RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781103|ref|YP_003065516.1| penicillin-binding transmembrane protein [Candidatus Liberibacter asiaticus str. psy62] (598 letters) >gnl|CDD|131269 TIGR02214, spoVD_pbp, stage V sporulation protein D. This model describes the spoVD subfamily of homologs of the cell division protein FtsI, a penicillin binding protein. This subfamily is restricted to Bacillus subtilis and related Gram-positive species with known or suspected endospore formation capability. In these species, the functional equivalent of FtsI is desginated PBP-2B, a paralog of spoVD. Length = 636 Score = 228 bits (583), Expect = 3e-60 Identities = 141/517 (27%), Positives = 226/517 (43%), Gaps = 41/517 (7%) Query: 116 RPDIIDRNGEILATDIPTFSLYVEPHKVISP-----DEIIEKLQIVLPNLDSEMIRRKLS 170 R I+DRNG LA + + ++P + EI +L VL ++ +R Sbjct: 49 RGRILDRNGNELAVSVSVDRVDLDPATIRKNKEPKQREIANELARVLEMDKEKVFKRITK 108 Query: 171 SETKFQW--LRRKLSPQQQKRILSFGLPGVGFRLEKSRFYPAASHASHVVGYVDIDNRGI 228 + F L RK+ + +++ + L GV + R+YP SHV+G+ + D RG+ Sbjct: 109 KNSPFVSAKLGRKIEKDKAEKVRNLKLNGVSVSPDSKRYYPNGDFLSHVLGFTNSDGRGL 168 Query: 229 TGIEKFLD-----MQGLTRVFTTNKGEKNLQPIR------------LALDLRIQNIVHQE 271 G+E + D + G+ + L +D IQ I+ +E Sbjct: 169 EGLELYYDKELRGLPGVRVAEYDANSLELPYAQHAYVKPVDGHDLVLTIDENIQYIIERE 228 Query: 272 LVENKKKYNAESVGTVILNVSTGEVISMVSIPDYDPHEAFKGKKEGW-FNRISYGIFEMG 330 + ++ + V +++N GE++ M + P YDP++ + NR +E G Sbjct: 229 ADKALRERKPKGVSIIVMNPKNGEILGMSNRPTYDPNDPRDKSPDTARRNRAVSDAYEPG 288 Query: 331 SIFKVFTIAMGIDSGLFTVKDLFDTRNPIKVGKHVIHDYHPQNR-ILTIPEIFRYSSNIG 389 S FK+ T + ++ G+ D F VG I + P T PE+ + S N G Sbjct: 289 STFKIITSSAAMEEGIVKESDKFYDDGSATVGGKKIKCWKPGGHGSQTFPEVVQNSCNPG 348 Query: 390 AAQIADAMGIQGHKEFLYRLGLLSKLETELP-EIQAPSYP-SQWKRIHSLTISFGHGLST 447 ++ +G + ++ G SK +LP E P + + TISFG + Sbjct: 349 FIELGMRLGAEKLNNYILAFGFGSKTGIDLPGEAAGILVPKKKVGPVDLATISFGQANTV 408 Query: 448 TPLQTAVAAAALINEGRLIPPTFM---------IRSREESEKVSRIVLKKNTVKTMRSLL 498 TP+Q A A+ N G+LI P M + +V R V+ K T + +R L Sbjct: 409 TPIQLMTAVNAVANGGKLIQPHIMKEISDSQNNAVDQTFEPEVKRQVVSKETTQKLRLAL 468 Query: 499 REGVTGGSGRRAFVPGFEVGGKTGTAQKV-IKKRYSDTLNFNSFLAVFPTTDPQYIVLSF 557 V+ GSG+ AF+ G+ VGGKTGTAQKV Y + SF+ P DP VL Sbjct: 469 ETVVSKGSGKNAFIEGYRVGGKTGTAQKVKPNGGYMEGEYIVSFVGFAPADDPAVAVLVV 528 Query: 558 MDSPKIKERNQLTAGINVAPMVGNIIRRSASMLGVKP 594 +D+PK Q G+ AP+ G++ + LG+KP Sbjct: 529 VDNPK---GVQQFGGLVAAPVFGSVFNDILNYLGIKP 562 >gnl|CDD|163256 TIGR03423, pbp2_mrdA, penicillin-binding protein 2. Members of this protein family are penicillin-binding protein 