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)