RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

Searching..................................................done

Query= gi|254780282|ref|YP_003064695.1| putative transcription
regulator protein [Candidatus Liberibacter asiaticus str. psy62]
         (299 letters)



>gnl|CDD|182990 PRK11139, PRK11139, DNA-binding transcriptional activator GcvA;
           Provisional.
          Length = 297

 Score =  108 bits (271), Expect = 2e-24
 Identities = 80/298 (26%), Positives = 134/298 (44%), Gaps = 33/298 (11%)

Query: 8   LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLH 67
           LR F   AR  SFT AAE+L ++Q+++S QI  LE  +G+KLF R  R L LTE+G +  
Sbjct: 11  LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYF 70

Query: 68  RVTSEVYHKL-ETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQL 126
               E++ +L E T+ +L+  S K +  L ++         L   L  F   +PDI ++L
Sbjct: 71  LDIREIFDQLAEATR-KLRARSAKGA--LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRL 127

Query: 127 ILDNKDIDISMDYADCAIRL---RKP-IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLS 182
              ++  D   D  D AIR      P ++   L+   L+ +      +P  L   +   +
Sbjct: 128 KAVDRLEDFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLLPV-----CSPALLNGGKPLKT 182

Query: 183 IQELDKHNLITFGDLIPKCMEDF-NW-----LATVDRPIGEPRISCLQVNSYLSIMQYCV 236
            ++L +H L+          ED+  W     L  ++   G P  S    +S +++ Q  +
Sbjct: 183 PEDLARHTLLHDDS-----REDWRAWFRAAGLDDLNVQQG-PIFS----HSSMAL-QAAI 231

Query: 237 LGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIF 291
            G G+AL    + +       LV   + V+      Y   P++     K+ AFR ++ 
Sbjct: 232 HGQGVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLL 289


>gnl|CDD|132382 TIGR03339, phn_lysR, aminoethylphosphonate catabolism associated
           LysR family transcriptional regulator.  This group of
           sequences represents a number of related clades with
           numerous examples of members adjacent to operons for the
           degradation of 2-aminoethylphosphonate (AEP) in
           Pseudomonas, Ralstonia, Bordetella and Burkholderia
           species. These are transcriptional regulators of the
           LysR family which contain a helix-turn-helix (HTH)
           domain (pfam00126) and a periplasmic substrate-binding
           protein-like domain (pfam03466).
          Length = 279

 Score = 99.4 bits (248), Expect = 9e-22
 Identities = 68/254 (26%), Positives = 117/254 (46%), Gaps = 15/254 (5%)

Query: 7   KLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL 66
           +L+ F+ VAR GSFT AAE+L LSQ +++ Q+  LE   G++LF+R+ R L LT+ G +L
Sbjct: 1   QLKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRL 60

Query: 67  HRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQL 126
             +   ++ +    +  L+ES     G LRIA T       +   +  F   YP I++ +
Sbjct: 61  LPIVERLFQQEAEAEFLLRESGALREGSLRIAAT---APYYVLDLVARFRQRYPGIEVSV 117

Query: 127 ILDNKDIDIS--MDY-ADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSI 183
            + N    +     Y  D A+          L +  L    + A     +    RE +++
Sbjct: 118 RIGNSQEVLQALQSYRVDVAVSSEVV-DDPRLDRVVLGNDPLVAVVHRQHPLAERESVTL 176

Query: 184 QELDKHNLI--TFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI 241
           +EL    L+    G +  +  E+    A V      PR   L++ S  +I +  + G G+
Sbjct: 177 EELAGQPLLMREPGSVTRQTTEEALAAAGV-----APR-PALEIGSREAIREAVLAGLGV 230

Query: 242 ALLPDYIVKDNPNL 255
           +++    V  +P L
Sbjct: 231 SVVSAAEVGRDPRL 244


>gnl|CDD|132459 TIGR03418, chol_sulf_TF, putative choline sulfate-utilization
           transcription factor.  Members of this protein family
           are transcription factors of the LysR family. Their
           genes typically are divergently transcribed from
           choline-sulfatase genes. That enzyme makes choline, a
           precursor to the osmoprotectant glycine-betaine,
           available by hydrolysis of choline sulfate.
          Length = 291

