ A+ W +VDT G + + + + + ++VV +V Sbjct: 311 --RDR-VSYDAE-----WAGTDFKLVDTGGWEADVEGIDSAIASQAQIAVSLADAVVFVV 362 Query: 114 DAAEGPMPQTKFVVGKALKIGLRPI-VVVNKVD 145 D G T + + L+ +P+ + VNK+D Sbjct: 363 DGQVGLT-STDERIVRMLRRAGKPVVLAVNKID 394 >gnl|CDD|184848 PRK14845, PRK14845, translation initiation factor IF-2; Provisional. Length = 1049 Score = 33.7 bits (77), Expect = 0.15 Identities = 67/264 (25%), Positives = 103/264 (39%), Gaps = 45/264 (17%) Query: 86 IVDTPGHADFGGEVERILCMVESVVVLVDAAEGPMPQTKFVVGKALKIGLRPIVV-VNKV 144 +DTPGH F +R + + V++VD EG PQT + L+ P VV NK+ Sbjct: 530 FIDTPGHEAFTSLRKRGGSLADLAVLVVDINEGFKPQTIEAI-NILRQYKTPFVVAANKI 588 Query: 145 DRSDARADEVINEVFDLFSALDATDAQLDFPI--------LYGSGRFGWMSDSSDGSRD- 195 D +E F L A + I LY G+ +D D +D Sbjct: 589 DLIPGWNISE-DEPFLLNFNEQDQHALTELEIKLYELIGKLY---ELGFDADRFDRVQDF 644 Query: 196 --------------QGMVPLLNLIV----DHVPPPVISEGEFKMIGTILE--KDPFLGRI 235 +G+ LL ++ ++ + E GTILE ++ LG Sbjct: 645 TRTVAIVPVSAKTGEGIPELLMMVAGLAQKYLEERLKLNVEGYAKGTILEVKEEKGLGTT 704 Query: 236 VTGRIHSGTIKSNQNIKALSPDGALVEVGRVSKILAFRGID--RQPIDEAHAGDIVSIAG 293 + I+ GT++ I PD +V +V +L + +D R P D+ D V+ A Sbjct: 705 IDAIIYDGTLRRGDTIVVGGPDDVIVT--KVRALLKPKPLDEIRDPRDKFDPVDEVTAAA 762 Query: 294 LVKATVADTFCDPSIDEPLKAQPI 317 VK P ++E L PI Sbjct: 763 GVKIAA------PGLEEVLAGSPI 780 >gnl|CDD|183441 PRK12326, PRK12326, preprotein translocase subunit SecA; Reviewed. Length = 764 Score = 32.6 bits (75), Expect = 0.31 Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 8/82 (9%) Query: 273 RGIDRQ-PIDEAHAGDIVSIAGLVKATV---ADTFCDPSIDEP---LKAQPIDPPTVTMT 325 R + RQ P+DE H + + L V +TF I + L + PT T T Sbjct: 681 RALGRQNPLDEFHRMAVDAFKSLAADAVERAQETFETAEITDDGADLDLAGLARPTATWT 740 Query: 326 FGVNDSPLAGTEGDKVTSRMIR 347 + V+D+PL+ +G V S + Sbjct: 741 YMVHDNPLSS-DGLSVLSGLPG 761 >gnl|CDD|168168 PRK05674, PRK05674, gamma-carboxygeranoyl-CoA hydratase; Validated. Length = 265 Score = 31.3 bits (71), Expect = 0.72 Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 12/60 (20%) Query: 141 VNKVDRSDARADEVINEVFDLFSALD--ATDAQLDFPILYGSGR-------FGWMSDSSD 191 +++ D+++A ++I E L ALD +DA L F +L G GR WM S+D Sbjct: 21 LSRADKNNAFNAQMIRE---LILALDQVQSDASLRFLLLRGRGRHFSAGADLAWMQQSAD 77 >gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional. Length = 201 Score = 31.0 bits (71), Expect = 0.85 Identities = 13/30 (43%), Positives = 21/30 (70%), Gaps = 1/30 (3%) Query: 133 IGLRPIVVVNKVDRSDARADEVINEVFDLF 162 +G+ PIV VNK+D+ R DEV++E+ + Sbjct: 129 LGIPPIVAVNKMDKIKNR-DEVLDEIAERL 157 >gnl|CDD|179275 PRK01294, PRK01294, lipase chaperone; Provisional. Length = 336 Score = 30.4 bits (69), Expect = 1.3 Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 5/46 (10%) Query: 348 DRLFKEAEGNIALKIEESSSKDAF--FVSGRGELQLAVLIETMRRE 391 L +A+G++A + +D F F+S GEL LA + + RE Sbjct: 72 PGLPLDAQGHLAD---TRALRDFFDYFLSALGELDLAAIDALVERE 114 >gnl|CDD|179996 