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)