2 (PBP-2), a protein whose gene (designated pbpA or mrdA) generally is found next to the gene for RodA, a protein required for rod (bacillus) shape in many bacteria. PBP-2 acts as a transpeptidase for cell elongation (hence, rod-shape). Length = 592 Score = 223 bits (572), Expect = 8e-59 Identities = 147/584 (25%), Positives = 239/584 (40%), Gaps = 123/584 (21%) Query: 73 RIGMTIVVCLVIYIILAIR-----IIQYGN---------IHPEPIAPSMNIDEYGMSRPD 118 R + + L ++ +LA R +I+ I PI P R Sbjct: 2 RALVAGGLVLALFGVLAARLFYLQVIRGEEYATLSEDNRIRLVPIPPP---------RGL 52 Query: 119 IIDRNGEILATDIPTFSLYVEPHKVISPDEIIEKLQIVLPNLDSEMIRRK---LSSETKF 175 I+DRNG +LA + P+FSL + P KV D +++L +L LD E I R L +F Sbjct: 53 ILDRNGVLLADNRPSFSLEIVPEKVDDLDATLDRLAKLLD-LDPEDIERFLKELKRSRRF 111 Query: 176 Q--WLRRKLSPQQQKRIL--SFGLPGVGFRLEKSRFYPAASHASHVVGYV-DIDNR---- 226 + L+ L+ ++ R + LPGV R+YP A+HV+GYV +I+ Sbjct: 112 EPIPLKSDLTEEEVARFAVNQYRLPGVEIEARLKRYYPYGELAAHVLGYVGEINEEDLER 171 Query: 227 ------------GITGIEKFLDMQ-----GLTRVFTTNKG----EKNLQP------IRLA 259 G +GIEK+ + + G V +G + P + L Sbjct: 172 LEPANYAGGDYIGKSGIEKYYEDELRGKPGYREVEVNARGRVIRTLSRVPPVPGKDLVLT 231 Query: 260 LDLRIQNIVHQELVENKKKYNAESVGT-VILNVSTGEVISMVSIPDYDPHEAFKG-KKEG 317 +D R+Q + L + G V+++ TGE+++MVS P +DP+ G + Sbjct: 232 IDARLQQAAEKALGGRR--------GAVVVMDPRTGEILAMVSTPSFDPNLFVDGISSKD 283 Query: 318 W-----------FNRISYGIFEMGSIFKVFTIAMGIDSGLFTVKDLFDTRNPIKVGKHVI 366 W NR G++ GS FK F ++ G+ T + ++G Sbjct: 284 WKALLNDPDRPLLNRAIQGVYPPGSTFKPFVALAALEEGVITPETRIYCPGYFQLGGRRF 343 Query: 367 HDYHPQNR-ILTIPEIFRYSSNIGAAQIADAMGIQGHKEFLYRLGLLSKLETELPEIQAP 425 + + + + S ++ Q+A +GI E+ + G K +LP ++ Sbjct: 344 RCWKRGGHGRVDLRKAIEESCDVYFYQLALRLGIDKIAEYAKKFGFGQKTGIDLPGEKSG 403 Query: 426 SYPS-QWKR-------IHSLTISFGHG---LSTTPLQTAVAAAALINEGRLIPPTFM--- 471 PS +WKR T++ G + TPLQ AVA AAL N G+L P + Sbjct: 404 LVPSREWKRKRFGQPWYPGDTLNVSIGQGYVLVTPLQLAVATAALANGGKLYKPHLVKSI 463 Query: 472 ------IRSREESEKVSRIVLKKNTVKTMRSLLREGVT--GGSGRRAFVP-GFEVGGKTG 522 + E E + + + + +R +R+ V GG+ RRA + +++ GKTG Sbjct: 464 EDPDGGVVQETEPEVLRPLPISPENLDVVREGMRDVVNEPGGTARRARLGLPYKMAGKTG 523 Query: 523 TAQKV------------IKKRYSDTLNFNSFLAVFPTTDPQYIV 554 TAQ V I +R D F+A P +P+ V Sbjct: 524 TAQVVSLKQGEKYDAEQIPERLRDH---ALFVAFAPYDNPKIAV 564 >gnl|CDD|185060 PRK15105, PRK15105, peptidoglycan synthase FtsI; Provisional. Length = 578 Score = 170 bits (433), Expect = 7e-43 Identities = 153/564 (27%), Positives = 264/564 (46%), Gaps = 76/564 (13%) Query: 78 IVVCLVIYIILAIRIIQYGNIHPEPI-----APSMNIDEYGMSRPDIIDRNGEILATDIP 132 I++ LV L R+ I+P+ + S+ + E SR I DR+G