RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

Searching..................................................done

Query= gi|254780805|ref|YP_003065218.1| chromosome partitioning
protein B [Candidatus Liberibacter asiaticus str. psy62]
         (300 letters)



>gnl|CDD|161748 TIGR00180, parB_part, ParB-like partition proteins.  This model
           represents the most well-conserved core of a set of
           chromosomal and plasmid partition proteins related to
           ParB, including Spo0J, RepB, and SopB. Spo0J has been
           shown to bind a specific DNA sequence that, when
           introduced into a plasmid, can serve as partition site.
           Study of RepB, which has nicking-closing activity,
           suggests that it forms a transient protein-DNA covalent
           intermediate during the strand transfer reaction.
          Length = 187

 Score =  161 bits (408), Expect = 3e-40
 Identities = 75/164 (45%), Positives = 113/164 (68%), Gaps = 4/164 (2%)

Query: 42  ISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDN--GLYKIIAGERRFR 99
           I I  + PNP+ PR  F  E L +L +SIK  G +QP++VR   +  G Y+IIAGERR+R
Sbjct: 8   IDIDLLQPNPYQPRKDFSEESLAELIESIKEQGQLQPILVRKHPDQPGRYEIIAGERRWR 67

Query: 100 AAKMASLSEVPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIG 159
           AAK+A L  +P I+R +D++  L  A++EN+QR+DL+P+EEA  Y++L+ ++  TQ D+ 
Sbjct: 68  AAKLAGLKTIPAIVRELDDEQMLADALIENIQREDLSPIEEAQAYKRLLEKFSMTQEDLA 127

Query: 160 SIVGKSRSHVANILRILKLPSSVREMI--RKEEISLGHARTLVS 201
             +GKSR+H+ N+LR+LKLPS ++  I      +S GHAR L++
Sbjct: 128 KKIGKSRAHITNLLRLLKLPSEIQSAIPEASGLLSSGHARLLLA 171


>gnl|CDD|163446 TIGR03734, PRTRC_parB, PRTRC system ParB family protein.  A novel
           genetic system characterized by six major proteins,
           included a ParB homolog and a ThiF homolog, is
           designated PRTRC, or ParB-Related,ThiF-Related Cassette.
           It is often found on plasmids. This protein family the
           member related to ParB, and is designated PRTRC system
           ParB family protein.
          Length = 554

 Score =  115 bits (290), Expect = 1e-26
 Identities = 51/181 (28%), Positives = 103/181 (56%), Gaps = 5/181 (2%)

Query: 52  HNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNG-LYKIIAGERRFRAAKMASLSE-- 108
           +NPR YF+   + +L +SI++ G++QP++VR +    LY+++AGERR+RAA      +  
Sbjct: 6   NNPRRYFDPAEMAELVESIRAKGVLQPILVRPVPGSDLYEVVAGERRYRAALEVFGEDYD 65

Query: 109 VPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSH 168
           +P +I+ + ++ +   A++ENVQR D++P EEA    +L+      + +    +G S + 
Sbjct: 66  IPALIKVLTDEEAEAAALIENVQRADMSPAEEAEAAARLLGRCKGDREEAARRLGWSPAT 125

Query: 169 VANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPL--SLAQVIVSKKMSVRDTEELV 226
           +   L ++     VR+ +   +I LGHA  L         ++   I+++K +V + ++++
Sbjct: 126 LDRRLALMNCTDEVRQALIDRKILLGHAELLAGLPKDKQDNVLTAILAEKPTVAELKKMI 185

Query: 227 Q 227
           +
Sbjct: 186 E 186


>gnl|CDD|128746 smart00470, ParB, ParB-like nuclease domain.  Plasmid RK2 ParB
           preferentially cleaves single-stranded DNA. ParB also
           nicks supercoiled plasmid DNA preferably at sites with
           potential single-stranded character, like AT-rich
           regions and sequences that can form cruciform
           structures. ParB also exhibits 5-->3 exonuclease
           activity.
          Length = 89

 Score = 91.2 bits (227), Expect = 3e-19
 Identities = 42/89 (47%), Positives = 64/89 (71%), Gaps = 2/89 (2%)

Query: 42  ISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAA 101
           + I  + PNP  PR   E   LE+L +SIK +G++QP+IVR  D G Y+II GERR RAA
Sbjct: 3   VPIEKLRPNPDQPRLTSEES-LEELAESIKENGLLQPIIVRPND-GRYEIIDGERRLRAA 60

Query: 102 KMASLSEVPVIIRNVDNKSSLEIAIVENV 130
           K+  L EVPVI+R++D++ ++ ++++EN+
Sbjct: 61  KLLGLKEVPVIVRDLDDEEAIALSLIENI 89


>gnl|CDD|184353 PRK13832, PRK13832, plasmid partitioning protein; Provisional.
          Length = 520

