RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781031|ref|YP_003065444.1| exsB protein [Candidatus
Liberibacter asiaticus str. psy62]
         (240 letters)



>gnl|CDD|129461 TIGR00364, TIGR00364, exsB protein.  This protein family is
           represented by a single member in nearly every completed
           large (> 1000 genes) prokaryotic genome. In Rhizobium
           meliloti, a species in which the exo genes make
           succinoglycan, a symbiotically important
           exopolysaccharide, exsB is located nearby and affects
           succinoglycan levels, probably through polar effects on
           exsA expression or the same polycistronic mRNA. In
           Arthrobacter viscosus, the homologous gene is designated
           ALU1 and is associated with an aluminum tolerance
           phenotype. The function is unknown.
          Length = 201

 Score =  236 bits (603), Expect = 5e-63
 Identities = 96/222 (43%), Positives = 133/222 (59%), Gaps = 26/222 (11%)

Query: 11  ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70
           A+++ SGGQDS+TCL+ A D    V  ++FDYGQR+  ELE      +KI E        
Sbjct: 1   AVVVLSGGQDSTTCLAIAKDEGYEVHAITFDYGQRHSRELESA----RKIAEA------- 49

Query: 71  LG-EDHILPLAILGDISHSSLTKNVAMKIQ----DNNLPNTFVPGRNIIFLVFAATLAYR 125
           LG E H++ L++L  +  S+LT    +  Q    ++ LPNTFVPGRN IFL  AA+ A  
Sbjct: 50  LGIEHHVIDLSLLKQLGGSALTDESEIPPQKSNEEDTLPNTFVPGRNAIFLSIAASYAEA 109

Query: 126 LGITNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQ 185
           LG   ++ GVCETD+SGYPDCR + ++A   A+NLGM + V +  PLM L K E  +LA 
Sbjct: 110 LGAEAVITGVCETDFSGYPDCRDEFVKAFNHALNLGMLTPVKIRAPLMDLTKAEIVQLAD 169

Query: 186 DIGGQDLVNLILEESHTCYLGKRDKRYEWGYGCNSCPACYLR 227
           ++G  DLV   ++ +++CY G        G GC  CP+C LR
Sbjct: 170 ELGVLDLV---IKLTYSCYAGG-------GEGCGKCPSCMLR 201


>gnl|CDD|182967 PRK11106, PRK11106, queuosine biosynthesis protein QueC;
           Provisional.
          Length = 231

 Score =  217 bits (555), Expect = 2e-57
 Identities = 97/226 (42%), Positives = 139/226 (61%), Gaps = 26/226 (11%)

Query: 11  ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70
           A+++FSGGQDS+TCL  AL ++D V  ++FDYGQR++ E++    V +++          
Sbjct: 4   AVVVFSGGQDSTTCLIQALQQYDEVHCVTFDYGQRHRAEID----VARELAL-------K 52

Query: 71  LG-EDH-ILPLAILGDISHSSLTKN----VAMKIQDNNLPNTFVPGRNIIFLVFAATLAY 124
           LG   H +L + +L +++ SSLT++       + + + LPNTFVPGRNI+FL  AA  AY
Sbjct: 53  LGARAHKVLDVTLLNELAVSSLTRDSIPVPDYEPEADGLPNTFVPGRNILFLTLAAIYAY 112

Query: 125 RLGITNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLA 184
           ++    ++ GVCETD+SGYPDCR + ++A+  A++LGM   +   TPLMWL K ETW LA
Sbjct: 113 QVKAEAVITGVCETDFSGYPDCRDEFVKALNHAVSLGMAKDIRFETPLMWLNKAETWALA 172

Query: 185 QDIGGQDLVNLILEESHTCYLGKRDKRYEWGYGCNSCPACYLRQKG 230
              G  DLV     E+ TCY G +      G GC  C AC+LR  G
Sbjct: 173 DYYGQLDLVR---HETLTCYNGIK------GDGCGHCAACHLRANG 209


>gnl|CDD|148238 pfam06508, ExsB, ExsB.  This family includes putative
           transcriptional regulators from Bacteria and Archaea.
          Length = 137

 Score =  184 bits (470), Expect = 1e-47
 Identities = 67/148 (45%), Positives = 92/148 (62%), Gaps = 18/148 (12%)

