RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

Searching..................................................done

Query= gi|254780901|ref|YP_003065314.1| single-stranded-DNA-specific
exonuclease protein [Candidatus Liberibacter asiaticus str. psy62]
         (600 letters)



>gnl|CDD|161976 TIGR00644, recJ, single-stranded-DNA-specific exonuclease RecJ.
           All proteins in this family are 5'-3' single-strand DNA
           exonucleases. These proteins are used in some aspects of
           mismatch repair, recombination, and recombinational
           repair.
          Length = 539

 Score =  536 bits (1382), Expect = e-153
 Identities = 211/553 (38%), Positives = 325/553 (58%), Gaps = 16/553 (2%)

Query: 39  IPDIVARVLVNRNV-SIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMI 97
           +  I+A++LV+R + + +  ++FL P +  L PDP +L D +KA  RI++AI N+EKI+I
Sbjct: 1   LNPILAQILVSRGIKTAEEFENFLEPDLIDL-PDPFLLKDMEKAVERIIEAIENNEKILI 59

Query: 98  FGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVD 157
           FGDYDVDG  S A+++ FL    VN + YIP+RI +GYG +P  + + I  G  LIITVD
Sbjct: 60  FGDYDVDGITSTAILVEFLKDLGVNVDYYIPNRITEGYGLSPEALREAIENGVSLIITVD 119

Query: 158 CGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFL 217
            G ++++ + YA   GIDVIV DHH+   +   A A+VNPNR D       L  AGV F 
Sbjct: 120 NGISAHEEIDYAKELGIDVIVTDHHEPPEDLPEAAAIVNPNRPDCDYPNKELAGAGVAFK 179

Query: 218 VLVLIYRILRQDNKVPLNFDLLSLLDLVALATVCDVVPLIGLNRAYVVKGLMVARRQGNP 277
           +   +   L +     L+      LDLVA+ T+ DV+PL G NRA V KGL   R+   P
Sbjct: 180 LCTALDEELPKLKPDLLDL-----LDLVAIGTIADVMPLTGENRALVKKGLKALRKGKRP 234

Query: 278 GLKALIERVNIS-SPITAENLGYMIGPSINAGGRIGESNLGSRLLISDDSQELEMLAMKL 336
           GLKAL++    +  P+++ ++G+ IGP INA GR+G+++L   LL++DD ++   LA +L
Sbjct: 235 GLKALLKVAGFNGKPLSSTDIGFSIGPRINAAGRLGDASLAVELLLTDDPKQARQLAEEL 294

Query: 337 DVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVEGDRWHPGIVGLLAARLKEKFGR 396
           D LN+ R+ +E  +L +AE         +   SVIVV G+ WHPG++G++A+RL E F +
Sbjct: 295 DELNEERKKIEQEVLAEAEKIAEAN--LLPNDSVIVVAGENWHPGVLGIVASRLAETFNK 352

Query: 397 PSFAISFEEDGKGIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAAGLTVERVNFGRL 456
           P   ++ +E     GS RSI G D+  ++S  + E + +K GGHAMAAGLT++R N    
Sbjct: 353 PVIVLAIDEGKGAKGSARSISGIDLYDLLS-ELREALFLKFGGHAMAAGLTLKRENLEEF 411

Query: 457 CDFFQKFAHNIVPALITTPVFKIDGVLNASAVNIALIDMLESAGPYGAGNPNPVFAFPNH 516
            +  ++    I+ A  +  +  +D  L A  +   LI+ +E   P+G GNP P+F   N 
Sbjct: 412 REKLEEKFKKILFADESEEILPVDAELKAEEITRELIEQIEKLEPFGQGNPEPLFLLKNL 471

Query: 517 KLQSIRVVNLAHLQMTFESQDSETLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLCVNYW 576
           +++ I+++   HL+++ +S     ++AIAF          L  + G+ + V G L +N W
Sbjct: 472 RVEDIKLLGENHLKLSLKSGGK-NIEAIAFNAGDLE----LELNLGRPLDVAGKLSINEW 526

Query: 577 RGSKRCQLRVLDA 589
           RG +  QL + D 
Sbjct: 527 RGRETPQLIIQDL 539


>gnl|CDD|182944 PRK11070, PRK11070, ssDNA exonuclease RecJ; Provisional.
          Length = 575

 Score =  291 bits (748), Expect = 3e-79
 Identities = 186/531 (35%), Positives = 286/531 (53%), Gaps = 36/531 (6%)

Query: 39  IPDIVARVLVNRNVSIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIF 98
           +P ++ R+  +R V    +   L  S++ L+P    L+  +KA   +  A+    +I++ 
Sbjct: 20  LPPLLRRLYASRGVR---SAQELERSVKGLLPWQQ-LSGIEKAVELLYNALREGTRIIVV 75

Query: 99  GDYDVDGAASVALMMRFL-SHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVD 157
           GD+D DGA S AL +  L S    N +  +P+R  DGYG +P ++++    GAQLI+TVD
Sbjct: 76  GDFDADGATSTALSVLALRSLGCSNVDYLVPNRFEDGYGLSPEVVDQAHARGAQLIVTVD 135

Query: 158 CGSTSYDALQYATNQGIDVIVIDHHQVKSEEIP-AYALVNPNRLDDLSGQGHLCAAGVVF 216
            G +S+  + +A   GI V+V DHH +  E +P A A++NPN  D       L   GV F
Sbjct: 136 NGISSHAGVAHAHALGIPVLVTDHH-LPGETLPAADAIINPNLRDCNFPSKSLAGVGVAF 194

Query: 217 LVLVLIYRILRQDN-------KVPLNFDLLSLLDLVALATVCDVVPLIGLNRAYVVKGLM 269
            +++ +   LR           +P   +L  LLDLVAL TV DVVPL   NR  V +GL 
Sbjct: 195 YLMLALRAFLRDQGWFDERGIAIP---NLAELLDLVALGTVADVVPLDANNRILVWQGLS 251

Query: 270 VARR-QGNPGLKALIERVN-ISSPITAENLGYMIGPSINAGGRIGESNLGSRLLISDDSQ 327
             R  +  PG+KAL+E  N  +  + A +LG+ +GP +NA GR+ + ++G  LL+ D+  
Sbjct: 252 RIRAGKCRPGIKALLEVANRDAQKLAASDLGFALGPRLNAAGRLDDMSVGVALLLCDNIG 311

Query: 328 ELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASV-----IVVEGDRWHPGI 382
           E  +LA +LD LNQ R+ +E  M  Q EA  LT C+ ++++S      + +    WH G+
Sbjct: 312 EARVLANELDALNQTRKEIEQGM--QVEA--LTLCEKLERSSDTLPYGLAMYHPEWHQGV 367

Query: 383 VGLLAARLKEKFGRPSFAISFEEDGKGI--GSGRSIEGFDIGKMVSF--AVEEGILVKGG 438
           VG+LA+R+KE+F RP   I+F   G G   GSGRSI+G  +   +     +  G+++K G
Sbjct: 368 VGILASRIKERFHRP--VIAFAPAGDGTLKGSGRSIQGLHMRDALERLDTLYPGLILKFG 425

Query: 439 GHAMAAGLTVERVNFGRLCDFFQKFAHNIVPALITTPVFKIDGVLNASAVNIALIDMLES 498
           GHAMAAGL++E   F      F +     +   +   V   DG L+ + +++ + ++L  
Sbjct: 426 GHAMAAGLSLEEDKFELFQQRFGELVTEWLDPSLLQGVVWSDGELSPAEMSLEVAELLRD 485

Query: 499 AGPYGAGNPNPVFAFPNHKLQSIRVVNLAHLQMTFESQD-SETLQAIAFRV 548
           AGP+G   P P+F      LQ  R+V   HL++  E       L  IAF V
Sbjct: 486 AGPWGQMFPEPLFDGRFRLLQQ-RLVGERHLKVMVEPVGGGPLLDGIAFNV 535


>gnl|CDD|184937 PRK14974, PRK14974, cell division protein FtsY; Provisional.
          Length = 336

 Score = 33.0 bits (76), Expect = 0.24
 Identities = 11/24 (45%), Positives = 19/24 (79%)

Query: 157 DCGSTSYDALQYATNQGIDVIVID 180
           D  + +YDA+++A  +GIDV++ID
Sbjct: 206 DPAAVAYDAIEHAKARGIDVVLID 229


>gnl|CDD|149172 pfam07948, Nairovirus_M, Nairovirus M polyprotein-like.  The
           sequences in this family are similar to the Dugbe virus
           M polyprotein precursor, which includes glycoproteins G1
           and G2. Both are thought to be inserted in the membrane
           of the Golgi complex of the infected host cell, and G1
           is known to have a role in infection of vertebrate
           hosts.
          Length = 645

 Score = 31.7 bits (72), Expect = 0.58
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 3/61 (4%)

