RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780255|ref|YP_003064668.1| 30S ribosomal protein S3 [Candidatus Liberibacter asiaticus str. psy62] (227 letters) >gnl|CDD|178972 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed. Length = 232 Score = 357 bits (918), Expect = 2e-99 Identities = 123/202 (60%), Positives = 159/202 (78%) Query: 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERT 60 MGQK+NPI FRLG+ W+SRW+A +Y LLHEDLKIR++L+ LK+AGV++I IER Sbjct: 1 MGQKVNPIGFRLGIIKDWDSRWYADKKDYADLLHEDLKIRKFLKKKLKKAGVSRIEIERP 60 Query: 61 HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSI 120 K R+ +++ARPG++IGKKG +IEK+RK+L +T + +++ EV KPE++A L+A+SI Sbjct: 61 AKRVRVTIHTARPGIVIGKKGAEIEKLRKELEKLTGKPVQINIVEVKKPELDAQLVAESI 120 Query: 121 AQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRA 180 AQQLERRV FRRAMKRA+Q AMR GA G+KV SGRL GAE++RTE Y EGRVPL TLRA Sbjct: 121 AQQLERRVSFRRAMKRAIQRAMRAGAKGIKVQVSGRLGGAEIARTEWYREGRVPLHTLRA 180 Query: 181 HIDYGTAVAETAYGSCGIKVYV 202 IDYGTA A T YG G+KV++ Sbjct: 181 DIDYGTAEAHTTYGIIGVKVWI 202 >gnl|CDD|130082 TIGR01009, rpsC_bact, ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea. Length = 211 Score = 296 bits (761), Expect = 2e-81 Identities = 115/202 (56%), Positives = 152/202 (75%) Query: 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERT 60 MGQK+NPI FRLG+ W SRW+A EY LLHEDLKIR Y++ L AG++ + IER Sbjct: 1 MGQKVNPIGFRLGITKDWKSRWYANPKEYAKLLHEDLKIRNYIKKELSNAGISDVEIERP 60 Query: 61 HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSI 120 R+ +++ARPG++IGKKG++IEK+RK L +T E+ +++ EV +PE++A L+A +I Sbjct: 61 ADKIRVTIHTARPGIVIGKKGSEIEKLRKDLQKLTGKEVQINIAEVKRPELDAQLVADNI 120 Query: 121 AQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRA 180 A+QLE RV FRRAMK+A+QSAM+ GA G+KV SGRL GAE++RTE Y EGRVPL TLRA Sbjct: 121 ARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGAEIARTEWYKEGRVPLHTLRA 180 Query: 181 HIDYGTAVAETAYGSCGIKVYV 202 IDY TA A T YG G+KV++ Sbjct: 181 DIDYATAEAHTTYGIIGVKVWI 202 >gnl|CDD|179775 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed. Length = 207 Score = 111 bits (279), Expect = 2e-25 Identities = 64/172 (37%), Positives = 98/172 (56%), Gaps = 14/172 (8%) Query: 37 LKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLS---N 93 + I EYL L +AG + I++T RI +Y+ RPG++IG+ G +I ++ + L Sbjct: 15 VMIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFG 74 Query: 94 MTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIA 153 + N +I V EV PE+NA ++A +A LER FRRA A++ M GA GV++I Sbjct: 75 LENPQI--DVKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGALGVEIII 132 Query: 154 SGRLNGAELSRTECYLEGRV-----PLQTLRAHIDYGTAVAETAYGSCGIKV 200 SG+L G E +RTE + EG + P + L +D G A+A+ G G++V Sbjct: 133 SGKLTG-ERARTEKFTEGYIKKSGEPAEEL---VDRGFAIAKLKLGIIGVEV 180 >gnl|CDD|130081 TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly. Length = 195 Score = 102 bits (257), Expect = 6e-23 Identities = 65/180 (36%), Positives = 98/180 (54%), Gaps = 9/180 (5%) Query: 37 LKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTN 96 I E+L+ L++AG + + + T ++I+++ RPGL+IG+ G I ++ +KL Sbjct: 13 TLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFG 72 Query: 97 SE-IHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASG 155 E + V EV PE+NA + A+ IA+ LER + FRRA AV+ M GA GV+V SG Sbjct: 73 LENPQIDVEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGAKGVEVTISG 132 Query: 156 RLNGAELSRTECYLEGRVPL--QTLRAHIDYGTAVAETAYGSCGIKVY-----VSLRDEV 208 +L G +RTE + G + + +D G A+A G G+KV V L DEV Sbjct: 133 KLTGER-ARTEKFAAGYLKHSGEPAEELVDKGFAIALLKLGVLGVKVKIMPPDVKLPDEV 191 >gnl|CDD|116265 pfam07650, KH_2, KH domain. Length = 55 Score = 64.0 bits (157), Expect = 3e-11 Identities = 18/54 (33%), Positives = 35/54 (64%) Query: 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIA 117 +++ +++PG++IGK G++I+K+ K+L ++ + V EV PE+ A L A Sbjct: 2 VIVVIRTSQPGIVIGKGGSNIKKLGKELRKRFGKKVQIEVLEVKNPELLAQLGA 55 >gnl|CDD|185435 PTZ00084, PTZ00084, 40S ribosomal protein S3; Provisional. Length = 220 Score = 49.7 bits (119), Expect = 6e-07 Identities = 31/122 (25%), Positives = 54/122 (44%), Gaps = 3/122 (2%) Query: 41 EYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIR---KKLSNMTNS 97 E+L L + G + + + T II+ + R ++G KG I ++ +K Sbjct: 23 EFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKRFGFPEG 82 Query: 98 EIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRL 157 ++ L V + A A+S+ +L + RRA ++ M GA G +VI SG+L Sbjct: 83 KVELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVIVSGKL 142 Query: 158 NG 159 Sbjct: 143 RA 144 >gnl|CDD|128617 smart00322, KH, K homology RNA-binding domain. Length = 69 Score = 40.0 bits (94), Expect = 5e-04 Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 3/64 (4%) Query: 65 RIIVYSARPGLIIGKKGTDIEKIRKKLS---NMTNSEIHLSVNEVPKPEINATLIAQSIA 121 +++ + + GLIIGK G+ I+KI ++ ++ V E+ P N A+ I Sbjct: 6 EVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELIL 65 Query: 122 QQLE 125 + LE Sbjct: 66 EILE 69 >gnl|CDD|178854 PRK00089, era, GTPase Era; Reviewed. Length = 292 Score = 32.3 bits (75), Expect = 0.10 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 16/54 (29%) Query: 53 AKILIER-THKNCRIIVYSARPGLIIGKKGTDIEKI----RKKLSNMTNSEIHL 101 A I +ER + K G+IIGK G ++KI RK + + ++ L Sbjct: 228 ATIYVERDSQK-----------GIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 >gnl|CDD|132714 TIGR03675, arCOG00543, arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782. Length = 630 Score = 30.7 bits (70), Expect = 0.29 Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 5/53 (9%) Query: 38 KIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKK 90 KI+E + ++AG+ I + +I+ + +PGL+IGK G+ + +I + Sbjct: 74 KIKEIVP---EEAGITDIYFDDV--TGEVIIEAEKPGLVIGKGGSTLREITAE 121 >gnl|CDD|177558 PHA03216, PHA03216, nuclear protein UL24; Provisional. Length = 272 Score = 30.4 bits (68), Expect = 0.43 Identities = 15/55 (27%), Positives = 26/55 (47%) Query: 125 ERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLR 179 E+R+ R ++ ++ RF V+ +AS + NG R VP +TL+ Sbjct: 4 EQRLTARSRLRAGIRCHNRFYNAMVQDLASAKANGVYGDRLAPLFSELVPAETLK 58 >gnl|CDD|184053 PRK13436, PRK13436, F0F1 ATP synthase subunit delta; Provisional. Length = 179 Score = 30.0 bits (68), Expect = 0.58 Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 6/36 (16%) Query: 82 TDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIA 117 I + KLS N ++HL +I+ LIA Sbjct: 122 VQISRFESKLSKKLNKKVHL------VNKIDPKLIA 151 >gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein. Length = 270 Score = 28.9 bits (65), Expect = 1.1 Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 4/32 (12%) Query: 74 GLIIGKKGTDIEKI----RKKLSNMTNSEIHL 101 +IIGK G+ I+ I RK + + + ++ L Sbjct: 234 KIIIGKNGSMIKAIGIAARKDILELFDCDVFL 265 >gnl|CDD|179528 PRK03031, rnpA, ribonuclease P; Reviewed. Length = 122 Score = 27.3 bits (61), Expect = 3.5 Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 4/55 (7%) Query: 111 INATLIAQSIAQQLERRVVFRRAMKRAVQSAMR----FGADGVKVIASGRLNGAE 161 T SI+Q++ ++ V R +KR +++A+R A G ++ + AE Sbjct: 44 PPPTRFGISISQKVSKKAVVRNRIKRQIRAALRQLLPRIAPGWDLVIIVKPTAAE 98 >gnl|CDD|163056 TIGR02877, spore_yhbH, sporulation protein YhbH. This protein family, typified by YhbH in Bacillus subtilis, is found in nearly every endospore-forming bacterium and in no other genome (but note that the trusted