Query: 11  ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70
           A++L SGG DS+TCL+WA      V  L+FDYGQR+  ELEC     KKI +        
Sbjct: 2   AVVLLSGGLDSTTCLAWAKKEGYEVYALTFDYGQRHSKELECA----KKIAKA------- 50

Query: 71  LGEDH-ILPLAILGDISHSSLTKNVAMKIQDNNL-----PNTFVPGRNIIFLVFAATLAY 124
           LG +H I+ L  L  I  S+LT + ++++ D+ L     PNT+VPGRN+IFL  AA+ A 
Sbjct: 51  LGVEHKIVDLDFLKQIGGSALTDD-SIEVPDSELESEEIPNTYVPGRNLIFLSIAASYAE 109

Query: 125 RLGITNIVIGVCETDYSGYPDCRHDTIR 152
            +G  +I IGV E D+SGYPDCR + ++
Sbjct: 110 AIGANDIFIGVNEEDFSGYPDCRPEFVK 137


>gnl|CDD|184745 PRK14561, PRK14561, hypothetical protein; Provisional.
          Length = 194

 Score = 35.2 bits (82), Expect = 0.014
 Identities = 15/39 (38%), Positives = 25/39 (64%), Gaps = 3/39 (7%)

Query: 13 LLFSGGQDSSTCLS-WALDRFDRVETLSFDYGQRNKVEL 50
          +LFSGG+DSS  L+   L+RF  VE ++ ++G  +  + 
Sbjct: 5  VLFSGGKDSS--LAAILLERFYDVELVTVNFGVLDSWKH 41


>gnl|CDD|173244 PRK14783, PRK14783, lipoprotein signal peptidase; Provisional.
          Length = 182

 Score = 32.1 bits (73), Expect = 0.12
 Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 3/43 (6%)

Query: 79  LAILGDISHSSLTKNVAM---KIQDNNLPNTFVPGRNIIFLVF 118
           L +LG     +LT N        QDN +P+    G  I+FL+ 
Sbjct: 44  LEVLGSFFRMTLTFNTGFVFGAFQDNAIPSLIATGFAIVFLIG 86


>gnl|CDD|129143 TIGR00032, argG, argininosuccinate synthase.  argG in bacteria,
          ARG1 in Saccharomyces cerevisiae. There is a very
          unusual clustering in the alignment, with a deep split
          between one cohort of E. coli, H. influenzae, and
          Streptomyces, and the other cohort of eukaryotes,
          archaea, and the rest of the eubacteria.
          Length = 394

 Score = 31.2 bits (71), Expect = 0.24
 Identities = 13/32 (40%), Positives = 18/32 (56%)

Query: 13 LLFSGGQDSSTCLSWALDRFDRVETLSFDYGQ 44
          L +SGG D+S CL W  ++   V   + D GQ
Sbjct: 4  LAYSGGLDTSVCLKWLREKGYEVIAYTADVGQ 35


>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
          Length = 475

 Score = 30.9 bits (70), Expect = 0.27
 Identities = 12/16 (75%), Positives = 13/16 (81%)

Query: 117 VFAATLAYRLGITNIV 132
           V A+ LAYRLGIT IV
Sbjct: 270 VLASALAYRLGITRIV 285


>gnl|CDD|184346 PRK13820, PRK13820, argininosuccinate synthase; Provisional.
          Length = 394

 Score = 30.3 bits (69), Expect = 0.48
 Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 2/36 (5%)

Query: 11 ALLLFSGGQDSSTCLSWALDR--FDRVETLSFDYGQ 44
           +L +SGG D+S C+    ++  +D V T++ D GQ
Sbjct: 5  VVLAYSGGLDTSVCVPLLKEKYGYDEVITVTVDVGQ 40


>gnl|CDD|178475 PLN02887, PLN02887, hydrolase family protein.
          Length = 580

 Score = 29.8 bits (67), Expect = 0.56
 Identities = 27/92 (29%), Positives = 37/92 (40%), Gaps = 27/92 (29%)

Query: 9   PSAL-LLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKW 67
           P A+ L F G +DS          +   +T   D G  + VEL   LC    I +L  +W
Sbjct: 129 PMAMKLAFDGLKDSK---------YKTRDTDISDVGGYDSVELSVMLCNDDFIRKLNKEW 179