LA +P Sbjct: 30 ILLALVF---LLGRVAWLQVINPDMLVREGDMRSLRVQEVSTSRGMITDRSGRPLAVSVP 86 Query: 133 TFSLYVEPHKV-----ISPDEIIEKLQIVLPNLDSEMIRRKLSSETK--FQWLRRKLSPQ 185 +++ +P +V IS D+ + L L N+ + + ++++ K F +L R+++P Sbjct: 87 VKAIWADPKEVHDAGGISVDDRWKALADAL-NIPLDQLSARINANPKGRFIYLARQVNPD 145 Query: 186 QQKRILSFGLPGVGFRLEKSRFYPAASHASHVVGYVDIDNRGITGIEKFLDMQGLTRVFT 245 I LPG+ R E R+YP+ +H++G+ ++D++GI G+EK D + T Sbjct: 146 MADYIKKLKLPGIHLREESRRYYPSGEVTAHLIGFTNVDSQGIEGVEKSFD-----KWLT 200 Query: 246 TNKGEKNLQPIR--------------------LALDLRIQNIVHQELVENKKKYN-AESV 284 GE+ ++ R L++D R+Q +V++EL N +N AES Sbjct: 201 GQPGERIVRKDRYGRVIEDISSTDSQAAHNLALSIDERLQALVYREL-NNAVAFNKAESG 259 Query: 285 GTVILNVSTGEVISMVSIPDYDPHEAFKGKKEGWFNRISYGIFEMGSIFKVFTIAMGIDS 344 V+++V+TGEV++M + P Y+P+ K+ NR +FE GS K + + Sbjct: 260 SAVLVDVNTGEVLAMANSPSYNPNNLSGTPKDAMRNRAITDVFEPGSTVKPMVVMTALQR 319 Query: 345 GLFTVKDLFDTRNPIKVGKHVIHDYHPQNRILTIPEIFRYSSNIGAAQIADAMGIQGHKE 404 G+ + +T P ++ H I D + LT+ + + SSN+G +++A AM + Sbjct: 320 GVVKENSVLNTV-PYRINGHEIKDVARYSE-LTLTGVLQKSSNVGVSKLALAMPSSALVD 377 Query: 405 FLYRLGLLSKLETELPEIQAPSYPSQ--WKRIHSLTISFGHGLSTTPLQTAVAAAALINE 462 R GL L ++ YP + W I T SFG+GL TPLQ A A + + Sbjct: 378 TYSRFGLGKATNLGLVGERSGLYPQKQRWSDIERATFSFGYGLMVTPLQLARVYATIGSY 437 Query: 463 G--------RLIPPTFMIRSREESEKVSRIVLKKNTVKTMRSLLREGVTGGSGRRAFVPG 514 G ++ PP + R E + R V V M S+ + GG G +A + G Sbjct: 438 GIYRPLSITKVDPP--VPGERVFPESIVRTV-----VHMMESV---ALPGGGGVKAAIKG 487 Query: 515 FEVGGKTGTAQKVIKKRYSDTLNFNSFLA----VFPTTDPQYIVLSFMDSPKIKERNQLT 570 + + KTGTA+KV D N ++A V P + P++ ++ ++ P+ + Sbjct: 488 YRIAIKTGTAKKV----GPDGRYINKYIAYTAGVAPASQPRFALVVVINDPQ---AGKYY 540 Query: 571 AGINVAPMVGNIIRRSASMLGVKP 594 G AP+ G I+ + ++P Sbjct: 541 GGAVSAPVFGAIMGGVLRTMNIEP 564 >gnl|CDD|162686 TIGR02074, PBP_1a_fam, penicillin-binding protein, 1A family. Bacterial that synthesize a cell wall of peptidoglycan (murein) generally have several transglycosylases and transpeptidases for the task. This family consists of bifunctional transglycosylase/transpeptidase penicillin-binding proteins (PBP). In the Proteobacteria, this family includes PBP 1A but not the paralogous PBP 1B (TIGR02071). This family also includes related proteins, often designated PBP 1A, from other bacterial lineages. Length = 530 Score = 93.1 bits (232), Expect = 2e-19 Identities = 74/290 (25%), Positives = 119/290 (41%), Gaps = 55/290 (18%) Query: 256 IRLALDLRIQ----NIVHQELVENKKKYNAES-VGTVILNVSTGEVISMVSIPDYDPHEA 310 I LDL +Q +++ L E ++ N + V ++ TG V ++V DY Sbjct: 224 