RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780217|ref|YP_003064630.1| DNA polymerase III subunit
delta' [Candidatus Liberibacter asiaticus str. psy62]
(347 letters)
>gnl|CDD|73174 COG0470, HolB, ATPase involved in DNA replication [DNA replication,
recombination, and repair].
Length = 325
Score = 120 bits (302), Expect = 5e-28
Identities = 81/322 (25%), Positives = 137/322 (42%), Gaps = 12/322 (3%)
Query: 14 LFGHEDIEKFLSQYYCSGRMHHALLFEGEQGIGKATLGFRYAGHVLQNPDFSKAPVRMCN 73
+ E +++ L Q SGR+ HALLF G G+GK T A +L P C
Sbjct: 4 VPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHC- 62
Query: 74 PDPCSPFVKQMASHALHDFLYLSYSLNPKTGKWRTVITVDEIRRIRYFLSLTANTGYWRV 133
K + + DFL L+ S + I V+++R + FLS + G ++V
Sbjct: 63 -----RSCKLIPAGNHPDFLELNPS-----DLRKIDIIVEQVRELAEFLSESPLEGGYKV 112
Query: 134 IMIDPVDGMNRNAANALLKSLEEPPQKVLFILISHASPTILSTIRSRCLSIKFNSLSENN 193
++ID D + +AANALLK+LEEPP+ FILI++ IL TIRSRC I+F S
Sbjct: 113 VIIDEADKLTEDAANALLKTLEEPPKNTRFILITNDPSKILPTIRSRCQRIRFKPPSRLE 172
Query: 194 LYKALEQLKIMGWDSKRDFVKIAAYGSVARAIKILHYDCDKIISSYIDLIHIPRQEYALQ 253
LE + + + A + +A+ L + I + + + + A
Sbjct: 173 AIAWLEDQGLEEIAAVAEGDARKA-INPLQALAALEIGEESIYEALLLALPESLAQLAAL 231
Query: 254 KMQQIADELLSQDQKIAFDFLIEFILKEICKSAKAAALSGQLEEADQIAQIYFSLVKRVH 313
++ ++A+ + + + L+ L + +L++A + L+ +
Sbjct: 232 ELLKLAENKFLEALEKLWLLLLLEGLLGEDLLDQLQRELLKLDKALIQEEKAAELLDALA 291
Query: 314 AFSMYNLDRRQMIFHLLSKARE 335
LD + L + E
Sbjct: 292 QARRRLLDGLLALIQLENLLAE 313
>gnl|CDD|32641 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 103 bits (258), Expect = 8e-23
Identities = 76/284 (26%), Positives = 121/284 (42%), Gaps = 28/284 (9%)
Query: 4 RAFDPVYNQRLFGHEDIEKFLSQYYCSGRMHHALLFEGEQGIGKATLGFRYAGHVLQNPD 63
R + P + G E + K LS +GR+ HA LF G +G+GK T+ A +
Sbjct: 8 RKYRPKTFDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENG 67
Query: 64 FSKAPVRMCNPDPCSPFVKQMASHALHDFLYLSYSLNPKTGKWRTVITVDEIRRIRYFLS 123
+ P C K++ +L D + + + N VD+IR I ++
Sbjct: 68 PTAEPCGKCI------SCKEINEGSLIDVIEIDAASN---------TGVDDIREIIEKVN 112
Query: 124 LTANTGYWRVIMIDPVDGMNRNAANALLKSLEEPPQKVLFILISHASPTILSTIRSRCLS 183
+ G ++V +ID V +++ A NALLK+LEEPP V FIL + I +TI SRC
Sbjct: 113 YAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTILSRCQR 172
Query: 184 IKFNSLSENNLYKALEQLKIMGW----DSKRDFVKIAAYGSVARAIKILHY---DCDKII 236
F L + K L + + + AA GS+ A+ +L + I
Sbjct: 173 FDFKRLDLEEIAKHLAAILDKEGINIEEDALSLIARAAEGSLRDALSLLDQAIAFGEGEI 232
Query: 237 SSYI--DLIHIPRQEYALQKMQQIADELLSQDQKIAFDFLIEFI 278
+ D++ + E L + + +L D K A + E I
Sbjct: 233 TLESVRDMLGLTDIEKLL----SLLEAILKGDAKEALRLINELI 272
>gnl|CDD|36207 KOG0989, KOG0989, KOG0989, Replication factor C, subunit RFC4
[Replication, recombination and repair].