 Score = 72.0 bits (177), Expect = 2e-13
 Identities = 54/187 (28%), Positives = 85/187 (45%), Gaps = 18/187 (9%)

Query: 49  PNPHNPRNYFESEGLED--LCQSIKSHGIIQPLIVRAI---DNGLYKIIAGERRFRAAKM 103
            NP N R    S    D  L  +IK+ GI+QP +V       NG   I AG RR + A  
Sbjct: 13  DNPDNTRRSKSSPQ-SDALLLATIKAVGIVQPPVVSPEEDGGNGYI-IQAGHRRVKQAIA 70

Query: 104 ASLSEVPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVG 163
           A L E+ V++    N +    ++VEN+ R+ LNP+++    E+L+   G+T+  I   + 
Sbjct: 71  AGLEEIEVLVTEAANDNGAMRSMVENIAREPLNPVDQWRAIERLV-ALGWTEEAIAVALA 129

Query: 164 KSRSHVANI--LRILK--LPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVIVSKKMSV 219
                V  I  LR+L   LP+ +  M + +  +    RT+ + S      Q  V K    
Sbjct: 130 LP---VRQIRKLRLLANVLPAMLDHMAKGDMPNEQQLRTIAAASLD---EQKEVWKAHKP 183

Query: 220 RDTEELV 226
           +  +  V
Sbjct: 184 KKGDPQV 190


>gnl|CDD|163272 TIGR03454, partition_RepB, plasmid partitioning protein RepB.
           Members of this family are the RepB protein involved in
           replicon partitioning. RepB is found, in general, as
           part of a repABC operon in plasmids and small
           chromosomes, separate from the main chromosome, in
           various bacteria. This model describes a rather narrow
           clade of proteins; it should be noted that additional
           homologs scoring below the trusted cutoff have very
           similar functions, although they may be named
           differently.
          Length = 325

 Score = 52.3 bits (126), Expect = 2e-07
 Identities = 46/191 (24%), Positives = 91/191 (47%), Gaps = 20/191 (10%)

Query: 11  GRGLAALIGEVNQSIDSPEKKTETIPE-SQDCISIHSIV--------PNPHNPRNYFESE 61
            R  +  +G + +S+    +K +   E  +      ++V        P+    R   + E
Sbjct: 27  QRVSSGAVGAMGRSLGELRQKAKRAEELEEQLAEGETVVELDPALIDPSFVRDRLDSDDE 86

Query: 62  GLEDLCQSIKSHGIIQPLIVRAI--DNGLYKIIAGERRFRAAKMASLSEVPV--IIRNVD 117
              DL +SI+ +G   P++VR      G Y+I  G RR RAA+       PV  ++R + 
Sbjct: 87  AFADLVESIRENGQQVPILVRPHPEAEGRYQIAYGHRRLRAAR---ELGRPVKAVVRELS 143

Query: 118 NKSSLEIAIV-ENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL 176
           ++  L IA   EN  R+DL+ +E AL + Q + + G+ ++ I + +   ++ ++ ++ + 
Sbjct: 144 DE-ELVIAQGQENSARRDLSFIERAL-FAQRLEDRGFDRDTIMAALSVDKTELSRMISVA 201

Query: 177 K-LPSSVREMI 186
           + +P  + E I
Sbjct: 202 RRIPEELIEAI 212


>gnl|CDD|172387 PRK13866, PRK13866, plasmid partitioning protein RepB; Provisional.
          Length = 336

 Score = 43.4 bits (102), Expect = 8e-05
 Identities = 44/136 (32%), Positives = 61/136 (44%), Gaps = 21/136 (15%)

Query: 9   RLGRGLAALIGEVNQSIDSPEKKTETIPESQDCISIHSIVPNPHNPRNYFESEGLEDLCQ 68
           RL   LAA  GE   S+D         P   D   I   +P   +P+        E L  
Sbjct: 54  RLQDQLAA--GEAVVSLD---------PSMIDGSPIADRLPADVDPK-------FEQLEA 95

Query: 69  SIKSHGIIQPLIVRAIDN--GLYKIIAGERRFRAAKMASLSEVPVIIRNVDNKSSLEIAI 126
           SI   G   P++VR      G Y+I+ G RR RAA      EV  I+RN+ ++  +    
Sbjct: 96  SISQEGQQVPILVRPHPEAAGRYQIVYGRRRLRAAVNLR-REVSAIVRNLTDRELVVAQG 154

Query: 127 VENVQRKDLNPLEEAL 142
            EN+ R DL+ +E+AL
Sbjct: 155 RENLDRADLSFIEKAL 170


>gnl|CDD|162028 TIGR00763, lon, ATP-dependent protease La.  This protein is induced
           by heat shock and other stresses in E. coli, B.
           subtilis, and other species. The yeast member,
           designated PIM1, is located in the mitochondrial matrix,
           required for mitochondrial function, and also induced by
           heat shock.
          Length = 775

