RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780202|ref|YP_003064615.1| hypothetical protein CLIBASIA_00435 [Candidatus Liberibacter asiaticus str. psy62] (211 letters) >gnl|CDD|132408 TIGR03365, Bsubt_queE, 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE. This uncharacterized enzyme, designated QueE, participates in the biosynthesis, from GTP, of 7-cyano-7-deazaguanosine, also called preQ0 because in many species it is a precursor of queuosine. In most Archaea, it is instead the precursor of a different tRNA modified base, archaeosine. Length = 238 Score = 55.0 bits (133), Expect = 1e-08 Identities = 41/142 (28%), Positives = 61/142 (42%), Gaps = 30/142 (21%) Query: 6 IKEIF-LTLQGEGGHAGRVAVFCRFSGCNLWSGREQDRLSAQCRFCDTDFVGIQGTKGGR 64 + EIF T+QGEG G+ +F R GC+ +C +CD+ F T G Sbjct: 5 VLEIFGPTIQGEGMVIGQKTMFVRTGGCDY-----------RCSWCDSLF-----TWDGS 48 Query: 65 YNVDQLADLIEEQW-----ITGEKEGRYCVLTGGEPLLQVDV-PLIQALNKRGFEIAVET 118 EE W + G + L+GG P LQ + LI +G+ A+ET Sbjct: 49 AKDTWRPMTAEEVWQELKALGGG-TPLHVSLSGGNPALQKPLGELIDLGKAKGYRFALET 107 Query: 119 NGTIEPPQG----IDWICVSPK 136 G++ Q +D + +SPK Sbjct: 108 QGSV--WQDWFRDLDDLTLSPK 127 >gnl|CDD|162888 TIGR02495, NrdG2, anaerobic ribonucleoside-triphosphate reductase activating protein. This enzyme is a member of the radical-SAM family (pfam04055). It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487) and presumably fulfills the identical function as NrdG which utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in NrdD. Length = 191 Score = 43.5 bits (103), Expect = 4e-05 Identities = 32/126 (25%), Positives = 61/126 (48%), Gaps = 26/126 (20%) Query: 21 GRVAVFCRFSGCNLWSGREQDRLSAQCRFC-DTDFVGIQGTKGGRYNVDQLADLIEEQWI 79 G++A F GCNL +C +C + + + +G+ G V+ L + + + Sbjct: 15 GKLAFTIFFQGCNL-----------KCPYCHNPELIDREGS--GEIEVEFLLEFLRSR-- 59 Query: 80 TGEKEGRYCVLTGGEPLLQVDVP-LIQALNKRGFEIAVETNGTIEPP------QG-IDWI 131 + V+TGGEP LQ +P ++ + + GFE+ ++TNG+ +G +D++ Sbjct: 60 --QGLIDGVVITGGEPTLQAGLPDFLRKVRELGFEVKLDTNGSNPRVLEELLEEGLVDYV 117 Query: 132 CVSPKA 137 + KA Sbjct: 118 AMDVKA 123 >gnl|CDD|131546 TIGR02493, PFLA, pyruvate formate-lyase 1-activating enzyme. An iron-sulfur protein with a radical-SAM domain (pfam04055). A single glycine residue in EC 2.3.1.54, formate C-acetyltransferase (formate-pyruvate lyase), is oxidized to the corresponding radical by transfer of H from its CH2 to AdoMet with concomitant cleavage of the latter. The reaction requires Fe2+. The first stage is reduction of the AdoMet to give methionine and the 5'-deoxyadenosin-5-yl radical, which then abstracts a hydrogen radical from the glycine residue. Length = 235 Score = 38.1 bits (89), Expect = 0.002 Identities = 29/120 (24%), Positives = 45/120 (37%), Gaps = 25/120 (20%) Query: 8 EIFLTLQGEGGHAGRVAVFCRFSGCNLWSGREQDRLSAQCRFC---DTDFVGIQGTKGGR 64 E T+ G G R VF GC L +C++C DT G Sbjct: 6 ESMGTVDGPGI---RFVVF--MQGCPL-----------RCQYCHNPDT----WDLKGGTE 45 Query: 65 YNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVD--VPLIQALNKRGFEIAVETNGTI 122 ++L + + G +GGEPLLQ + L +A + G ++T+G + Sbjct: 46 VTPEELIKEVGSYKDFFKASGGGVTFSGGEPLLQPEFLSELFKACKELGIHTCLDTSGFL 105 >gnl|CDD|162887 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein family. This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2, ) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0 to 8 additional cysteines. Length = 295 Score = 37.7 bits (88), Expect = 0.002 Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 2/65 (3%) Query: 59 GTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVD--VPLIQALNKRGFEIAV 116 G V+++ ++ I G L+GGEPLLQ + + L+QA ++RG AV Sbjct: 100 SIVGEEMTVEEVMRVVLRDSIFYRNSGGGVTLSGGEPLLQPEFALALLQACHERGIHTAV 159 Query: 117 ETNGT 121 ET+G Sbjct: 160 ETSGF 164 >gnl|CDD|162966 TIGR02666, moaA, molybdenum cofactor biosynthesis protein A, bacterial. The model for this family describes molybdenum cofactor biosynthesis protein A, or MoaA, as found in bacteria. It does not include the family of probable functional equivalent proteins from the archaea. MoaA works together with MoaC to synthesize precursor Z from guanine. Length = 334 Score = 35.3 bits (82), Expect = 0.012 Identities = 18/35 (51%), Positives = 22/35 (62%), Gaps = 3/35 (8%) Query: 90 LTGGEPLLQVDVP-LIQALNK-RGFE-IAVETNGT 121 LTGGEPLL+ D+ L+ L G E IA+ TNG Sbjct: 65 LTGGEPLLRKDLVELVARLAALPGIEDIALTTNGL 99 >gnl|CDD|162967 TIGR02668, moaA_archaeal, probable molybdenum cofactor biosynthesis protein A, archaeal. This model describes an archaeal family related, and predicted to be functionally equivalent, to molybdenum cofactor biosynthesis protein A (MoaA) of bacteria (see TIGR02666). Length = 302 Score = 35.0 bits (81), Expect = 0.016 Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 2/34 (5%) Query: 90 LTGGEPLLQVDVPLIQA-LNKRGF-EIAVETNGT 121 +TGGEPLL+ D+ I + G ++++ TNG Sbjct: 62 ITGGEPLLRKDLIEIIRRIKDYGIKDVSMTTNGI 95 >gnl|CDD|178909 PRK00164, moaA, molybdenum cofactor biosynthesis protein A; Reviewed. Length = 331 Score = 34.7 bits (81), Expect = 0.017 Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 3/35 (8%) Query: 90 LTGGEPLLQVDVP-LIQAL--NKRGFEIAVETNGT 121 LTGGEPLL+ D+ +I AL ++A+ TNG Sbjct: 71 LTGGEPLLRKDLEDIIAALAALPGIRDLALTTNGY 105 >gnl|CDD|184000 PRK13361, PRK13361, molybdenum cofactor biosynthesis protein A; Provisional. Length = 329 Score = 31.1 bits (71), Expect = 0.19 Identities = 31/113 (27%), Positives = 46/113 (40%), Gaps = 33/113 (29%) Query: 21 GRVAVFCRFSGCNLWSGREQDRLSAQCRFC---DTDFVGIQGTKGGRYNVDQLADLIEEQ 77 GR + R S DR +C +C D F+ DQ+ L E Sbjct: 10 GRTVTYLRLS--------VTDRCDFRCVYCMSEDPCFL----------PRDQVLSLEELA 51 Query: 78 WIT------GEKEGRYCVLTGGEPLLQVD-VPLIQALNKRG--FEIAVETNGT 121 W+ G ++ R LTGGEPL++ L+ L K E+++ TNG+ Sbjct: 52 WLAQAFTELGVRKIR---LTGGEPLVRRGCDQLVARLGKLPGLEELSLTTNGS 101 >gnl|CDD|178737 PLN03195, PLN03195, fatty acid omega-hydroxylase; Provisional. Length = 516 Score = 30.9 bits (70), Expect = 0.22 Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 4/41 (9%) Query: 164 IGFDFERFSLQPM--DGPFLE--ENTNLAISYCFQNPKWRL 200 +GF E +L P + PF + + N+ ++ F +P W+L Sbjct: 185 VGFGVEIGTLSPSLPENPFAQAFDTANIIVTLRFIDPLWKL 