IYTTLDLDMQKAAEKVLNNGLREAGRRANDDLQAALVAIDPDTGAVRALVGGRDY----- 278 Query: 311 FKGKKEGWFNRISYGIFEMGSIFKVFTIAMGIDSGLFTVKDLFDTRNPIKVGKHVIHDYH 370 G+ + FNR + + GS FK F A ++ G +T + D PI + Sbjct: 279 --GESQ--FNRATQAKRQPGSTFKPFVYAAALEKG-WTPASIVDDE-PITYSNG---PWS 329 Query: 371 PQN-------RILTIPEIFRYSSNIGAAQIADAMGIQGHKEFLYRLGLLSKLETELPEIQ 423 P+N + T+ + S NI A ++ D +G+ R G+ S L Sbjct: 330 PKNYGGGYRGNV-TLRQALAQSRNIPAVRLLDEVGLNKVVALAKRFGITSPL-------- 380 Query: 424 APSYPSQWKRIHSLTISFGHGLSTTPLQTAVAAAALINEGRLIPPTFMIRS--------R 475 L+++ G + +PL+ A A A N G+ + P IR Sbjct: 381 ----------PPVLSLALG-TVEVSPLEMASAYAVFANGGKYVEPHG-IRKIVDRDGKVI 428 Query: 476 EESEKVSRIVLKKNTVKTMRSLLREGVTGGSGRRAFVPGFEVGGKTGTAQ 525 E++ + V+ T M +L+ V G+GR A +PG V GKTGT Q Sbjct: 429 YENKPTTTQVISPATAYIMTDMLKGVVESGTGRSARLPGRPVAGKTGTTQ 478 >gnl|CDD|182738 PRK10795, PRK10795, penicillin-binding protein 2; Provisional. Length = 634 Score = 92.9 bits (231), Expect = 2e-19 Identities = 118/509 (23%), Positives = 207/509 (40%), Gaps = 107/509 (21%) Query: 102 PIAPSMNIDEYGMSRPDIIDRNGEILATDIPTFSLYVEPHKVISPDEIIEKLQIV--LPN 159 PIAPS I I DRNG LA + + L + P KV + + ++ L+ V L + Sbjct: 64 PIAPSRGI---------IYDRNGTPLALNRTIYQLEMMPEKVDNLQQTLDALRSVVDLTD 114 Query: 160 LDSEMIRRKLSSETKFQW--LRRKLSPQQQKR--ILSFGLPGVGFRLEKSRFYPAASHAS 215 D R++ + +F ++ L+ Q R + + PGV + + R+YP S + Sbjct: 115 DDIAAFRKERARSRRFTSIPVKTNLTEVQVARFAVNQYRFPGVEVKGYQRRYYPYGSALT 174 Query: 216 HVVGYVD---------IDNRGI------------TGIEKFLD-----MQGLTRVFTTNKG 249 HV+GYV +D G GIE++ + G V N+G Sbjct: 175 HVIGYVSKINDKDVERLDKEGKLANYAATHDIGKLGIERYYEDVLHGKTGYEEVEVNNRG 234 Query: 250 E--KNL--QP------IRLALDLRIQNIVHQELVENKKKYNAESVGTVILNVSTGEVISM 299 + L QP I L LDL++Q + L ++ V+ + TG ++++ Sbjct: 235 RVIRQLHEQPPQAGHDIYLTLDLKLQQYIETLLAGSR-------AAVVVTDPRTGGILAL 287 Query: 300 VSIPDYDP------------HEAFKGKKEGWFNRISYGIFEMGSIFKVFTIAMGIDSGLF 347 VS P YDP NR + G++ S K + + +G+ Sbjct: 288 VSTPSYDPNLFVDGISSKDYSGLLNDPNRPLINRATQGVYPPASTVKPYVAVSALSAGVI 347 Query: 348 TVK-DLFD--------TRNPIKVGKHVIHDYHPQNRILTIPEIFRYSSNIGAAQIADAMG 398 T LFD + + K H L + + S++ Q+A MG Sbjct: 348 TRNTSLFDPGWWQLPGSEKRYRDWKKWGHGR------LNVTKSLEESADTFFYQVAYDMG 401 Query: 399 IQGHKEFLYRLGLLSKLETELPEIQAPSYPS-QWK--RIH-------SLTISFGHGLST- 447 I E++ + G +L E ++ + P+ +WK R ++ + G G T Sbjct: 402 IDRLSEWMGKFGYGHYTGIDLAEERSGNMPTREWKQKRFKKPWYQGDTIPVGIGQGYWTA 461 Query: 448 TPLQTAVAAAALINEGRLIPPTFMIRSREESEKVSRIVLKKNTVKTMRS----LLREGVT 503 TP+Q + A LIN+G + P ++ + E+ ++V + + V + S + ++G+ Sbjct: 462 TPIQMSKALMTLINDGIVKVPHLLMSTAEDGKQVPWVQPHEPPVGDIHSGYWEIAKDGMY 521 Query: 504 