RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781218|ref|YP_003065631.1| hypothetical protein CLIBASIA_05625 [Candidatus Liberibacter asiaticus str. psy62] (205 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 = 54.4 bits (131), Expect = 2e-08 Identities = 21/58 (36%), Positives = 34/58 (58%) Query: 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172 G RLK +RK+KG++Q E + LG+ ST+S E G+ P ++ K+ + LD + Sbjct: 1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58 Score = 38.2 bits (89), Expect = 0.002 Identities = 17/58 (29%), Positives = 28/58 (48%) Query: 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI 90 G R+K++RK TQ+E+A S ++ ENG + S+ L +S D + Sbjct: 1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 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 = 52.1 bits (126), Expect = 1e-07 Identities = 18/55 (32%), Positives = 32/55 (58%) Query: 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172 LK +R++ G+SQ E + LG+ ST+S E G+ P ++ +K+ + LD + Sbjct: 1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55 Score = 29.4 bits (67), Expect = 0.69 Identities = 13/55 (23%), Positives = 25/55 (45%) Query: 36 IKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI 90 +K++R+ +Q+E+A S ++ ENG S+ L +S D + Sbjct: 1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55 >gnl|CDD|32767 COG2944, COG2944, Predicted transcriptional regulator [Transcription]. Length = 104 Score = 46.5 bits (110), Expect = 6e-06 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%) Query: 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKH 168 +K+IR+ G+SQ F + LG+ ST+ +EQGR P A K+ ++ + H Sbjct: 46 PTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPS-GAALKLLRIVQNH 98 >gnl|CDD|31665 COG1476, COG1476, Predicted transcriptional regulators [Transcription]. Length = 68 Score = 39.8 bits (93), Expect = 5e-04 Identities = 20/61 (32%), Positives = 37/61 (60%) Query: 117 RLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFGD 176 +LK +R + G++Q E KL+G+ T+ E+G+ P ++ A KI +V K ++ I+ + Sbjct: 5 KLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDIFQLE 64 Query: 177 E 177 E Sbjct: 65 E 65 Score = 27.5 bits (61), Expect = 2.8 Identities = 13/61 (21%), Positives = 27/61 (44%) Query: 34 TRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDG 93 ++K++R TQ+E+A + E G + S+ AL + + + + I+ Sbjct: 4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDIFQL 63 Query: 94 E 94 E Sbjct: 64 E 64 >gnl|CDD|31586 COG1396, HipB, Predicted transcriptional regulators [Transcription]. Length = 120 Score = 39.6 bits (90), Expect = 7e-04 Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 1/85 (1%) Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRT-IPEIKPARKIKQVTKKHLDWI 172 IG RLK +RK KG+SQ E + LG+ ST+S E+GR+ P ++ ++ LD + Sbjct: 2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDEL 61 Query: 173 YFGDEVIVPKSIKRAKGNQSSKKSK 197 +E + + + ++ + Sbjct: 62 LEEEEELEIEELNELAKLLLLEEEE 86 Score = 31.9 bits (70), Expect = 0.12 Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 1/85 (1%) Query: 31 DVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCST-SIRYALYLRNEYEISFDW 89 +G R+K++RK +Q+E+A S ++ E G + S+ L +S D Sbjct: 1 SIGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDE 60 Query: 90 IYDGEVIDRRYEDVTNKKRLDPYAI 114 + + E E K L Sbjct: 61 LLEEEEELEIEELNELAKLLLLEEE 85 >gnl|CDD|31998 COG1813, COG1813, Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]. Length = 165 Score = 37.3 bits (86), Expect = 0.003 Identities = 16/57 (28%), Positives = 29/57 (50%) Query: 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDW 171 G R++ R+ +G+SQ + L S + E+G P IK A+K++++ L Sbjct: 81 GERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVE 137 >gnl|CDD|31585 COG1395, COG1395, Predicted transcriptional regulator [Transcription]. Length = 313 Score = 34.1 bits (78), Expect = 0.028 Identities = 18/86 (20%), Positives = 43/86 (50%), Gaps = 9/86 (10%) Query: 