RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780522|ref|YP_003064935.1| flagellar biosynthesis
regulatory protein FlaF [Candidatus Liberibacter asiaticus str. psy62]
         (114 letters)



>gnl|CDD|183750 PRK12793, flaF, flagellar biosynthesis regulatory protein FlaF;
           Reviewed.
          Length = 115

 Score =  136 bits (345), Expect = 1e-33
 Identities = 52/110 (47%), Positives = 78/110 (70%)

Query: 5   YHETIQESSIECRKREHWILDRSISLLSIAHKSLPNSKQAVEALFYTSRVWVVFIQDLVS 64
           Y E +++S    R+RE    DRSI LL  A      S++A+EAL++T R+W V I+DL S
Sbjct: 6   YAEVMEDSVASARERERQAFDRSIDLLEAARAKGAYSREAIEALYFTRRLWTVLIEDLGS 65

Query: 65  EDNHLPQEVKLNLISIGLWVLKECERIRRNKSNSYQDIIDVISIVRDGLK 114
            +N LP+E++ +LISIGLWVLKE +RIR+ +SN++  +I++ + +RDGLK
Sbjct: 66  PENALPEELRADLISIGLWVLKEADRIRQGESNNFAGLIEINTSIRDGLK 115


>gnl|CDD|148743 pfam07309, FlaF, Flagellar protein FlaF.  This family consists of
           several bacterial FlaF flagellar proteins. FlaF and FlaG
           are trans-acting, regulatory factors that modulate
           flagellin synthesis during flagellum biogenesis.
          Length = 113

 Score =  110 bits (277), Expect = 1e-25
 Identities = 38/112 (33%), Positives = 64/112 (57%), Gaps = 1/112 (0%)

Query: 2   RQYYHETIQESSIECRKREHWILDRSISLLSIAHKSLPNSKQAVEALFYTSRVWVVFIQD 61
           +  Y    Q ++   R+RE   L R+ + L  A K+    ++A+EAL +  ++W +F  D
Sbjct: 3   QSAYARVAQSTATP-REREAQALARATARLQQARKAGAAGREALEALHFNRKLWTIFAAD 61

Query: 62  LVSEDNHLPQEVKLNLISIGLWVLKECERIRRNKSNSYQDIIDVISIVRDGL 113
           L S DN LPQE++ NLIS+GL+VLK   ++    ++    +I++   + DGL
Sbjct: 62  LASPDNPLPQELRANLISLGLFVLKHTSKVLAGPADDLDPLIEINRAIADGL 113


>gnl|CDD|183751 PRK12794, flaF, flagellar biosynthesis regulatory protein FlaF;
           Reviewed.
          Length = 122

 Score = 49.9 bits (120), Expect = 2e-07
 Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 45  VEALFYTSRVWVVFIQDLVSEDNHLPQEVKLNLISIGLWVLKECERIRRNKSNSYQDIID 104
            EAL +  ++W +F  D+   DN LP E++  + ++ L+V K   ++ R        +ID
Sbjct: 48  AEALHFNRKLWSIFASDVADPDNPLPIELRARIFNLSLFVQKHSSKVLRKP-EKLTPLID 106

Query: 105 VISIVRDGLK 114
           +   +  GL 
Sbjct: 107 INRNIAAGLS 116


>gnl|CDD|179574 PRK03378, ppnK, inorganic polyphosphate/ATP-NAD kinase;
          Provisional.
          Length = 292

 Score = 26.8 bits (60), Expect = 1.4
 Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 2/51 (3%)

Query: 33 IAHKSLPNSKQAVEALFY--TSRVWVVFIQDLVSEDNHLPQEVKLNLISIG 81
          + H   P +    E L++  TS+ + V ++  ++ +  L       L  IG
Sbjct: 11 VGHPRHPTALTTHEMLYHWLTSKGYEVIVEQQIAHELQLKNVKTGTLAEIG 61


>gnl|CDD|105645 PRK12430, PRK12430, putative bifunctional flagellar biosynthesis
           protein FliO/FliP; Provisional.
          Length = 379

 Score = 26.4 bits (58), Expect = 1.8
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 75  LNLISIGLWVLKECERIRRNKSNSYQDIIDVISI 108
           + LI I  W+LK+    + NK  S   II+ +S+
Sbjct: 34  ILLILILSWILKKISLFKINKIISRMKIIERLSL 67


>gnl|CDD|162306 TIGR01340, aconitase_mito, aconitate hydratase, mitochondrial.
           This model represents mitochondrial forms of the TCA
           cycle enzyme aconitate hydratase, also known as
           aconitase and citrate hydro-lyase.
          Length = 745

 Score = 26.4 bits (58), Expect = 1.9
 Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 13/51 (25%)

Query: 64  SEDNHLPQEVKLNLISIGLWVLKECERIRRNKSNSYQDIIDVISIVRDGLK 114
            + N  P+++   LI         C       ++SY+D+    SIV+D  +
Sbjct: 334 VQKNGWPEKLSAGLIG-------SC------TNSSYEDMSRCASIVKDAEQ 371


>gnl|CDD|149788 pfam08841, DDR, Diol dehydratase reactivase ATPase-like domain.
          Diol dehydratase (DDH, EC:4.2.1.28) and its
          isofunctional homologue glycerol dehydratase (GDH,
          EC.4.2.1.30) are enzymes which catalyse the conversion
          of glycerol 1,2-propanediol, and 1,2-ethanediol to
          aldehydes. These reactions require coenzyme B12.
          Cleavage of the Co-C bond of coenzyme B12 by substrates
          or coenzyme analogues results in inactivation during
          which coenzyme B12 remains tightly bound to the
          apoenzyme. This family comprises of the large subunit
          of the diol dehydratase and glycerol dehydratase
          reactivating factors whose function is to reactivate
          the holoenzyme by exchange of a damaged cofactor for
          intact coenzyme.
          Length = 332

