RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781196|ref|YP_003065609.1| DNA ligase, NAD-dependent [Candidatus Liberibacter asiaticus str. psy62] (119 letters) >gnl|CDD|128805 smart00532, LIGANc, Ligase N family. Length = 441 Score = 56.1 bits (136), Expect = 2e-09 Identities = 24/60 (40%), Positives = 31/60 (51%) Query: 59 AMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118 A E+ L K+ H YY LD P+ +D YDR+ L L+E+ PEL D P VG Sbjct: 1 AQKEISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELKTPDSPTQRVG 60 >gnl|CDD|181181 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated. Length = 665 Score = 55.1 bits (134), Expect = 4e-09 Identities = 25/61 (40%), Positives = 31/61 (50%) Query: 58 EAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTV 117 EA +E L + HH YY LD P +D YDR+ L AL+ + PEL D P V Sbjct: 4 EAKKRIEELREELNHHAYAYYVLDAPSISDAEYDRLYRELVALEAEHPELITPDSPTQRV 63 Query: 118 G 118 G Sbjct: 64 G 64 >gnl|CDD|161936 TIGR00575, dnlj, DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed. Length = 652 Score = 50.7 bits (122), Expect = 9e-08 Identities = 23/53 (43%), Positives = 28/53 (52%) Query: 66 LVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118 L K+ HH YY LD P +D YDR+ L L+E+ PEL D P VG Sbjct: 1 LRKLIRHHDYRYYVLDEPSISDAEYDRLYRELQELEEKHPELITPDSPTQRVG 53 >gnl|CDD|184640 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisional. Length = 689 Score = 42.8 bits (101), Expect = 2e-05 Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 1/68 (1%) Query: 51 VTSLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDE 110 V LS+ EA + E L + H YY +P+ D YD + RL AL++ F +L E Sbjct: 24 VEELSEDEAEEQAEQLREAIREHDHRYYVEADPVIADRAYDALFARLQALEDAF-DLDTE 82 Query: 111 DHPWNTVG 118 + P VG Sbjct: 83 NSPTRRVG 90 >gnl|CDD|181228 PRK08097, ligB, NAD-dependent DNA ligase LigB; Reviewed. Length = 562 Score = 30.7 bits (70), Expect = 0.10 Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 5/49 (10%) Query: 70 ALHHQ--KW---YYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHP 113 AL Q +W Y+R D +YD++ RL Q F D P Sbjct: 36 ALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLTQWQRCFGGPEPRDVP 84 >gnl|CDD|163456 TIGR03744, traC_PFL_4706, conjugative transfer ATPase, PFL_4706 family. Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves. Length = 893 Score = 27.7 bits (62), Expect = 0.76 Identities = 9/17 (52%), Positives = 12/17 (70%), Gaps = 2/17 (11%) Query: 98 DALQEQFPELFDEDHPW 114 DALQ+ F EL ++ PW Sbjct: 67 DALQDSFDEL--DEAPW 81 >gnl|CDD|172826 PRK14350, ligA, NAD-dependent DNA ligase LigA; Provisional. Length = 669 Score = 26.3 bits (58), Expect = 1.7 Identities = 17/52 (32%), Positives = 24/52 (46%) Query: 62 EVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHP 113 E+ L K+ K YY +P D YD+ RL L+ ++PE D P Sbjct: 8 EILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQELESKYPEYKTLDSP 59 >gnl|CDD|162228 TIGR01161, purK, phosphoribosylaminoimidazole carboxylase, PurK protein. Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, N5-carboxyaminoimidazole ribonucleotide synthetase, which hydrolyzes ATP and converts AIR to N5-CAIR. