RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780444|ref|YP_003064857.1| bacteriophage repressor
protein C1 [Candidatus Liberibacter asiaticus str. psy62]
         (223 letters)



>gnl|CDD|185600 PTZ00410, PTZ00410, NAD-dependent SIR2; Provisional.
          Length = 349

 Score = 31.8 bits (72), Expect = 0.13
 Identities = 14/35 (40%), Positives = 19/35 (54%)

Query: 119 GVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRK 153
           G+P+ RSPH GIYA   +   +   D   L L R+
Sbjct: 45  GIPDFRSPHTGIYAKLGKYNLNSPTDAFSLTLLRE 79


>gnl|CDD|162030 TIGR00767, rho, transcription termination factor Rho.  Members of
           this family differ in the specificity of RNA binding.
          Length = 415

 Score = 29.7 bits (67), Expect = 0.57
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 6/51 (11%)

Query: 6   HKK----IWEAIDRMAERHNLT--PSGLARKAGLDPTSFNKSKRFGIEGRN 50
           HKK    + ++I R+A  +N     SG     G+D  + ++ KRF    RN
Sbjct: 253 HKKDVVILLDSITRLARAYNTVTPASGKVLSGGVDANALHRPKRFFGAARN 303


>gnl|CDD|178066 PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme.
          Length = 758

 Score = 29.6 bits (67), Expect = 0.64
 Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 2/34 (5%)

Query: 98  SGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIY 131
           +  G + D    P   K+      EI +P+NG+Y
Sbjct: 177 TPDGRWVDR--IPAWIKYAVQAPGEIGAPYNGVY 208


>gnl|CDD|128803 smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins. 
          Length = 56

 Score = 28.7 bits (65), Expect = 1.2
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 5/60 (8%)

Query: 13 IDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQL 72
          +  + E   LT   LA K G+  ++ ++     IE   R PS E++ K+  A   ++ +L
Sbjct: 2  LKELREEKGLTQEELAEKLGVSRSTLSR-----IENGKRKPSLETLKKLAKALGVSLDEL 56


>gnl|CDD|132276 TIGR03232, benzo_1_2_benB, benzoate 1,2-dioxygenase, small subunit.
            Benzoate 1,2-dioxygenase (EC 1.14.12.10) belongs to the
           larger family of aromatic ring-hydroxylating
           dioxygenases. Members of this family should all act on
           benzoate, but several have additional known activities
           on various benozate analogs. Some members actually may
           be named more suitably according to such alternate an
           activity, such as 2-chlorobenzoate 1,2-dioxygenase
           (1.14.12.13).
          Length = 155

 Score = 28.6 bits (64), Expect = 1.2
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 79  DGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHN 128
           D + TE  + EI L+Y+P     G  D  VF    + ++  VP+ R+ HN
Sbjct: 38  DDQLTEDPQSEISLIYYP--NRQGLEDR-VFRIKTERSSATVPDTRTSHN 84


>gnl|CDD|152766 pfam12331, DUF3636, Protein of unknown function (DUF3636).  This
           domain family is found in eukaryotes, and is
           approximately 160 amino acids in length.
          Length = 155

 Score = 27.3 bits (61), Expect = 3.4
 Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 5/28 (17%)

Query: 195 LMSLNCCYPVDTVEMSDIEWIARILWAS 222
           LM LN   P+      DI  +  +L  S
Sbjct: 36  LMMLNPSQPIR-----DITLMLSLLSTS 58


>gnl|CDD|147833 pfam05895, DUF859, Siphovirus protein of unknown function (DUF859).
            This family consists of several uncharacterized
           proteins from the Siphoviruses as well as one bacterial
           sequence. Some of the members of this family are
           described as putative minor structural proteins.
          Length = 534

 Score = 27.0 bits (60), Expect = 3.8
 Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 6/44 (13%)

Query: 78  SDGRTTEKKEKEIPLL-YFPPSGSGGFFDSGVFPTGNKWNTVGV 120
           S GR ++  E  I +L YF P+         V  TG   N + V
Sbjct: 309 SRGRQSDPVETTITVLEYFGPA-----LSFSVQRTGETSNQLVV 347


>gnl|CDD|162065 TIGR00844, c_cpa1, na(+)/h(+) antiporter.  This model is specific
           for the fungal members of this family.
          Length = 810

