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)