RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780454|ref|YP_003064867.1| DNA polymerase III subunit
beta [Candidatus Liberibacter asiaticus str. psy62]
(385 letters)
>gnl|CDD|29053 cd00140, beta_clamp, Beta clamp domain. The beta subunit
(processivity factor) of DNA polymerase III holoenzyme,
refered to as the beta clamp, forms a ring shaped dimer
that encircles dsDNA (sliding clamp) in bacteria. The
beta-clamp is structurally similar to the trimeric ring
formed by PCNA (found in eukaryotes and archaea) and the
processivity factor (found in bacteriophages T4 and
RB69). This structural correspondence further
substantiates the mechanistic connection between
eukaryotic and prokaryotic DNA replication that has been
suggested on biochemical grounds. .
Length = 365
Score = 311 bits (798), Expect = 2e-85
Identities = 151/385 (39%), Positives = 229/385 (59%), Gaps = 21/385 (5%)
Query: 1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPA- 59
MK T+ R +LE L R IE +NTIP+ +VL++A+DG L + A+ EI I IPA
Sbjct: 1 MKFTINREALLEALQKVSRAIESRNTIPILSNVLIEASDGGLTLTATDLEISIKTTIPAE 60
Query: 60 SVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFP 119
V+ GS+TV A L DIVRKL D +++ E + I G S F L + P EFP
Sbjct: 61 EVEEEGSVTVPAKKLLDIVRKLPDE-EVTLETEEN---RLTIKSGKSRFSLNTLPAEEFP 116
Query: 120 STKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGH 179
E E SF + +S LK L+++T FA++T+E R LNG+ I + KL AVATDGH
Sbjct: 117 ELPEIENGSSFTIPASELKELIKKTAFAVSTDETRPILNGVLLEIEDN--KLRAVATDGH 174
Query: 180 RLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSV 239
RLA+ E+++ + + ++IVPRK + E+L++L D V++S+SE++I + + + +
Sbjct: 175 RLALREIELESGAEEDFNVIVPRKTLNELLKLLEDDDEEVEISISENQILFKLGNTTFTS 234
Query: 240 RLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTV 299
RLI+GEFP+Y+ VIP +K L V+ L +A+ RVS++S+ + + VKL +S +L ++
Sbjct: 235 RLIEGEFPDYERVIPKEFEKSLTVDREELLEALKRVSLLSNEKNRGVKLEISEGQLKLSA 294
Query: 300 DNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFI 359
+NP++G+A E + V Y ++I FN KYLL+ + I S +EV SNS V I
Sbjct: 295 NNPEIGEAEEELEVEYEGEELEIGFNPKYLLDALKAIDS-----EEVRLSFTDSNSPVLI 349
Query: 360 RGKDKDSKNNKDNKVNAFYVLMPMR 384
+D D N Y++MP+R
Sbjct: 350 TPEDDD---------NFLYLIMPVR 365
>gnl|CDD|30937 COG0592, DnaN, DNA polymerase sliding clamp subunit (PCNA homolog)
[DNA replication, recombination, and repair].
Length = 364
Score = 244 bits (625), Expect = 2e-65
Identities = 130/385 (33%), Positives = 215/385 (55%), Gaps = 21/385 (5%)
Query: 1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS 60
MK ++ER ++L+ L RI+E + TIP+ +VL++A + L + + EI + IPA
Sbjct: 1 MKFSIERENLLKALQLVSRIVESRPTIPILSNVLIEAKENGLTLTGTDLEISLEARIPAE 60
Query: 61 VDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPS 120
V+ G + V A L DI+ KL D A ++ + G S F L + P +FP
Sbjct: 61 VEAEGEVAVPAKKLLDIISKLPDEAVFLVTEDGISLLA--VDSGKSAFVLLTLPAEDFPE 118
Query: 121 TKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHR 180
+E F L + +LK +++RT FA + E RY LNG+ I E KL VATDGHR
Sbjct: 119 YPVDEEEVEFGLPTELLKKIIKRTKFADSLLETRYELNGVLLEI--EGTKLRLVATDGHR 176
Query: 181 LAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVR 240
LAV E++I ++ + S+I+P K + E++++L KD+ V++ L +I + +
Sbjct: 177 LAVEELEI-PELEEDASVIIPAKTLKELIKLL--KDADVEIFLVSDQIRFKAGETILFSK 233
Query: 241 LIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVD 300
LI+GEFP+Y+ VIP +KEL ++ L++A+ RV +S ++ + KLSL+ ++ +++
Sbjct: 234 LIEGEFPDYERVIPKEFEKELTLDRLELKEALKRVYSLSYLKDRGKKLSLADGEVKLSLG 293
Query: 301 NPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIR 360
N + GKA E ++V Y + I FN YLL+++ + S +EV F + S+S IR
Sbjct: 294 NDEPGKAEEEIDVGYTGEELKIGFNLAYLLDVLKALDS-----EEVQFGFNDSSSPFLIR 348
Query: 361 GKDKDSKNNKDNKVNAFYVLMPMRI 385
++ D + Y++MPMR+
Sbjct: 349 PEEND---------DFKYLIMPMRL 364
>gnl|CDD|111640 pfam02767, DNA_pol3_beta_2, DNA polymerase III beta subunit,
central domain. A dimer of the beta subunit of DNA
polymerase beta forms a ring which encircles duplex DNA.
Each monomer contains three domains of identical
topology and DNA clamp fold.