G------GSGRRAFVPG-FEVGGKTGTAQ 525 G G+ + F +++ K+GTAQ Sbjct: 522 GVANRPNGTAHKYFASAPYKIAAKSGTAQ 550 >gnl|CDD|162685 TIGR02073, PBP_1c, penicillin-binding protein 1C. This subfamily of the penicillin binding proteins includes the member from E. coli designated penicillin-binding protein 1C. Members have both transglycosylase and transpeptidase domains and are involved in forming cross-links in the late stages of peptidoglycan biosynthesis. All members of this subfamily are presumed to have the same basic function. Length = 727 Score = 42.4 bits (100), Expect = 3e-04 Identities = 60/287 (20%), Positives = 97/287 (33%), Gaps = 52/287 (18%) Query: 256 IRLALDLRIQNIVHQELVEN----KKKYNAESVGTVILNVSTGEVISMVSIPDYDPHEAF 311 I LD +Q + +EL + ++ ++++ +G V++ V D+ Sbjct: 244 IVSTLDADLQRRL-EELARRYLSALRPRGISNLAILVVDNRSGAVLAYVGSADFFDDSNS 302 Query: 312 KGKKEGWFNRISYGIFEMGSIFKVFTIAMGIDSGLFTVKDLFDTRNPIKVGKHVIHDYHP 371 G + + GS K F A+ +D GL L P++ G DY P Sbjct: 303 -----GQVDGVR-APRSPGSTLKPFLYALALDDGLLHPDSLLKDV-PLRFG-----DYAP 350 Query: 372 QN------RILTIPEIFRYSSNIGAAQIADAMGIQGHKEFLYRLGLLSKLETELPEIQAP 425 +N + E S NI A ++ + +G +FL + G L P+ Sbjct: 351 ENFDKTFHGPVPAREALARSLNIPAVRLLERVGPPRFADFLRQAG----LNLLKPKSDYY 406 Query: 426 SYPSQWKRIHSLTISFGHGLSTTPLQTAVAAAALINEGRLIPPTFM-------IRSREES 478 SL + G T A A L N+G P F+ R R S Sbjct: 407 GL--------SLALG---GAEITLQDLANLYAMLANQGLSGPLRFLQTDAKRPERERLLS 455 Query: 479 EKVSRIVLKKNTVKTMRSLLREGVTGGSGRRAFVPGFEVGGKTGTAQ 525 + IVL ++ R A + KTGT+ Sbjct: 456 PGAAWIVL-----DILKDRPRPD--DTLPLSALPTRLPLAWKTGTSY 495 >gnl|CDD|183248 PRK11636, mrcA, penicillin-binding protein 1a; Provisional. Length = 850 Score = 36.6 bits (85), Expect = 0.019 Identities = 49/204 (24%), Positives = 81/204 (39%), Gaps = 40/204 (19%) Query: 287 VILNVSTGEVISMVSIPDYDPHEAFKGKKEGWFNRISYGIFEMGSIFKVFTIAMGIDSGL 346 V +N G V+++V D++ + FNR + + ++GS K F +D GL Sbjct: 430 VSINPQNGAVMALVGGFDFNQSK---------FNRATQALRQVGSNIKPFLYTAAMDKGL 480 Query: 347 FTVKDLFD---TRNPIKVGKHVIHDYHPQNRILTIPEIFRY------SSNIGAAQIADAM 397 L D +R G D+ P+N R S N+ + AM Sbjct: 481 TLASMLNDVPISRWDAGAGS----DWRPKNSPPQYAGPIRLRQGLGQSKNVVMVRAMRAM 536 Query: 398 GIQGHKEFLYRLGLLSKLETELPEIQAPSYPSQWKRIHSLTISFGHGLSTTPLQTAVAAA 457 G+ E+L R G +P+Q +H+ +++ G S TP+Q A A Sbjct: 537 GVDYAAEYLQRFG----------------FPAQ-NIVHTESLALGSA-SFTPMQVARGYA 578 Query: 458 ALINEGRLIPPTFMIRSREESEKV 481 + N G L+ P F+ + + V Sbjct: 579 VMANGGFLVDPYFISKIENDQGGV 602 >gnl|CDD|184852 PRK14850, PRK14850, penicillin-binding protein 1b; Provisional. Length = 764 Score = 33.3 bits (76), Expect = 0.20 Identities = 62/306 (20%), Positives = 120/306 (39%), Gaps = 52/306 (16%) Query: 234 FLDMQGLTRVFTTNKGEKNLQPIRLALDLRIQNIVHQ----ELVENKKKYNAE--SVGTV 287 F + G T++FTT LD QN Q + K+K + V V Sbjct: 374 FKNFSG-TKIFTT-------------LDYISQNAAEQAVKIGIPILKRKKRLKDLEVAMV 419 Query: 288 ILNVSTGEVISMVSIPDYDPHEAFKGKKEGWFNRISYGIFEMGSIFKVFTIAMGIDSGLF 347 I++ +GEV +++ P F G +NR +GS+ K T + Sbjct: 420 IIDRFSGEVRALIG--SSKPE--FNG-----YNRALKARRSIGSLSKPITYLTALSQPEK 470 Query: 348 TVKDLFDTRNPIKVGKHVIHDYHPQN-------RILTIPEIFRYSSNIGAAQIADAMGIQ 400 + + + PI + + P+N +++ I + +S NI ++ +G++ Sbjct: 471 YHLNTWISDTPISIKLDNGQYWTPKNNNFSFSGKVMLI-DALIHSINIPTVHLSINLGLK 529 Query: 401 GHKEFLYRLGLLSKLETELPEIQAPSY---PSQWKRIHSLTISFGHGLSTTPLQTAVAAA 457 + LG+ S T LP I + P + ++ + S G+ S + +++ ++ Sbjct: 530 KLVDSWILLGISSNYITPLPSISLGAINLTPMEVAQVFQIIGSGGYKSSLSSIRSIIS-- 587 Query: 458 ALINEGRLIPPTFMIRSREESEKVSRIVLKKNTVKTMRSLLREGVTGGSGRRAFVPGFEV 517 ++ +++ F ES + S + L M+ +++ G G F + Sbjct: 588 ---DDNKVLYQNFPQSKHVESSQASYLTL-----YAMQQVVKSGTAKSLGT--IFKEFSL 637 Query: 518 GGKTGT 523 GKTGT Sbjct: 638 AGKTGT 643 >gnl|CDD|182045 PRK09718, PRK09718, hypothetical protein; Validated. Length = 512 Score = 30.0 bits (67), Expect = 2.0 Identities = 11/28 (39%), Positives = 20/28 (71%) Query: 251 KNLQPIRLALDLRIQNIVHQELVENKKK 278 K++ ++L + L+I NIV++ +EN KK Sbjct: 280 KSVLAVKLVMQLKILNIVNKNFIENMKK 307 >gnl|CDD|148274 pfam06570, DUF1129, Protein of unknown function (DUF1129). This family consists of several hypothetical bacterial proteins of unknown function. Length = 206 Score = 29.5 bits (67), Expect = 2.6 Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 1/66 (1%) Query: 275 NKKKYNAESVGTVILNVSTGEVISMVSIPDY-DPHEAFKGKKEGWFNRISYGIFEMGSIF 333 +K A S T +L S ++M + Y + K K+ W+ + + + Sbjct: 102 SKNAQPAYSGITTLLLTSLVGGLAMYYMYRYLYRYLKDKSKRPPWWKSLLILVLAVVVWM 161 Query: 334 KVFTIA 339 VFT+ Sbjct: 162 AVFTLT 167 >gnl|CDD|177587 PHA03334, PHA03334, putative DNA polymerase catalytic subunit; Provisional. Length = 1545 Score = 29.4 bits (66), Expect = 2.9 Identities = 7/51 (13%), Positives = 15/51 (29%), Gaps = 2/51 (3%) Query: 39 MESGHNLCQKGCHMEDGQDLFQKRRRKVIA--HSKNRIGMTIVVCLVIYII 87 C+K ++ + K R V + + + +II Sbjct: 422 KAQFKATCRKAAARKEEIGSYMKTRDTVQDFNDNDKKYLNSTSHGFGAHII 472 >gnl|CDD|177860 PLN02210, PLN02210, UDP-glucosyl transferase. Length = 456 Score = 29.2 bits (65), Expect = 2.9 Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%) Query: 439 ISFGHGLSTTPLQTAVAAAALINEGRLIPPTFMIRSREESEKVS 482 ISFG L + Q A AL N G +P ++IR +E+++ V Sbjct: 274 ISFGSMLESLENQVETIAKALKNRG--VPFLWVIRPKEKAQNVQ 