 Score = 26.8 bits (59), Expect = 4.1
 Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 116 NTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKP 175
            T     I S  + +Y  +       + +   +   R+ +     + I     ++++I+ 
Sbjct: 604 PTSRYDGIESEIDDVYTYENDSESIASSERRRIKKLREEE---QQAYIAYTEDNQVIIEN 660

Query: 176 RTGDIVAKVLISRRG 190
           R G+I+  V I  RG
Sbjct: 661 RQGEILEYVDIHDRG 675


>gnl|CDD|131387 TIGR02334, prpF, probable AcnD-accessory protein PrpF.  The
           2-methylcitrate cycle is one of at least five
           degradation pathways for propionate via propionyl-CoA.
           Degradation of propionate toward pyruvate consumes
           oxaloacetate and releases succinate. Oxidation of
           succinate back into oxaloacetate by the TCA cycle makes
           the 2-methylcitrate pathway a cycle. This family
           consists of PrpF, an incompletely characterized protein
           that appears to be an essential accessory protein for
           the Fe/S-dependent 2-methylisocitrate dehydratase AcnD
           (TIGR02333). This protein is related to but distinct
           from FldA (part of Pfam family pfam04303), a putative
           fluorene degradation protein of Sphingomonas sp. LB126.
          Length = 390

 Score = 26.7 bits (59), Expect = 5.1
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 13/59 (22%)

Query: 75  LPFSDGRTTEKKEKEIPLLYFP----------PSGSGGFFDSGVFPTGNKWNTVGVPEI 123
           +P S G+  E  + E+  + FP          P+  G   +  +FPTGN  + + VP +
Sbjct: 146 VPISGGQVQETGDFELDGVTFPAAEVQLEFLDPADDG---EGAMFPTGNLVDDLEVPGV 201


>gnl|CDD|162812 TIGR02346, chap_CCT_theta, T-complex protein 1, theta subunit.
           Members of this family, all eukaryotic, are part of the
           group II chaperonin complex called CCT (chaperonin
           containing TCP-1) or TRiC. The archaeal equivalent group
           II chaperonin is often called the thermosome. Both are
           somewhat related to the group I chaperonin of bacterial,
           GroEL/GroES. This family consists exclusively of the CCT
           alpha chain (part of a paralogous family) from animals,
           plants, fungi, and other eukaryotes.
          Length = 531

 Score = 26.6 bits (59), Expect = 5.7
 Identities = 11/25 (44%), Positives = 14/25 (56%)

Query: 12  AIDRMAERHNLTPSGLARKAGLDPT 36
           AI + AE   + P  LA  AGL+P 
Sbjct: 429 AIKKFAEAFEIIPRTLAENAGLNPN 453


>gnl|CDD|178277 PLN02672, PLN02672, methionine S-methyltransferase.
          Length = 1082

 Score = 26.3 bits (58), Expect = 6.5
 Identities = 20/60 (33%), Positives = 24/60 (40%), Gaps = 17/60 (28%)

Query: 58  IFKILAATNETICQLLDLPFSDGRTTEKKEKEIPLL-----------YFP---PSGSGGF 103
           IFK L      +   LDL F D    ++K   IP L           YFP   P+GS  F
Sbjct: 375 IFKFLKNGFHEVSGSLDLSFEDESVADEK---IPFLAYLASALKGLSYFPCEPPAGSKRF 431


>gnl|CDD|180973 PRK07424, PRK07424, bifunctional sterol desaturase/short chain
           dehydrogenase; Validated.
          Length = 406

 Score = 26.2 bits (58), Expect = 6.8
 Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 1/28 (3%)

Query: 143 QDTSMLPLYRKGDILILNSAIQVNCGDR 170
           Q+ ++  L  K DILI+N  I V+ G+R
Sbjct: 235 QEAALAELLEKVDILIINHGINVH-GER 261


  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
   0.319    0.136    0.418 

Gapped
Lambda     K      H
   0.267   0.0637    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,724,028
Number of extensions: 229232
Number of successful extensions: 418
Number of sequences better than 10.0: 1
Number of HSP's gapped: 418
Number of HSP's successfully gapped: 20
Length of query: 223
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 133
Effective length of database: 4,049,753
Effective search space: 538617149
Effective search space used: 538617149
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 (21.8 bits)
S2: 55 (25.2 bits)