225 >gnl|CDD|184309 PRK13762, PRK13762, tRNA-modifying enzyme; Provisional. Length = 322 Score = 30.2 bits (69), Expect = 0.35 Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 1/30 (3%) Query: 93 GEPLLQVDVP-LIQALNKRGFEIAVETNGT 121 GEP L +P LI+ +KRGF + TNGT Sbjct: 139 GEPTLYPYLPELIEEFHKRGFTTFLVTNGT 168 >gnl|CDD|183551 PRK12484, PRK12484, nicotinate phosphoribosyltransferase; Provisional. Length = 443 Score = 29.7 bits (67), Expect = 0.63 Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 9/42 (21%) Query: 84 EGRYCVLTGGEPLLQVDVPLIQA-------LNKRGFEIAVET 118 EG V+ EPLL+V PLI+A LN+ + + + Sbjct: 97 EGT--VVFPNEPLLEVTAPLIEAQLVETFLLNQINHQSLIAS 136 >gnl|CDD|163534 TIGR03822, AblA_like_2, lysine-2,3-aminomutase-related protein. Members of this protein form a distinctive clade, homologous to lysine-2,3-aminomutase (of Bacillus, Clostridium, and methanogenic archaea) and likely similar in function. Members of this family are found in Rhodopseudomonas, Caulobacter crescentus, Bradyrhizobium, etc. Length = 321 Score = 29.3 bits (66), Expect = 0.70 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 5/52 (9%) Query: 47 CRFC-DTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLL 97 CRFC + VG +G G + +L +I E +LTGG+PL+ Sbjct: 102 CRFCFRREMVGPEG--LGVLSPAELD--AAFAYIADHPEIWEVILTGGDPLV 149 >gnl|CDD|181722 PRK09243, PRK09243, nicotinate phosphoribosyltransferase; Validated. Length = 464 Score = 29.0 bits (66), Expect = 0.91 Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 2/28 (7%) Query: 79 ITGEKEGRYCVLTGGEPLLQVDVPLIQA 106 + EG ++ EPLL+V+ PL +A Sbjct: 98 VRAVPEGE--LVFPNEPLLRVEGPLAEA 123 >gnl|CDD|163535 TIGR03823, FliZ, flagellar regulatory protein FliZ. FliZ is involved in the regulation of flagellar assembly and possibly also the down-regulation of the motile phenotype. FliZ interacts with the flagellar translational activator FlhCD complex. Length = 168 Score = 27.9 bits (62), Expect = 2.0 Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 8/36 (22%) Query: 33 NLWSGREQDRLSAQCRFC-------DTDFVGIQGTK 61 N WS Q L+A CRFC +D+ I K Sbjct: 59 NGWSV-LQQELAALCRFCSEIYCNTTSDYFDIMAFK 93 >gnl|CDD|162339 TIGR01399, hrcV, type III secretion protein, HrcV family. Members of this family are closely homologous to the flagellar biosynthesis protein FlhA (TIGR01398) and should all participate in type III secretion systems. Examples include InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc. Type III secretion systems resemble flagellar biogenesis systems, and may share the property of translocating special classes of peptides through the membrane. Length = 677 Score = 27.7 bits (62), Expect = 2.5 Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 7/39 (17%) Query: 42 RLSAQCRFCDTDFVGIQGTKGGRYNVDQL----ADLIEE 76 RL A +F+GIQ T RY +DQ+ +L++E Sbjct: 475 RLKATLLRNAQEFIGIQET---RYLLDQMEREYPELVKE 510 >gnl|CDD|152611 pfam12176, MtaB, Methanol-cobalamin methyltransferase B subunit. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 460 amino acids in length. MtaB folds as a TIM barrel and contains a novel zinc-binding motif. Zinc(II) lies at the bottom of a funnel formed at the C-terminal beta-barrel end and ligates to two cysteinyl sulfurs (Cys-220 and Cys-269) and one carboxylate oxygen (Glu-164). The function of this protein is to catalyse the cleavage of the C O bond in methanol by an SN2 mechanism. It complexes with MtaA and MtaC to perform this function. Length = 460 Score = 27.4 bits (61), Expect = 2.8 Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 5/33 (15%) Query: 131 ICVSP-KAGCDLKIKGGQELKLVFPQVNVSPEN 162 P KAG L+I G V P++N +P Sbjct: 20 KAKHPVKAGLGLEIGAGY----VIPEINYAPRP 48 >gnl|CDD|185626 PTZ00447, PTZ00447, apical membrane antigen 1-like protein; Provisional. Length = 508 Score = 27.3 bits (60), Expect = 2.9 Identities = 11/23 (47%), Positives = 16/23 (69%) Query: 184 NTNLAISYCFQNPKWRLSVQTHK 206 NTN I Y +QN K++LS+ + K Sbjct: 318 NTNANIIYTYQNEKYQLSIHSEK 340 >gnl|CDD|162398 TIGR01513, NAPRTase_put, putative nicotinate phosphoribosyltransferase. Most members of this family are Gram-positive bacteria. An additional set of mutually closely related archaeal sequences score between the trusted and noise cutoffs. Length = 443 Score = 26.9 bits (60), Expect = 3.8 Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 9/48 (18%) Query: 79 ITGEKEGRYCVLTGGEPLLQVDVPLIQA-------LNKRGFEIAVETN 119 + EG ++ EPLLQV+ PLI+A LN F+ + T Sbjct: 89 VRALPEGS--LVFPNEPLLQVEGPLIEAQLLETLVLNIINFQTLIATK 134 >gnl|CDD|161784 TIGR00238, TIGR00238, KamA family protein. Note that the E. coli homolog was expressed in E. coli and purified and found not to display display lysine 2,3-aminomutase activity. Active site residues are found in 100 residue extension in B. subtilis. Name changed to KamA family protein. Length = 331 Score = 26.7 bits (59), Expect = 4.0 Identities = 14/63 (22%), Positives = 25/63 (39%), Gaps = 5/63 (7%) Query: 47 CRFCDTDFVGIQGTKGGRYNVDQLADLIEEQWITGEKEGRYCVLTGGEPLLQVDVPLIQA 106 CR+C + G + + D +I E +++GG+PL+ D L Sbjct: 127 CRYCFRRHFPYKENPGNKKKWQKALD-----YIAEHPEIIEILISGGDPLMAKDHELEWL 181 Query: 107 LNK 109 L + Sbjct: 182 LKR 184 >gnl|CDD|179152 PRK00881, purH, bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional. Length = 513 Score = 26.6 bits (60), Expect = 4.4 Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 1/21 (4%) Query: 101 VPLIQALNKRGFEIAVETNGT 121 V +AL + G EI + T GT Sbjct: 18 VEFAKALVELGVEI-LSTGGT 37 >gnl|CDD|116601 pfam07991, IlvN, Acetohydroxy acid isomeroreductase, catalytic domain. Acetohydroxy acid isomeroreductase catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine. Length = 165 Score = 26.7 bits (60), Expect = 5.1 Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 3/27 (11%) Query: 111 GFEIAVETNGTIEPPQGIDWICVSPKA 137 GF I G I+PP+ +D I V+PK Sbjct: 96 GFNIHF---GQIKPPKDVDVIMVAPKG 119 >gnl|CDD|183213 PRK11582, PRK11582, flagella biosynthesis protein FliZ; Provisional. Length = 169 Score = 26.5 bits (59), Expect = 5.7 Identities = 8/18 (44%), Positives = 9/18 (50%), Gaps = 1/18 (5%) Query: 33 NLWSGREQDRLSAQCRFC 50 N W + Q A CRFC Sbjct: 59 NGWQ-KLQQEWVALCRFC 