RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780776|ref|YP_003065189.1| ribosome recycling factor [Candidatus Liberibacter asiaticus str. psy62] (186 letters) >1y69_8 Ribosome recycling factor; RRF; 3.33A {Deinococcus radiodurans} (8:) Length = 113 Score = 126 bits (319), Expect = 1e-30 Identities = 37/120 (30%), Positives = 65/120 (54%), Gaps = 7/120 (5%) Query: 67 VVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSK 126 ++S K+ +++ + ++ I G TEERR L K+ AE+++ Sbjct: 1 MISDIRKDAEVRMDKCVEAFKTQISKIRTG-------GGGTEERRKDLTKIVRGEAEQAR 53 Query: 127 ISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIMHF 186 ++VRN+RRD D +K K + SED ++D+QK+TD+ IK I++ +K+ E+M F Sbjct: 54 VAVRNVRRDANDKVKALLKDKEISEDDDRRSQDDVQKLTDAAIKKIEAALADKEAELMQF 113 >1wih_A Mitochondrial ribosome recycling factor; structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} (A:) Length = 84 Score = 119 bits (300), Expect = 3e-28 Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 1/82 (1%) Query: 31 GRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWD-KEMVASVERGIHESNLG 89 G S LD + V V LNQ+ +++ P++++V++ E A+ + I ES + Sbjct: 1 GSSGSSGLDHITVVTADGKVALNQIGQISMKSPQVILVNMASFPECTAAAIKAIRESGMN 60 Query: 90 LNPIVEGQVLRIPVPETTEERR 111 LNP VEG ++R+P+P+ T Sbjct: 61 LNPEVEGTLIRVPIPKVTSGPS 82 >1wqg_A Ribosome recycling factor; translation factor, triple-helix bundle, protein synthesis; 2.15A {Mycobacterium tuberculosis} (A:33-104) Length = 72 Score = 109 bits (275), Expect = 2e-25 Identities = 22/72 (30%), Positives = 46/72 (63%) Query: 34 SPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPI 93 +P M + ++ YG+ P+ Q+A++ V E R++V+ ++ + ++E I S+LG+NP Sbjct: 1 NPGMFSRITIDYYGAATPITQLASINVPEARLVVIKPYEANQLRAIETAIRNSDLGVNPT 60 Query: 94 VEGQVLRIPVPE 105 +G ++R+ VP+ Sbjct: 61 NDGALIRVAVPQ 72 >1dd5_A Ribosome recycling factor; three-helix bundle, beta-alpha-beta sandwich; 2.55A {Thermotoga maritima} (A:34-104) Length = 71 Score = 109 bits (275), Expect = 2e-25 Identities = 30/71 (42%), Positives = 51/71 (71%) Query: 35 PSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPIV 94 P++L+ +KV+ YG P+NQ+A +++ E R LV+ WDK +++ +E+ I+ S+LGLNPI Sbjct: 1 PAILEEIKVDYYGVPTPVNQLATISISEERTLVIKPWDKSVLSLIEKAINASDLGLNPIN 60 Query: 95 EGQVLRIPVPE 105 +G V+R+ P Sbjct: 61 DGNVIRLVFPS 71 >1ise_A Ribosome recycling factor; translation; 2.20A {Escherichia coli} (A:33-104) Length = 72 Score = 108 bits (272), Expect = 5e-25 Identities = 34/72 (47%), Positives = 50/72 (69%) Query: 34 SPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPI 93 SPS+LD + VE YG+ PL Q+A+VTV + R L ++V+D+ M +VE+ I S+LGLNP Sbjct: 1 SPSLLDGIVVEYYGTPTPLRQLASVTVEDSRTLKINVFDRSMSPAVEKAIMASDLGLNPN 60 Query: 94 VEGQVLRIPVPE 105 G +R+P+P Sbjct: 61 SAGSDIRVPLPP 72 >1is1_A Ribosome recycling factor; translation; 2.20A {Vibrio parahaemolyticus} (A:33-104) Length = 72 Score = 107 bits (268), Expect = 1e-24 Identities = 34/70 (48%), Positives = 49/70 (70%) Query: 35 PSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPIV 94 PS+L + VE YG+ PLNQVANV + R L ++V+DKE+ VE+ I S+LGLNP+ Sbjct: 2 PSLLSGISVEYYGAATPLNQVANVVAEDARTLAITVFDKELTQKVEKAIMMSDLGLNPMS 61 Query: 95 EGQVLRIPVP 104 G ++R+P+P Sbjct: 62 AGTIIRVPLP 71 >1eh1_A Ribosome