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYF 174 G +L+ R++ G+S + +LG+ T+ YE+G + ++ A K++++ F Sbjct: 127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEI---------F 177 Query: 175 GDEVIVPKSIKRAKGNQSSKKSKKDK 200 G++++ P I + + + + D Sbjct: 178 GEDIVKPIDILKIPEDDIKLEEEPDD 203 >gnl|CDD|31895 COG1709, COG1709, Predicted transcriptional regulator [Transcription]. Length = 241 Score = 32.5 bits (74), Expect = 0.085 Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%) Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR-TIPEIKPARKI 161 G L+ R+ +SQ E + LG+ S +S+YE GR P I +K Sbjct: 28 PGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKF 76 >gnl|CDD|38608 KOG3398, KOG3398, KOG3398, Transcription factor MBF1 [Transcription]. Length = 135 Score = 32.0 bits (72), Expect = 0.11 Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 2/75 (2%) Query: 99 RYEDVTNKKRLD--PYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIK 156 + + T + D P +G ++ R KGMSQ + + + + +YE GR IP + Sbjct: 57 KLDRETEELGHDRVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQ 116 Query: 157 PARKIKQVTKKHLDW 171 K+++ L Sbjct: 117 ILSKMERALGVKLRG 131 >gnl|CDD|34409 COG4800, COG4800, Predicted transcriptional regulator with an HTH domain [Transcription]. Length = 170 Score = 29.6 bits (66), Expect = 0.66 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 1/47 (2%) Query: 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI 161 G+ L+ + + G++ EF K +P STL +G P +I Sbjct: 18 GSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKGSD-PRYDTLTRI 63 >gnl|CDD|32592 COG2522, COG2522, Predicted transcriptional regulator [General function prediction only]. Length = 119 Score = 29.1 bits (65), Expect = 0.95 Identities = 14/38 (36%), Positives = 21/38 (55%) Query: 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR 150 AI A L ++G+SQ KLLG+ + +S Y G+ Sbjct: 9 AIRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSGK 46 >gnl|CDD|31615 COG1426, COG1426, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 284 Score = 28.5 bits (63), Expect = 1.2 Identities = 11/37 (29%), Positives = 19/37 (51%) Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGR 150 +G RL+ R++KG+S + + S L E+G Sbjct: 4 LGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGN 40 >gnl|CDD|33419 COG3620, COG3620, Predicted transcriptional regulator with C-terminal CBS domains [Transcription]. Length = 187 Score = 27.6 bits (61), Expect = 2.3 Identities = 10/44 (22%), Positives = 23/44 (52%) Query: 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI 161 L+ RK+ G++Q + + G+ ++ E G+ P + ++I Sbjct: 10 LRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRI 53 >gnl|CDD|133048 cd06426, NTP_transferase_like_2, NTP_trnasferase_like_2 is a member of the nucleotidyl transferase family. This is a subfamily of nucleotidyl transferases. Nucleotidyl transferases transfer nucleotides onto phosphosugars. The activated sugars are precursors for synthesis of lipopolysaccharide, glycolipids and polysaccharides. Other subfamilies of nucleotidyl transferases include Alpha-D-Glucose-1-Phosphate Cytidylyltransferase, Mannose-1-phosphate guanyltransferase, and Glucose-1-phosphate thymidylyltransferase. Length = 220 Score = 26.7 bits (60), Expect = 4.1 Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 1/19 (5%) Query: 25 IRQYWKDVGTRIKDIRKAN 43 I +YW D+G R +D KAN Sbjct: 203 IHEYWLDIG-RPEDYEKAN 220 >gnl|CDD|36179 KOG0961, KOG0961, KOG0961, Predicted Zn2+-dependent endopeptidase, insulinase superfamily [Posttranslational modification, protein turnover, chaperones]. Length = 1022 Score = 26.2 bits (57), Expect = 6.0 Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 6/43 (13%) Query: 88 DWIYDGEVI-----DRR-YEDVTNKKRLDPYAIGARLKSIRKD 124 D DG + Y + K D + L+ I KD Sbjct: 681 DRKRDGCTVLSSAVASMLYGKNSLKISFDELVLEKLLEEISKD 723 >gnl|CDD|144176 pfam00483, NTP_transferase, Nucleotidyl transferase. This family includes a wide