RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780347|ref|YP_003064760.1| riboflavin synthase subunit alpha [Candidatus Liberibacter asiaticus str. psy62] (204 letters) >gnl|CDD|30655 COG0307, RibC, Riboflavin synthase alpha chain [Coenzyme metabolism]. Length = 204 Score = 202 bits (515), Expect = 5e-53 Identities = 88/201 (43%), Positives = 125/201 (62%), Gaps = 10/201 (4%) Query: 1 MFTGIVTDIGKIIAMTPIAKGMRLRVMT-SYNTSKMKLGCSIAHAGICLTVVRLSEEHSV 59 MFTGIV +IGK+ + G+ L + + +KLG SIA G+CLTV +E+ Sbjct: 1 MFTGIVEEIGKV---KKVENGITLTIESAKLILEDVKLGDSIAVNGVCLTVTEFNEDG-- 55 Query: 60 DNWYEVEVWAETNRITNIASWGIGTFINLERSVKLGDRLDGHLVSGHIDGTVEILFLDFI 119 + V+V ET R TN+ +G +NLER++KLGDRL GHLVSGH+DGT EI+ ++ Sbjct: 56 ---FSVDVMPETLRRTNLGDLKVGDKVNLERALKLGDRLGGHLVSGHVDGTGEIVKIEKD 112 Query: 120 GDSMYCRLSL-PHNLEQFIAVKGSVCLNGVSLTVNLVGKNFFDVLLIRHTIEETTWKMHK 178 G+++ P L ++I KGS+ ++G+SLTVN V + F V LI HT+E TT K Sbjct: 113 GNAVRFWFKAPPEELAKYIVEKGSIAVDGISLTVNEVEDDTFSVSLIPHTLERTTLGEKK 172 Query: 179 VGDLINIEVDSMMRYIARLYA 199 VGD +NIE+D + +Y+ RL A Sbjct: 173 VGDRVNIEIDVLAKYVERLLA 193 >gnl|CDD|38520 KOG3310, KOG3310, KOG3310, Riboflavin synthase alpha chain [Coenzyme transport and metabolism]. Length = 210 Score = 116 bits (291), Expect = 5e-27 Identities = 66/201 (32%), Positives = 109/201 (54%), Gaps = 9/201 (4%) Query: 1 MFTGIVTDIGKIIAMTP-IAKGMRLRVMTSYNTSKMKLGCSIAHAGICLTVVRLSEEHSV 59 MFTGIV +G++ + G L++ LG SIA G CLTV + E Sbjct: 1 MFTGIVECMGEVKDLGMADDGGFDLKIGARVILEDCHLGDSIAVNGTCLTVTEFNAEE-- 58 Query: 60 DNWYEVEVWAETNRITNIASWGIGTFINLERSVKLGDRLDGHLVSGHIDGTVEILFLDFI 119 + V + ET R TN+ G+ +NLER+V+ R+ GH+V GH+D I+ ++ Sbjct: 59 ---FTVGIAPETLRKTNLEELKKGSPVNLERAVQPVSRMGGHVVQGHVDTVAVIVSMEVE 115 Query: 120 GDSMYCRLSL-PHNLEQFIAVKGSVCLNGVSLTVNLV--GKNFFDVLLIRHTIEETTWKM 176 GDS++ + L L ++I KG + ++G SLT+ V ++ F++++I +T + Sbjct: 116 GDSIWFKFKLRDKGLLKYIVPKGFIAVDGTSLTIVDVDDEESCFNIMMIAYTQQNVIMPT 175 Query: 177 HKVGDLINIEVDSMMRYIARL 197 K+GD +N+EVD M +Y+ +L Sbjct: 176 KKIGDKVNLEVDIMGKYVEKL 196 >gnl|CDD|144321 pfam00677, Lum_binding, Lumazine binding domain. This domain binds to derivatives of lumazine in some proteins. Some proteins have lost the residues involved in binding lumazine. Length = 86 Score = 62.2 bits (152), Expect = 1e-10 Identities = 30/86 (34%), Positives = 47/86 (54%), Gaps = 1/86 (1%) Query: 104 SGHIDGTVEILFLDFIGDSMYCRLSLP-HNLEQFIAVKGSVCLNGVSLTVNLVGKNFFDV 162 +G ++G EI + G++ + LP L + + K S+ +NG+SLTV V N F Sbjct: 1 TGIVEGVGEIAEIIENGNARSIWIKLPDKMLTKVLIGKDSIAVNGISLTVTEVTGNQFTF 60 Query: 163 LLIRHTIEETTWKMHKVGDLINIEVD 188 LI T++ T KVGD +N+E+D Sbjct: 61 DLIPETLKRTNLGSLKVGDKVNLEID 86 Score = 44.9 bits (107), Expect = 2e-05 Identities = 26/94 (27%), Positives = 41/94 (43%), Gaps = 15/94 (15%) Query: 3 TGIVTDIGKIIAMTPIAKGMRLRV------MTSYNTSKMKLGCSIAHAGICLTVVRLSEE 56 TGIV +G+I + + + +T K SIA GI LTV ++ Sbjct: 1 TGIVEGVGEIAEIIENGNARSIWIKLPDKMLTKVLIGK----DSIAVNGISLTVTEVT-- 54 Query: 57 HSVDNWYEVEVWAETNRITNIASWGIGTFINLER 90 N + ++ ET + TN+ S +G +NLE Sbjct: 55 ---GNQFTFDLIPETLKRTNLGSLKVGDKVNLEI 85 >gnl|CDD|31266 COG1067, LonB, Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]. Length = 647 Score = 30.3 bits (68), Expect = 0.36 Identities = 28/133 (21%), Positives = 45/133 (33%), Gaps = 41/133 (30%) Query: 48 LTVVRLSEEHSVDNWYEVEVWAETNRITNIASWGIGTFINLERSVKLGD----------- 96 L+V+ + H+ E RI+ G G +++ER +L Sbjct: 434 LSVIEVPGHHAFG---------EPARISCAVHKGDGEIVDIERKAELAGNIHNKGMMIKQ 484 Query: 97 -------RLDGHL-VSGHIDGTVEILFLDFIGDS----MYCRL-----SLPHNLEQFIAV 139 D H+ S + +D GDS C L +P ++Q IA+ Sbjct: 485 AFLMSILNYDIHIPFSASLVFEQSYGEVD--GDSASLAEACALISALSKIP--VDQDIAI 540 Query: 140 KGSVCLNGVSLTV 152 GS+ G V Sbjct: 541 TGSIDQFGEVQPV 553 >gnl|CDD|153084 cd01675, RNR_III, Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit which contains the active and allosteric sites. Length = 555 Score = 26.9 bits (60), Expect = 4.3 Identities = 9/41 (21%), Positives = 18/41 (43%), Gaps = 3/41 (7%) Query: 97 RLDGHLVSGHIDGTVEILFLDFIGDSMYCRLSLPHNLEQFI 137 L + H++G + I LD++ + YC +L + Sbjct: 29 ILPKEIARAHLNGDIHIHDLDYLPLTPYCCG---WDLRPLL 66 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.324 0.138 0.416 Gapped Lambda K H 0.267 0.0714 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,418,808 Number of extensions: 122765 Number of successful extensions: 311 Number of sequences better than 10.0: 1 Number of HSP's gapped: 296 Number of HSP's successfully gapped: 8 Length of query: 204 Length of database: 6,263,737 Length adjustment: 89 Effective length of query: 115 Effective length of database: 4,340,536 Effective search space: 499161640 Effective search space used: 499161640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 55 (25.0 bits)