 Score = 94.8 bits (236), Expect = 2e-20
 Identities = 81/301 (26%), Positives = 129/301 (42%), Gaps = 28/301 (9%)

Query: 4   DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
               LRVF   AR  SFT AA +L  +Q ++S+Q+  LE E+G  LF R  RG+ LTE G
Sbjct: 2   SLQALRVFESAARLASFTAAARELGSTQPAVSQQVKRLEEELGTPLFERGHRGIELTEDG 61

Query: 64  SKLHRVTSEVYHKLETTQIELQE-SSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDI 122
            +L      V   L+T  +   +  + +    L +AT        L   L  F    PD+
Sbjct: 62  QRLFEA---VRAGLDTIDLATAQLRARREHETLTLATDFAFATYWLMPRLHRFKRAMPDV 118

Query: 123 QIQLILDNKDIDISMDYADCAIRL---RKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCRE 179
            + L+     +D   D  D AI     R P   +  +  + VT       +P  L     
Sbjct: 119 DVSLVTSQDSLDPQRDDIDVAILFGDGRWPGGEAHRLFSEEVT----PVCSPALLAARAT 174

Query: 180 PLSIQELDKHNLITFGDLIPKCMED-FNWLA-----TVDRPIGEPRISCLQVNSYLSIMQ 233
           PLS  +L +  L+    L P      F+W        ++RP   P    L  N+Y  ++Q
Sbjct: 175 PLSAADLLRLPLL---HLEPTQPARWFDWAGWFDAHGLERP---PAPGGLTFNNYTLVIQ 228

Query: 234 YCVLGSGIAL----LPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNF 289
             + G G+AL    L D +++    LVR++++ +      Y   P   +    ++ FR++
Sbjct: 229 AAIGGQGVALGWAPLVDELLEAG-QLVRLIDEPVVTERGYYLVRPPRKRRGPAVRRFRDW 287

Query: 290 I 290
           +
Sbjct: 288 L 288


>gnl|CDD|182231 PRK10086, PRK10086, DNA-binding transcriptional regulator DsdC;
           Provisional.
          Length = 311

 Score = 94.7 bits (236), Expect = 3e-20
 Identities = 54/181 (29%), Positives = 88/181 (48%), Gaps = 8/181 (4%)

Query: 7   KLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL 66
           KL  F V AR  SF  AA++L L+ S++S +I+ LE E+GIKLF R  R + LTE+G   
Sbjct: 18  KLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGK-- 75

Query: 67  HRVTSEVYHKLETTQIELQE-SSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQ 125
            RV   +   L+T   E+ +  + + SG L + +   + Q  L   L +F   YP I + 
Sbjct: 76  -RVFWALKSSLDTLNQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLT 134

Query: 126 LILDNKDIDISMDYADCAI----RLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPL 181
           ++  N++++      D AI         +    L+  +++ +    YA  H L    + L
Sbjct: 135 ILTGNENVNFQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAERHALTGNPDNL 194

Query: 182 S 182
            
Sbjct: 195 R 195


>gnl|CDD|182085 PRK09801, PRK09801, transcriptional activator TtdR; Provisional.
          Length = 310

 Score = 94.3 bits (234), Expect = 3e-20
 Identities = 73/287 (25%), Positives = 135/287 (47%), Gaps = 9/287 (3%)

Query: 8   LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLH 67
           L+V   +  SGSF+ AA  L  + + ++++I  LE  +   L  R ARG+ LTE G + +
Sbjct: 11  LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCY 70

Query: 68  RVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLI 127
               E+  + +    ++ +   +P G +RI  +   G++ +   + E +  YP++Q+   
Sbjct: 71  EHALEILTQYQRLVDDVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFE 130

Query: 128 LDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELD 187
           L ++ ID+  D  D  IR+   I     I   L        AAP YL+   +P S+QEL 
Sbjct: 131 LFDRQIDLVQDNIDLDIRINDEI-PDYYIAHLLTKNKRILCAAPEYLQKYPQPQSLQELS 189

Query: 188 KHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISC-LQVNSYLSIMQYCVLGSGIALLPD 246
           +H+ +   +   + M    W     +     ++S  L  NS   ++Q+ + G GI L  +
Sbjct: 190 RHDCLVTKE---RDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSE 246