Length = 346
Score = 58.4 bits (141), Expect = 3e-09
Identities = 31/101 (30%), Positives = 52/101 (51%), Gaps = 4/101 (3%)
Query: 132 RVIMIDPVDGMNRNAANALLKSLEEPPQKVLFILISHASPTILSTIRSRCLSIKFNSLSE 191
++I++D D M +A AL +++E+ + FILI + I+ + SRC +F L +
Sbjct: 131 KIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKD 190
Query: 192 NNLYKALEQLKIM-GWDSKRDFVK-IAAY--GSVARAIKIL 228
++ LE++ G D D +K IA G + RAI L
Sbjct: 191 EDIVDRLEKIASKEGVDIDDDALKLIAKISDGDLRRAITTL 231
>gnl|CDD|36209 KOG0991, KOG0991, KOG0991, Replication factor C, subunit RFC2
[Replication, recombination and repair].
Length = 333
Score = 46.9 bits (111), Expect = 8e-06
Identities = 46/199 (23%), Positives = 79/199 (39%), Gaps = 38/199 (19%)
Query: 6 FDPVYNQRLFGHEDIEKFLSQYYCSGRMHHALLFEGEQGIGKATLGFRYAGHVLQNPDFS 65
+ P Q + G+ED + LS G M + L+ G G GK T A L +
Sbjct: 21 YRPSVLQDIVGNEDTVERLSVIAKEGNMPN-LIISGPPGTGKTTSILCLA-RELLGDSYK 78
Query: 66 KAPVRMCNPDPCSPFVKQMASHALHDFLYLSYSLNPKTGKWRTVITVDEIR-RIRYFLS- 123
+A + LN + +D +R +I+ F
Sbjct: 79 EAVLE----------------------------LNASDER-----GIDVVRNKIKMFAQK 105
Query: 124 -LTANTGYWRVIMIDPVDGMNRNAANALLKSLEEPPQKVLFILISHASPTILSTIRSRCL 182
+T G ++I++D D M A AL +++E F L + S I+ I+SRC
Sbjct: 106 KVTLPPGRHKIIILDEADSMTAGAQQALRRTMEIYSNTTRFALACNQSEKIIEPIQSRCA 165
Query: 183 SIKFNSLSENNLYKALEQL 201
++++ LS+ + K L ++
Sbjct: 166 ILRYSKLSDQQILKRLLEV 184
>gnl|CDD|36208 KOG0990, KOG0990, KOG0990, Replication factor C, subunit RFC5
[Replication, recombination and repair].