cutoff score is set high to exclude a single high-scoring sequence from Nitrosococcus oceani ATCC 19707, which is classified in the Gammaproteobacteria). The gene in Bacillus subtilis was shown to be in the regulon of the sporulation sigma factor, sigma-E, and its mutation was shown to create a sporulation defect. Length = 371 Score = 27.4 bits (61), Expect = 3.6 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 8/49 (16%) Query: 77 IGKKGTDIEKIRKKLS-------NMTNSEIHLS-VNEVPKPEINATLIA 117 + KK T IE +++ +T ++ E KPE NA +IA Sbjct: 159 LDKKRTVIEALKRNQLRGRPELYPITKEDLRYKTWKENEKPESNAVVIA 207 >gnl|CDD|180352 PRK06019, PRK06019, phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed. Length = 372 Score = 27.0 bits (61), Expect = 3.8 Identities = 16/46 (34%), Positives = 17/46 (36%), Gaps = 5/46 (10%) Query: 136 RAVQSAMRFGADG--VKVIASG---RLNGAELSRTECYLEGRVPLQ 176 AV R G DG VI S A L C LE VP + Sbjct: 137 PAVLKTRRGGYDGKGQWVIRSAEDLEAAWALLGSVPCILEEFVPFE 182 >gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional. Length = 602 Score = 27.1 bits (61), Expect = 3.8 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 7/56 (12%) Query: 38 KIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARP--GLIIGKKGTDIEKIRKKL 91 +I ++ +L +++ + + +VY +IGK G I+KI KKL Sbjct: 460 EIEREIKRYLPGPVEVEVV-----SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKL 510 >gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit clpA. Length = 731 Score = 26.5 bits (59), Expect = 5.7 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 13/80 (16%) Query: 76 IIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPK-PEINATLIAQSIAQQLERRVVFRRAM 134 I+ + G D+E +RK L + +L N +P E N Q++ Q V +RA+ Sbjct: 42 ILEECGGDVEALRKDLED------YLE-NNLPSITEENEADPEQTVGVQ----RVLQRAL 90 Query: 135 KRAVQSAMRFGADGVKVIAS 154 V+SA + ++ + Sbjct: 91 -LHVKSAGKKEIGIGDILVA 109 >gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed. Length = 725 Score = 26.2 bits (58), Expect = 7.0 Identities = 9/30 (30%), Positives = 15/30 (50%) Query: 12 LGVNCTWNSRWFARGSEYGALLHEDLKIRE 41 LG++ RW A+G +Y L +L+ Sbjct: 665 LGIDSKLIKRWLAQGPDYRQALATNLEEER 694 >gnl|CDD|184049 PRK13429, PRK13429, F0F1 ATP synthase subunit delta; Provisional. Length = 181 Score = 26.3 bits (59), Expect = 7.2 Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 13/63 (20%) Query: 83 DIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQ--------SIAQQLERRVVFRRAM 134 E IR+KL MT ++ L V P + ++ + S+ QL R + + Sbjct: 123 QQEAIRQKLEKMTGKKVELDT-AV-DPSLIGGVVVKIGDKVLDASVRTQLRR---LKETL 177 Query: 135 KRA 137 K+ Sbjct: 178 KKG 180 >gnl|CDD|180527 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein; Validated. Length = 860 Score = 25.9 bits (57), Expect = 8.4 Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 11/66 (16%) Query: 84 IEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLER-----RVVFRRAMKRAV 138 I KI K ++LS P P+ IA IA QL + R+ F K AV Sbjct: 64 INKICKLAKKC--DVVYLS----PDPDREGEAIAWHIANQLPKNTKIQRISFNAITKGAV 117 Query: 139 QSAMRF 144 A++ Sbjct: 118 TEALKH 123 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 0.134 0.387 Gapped Lambda K H 0.267 0.0763 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,650,430 Number of extensions: 228435 Number of successful extensions: 518 Number of sequences better than 10.0: 1 Number of HSP's gapped: 514 Number of HSP's successfully gapped: 38 Length of query: 227 Length of database: 5,994,473 Length adjustment: 90 Effective length of query: 137 Effective length of database: 4,049,753 Effective search space: 554816161 Effective search space used: 554816161 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 (24.9 bits)