Query: 247 YIVK---DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
           + V    ++  LV+++ +    S  ++  Y E L  + KL+    F+
Sbjct: 247 WDVLPFLESGKLVQVLPEY-AQSANIWAVYREPLYRSMKLRVCVEFL 292


>gnl|CDD|182601 PRK10632, PRK10632, transcriptional regulator; Provisional.
          Length = 309

 Score = 94.1 bits (234), Expect = 4e-20
 Identities = 73/249 (29%), Positives = 110/249 (44%), Gaps = 30/249 (12%)

Query: 10  VFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRV 69
           VF  V   GSFT AA QL +S SSIS+ +S LE E+ +KL  R  R + LTE G   ++ 
Sbjct: 9   VFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQG 68

Query: 70  TSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILD 129
              + H+++    +L   +  P G LRI  +  + QN+L G   + L  YP + + L+  
Sbjct: 69  CRRMLHEVQDVHEQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTG 128

Query: 130 NKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKH 189
               D+  D  D  IR+   +Q SSL  R+L  + M   AA  YL     P         
Sbjct: 129 IPAPDLIADGLDVVIRV-GALQDSSLFSRRLGAMPMVVCAAKSYLAQYGTPEK------- 180

Query: 190 NLITFGDLIPKCMEDFNWLATVDRPIGE-----PRISCLQV--------NSYLSIMQYCV 236
                    P  +   +WL    RP  E     P     ++        N   +++++  
Sbjct: 181 ---------PADLSSHSWLEYSVRPDNEFELIAPEGISTRLIPQGRFVTNDPQTLVRWLT 231

Query: 237 LGSGIALLP 245
            G+GIA +P
Sbjct: 232 AGAGIAYVP 240


>gnl|CDD|131091 TIGR02036, dsdC, D-serine deaminase transcriptional activator.
           This family, part of the LysR family of transcriptional
           regulators, activates transcription of the gene for
           D-serine deaminase, dsdA. Trusted members of this family
           so far are found adjacent to dsdA and only in
           Gammaproteobacteria, including E. coli, Vibrio cholerae,
           and Colwellia psychrerythraea.
          Length = 302

 Score = 81.1 bits (200), Expect = 3e-16
 Identities = 49/145 (33%), Positives = 74/145 (51%), Gaps = 6/145 (4%)

Query: 2   SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61
           SF   K+  F V AR  SF+ AAE+L L+ S+IS +I+ LE E+GI+LF R  R + LT 
Sbjct: 7   SFQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGIQLFVRSHRKVELTH 66

Query: 62  QGSKLHRVTSEVYHKL--ETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLY 119
           +G +++         L  E   I+ QE     SG L + +     Q  L   + +F   Y
Sbjct: 67  EGKRIYWALKSSLDTLNQEILDIKNQEL----SGTLTLYSRPSFAQCWLVPRIGDFTRRY 122

Query: 120 PDIQIQLILDNKDIDISMDYADCAI 144
           P I + ++  N++I+      D AI
Sbjct: 123 PSISLTVLTGNENINFQGAGIDVAI 147


>gnl|CDD|184959 PRK14997, PRK14997, LysR family transcriptional regulator;
           Provisional.
          Length = 301

 Score = 80.8 bits (199), Expect = 4e-16
 Identities = 50/185 (27%), Positives = 85/185 (45%), Gaps = 6/185 (3%)

Query: 3   FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62
           F W     F  V   G F  A   L   +S +SR+I+ LE  +G++L  R  R   +TE 
Sbjct: 7   FAW-----FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEV 61

Query: 63  GSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDI 122
           G   +     +  + +  Q  +    V+P G +++   + L    +   L +F+  YPD+
Sbjct: 62  GQTFYEHCKAMLVEAQAAQDAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDV 121

Query: 123 QIQLILDNKDIDISMDYADCAIRLR-KPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPL 181
            +QL   N+ +D+  +  D AIR+R +P + S L+ R L       +A+P  +     P 
Sbjct: 122 SLQLEATNRRVDVVGEGVDVAIRVRPRPFEDSDLVMRVLADRGHRLFASPDLIARMGIPS 181

