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)