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)