RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780915|ref|YP_003065328.1| oligoendopeptidase F [Candidatus Liberibacter asiaticus str. psy62] (626 letters) >gnl|CDD|162797 TIGR02290, M3_fam_3, oligoendopeptidase, pepF/M3 family. The M3 family of metallopeptidases contains several distinct clades. Oligoendopeptidase F as characterized in Lactococcus, the functionally equivalent oligoendopeptidase B of group B Streptococcus, and closely related sequences are described by TIGR00181. The present family is quite similar but forms a distinct clade, and a number of species have one member of each. A greater sequence difference separates members of TIGR02289, probable oligoendopeptidases of the M3 family that probably should not be designated PepF. Length = 587 Score = 509 bits (1314), Expect = e-145 Identities = 213/598 (35%), Positives = 324/598 (54%), Gaps = 20/598 (3%) Query: 38 RWNLEDLYPSHDSQEISNDMECIEHESLAFKTRWEGNLAHATNQKNCHSLGAAIAEYERI 97 W+L DLYP S E D++ I+ + F++ ++ L + K L A+ YE + Sbjct: 1 EWDLSDLYPGGSSPEFEEDLKKIKALADEFESLYQEKLT-PLDAKGKEKLQNALKRYEAL 59 Query: 98 CELIGRIASYAMLSYNCNLSSPTIRKFYTDINAKLADFEKVLIFFALEINTLDE----AL 153 EL+ ++ +YA L Y+ + S P + ++ A ++ ++ L+FF LE+ L + AL Sbjct: 60 GELLSKVGAYASLLYSADTSDPEAKALLGELEALSSEIQQALLFFTLELMRLSDEVWAAL 119 Query: 154 LEQSYAQDPLTLKYSAWIKNIRKIKKHLLSNDMECLLSDTSQVGREALKRFFCENIESLR 213 L Y ++K +RK H LS + E L++ S GR A R + E +LR Sbjct: 120 LSDPDLAP-----YRFYLKELRKEAPHTLSEEEEKLINALSLTGRAAWSRLYDELTGTLR 174 Query: 214 FKIN-----DQKIPLTKAYKSFFDSDREVRKSAAKALSHTFNKSSHIFSFITNTLAKDEE 268 ++ ++ + L +A D D EVRK A KAL + K++ + I N LA D Sbjct: 175 IPVDGKDGEEETLSLEQALNLLRDPDAEVRKKAFKALLKAWEKNAPTLAAILNALAGDRL 234 Query: 269 IQDRWRKYEKIADSRHLSNNVEPYVIEALMQSVKNYYPKTSHRYYELKKKWLKLDTMYFW 328 + R R Y+ + R L N ++ ++A+++++K YP RYY+LK K L + + F+ Sbjct: 235 TEYRLRGYDHPLEPRLLYNRIDQETLDAMLEAIKENYP-LFRRYYKLKAKLLGKEKLDFY 293 Query: 329 DRLAPLPGTSQDIIPFEVARDLVLQSYAKFSPQMSIIAEKFFTHNWIDAPQYDGKGSGAF 388 D APL +S F+ A++LVL+++ KFSP+M+ AEK F WIDA GK GAF Sbjct: 294 DLYAPLGDSSAKTYTFDEAKELVLEAFGKFSPEMADFAEKAFEEGWIDAEPRPGKRGGAF 353 Query: 389 AHGTIPSVHPYILLNYLGKPQDVMTLAHELGHGIHFVLSSETQGILTNNSSLTLAETASI 448 G PS P +L+NY G +DV TLAHELGH H L+ + Q +L +TLAETASI Sbjct: 354 CTGFPPSKEPRVLMNYDGSRRDVSTLAHELGHAYHSELAKD-QPLLNARYPMTLAETASI 412 Query: 449 FGETLTFDSLLQAASSKEERKILLANKIEDMLNSIVRQISFYDFELKLHTERRSTGDIPT 508 F E L FD+LL+ A + EE+ LLA K+ED + ++VR + + FE + H E R G++ Sbjct: 413 FAEMLLFDALLKEAKTDEEKLSLLAEKLEDAIATLVRIHARFLFERRFH-EARKEGELSA 471 Query: 509 HRINEIWLETQKESLGPAFDLSDLEYGSFWMMVPHFIESSFYVYAYAFGNCLVNSLYDIY 568 I ++ LE QKES G A D S+L + W PHF + FY Y Y FG V LY Y Sbjct: 472 DDICDLMLEAQKESYGDALDESEL-HPYMWAYKPHFYHAPFYNYPYTFGYLFVLGLYAKY 530 Query: 569 KSNTVDCFKEKYLNILRAGNSKHYSELLLPLNINLSDPNFWERGLQTVEKMIDDVEKM 