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Length = 352 Score = 25.8 bits (57), Expect = 2.6 Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 1/37 (2%) Query: 13 FENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAK 49 FE EH A +KL K P+ AL D+ Sbjct: 66 FEFEHVDVEA-LEKLEARGVKLFPSPDALAIIQDRLT 101 >gnl|CDD|183822 PRK12900, secA, preprotein translocase subunit SecA; Reviewed. Length = 1025 Score = 25.9 bits (57), Expect = 2.8 Identities = 11/43 (25%), Positives = 20/43 (46%) Query: 64 EYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPE 106 L I + +LDNP + + ++E LD L +++ E Sbjct: 55 GALEPIEQKKKDLEKKLDNPDISLEEAESINEELDTLAKEYEE 97 >gnl|CDD|118860 pfam10339, Vel1p, Velum formation protein. This is a small family of putative velum formation proteins found in fungi. They are of unknown function but are highly induced in zinc-depleted conditions and have increased expression in NAP1 deletion mutants. Length = 201 Score = 25.7 bits (56), Expect = 3.0 Identities = 16/82 (19%), Positives = 29/82 (35%), Gaps = 14/82 (17%) Query: 24 WKKLLTLEAKFLPNKRALESWLDKAKKVTSL------------SKGEAMIEVEYLVKIAL 71 + ++L E +F+P + + + L S +AMI V + Sbjct: 66 FARMLEQEPRFIPKLFTIAE--NDTANFSPLIFTTNIKTCNPQSIEDAMIPFANTVTGEI 123 Query: 72 HHQKWYYRLDNPLFTDGLYDRV 93 W DN F GL +++ Sbjct: 124 EFDAWADTADNASFITGLANQL 145 >gnl|CDD|184948 PRK14986, PRK14986, glycogen phosphorylase; Provisional. Length = 815 Score = 25.6 bits (56), Expect = 3.4 Identities = 13/32 (40%), Positives = 18/32 (56%) Query: 80 LDNPLFTDGLYDRVSERLDALQEQFPELFDED 111 L N L + G+YD V L+A+ EL DE+ Sbjct: 85 LSNALLSLGIYDDVQGALEAMGLDLEELIDEE 116 >gnl|CDD|147874 pfam05957, DUF883, Bacterial protein of unknown function (DUF883). This family consists of several hypothetical bacterial proteins of unknown function. Length = 94 Score = 25.2 bits (56), Expect = 3.8 Identities = 9/45 (20%), Positives = 15/45 (33%), Gaps = 17/45 (37%) Query: 91 DRVSERLDALQEQFPELFDE-----------------DHPWNTVG 118 +R LD +E+ + D ++PW VG Sbjct: 34 ERAEAALDDARERLGDAADAAAERARDAADAADDYVHENPWQAVG 78 >gnl|CDD|128619 smart00324, RhoGAP, GTPase-activator protein for Rho-like GTPases. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases. etter domain limits and outliers. Length = 174 Score = 25.3 bits (56), Expect = 3.8 Identities = 12/40 (30%), Positives = 15/40 (37%), Gaps = 9/40 (22%) Query: 80 LDNPLFTDGLYDR---------VSERLDALQEQFPELFDE 110 L PL LY+ +ERL AL+E L Sbjct: 70 LPEPLIPYELYEEFIEAAKVEDETERLRALRELISLLPPA 109 >gnl|CDD|181731 PRK09257, PRK09257, aromatic amino acid aminotransferase; Provisional. Length = 396 Score = 25.1 bits (56), Expect = 4.2 Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 7/27 (25%) Query: 17 HN-----ITPAQWKKL--LTLEAKFLP 36 HN +TP QW +L L E +P Sbjct: 182 HNPTGADLTPEQWDELAELLKERGLIP 208 >gnl|CDD|185028 PRK15068, PRK15068, tRNA mo(5)U34 methyltransferase; Provisional. Length = 322 Score = 25.2 bits (56), Expect = 4.7 Identities = 7/16 (43%), Positives = 13/16 (81%) Query: 34 FLPNKRALESWLDKAK 49 F+P+ AL++WL++A Sbjct: 251 FIPSVPALKNWLERAG 266 >gnl|CDD|177793 PLN00203, PLN00203, glutamyl-tRNA reductase. Length = 519 Score = 25.1 bits (55), Expect = 4.8 Identities = 8/16 (50%), Positives = 13/16 (81%) Query: 91 DRVSERLDALQEQFPE 106 +R ER+ AL+E+FP+ Sbjct: 297 NRSEERVAALREEFPD 312 >gnl|CDD|183163 PRK11498, bcsA, cellulose synthase catalytic subunit; Provisional. Length = 852 Score = 25.0 bits (55), Expect = 5.2 Identities = 8/12 (66%), Positives = 9/12 (75%) Query: 78 YRLDNPLFTDGL 89 +RLDNPL GL Sbjct: 492 FRLDNPLTGKGL 503 >gnl|CDD|163239 TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export. Length = 694 Score = 24.8 bits (55), Expect = 5.6 Identities = 11/37 (29%), Positives = 13/37 (35%), Gaps = 13/37 (35%) Query: 70 ALHHQKWYYR-------------LDNPLFTDGLYDRV 93 L YR L +PLF +YDRV Sbjct: 141 TLKESWPLYRDVLIASLLINLLALASPLFVMNVYDRV 177 >gnl|CDD|178811 