RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781147|ref|YP_003065560.1| transcriptional regulator [Candidatus Liberibacter asiaticus str. psy62] (83 letters) >gnl|CDD|28977 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.. Length = 58 Score = 46.7 bits (111), Expect = 1e-06 Identities = 19/57 (33%), Positives = 32/57 (56%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80 + +RKE LTQ+E+ + G ++S IS +E GK +++ + LA L L +L Sbjct: 2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58 >gnl|CDD|144828 pfam01381, HTH_3, Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI. Length = 55 Score = 42.9 bits (102), Expect = 2e-05 Identities = 16/51 (31%), Positives = 31/51 (60%) Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPL 77 + +R+E L+Q+E+ + G ++S IS++E GK +++ + LA L L Sbjct: 2 KELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSL 52 >gnl|CDD|33419 COG3620, COG3620, Predicted transcriptional regulator with C-terminal CBS domains [Transcription]. Length = 187 Score = 34.9 bits (80), Expect = 0.005 Identities = 15/32 (46%), Positives = 21/32 (65%) Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGK 58 R RKE +TQK++ R G +Q +I+ LE GK Sbjct: 11 RKRRKELGITQKDLARRAGVSQPYIARLEAGK 42 >gnl|CDD|31586 COG1396, HipB, Predicted transcriptional regulators [Transcription]. Length = 120 Score = 32.3 bits (71), Expect = 0.030 Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 1/64 (1%) Query: 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKS-TINIDNMIILAHTLDTPLWK 79 + +RK+ L+Q+E+ R G ++S IS +E G+S + +++ + LA L L + Sbjct: 1 SIGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDE 60 Query: 80 LLKP 83 LL+ Sbjct: 61 LLEE 64 >gnl|CDD|31665 COG1476, COG1476, Predicted transcriptional regulators [Transcription]. Length = 68 Score = 28.6 bits (64), Expect = 0.33 Identities = 13/54 (24%), Positives = 26/54 (48%) Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPL 77 N + +R E LTQ+E+ G ++ I +E GK +++ + +A + Sbjct: 4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTI 57 >gnl|CDD|31895 COG1709, COG1709, Predicted transcriptional regulator [Transcription]. Length = 241 Score = 27.9 bits (62), Expect = 0.69 Identities = 10/32 (31%), Positives = 18/32 (56%) Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGK 58 R R+ ++Q E+ G + S IS+ E+G+ Sbjct: 33 RKWREIFNVSQTELARELGVSPSVISDYESGR 64 >gnl|CDD|31615 COG1426, COG1426, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 284 Score = 25.8 bits (56), Expect = 2.9 Identities = 10/33 (30%), Positives = 18/33 (54%) Query: 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETGK 58 R R+E L+ +++ RT +S++ LE G Sbjct: 8 LRQAREEKGLSLEDVAARTKIRKSYLRALEEGN 40 >gnl|CDD|31384 COG1191, FliA, DNA-directed RNA polymerase specialized sigma subunit [Transcription]. Length = 247 Score = 24.9 bits (54), Expect = 4.5 Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 5/40 (12%) Query: 17 RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 RE+++ V R + +LTQKEI G ++S +S L Sbjct: 200 REKLVLVL-----RYKEELTQKEIAEVLGISESRVSRLHK 234 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 0.321 0.135 0.398 Gapped Lambda K H 0.267 0.0762 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,018,805 Number of extensions: 42462 Number of successful extensions: 116 Number of sequences better than 10.0: 1 Number of HSP's gapped: 116 Number of HSP's successfully gapped: 17 Length of query: 83 Length of database: 6,263,737 Length adjustment: 53 Effective length of query: 30 Effective length of database: 5,118,460 Effective search space: 153553800 Effective search space used: 153553800 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: 51 (23.4 bits)