626 + F KY+ +LR S EL+ +L+ P+FW++G+ +E+ ID+ E++ Sbjct: 531 REEGES-FVPKYIALLRDTGSMTPEELVKKFGFDLTSPDFWQKGIDVIEEKIDEFEEL 587 >gnl|CDD|161749 TIGR00181, pepF, oligoendopeptidase F. This family represents the oligoendopeptidase F clade of the family of larger M3 or thimet (for thiol-dependent metallopeptidase) oligopeptidase family. Lactococcus lactis PepF hydrolyzed peptides of 7 and 17 amino acids with fairly broad specificity. The homolog of lactococcal PepF in group B Streptococcus was named PepB (PubMed:8757883), with the name difference reflecting a difference in species of origin rather activity; substrate profiles were quite similar. Differences in substrate specificity should be expected in other species. The gene is duplicated in Lactococcus lactis on the plasmid that bears it. A shortened second copy is found in Bacillus subtilis. Length = 591 Score = 278 bits (712), Expect = 4e-75 Identities = 171/597 (28%), Positives = 276/597 (46%), Gaps = 24/597 (4%) Query: 38 RWNLEDLYPSHDSQEISND-MECIEHESLAFKTRWEGNLAHATNQKNCHSLGAAIAEYER 96 +W+L+DLY + + E+ + +E E AFK + A+A E+ Sbjct: 9 KWDLDDLYKNKEEWELFLEALEEDIKEIKAFKKGLLHSKET---------FLEALALEEK 59 Query: 97 ICELIGRIASYAMLSYNCNLSSPTIRKFYTDINAKLADFEKVLIFFALEINTLDEALLEQ 156 I L+ R+ +YA + + +++ P ++ FF EI ++E ++ + Sbjct: 60 ILILLNRLYNYASMKLSTDVTDPEANAISQKLSNLYTKVASATSFFEPEILEIEEKII-K 118 Query: 157 SYAQDPLTLK-YSAWIKNIRKIKKHLLSNDMECLLSDTSQVGREALKRFFCENIESLRFK 215 + +DP L Y ++ I + K H+LS ++E LLS S+V + + F Sbjct: 119 EWLKDPEELADYKRALEEIFRDKPHILSEEVEKLLSALSEVFGSPSDIYSTLTNADMDFG 178 Query: 216 -IND---QKIPLTKAYKSFF---DSDREVRKSAAKALSHTFNKSSHIFSFITNTLAKDEE 268 I D +K P+T + F + DRE+RK A ++ + K + F+ + + Sbjct: 179 SIEDYKGKKYPITNSTYENFLQKNKDREIRKKAYESFYKAYRKHKNTFAALYYGNVQKNV 238 Query: 269 IQDRWRKYEKIADSRHLSNNVEPYVIEALMQSVKNYYPKTSHRYYELKKKWLKLDTMYFW 328 + R YE D+ S+ V V + L ++K P RYY+L+KK LKLD M + Sbjct: 239 FLAKLRNYESYIDASLFSDEVPREVYDNLYDTIKKNAP-VLQRYYKLRKKVLKLDKMEPY 297 Query: 329 DRLAPLPGTSQDIIPFEVARDLVLQSYAKFSPQMSIIAEKFFTHNWIDAPQYDGKGSGAF 388 D PL E A++L+L+S + I ++ F W+D + GK SGA+ Sbjct: 298 DLYLPLVKEKNPKFSIEEAKELILKSLEPLGEEYIKILKRAFNERWVDYAENKGKRSGAY 357 Query: 389 AHGTIPSVHPYILLNYLGKPQDVMTLAHELGHGIHFVLSSETQGILTNNSSLTLAETASI 448 + G V PYIL+N+ G V TLAHELGH +H SS+ Q ++ S+ AE AS Sbjct: 358 SIG-GYKVKPYILMNWDGTLNSVFTLAHELGHSMHSYFSSKHQPYPNSDYSIFYAEIAST 416 Query: 449 FGETLTFDSLLQAASSKEERKILLANKIEDMLNSIVRQISFYDFELKLHTERRSTGDIPT 508 F E L D LL+ ++ E + +L +I + + RQ F +FE + + + Sbjct: 417 FNELLLADYLLKNSNDPEMKIYILLERISNFFGTFTRQTLFAEFEYEAYELIEEGEPLTA 476 Query: 509 HRINEIWLETQKESLGPAFDLSDLEYGSFWMMVPHFIESSFYVYAYAFGNCLVNSLYDIY 568 +NEI+ K+ G D G WM +PHF FYVY YA G +LY+ Sbjct: 477 ETLNEIYANLLKKYFGDLVK-IDEGAGLTWMRIPHFY-MGFYVYKYATGQVAATALYEKI 534 Query: 569 KSNTVDCFKEKYLNILRAGNSKHYSELLLPLNINLSDPNFWERGLQTVEKMIDDVEK 