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)