Length = 360
Score = 44.6 bits (105), Expect = 4e-05
Identities = 49/303 (16%), Positives = 93/303 (30%), Gaps = 47/303 (15%)
Query: 14 LFGHEDIEKFLSQYYCSGRMHHALLFEGEQGIGKATLGFRYAGHVLQNPDFSKAPVRMCN 73
+ E I ++Y + H LLF G G GK + A + + +
Sbjct: 43 VIKQEPIWSTENRYSGMPGLPH-LLFYGPPGTGKTSTILANARDFYSPHPTTSMLLELNA 101
Query: 74 PDPCSPFVKQMASHALHDFLYLSYSLNPKTGKWRTVITVDEIRRIRYFLSLTANTGYWRV 133
D + +H F + + +++
Sbjct: 102 SDDRGIDPVR---QQIHLFAST------------------------QQPTTYSTHAAFKL 134
Query: 134 IMIDPVDGMNRNAANALLKSLEEPPQKVLFILISHASPTILSTIRSRCLSIKFNSLSENN 193
+++D D M R+A NAL + +E+ F IS+ I +SRC +F L+
Sbjct: 135 VILDEADAMTRDAQNALRRVIEKYTANTRFATISNPPQKIHPAQQSRCTRFRFAPLTMAQ 194
Query: 194 LYKAL------EQLKIMGWDSKRDFVKIAAYGSVARAIKIL---HYDCDKIISSYIDLIH 244
+ EQ + + + G + A+ L +
Sbjct: 195 QTERQSHIRESEQKETN--PEGYSALGRLSVGDMRVALNYLQSILKKVMERKELNNPNDL 252
Query: 245 IPRQEYALQKM--QQIADELLSQDQKIAFDFLIEFILKEICKSAKAAALSGQLEEADQIA 302
+ + + A Q +QI ++ ++ + E K K A + E +Q
Sbjct: 253 VYQCKGAPQPSDIRQIIEKRMNGEDIELMLDDSEL------KKPKGLARQDRRAELEQRF 306
Query: 303 QIY 305
I
Sbjct: 307 AIV 309
>gnl|CDD|37246 KOG2035, KOG2035, KOG2035, Replication factor C, subunit RFC3
[Energy production and conversion, Replication,
recombination and repair].
Length = 351
Score = 40.3 bits (94), Expect = 8e-04
Identities = 34/139 (24%), Positives = 73/139 (52%), Gaps = 5/139 (3%)
Query: 131 WRVIMIDPVDGMNRNAANALLKSLEEPPQKVLFILISHASPTILSTIRSRCLSIKFNSLS 190
++V++I+ D + R+A +AL +++E+ IL+ +++ I+ IRSRCL I+ + S
Sbjct: 128 FKVVVINEADELTRDAQHALRRTMEKYSSNCRLILVCNSTSRIIEPIRSRCLFIRVPAPS 187
Query: 191 ENNLYKALEQ-LKIMGWDSKRDF-VKIA--AYGSVARAIKILHYDCDKIISSYIDLIHIP 246
+ + L + LK G ++ +IA + ++ RA+ +L + IP
Sbjct: 188 DEEITSVLSKVLKKEGLQLPKELLKRIAEKSNRNLRRALLMLEAVRVNNEPFTANSQVIP 247
Query: 247 RQEYALQKMQQIADELLSQ 265
+ ++ + +Q+IA +L +
Sbjct: 248 KPDWEIY-IQEIARVILKE 265
>gnl|CDD|32437 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 33.7 bits (77), Expect = 0.079
Identities = 18/95 (18%), Positives = 39/95 (41%), Gaps = 4/95 (4%)
Query: 108 TVITVDEIRRIRYFLSLTANTGYWRVIMIDPVDGMNRNAANALLKSLEEPPQKVLFILIS 167
V ++R I G ++ +D + N+ +ALL +E ++ I +
Sbjct: 82 VTSGVKDLREIIEEARKNRLLGRRTILFLDEIHRFNKAQQDALLPHVEN--GTIILIGAT 139
Query: 168 HASPT--ILSTIRSRCLSIKFNSLSENNLYKALEQ 200
+P+ + + SR + LS ++ K L++
Sbjct: 140 TENPSFELNPALLSRARVFELKPLSSEDIKKLLKR 174
>gnl|CDD|144377 pfam00753, Lactamase_B, Metallo-beta-lactamase superfamily.
Length = 148
Score = 31.9 bits (72), Expect = 0.25
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 132 RVIMIDPVDGMNRNAANALLKSLEEPPQKVLFILISHA 169
I+ID G+ + A LL +L P+ + I+++HA
Sbjct: 16 GAILIDT--GLGADDALLLLAALGLDPKDIDAIILTHA 51
>gnl|CDD|39359 KOG4157, KOG4157, KOG4157,
beta-1,6-N-acetylglucosaminyltransferase, contains WSC
domain [Carbohydrate transport and metabolism,
Posttranslational modification, protein turnover,
chaperones].