75 >gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated. Length = 740 Score = 26.3 bits (58), Expect = 5.8 Identities = 8/32 (25%), Positives = 17/32 (53%) Query: 34 LWSGREQDRLSAQCRFCDTDFVGIQGTKGGRY 65 L G +D++ +C C +D + + +G R+ Sbjct: 579 LREGLREDKIIGKCPLCGSDLMVRRSKRGSRF 610 >gnl|CDD|180113 PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional. Length = 330 Score = 26.2 bits (59), Expect = 5.9 Identities = 9/18 (50%), Positives = 11/18 (61%) Query: 120 GTIEPPQGIDWICVSPKA 137 G I PP +D I V+PK Sbjct: 115 GQIVPPADVDVIMVAPKG 132 >gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional. Length = 1560 Score = 26.2 bits (57), Expect = 6.1 Identities = 9/12 (75%), Positives = 10/12 (83%) Query: 44 SAQCRFCDTDFV 55 S QC FCDTDF+ Sbjct: 731 SVQCVFCDTDFL 742 >gnl|CDD|129783 TIGR00700, GABAtrnsam, 4-aminobutyrate aminotransferase, prokaryotic type. Alternate names include GABA transaminase, gamma-amino-N-butyrate transaminase, and beta-alanine--oxoglutarate aminotransferase. Length = 420 Score = 25.6 bits (56), Expect = 8.8 Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 2/34 (5%) Query: 97 LQVDVPLIQALNKRGFEIAVETN--GTIEPPQGI 128 L+ P I + G IAVE GT EP G+ Sbjct: 336 LKAVDPRIGDVRGLGAMIAVELVDPGTTEPDAGL 369 >gnl|CDD|184040 PRK13412, fkp, bifunctional fucokinase/L-fucose-1-P-guanylyltransferase; Provisional. Length = 974 Score = 25.6 bits (56), Expect = 9.0 Identities = 7/27 (25%), Positives = 11/27 (40%) Query: 178 GPFLEENTNLAISYCFQNPKWRLSVQT 204 G EN L I W+L+ ++ Sbjct: 341 GKLTAENATLWIENSHVGEGWKLASRS 367 >gnl|CDD|180002 PRK05301, PRK05301, pyrroloquinoline quinone biosynthesis protein PqqE; Provisional. Length = 378 Score = 25.6 bits (57), Expect = 9.1 Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 1/24 (4%) Query: 90 LTGGEPLLQVDVP-LIQALNKRGF 112 +GGEPLL+ D+ L+ + G Sbjct: 68 FSGGEPLLRKDLEELVAHARELGL 91 >gnl|CDD|172997 PRK14531, PRK14531, adenylate kinase; Provisional. Length = 183 Score = 25.5 bits (56), Expect = 9.2 Identities = 10/22 (45%), Positives = 13/22 (59%) Query: 102 PLIQALNKRGFEIAVETNGTIE 123 PLI +RG +VE G+IE Sbjct: 151 PLIDHYRQRGLLQSVEAQGSIE 172 >gnl|CDD|184709 PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein; Provisional. Length = 229 Score = 25.7 bits (57), Expect = 9.9 Identities = 9/22 (40%), Positives = 13/22 (59%) Query: 55 VGIQGTKGGRYNVDQLADLIEE 76 + I K G +D+LADL+ E Sbjct: 121 LAIDDFKYGTEEIDELADLVLE 142 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 0.322 0.142 0.450 Gapped Lambda K H 0.267 0.0632 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,540,607 Number of extensions: 220474 Number of successful extensions: 434 Number of sequences better than 10.0: 1 Number of HSP's gapped: 431 Number of HSP's successfully gapped: 37 Length of query: 211 Length of database: 5,994,473 Length adjustment: 89 Effective length of query: 122 Effective length of database: 4,071,361 Effective search space: 496706042 Effective search space used: 496706042 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 (21.9 bits) S2: 55 (25.2 bits)