RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780238|ref|YP_003064651.1| 30S ribosomal protein S11 [Candidatus Liberibacter asiaticus str. psy62] (129 letters) >gnl|CDD|180007 PRK05309, PRK05309, 30S ribosomal protein S11; Validated. Length = 128 Score = 192 bits (490), Expect = 3e-50 Identities = 70/127 (55%), Positives = 94/127 (74%) Query: 3 KSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFA 62 K ++ + +KNI SG AH+ +TFNNT +TITD GN I+W+S +GF GSRK++P+A Sbjct: 2 KKKKTVKKKVKKNIPSGVAHIHATFNNTIVTITDRQGNVISWASAGGLGFKGSRKSTPYA 61 Query: 63 AQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCR 122 AQVA +D + KA+ HGM ++EV V G G+GR+SA+RAL+A G + SI DVT I HNGCR Sbjct: 62 AQVAAEDAAKKAKEHGMKTVEVFVKGPGSGRESAIRALQAAGLEVTSIKDVTPIPHNGCR 121 Query: 123 PRKRRRI 129 P KRRR+ Sbjct: 122 PPKRRRV 128 >gnl|CDD|163365 TIGR03632, bact_S11, 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected. Length = 108 Score = 163 bits (414), Expect = 2e-41 Identities = 61/108 (56%), Positives = 82/108 (75%) Query: 19 GRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHG 78 G AH+ +TFNNT +TITDP GN ++W+S VGF GS+K++P+AAQ+A +D + KA+ G Sbjct: 1 GVAHIHATFNNTIVTITDPQGNVLSWASAGAVGFKGSKKSTPYAAQLAAEDAAKKAKEFG 60 Query: 79 MSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKR 126 M +++V V G GAGR+SA+RAL+A G + SI DVT I HNGCRP KR Sbjct: 61 MKTVDVYVKGPGAGRESAIRALQAAGLEVTSIKDVTPIPHNGCRPPKR 108 >gnl|CDD|181987 PRK09607, rps11p, 30S ribosomal protein S11P; Reviewed. Length = 132 Score = 72.7 bits (179), Expect = 2e-14 Identities = 47/126 (37%), Positives = 66/126 (52%), Gaps = 9/126 (7%) Query: 12 ERKNIVSGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDC 70 + G AH+ ++FNNT ITITD G TIA SS +V + ++SP+AA A + Sbjct: 3 SMRKEKWGIAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKA 62 Query: 71 SAKAQNHGMSSLEVKVSGLGA--------GRDSALRALRAIGFTIVSICDVTMIAHNGCR 122 + A+ G++ + +KV G G +A+RAL G I I DVT I H+G R Sbjct: 63 AEDAKEKGITGVHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGTR 122 Query: 123 PRKRRR 128 P RR Sbjct: 123 PPGGRR 128 >gnl|CDD|132667 TIGR03628, arch_S11P, archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria. Length = 114 Score = 67.5 bits (165), Expect = 8e-13 Identities = 46/112 (41%), Positives = 61/112 (54%), Gaps = 9/112 (8%) Query: 19 GRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNH 77 G AH+ S+FNNT ITITD G TIA SS +V + ++SP+AA A + KA+ Sbjct: 3 GIAHIYSSFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKER 62 Query: 78 GMSSLEVKVSGLGA--------GRDSALRALRAIGFTIVSICDVTMIAHNGC 121 G++ L +KV G G +A+RAL G I I DVT I H+G Sbjct: 63 GITGLHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGT 114 >gnl|CDD|185465 PTZ00129, PTZ00129, 40S ribosomal protein S14; Provisional. Length = 149 Score = 52.6 bits (126), Expect = 3e-08 Identities = 39/122 (31%), Positives = 64/122 (52%), Gaps = 9/122 (7%) Query: 16 IVSGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKA 74 +V G AH+ ++FN+T I +TD G T+ + + + ++SP+AA +A D +A+ Sbjct: 26 LVFGVAHIFASFNDTFIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARC 85 Query: 75 QNHGMSSLEVKVSGLGA--------GRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKR 126 + G+++L +K+ G G +ALRAL G I I DVT I + R + Sbjct: 86 KELGINALHIKLRATGGVRTKTPGPGAQAALRALARAGLKIGRIEDVTPIPTDSTRRKGG 145 Query: 127 RR 128 RR Sbjct: 146 RR 147 >gnl|CDD|178421 PLN02826, PLN02826, dihydroorotate