 Score = 41.9 bits (99), Expect = 2e-04
 Identities = 48/226 (21%), Positives = 82/226 (36%), Gaps = 52/226 (23%)

Query: 75  IIQPLIVRAIDNGLYKIIA-GERRFRAAKMASLSEVPVIIRNVDNKSSLEIAIVENVQRK 133
           I++ L + +     YK++  G RR R  ++    +   ++  VDN       + E    K
Sbjct: 67  ILEMLPLPSSGTATYKVVVEGLRRIRIKEL--SDKGGYLVVRVDN-------LKEEPFDK 117

Query: 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISL 193
           D +   +AL                             I    +   S+ ++ R      
Sbjct: 118 D-DEEIKAL--------------------------TREIKETFRELISLSKLFR---EQP 147

Query: 194 GHARTLVSTSDPLSLAQVIVSKKMSVRDTEEL--VQEQDNKKEKRKKIFEGSREKEKYLT 251
                L    +P  LA  + +  + +++ +EL  V E  N +++ KK  E   +KE  L 
Sbjct: 148 ALLSALEDIDEPGRLADFVAAS-LQLKEKDELQEVLETVNIEKRLKKALE-LLKKELELL 205

Query: 252 DLEKKISSKVGLNISIKHRNNKGQFCIKYETNEQLKIICSLLGEND 297
            L+ KI+ KV   +    R        +Y   EQLK I   LG   
Sbjct: 206 KLQNKITKKVEEKMEKTQR--------EYYLREQLKAIKKELGIEK 243


>gnl|CDD|149550 pfam08535, KorB, KorB domain.  This family consists of several KorB
           transcriptional repressor proteins. The korB gene is a
           major regulatory element in the replication and
           maintenance of broad host-range plasmid RK2. It
           negatively controls the replication gene trfA, the
           host-lethal determinants kilA and kilB, and the
           korA-korB operon. This domain includes the DNA-binding
           HTH motif.
          Length = 93

 Score = 37.4 bits (87), Expect = 0.004
 Identities = 14/43 (32%), Positives = 21/43 (48%)

Query: 150 EYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEIS 192
             G  Q +I   +GKS+S V+  L +L +P  +RE       S
Sbjct: 1   AKGVKQAEIAKKLGKSKSFVSQHLALLDMPDCIREAYDSGRCS 43


>gnl|CDD|178143 PLN02528, PLN02528, 2-oxoisovalerate dehydrogenase E2 component.
          Length = 416

 Score = 30.1 bits (68), Expect = 0.79
 Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 20/83 (24%)

Query: 109 VPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQL----ISEYGYTQNDIGSIVGK 164
           VP I +NV + S LEI        K+L+ L+      +L    I+    T ++IG+I GK
Sbjct: 290 VPNI-KNVQSLSLLEIT-------KELSRLQHLAAENKLNPEDITGGTITLSNIGAIGGK 341

Query: 165 SRSHVAN--------ILRILKLP 179
             S V N        + RI K+P
Sbjct: 342 FGSPVLNLPEVAIIALGRIQKVP 364


>gnl|CDD|162669 TIGR02033, D-hydantoinase, D-hydantoinase.  This model represents
           the D-hydantoinase (dihydropyrimidinase) which primarily
           converts 5,6-dihydrouracil to 3-ureidopropanoate but
           also acts on dihydrothymine and hydantoin. The enzyme is
           a metalloenzyme.
          Length = 454

 Score = 30.0 bits (68), Expect = 0.82
 Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 10/68 (14%)

Query: 66  LCQSIKSHGIIQPLIVRAIDNGL----YKIIA------GERRFRAAKMASLSEVPVIIRN 115
           L    ++  +I  L  R +  G     Y  ++       E   RA  +A+L+  P+ + +
Sbjct: 179 LQVHAENGDVIAELQARLLAQGKTGPEYHALSRPPESEAEAVARAIALAALANAPLYVVH 238

Query: 116 VDNKSSLE 123
           V   S+++
Sbjct: 239 VSTASAVD 246


>gnl|CDD|183338 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed.
          Length = 547

 Score = 29.8 bits (68), Expect = 0.97
 Identities = 12/17 (70%), Positives = 14/17 (82%), Gaps = 1/17 (5%)

Query: 109 VPVIIRNVDNKSSLEIA 125
           VPVI ++VD KS LEIA
Sbjct: 425 VPVI-KDVDKKSLLEIA 440


>gnl|CDD|180066 PRK05419, PRK05419, putative sulfite oxidase subunit YedZ;
           Reviewed.
          Length = 205

 Score = 27.5 bits (62), Expect = 4.3
 Identities = 6/11 (54%), Positives = 8/11 (72%)

