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)