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed. Length = 449 Score = 30.5 bits (70), Expect = 1.3 Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 10/89 (11%) Query: 76 SIVWNDVRINIVDTPGHADFGGEVERI-----LCMVES---VVVLVDAAEGPMPQTKFVV 127 I + + + ++DT G + EVE+I +E V++++DA+E + ++ Sbjct: 257 HINLDGIPLRLIDTAGIRETDDEVEKIGIERSREAIEEADLVLLVLDASEPLTEEDDEIL 316 Query: 128 GKALKIGLRPIVVVNKVDRSDARADEVIN 156 + + IVV+NK D + E N Sbjct: 317 EELKDKPV--IVVLNKADLTGEIDLEEEN 343 >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 = 30.6 bits (70), Expect = 1.3 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 1/79 (1%) Query: 411 LLEPIEEVVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVFLSPTRGLIGYQSQL 470 LLEPI +V + V EE+ G V+ + + ++ + G +V + P + GY + L Sbjct: 1 LLEPIMKVEVTVPEEYMGDVIGDLNSRRGKIEGMEQRGGAQVIKAKV-PLSEMFGYATDL 59 Query: 471 MTDTRGTAIMNRLFHSYQP 489 + T+G A + F Y+ Sbjct: 60 RSATQGRATWSMEFSHYEE 78 >gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed. Length = 472 Score = 29.2 bits (66), Expect = 3.0 Identities = 38/148 (25%), Positives = 59/148 (39%), Gaps = 41/148 (27%) Query: 22 IAIIAHVDHGKTTLVDELLKQS--------GVFRDNQRVSERVMDCNDLEKERGITILAK 73 +A++ + GK+TLV+ +L + GV RD RVS Sbjct: 41 VAVVGRPNVGKSTLVNRILGRREAVVEDVPGVTRD--RVSYDAE---------------- 82 Query: 74 VTSIVWNDVRINIVDTPG--------HADFGGEVERILCMVESVVVLVDAAEGPMPQTKF 125 WN R +VDT G A + E + ++V+ +VDA G T Sbjct: 83 -----WNGRRFTVVDTGGWEPDAKGLQASVAEQAEVAMRTADAVLFVVDATVGAT-ATDE 136 Query: 126 VVGKALKIGLRPIVVV-NKVDRSDARAD 152 V + L+ +P+++ NKVD AD Sbjct: 137 AVARVLRRSGKPVILAANKVDDERGEAD 164 >gnl|CDD|148110 pfam06303, MatP, Organiser of macrodomain of Terminus of chromosome. This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localizes with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial chromosome management during the cell cycle. Length = 148 Score = 28.9 bits (65), Expect = 4.2 Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 4/66 (6%) Query: 563 SGKDEAVKLVPAVKMTLEQALSWIQ---NDELVEVTPKSIRL-RKMYLDPNERKRKGKSV 618 S + AV+ + ++ + L WI+ N EL ++IR RK + + ++ + KS+ Sbjct: 35 SLAEAAVQELLKLEHEPVKVLEWIKAHMNPELENKMKQAIRARRKRHFNAEKQHTRKKSI 94 Query: 619 NLEYNV 624 +LEY V Sbjct: 95 DLEYRV 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 = 28.6 bits (64), Expect = 5.0 Identities = 31/143 (21%), Positives = 62/143 (43%), Gaps = 29/143 (20%) Query: 15 GYMQIRN---IAIIAHVDHGKTTLVDELLKQSGVFRDNQRVSERVMDCNDLEKERGITIL 71 ++ + +AI+ + GK++L++ LLKQ D VS+ D+ + Sbjct: 196 KLEKLDDGFKLAIVGSPNVGKSSLLNALLKQ-----DRAIVSDIKGTTRDVVEG------ 244 Query: 72 AKVTSIVWNDVRINIVDTPGHADFGGEVERI--------LCMVESVVVLVDAAEGPMPQT 123 N + I ++DT G + VER+ + + V+ ++DA++ Sbjct: 245 ----DFELNGILIKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIYVLDASQPLTKDD 300 Query: 124 KFVVGKALKIGLRP-IVVVNKVD 145 ++ L +P I+V+NK+D Sbjct: 301 FLII--DLNKSKKPFILVLNKID 321 >gnl|CDD|183557 