Query: 182 SIQEL 186
           +  EL
Sbjct: 182 APAEL 186


>gnl|CDD|183051 PRK11242, PRK11242, DNA-binding transcriptional regulator CynR;
           Provisional.
          Length = 296

 Score = 78.8 bits (195), Expect = 2e-15
 Identities = 75/274 (27%), Positives = 114/274 (41%), Gaps = 47/274 (17%)

Query: 8   LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLH 67
           +R F  VA  G+FT AAE LH+SQ ++S+QI  LE  +G++LF R  R + LT+ G    
Sbjct: 6   IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYL 65

Query: 68  RVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQI--- 124
           R        LE  +  + + +    G LR+A T      L+   +  F   YP I +   
Sbjct: 66  RYARRALQDLEAGRRAIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIR 125

Query: 125 ---------QLILDNKDIDISMDYADCAIRLRKP-IQSSSLI--QRKLVTIHMHAYAAPH 172
                     L  D  D+ I+            P I++  L      LV    H  AA  
Sbjct: 126 EMSQERIEALLADDELDVGIAFAPV------HSPEIEAQPLFTETLALVVGRHHPLAA-- 177

Query: 173 YLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLAT---VDRPIGE----PRISCLQV 225
                R+ L++ EL    L+           +F   AT   +DR        PR++ ++ 
Sbjct: 178 ----RRKALTLDELADEPLVLLSA-------EF---ATREQIDRYFRRHGVTPRVA-IEA 222

Query: 226 NSYLSIMQYCVLGSGIA-LLPDYIVKDNPNLVRI 258
           NS +S +   V    +A LLP  I +++  L  I
Sbjct: 223 NS-ISAVLEIVRRGRLATLLPAAIAREHDGLCAI 255


>gnl|CDD|183679 PRK12682, PRK12682, transcriptional regulator CysB-like protein;
           Reviewed.
          Length = 309

 Score = 76.2 bits (188), Expect = 1e-14
 Identities = 66/265 (24%), Positives = 110/265 (41%), Gaps = 22/265 (8%)

Query: 21  THAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-LTEQGSKLHRVTSEVYHKLET 79
           T AA+ LH SQ  +S+ I  LE E+GI++F RH + L  LTE G  +  V   +  ++  
Sbjct: 20  TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLTEPGKAVLDVIERILREVGN 79

Query: 80  TQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISM-- 137
            +    + S + SG L IATT    + +L   +  F   YP + + L   + D    M  
Sbjct: 80  IKRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVI 139

Query: 138 -DYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAP--HYLKNCREPLSIQELDKHNLITF 194
              AD  I          L          HA   P  H L    E +++++L ++ LIT+
Sbjct: 140 SGEADIGIATESLADDPDLATLPCYDWQ-HAVIVPPDHPLA-QEERITLEDLAEYPLITY 197

Query: 195 GDLIPKCMEDFNWLATVDRPIG----EPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVK 250
                     F   + +DR       +P I    ++S + I  Y  LG G+ ++ +   +
Sbjct: 198 H-------PGFTGRSRIDRAFAAAGLQPDIVLEAIDSDV-IKTYVRLGLGVGIVAEMAYR 249

Query: 251 D--NPNLVRIMEDVITPSFTVYFCY 273
              + +LV +    +    T +   
Sbjct: 250 PDRDGDLVALPAGHLFGPNTAWVAL 274


>gnl|CDD|185048 PRK15092, PRK15092, DNA-binding transcriptional repressor LrhA;
           Provisional.
          Length = 310

 Score = 68.1 bits (167), Expect = 3e-12
 Identities = 72/287 (25%), Positives = 119/287 (41%), Gaps = 57/287 (19%)

Query: 1   MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT 60
           ++ D D LR F  VA   +F  AA  +  +QS++S+Q+  LE  VG +LF RH R   LT
Sbjct: 9   INLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLT 68

Query: 61  EQG-------SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLK 113
           E G        K+ R   E    L  + ++         G L I  + D    +L   L 
Sbjct: 69  EHGIQLLGYARKILRFNDEACSSLMYSNLQ---------GVLTIGASDDTADTILPFLLN 119