Query: 136 GPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALV 195
           G      + +  +G    +T D G  S      A+N G+ +I +  H +K +  P   + 
Sbjct: 98  GLTAEPFKSYYAKG---FLTFDSGYFSAKCYSAASNSGLQLINVTQHSIKIQNTPGPKIS 154

Query: 196 N 196
           N
Sbjct: 155 N 155


>gnl|CDD|162105 TIGR00916, 2A0604s01, protein-export membrane protein, SecD/SecF
           family.  The SecA,SecB,SecD,SecE,SecF,SecG and SecY
           proteins form the protein translocation appartus in
           prokaryotes. This family is specific for the SecD and
           SecF proteins.
          Length = 192

 Score = 31.1 bits (71), Expect = 0.92
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 4/61 (6%)

Query: 167 QYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRIL 226
            +A N G   IV+D+ +V S   P    V P    +L   G +  A ++ LVLVL+Y +L
Sbjct: 11  DFAANIGKPAIVLDNAKVISA--PVVGTVGPTLGGELIKAGII--ALLIGLVLVLLYMLL 66

Query: 227 R 227
           R
Sbjct: 67  R 67


>gnl|CDD|131525 TIGR02472, sucr_P_syn_N, sucrose-phosphate synthase, putative,
          glycosyltransferase domain.  This family consists of
          the N-terminal regions, or in some cases the entirety,
          of bacterial proteins closely related to plant
          sucrose-phosphate synthases (SPS). The C-terminal
          domain (TIGR02471), found with most members of this
          family, resembles both bona fide plant
          sucrose-phosphate phosphatases (SPP) and the SPP-like
          domain of plant SPS. At least two members of this
          family lack the SPP-like domain, which may have binding
          or regulatory rather than enzymatic activity by analogy
          to plant SPS. This enzyme produces sucrose 6-phosphate
          and UDP from UDP-glucose and D-fructose 6-phosphate,
          and may be encoded near the gene for fructokinase.
          Length = 439

 Score = 30.9 bits (70), Expect = 1.0
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 2/42 (4%)

Query: 29 RALAITQKHAIPDIVARVLVNRNVSIDYAK--DFLNPSIRLL 68
          RALA   +    D+V R++ +  VS DYA+  + + P  R++
Sbjct: 37 RALARRSEVEQVDLVTRLIKDAKVSPDYAQPIERIAPGARIV 78


>gnl|CDD|182695 PRK10747, PRK10747, putative protoheme IX biogenesis protein;
           Provisional.
          Length = 398

 Score = 30.1 bits (68), Expect = 1.9
 Identities = 13/36 (36%), Positives = 21/36 (58%)

Query: 340 NQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVEG 375
           NQ+R+      L+ A A+ L +CDD   A  I+++G
Sbjct: 254 NQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDG 289


>gnl|CDD|180539 PRK06352, PRK06352, threonine synthase; Validated.
          Length = 351

 Score = 30.0 bits (67), Expect = 2.0
 Identities = 13/36 (36%), Positives = 19/36 (52%)

Query: 144 KFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVI 179
           K   EGA+ +I    G+TS  A  YAT  G+   ++
Sbjct: 69  KAKEEGAEAVICASTGNTSAAAAAYATRAGLKAYIV 104


>gnl|CDD|185455 PTZ00114, PTZ00114, Heat shock protein 60; Provisional.
          Length = 555

 Score = 29.5 bits (67), Expect = 2.6
 Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 4/59 (6%)

Query: 428 AVEEGILVKGGGHAMA-AGLTVERVNFGRLCDFFQKFAHNIVPALITTPVFKIDGVLNA 485
           AVEEGI V GGG A+  A   ++++         Q+    IV   +  P  +I    NA
Sbjct: 418 AVEEGI-VPGGGVALLRASKLLDKLEEDNELTPDQRTGVKIVRNALRLPTKQI--AENA 473


>gnl|CDD|129577 TIGR00486, YbgI_SA1388, dinuclear metal center protein, YbgI/SA1388
           family.  The characterization of this family of
           uncharacterized proteins as orthologous is tentative.
           Members are found in all three domains of life. Several
           members (from Bacillus subtilis, Listeria monocytogenes,
           and Mycobacterium tuberculosis - all classified as
           Firmicutes within the Eubacteria) share a long insert
           relative to other members.
          Length = 249

 Score = 29.3 bits (66), Expect = 3.3
 Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 6/65 (9%)

Query: 119 CSVNANMYIPD-RIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVI 177
              N   Y+    +V G G   S + K + EG    IT   G  S+     A   G++VI
Sbjct: 159 VVKNGPEYVKKVAVVSGSGL--SFIMKALREGVDAYIT---GDLSHHTAHLARELGLNVI 213