625 K EKYL L++G SK+ E L ++L+ P W+ + ID++E+ Sbjct: 535 KEEGKGA-VEKYLKFLKSGGSKYPLETLKIAGVDLTKPQPWQAAINIFSDWIDELEE 590 >gnl|CDD|131342 TIGR02289, M3_not_pepF, oligoendopeptidase, M3 family. This family consists of probable oligoendopeptidases in the M3 family, related to lactococcal PepF and group B streptococcal PepB (TIGR00181) but in a distinct clade with considerable sequence differences. The likely substrate is small peptides and not whole proteins, as with PepF, but members are not characterized and the activity profile may differ. Several bacteria have both a member of this family and a member of the PepF family. Length = 549 Score = 83.6 bits (207), Expect = 1e-16 Identities = 82/373 (21%), Positives = 137/373 (36%), Gaps = 15/373 (4%) Query: 232 DSDREVRKSAAKALSHTFNKSSHIFSFITNTLAKDEEIQDRWRKYEKIADSRHLSNNVEP 291 D +R RK A A S F I + L + + D + N Sbjct: 155 DPNRSTRKKAWYARSEFFAVVEEELDRIYDELVQIRTQIALNLGFSNYRDYMYKLKNRTD 214 Query: 292 YVIE---ALMQSVKNYYPKTSHRYYELKKKWLKLDTMYFWDRLAPLPGTSQDIIPFEVAR 348 Y E +S+ Y + ++KKK L + T+ WD A ++ PF Sbjct: 215 YSAEDCYKYRESILKYVVPLWTKLRKIKKKRLGIKTLRPWDESAVFL--DGNVKPFGNVD 272 Query: 349 DLVLQS---YAKFSPQMSIIAEKFFTHNWIDAPQYDGKGSGAFAHGTIPSVHPYILLNYL 405 L+ ++ Y + S + N +D GK +G + P+I N+ Sbjct: 273 FLLEKAEKMYKELSLEFYEFFNFMREKNLLDLESRKGKAAGGYCTYLPKYKAPFIFSNFN 332 Query: 406 GKPQDVMTLAHELGHGIHFVLSSETQGILTNNSSLTLAETASIFGETLTFDSLLQAASSK 465 G D+ L HE GH H S + + AE AS+ E L+ + + Sbjct: 333 GTSGDIDVLTHEAGHAFHVYESRKDLLPEYRWPTYEAAELASMSMELLSMPWWDLFYTDE 392 Query: 466 EERKILLANKIEDMLNSIVRQISFYDFELKLHTERRSTGDIPTHRINEIWLETQKESLGP 525 ++ K + ++ L+ + + F+ ++ T P R +E + E +K Sbjct: 393 KDLKKAKISHLKGALSFLPYGVIVDHFQHWVYENPNHT---PEER-DEKYAELEKRYQPS 448 Query: 526 AFDLSDLEY--GSFWMMVPHFIESSFYVYAYAFGNCLVNSLYDIYKSNTVDCFKEKYLNI 583 ++ LE G+FW+ H E FY Y +Y IYK + K+ Y + Sbjct: 449 TVYIAGLELEIGTFWLRQLHIFEVPFYYIEYTIAQIGALQIYKIYKEDPEKALKD-YKKL 507 Query: 584 LRAGNSKHYSELL 596 AG S+ + EL Sbjct: 508 CSAGGSQSFLELY 520 >gnl|CDD|149486 pfam08439, Peptidase_M3_N, Oligopeptidase F. This domain is found to the N-terminus of the pfam01432 domain in bacterial and archaeal proteins including Oligoendopeptidase F. An example of this protein is Lactococcus lactis PepF. Length = 70 Score = 43.7 bits (104), Expect = 2e-04 Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 1/61 (1%) Query: 145 EINTLDEALLEQSYAQDPLTLKYSAWIKNIRKIKKHLLSNDMECLLSDTSQVGREALKRF 204 E+ L E LE +DP Y +++ +R+ K H LS + E LL+ S G A R Sbjct: 1 ELLALPEEKLEALLEEDPELKPYRFYLEELRRQKPHTLSEEEEKLLAALS-DGLGAWSRL 59 Query: 205 F 205 F Sbjct: 60 F 60 >gnl|CDD|182832 PRK10911, PRK10911, oligopeptidase A; Provisional. Length = 680 Score = 36.7 bits (85), Expect = 0.019 Identities = 41/147 (27%), Positives = 65/147 (44%), Gaps = 25/147 (17%) Query: 