Query: 114 EFLLLYP----DIQIQL------ILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTI 163
               +YP    D++++       +L+++++D+       A+   +P    +L  R   T 
Sbjct: 120 RVSSVYPKLALDVRVKRNAFMMEMLESQEVDL-------AVTTHRPSSFPALNLR---TS 169

Query: 164 HMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFN--W-LATVDRPIGEPRI 220
               Y A  Y+    EP+ +  LD+ +   F D+    +      W +A V   +   R 
Sbjct: 170 PTLWYCAAEYVLQKGEPIPLVLLDEPS--PFRDMALATLNAAGIPWRIAYVASTLSAVRA 227

Query: 221 SCLQVNSYLSIM---------QYCVLGS--GIALLPD--YIVKDNPN 254
           +   V + L +             VLG   G+  LPD  Y++  +PN
Sbjct: 228 A---VKAGLGVTARPVEMMSPDLRVLGESEGLPPLPDTEYLLCRDPN 271


>gnl|CDD|182137 PRK09906, PRK09906, DNA-binding transcriptional regulator HcaR;
           Provisional.
          Length = 296

 Score = 67.5 bits (165), Expect = 4e-12
 Identities = 70/293 (23%), Positives = 114/293 (38%), Gaps = 54/293 (18%)

Query: 8   LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLH 67
           LR F  VA   +FT AAE+LH +Q S+S+QI  LE  VG+ L  R  R + LT  G    
Sbjct: 6   LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAG---- 61

Query: 68  RVTSEVYHKLETTQIELQESS---------VKPSGKLRIATTIDLGQNLLQGNLKEFLLL 118
               EV+  L+  +  L+++          V+   +L I        NLL   L  F L 
Sbjct: 62  ----EVF--LQDARAILEQAEKAKLRARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLR 115

Query: 119 YPDIQIQLI----------LDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAY 168
           +PD  I+L+          L   ++D+          +R P+ S   I    +       
Sbjct: 116 HPDTLIELVSLITTQQEEKLRRGELDVGF--------MRHPVYSDE-IDYLELLDEPLVV 166

Query: 169 AAP--HYLKNCREPLSIQELDKHNLIT----FGDLIPKCMEDFNWLATVDRPIGEPRISC 222
             P  H L +  + ++  +LD  N I+    +   +   ++ +         I       
Sbjct: 167 VLPVDHPLAHE-KEITAAQLDGVNFISTDPAYSGSLAPIIKAWFAQHNSQPNI------- 218

Query: 223 LQV-NSYLSIMQYCVLGSGIALLPDYIVKDNP-NLVRIMEDVITPSFTVYFCY 273
           +QV  + L  M    +G G  ++P Y+   N   +V        PS  +   +
Sbjct: 219 VQVATNILVTMNLVGMGLGCTIIPGYMNNFNTGQVVFRPLAGNVPSIALLMAW 271


>gnl|CDD|182237 PRK10094, PRK10094, DNA-binding transcriptional activator AllS;
          Provisional.
          Length = 308

 Score = 67.1 bits (164), Expect = 5e-12
 Identities = 34/84 (40%), Positives = 48/84 (57%)

Query: 3  FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62
          FD + LR F  VA +GSF+ AAE+L  + ++IS +I  LE   G+ LF+R  R +TLT  
Sbjct: 2  FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAA 61

Query: 63 GSKLHRVTSEVYHKLETTQIELQE 86
          G  L     +    LE+   ELQ+
Sbjct: 62 GEHLLSQARDWLSWLESMPSELQQ 85


>gnl|CDD|183681 PRK12684, PRK12684, transcriptional regulator CysB-like protein;
           Reviewed.
          Length = 313

 Score = 65.0 bits (159), Expect = 2e-11
 Identities = 52/199 (26%), Positives = 89/199 (44%), Gaps = 19/199 (9%)

Query: 8   LRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-LTEQGSK 65
           LR      R   + T AA+ L+ SQ  +S+ I  LE E+G+++F RH + L  LTE G  
Sbjct: 6   LRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEPGRI 65

Query: 66  LHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQ 125
           +      +  ++E  +   +E + +  G L IATT    +  L   +KEF   YP +++ 
Sbjct: 66  ILASVERILQEVENLKRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLS 125