range of enzymes which transfer nucleotides onto phosphosugars. Length = 247 Score = 26.0 bits (58), Expect = 7.1 Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 1/22 (4%) Query: 28 YWKDVGTRIKDIRKANNKTQKE 49 YW DVGT + +AN K Sbjct: 227 YWSDVGT-WDSLWEANLKLLTG 247 >gnl|CDD|145863 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel transmembrane region. This family includes the four transmembrane helices that form the ion channel. Length = 228 Score = 26.1 bits (58), Expect = 7.1 Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 1/20 (5%) Query: 80 RNEY-EISFDWIYDGEVIDR 98 R+E+ E+ DW Y VIDR Sbjct: 191 RDEFDEVKEDWKYVAMVIDR 210 >gnl|CDD|58600 cd04234, AAK_AK, AAK_AK: Amino Acid Kinase Superfamily (AAK), Aspartokinase (AK); this CD includes the N-terminal catalytic domain of aspartokinase (4-L-aspartate-4-phosphotransferase;). AK is the first enzyme in the biosynthetic pathway of the aspartate family of amino acids (lysine, threonine, methionine, and isoleucine) and the bacterial cell wall component, meso-diaminopimelate. It also catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. One mechanism for the regulation of this pathway is by the production of several isoenzymes of aspartokinase with different repressors and allosteric inhibitors. Pairs of ACT domains are proposed to specifically bind amino acids leading to allosteric regulation of the enzyme. In Escherichia coli, three different aspartokinase isoenzymes are regulated specifically by lysine, methionine, and threonine. AK-HSDHI (ThrA) and AK-HSDHII (MetL) are bifunctional enzymes that consist of an N-terminal AK and a C-terminal homoserine dehydrogenase (HSDH). ThrA and MetL are involved in threonine and methionine biosynthesis, respectively. The third isoenzyme, AKIII (LysC), is monofunctional and is involved in lysine synthesis. The three Bacillus subtilis isoenzymes, AKI (DapG), AKII (LysC), and AKIII (YclM), are feedback-inhibited by meso-diaminopimelate, lysine, and lysine plus threonine, respectively. The E. coli lysine-sensitive AK is described as a homodimer, whereas, the B. subtilis lysine-sensitive AK is described as a heterodimeric complex of alpha- and beta- subunits that are formed from two in-frame overlapping genes. A single AK enzyme type has been described in Pseudomonas, Amycolatopsis, and Corynebacterium. The fungal aspartate pathway is regulated at the AK step, with L-Thr being an allosteric inhibitor of the Saccharomyces cerevisiae AK (Hom3). At least two distinct AK isoenzymes can occur in higher plants, one is a monofunctional lysine-sensitive isoenzyme, which is involved in the overall regulation of the pathway and can be synergistically inhibited by S-adenosylmethionine. The other isoenzyme is a bifunctional, threonine-sensitive AK-HSDH protein. Also included in this CD is the catalytic domain of the Methylomicrobium alcaliphilum ectoine AK, the first enzyme of the ectoine biosynthetic pathway, found in this bacterium, and several other halophilic/halotolerant bacteria.. Length = 227 Score = 25.5 bits (56), Expect = 9.7 Identities = 9/38 (23%), Positives = 21/38 (55%), Gaps = 1/38 (2%) Query: 155 IKPARKIKQVTKKHLDWI-YFGDEVIVPKSIKRAKGNQ 191 + AR I +++ + YFG +V+ P++++ A+ Sbjct: 171 VPEARLIPEISYDEALELAYFGAKVLHPRAVEPARKAN 208 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 0.315 0.133 0.379 Gapped Lambda K H 0.267 0.0718 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,410,994 Number of extensions: 120753 Number of successful extensions: 276 Number of sequences better than 10.0: 1 Number of HSP's gapped: 276 Number of HSP's successfully gapped: 34 Length of query: 205 Length of database: 6,263,737 Length adjustment: 89 Effective length of query: 116 Effective length of database: 4,340,536 Effective search space: 503502176 Effective search space used: 503502176 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 55 (25.0 bits)