RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|255764496|ref|YP_003065012.2| excinuclease ABC subunit C [Candidatus Liberibacter asiaticus str. psy62] (616 letters) >gnl|CDD|30670 COG0322, UvrC, Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]. Length = 581 Score = 517 bits (1334), Expect = e-147 Identities = 250/605 (41%), Positives = 337/605 (55%), Gaps = 40/605 (6%) Query: 7 PECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTE 66 P PGVY M D G VLYVGKA NL+KR+ SY + ++ I +I + VT TE Sbjct: 13 PHSPGVYLMKDENGTVLYVGKAKNLRKRVSSYFRGRLD-PKTAALVENIADIEYIVTDTE 71 Query: 67 VEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFA 126 EALLLE N+IK+ KPR+N+LL+DDKS+PYI IT + P + R +G YFGP+ Sbjct: 72 TEALLLENNLIKKHKPRYNVLLKDDKSYPYIKITLHEEFPRIAITRGLRKDKGKYFGPYP 131 Query: 127 SVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHE 186 S AV +T+N LQR F LR+C+DSV R+R RPCL +QI RC PC G IS E+Y E V E Sbjct: 132 SAGAVRETLNLLQRLFPLRTCSDSVKRNRRRPCLYYQIGRCLAPCVGLISEEEYREIVEE 191 Query: 187 AKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNH---NDSIYNRMD 243 K FL G + + +++ M +A+ D+E A RD++ AL +Q + +D Sbjct: 192 VKGFLKGKDDAVLQELEEKMEEASENLDFERAARLRDQIKALEKLQEKQAVSLFKLQDLD 251 Query: 244 CFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENI 303 + + AC+Q F G+ G +F + L F+ QFY P+ I Sbjct: 252 VIAGAVDGGEACVQVFFVRGGKLLGRRAYFPLENEAEEE---LEAFILQFYKSNEIPKEI 308 Query: 304 LLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISHQ 363 LL +E E L E + G +I VPK+GEK+ ++E A NA + Q Q Sbjct: 309 LLPQELPEEELEEA-LSEAAGL--EIRVPKRGEKKSLLELATKNAKEALEQLKERSDEKQ 365 Query: 364 MILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVK 423 L+ LP P RIE +D SHI G VG MVV + G K YR++N+ + Sbjct: 366 -ALEALAALLGLP-APYRIECFDISHIQGEDTVGSMVVFEDGGPSKKDYRRYNI---KIT 420 Query: 424 TQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVL 483 DD A MR VL RR+S+L+K E PD++++DGGKGQL+AA+ VL Sbjct: 421 GGDDYASMREVLTRRYSRLLKEE----------------LPDLILIDGGKGQLNAAKEVL 464 Query: 484 KKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAIT 543 K+L ++ I +I +AKG + E GE L P LY +QR+RDEAHRFAIT Sbjct: 465 KELGLD--IPVIGLAKGEE-----ELLLPGPGEEFDLPPNSPALYLLQRIRDEAHRFAIT 517 Query: 544 THRKRRKKAAY-SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACK 602 HRK+R KA S LD+I GIGP R++ LL+ FG++K I +S E LA + GISKK+A K Sbjct: 518 YHRKKRSKAMLQSSLDDIPGIGPKRRKALLKHFGSLKGIKSASVEELAKV-GISKKLAEK 576 Query: 603 IYNHF 607 IY Sbjct: 577 IYEAL 581 >gnl|CDD|144946 pfam01541, GIY-YIG, GIY-YIG catalytic domain. This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site. Length = 77 Score = 47.8 bits (114), Expect = 1e-05 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 3/75 (4%) Query: 10 PGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEV-E 68 PGVY + + +VLYVG NL++R+K H + + T ++ + E Sbjct: 2 PGVYIITNKDNKVLYVGSTKNLKRRLKQ--HFSGKGAKKTRNKAKPFELIILEEFPTKEE 59 Query: 69 ALLLEANMIKRLKPR 83 AL LE +IK+ KP Sbjct: 60 ALELEKYLIKKYKPN 74 >gnl|CDD|32131 COG1948, MUS81, ERCC4-type nuclease [DNA replication, recombination, and repair]. Length = 254 Score = 46.4 bits (110), Expect = 2e-05 Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 6/87 (6%) Query: 526 ILYFIQRLRDEAHRFAITTHRKRRKKAAYSPLDE-----INGIGPLRKRLLLQSFGTVKM 580 +++ + R E + ++ H K++ K L I GIGP LL+ FG+V+ Sbjct: 149 LIHELARREQEERKRSVNPHGKKKAKT-LKELQLYILESIPGIGPKLAERLLKKFGSVED 207 Query: 581 ISRSSPETLASIEGISKKIACKIYNHF 607 + +S E L ++GI +K A +IY Sbjct: 208 VLTASEEELMKVKGIGEKKAREIYRFL 234 >gnl|CDD|30621 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]. Length = 667 Score = 39.8 bits (93), Expect = 0.002 Identities = 17/50 (34%), Positives = 26/50 (52%) Query: 560 INGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 I +G + L + FGT++ + +S E LASI GI + +A I F Sbjct: 