Query: 178 VIDHH 182
              H+
Sbjct: 214 DAGHY 218


>gnl|CDD|182441 PRK10416, PRK10416, signal recognition particle-docking protein
           FtsY; Provisional.
          Length = 318

 Score = 28.9 bits (66), Expect = 3.9
 Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 6/34 (17%)

Query: 147 NEGAQLIITVDCGSTSYDALQYATNQGIDVIVID 180
            EGA      D  S ++DA+Q A  +GIDV++ID
Sbjct: 176 KEGA------DPASVAFDAIQAAKARGIDVLIID 203


>gnl|CDD|181451 PRK08506, PRK08506, replicative DNA helicase; Provisional.
          Length = 472

 Score = 28.8 bits (65), Expect = 4.2
 Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 5/42 (11%)

Query: 312 GESNLGSR-LLISDDSQELEMLAMKLDV----LNQNRRLMES 348
           G  N   R L IS+ S+ L++LA +LD+    L+Q  R +ES
Sbjct: 316 GSGNFKDRHLQISEISRGLKLLARELDIPIIALSQLNRSLES 357


>gnl|CDD|165230 PHA02914, PHA02914, Immunoglobulin-like domain protein;
           Provisional.
          Length = 500

 Score = 28.5 bits (63), Expect = 4.7
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 6/51 (11%)

Query: 9   VECSISGFRWVSLLGQEGINRALAITQKHAIPDIVARVLVNRNVSIDYAKD 59
           +EC  S      + G E I+ A  I     I  ++  V     V  D+A+D
Sbjct: 284 IECFFS------MCGNENISNAKWIDTGFEIGPLIGTVKSKDIVEGDFAED 328


>gnl|CDD|180907 PRK07251, PRK07251, pyridine nucleotide-disulfide oxidoreductase;
           Provisional.
          Length = 438

 Score = 28.6 bits (64), Expect = 4.9
 Identities = 9/24 (37%), Positives = 16/24 (66%)

Query: 147 NEGAQLIITVDCGSTSYDALQYAT 170
           N+G Q+++  +  +  +DAL YAT
Sbjct: 226 NDGDQVLVVTEDETYRFDALLYAT 249


>gnl|CDD|161686 TIGR00064, ftsY, signal recognition particle-docking protein FtsY. 
           There is a weak division between FtsY and SRP54; both
           are GTPases. In E.coli, ftsY is an essential gene
           located in an operon with cell division genes ftsE and
           ftsX, but its apparent function is as the signal
           recognition particle docking protein.
          Length = 272

 Score = 28.4 bits (64), Expect = 5.7
 Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 6/34 (17%)

Query: 147 NEGAQLIITVDCGSTSYDALQYATNQGIDVIVID 180
            EGA      D  + ++DA+Q A  + IDV++ID
Sbjct: 134 KEGA------DPAAVAFDAIQKAKARNIDVVLID 161


>gnl|CDD|161830 TIGR00344, alaS, alanine--tRNA ligase.  The model describes
           alanine--tRNA ligase. This enzyme catalyzes the reaction
           (tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
           pyrophosphate + AMP).
          Length = 851

 Score = 28.1 bits (63), Expect = 6.8
 Identities = 24/117 (20%), Positives = 48/117 (41%), Gaps = 10/117 (8%)

Query: 337 DVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVEGDRWHPGIVGLLAARLKEKFGR 396
            +  +   L      ++ +  +  + + I    V+V   D      +  +A RLK K G 
Sbjct: 737 ALQKELESLKLKIADQKIDE-LKDKAETINGVKVLVEVVDAKDMKSLKTMADRLKSKLGS 795

Query: 397 PSFAISFEEDGKG-IGSGRS----IEGFDIGKMVSFAVEEGILVKGGGH---AMAAG 445
             + ++   +GK  +  G S     +G   G++++  + + +  KGGG    A A G
Sbjct: 796 AIYVLASFANGKVKLVCGVSNDVLNKGIKAGELIN-QIAQVLGGKGGGRPDLAQAGG 851


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.322    0.139    0.406 

Gapped
Lambda     K      H
   0.267   0.0676    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 10,038,623
Number of extensions: 685056
Number of successful extensions: 1397
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1383
Number of HSP's successfully gapped: 26
Length of query: 600
Length of database: 5,994,473
Length adjustment: 99
Effective length of query: 501
Effective length of database: 3,855,281
Effective search space: 1931495781
Effective search space used: 1931495781
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 (27.0 bits)