RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781181|ref|YP_003065594.1| hypothetical protein CLIBASIA_05440 [Candidatus Liberibacter asiaticus str. psy62] (85 letters) >gnl|CDD|180635 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed. Length = 284 Score = 28.6 bits (65), Expect = 0.36 Identities = 14/36 (38%), Positives = 16/36 (44%), Gaps = 8/36 (22%) Query: 55 NSIMFLYPEQRQELAKRYKEKYND-------VLIHL 83 N I L E+ LAKR +E D VL HL Sbjct: 24 NKIPMLTAEEEYMLAKRLREH-GDLEAAKQLVLSHL 58 >gnl|CDD|162835 TIGR02392, rpoH_proteo, alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. Length = 270 Score = 26.5 bits (59), Expect = 1.8 Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 8/36 (22%) Query: 55 NSIMFLYPEQRQELAKRYKEKYND-------VLIHL 83 N I L PE+ +LAKR +E D VL HL Sbjct: 11 NRIPMLTPEEEYQLAKRLREH-GDLDAAKKLVLSHL 45 >gnl|CDD|183827 PRK12906, secA, preprotein translocase subunit SecA; Reviewed. Length = 796 Score = 25.4 bits (56), Expect = 3.1 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 10/55 (18%) Query: 28 LKRIVKVQKQAKSLANASQKLTVDQIDNSIMFLYPEQRQELAKRYK--EKYNDVL 80 LKR+ K+ + +L + +KL+ +Q+ E R K E +D+L Sbjct: 16 LKRLEKIADKVNALEDEYEKLSDEQLQAKTP--------EFRDRIKDGESLDDLL 62 >gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family. Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. Length = 319 Score = 25.4 bits (56), Expect = 3.1 Identities = 6/11 (54%), Positives = 8/11 (72%) Query: 23 NFGCPLKRIVK 33 N GCP+ +I K Sbjct: 95 NMGCPVPKITK 105 >gnl|CDD|177416 PHA02587, 30, DNA ligase; Provisional. Length = 488 Score = 24.3 bits (53), Expect = 7.3 Identities = 9/16 (56%), Positives = 10/16 (62%) Query: 60 LYPEQRQELAKRYKEK 75 L PEQ Q LA + EK Sbjct: 129 LIPEQPQMLASSFSEK 144 >gnl|CDD|150842 pfam10231, DUF2315, Uncharacterized conserved protein (DUF2315). This is a family of small conserved proteins found from worms to humans. The function is not known. Length = 127 Score = 24.4 bits (53), Expect = 7.3 Identities = 4/23 (17%), Positives = 9/23 (39%) Query: 57 IMFLYPEQRQELAKRYKEKYNDV 79 I+ PE L ++ + + Sbjct: 17 IVLHIPENETPLERKLRLLRQET 39 >gnl|CDD|183248 PRK11636, mrcA, penicillin-binding protein 1a; Provisional. Length = 850 Score = 24.3 bits (53), Expect = 7.9 Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 1/28 (3%) Query: 52 QIDNSIMFLYPEQRQELAKRYKEK-YND 78 +I S +L RQE+ RY E Y D Sbjct: 256 EIAFSAPYLSEMVRQEMYNRYGENAYED 283 >gnl|CDD|183692 PRK12704, PRK12704, phosphodiesterase; Provisional. Length = 520 Score = 24.0 bits (53), Expect = 9.5 Identities = 9/16 (56%), Positives = 12/16 (75%), Gaps = 2/16 (12%) Query: 67 ELAKRYKEKYNDVLIH 82 ELAK+YKE V+I+ Sbjct: 388 ELAKKYKES--PVVIN 401 >gnl|CDD|179016 PRK00419, PRK00419, DNA primase small subunit; Reviewed. Length = 376 Score = 23.8 bits (52), Expect = 9.9 Identities = 6/24 (25%), Positives = 11/24 (45%) Query: 62 PEQRQELAKRYKEKYNDVLIHLPD 85 R+ L R+++ Y + LP Sbjct: 3 ERTREYLKSRFRDYYRRAELPLPP 26 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 0.323 0.137 0.387 Gapped Lambda K H 0.267 0.0769 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,324,303 Number of extensions: 65703 Number of successful extensions: 219 Number of sequences better than 10.0: 1 Number of HSP's gapped: 219 Number of HSP's successfully gapped: 29 Length of query: 85 Length of database: 5,994,473 Length adjustment: 54 Effective length of query: 31 Effective length of database: 4,827,641 Effective search space: 149656871 Effective search space used: 149656871 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 50 (23.0 bits)