RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780612|ref|YP_003065025.1| putative transmembrane protein
[Candidatus Liberibacter asiaticus str. psy62]
         (503 letters)



>gnl|CDD|180131 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 559

 Score = 31.4 bits (72), Expect = 0.52
 Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 6/75 (8%)

Query: 47  KEILERQFNKLEQAILQVEKQNQKSLHTSKQDKESDIPKSSVTSKENIFLEPRLRSISSI 106
            E+L ++  +LEQ + Q++ Q        K+ K+          K           I  +
Sbjct: 371 LEVLLQRVEQLEQELKQLKAQPVGVAPEQKEKKKEKKKNKKKKYKVP------RGKIYKV 424

Query: 107 LRSNKHKKLANILSV 121
           L+    + L  + +V
Sbjct: 425 LKEATRQDLELLKNV 439


>gnl|CDD|130217 TIGR01147, V_ATP_synt_G, vacuolar ATP synthase, subunit G.  This
          model describes the vacuolar ATP synthase G subunit in
          eukaryotes and includes members from diverse groups
          e.g., fungi, plants, parasites etc. V-ATPases are
          multi-subunit enzymes composed of two functional
          domains: A transmembrane Vo domain and a peripheral
          catalytic domain V1. The G subunit is one of the
          subunits of the catalytic domain. V-ATPases are
          responsible for the acidification of endosomes and
          lysosomes, which are part of the central vacuolar
          system.
          Length = 113

 Score = 29.8 bits (67), Expect = 1.8
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 21 ERRSH-IYEHARNSVARRLESMKPRLPKEI------LERQFNKLEQAILQVEKQNQKSLH 73
          E+R+      AR    +RL+  K    KE+       E++F + E   L      ++   
Sbjct: 15 EKRAAEKVSEARKRKTKRLKQAKEEAQKEVEKYKQQREKEFKEFEAKHLGGNGAAEEKAE 74

Query: 74 TSKQDKESDIPKSSVTSKENI 94
             Q K  +I K+   +K+ +
Sbjct: 75 AETQAKIREIKKAVQKNKDAV 95


>gnl|CDD|181447 PRK08487, PRK08487, DNA polymerase III subunit delta; Validated.
          Length = 328

 Score = 29.5 bits (67), Expect = 1.8
 Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 5/65 (7%)

Query: 45  LPKEILERQFNKLEQAILQVEKQNQKSLHTSKQDKESDIPKSSVTSKENIFLEPRLRSIS 104
            PK+I E   N  +QAI   E Q ++ +     + E ++        +N+FL   L  I 
Sbjct: 269 PPKQIAE---NLAKQAIKIKEAQYKE-IFELLLEWELELKTGQKI-DKNLFLLSTLIKIQ 323

Query: 105 SILRS 109
            IL  
Sbjct: 324 KILNP 328


>gnl|CDD|182989 PRK11138, PRK11138, outer membrane biogenesis protein BamB;
           Provisional.
          Length = 394

 Score = 29.1 bits (66), Expect = 2.9
 Identities = 7/34 (20%), Positives = 16/34 (47%), Gaps = 3/34 (8%)

Query: 324 PLIGEGRVFINKGRGQSSIL---SGKILWSLQQE 354
           P++ +G V ++   G    L    G + W++  +
Sbjct: 156 PVVSDGLVLVHTSNGMLQALNESDGAVKWTVNLD 189


>gnl|CDD|183879 PRK13182, racA, polar chromosome segregation protein; Reviewed.
          Length = 175

 Score = 28.9 bits (65), Expect = 3.0
 Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 19/97 (19%)

Query: 7   VIQRAVDNLPENTPERRSHIYEHARNSVARRLESMKPRLPK------------------E 48
           V +  V+ + +N         E   N++ RRL+ ++ +L +                  E
Sbjct: 70  VEETQVNTIVQNISSVDFEQLEAQLNTITRRLDELERQLQQKADDVVSYQLLQHRREMEE 129

