RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780266|ref|YP_003064679.1| 30S ribosomal protein S12
[Candidatus Liberibacter asiaticus str. psy62]
         (124 letters)



>gnl|CDD|179949 PRK05163, rpsL, 30S ribosomal protein S12; Validated.
          Length = 124

 Score =  210 bits (536), Expect = 9e-56
 Identities = 87/124 (70%), Positives = 101/124 (81%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPT+NQL+RK RK S    +K  AL   PQKRGVC RVYT TPKKPNSALRKV + RLT+
Sbjct: 1   MPTINQLVRKGRK-SKVKKSKSPALNACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTN 59

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RG LD  GVK+RKQ RS+YGA
Sbjct: 60  GFEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKDRKQGRSKYGA 119

Query: 121 ERPK 124
           +RPK
Sbjct: 120 KRPK 123


>gnl|CDD|130054 TIGR00981, rpsL_bact, ribosomal protein S12, bacterial/organelle.
           This model recognizes ribosomal protein S12 of Bacteria,
           mitochondria, and chloroplasts. The homologous ribosomal
           proteins of Archaea and Eukarya, termed S23 in Eukarya
           and S12 or S23 in Archaea, score below the trusted
           cutoff.
          Length = 124

 Score =  182 bits (464), Expect = 2e-47
 Identities = 88/124 (70%), Positives = 101/124 (81%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPT+NQLIRK RK   +  +K  AL   PQKRGVC RVYT TPKKPNSALRKV + RLT+
Sbjct: 1   MPTINQLIRKGRKKKKKK-SKSPALEACPQKRGVCTRVYTTTPKKPNSALRKVARVRLTN 59

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RG LD  GVKNRKQ RS+YGA
Sbjct: 60  GFEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVKNRKQGRSKYGA 119

Query: 121 ERPK 124
           +RPK
Sbjct: 120 KRPK 123


>gnl|CDD|185456 PTZ00115, PTZ00115, 40S ribosomal protein S12; Provisional.
          Length = 290

 Score =  124 bits (313), Expect = 6e-30
 Identities = 53/95 (55%), Positives = 70/95 (73%)

Query: 25  LRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLC 84
           L G PQK+G+C++V   TP+KPNS LRKV + RL++G  V  Y+PG GHNL  HSVV++ 
Sbjct: 120 LEGAPQKKGICVKVRVQTPRKPNSGLRKVARVRLSTGRTVTVYIPGIGHNLNTHSVVLVR 179

Query: 85  GGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYG 119
           GGR KD+PG  Y+ +RGV D   VKNR ++RS+YG
Sbjct: 180 GGRCKDVPGCNYKAVRGVYDLLPVKNRARSRSKYG 214


>gnl|CDD|179789 PRK04211, rps12P, 30S ribosomal protein S12P; Reviewed.
          Length = 145

 Score = 54.6 bits (132), Expect = 7e-09
 Identities = 41/108 (37%), Positives = 62/108 (57%), Gaps = 11/108 (10%)

Query: 21  KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLT-SGVEVIAYVPGEG--HNLQE 77
           K   L G P  RG+ L    V  K+PNSA+RK ++ +L  +G +V A+ PG+G  + + E
Sbjct: 38  KADPLEGAPMARGIVLEKVGVEAKQPNSAIRKCVRVQLIKNGKQVTAFCPGDGAINFIDE 97

Query: 78  HSVVMLCG-----GRVK-DLPGVKYRVIR--GVLDAQGVKNRKQARSR 117
           H  V++ G     GR   D+PGV+Y+VI+  GV   + VK +K+   R
Sbjct: 98  HDEVVIEGIGGPKGRSMGDIPGVRYKVIKVNGVSLKELVKGKKEKPVR 145


>gnl|CDD|130055 TIGR00982, S23_S12_E_A, ribosomal protein S23 (S12).  This model
           represents the eukaryotic and archaeal homologs of
           bacterial ribosomal protein S12. This protein is known
           typically as S23 in eukaryotes and as either S12 or S23
           in the Archaea.
          Length = 139

 Score = 54.1 bits (130), Expect = 1e-08
 Identities = 38/120 (31%), Positives = 64/120 (53%), Gaps = 11/120 (9%)

