RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780252|ref|YP_003064665.1| 30S ribosomal protein S17 [Candidatus Liberibacter asiaticus str. psy62] (79 letters) >gnl|CDD|180162 PRK05610, rpsQ, 30S ribosomal protein S17; Reviewed. Length = 84 Score = 112 bits (283), Expect = 2e-26 Identities = 42/75 (56%), Positives = 57/75 (76%) Query: 1 MPKRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIE 60 MP++ LQG VVSDK +KTI+VLVERR HP + K ++RSK+Y HDENN+ K+GD V I Sbjct: 4 MPRKTLQGRVVSDKMDKTIVVLVERRVKHPLYGKIVKRSKKYHAHDENNEAKIGDVVRIM 63 Query: 61 ESAPISKKKSWLVID 75 E+ P+SK K W +++ Sbjct: 64 ETRPLSKTKRWRLVE 78 >gnl|CDD|163368 TIGR03635, S17_bact, 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17. Length = 71 Score = 106 bits (266), Expect = 2e-24 Identities = 40/71 (56%), Positives = 54/71 (76%) Query: 3 KRVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEES 62 ++ LQG+VVSDK +KTI+VLVERR HP + K ++R+K+Y HDENN+ KVGD V I E+ Sbjct: 1 RKTLQGVVVSDKMDKTIVVLVERRVKHPLYGKIVKRTKKYHAHDENNECKVGDVVRIIET 60 Query: 63 APISKKKSWLV 73 P+SK K W + Sbjct: 61 RPLSKTKRWRL 71 >gnl|CDD|181479 PRK08572, rps17p, 30S ribosomal protein S17P; Reviewed. Length = 108 Score = 54.5 bits (132), Expect = 6e-09 Identities = 29/72 (40%), Positives = 43/72 (59%), Gaps = 1/72 (1%) Query: 4 RVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHD-ENNKYKVGDFVSIEES 62 +VL+G VVSDK KT++V E P++++ +R R H+ KVGD V I E Sbjct: 30 QVLEGTVVSDKMHKTVVVEREYLHYVPKYERYEKRRSRIHAHNPPCIDAKVGDKVKIAEC 89 Query: 63 APISKKKSWLVI 74 P+SK KS++V+ Sbjct: 90 RPLSKTKSFVVV 101 >gnl|CDD|132669 TIGR03630, arch_S17P, archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria. Length = 102 Score = 52.3 bits (126), Expect = 3e-08 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 1/72 (1%) Query: 4 RVLQGMVVSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHD-ENNKYKVGDFVSIEES 62 ++L+G+VVSDK KT++V E + ++++ RR + H+ K GD V I E+ Sbjct: 28 QILEGVVVSDKMNKTVVVEREYLYYDRKYERYERRRSKIHAHNPPCIDVKEGDIVIIGET 87 Query: 63 APISKKKSWLVI 74 P+SK KS++V+ Sbjct: 88 RPLSKTKSFVVL 99 >gnl|CDD|185523 PTZ00241, PTZ00241, 40S ribosomal protein S11; Provisional. Length = 158 Score = 34.3 bits (79), Expect = 0.007 Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 5/67 (7%) Query: 4 RVLQGMVVSDKSEKTIIVLVERRFSH--PRFQKTIRRSKRYAVHDENN-KYKVGDFVSIE 60 R+L+G+V+S K ++TII + R + H ++ + +R K VH K GD V + Sbjct: 69 RILRGVVISTKMKRTII--IRRDYLHYVKKYNRYEKRHKNIPVHCSPCFDVKEGDIVVVG 126 Query: 61 ESAPISK 67 + P+SK Sbjct: 127 QCRPLSK 133 >gnl|CDD|152630 pfam12195, End_beta_barrel, Beta barrel domain of bacteriophage endosialidase. This domain family is found in bacteria and viruses, and is approximately 80 amino acids in length.This domain is the beta barrel domain of bacteriophage endosialidase which represents the one of the two sialic acid binding sites of the enzyme. The domain is nested in the beta propeller domain of the endosialidase enzyme. The endosialidase protein complexes to form homotrimeric molecules. Length = 83 Score = 28.8 bits (64), Expect = 0.35 Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 1/39 (2%) Query: 26 RFSHPRFQKTIRRSKRYA-VHDENNKYKVGDFVSIEESA 63 R H T ++RYA +H ++ GDFV+ SA Sbjct: 2 RSLHLTGGITKAANQRYATIHIPDHGLFAGDFVNFSNSA 40 >gnl|CDD|152652 pfam12217, End_beta_propel, Catalytic beta propeller domain of bacteriophage endosialidase. This domain family is found in bacteria and viruses, and is typically between 443 and 460 amino acids in length. This domain is the highly conserved beta propeller of bacteriophage endosialidase which represents the catalytically active part of the enzymes. This core domain forms stable SDS-resistant trimers. There is a nested beta barrel domain in this domain (pfam12195). The endosialidase protein complexes to form a homotrimeric molecule. Length = 449 Score = 27.6 bits (61), Expect = 0.69 Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 1/39 (2%) Query: 26 RFSHPRFQKTIRRSKRYA-VHDENNKYKVGDFVSIEESA 63 R H T +++YA +H ++ GDFV+ SA Sbjct: 113 RSLHLTGGITKAANQQYATIHIPDHGLFAGDFVNFSNSA 151 >gnl|CDD|130337 TIGR01270, Trp_5_monoox, tryptophan 5-monooxygenase, tetrameric. This model describes tryptophan 5-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tyrosine 3-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria. Length = 464 Score = 27.5 bits (61), Expect = 0.87 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 1/46 (2%) Query: 29 HPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESAPISKKKSWLVI 74 HP F+ T R +R D YK G+ + E ++K+W I