Query: 68  KDSLGEDHI--------------LPLAILGDI 85
           +    EDH               LP+ +LGDI
Sbjct: 180 RG---EDHATDVLSMSQHVPGLKLPVLMLGDI 208


>gnl|CDD|179917 PRK05031, PRK05031, tRNA (uracil-5-)-methyltransferase; Validated.
          Length = 362

 Score = 29.0 bits (66), Expect = 1.1
 Identities = 8/38 (21%), Positives = 17/38 (44%)

Query: 40  FDYGQRNKVELECRLCVRKKIVELMPKWKDSLGEDHIL 77
           FD   + ++ ++      + I  LMP    +L  + +L
Sbjct: 64  FDQQTKQRIRIDQFPIASELINALMPALLAALRANPVL 101


>gnl|CDD|162012 TIGR00728, OPT_sfam, oligopeptide transporters, OPT superfamily.
           Homology between the two branches of the superfamily is
           seen most easily at the ends of the protein. The central
           regions are poorly conserved within each branch and may
           not be homologous between branches.
          Length = 654

 Score = 28.6 bits (64), Expect = 1.6
 Identities = 10/23 (43%), Positives = 12/23 (52%)

Query: 113 IIFLVFAATLAYRLGITNIVIGV 135
           II  V A  +    GITN V G+
Sbjct: 415 IIAFVLAIPIGILAGITNPVSGL 437


>gnl|CDD|163392 TIGR03679, arCOG00187, arCOG00187 universal archaeal
          metal-binding-domain/4Fe-4S-binding-domain containing
          ABC transporter, ATP-binding protein.  This model has
          the same scope as an archaeal COG (arCOG00187) and is
          found in all completely sequenced archaea and does not
          recognize any known non-archaeal genes.
          Length = 218

 Score = 28.4 bits (64), Expect = 1.9
 Identities = 11/25 (44%), Positives = 15/25 (60%)

Query: 14 LFSGGQDSSTCLSWALDRFDRVETL 38
          L+SGG+DS+  L  AL+    V  L
Sbjct: 3  LYSGGKDSNYALYKALEEGHEVRCL 27


>gnl|CDD|129390 TIGR00289, TIGR00289, conserved hypothetical protein TIGR00289.
          Homologous proteins related to MJ0570 of Methanococcus
          jannaschii include both the apparent orthologs found by
          this model above the trusted cutoff, the much longer
          protein YLR143W from Saccharomyces cerevisiae, and
          second homologous proteins from Archaeoglobus fulgidus
          and Pyrococcus horikoshii that appear to represent a
          second orthologous group.
          Length = 222

 Score = 28.3 bits (63), Expect = 2.0
 Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)

Query: 14 LFSGGQDSSTCLSWALDRFDRVETL 38
          L+SGG+DS   L  AL+  + V +L
Sbjct: 6  LYSGGKDSILALYKALEEHE-VISL 29


>gnl|CDD|181483 PRK08576, PRK08576, hypothetical protein; Provisional.
          Length = 438

 Score = 27.7 bits (62), Expect = 2.5
 Identities = 11/29 (37%), Positives = 15/29 (51%)

Query: 15  FSGGQDSSTCLSWALDRFDRVETLSFDYG 43
           +SGG+DS+  L  A   F  V  +  D G
Sbjct: 241 WSGGKDSTAALLLAKKAFGDVTAVYVDTG 269


>gnl|CDD|178336 PLN02735, PLN02735, carbamoyl-phosphate synthase.
          Length = 1102

 Score = 27.8 bits (62), Expect = 2.7
 Identities = 13/23 (56%), Positives = 14/23 (60%), Gaps = 1/23 (4%)

Query: 126 LGITNIVIG-VCETDYSGYPDCR 147
           LG   IVIG  CE DYSG   C+
Sbjct: 29  LGAGPIVIGQACEFDYSGTQACK 51


>gnl|CDD|172452 PRK13943, PRK13943, protein-L-isoaspartate O-methyltransferase;
           Provisional.
          Length = 322

 Score = 27.1 bits (60), Expect = 3.6
 Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 1/31 (3%)