516 IRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEVVARSIIEFFAN 565 >gnl|CDD|38052 KOG2841, KOG2841, KOG2841, Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]. Length = 254 Score = 35.3 bits (81), Expect = 0.051 Identities = 16/52 (30%), Positives = 26/52 (50%) Query: 557 LDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFH 608 L I G+ +LLLQ FG+++ IS +S L G+ A +++ H Sbjct: 197 LTTIPGVNKTDAQLLLQKFGSLQQISNASEGELEQCPGLGPAKAKRLHKFLH 248 >gnl|CDD|145355 pfam02151, UVR, UvrB/uvrC motif. Length = 36 Score = 34.7 bits (81), Expect = 0.071 Identities = 11/33 (33%), Positives = 19/33 (57%) Query: 197 NLKEKIARNMNQATLKEDYESAIIHRDRLAALS 229 L +++ M +A +ED+E A RD++ AL Sbjct: 2 KLIKELEEEMEEAAEEEDFEKAAKLRDQIKALE 34 >gnl|CDD|30977 COG0632, RuvA, Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]. Length = 201 Score = 31.4 bits (71), Expect = 0.78 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 7/82 (8%) Query: 526 ILYFIQRLRDEAHR-FAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGT---VKMI 581 L+ +R++AH + T ++ + L +NGIGP +L + + I Sbjct: 46 KLFTHLVVREDAHLLYGFLT---EEERELFRLLISVNGIGPKLALAILSNLDPEELAQAI 102 Query: 582 SRSSPETLASIEGISKKIACKI 603 + + L+ I GI KK A +I Sbjct: 103 ANEDVKALSKIPGIGKKTAERI 124 >gnl|CDD|31810 COG1623, COG1623, Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]. Length = 349 Score = 30.2 bits (68), Expect = 1.9 Identities = 13/35 (37%), Positives = 21/35 (60%) Query: 569 RLLLQSFGTVKMISRSSPETLASIEGISKKIACKI 603 L+++FGT+ I +S E L ++EGI + A I Sbjct: 307 ENLVRAFGTLDGILEASAEDLDAVEGIGEARARAI 341 >gnl|CDD|144362 pfam00731, AIRC, AIR carboxylase. Members of this family catalyse the decarboxylation of 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR). This family catalyse the sixth step of de novo purine biosynthesis. Some members of this family contain two copies of this domain. Length = 150 Score = 28.6 bits (65), Expect = 4.6 Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 3/43 (6%) Query: 464 PDVVILDGGKGQLSAAQG---VLKKLNVENRITIISIAKGPKR 503 P V I+ G L + VLK+ + + ++S + P+R Sbjct: 1 PKVGIIMGSDSDLPTMEKAAKVLKEFGIPYEVRVVSAHRTPER 43 >gnl|CDD|145477 pfam02350, Epimerase_2, UDP-N-acetylglucosamine 2-epimerase. This family consists of UDP-N-acetylglucosamine 2-epimerases EC:5.1.3.14 this enzyme catalyses the production of UDP-ManNAc from UDP-GlcNAc. Note that some of the enzymes is this family are bifunctional, in this instance Pfam matches only the N-terminal half of the protein suggesting that the additional C-terminal part (when compared to mono-functional members of this family) is responsible for the UPD-N-acetylmannosamine kinase activity of these enzymes. This hypothesis is further supported by the assumption that the C-terminal part of rat bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase is the kinase domain. Length = 346 Score = 28.6 bits (65), Expect = 5.4 Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 2/41 (4%) Query: 60 FTVTCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILIT 100 F T ++ALLL I+ IL K YIL+T Sbjct: 148 FVTGNTVIDALLLSREEIEESLEISGILADLGK--RYILVT 186 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 0.322 0.135 0.399 Gapped Lambda K H 0.267 0.0749 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 7,338,438 Number of extensions: 391277 Number of successful extensions: 981 Number of sequences better than 10.0: 1 Number of HSP's gapped: 971 Number of HSP's successfully gapped: 17 Length of query: 616 Length of database: 6,263,737 Length adjustment: 100 Effective length of query: 516 Effective length of database: 4,102,837 Effective search space: 2117063892 Effective search space used: 2117063892 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 60 (26.9 bits)