Length = 418
Score = 30.9 bits (69), Expect = 0.52
Identities = 21/121 (17%), Positives = 33/121 (27%), Gaps = 11/121 (9%)
Query: 11 NQRLFGHEDIEKFLSQYYCSG--RMHHALLFEGEQGIGKATLGFRYAGHVLQNPDFSKAP 68
+ L G S +C F E G Y G L ++A
Sbjct: 37 IRALTGTSKTSYKQSVSHCQNFCAEQGYRFFGLEAGYEC------YCGGSLPLMSNTEAS 90
Query: 69 VRMCNPDPCSPFVKQMASHALHDFLYLSYSLNPKTGKWRTVITVDEIRRIRYFLSLTANT 128
CN C + Q+ A D L + + + +T F S ++
Sbjct: 91 SSECNT-KCFGYGYQICGGA--DRLSVYVTSVGMPSGNSSSMTSRTCTSSSDFPSSYTSS 147
Query: 129 G 129
Sbjct: 148 T 148
>gnl|CDD|35796 KOG0576, KOG0576, KOG0576, Mitogen-activated protein kinase kinase
kinase kinase (MAP4K), germinal center kinase family
[Signal transduction mechanisms].
Length = 829
Score = 29.6 bits (66), Expect = 1.3
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 6/50 (12%)
Query: 59 LQNPDFSKAPVRM------CNPDPCSPFVKQMASHALHDFLYLSYSLNPK 102
LQ P F P+R P + K S H+F+ + + NPK
Sbjct: 211 LQPPLFDLHPMRALFLMTKSGFQPPTLKDKTKWSEFFHNFVKGALTKNPK 260
>gnl|CDD|147774 pfam05800, GvpO, Gas vesicle synthesis protein GvpO. This family
consists of archaeal GvpO proteins which are required
for gas vesicle synthesis. The family also contains two
related sequences from Streptomyces coelicolor.
Length = 101
Score = 28.5 bits (64), Expect = 2.6
Identities = 18/41 (43%), Positives = 22/41 (53%), Gaps = 11/41 (26%)
Query: 104 GKWRTVITVDEIRRI--------RYFLSLTAN---TGYWRV 133
G WR V+ V E RRI RY ++L A+ TGY RV
Sbjct: 51 GGWRVVVEVVERRRIPDTQDILARYEVTLDADGELTGYRRV 91
>gnl|CDD|33926 COG4191, COG4191, Signal transduction histidine kinase regulating
C4-dicarboxylate transport system [Signal transduction
mechanisms].
Length = 603
Score = 27.9 bits (62), Expect = 4.2
Identities = 12/43 (27%), Positives = 17/43 (39%)
Query: 114 EIRRIRYFLSLTANTGYWRVIMIDPVDGMNRNAANALLKSLEE 156
+ R +L A R + P D R AAN L+ + E
Sbjct: 54 TLERYESLPALLALDDDLREALTGPGDPALRAAANRYLEQINE 96
>gnl|CDD|31932 COG1746, CCA1, tRNA nucleotidyltransferase (CCA-adding enzyme)
[Translation, ribosomal structure and biogenesis].
Length = 443
Score = 27.5 bits (61), Expect = 6.1
Identities = 25/86 (29%), Positives = 36/86 (41%), Gaps = 20/86 (23%)
Query: 134 IMIDPVDGMNRNAANAL-LKS-----------LEEPPQKVLFILISHASPTILSTIRSR- 180
I++DPVD RN A AL L++ L+ P + F P +LS +R R
Sbjct: 226 IVVDPVD-PKRNVAAALSLENLARFVHAAREFLKNPSPE--FFFPRKPKPLLLSKLRRRG 282
Query: 181 ----CLSIKFNSLSENNLYKALEQLK 202
L L ++ LY LE+
Sbjct: 283 THVLALVFPKPDLVDDILYPQLERTA 308
>gnl|CDD|37648 KOG2437, KOG2437, KOG2437, Muskelin [Signal transduction
mechanisms].