Query: 126 LILDN-KDID--ISMDYADCAIRLRKPIQSSSLI-------QRKLVTIHMHAYAAPHYLK 175
           ++  +   I   +    AD AI          L+          +V    H         
Sbjct: 126 ILQGSPTQIAEMVLHGQADLAIATEAIADYKELVSLPCYQWNHCVVVPPDHPLLE----- 180

Query: 176 NCREPLSIQELDKHNLITF 194
             R+PL++++L ++ LIT+
Sbjct: 181 --RKPLTLEDLAQYPLITY 197


>gnl|CDD|182077 PRK09791, PRK09791, putative DNA-binding transcriptional regulator;
           Provisional.
          Length = 302

 Score = 64.8 bits (158), Expect = 2e-11
 Identities = 30/121 (24%), Positives = 70/121 (57%)

Query: 7   KLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL 66
           ++R F  VAR GS   A+  L++SQ ++++ I  LE  +  +LF+R ++G+TLT+ G   
Sbjct: 9   QIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESF 68

Query: 67  HRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQL 126
           ++  S +  +L   Q ++++   + +G++ I     + ++L+   +  F   +P +++++
Sbjct: 69  YQHASLILEELRAAQEDIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRI 128

Query: 127 I 127
           +
Sbjct: 129 M 129


>gnl|CDD|183288 PRK11716, PRK11716, DNA-binding transcriptional regulator IlvY;
           Provisional.
          Length = 269

 Score = 63.3 bits (155), Expect = 8e-11
 Identities = 31/99 (31%), Positives = 51/99 (51%)

Query: 28  HLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQES 87
           H+S S++SRQI  LE E+G  LF R  R +TLTE G +L     +   + +  +  L + 
Sbjct: 2   HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQ 61

Query: 88  SVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQL 126
               SG+L +  ++    + L   L  F   +P ++I+L
Sbjct: 62  GPSLSGELSLFCSVTAAYSHLPPILDRFRAEHPLVEIKL 100


>gnl|CDD|182768 PRK10837, PRK10837, putative DNA-binding transcriptional regulator;
           Provisional.
          Length = 290

 Score = 62.8 bits (153), Expect = 9e-11
 Identities = 51/185 (27%), Positives = 92/185 (49%), Gaps = 13/185 (7%)

Query: 7   KLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL 66
           +L VF  V +SGS T A+  L LSQS++S  ++ LE ++G++LF R  + L + E G  L
Sbjct: 7   QLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLL 66

Query: 67  H-RVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQ 125
           + R  + +   +E  Q+  ++     +G LRI  +  +G  +L   +  +   YP + ++
Sbjct: 67  YPRALALLEQAVEIEQLFRED-----NGALRIYASSTIGNYILPAMIARYRRDYPQLPLE 121

Query: 126 LILDNKDIDISMDYADCAIRL---RKPIQSSSLIQRKLVTIHMHAYAAP-HYLKNCREPL 181
           L + N   D+     D  + +     P  S  LI    +   +  +AAP   L   R P+
Sbjct: 122 LSVGNSQ-DVINAVLDFRVDIGLIEGPCHSPELISEPWLEDELVVFAAPDSPL--ARGPV 178

Query: 182 SIQEL 186
           ++++L
Sbjct: 179 TLEQL 183


>gnl|CDD|183676 PRK12679, cbl, transcriptional regulator Cbl; Reviewed.
          Length = 316

 Score = 62.9 bits (153), Expect = 1e-10
 Identities = 85/324 (26%), Positives = 133/324 (41%), Gaps = 62/324 (19%)

Query: 1   MSFDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-RGLT 58
           M+F   +L++    AR   + T  A  L  SQS +SR I  LE E+GI++F R   R L 
Sbjct: 1   MNFQ--QLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLG 58

Query: 59  LTEQGSKL----HRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKE 114
           +TE G  L     R+ +E  +      +   ++    SG L IATT    +  L   +K 
Sbjct: 59  MTEPGKALLVIAERILNEASNVRRLADLFTNDT----SGVLTIATTHTQARYSLPEVIKA 114