PRK00035, hemH, ferrochelatase; Reviewed. Length = 333 Score = 24.4 bits (54), Expect = 7.0 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 6/51 (11%) Query: 61 IEVEYLVKIALHHQKWYYRL-----DNPLFTDGLYDRVSERLDALQEQFPE 106 I++EY +IA +R D+P F + L D V E L + Sbjct: 283 IDIEYR-EIAEEAGGEEFRRIPCLNDSPEFIEALADLVRENLQGWPPRLLG 332 >gnl|CDD|130387 TIGR01320, mal_quin_oxido, malate:quinone-oxidoreductase. This membrane-associated enzyme is an alternative to the better-known NAD-dependent malate dehydrogenase as part of the TCA cycle. The reduction of a quinone rather than NAD+ makes the reaction essentially irreversible in the direction of malate oxidation to oxaloacetate. Both forms of malate dehydrogenase are active in E. coli; disruption of this form causes less phenotypic change. In some bacteria, this form is the only or the more important malate dehydrogenase. Length = 483 Score = 24.4 bits (53), Expect = 7.1 Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 2/23 (8%) Query: 95 ERLDALQEQFPELFDEDHPWNTV 117 ER+ AL+E +PE D D W + Sbjct: 364 ERVSALREFYPEAIDSD--WELI 384 >gnl|CDD|179484 PRK02854, PRK02854, primosomal protein DnaI; Provisional. Length = 179 Score = 24.4 bits (53), Expect = 7.1 Identities = 8/16 (50%), Positives = 11/16 (68%) Query: 19 ITPAQWKKLLTLEAKF 34 +TPA+ +LL LE K Sbjct: 45 VTPARLAELLALEEKL 60 >gnl|CDD|162549 TIGR01828, pyru_phos_dikin, pyruvate, phosphate dikinase. This model represents pyruvate,phosphate dikinase, also called pyruvate,orthophosphate dikinase. It is similar in sequence to other PEP-utilizing enzymes. Length = 856 Score = 24.2 bits (53), Expect = 7.7 Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 1/38 (2%) Query: 77 YYRLDNPLFTDGLYDRVSERLDALQEQFPELF-DEDHP 113 Y + F GL + + E L L+E+ + F D ++P Sbjct: 48 EYYANGKQFPKGLQEEIKEALTLLEEKTGKKFGDTENP 85 >gnl|CDD|151766 pfam11325, DUF3127, Protein of unknown function (DUF3127). This bacterial family of proteins has no known function. Length = 84 Score = 24.1 bits (53), Expect = 8.7 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 5/57 (8%) Query: 24 WKK---LLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVEYLVKIALHHQKWY 77 WKK +L E ++ P K E W DK + SL+ G+ ++V + ++ + KW+ Sbjct: 21 WKKREFVLETEGQY-PQKICFEFWGDKIDLLDSLNVGD-EVKVSFDLEGREWNGKWF 75 >gnl|CDD|139424 PRK13247, PRK13247, dihydrobiliverdin:ferredoxin oxidoreductase; Provisional. Length = 238 Score = 24.2 bits (53), Expect = 8.8 Identities = 13/26 (50%), Positives = 17/26 (65%), Gaps = 1/26 (3%) Query: 83 PLFTDGLY-DRVSERLDALQEQFPEL 107 PL D Y DR E L +L+E+FP+L Sbjct: 102 PLVQDKDYLDRYFEGLKSLKERFPDL 127 >gnl|CDD|183961 PRK13304, PRK13304, L-aspartate dehydrogenase; Reviewed. Length = 265 Score = 23.8 bits (52), Expect = 9.7 Identities = 7/24 (29%), Positives = 16/24 (66%) Query: 45 LDKAKKVTSLSKGEAMIEVEYLVK 68 L+KA+ + S + +A + ++ LV+ Sbjct: 37 LEKAENLASKTGAKACLSIDELVE 60 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 0.135 0.419 Gapped Lambda K H 0.267 0.0710 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,014,369 Number of extensions: 114313 Number of successful extensions: 348 Number of sequences better than 10.0: 1 Number of HSP's gapped: 348 Number of HSP's successfully gapped: 41 Length of query: 119 Length of database: 5,994,473 Length adjustment: 81 Effective length of query: 38 Effective length of database: 4,244,225 Effective search space: 161280550 Effective search space used: 161280550 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 (23.5 bits)