Query: 2   SNNYSKRRLGR 12
           S   S+RRLG+
Sbjct: 134 STRASQRRLGK 144


>gnl|CDD|152322 pfam11886, DUF3406, Domain of unknown function (DUF3406).  This
           domain is functionally uncharacterized. This domain is
           found in eukaryotes. This presumed domain is about 270
           amino acids in length. This domain is found associated
           with pfam04548.
          Length = 275

 Score = 27.3 bits (61), Expect = 4.4
 Identities = 11/39 (28%), Positives = 23/39 (58%), Gaps = 7/39 (17%)

Query: 258 SSKVGLNISIKHRNNK--GQFCIKYETNEQLKIICSLLG 294
            S +  + ++   NN+  GQ  ++  ++EQL+I  +L+G
Sbjct: 228 GSNMAGHANL---NNRGTGQISVRTSSSEQLQI--ALIG 261


>gnl|CDD|163476 TIGR03764, ICE_PFGI_1_parB, integrating conjugative element, PFGI_1
           class, ParB family protein.  Members of this protein
           family carry the ParB-type nuclease domain and are found
           in integrating conjugative elements (ICE) in the same
           class as PFGI-1 of Pseudomonas fluorescens Pf-5.
          Length = 258

 Score = 27.3 bits (61), Expect = 5.7
 Identities = 26/124 (20%), Positives = 49/124 (39%), Gaps = 27/124 (21%)

Query: 42  ISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPL-----------IVRAIDNGLYK 90
           +++  + P   NPR     +  +++  SI+  G+ QP            I+R   N   +
Sbjct: 11  LTLDQLRPYEDNPRTTRNPK-YDEIKASIRERGLDQPPKVTRRPGESDYIIRNGGNTRLQ 69

Query: 91  II------AGERRFRAAKMASLSEVPVIIRNVDNKSSLEIA-IVENVQRKDLNPLEEALG 143
           I+       G+ RF          +  + +    +    I  + EN  R DL  +E+ALG
Sbjct: 70  ILKELWQETGDERFF--------RIHCLFKPWPGELQALIGHLAENDLRGDLTFIEKALG 121

Query: 144 YEQL 147
            ++ 
Sbjct: 122 VQKA 125


>gnl|CDD|116230 pfam07611, DUF1574, Protein of unknown function (DUF1574).  A
           family of hypothetical proteins in Leptospira
           interrogans.
          Length = 345

 Score = 27.1 bits (60), Expect = 6.2
 Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 223 EELVQEQDNKKEKRKKI--FEGSREKEKYLTDLEKKISSKVGLNIS 266
           EELV+     KEK+K +  F  SR       D+EKK       N S
Sbjct: 50  EELVKYSKKPKEKKKLLILFGSSRMLYFSNDDIEKKYPDWDLYNFS 95


>gnl|CDD|149891 pfam08964, DUF1881, Protein of unkown function (DUF1881).  This
           domain is found in a set of hypothetical bacterial and
           eukaryotic proteins, as well as in various
           calcium-dependent cell adhesion molecules.
          Length = 199

 Score = 27.0 bits (60), Expect = 6.5
 Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 2/28 (7%)

Query: 143 GYEQLISEYGYTQNDIGSIVGKSRSHVA 170
            Y+Q   E+G +Q DI SI G S+  VA
Sbjct: 59  KYQQR--EWGSSQPDITSIGGLSKFQVA 84


>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
           Provisional.
          Length = 784

 Score = 26.4 bits (58), Expect = 9.0
 Identities = 30/101 (29%), Positives = 47/101 (46%), Gaps = 11/101 (10%)

Query: 198 TLVSTSDPLSLAQVIVSK-KMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLEKK 256
           +L S  DP  LA  I +   + + D + +++  D    +R +      E E  L  +EK+
Sbjct: 155 SLNSIDDPARLADTIAAHMPLKLADKQSVLEMSD--VNERLEYLMAMMESEIDLLQVEKR 212

Query: 257 ISSKVGLNISIKHRNNKGQFCIKYETNEQLKIICSLLGEND 297
           I ++V      K +  K Q   +Y  NEQ+K I   LGE D
Sbjct: 213 IRNRV------KKQMEKSQR--EYYLNEQMKAIQKELGEMD 245


  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
   0.313    0.132    0.356 

Gapped
Lambda     K      H
   0.267   0.0732    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,705,889
Number of extensions: 298202
Number of successful extensions: 595
Number of sequences better than 10.0: 1
Number of HSP's gapped: 582
Number of HSP's successfully gapped: 58
Length of query: 300
Length of database: 5,994,473
Length adjustment: 93
Effective length of query: 207
Effective length of database: 3,984,929
Effective search space: 824880303
Effective search space used: 824880303
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.7 bits)