Query: 9   RKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLT-SGVEVIAY 67
           R+ ++   R   K   L G P  RG+ L    V  ++PNSA+RK ++ +L  +G  V A+
Sbjct: 20  RRFKRRMLRLKRKADPLEGAPMARGIVLEKVGVEARQPNSAIRKCVRVQLIKNGKVVTAF 79

Query: 68  VPGEG--HNLQEHSVVML------CGGRVKDLPGVKYRVIR--GVLDAQGVKNRKQARSR 117
            PG+G  + + EH  V++       G  + D+PGV+Y+V++   V   + VK +K+   R
Sbjct: 80  CPGDGAINFIDEHDEVIIEGIGGPRGRSMGDIPGVRYKVVKVNNVSLKELVKGKKEKPRR 139


>gnl|CDD|185422 PTZ00067, PTZ00067, 40S ribosomal S23; Provisional.
          Length = 143

 Score = 43.6 bits (103), Expect = 2e-05
 Identities = 28/97 (28%), Positives = 54/97 (55%), Gaps = 8/97 (8%)

Query: 12  RKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLT-SGVEVIAYVPG 70
           +K       K     G    +G+ +    +  K+PNSA+RK ++ +L  +G ++ A+VP 
Sbjct: 28  KKAHLGTRYKANPFGGASHAKGIVVEKIGIEAKQPNSAIRKCVRVQLIKNGKKITAFVPN 87

Query: 71  EG--HNLQEHSVVMLCG-GR----VKDLPGVKYRVIR 100
           +G  + + E+  V++ G GR    V D+PGV+++V++
Sbjct: 88  DGCLNFINENDEVLVSGFGRSGHAVGDIPGVRFKVVK 124


>gnl|CDD|179368 PRK02106, PRK02106, choline dehydrogenase; Validated.
          Length = 560

 Score = 28.6 bits (65), Expect = 0.48
 Identities = 9/18 (50%), Positives = 13/18 (72%)

Query: 61  GVEVIAYVPGEGHNLQEH 78
           G+ V+  +PG G NLQ+H
Sbjct: 282 GIPVVHDLPGVGENLQDH 299


>gnl|CDD|185641 PTZ00462, PTZ00462, Serine-repeat antigen protein; Provisional.
          Length = 1004

 Score = 28.1 bits (62), Expect = 0.68
 Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 3/45 (6%)

Query: 49  ALRKVIKARLTSGVEVIAYVPGE---GHNLQEHSVVMLCGGRVKD 90
           A  K+IK  + +   VIAY+  E   G+      V  LCG    D
Sbjct: 678 AFIKIIKDEIMNKGSVIAYIKAENVLGYEFNGKKVQNLCGDDTAD 722


>gnl|CDD|163029 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
            synthase PfaA.  Members of the seed for this alignment
            are involved in omega-3 polyunsaturated fatty acid
            biosynthesis, such as the protein PfaA from the
            eicosapentaenoic acid biosynthesis operon in
            Photobacterium profundum strain SS9. PfaA is encoded
            together with PfaB, PfaC, and PfaD, and the functions of
            the individual polypeptides have not yet been described.
            More distant homologs of PfaA, also included with the
            reach of this model, appear to be involved in
            polyketide-like biosynthetic mechanisms of
            polyunsaturated fatty acid biosynthesis, an alternative
            to the more familiar iterated mechanism of chain
            extension and desaturation, and in most cases are encoded
            near genes for homologs of PfaB, PfaC, and/or PfaD.
          Length = 2582

 Score = 25.7 bits (56), Expect = 3.1
 Identities = 17/56 (30%), Positives = 21/56 (37%), Gaps = 5/56 (8%)

Query: 39   YTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGV 94
            Y  +   P  A    +   + + VE IA       NL  HS V L     K LP V
Sbjct: 1690 YMQSKVSPTDATDPKVATTVPAAVEAIARTVETAVNLPPHSEVEL-----KKLPAV 1740


>gnl|CDD|181677 PRK09169, PRK09169, hypothetical protein; Validated.
          Length = 2316

 Score = 25.4 bits (56), Expect = 3.9
 Identities = 10/29 (34%), Positives = 13/29 (44%)