dehydrogenase. Length = 409 Score = 28.2 bits (63), Expect = 0.59 Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 4/42 (9%) Query: 88 GLGAGRDS---ALRALRAIGFTIVSICDVTMIAHNGCRPRKR 126 GL AG D A+ L +GF V I VT + G P+ R Sbjct: 88 GLAAGFDKNAEAVEGLLGLGFGFVEIGSVTPLPQPG-NPKPR 128 >gnl|CDD|173384 PTZ00090, PTZ00090, 40S ribosomal protein S11; Provisional. Length = 233 Score = 28.0 bits (62), Expect = 0.66 Identities = 28/121 (23%), Positives = 50/121 (41%), Gaps = 18/121 (14%) Query: 20 RAHVVSTFNNTRITITDPHGN--TIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNH 77 + ++ NN + + N T+ S VGF + S A ++ + K + Sbjct: 120 MLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNVGFRKKLQQSERCAYRIGENIAKKCRRL 179 Query: 78 GMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAH---------NGCRPRKRRR 128 G+ ++++K + ++ L+A A G VT I H N +PRKRRR Sbjct: 180 GIFAVDIKFRRI-MRVETVLQAFYANGL------QVTQIIHEPRLPKCGLNAVKPRKRRR 232 Query: 129 I 129 + Sbjct: 233 V 233 >gnl|CDD|180064 PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional. Length = 288 Score = 27.8 bits (63), Expect = 0.84 Identities = 13/24 (54%), Positives = 17/24 (70%), Gaps = 1/24 (4%) Query: 86 VSGL-GAGRDSALRALRAIGFTIV 108 V+GL GAG+ ALRAL +G+ V Sbjct: 11 VTGLSGAGKSVALRALEDLGYYCV 34 >gnl|CDD|162334 TIGR01391, dnaG, DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751). Length = 415 Score = 26.0 bits (58), Expect = 2.6 Identities = 17/49 (34%), Positives = 17/49 (34%), Gaps = 21/49 (42%) Query: 23 VVSTFNNTRIT--ITDPHGNTIAWSSPKVVGFSGSRK---------NSP 60 F N RI I DP G VVGF G R NSP Sbjct: 195 YYDRFRN-RIMFPIHDPKGR--------VVGFGG-RALGDEKPKYLNSP 233 >gnl|CDD|164924 PHA02523, 43B, DNA polymerase subunit B; Provisional. Length = 391 Score = 25.8 bits (56), Expect = 3.0 Identities = 13/52 (25%), Positives = 23/52 (44%) Query: 32 ITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLE 83 + + D G A K++G R ++P A Q + + + G SSL+ Sbjct: 197 LNVYDMEGTRYAEPHLKIMGLETQRSSTPLACQKSLKESIRRLLQEGESSLQ 248 >gnl|CDD|131199 TIGR02144, LysX_arch, Lysine biosynthesis enzyme LysX. The family of proteins found in this equivalog include the characterized LysX from Thermus thermophilus which is part of a well-organized lysine biosynthesis gene cluster. LysX is believed to carry out an ATP-dependent acylation of the amino group of alpha-aminoadipate in the prokaryotic version of the fungal AAA lysine biosynthesis pathway. No species having a sequence in this equivalog contains the elements of the more common diaminopimelate lysine biosythesis pathway, and none has been shown to be a lysine auxotroph. These sequences have mainly recieved the name of the related enzyme, "ribosomal protein S6 modification protein RimK". RimK has been characterized in E. coli, and acts by ATP-dependent condensation of S6 with glutamate residues. Length = 280 Score = 25.8 bits (57), Expect = 3.3 Identities = 7/23 (30%), Positives = 14/23 (60%) Query: 87 SGLGAGRDSALRALRAIGFTIVS 109 + L R++AL+ A+G+ +V Sbjct: 105 TYLAFDREAALKLAEALGYPVVL 127 >gnl|CDD|182962 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional. Length = 475 Score = 25.6 bits (57), Expect = 3.5 Identities = 10/31 (32%), Positives = 15/31 (48%) Query: 28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKN 58 + R+ +TD G + S + VG SR N Sbjct: 91 VDYRVYVTDAQGIVLFDSEGRAVGQDYSRWN 121 >gnl|CDD|140255 