RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780644|ref|YP_003065057.1| hypothetical protein
CLIBASIA_02655 [Candidatus Liberibacter asiaticus str. psy62]
         (289 letters)



>gnl|CDD|185150 PRK15235, PRK15235, outer membrane fimbrial usher protein SefC;
           Provisional.
          Length = 814

 Score = 30.1 bits (67), Expect = 0.67
 Identities = 12/37 (32%), Positives = 19/37 (51%)

Query: 90  QAVEYEKPYSTVIANLTDSHQKYATNIATYMPIGEEF 126
           Q   Y  PYST + +L D + KY+  I  Y  +  ++
Sbjct: 317 QVQNYTVPYSTPVLSLPDGYSKYSVTIGRYREVNNDY 353


>gnl|CDD|132534 TIGR03495, phage_LysB, phage lysis regulatory protein, LysB family.
            Members of this protein family are phage lysis
           regulatory protein, including the well-studied protein
           LysB (lysis protein B) of Enterobacteria phage P2. For
           members of this family, genes are found in phage or in
           prophage regions of bacterial genomes, typically near a
           phage lysozyme or phage holin.
          Length = 135

 Score = 28.1 bits (63), Expect = 2.5
 Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 15/84 (17%)

Query: 127 AHSLSARIASSENAQVIEALYDIVKNRNDIMLLTKYGESLQILRRLTQETEKHINNLQDK 186
             +  A +AS  N   +  L   +  RN+        E+   LR+   +    +   + +
Sbjct: 35  LKAQQAELASKAN--QLIVLL-ALAKRNE--------EAQAQLRQQLAQARALLAQREQR 83

Query: 187 I--LQDRAKEIKHWYDTLIPHPDD 208
           I  L+   ++++ W DT  P PDD
Sbjct: 84  IERLKRENEDLRRWADT--PLPDD 105


>gnl|CDD|162709 TIGR02110, PQQ_syn_pqqF, coenzyme PQQ biosynthesis probable
           peptidase PqqF.  In a subset of species that make
           coenzyme PQQ (pyrrolo-quinoline-quinone), this probable
           peptidase is found in the PQQ biosynthesis region and is
           thought to act as a protease on PqqA (TIGR02107), a
           probable peptide precursor of the coenzyme. PQQ is
           required for some glucose dehydrogenases and alcohol
           dehydrogenases.
          Length = 696

 Score = 27.5 bits (61), Expect = 4.3
 Identities = 18/96 (18%), Positives = 33/96 (34%), Gaps = 6/96 (6%)

Query: 6   EKLKEACDVATDSIRSFFMQAKPYILPALSKEEQ--KSLKYFFLPEN---TLCQKFFNAF 60
             L          +  F     P  L A  +E    +S+   +L ++    L    F+A 
Sbjct: 247 AGLPATARDNVTLLCEFLQDEAPGGLLAQLRERGLAESVAATWLYQDAGQALLALEFSAR 306

Query: 61  DRHATAGIEIKKTMNATLQFLQKVPTADPQAVEYEK 96
              A A  +I++ +   L  L +   A+     Y +
Sbjct: 307 CISAAAAQQIEQLLTQWLGALAEQTWAEQLE-HYAQ 341


>gnl|CDD|161982 TIGR00657, asp_kinases, aspartate kinase.  The Lys-sensitive enzyme
           of Bacillus subtilis resembles the E. coli form but is
           an alpha 2/beta 2 heterotetramer, where the beta subunit
           is translated from an in-phase alternative initiator at
           Met-246. This may be a feature of a number of closely
           related forms, including a paralog from B. subtilis.
          Length = 441

 Score = 27.3 bits (61), Expect = 5.0
 Identities = 18/98 (18%), Positives = 42/98 (42%), Gaps = 2/98 (2%)

Query: 181 NNLQDKILQDRAKEIKHWYDTLIPHPDDSSPNSGVSFDIMEPGHEKTNIYALSYGEQMSA 240
              ++ + + R K I+   + LIP          +  +++     +     LS+GE++SA
Sbjct: 59  GPSKEFLEKIREKHIEI-LERLIPQAIAEELKRLLDAELVLEEKPREMDRILSFGERLSA 117

Query: 241 PANLSECQ-LNCLGLAVWGSCAPLLNNHHLALSFSIIQ 277
               +  + L    +++ G  A +L + +   +  II+
Sbjct: 118 ALLSAALEELGVKAVSLLGGEAGILTDSNFGRARVIIE 155


>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein.  These
            proteins are found in P. falciparum, P. vivax and P.
            yoelii.
          Length = 2757

 Score = 27.3 bits (60), Expect = 5.2
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 139  NAQVIEALYDIVKNRNDIMLLTKYGESLQILRRLTQETEKHINNLQDKILQDRAKEIKHW 198
               +I  L D  K+ N+  L+ K  E+ +I+  LT+      NN    IL +   +I ++
Sbjct: 2210 KKHMISILADATKDHNN--LIEKEKEATKIINNLTELFTIDFNNADADILHNNKIQIIYF 2267

Query: 199  YDTL 202
               L
Sbjct: 2268 NSEL 2271


>gnl|CDD|130083 TIGR01010, BexC_CtrB_KpsE, polysaccharide export inner-membrane
           protein, BexC/CtrB/KpsE family.  This family contains
           gamma proteobacterial proteins involved in capsule
           polysaccharide export.
          Length = 362

 Score = 27.0 bits (60), Expect = 5.9
 Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 12/60 (20%)