Query: 1    MPTVNQLIRKPRKGSFRACAKVTALRGNP 29
            +P      R+ R G F A A +  L  NP
Sbjct: 1814 VPYTKSTARELRDGRFDAEAALARLEDNP 1842


>gnl|CDD|183935 PRK13271, treA, trehalase; Provisional.
          Length = 569

 Score = 25.3 bits (55), Expect = 5.0
 Identities = 12/29 (41%), Positives = 15/29 (51%)

Query: 50  LRKVIKARLTSGVEVIAYVPGEGHNLQEH 78
           LR  +    T   E   YVP EG +L+EH
Sbjct: 94  LRHFVNVNFTLPKEGEKYVPPEGQSLREH 122


>gnl|CDD|179894 PRK04926, dgt, deoxyguanosinetriphosphate triphosphohydrolase;
           Provisional.
          Length = 503

 Score = 24.9 bits (55), Expect = 5.1
 Identities = 7/9 (77%), Positives = 8/9 (88%)

Query: 96  YRVIRGVLD 104
           YRVI G+LD
Sbjct: 403 YRVISGLLD 411


>gnl|CDD|162541 TIGR01810, betA, choline dehydrogenase.  This enzyme is a member of
           the GMC oxidoreductase family (pfam00732 and pfam05199),
           sharing a common evoluntionary origin and enzymatic
           reaction with alcohol dehydrogenase. Outgrouping from
           this model, Caulobacter crescentus shares sequence
           homology with choline dehydrogenase, yet other genes
           participating in this enzymatic reaction have not
           currently been identified.
          Length = 532

 Score = 24.8 bits (54), Expect = 6.4
 Identities = 9/18 (50%), Positives = 13/18 (72%)

Query: 61  GVEVIAYVPGEGHNLQEH 78
           G+E   ++PG G NLQ+H
Sbjct: 275 GIEPRIHLPGVGENLQDH 292


>gnl|CDD|117685 pfam09129, Chol_subst-bind, Cholesterol oxidase,
          substrate-binding.  The substrate-binding domain found
          in Cholesterol oxidase is composed of an eight-stranded
          mixed beta-pleated sheet and six alpha-helices. This
          domain is positioned over the isoalloxazine ring system
          of the FAD cofactor bound by FAD_binding_4 (PF:PF01565)
          and forms the roof of the active site cavity, allowing
          for catalysis of oxidation and isomerisation of
          cholesterol to cholest-4-en-3-one.
          Length = 321

 Score = 24.9 bits (54), Expect = 6.5
 Identities = 8/14 (57%), Positives = 12/14 (85%)

Query: 36 LRVYTVTPKKPNSA 49
          L+V+TV+P KP+ A
Sbjct: 49 LKVWTVSPTKPDGA 62


>gnl|CDD|182549 PRK10560, hofQ, outer membrane porin HofQ; Provisional.
          Length = 386

 Score = 24.4 bits (53), Expect = 8.4
 Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 2/52 (3%)

Query: 7  LIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARL 58
          L   P K + +   K   L    ++ G  L V++   +  N A ++  +AR 
Sbjct: 36 LTDVPWKQALQTVVKSAGLI--LRQEGNILSVHSQAWQNENIARQEAEQARA 85


>gnl|CDD|148074 pfam06246, Isy1, Isy1-like splicing family.  Isy1 protein is
           important in the optimisation of splicing.
          Length = 253

 Score = 24.2 bits (53), Expect = 8.7
 Identities = 8/10 (80%), Positives = 9/10 (90%)

Query: 86  GRVKDLPGVK 95
           GR K+LPGVK
Sbjct: 128 GRAKELPGVK 137


  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
   0.320    0.136    0.400 

Gapped
Lambda     K      H
   0.267   0.0751    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,989,323
Number of extensions: 114572
Number of successful extensions: 197
Number of sequences better than 10.0: 1
Number of HSP's gapped: 192
Number of HSP's successfully gapped: 23
Length of query: 124
Length of database: 5,994,473
Length adjustment: 82
Effective length of query: 42
Effective length of database: 4,222,617
Effective search space: 177349914
Effective search space used: 177349914
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: 51 (23.4 bits)