 Score = 25.8 bits (57), Expect = 2.5
 Identities = 8/18 (44%), Positives = 14/18 (77%)

Query: 57 VFIQDLVSEDNHLPQEVK 74
          +FIQDL++ D  +P +V+
Sbjct: 54 IFIQDLLAVDTFVPVKVR 71


>gnl|CDD|180841 PRK07106, PRK07106, 5-aminoimidazole-4-carboxamide ribonucleotide
           transformylase; Provisional.
          Length = 390

 Score = 25.0 bits (55), Expect = 4.1
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 14/55 (25%)

Query: 58  FIQDLVSEDNHLPQEVKLNLISIGLWVLKECERIRRNKSNSYQDIIDVISIVRDG 112
            ++++V+E+  LP E K +LI I L  LK        +SNS       +   +DG
Sbjct: 197 LLKNIVTENKELPDEAKRDLI-IALITLK------YTQSNS-------VCYAKDG 237


>gnl|CDD|183730 PRK12765, PRK12765, flagellar capping protein; Provisional.
          Length = 595

 Score = 24.5 bits (53), Expect = 5.9
 Identities = 7/19 (36%), Positives = 12/19 (63%)

Query: 94  NKSNSYQDIIDVISIVRDG 112
           +KS +Y+D+ D I+    G
Sbjct: 149 DKSTTYRDLADKINEASGG 167


>gnl|CDD|178424 PLN02830, PLN02830, UDP-sugar pyrophosphorylase.
          Length = 615

 Score = 24.3 bits (53), Expect = 6.9
 Identities = 11/27 (40%), Positives = 13/27 (48%), Gaps = 10/27 (37%)

Query: 45  VEALFYTS----------RVWVVFIQD 61
           V AL Y+S          + WVVF QD
Sbjct: 256 VHALLYSSGLLDKWLSAGKKWVVFFQD 282


>gnl|CDD|177824 PLN02167, PLN02167, UDP-glycosyltransferase family protein.
          Length = 475

 Score = 24.4 bits (53), Expect = 7.2
 Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 3/34 (8%)

Query: 12 SSIECRKREHWI-LDRSISLLSIAHKSLPNSKQA 44
           +IE  KR   I LDR I  ++I + SLP + QA
Sbjct: 19 VTIEFAKR--LINLDRRIHTITILYWSLPFAPQA 50


>gnl|CDD|131719 TIGR02671, cas_csx9, CRISPR-associated protein (provisional), Csx9
           family.  Members of this family, so far, are archaeal
           proteins found in CRISPR-associated (cas) gene regions.
           So far, this rare cas protein is found in only three
           genomes: Pyrococcus horikoshii shinkaj OT3, Pyrococcus
           abyssi GE5, and Thermococcus kodakarensis KOD1. In each
           case it is found immediately upstream of cas3 in loci
           that resemble the Apern type but lack Csa1 and Csa4
           genes.
          Length = 377

 Score = 24.1 bits (52), Expect = 7.7
 Identities = 12/49 (24%), Positives = 21/49 (42%)

Query: 55  WVVFIQDLVSEDNHLPQEVKLNLISIGLWVLKECERIRRNKSNSYQDII 103
           WVV    L  +   L   ++  L S+    +    +I RN  NS+  ++
Sbjct: 3   WVVMDAGLEPDPEELADALEGALDSLKSRAMINTSKIGRNDRNSFDRVL 51


>gnl|CDD|118190 pfam09658, Cas_Csx9, CRISPR-associated protein (Cas_Csx9).
           Clusters of short DNA repeats with nonhomologous
           spacers, which are found at regular intervals in the
           genomes of phylogenetically distinct prokaryotic
           species, comprise a family with recognisable features.
           This family is known as CRISPR (short for Clustered,
           Regularly Interspaced Short Palindromic Repeats). A
           number of protein families appear only in association
           with these repeats and are designated Cas
           (CRISPR-Associated) proteins. This entry describes
           archaeal proteins encoded in cas gene regions.
          Length = 377

 Score = 24.1 bits (52), Expect = 7.7
 Identities = 12/49 (24%), Positives = 21/49 (42%)

Query: 55  WVVFIQDLVSEDNHLPQEVKLNLISIGLWVLKECERIRRNKSNSYQDII 103
           WVV    L  +   L   ++  L S+    +    +I RN  NS+  ++
Sbjct: 3   WVVMDAGLEPDPEELADALEGALDSLKSRAMINTSKIGRNDRNSFDRVL 51


>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
          Length = 567

 Score = 24.1 bits (52), Expect = 9.5
 Identities = 9/18 (50%), Positives = 14/18 (77%)

Query: 13  SIECRKREHWILDRSISL 30
           ++ECR  +H+I  RSI+L
Sbjct: 407 TVECRNCKHYIPSRSIAL 424


  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
   0.321    0.135    0.396 

Gapped
Lambda     K      H
   0.267   0.0589    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,789,679
Number of extensions: 95717
Number of successful extensions: 164
Number of sequences better than 10.0: 1
Number of HSP's gapped: 164
Number of HSP's successfully gapped: 23
Length of query: 114
Length of database: 5,994,473
Length adjustment: 79
Effective length of query: 35
Effective length of database: 4,287,441
Effective search space: 150060435
Effective search space used: 150060435
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: 50 (23.3 bits)