Query: 115 FLLLYPDIQIQLILDNKDIDISM---DYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAP 171
           F  L+P+++++LI        ++     AD  I   +      L+       H H+   P
Sbjct: 115 FRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVAFPWFRWH-HSLLVP 173

Query: 172 --HYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRI------SCL 223
             H L     PL+++ + K  LIT+   I                 G  RI        L
Sbjct: 174 HDHPLTQ-ITPLTLESIAKWPLITYRQGI----------------TGRSRIDDAFARKGL 216

Query: 224 QVNSYLS------IMQYCVLGSGIALLPDYIVKDNP--NLVRIMEDVITPSFTVYFCYPE 275
             +  LS      I  Y  LG GI L+ +    +    NL+R+    +  + TV+     
Sbjct: 217 LADIVLSAQDSDVIKTYVALGLGIGLVAEQSSGEQEESNLIRLDTRHLFDANTVWL---- 272

Query: 276 ALKNTGKLKAFRNFIFLKARDWKF 299
            LK  G+L+  RN++      W+F
Sbjct: 273 GLKR-GQLQ--RNYV------WRF 287


>gnl|CDD|182391 PRK10341, PRK10341, DNA-binding transcriptional activator TdcA;
           Provisional.
          Length = 312

 Score = 63.0 bits (153), Expect = 1e-10
 Identities = 31/119 (26%), Positives = 58/119 (48%)

Query: 8   LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLH 67
           L VF  V RSGS   AA++L L+Q ++S+ I+ +E   G++L  R   G+TLT  G  L 
Sbjct: 12  LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLL 71

Query: 68  RVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQL 126
             +  +  +++    E+   S +    +       +G   +   + +F  ++P  Q+ +
Sbjct: 72  SRSESITREMKNMVNEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSM 130


>gnl|CDD|183680 PRK12683, PRK12683, transcriptional regulator CysB-like protein;
           Reviewed.
          Length = 309

 Score = 62.4 bits (152), Expect = 1e-10
 Identities = 53/210 (25%), Positives = 101/210 (48%), Gaps = 29/210 (13%)

Query: 1   MSFDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT- 58
           M+F   +LR+     R   + T  A  L+ SQS +S+QI  LE E+G+++F R  + LT 
Sbjct: 1   MNFQ--QLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTG 58

Query: 59  LTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLL 118
           LTE G +L ++   +    E  +   ++ + + SG L +ATT    +  L   +++F  +
Sbjct: 59  LTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEV 118

Query: 119 YPDIQI-----------QLILDNK-DIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMH 166
           +P + +           +++L+ + DI I+ +  D         +   L+     + H H
Sbjct: 119 FPKVHLALRQGSPQEIAEMLLNGEADIGIATEALD---------REPDLVSFPYYSWH-H 168

Query: 167 AYAAP--HYLKNCREPLSIQELDKHNLITF 194
               P  H L   RE L+++ + ++ +IT+
Sbjct: 169 VVVVPKGHPLTG-RENLTLEAIAEYPIITY 197


>gnl|CDD|162852 TIGR02424, TF_pcaQ, pca operon transcription factor PcaQ.
          Members of this family are LysR-family transcription
          factors associated with operons for catabolism of
          protocatechuate. Members occur only in Proteobacteria.
          Length = 300

 Score = 60.5 bits (147), Expect = 5e-10
 Identities = 25/56 (44%), Positives = 34/56 (60%)

Query: 8  LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
          L+ F  VAR GS   AAE LH++Q ++S+ +  LE  +G  LF R  RG+ LT  G
Sbjct: 8  LQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYG 63


>gnl|CDD|182183 PRK09986, PRK09986, DNA-binding transcriptional activator XapR;
           Provisional.
          Length = 294

 Score = 60.1 bits (146), Expect = 6e-10
 Identities = 69/266 (25%), Positives = 106/266 (39%), Gaps = 53/266 (19%)

Query: 8   LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL- 66
           LR F  VA    F  AA +L++SQ  +S  I  LE ++G  LF RH+R + LT  G  L 
Sbjct: 12  LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILM 71

Query: 67  ---HRVTSEVYHKL---------ETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKE 114
               R+       L         E  +IE+        G+LR A             ++ 
Sbjct: 72  EESRRLLDNAEQSLARVEQIGRGEAGRIEIGIVGTALWGRLRPA-------------MRH 118