Query: 115 FLVFAATLAYRLGITNIVIGVCETDYSGYPD 145
               A     RLGI N++  VC   Y G P+
Sbjct: 117 ICEIAKRNVRRLGIENVIF-VCGDGYYGVPE 146


>gnl|CDD|177791 PLN00200, PLN00200, argininosuccinate synthase; Provisional.
          Length = 404

 Score = 27.0 bits (60), Expect = 3.9
 Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 7  KAPSALLLFSGGQDSSTCLSWALDRFD-RVETLSFDYGQRNKVELE 51
          K    +L +SGG D+S  L W  + +   V   + D GQ  + ELE
Sbjct: 4  KLNKVVLAYSGGLDTSVILKWLRENYGCEVVCFTADVGQGIE-ELE 48


>gnl|CDD|185096 PRK15174, PRK15174, Vi polysaccharide export protein VexE;
           Provisional.
          Length = 656

 Score = 27.0 bits (59), Expect = 4.0
 Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 14/62 (22%)

Query: 70  SLGEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGIT 129
           +L     L +AI G ++ S+              P     G+ I +  F + LA+++ + 
Sbjct: 541 TLHSGQSLVVAIDGALNLSA--------------PTIDFFGQQITYSTFCSRLAWKMHLP 586

Query: 130 NI 131
            +
Sbjct: 587 TV 588


>gnl|CDD|182369 PRK10307, PRK10307, putative glycosyl transferase; Provisional.
          Length = 412

 Score = 26.9 bits (60), Expect = 4.7
 Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 11/47 (23%)

Query: 26  SWALDRFDRVETLS---FDYGQRNKVELECRLCVRKKIVELMPKWKD 69
              L RFD V T+S    +  +   V         +K++   P W +
Sbjct: 166 RSLLRRFDNVSTISRSMMNKAREKGV-------AAEKVIFF-PNWSE 204


>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 = 26.9 bits (60), Expect = 5.5
 Identities = 18/99 (18%), Positives = 38/99 (38%), Gaps = 23/99 (23%)

Query: 1   MNDIIKKAPSALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKI 60
           + D++ +   AL L  GG   +  L+                 +R  +E       R+K+
Sbjct: 377 LYDLLSELREALFLKFGGHAMAAGLTL----------------KRENLEE-----FREKL 415

Query: 61  VELMPKWKDSLGEDHILPLAILGDISHSSLTKNVAMKIQ 99
            E   K   +   + ILP  +  ++    +T+ +  +I+
Sbjct: 416 EEKFKKILFADESEEILP--VDAELKAEEITRELIEQIE 452


>gnl|CDD|119242 pfam10722, YbjN, Putative bacterial sensory transduction regulator.
            YbjN is a putative sensory transduction regulator
           protein found in Proteobacteria. As it is a multi-copy
           suppressor of the coenzyme A-associated temperature
           sensitivity in temperature-sensitive mutant strains of
           Escherichia coli the suggestion is that it both helps
           CoA-A1 and possibly works as a general stabilizer for
           some other unstable proteins.
          Length = 157

 Score = 26.5 bits (59), Expect = 5.7
 Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 1/30 (3%)

Query: 76  ILPL-AILGDISHSSLTKNVAMKIQDNNLP 104
           +LPL A L  I+ S LT    + IQD+NLP
Sbjct: 68  LLPLVADLSRINASYLTVKAFLDIQDDNLP 97


>gnl|CDD|178474 PLN02886, PLN02886, aminoacyl-tRNA ligase.
          Length = 389

 Score = 26.7 bits (59), Expect = 5.9
 Identities = 8/13 (61%), Positives = 9/13 (69%)

Query: 163 ESHVTVHTPLMWL 175
           +SHV  H  LMWL
Sbjct: 125 QSHVPAHAELMWL 137


>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
           subunit 1/adenylylsulfate kinase protein; Provisional.
          Length = 632

 Score = 26.4 bits (59), Expect = 6.8
 Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 2/49 (4%)

Query: 122 LAYRLGITNIVIGVCETDYSGYPDCRHDTIRA--IETAINLGMESHVTV 168
           +A  LGI ++V+ V + D   Y     D I A     A  LG+     +
Sbjct: 151 IASLLGIRHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGLHDVTFI 199


>gnl|CDD|184427 PRK13969, PRK13969, proline racemase; Provisional.
          Length = 334