Length = 116
Score = 115 bits (289), Expect = 3e-26
Identities = 46/118 (38%), Positives = 71/118 (60%), Gaps = 2/118 (1%)
Query: 131 ELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVA 190
L VLK L+E+T FAM +E RY LNG+ +L VATDGHRLAV ++++
Sbjct: 1 TLPQKVLKELIEQTAFAMGRDETRYVLNGVNLETEGN--ELRLVATDGHRLAVRKLELSV 58
Query: 191 QIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFPN 248
+ + S+IVPRK + E+ ++L+ VK+ + E +I ++ + RLIDG+FP+
Sbjct: 59 ENPDIFSVIVPRKTLLELAKLLTDNGELVKLQIGEGQIRFEFGNVIFTSRLIDGKFPD 116
>gnl|CDD|109756 pfam00712, DNA_pol3_beta, DNA polymerase III beta subunit,
N-terminal domain. A dimer of the beta subunit of DNA
polymerase beta forms a ring which encircles duplex DNA.
Each monomer contains three domains of identical
topology and DNA clamp fold.
Length = 120
Score = 87.3 bits (217), Expect = 7e-18
Identities = 36/120 (30%), Positives = 57/120 (47%), Gaps = 4/120 (3%)
Query: 1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS 60
MK T+ER +L+ L R++ + TIP+ +LL+ D L + + EI I I A
Sbjct: 1 MKFTIERDQLLKALQKVARVLSNRPTIPILSGILLEVKDDQLSLTGTDLEISIESTISAE 60
Query: 61 VD-VCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFP 119
++ GS+ + A DIVR L D + + I G+S F L + P ++P
Sbjct: 61 IESEPGSVLIPARKFLDIVRALPDDKDVKLSVNEDRLL---IISGNSRFSLPTLPAEDYP 117
>gnl|CDD|111641 pfam02768, DNA_pol3_beta_3, DNA polymerase III beta subunit,
C-terminal domain. A dimer of the beta subunit of DNA
polymerase beta forms a ring which encircles duplex DNA.
Each monomer contains three domains of identical
topology and DNA clamp fold.
Length = 121
Score = 79.6 bits (197), Expect = 1e-15
Identities = 37/133 (27%), Positives = 70/133 (52%), Gaps = 14/133 (10%)
Query: 252 VIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESM 311
V+P + ++ V+ L++A+ RV+++++ + + V+LS +L +T +NP++G+A E +
Sbjct: 3 VLPKEFETKITVDNKELKKALARVALLANEKNRGVRLSFEEGQLKLTANNPEIGRAEEEV 62
Query: 312 NVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKD 371
+V Y P++I FN YLL+ + + S +E+ + S I D
Sbjct: 63 DVDYIGEPLEIAFNVSYLLDALKALKS-----EEIELQFTDSTKPALISPPGDDD----- 112
Query: 372 NKVNAFYVLMPMR 384
YV+MPMR
Sbjct: 113 ----LKYVVMPMR 121
>gnl|CDD|32727 COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid
transport and metabolism].
Length = 1592
Score = 31.1 bits (70), Expect = 0.61
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 327 KYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDK 364
LL+I DNI D+VV V RLD + + + DK
Sbjct: 863 SGLLDITDNIIDDQVVPPADVVRLDGDDPYLVV-AADK 899
>gnl|CDD|36161 KOG0943, KOG0943, KOG0943, Predicted ubiquitin-protein
ligase/hyperplastic discs protein, HECT superfamily
[Posttranslational modification, protein turnover,
chaperones].
Length = 3015
Score = 29.0 bits (64), Expect = 2.4
Identities = 28/147 (19%), Positives = 49/147 (33%), Gaps = 2/147 (1%)
Query: 165 NEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLS 224
+ + ++A A A + A+ A S P + I R + SS LS
Sbjct: 1877 APRPMIMASIAAQSAARARALEALAARRAAAASR-TPAASSAGIERFDPYRFSSRSSFLS 1935
Query: 225 ESRIHLNIESLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQ 284
R +I S + GE + N +RQ D + ++ +
Sbjct: 1936 NLREDGSI-SQGAAAAAAAGEASGAGSSALAPASALAGANNIQIRQIPDLMGLIPKSNHE 1994
Query: 285 AVKLSLSSDKLCMTVDNPDMGKAIESM 311
+ ++ KL D P++ A E
Sbjct: 1995 SSPAINAAKKLNDNQDAPNLENAREEK 2021
>gnl|CDD|113695 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes
the fifth essential DNA polymerase in yeast EC:2.7.7.7.
Pol5p is localized exclusively to the nucleolus and
binds near or at the enhancer region of rRNA-encoding
DNA repeating units.
Length = 784
Score = 27.5 bits (61), Expect = 6.3
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 337 SSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNK 373
+E +DDE + RLD+ + +F K++ + K
Sbjct: 724 EDEEGMDDEQMMRLDTYLAQIFKEKKERIQAGGETKK 760
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
0.318 0.134 0.374
Gapped
Lambda K H
0.267 0.0612 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,348,565
Number of extensions: 222501
Number of successful extensions: 550
Number of sequences better than 10.0: 1
Number of HSP's gapped: 537
Number of HSP's successfully gapped: 19
Length of query: 385
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 289
Effective length of database: 4,189,273
Effective search space: 1210699897
Effective search space used: 1210699897
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.4 bits)