RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780937|ref|YP_003065350.1| DNA-directed RNA polymerase subunit omega [Candidatus Liberibacter asiaticus str. psy62] (122 letters) >gnl|CDD|178998 PRK00392, rpoZ, DNA-directed RNA polymerase subunit omega; Reviewed. Length = 69 Score = 96.9 bits (242), Expect = 1e-21 Identities = 39/69 (56%), Positives = 48/69 (69%) Query: 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSP 60 MAR T+ED ++KVDNR+ LVLLA+ R R L GAKP VD DK V+ALREIA G ++ Sbjct: 1 MARPTIEDLLEKVDNRYELVLLAAKRARQLRAGAKPPVDKSSDKPVVIALREIAEGKVTY 60 Query: 61 DDLEEDFIH 69 + LEE I Sbjct: 61 EILEEVEIE 69 >gnl|CDD|161999 TIGR00690, rpoZ, DNA-directed RNA polymerase, omega subunit. The trusted cutoff excludes archaeal homologs but captures some organellar sequences. Length = 59 Score = 55.2 bits (133), Expect = 5e-09 Identities = 26/59 (44%), Positives = 38/59 (64%), Gaps = 1/59 (1%) Query: 2 ARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGK-DKNTVVALREIASGTLS 59 AR T+ED + K+ +R+ LVL+A+ R R L + + DK TV+ALREIA+G +S Sbjct: 1 ARPTIEDAMKKIGSRYDLVLVAARRARQLQLKGTDPIVPEENDKPTVIALREIAAGLVS 59 >gnl|CDD|184839 PRK14829, PRK14829, undecaprenyl pyrophosphate synthase; Provisional. Length = 243 Score = 27.1 bits (60), Expect = 1.2 Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 5/33 (15%) Query: 51 REIASGTLSPDDLEEDFIHSLQKHVEIDEPDSP 83 RE+ G +S D + E I + PD P Sbjct: 157 REVRDGKISGDRVTEKMISDH-----LYNPDMP 184 >gnl|CDD|183725 PRK12755, PRK12755, phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional. Length = 353 Score = 26.0 bits (58), Expect = 2.7 Identities = 6/19 (31%), Positives = 11/19 (57%) Query: 2 ARTTVEDCIDKVDNRFLLV 20 +R + D + D+R L+V Sbjct: 40 SRQAIADILHGRDDRLLVV 58 >gnl|CDD|184947 PRK14985, PRK14985, maltodextrin phosphorylase; Provisional. Length = 798 Score = 25.8 bits (57), Expect = 2.8 Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 2/46 (4%) Query: 30 LSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLE--EDFIHSLQK 73 L++G P KDK L+E+ SG S D + +HSL++ Sbjct: 690 LAKGYDPVKWRKKDKVLDAVLKELESGKYSDGDKHAFDQMLHSLKQ 735 >gnl|CDD|150933 pfam10337, DUF2422, Protein of unknown function (DUF2422). This is a family of proteins conserved in fungi. The function is not known. This family is the C-terminal half of some member proteins which contain the DUF2421 pfam10334 domain at their N-terminus. Length = 448 Score = 25.4 bits (56), Expect = 4.3 Identities = 7/20 (35%), Positives = 9/20 (45%) Query: 51 REIASGTLSPDDLEEDFIHS 70 E + G LS DDL+ Sbjct: 280 LEFSYGRLSADDLKTIRRLL 299 >gnl|CDD|165718 PLN00150, PLN00150, potassium ion transporter family protein; Provisional. Length = 779 Score = 24.8 bits (54), Expect = 5.0 Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%) Query: 61 DDLEEDFIHSLQKHVEID--EPDSPTENSDFSWHKPEALSFGQMSEGD 106 D+ E+ I SL++ +EI+ S E+ SW PE L S G Sbjct: 625 DNFEQLLIASLERFIEIESFREQSDLESMAASW-TPEELMGEGNSVGS 671 >gnl|CDD|162992 TIGR02739, TraF, type-F conjugative transfer system pilin assembly protein TraF. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm. Unlike the related protein TrbB (TIGR02738), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. Even more closely related than TrbB is a clade of genes (TIGR02740) which do contain the CXXC motif, but it is unclear whether these genes are involved in type-F conjugation systems per se. Length = 256 Score = 25.1 bits (55), Expect = 5.4 Identities = 12/31 (38%), Positives = 19/31 (61%) Query: 92 HKPEALSFGQMSEGDLLEGINNIVTPDKRDD 122 K L++G +S+ +L E I N++T KR D Sbjct: 225 QKMSPLAYGFISQDELKERILNVLTQFKRPD 255 >gnl|CDD|184096 PRK13505, PRK13505, formate--tetrahydrofolate ligase; Provisional. Length = 557 Score = 24.8 bits (55), Expect = 5.5 Identities = 12/25 (48%), Positives = 13/25 (52%), Gaps = 7/25 (28%) Query: 35 KPTVDVG-------KDKNTVVALRE 52 K TV VG K TV+ALRE Sbjct: 72 KSTVTVGLGDALNKIGKKTVIALRE 96 >gnl|CDD|150974 pfam10390, ELL, RNA polymerase II elongation factor ELL. ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF. Some members carry an Occludin domain pfam07303 just downstream. There is no S. cerevisiae member. Length = 285 Score = 24.7 bits (54), Expect = 6.3 Identities = 8/23 (34%), Positives = 14/23 (60%) Query: 71 LQKHVEIDEPDSPTENSDFSWHK 93 Q +++I PDSP+ FS++ Sbjct: 53 NQGYIKIPSPDSPSSVRTFSFYL 75 >gnl|CDD|162698 TIGR02093, P_ylase, glycogen/starch/alpha-glucan phosphorylases. This family consists of phosphorylases. Members use phosphate to break alpha 1,4 linkages between pairs of glucose residues at the end of long glucose polymers, releasing alpha-D-glucose 1-phosphate. The nomenclature convention is to preface the name according to the natural substrate, as in glycogen phosphorylase, starch phosphorylase, maltodextrin phosphorylase, etc. Name differences among these substrates reflect differences in patterns of branching with alpha 1,6 linkages. Members include allosterically regulated and unregulated forms. A related family, TIGR02094, contains examples known to act well on particularly small alpha 1,4 glucans, as may be found after import from exogenous sources. Length = 794 Score = 24.5 bits (54), Expect = 7.1 Identities = 18/63 (28%), Positives = 22/63 (34%), Gaps = 2/63 (3%) Query: 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDD--LEEDFIHSL 71 +N F+ L +G P D L I+SGT SP D L SL Sbjct: 672 ENIFIFGLTVEEVEALREKGYNPREYYEADPELKRVLDLISSGTFSPGDPGLFRPLYDSL 731 Query: 72 QKH 74 H Sbjct: 732 LNH 734 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 0.313 0.132 0.380 Gapped Lambda K H 0.267 0.0622 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,026,041 Number of extensions: 117727 Number of successful extensions: 172 Number of sequences better than 10.0: 1 Number of HSP's gapped: 171 Number of HSP's successfully gapped: 20 Length of query: 122 Length of database: 5,994,473 Length adjustment: 82 Effective length of query: 40 Effective length of database: 4,222,617 Effective search space: 168904680 Effective search space used: 168904680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (23.7 bits)