Sbjct: 157 HPGFKDTEYRKRRMMFADLALNYKHGEPIPRVEYTE-EERKTWGTI 201 >gnl|CDD|162801 TIGR02302, aProt_lowcomp, conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model. Length = 851 Score = 25.7 bits (56), Expect = 2.6 Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 7/62 (11%) Query: 3 KRVLQGMVVSD------KSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDF 56 V +V D SE I L ER F+ P + + + A+ D N +V D Sbjct: 384 AEVTLTLVAKDAAGNQGHSEPFTIRLPERLFTKPLARAVAEQRRILAL-DANQNSQVYDA 442 Query: 57 VS 58 + Sbjct: 443 LD 444 >gnl|CDD|173501 PTZ00265, PTZ00265, multidrug resistance protein (mdr1); Provisional. Length = 1466 Score = 25.0 bits (54), Expect = 4.1 Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 9/50 (18%) Query: 11 VSDKSEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIE 60 + DK++KTII + R S I+RS + V NN + G FV Sbjct: 1404 IKDKADKTIITIAHRIAS-------IKRSDKIVVF--NNPDRTGSFVQAH 1444 >gnl|CDD|148097 pfam06283, ThuA, Trehalose utilisation. This family consists of several bacterial ThuA like proteins. ThuA appears to be involved in utilisation of trehalose. The thuA and thuB genes form part of the trehalose/sucrose transport operon thuEFGKAB, which is located on the pSymB megaplasmid. The thuA and thuB genes are induced in vitro by trehalose but not by sucrose and the extent of its induction depends on the concentration of trehalose available in the medium. Length = 216 Score = 24.9 bits (55), Expect = 4.7 Identities = 7/18 (38%), Positives = 10/18 (55%) Query: 27 FSHPRFQKTIRRSKRYAV 44 + P FQK + R R+A Sbjct: 198 YDDPGFQKLLLRGIRWAA 215 >gnl|CDD|151541 pfam11097, DUF2883, Protein of unknown function (DUF2883). This family of proteins have no known function but appear to be restricted to phage. Length = 75 Score = 25.0 bits (54), Expect = 4.9 Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 1/28 (3%) Query: 31 RFQKTIRRSKRYA-VHDENNKYKVGDFV 57 RFQ T RR K Y +H + K G FV Sbjct: 38 RFQDTPRRGKNYTQMHILKQRSKTGAFV 65 >gnl|CDD|184251 PRK13695, PRK13695, putative NTPase; Provisional. Length = 174 Score = 24.9 bits (55), Expect = 5.0 Identities = 10/25 (40%), Positives = 13/25 (52%) Query: 14 KSEKTIIVLVERRFSHPRFQKTIRR 38 SEK +I + RR HP Q+ R Sbjct: 124 DSEKPVIATLHRRSVHPFVQEIKSR 148 >gnl|CDD|180431 PRK06155, PRK06155, crotonobetaine/carnitine-CoA ligase; Provisional. Length = 542 Score = 24.7 bits (54), Expect = 5.8 Identities = 14/44 (31%), Positives = 18/44 (40%), Gaps = 6/44 (13%) Query: 21 VLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEESAP 64 ++E RFS F +RR Y +G VSI S P Sbjct: 249 YVLEPRFSASGFWPAVRRHGATVT------YLLGAMVSILLSQP 286 >gnl|CDD|150107 pfam09328, Phytochelatin_C, Domain of unknown function (DUF1984). Members of this family of functionally uncharacterized domains are found at the C-terminus of plant phytochelatin synthases. Length = 264 Score = 24.6 bits (54), Expect = 5.8 Identities = 12/23 (52%), Positives = 15/23 (65%) Query: 1 MPKRVLQGMVVSDKSEKTIIVLV 23 P V+ G VVSD SE+ + VLV Sbjct: 166 GPTTVVSGTVVSDGSEQGVDVLV 188 >gnl|CDD|178286 PLN02682, PLN02682, pectinesterase family protein. Length = 369 Score = 24.3 bits (53), Expect = 6.7 Identities = 9/36 (25%), Positives = 14/36 (38%) Query: 27 FSHPRFQKTIRRSKRYAVHDENNKYKVGDFVSIEES 62 H FQK + + K GDF +I+ + Sbjct: 53 LKHSVFQKAKNKLFPSYTIVVDKKPAAGDFTTIQAA 88 >gnl|CDD|161715 TIGR00113, queA, S-adenosylmethionine:tRNA ribosyltransferase-isomerase. This model describes the enzyme for S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA). QueA synthesizes Queuosine which is usually in the first position of the anticodon of tRNAs specific for asparagine, aspartate, histidine, and tyrosine. Length = 344 Score = 23.9 bits (52), Expect = 9.1 Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 3/41 (7%) Query: 15 SEKTIIVLVERRFSHPRFQKTIRRSKRYAVHDENNKYKVGD 55 S + VL+ R R+ I+ SK+ + K K G+ Sbjct: 73 SGGKVEVLLLRMLDENRWLALIKPSKKPKI---GAKVKFGE 110 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 0.317 0.132 0.368 Gapped Lambda K H 0.267 0.0821 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,243,762 Number of extensions: 61626 Number of successful extensions: 146 Number of sequences better than 10.0: 1 Number of HSP's gapped: 143 Number of HSP's successfully gapped: 27 Length of query: 79 Length of database: 5,994,473 Length adjustment: 49 Effective length of query: 30 Effective length of database: 4,935,681 Effective search space: 148070430 Effective search space used: 148070430 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: 50 (22.9 bits)