Length = 723
Score = 27.3 bits (60), Expect = 6.8
Identities = 23/108 (21%), Positives = 33/108 (30%), Gaps = 1/108 (0%)
Query: 224 AIKILHYDCDKIISSYIDLIHIPRQEYALQKMQQIADELLSQDQKIAFDFLIEFILKEIC 283
++KI D ++ LI R E Q A + L D I D KE
Sbjct: 608 SLKICRPSKDYLLRHCKYLIRKHRFEEKAQVDPLSALKYLQNDLYITVDHSDPEETKEFQ 667
Query: 284 KSAKAAALSGQLEEADQIAQIYFSLVKRVHAF-SMYNLDRRQMIFHLL 330
A A SG + + +R F ++ N M
Sbjct: 668 LLASALFKSGSDFTKLGFSDRDHTYAQRTDLFDTLVNFVPDSMTPPKG 715
>gnl|CDD|99958 cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repeat I_like
subfamily. WDR9 is a human gene located in the Down
Syndrome critical region-2 of chromosome 21. It encodes
for a nuclear protein containing WD40 repeats and two
bromodomains, which may function as a transcriptional
regulator involved in chromatin remodeling and play a
role in embryonic development. Bromodomains are 110
amino acid long domains, that are found in many
chromatin associated proteins. Bromodomains can interact
specifically with acetylated lysine..
Length = 128
Score = 26.9 bits (60), Expect = 8.4
Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 20/74 (27%)
Query: 171 PTILSTIRSRCLSIKFNSLSENNLYKALEQLKIMGWDSKRDFVKIAAY------GSVARA 224
P L TIRSR EN Y++LE L+ D + + A +A+
Sbjct: 68 PMDLETIRSRL---------ENRYYRSLEALR---HDVRL--ILSNAETFNEPNSEIAKK 113
Query: 225 IKILHYDCDKIISS 238
K L +I+SS
Sbjct: 114 AKRLSDWLLRILSS 127
>gnl|CDD|176523 cd08581, GDPD_like_1, Glycerophosphodiester phosphodiesterase
domain of uncharacterized bacterial
glycerophosphodiester phosphodiesterases. This
subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in a group of
uncharacterized bacterial glycerophosphodiester
phosphodiesterase and similar proteins. They show high
sequence similarity to Escherichia coli
glycerophosphodiester phosphodiesterase, which catalyzes
the degradation of glycerophosphodiesters to produce
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols.
Length = 229
Score = 26.9 bits (60), Expect = 9.5
Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 6/42 (14%)
Query: 91 DFLYLSYSLNPKTGK-----WRTVI-TVDEIRRIRYFLSLTA 126
D+L+ +L P TG W+ VI V+E +
Sbjct: 180 DYLFCDKNLLPDTGDLWAGTWKWVIYEVNEPAEALALAARGV 221
>gnl|CDD|31434 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 26.8 bits (59), Expect = 9.8
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 7/49 (14%)
Query: 133 VIMIDPVDGMNRNAANALLKSLEEPPQKVLFILISHASPTILSTIRSRC 181
V ID D MN A+ +++E+ Q IS A I +T+ +RC
Sbjct: 386 VCCIDEFDKMNEEDRVAIHEAMEQ--QT-----ISIAKAGITATLNARC 427
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.326 0.139 0.415
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,350,296
Number of extensions: 231267
Number of successful extensions: 876
Number of sequences better than 10.0: 1
Number of HSP's gapped: 874
Number of HSP's successfully gapped: 29
Length of query: 347
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 252
Effective length of database: 4,210,882
Effective search space: 1061142264
Effective search space used: 1061142264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.1 bits)