Query: 49  ILERQFNKLEQAILQVEKQNQKSLHTSKQDKESDIPK 85
           +LER   KLE  + ++E            ++E    +
Sbjct: 130 MLER-LQKLEARLKKLEPIYITPDTEPTYEREKKPKR 165


>gnl|CDD|128712 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota).  DNA
           Topoisomerase I (eukaryota), DNA topoisomerase V,
           Vaccina virus topoisomerase, Variola virus
           topoisomerase, Shope fibroma virus topoisomeras.
          Length = 391

 Score = 28.9 bits (65), Expect = 3.6
 Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 3/61 (4%)

Query: 42  KPRLPKEILERQFNKLEQAILQVEKQNQK--SLHTSKQDKESDIPKSSVTSKENIFLEPR 99
           K     +  +++  K E+   Q+E+  ++   L     DKE +   +  TSK N +++PR
Sbjct: 323 KLDAEVKEKKKEKKKEEKKKKQIERLEERIEKLEVQATDKEENKTVALGTSKIN-YIDPR 381

Query: 100 L 100
           +
Sbjct: 382 I 382


>gnl|CDD|129587 TIGR00496, frr, ribosome recycling factor.  This model finds only
           eubacterial proteins. Mitochondrial and/or chloroplast
           forms might be expected but are not currently known.
           This protein was previously called ribosome releasing
           factor. By releasing ribosomes from mRNA at the end of
           protein biosynthesis, it prevents inappropriate
           translation from 3-prime regions of the mRNA and frees
           the ribosome for new rounds of translation.
           EGAD|53116|YHR038W is part of the frr superfamily.
          Length = 176

 Score = 28.6 bits (64), Expect = 4.5
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 12/82 (14%)

Query: 14  NLPENTPERRSHIYEHARN----------SVARRLESMKPRLPK--EILERQFNKLEQAI 61
           N P  T ERR  + +HA+           +V R       +L K  EI E +  +L++ I
Sbjct: 92  NFPPLTEERRKELVKHAKKIAEQAKVAVRNVRRDANDKVKKLEKDKEISEDEERRLQEEI 151

Query: 62  LQVEKQNQKSLHTSKQDKESDI 83
            ++  +  K +    +DKE ++
Sbjct: 152 QKLTDEYIKKIDEILKDKEKEL 173


>gnl|CDD|166000 PLN02359, PLN02359, ethanolaminephosphotransferase.
          Length = 389

 Score = 28.2 bits (63), Expect = 5.6
 Identities = 14/60 (23%), Positives = 30/60 (50%), Gaps = 3/60 (5%)

Query: 176 LAGIFSFPTGSIFWSVHNYFFNKTRGLLSFYSALSEHHLFKYFVFLIILLGMAIGVSYSI 235
            A  F+   G+ +W+     F K+   LS+   +SE   ++  +FL+I   +   V++++
Sbjct: 182 CAHFFTAIVGAEWWAQD---FGKSIPFLSWVPFVSEIQTYRIVLFLMIAFAVIPTVAFNV 238


>gnl|CDD|178370 PLN02771, PLN02771, carbamoyl-phosphate synthase
           (glutamine-hydrolyzing).
          Length = 415

 Score = 28.0 bits (62), Expect = 6.2
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 264 GIRPKITRRLLEDGSEVDVGPSTIPVAD 291
           GI+  I RRL   G ++ V PST P ++
Sbjct: 249 GIKHNILRRLASYGCKITVVPSTWPASE 276


>gnl|CDD|183250 PRK11638, PRK11638, lipopolysaccharide biosynthesis protein WzzE;
           Provisional.
          Length = 342

 Score = 28.1 bits (63), Expect = 6.4
 Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 10/70 (14%)

Query: 24  SHIYEHARNSVARRLESMKPRLPKE------ILERQFNKLEQAILQVEKQNQKSLHTSKQ 77
           SH+ +  + + A R   MK ++ ++      I +R+ N +EQA+   E+Q    +  S+ 
Sbjct: 182 SHLNDELKGAWAARTIQMKAQVKRQEAVAKAIYDREVNSVEQALKIAEQQG---ISRSQT 238