374 WIDAPQYDGKGSGAFAHGTIPSVHPYILLNY----LGKP-----QDVMTLAHELGHGIHF 424 W+D D G A G++ Y+ N+ GKP +V+TL HE GHG+H Sbjct: 422 WMD----DCVGQMRKADGSLQKPVAYLTCNFNRPVNGKPALFTHDEVITLFHEFGHGLHH 477 Query: 425 VLSS-ETQGIL-TNNSSLTLAETASIFGETLTF--DSLLQAASSKEERKILLANKIEDML 480 +L+ ET G+ + E S F E + ++L + E + L ++ ML Sbjct: 478 MLTRIETAGVSGISGVPWDAVELPSQFMENWCWEPEALAFISGHYETGEPLPKELLDKML 537 Query: 481 NS--------IVRQISFYDFELKLHTE 499 + I+RQ+ F F+ +LH E Sbjct: 538 AAKNYQAALFILRQLEFGLFDFRLHAE 564 >gnl|CDD|178902 PRK00149, dnaA, chromosomal replication initiation protein; Reviewed. Length = 450 Score = 30.5 bits (70), Expect = 1.3 Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 4/35 (11%) Query: 549 FYVYAYAFGNCLVNSLYDIYKSNTVDCFKEKYLNI 583 YV + F N VN+L ++NT++ FKEKY ++ Sbjct: 182 VYVTSEKFTNDFVNAL----RNNTMEEFKEKYRSV 212 >gnl|CDD|178464 PLN02876, PLN02876, acyl-CoA dehydrogenase. Length = 822 Score = 30.1 bits (68), Expect = 1.8 Identities = 30/110 (27%), Positives = 45/110 (40%), Gaps = 22/110 (20%) Query: 12 NAFFRKALRSSDMTTMDSQENLGNLPR----WNLEDLYPSHDSQEISNDMECIEHESLAF 67 N F++ A SS T +E L L + WNL + DS A Sbjct: 426 NEFYKLAQSSSRWTVHPEEERLKELAKKEGLWNL---WIPLDSAA------------RAR 470 Query: 68 KTRWEGNLAHATNQKNCHSLGAAIA--EYERICELIGRIASYAMLSYNCN 115 K +E N + LGA ++ EY +CE++GR + +A +NC Sbjct: 471 KLLFEDNKHMVSGDSADQLLGAGLSNLEYGYLCEIMGR-SVWAPQVFNCG 519 >gnl|CDD|161840 TIGR00362, DnaA, chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006). Length = 405 Score = 29.8 bits (68), Expect = 2.0 Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 4/35 (11%) Query: 549 FYVYAYAFGNCLVNSLYDIYKSNTVDCFKEKYLNI 583 YV + F N VN+L ++N ++ FKEKY ++ Sbjct: 170 VYVSSEKFTNDFVNAL----RNNKMEEFKEKYRSV 200 >gnl|CDD|129223 TIGR00117, acnB, aconitate hydratase 2. Aconitate hydratase (aconitase) is an enzyme of the TCA cycle. This model describes aconitase 2, AcnB, which has weak similarity to aconitase 1. It is found almost exclusively in the Proteobacteria. Length = 844 Score = 29.5 bits (66), Expect = 2.6 Identities = 19/58 (32%), Positives = 22/58 (37%), Gaps = 13/58 (22%) Query: 222 PLTKAYKSFFDSDREVRKSAAKALSHT------FNKSSHIFSFITNTLAKDEEIQDRW 273 PL A S D + AAKALSHT F TN AK ++ W Sbjct: 101 PLIDALDS---QDANIAPIAAKALSHTLLVFDNFYDVEEKSK--TNEYAK--QVMQSW 151 >gnl|CDD|165718 PLN00150, PLN00150, potassium ion transporter family protein; Provisional. Length = 779 Score = 29.5 bits (66), Expect = 2.7 Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 10/73 (13%) Query: 90 AIAEYERICELIGRIASYAMLSYNCNLSSPTIRKFYTDINAKLADFEKVLIFFA---LEI 146 + + ER LI RI A Y C R YTD+ K +FE++LI +EI Sbjct: 589 TVPQDERF--LIRRIGPRAYSMYRC-----AARYGYTDLEKKDDNFEQLLIASLERFIEI 641 Query: 147 NTLDEALLEQSYA 159 + E +S A Sbjct: 642 ESFREQSDLESMA 654 >gnl|CDD|147984 pfam06114, DUF955, Domain of