 Score = 26.4 bits (58), Expect = 7.1
 Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 7/45 (15%)

Query: 134 GVCETDYSGYPD-CRHDTIRAIETAINLGME------SHVTVHTP 171
           G+   D  GY + C H +I A   A+  G+       +H+ +  P
Sbjct: 78  GIIFMDGGGYLNMCGHGSIGAATCAVETGIVKVEEPYTHIKLEAP 122


>gnl|CDD|179998 PRK05294, carB, carbamoyl phosphate synthase large subunit;
           Reviewed.
          Length = 1066

 Score = 26.2 bits (59), Expect = 7.2
 Identities = 10/13 (76%), Positives = 10/13 (76%), Gaps = 1/13 (7%)

Query: 131 IVIG-VCETDYSG 142
           IVIG  CE DYSG
Sbjct: 18  IVIGQACEFDYSG 30


>gnl|CDD|161881 TIGR00442, hisS, histidyl-tRNA synthetase.  This model finds a
           histidyl-tRNA synthetase in every completed genome.
           Apparent second copies from Bacillus subtilis,
           Synechocystis sp., and Aquifex aeolicus are slightly
           shorter, more closely related to each other than to
           other hisS proteins, and actually serve as regulatory
           subunits for an enzyme of histidine biosynthesis. They
           were excluded from the seed alignment and score much
           lower than do single copy histidyl-tRNA synthetases of
           other genomes not included in the seed alignment. These
           putative second copies of HisS score below the trusted
           cutoff. The regulatory protein kinase GCN2 of
           Saccharomyces cerevisiae (YDR283c), and related proteins
           from other species designated eIF-2 alpha kinase, have a
           domain closely related to histidyl-tRNA synthetase that
           may serve to detect and respond to uncharged tRNA(his),
           an indicator of amino acid starvation; these regulatory
           proteins are not orthologous and so score below the
           noise cutoff.
          Length = 397

 Score = 25.9 bits (58), Expect = 8.6
 Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 5/40 (12%)

Query: 50  LECRLCVRKKIVELMPKWKDSLGED-----HILPLAILGD 84
           LE RL  R+ ++  + K  D LGED        PL IL  
Sbjct: 165 LEGRLEYREALLRYLDKHLDKLGEDSVRRLEKNPLRILDS 204


>gnl|CDD|150923 pfam10327, 7TM_GPCR_Sri, Serpentine type 7TM GPCR chemoreceptor
           Sri.  Chemoreception is mediated in Caenorhabditis
           elegans by members of the seven-transmembrane
           G-protein-coupled receptor class (7TM GPCRs) of proteins
           which are of the serpentine type. Sri is part of the Str
           superfamily of chemoreceptors. Chemoperception is one of
           the central senses of soil nematodes like C. elegans
           which are otherwise 'blind' and 'deaf'.
          Length = 303

 Score = 26.0 bits (58), Expect = 9.3
 Identities = 7/31 (22%), Positives = 11/31 (35%)

Query: 75  HILPLAILGDISHSSLTKNVAMKIQDNNLPN 105
           HI P         S L++   ++    N P 
Sbjct: 141 HIFPFLTAFLFYQSGLSREEQLEYVKENYPE 171


>gnl|CDD|179051 PRK00509, PRK00509, argininosuccinate synthase; Provisional.
          Length = 399

 Score = 25.8 bits (58), Expect = 9.4
 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%)

Query: 13 LLFSGGQDSSTCLSWALDRFDR-VETLSFDYGQRNKVELE 51
          L +SGG D+S  + W  + +   V   + D GQ    ELE
Sbjct: 7  LAYSGGLDTSVIIKWLKETYGCEVIAFTADVGQGE--ELE 44


  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    0.138    0.438 

Gapped
Lambda     K      H
   0.267   0.0755    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,925,980
Number of extensions: 236463
Number of successful extensions: 506
Number of sequences better than 10.0: 1
Number of HSP's gapped: 498
Number of HSP's successfully gapped: 32
Length of query: 240
Length of database: 5,994,473
Length adjustment: 91
Effective length of query: 149
Effective length of database: 4,028,145
Effective search space: 600193605
Effective search space used: 600193605
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: 56 (25.3 bits)