RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780417|ref|YP_003064830.1| transcriptional regulator CarD
family protein [Candidatus Liberibacter asiaticus str. psy62]
         (188 letters)



>gnl|CDD|161938 TIGR00580, mfd, transcription-repair coupling factor (mfd).  All
           proteins in this family for which functions are known
           are DNA-dependent ATPases that function in the process
           of transcription-coupled DNA repair in which the repair
           of the transcribed strand of actively transacribed genes
           is repaired at a higher rate than the repair of
           non-transcribed regions of the genome and than the
           non-transcribed strand of the same gene. This family is
           based on the phylogenomic analysis of JA Eisen (1999,
           Ph.D. Thesis, Stanford University). This family is
           closely related to the RecG and UvrB families.
          Length = 926

 Score = 35.4 bits (82), Expect = 0.010
 Identities = 15/67 (22%), Positives = 32/67 (47%), Gaps = 6/67 (8%)

Query: 2   TFQQKRDAMRQGF---RTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIA-FDKDKMCL 57
              + +    +       G+++V+  HG+G    ++  EV G++ ++ V+    +DK  L
Sbjct: 313 KKSRLKSKPIESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDK--L 370

Query: 58  KVPVGKA 64
            VPV + 
Sbjct: 371 YVPVEQL 377


>gnl|CDD|179244 PRK01198, PRK01198, V-type ATP synthase subunit C; Provisional.
          Length = 352

 Score = 31.8 bits (73), Expect = 0.11
 Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 18/93 (19%)

Query: 89  ARVKRTMWSRRA-----QEYDAKINSGDLIAIAEVVRDLHRTDSQPE-----KSYSERQL 138
           ARV+     R A     ++Y+  +    L    E++R L  T+ + E       YS   L
Sbjct: 16  ARVR----VREAKLLDREKYERLLEMKSL---EEIIRFLEETEYKEEIDELGSRYSGPDL 68

Query: 139 YESALNR-MVREIAAVNSISEPEAINLIEVNLS 170
            E ALNR + +    +  IS      L++V L 
Sbjct: 69  IEKALNRNLAKTYELLLEISPGRLKELVDVYLR 101


>gnl|CDD|106078 PRK13041, PRK13041, superantigen-like protein; Reviewed.
          Length = 231

 Score = 27.3 bits (60), Expect = 2.7
 Identities = 24/100 (24%), Positives = 42/100 (42%), Gaps = 7/100 (7%)

Query: 33  IKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMRKLSEAHFVERALKLVRGKARVK 92
           IK   +     +FF    DK+ M L     K ID  +RK    ++     ++  GK  VK
Sbjct: 139 IKADHIGEYDYDFFPFKIDKEAMSL-----KEIDFKLRKYLIDNYGLYG-EMSTGKITVK 192

Query: 93  RTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKS 132
           +  + +   E D K+    +  +  V  D+ R + +  K+
Sbjct: 193 KKYYGKYTFELDKKLQEDRMSDVINVT-DIDRIEIKVRKA 231


>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
           Provisional.
          Length = 1147

 Score = 27.0 bits (60), Expect = 3.1
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 15  RTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPV 61
             G+ +V+  HGVG    +   E  G+K E+ ++ +  D   L VPV
Sbjct: 478 HPGQPVVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYANDAK-LYVPV 523


>gnl|CDD|184850 PRK14848, PRK14848, deubiquitinase SseL; Provisional.
          Length = 317

 Score = 26.1 bits (57), Expect = 5.0
 Identities = 11/25 (44%), Positives = 15/25 (60%)

Query: 147 VREIAAVNSISEPEAINLIEVNLSS 171
           + E A +  ISE E +N IE NL +
Sbjct: 232 IIEAAKIAGISENEDVNFIETNLQN 256


>gnl|CDD|172935 PRK14460, PRK14460, ribosomal RNA large subunit methyltransferase
           N; Provisional.
          Length = 354

 Score = 26.2 bits (58), Expect = 5.4
 Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 8/58 (13%)

Query: 125 TDSQPEKSYSERQLYESALNRMVREIAAVNSISEP--------EAINLIEVNLSSKSS 174
           T    E  +  RQ+++    +  R+  ++ ++S+           IN  EV     SS
Sbjct: 17  TAELGEPRFRARQIWQWLWQKGARDFDSMTNVSKALRARLAEKAVINWPEVETVQTSS 74


>gnl|CDD|148640 pfam07147, PDCD9, Mitochondrial 28S ribosomal protein S30 (PDCD9). 
           This family consists of several eukaryotic mitochondrial
           28S ribosomal protein S30 (or programmed cell death
           protein 9 PDCD9) sequences. The exact function of this
           family is unknown although it is known to be a component
           of the mitochondrial ribosome and a component in
           cellular apoptotic signaling pathways.
          Length = 423

 Score = 25.5 bits (56), Expect = 8.4
 Identities = 13/39 (33%), Positives = 15/39 (38%), Gaps = 7/39 (17%)

Query: 9   AMRQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFV 47
           AM QGF  GE +  P      IT+       G    FF 
Sbjct: 334 AMYQGFWQGEDVTRPFTSQCVITD-------GKYFSFFC 365


>gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase;
           Provisional.
          Length = 336

 Score = 25.4 bits (56), Expect = 9.6
 Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 1/27 (3%)

Query: 136 RQLYESALNRMVREIAAVNSISEPEAI 162
           R LYES   R    + A+N +++ E +
Sbjct: 18  RALYESG-RRAEITVVAINELADAEGM 43


  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
   0.315    0.129    0.348 

Gapped
Lambda     K      H
   0.267   0.0631    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,902,701
Number of extensions: 177907
Number of successful extensions: 360
Number of sequences better than 10.0: 1
Number of HSP's gapped: 360
Number of HSP's successfully gapped: 24
Length of query: 188
Length of database: 5,994,473
Length adjustment: 88
Effective length of query: 100
Effective length of database: 4,092,969
Effective search space: 409296900
Effective search space used: 409296900
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 (21.6 bits)
S2: 54 (24.8 bits)