Query: 78  DKESD-IPKS 86
           D  ++ +P S
Sbjct: 239 DVPAEELPDS 248


>gnl|CDD|149683 pfam08703, PLC-beta_C, PLC-beta C terminal.  This domain
           corresponds to the alpha helical C terminal domain of
           phospholipase C beta.
          Length = 185

 Score = 27.9 bits (62), Expect = 6.7
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 23  RSHIYEHARNSVARRLESMKPRLPKEILERQFNKLEQAILQVEKQNQKSLHTSKQDKESD 82
           RSHI E    S+ R  E+ K R  +E L  +  ++ Q I + E + Q  L    + K   
Sbjct: 104 RSHIQE-VVQSIKRLEEAQKRR--QEKLVEKQQEILQQIQEEEPKLQAQLTAEYEAKLKR 160

Query: 83  IPKS 86
           +P+ 
Sbjct: 161 LPQE 164


>gnl|CDD|151311 pfam10862, DUF2662, Protein of unknown function (DUF2662).  This
           bacterial family of proteins has no known function.
          Length = 157

 Score = 27.5 bits (61), Expect = 8.9
 Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 2/45 (4%)

Query: 96  LEPRLRSISSILRSNKHKKLANILSVQGKSRTNTNLSPKNFSCRL 140
           L P LR  S  +      +L++IL V+  SR    ++P  FS RL
Sbjct: 76  LIPGLRGWS--IDDYFRHQLSDILIVKFSSRFRKPINPAKFSGRL 118


>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC.  This family is based on the
           phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
           Stanford University).
          Length = 1042

 Score = 27.2 bits (60), Expect = 9.3
 Identities = 13/79 (16%), Positives = 25/79 (31%), Gaps = 9/79 (11%)

Query: 23  RSHIYEHARNSVARRLESMKPRLPKEILERQFNKLEQ---------AILQVEKQNQKSLH 73
           R+ +       V ++    + R   + L  Q   +            I   +    + +H
Sbjct: 323 RAKLLMKRAAHVKQQSSIEEQRRLLQTLHSQEIHIRDAHEVATSIREISCQQHTLTQHIH 382

Query: 74  TSKQDKESDIPKSSVTSKE 92
           T +Q K +   K     KE
Sbjct: 383 TLQQQKTTLTQKLQSLCKE 401


>gnl|CDD|163143 TIGR03121, one_C_dehyd_A, formylmethanofuran dehydrogenase subunit
           A.  Members of this largely archaeal protein family are
           subunit A of the formylmethanofuran dehydrogenase.
           Nomenclature in some bacteria may reflect inclusion of
           the formyltransferase described by TIGR03119 as part of
           the complex, and therefore call this protein
           formyltransferase/hydrolase complex Fhc subunit A. Note
           that this model does not distinguish tungsten (FwdA)
           from molybdenum-containing (FmdA) forms of this enzyme;
           a single gene from this family is expressed
           constitutively in Methanobacterium thermoautotrophicum,
           which has both tungsten and molybdenum forms and may
           work interchangeably.
          Length = 556

 Score = 27.3 bits (61), Expect = 9.5
 Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 3/36 (8%)

Query: 456 KILEEYRFIDIPITYRSGQ-KILFTIDKG--KKGAD 488
            I  EY   +I I  R+G  K+L   D+G    GAD
Sbjct: 425 GIDREYSLYEIAIMTRAGPAKLLGLTDRGHLGVGAD 460


  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
   0.317    0.134    0.374 

Gapped
Lambda     K      H
   0.267   0.0753    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 7,992,026
Number of extensions: 516123
Number of successful extensions: 1137
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1135
Number of HSP's successfully gapped: 31
Length of query: 503
Length of database: 5,994,473
Length adjustment: 97
Effective length of query: 406
Effective length of database: 3,898,497
Effective search space: 1582789782
Effective search space used: 1582789782
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: 59 (26.5 bits)