315 >gnl|CDD|178660 PLN03113, PLN03113, DNA ligase 1; Provisional. Length = 744 Score = 28.8 bits (64), Expect = 3.6 Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 2/77 (2%) Query: 444 GLSTTPLQTAVAAAALINEGRLIPPTFMIRSREESEKVSRIVLKKNTV--KTMRSLLREG 501 GL+ L A+ AA+ NE PP + EE+ K+ + V V K + +LL G Sbjct: 295 GLAGQTLLAALGQAAVYNEEHSTPPPNIQSPLEEAAKIVKQVYSVLPVYDKIVPALLSGG 354 Query: 502 VTGGSGRRAFVPGFEVG 518 V +F PG VG Sbjct: 355 VWNLPKTCSFTPGVPVG 371 >gnl|CDD|162859 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis. Length = 633 Score = 28.5 bits (64), Expect = 4.7 Identities = 30/120 (25%), Positives = 47/120 (39%), Gaps = 31/120 (25%) Query: 107 MNIDEYGMSRPDIIDRNGEILATDIPTFSLYVEPHKVISPDEIIEKLQIVLPNL----DS 162 MN +E G RP ++DR F L V+ P+E +E I+ L D Sbjct: 176 MNPEE-GDLRPQLLDR-----------FGLCVDVAAPRDPEERVE---IIRRRLAFDADP 220 Query: 163 EMIRRKLSSETKFQWLRRKLSPQQQKRILSFGLPGVGFRLEKS--RFYPAASHASHVVGY 220 E + ++E + LR +++ + LP V R+ S RF V G+ Sbjct: 221 EAFAARWAAEQEE--LRNRIARARSL------LPSV--RISDSLIRFISELCIEFGVDGH 270 >gnl|CDD|162683 TIGR02071, PBP_1b, penicillin-binding protein 1B. Bacterial that synthesize a cell wall of peptidoglycan (murein) generally have several transglycosylases and transpeptidases for the task. This family consists of a particular bifunctional transglycosylase/transpeptidase in E. coli and other Proteobacteria, designated penicillin-binding protein 1B. Length = 730 Score = 28.1 bits (63), Expect = 5.7 Identities = 31/114 (27%), Positives = 43/114 (37%), Gaps = 33/114 (28%) Query: 232 EKFLDMQGLTRVFTTNKGEKNLQPIRLALDLRIQNIVHQELVEN------KKKYNAESVG 285 +K D+ GL R+FTT LD Q+ Q + E KKK Sbjct: 362 DKVKDLSGL-RIFTT-------------LDPVSQSAAEQAVQETIPALKKKKKLPDLEAA 407 Query: 286 TVILNVSTGEVISMV--SIPDYDPHEAFKGKKEGWFNRISYGIFEMGSIFKVFT 337 V+ + TGEV +MV S P + FNR ++GS+ K Sbjct: 408 MVVTDRFTGEVRAMVGGSDPQFAG-----------FNRALQARRQIGSLVKPAV 450 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 0.322 0.138 0.401 Gapped Lambda K H 0.267 0.0822 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 10,034,055 Number of extensions: 674604 Number of successful extensions: 1294 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1268 Number of HSP's successfully gapped: 21 Length of query: 598 Length of database: 5,994,473 Length adjustment: 99 Effective length of query: 499 Effective length of database: 3,855,281 Effective search space: 1923785219 Effective search space used: 1923785219 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 (21.9 bits) S2: 60 (26.7 bits)