Query: 144 EALYDIVKNRNDIMLLTKYG------------ESLQILRRLTQETEKHINNLQDKILQDR 191
           EA Y   K R  + + +  G            E+ +I +RL +E E+ IN L ++  +D 
Sbjct: 112 EAFYRYYKKRLSVDVDSVSGILTLNVTAFDAEEAQKINQRLLKEGERLINRLNERARKDT 171


>gnl|CDD|180515 PRK06291, PRK06291, aspartate kinase; Provisional.
          Length = 465

 Score = 26.8 bits (60), Expect = 6.9
 Identities = 8/12 (66%), Positives = 11/12 (91%)

Query: 230 YALSYGEQMSAP 241
           Y LS+GE++SAP
Sbjct: 124 YILSFGERLSAP 135


>gnl|CDD|152763 pfam12328, Rpp20, Rpp20 subunit of nuclear RNase MRP and P.  The
          nuclear RNase P of Saccharomyces cerevisiae is made up
          of at least nine protein subunits; Pop1, Pop3, Pop4,
          Pop5, Pop6, Pop7, Pop8, Rpr2 and Rpp1. Many of these
          subunits seem to be present also in the RNase MRP, with
          the exception of Rpr2 (Rpp21) which is unique to RNase
          P. Human nuclear RNase P and MRP appear to contain at
          least 10 protein subunits, Rpp14, Rpp20, Rpp21, Rpp25,
          Rpp29, Rpp30, Rpp38, Rpp40, hPop1 and hPop5, although
          there is recent evidence that not all of these subunits
          are shared between P and MRP. Archaeal RNase P has at
          least four protein subunits homologous to eukaryotic
          RNase P/MRP proteins. In the yeast RNase P, Pop6 and
          Pop7 (the Rpp20 homologue) interact with each other and
          they are both interaction partners of Pop4; in the
          human MRP Rpp25 and Rpp20 interact with each other and
          Rpp25 binds to Rpp29 (Pop4).
          Length = 120

 Score = 26.9 bits (60), Expect = 7.0
 Identities = 8/32 (25%), Positives = 16/32 (50%)

Query: 53 CQKFFNAFDRHATAGIEIKKTMNATLQFLQKV 84
           QK  +  ++ AT+  E+ K      + L++V
Sbjct: 21 IQKLLDKAEKRATSSEELAKDRKNGGKKLEEV 52


>gnl|CDD|182751 PRK10811, rne, ribonuclease E; Reviewed.
          Length = 1068

 Score = 26.5 bits (59), Expect = 7.9
 Identities = 10/15 (66%), Positives = 10/15 (66%), Gaps = 2/15 (13%)

Query: 218 DIMEPGHE--KTNIY 230
           DI  PGHE  K NIY
Sbjct: 28  DIESPGHEQKKANIY 42


>gnl|CDD|177917 PLN02278, PLN02278, succinic semialdehyde dehydrogenase.
          Length = 498

 Score = 26.6 bits (59), Expect = 8.3
 Identities = 7/19 (36%), Positives = 14/19 (73%)

Query: 190 DRAKEIKHWYDTLIPHPDD 208
           +R+K ++ WYD +I + +D
Sbjct: 85  ERSKILRRWYDLIIANKED 103


>gnl|CDD|162167 TIGR01034, metK, S-adenosylmethionine synthetase.  Tandem isozymes
           of this S-adenosylmethionine synthetase in E. coli are
           designated MetK and MetX.
          Length = 377

 Score = 26.6 bits (59), Expect = 8.7
 Identities = 11/25 (44%), Positives = 12/25 (48%), Gaps = 1/25 (4%)

Query: 112 YATNIA-TYMPIGEEFAHSLSARIA 135
           YATN     MP+    AH L  R A
Sbjct: 122 YATNETPELMPLPITLAHKLLKRAA 146


>gnl|CDD|129550 TIGR00458, aspS_arch, aspartyl-tRNA synthetase, archaeal type.  In
           a multiple sequence alignment of representative
           asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic
           type aspartyl-tRNA synthetases (aspS_arch), and
           bacterial type aspartyl-tRNA synthetases (aspS_bact),
           there is a striking similarity between asnS and
           aspS_arch in gap pattern and in sequence, and a striking
           divergence of aspS_bact. Consequently, a separate model
           was built for each of the three groups. This model,
           aspS_arch, represents aspartyl-tRNA synthetases from the
           eukaryotic cytosol and from the Archaea. In some
           species, this enzyme aminoacylates tRNA for both Asp and
           Asn; Asp-tRNA(asn) is subsequently transamidated to
           Asn-tRNA(asn).
          Length = 428

 Score = 26.3 bits (58), Expect = 9.6
 Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 16/76 (21%)

Query: 162 YGESLQILRR----------LTQETEKHINNLQDKI--LQDRAKEIKHWYDTLIPHPDDS 209
           Y E++++             L+ E EK +    D +  + D   EI+ +Y      PD+ 
Sbjct: 280 YDEAIEMANAKGVEIGWGEDLSTEAEKALGEEMDGLYFITDWPTEIRPFYTM----PDED 335

Query: 210 SPNSGVSFDIMEPGHE 225
           +P    SFD+M    E
Sbjct: 336 NPEISKSFDLMYRDLE 351


  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
   0.318    0.131    0.383 

Gapped
Lambda     K      H
   0.267   0.0686    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,509,067
Number of extensions: 270274
Number of successful extensions: 578
Number of sequences better than 10.0: 1
Number of HSP's gapped: 578
Number of HSP's successfully gapped: 18
Length of query: 289
Length of database: 5,994,473
Length adjustment: 92
Effective length of query: 197
Effective length of database: 4,006,537
Effective search space: 789287789
Effective search space used: 789287789
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: 57 (25.8 bits)