PRK12494, PRK12494, NADH dehydrogenase subunit J; Provisional. Length = 172 Score = 28.0 bits (63), Expect = 7.8 Identities = 11/32 (34%), Positives = 18/32 (56%) Query: 255 SPDGALVEVGRVSKILAFRGIDRQPIDEAHAG 286 +P+ A+VE G VS+ L G + + + H G Sbjct: 8 TPEAAIVEAGPVSQWLTENGFEHESLGPDHLG 39 >gnl|CDD|162404 TIGR01533, lipo_e_P4, 5'-nucleotidase, lipoprotein e(P4) family. which in turn belongs to the haloacid dehalogenase (HAD) superfamily of aspartate-dependent hydrolases. Members are found on the outer membrane of Gram-negative bacteria and the cytoplasmic membrane of Gram-positive bacteria. Most members have classic lipoprotein signal sequences. A critical role of this 5'-nucleotidase in Haemophilus influenzae is the degradation of external riboside in order to allow transport into the cell. An earlier suggested role in hemin transport is no longer current. This enzyme may also have other physiologically significant roles. Length = 266 Score = 27.9 bits (62), Expect = 7.9 Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 1/42 (2%) Query: 369 DAFFVSGRGELQLAVLIETMRREGFELAVSRPRVVIKKEGDS 410 F+VS R E + A ++ ++R GF A +++KK+ S Sbjct: 136 KIFYVSNRSEKEKAATLKNLKRFGFPQA-DEEHLLLKKDKSS 176 >gnl|CDD|184709 PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein; Provisional. Length = 229 Score = 27.6 bits (62), Expect = 8.9 Identities = 11/25 (44%), Positives = 17/25 (68%) Query: 19 IRNIAIIAHVDHGKTTLVDELLKQS 43 +R I +I D GKTTL++++LK Sbjct: 1 MRAIGVIGFKDSGKTTLIEKILKNL 25 >gnl|CDD|183316 PRK11790, PRK11790, D-3-phosphoglycerate dehydrogenase; Provisional. Length = 409 Score = 27.8 bits (63), Expect = 9.1 Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 9/39 (23%) Query: 418 VVIDVDEEHSGAVVQKMTLHKSEMIELRPSGTGRVRLVF 456 VVIDVD +++ + + GT R RL++ Sbjct: 380 VVIDVDADYAEEALDALKAIP---------GTIRARLLY 409 >gnl|CDD|167016 PRK00635, PRK00635, excinuclease ABC subunit A; Provisional. Length = 1809 Score = 27.5 bits (61), Expect = 9.9 Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 12/64 (18%) Query: 331 SPLAGTEGDKVTSRMIRDRLFKE-AEGNIALKIEESSSKDAFFVSGRGELQLAVLIETMR 389 SPL+G K+T + I + L +G + + +D L + ++ Sbjct: 1058 SPLSGDALRKITPQTIAEELLTHYTKGYVTITSPIPKEED-----------LFIYLQEKL 1106 Query: 390 REGF 393 +EGF Sbjct: 1107 KEGF 1110 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 0.318 0.138 0.390 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: 10,379,458 Number of extensions: 710806 Number of successful extensions: 1581 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1474 Number of HSP's successfully gapped: 107 Length of query: 624 Length of database: 5,994,473 Length adjustment: 99 Effective length of query: 525 Effective length of database: 3,855,281 Effective search space: 2024022525 Effective search space used: 2024022525 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 60 (26.9 bits)