unknown function (DUF955). Family of bacterial and viral proteins with undetermined function. A conserved H-E-X-X-H motif is suggestive of a catalytic active site and shows similarity to pfam01435. Length = 121 Score = 29.3 bits (66), Expect = 3.0 Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 7/51 (13%) Query: 374 WIDAPQYDGKGSGAFAHGTIPSVHPYILLN-YLGKPQDVMTLAHELGHGIH 423 + D DG G H + I +N L + TLAHELGH + Sbjct: 10 YEDLGAMDGDGRRYDRH------NKVIFINENLSPERQRFTLAHELGHLLL 54 >gnl|CDD|151809 pfam11369, DUF3160, Protein of unknown function (DUF3160). This family of proteins has no known function. Length = 637 Score = 29.3 bits (66), Expect = 3.0 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%) Query: 259 ITNTLAKDEEIQDRW-RKYEKIADSRHLSNNVEPYVIEALMQSVKNYYPK 307 I++ L D+E++ +W R Y+ A LS+++ PY ++SV K Sbjct: 219 ISSALDNDKELRKKWDRVYDPTAFYVGLSDDLGPYEYAEALKSVFGGDRK 268 >gnl|CDD|182353 PRK10280, PRK10280, dipeptidyl carboxypeptidase II; Provisional. Length = 681 Score = 28.6 bits (64), Expect = 4.3 Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 18/66 (27%) Query: 381 DGKGSGAFA-----HGTIPSVHPYI--LLNYLGKPQ----------DVMTLAHELGHGIH 423 D K GA+ T+ P I + NY KP DV+TL HE GH +H Sbjct: 419 DSKSGGAWMGNFVEQSTLNETRPVIYNVCNYQ-KPAAGQPALLLWDDVITLFHEFGHTLH 477 Query: 424 FVLSSE 429 + + + Sbjct: 478 GLFARQ 483 >gnl|CDD|179368 PRK02106, PRK02106, choline dehydrogenase; Validated. Length = 560 Score = 28.6 bits (65), Expect = 5.5 Identities = 18/53 (33%), Positives = 22/53 (41%), Gaps = 19/53 (35%) Query: 377 APQYDGK----GSGAFAH---------GTI------PSVHPYILLNYLGKPQD 410 A +YDG G G AH G++ P HP IL NY+ QD Sbjct: 368 AIRYDGSNAVKGHGFQAHVGPMRSPSRGSVKLKSADPRAHPSILFNYMSTEQD 420 >gnl|CDD|180621 PRK06556, PRK06556, vitamin B12-dependent ribonucleotide reductase; Validated. Length = 953 Score = 28.0 bits (63), Expect = 8.0 Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 12/65 (18%) Query: 114 CNLSSPTIRKFYTDINA-KLADFEKV--LIFFALEIN-------TLDEALLEQSYAQDPL 163 CNL+S + KF D + F L+ A+EI+ T E + + A L Sbjct: 369 CNLASLNLMKFLRDDGTFDVESFRHAVELVITAMEISICFADFPT--EKIARNTRAFRQL 426 Query: 164 TLKYS 168 L Y+ Sbjct: 427 GLGYA 431 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.319 0.134 0.396 Gapped Lambda K H 0.267 0.0688 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 10,146,089 Number of extensions: 648558 Number of successful extensions: 1245 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1224 Number of HSP's successfully gapped: 34 Length of query: 626 Length of database: 5,994,473 Length adjustment: 99 Effective length of query: 527 Effective length of database: 3,855,281 Effective search space: 2031733087 Effective search space used: 2031733087 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 (21.8 bits) S2: 60 (27.0 bits)