PTZ00228, PTZ00228, variable surface protein Vir21; Provisional. Length = 350 Score = 25.5 bits (56), Expect = 3.9 Identities = 8/19 (42%), Positives = 11/19 (57%), Gaps = 2/19 (10%) Query: 6 SRIRNRERKNIVS--GRAH 22 S +R + KNIV+ AH Sbjct: 313 SSLRKGKGKNIVNIDEEAH 331 >gnl|CDD|181813 PRK09382, ispDF, bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional. Length = 378 Score = 25.6 bits (57), Expect = 4.2 Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 1/22 (4%) Query: 96 ALRALRAIGFTIVSICDVTMIA 117 A +R G I++ DVT+IA Sbjct: 297 AADFVREAGGEIIN-ADVTIIA 317 >gnl|CDD|178328 PLN02727, PLN02727, NAD kinase. Length = 986 Score = 25.2 bits (55), Expect = 4.7 Identities = 7/19 (36%), Positives = 15/19 (78%) Query: 10 NRERKNIVSGRAHVVSTFN 28 N+ R+ ++SGR+ ++S+F Sbjct: 147 NKGREEVLSGRSSIMSSFR 165 >gnl|CDD|182226 PRK10078, PRK10078, ribose 1,5-bisphosphokinase; Provisional. Length = 186 Score = 24.7 bits (54), Expect = 6.6 Identities = 8/13 (61%), Positives = 10/13 (76%) Query: 90 GAGRDSALRALRA 102 G+G+DS L ALR Sbjct: 12 GSGKDSLLAALRQ 24 >gnl|CDD|180189 PRK05667, dnaG, DNA primase; Validated. Length = 580 Score = 24.8 bits (55), Expect = 7.4 Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 7/49 (14%) Query: 88 GLG---AGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRK----RRRI 129 G+G G D+ L+ L GF+ + + ++ N R RI Sbjct: 151 GIGYAPDGWDALLKHLGGKGFSEKELEEAGLLIKNEDGGGPYDRFRNRI 199 >gnl|CDD|183478 PRK12372, PRK12372, ribonuclease III; Reviewed. Length = 413 Score = 24.5 bits (53), Expect = 7.5 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 12/61 (19%) Query: 39 GNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALR 98 G+ IA + VV G+ N F + C+ + L+VKVSG GA R +A + Sbjct: 163 GHKIALPTYTVVATHGAAHNQQFEVE-----CT-------VPKLDVKVSGSGASRRAAEQ 210 Query: 99 A 99 A Sbjct: 211 A 211 >gnl|CDD|178970 PRK00302, lnt, apolipoprotein N-acyltransferase; Reviewed. Length = 505 Score = 24.5 bits (54), Expect = 7.6 Identities = 9/16 (56%), Positives = 10/16 (62%), Gaps = 1/16 (6%) Query: 29 NTRIT-ITDPHGNTIA 43 NT IT + DP G IA Sbjct: 438 NTGITAVIDPLGRIIA 453 >gnl|CDD|185007 PRK15047, PRK15047, N-hydroxyarylamine O-acetyltransferase; Provisional. Length = 281 Score = 24.4 bits (53), Expect = 8.8 Identities = 8/32 (25%), Positives = 17/32 (53%) Query: 98 RALRAIGFTIVSICDVTMIAHNGCRPRKRRRI 129 R LR +GF + S+ ++++ P + R+ Sbjct: 78 RVLRELGFNVRSLLGRVVLSNPPALPPRTHRL 109 >gnl|CDD|179576 PRK03381, PRK03381, PII uridylyl-transferase; Provisional. Length = 774 Score = 24.2 bits (53), Expect = 9.3 Identities = 13/42 (30%), Positives = 14/42 (33%), Gaps = 1/42 (2%) Query: 89 LGAG-RDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRRI 129 LG G R RAL TI DV PR+ Sbjct: 256 LGLGDRFDLARALSDAARTISYAVDVGWRTAANALPRRGLSA 297 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 0.319 0.130 0.385 Gapped Lambda K H 0.267 0.0784 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,065,544 Number of extensions: 113915 Number of successful extensions: 263 Number of sequences better than 10.0: 1 Number of HSP's gapped: 257 Number of HSP's successfully gapped: 34 Length of query: 129 Length of database: 5,994,473 Length adjustment: 83 Effective length of query: 46 Effective length of database: 4,201,009 Effective search space: 193246414 Effective search space used: 193246414 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 (23.3 bits)