recycling factor; translation, hinge variability; 2.60A {Thermus thermophilus} (A:36-105) Length = 70 Score = 104 bits (261), Expect = 8e-24 Identities = 34/69 (49%), Positives = 49/69 (71%) Query: 36 SMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPIVE 95 ++L +KVE YG+HVPLNQ+A VT +PR LVV WD+ + ++E+ I +S+LGLNP + Sbjct: 1 ALLLHLKVEYYGAHVPLNQIATVTAPDPRTLVVQSWDQNALKAIEKAIRDSDLGLNPSNK 60 Query: 96 GQVLRIPVP 104 G L I +P Sbjct: 61 GDALYINIP 69 >1ge9_A Ribosome recycling factor; three-helix bundle; NMR {Aquifex aeolicus} (A:37-106) Length = 70 Score = 102 bits (256), Expect = 4e-23 Identities = 27/69 (39%), Positives = 46/69 (66%), Gaps = 1/69 (1%) Query: 36 SMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPIVE 95 ++++ +KVE YGS VP+ Q+ ++V E +V+ VWD+ V ++E+ I L LNP V+ Sbjct: 2 ALVEEIKVEYYGSKVPIKQLGTISVPEHNQIVIQVWDQNAVPAIEKAI-REELNLNPTVQ 60 Query: 96 GQVLRIPVP 104 G V+R+ +P Sbjct: 61 GNVIRVTLP 69 >1eh1_A Ribosome recycling factor; translation, hinge variability; 2.60A {Thermus thermophilus} (A:1-35,A:106-185) Length = 115 Score = 101 bits (254), Expect = 5e-23 Identities = 36/78 (46%), Positives = 49/78 (62%) Query: 107 TEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITD 166 TEERR LV+ YAE+ ++++RNIRR+ +D LKK K SED E +IQKITD Sbjct: 37 TEERRKDLVRAVRQYAEEGRVAIRNIRREALDKLKKLAKELHLSEDETKRAEAEIQKITD 96 Query: 167 STIKNIDSFFEEKKKEIM 184 I D E+K++EI+ Sbjct: 97 EFIAKADQLAEKKEQEIL 114 >1ise_A Ribosome recycling factor; translation; 2.20A {Escherichia coli} (A:1-32,A:105-185) Length = 113 Score = 101 bits (253), Expect = 8e-23 Identities = 32/80 (40%), Positives = 51/80 (63%) Query: 107 TEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITD 166 TEERR L K+ AE+++++VRN+ RD D +K K + SED ++D+QK+TD Sbjct: 34 TEERRKDLTKIVRGEAEQARVAVRNVGRDANDKVKALLKDKEISEDDDRRSQDDVQKLTD 93 Query: 167 STIKNIDSFFEEKKKEIMHF 186 + IK I++ +K+ E+M F Sbjct: 94 AAIKKIEAALADKEAELMQF 113 >1wqg_A Ribosome recycling factor; translation factor, triple-helix bundle, protein synthesis; 2.15A {Mycobacterium tuberculosis} (A:1-32,A:105-185) Length = 113 Score = 100 bits (252), Expect = 1e-22 Identities = 35/78 (44%), Positives = 47/78 (60%) Query: 107 TEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITD 166 TEERR LVK A E++K+SVRNIRR M+ L + RK G+A ED V E D+ K T Sbjct: 34 TEERRRELVKQAKHKGEEAKVSVRNIRRKAMEELHRIRKEGEAGEDEVGRAEKDLDKTTH 93 Query: 167 STIKNIDSFFEEKKKEIM 184 + ID + K+ E++ Sbjct: 94 QYVTQIDELVKHKEGELL 111 >1is1_A Ribosome recycling factor; translation; 2.20A {Vibrio parahaemolyticus} (A:1-32,A:105-185) Length = 113 Score = 100 bits (251), Expect = 1e-22 Identities = 35/80 (43%), Positives = 47/80 (58%) Query: 107 TEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITD 166 TEERR LVK+ AE +++VRNIRRD + LK K + SED + +IQK+TD Sbjct: 34 TEERRKDLVKIVRGEAEGGRVAVRNIRRDANNDLKALLKDKEISEDEDRKAQEEIQKLTD 93 Query: 167 STIKNIDSFFEEKKKEIMHF 186 +K ID K+KE+M Sbjct: 94 VAVKKIDEVLAAKEKELMEV 113 >1dd5_A Ribosome recycling factor; three-helix bundle, beta-alpha-beta sandwich; 2.55A {Thermotoga maritima} (A:1-33,A:105-185) Length = 114 Score = 100 bits (250), Expect = 2e-22 Identities = 39/88 (44%), Positives = 54/88 (61%) Query: 99 LRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLE 158 +R P T E+R VK A E+ KI++RNIRR+ + +K+ +K G ED LE Sbjct: 27 MRTGKPSPTTEQREKWVKKAKEIVEEGKIAIRNIRREILKKIKEDQKEGLIPEDDAKRLE 86 Query: 159 NDIQKITDSTIKNIDSFFEEKKKEIMHF 186 N+IQK+TD I+ +D FE KK+EIM F Sbjct: 87 NEIQKLTDEFIEKLDEVFEIKKEEIMEF 114 >1ge9_A Ribosome recycling factor; three-helix bundle; NMR {Aquifex aeolicus} (A:1-36,A:107-184) Length = 114 Score = 92.5 bits (230), Expect = 3e-20 Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 3/78 (3%) Query: 107 TEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITD 166 TEERR LV++ H E++++ VRN+RR+ + ++ + SED +QK+TD Sbjct: 38 TEERRRELVRLLHKITEEARVRVRNVRREAKEMIE---ELEGISEDEKKRALERLQKLTD 94 Query: 167 STIKNIDSFFEEKKKEIM 184 I I+ E K+KEIM Sbjct: 95 KYIDEINKLMEAKEKEIM 112 >2gu1_A Zinc peptidase; alpha/beta, beta barrel, structural genomics, PSI, protein structure initiative; 1.90A {Vibrio cholerae} (A:1-95) Length = 95 Score = 26.4 bits (58), Expect = 2.3 Identities = 9/71 (12%), Positives = 22/71 (30%), Gaps = 8/71 (11%) Query: 68 VSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVA----HAYAE 123 V + + SV+ + ++ I G+ L + + + + RL E Sbjct: 27 VPYSILQKILSVDLDHLQLDM----IQPGEELELMMDDMGQLSRLIYHMSIVEKAIYTRE 82 Query: 124 KSKISVRNIRR 134 + + Sbjct: 83 NDGSFSYDFQE 93 >1miu_A BRCA2, breast cancer type 2 susceptibility protein; tumor suppressor, breast cancer susceptibility, DNA-binding; 3.10A {Mus musculus} (A:597-738) Length = 142 Score = 26.3 bits (58), Expect = 2.4 Identities = 8/18 (44%), Positives = 16/18 (88%) Query: 168 TIKNIDSFFEEKKKEIMH 185 I+NID+F++E +K+++H Sbjct: 110 AIENIDTFYKEAEKKLIH 127 >1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning, protein-DNA complex, heilx-turn- helix motif, transcription factor; HET: BRU; 2.20A {Escherichia coli} (A:77-178) Length = 102 Score = 26.0 bits (57), Expect = 3.3 Identities = 13/35 (37%), Positives = 23/35 (65%) Query: 148 KASEDMVASLENDIQKITDSTIKNIDSFFEEKKKE 182 K E++ A L++D Q+IT T+K + F +EK ++ Sbjct: 30 KRPEEVEAWLDDDTQEITRGTVKLLREFLDEKGRD 64 >2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis S2} (C:359-648) Length = 290 Score = 24.8 bits (54), Expect = 7.4 Identities = 5/24 (20%), Positives = 8/24 (33%), Gaps = 2/24 (8%) Query: 103 VPETTEERRLA--LVKVAHAYAEK 124 VP E L L++ + Sbjct: 23 VPVMDEIYDLTKELIESCVKNKDL 46 >2odr_D Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis S2} (D:363-647) Length = 285 Score = 24.8 bits (54), Expect = 8.5 Identities = 5/24 (20%), Positives = 8/24 (33%), Gaps = 2/24 (8%) Query: 103 VPETTEERRLA--LVKVAHAYAEK 124 VP E L L++ + Sbjct: 19 VPVMDEIYDLTKELIESCVKNKDL 42 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.316 0.131 0.355 Gapped Lambda K H 0.267 0.0555 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 1,311,441 Number of extensions: 54950 Number of successful extensions: 199 Number of sequences better than 10.0: 1 Number of HSP's gapped: 195 Number of HSP's successfully gapped: 33 Length of query: 186 Length of database: 4,956,049 Length adjustment: 83 Effective length of query: 103 Effective length of database: 2,150,234 Effective search space: 221474102 Effective search space used: 221474102 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: 52 (24.2 bits)