Query: 115 FLLLYPDIQIQL----------ILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIH 164
           FL   P+++  L           L+ +++D  +       R+     +     R+L    
Sbjct: 119 FLKENPNVEWLLRELSPSMQMAALERRELDAGIW------RMADLEPNPGFTSRRL-HES 171

Query: 165 MHAYAAP--HYLKNCREPLSIQELDKHNLITFGDLIPKCMEDF-NWLATVDRPIG-EPRI 220
             A A P  H L   R  + ++ L     IT    +P    D+  +L  V +  G  P+I
Sbjct: 172 AFAVAVPEEHPLA-SRSSVPLKALRNEYFIT----LPFVHSDWGKFLQRVCQQAGFSPQI 226

Query: 221 SCLQVNSYLSIMQYCVLGSGIALLPD 246
              QVN   +++    +G GI LLPD
Sbjct: 227 I-RQVNEPQTVLAMVSMGIGITLLPD 251


>gnl|CDD|183678 PRK12681, cysB, transcriptional regulator CysB; Reviewed.
          Length = 324

 Score = 58.0 bits (141), Expect = 3e-09
 Identities = 35/103 (33%), Positives = 56/103 (54%), Gaps = 1/103 (0%)

Query: 21  THAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-LTEQGSKLHRVTSEVYHKLET 79
           +  AE L+ SQ  IS+Q+  LE E+GI++F R  + LT +T  G ++ R+  E+  K+E+
Sbjct: 20  SATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTPAGEEIIRIAREILSKVES 79

Query: 80  TQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDI 122
            +    E +    G L IATT    +  L   +K F+  YP +
Sbjct: 80  IKSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIERYPRV 122


>gnl|CDD|182948 PRK11074, PRK11074, putative DNA-binding transcriptional
          regulator; Provisional.
          Length = 300

 Score = 57.3 bits (139), Expect = 4e-09
 Identities = 23/56 (41%), Positives = 33/56 (58%)

Query: 8  LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
          L V   VAR+GSF+ AA++LH   S++S  +  LE  + + LF R  R + LT  G
Sbjct: 7  LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAG 62


>gnl|CDD|163206 TIGR03298, argP, transcriptional regulator, ArgP family.  ArgP
          used to be known as IciA. ArgP is a positive regulator
          of argK. It is a negative autoregulator in presence of
          arginine. It competes with DnaA for oriC iteron
          (13-mer) binding. It activates dnaA and nrd
          transcription. It has been demonstrated to be part of
          the pho regulon (PubMed:10589831). ArgP mutants convey
          canavanine (an L-arginine structural homolog)
          sensitivity (PubMed: 15150242).
          Length = 292

 Score = 55.7 bits (135), Expect = 2e-08
 Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 1/64 (1%)

Query: 3  FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62
           D+ +L     V   GSF  AA  L ++ S++S++I  LE  +G  L  R  +    TE 
Sbjct: 1  LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEA 59

Query: 63 GSKL 66
          G +L
Sbjct: 60 GQRL 63


>gnl|CDD|182228 PRK10082, PRK10082, cell density-dependent motility repressor;
           Provisional.
          Length = 303

 Score = 55.1 bits (132), Expect = 2e-08
 Identities = 32/98 (32%), Positives = 50/98 (51%)

Query: 11  FYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVT 70
           F  + +  +F+ AA   ++SQ + SR+I  LE  +G++LF R    L L+EQG   H   
Sbjct: 19  FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQI 78

Query: 71  SEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLL 108
             +  +LE+   EL+  S     K++IA    L   LL
Sbjct: 79  RHLLQQLESNLAELRGGSDYAQRKIKIAAAHSLSLGLL 116


>gnl|CDD|182899 PRK11013, PRK11013, DNA-binding transcriptional regulator LysR;
           Provisional.
          Length = 309

 Score = 54.2 bits (131), Expect = 4e-08
 Identities = 43/130 (33%), Positives = 68/130 (52%), Gaps = 6/130 (4%)

Query: 1   MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG-LTL 59
            +     + +F+ V  +GS T AA  LH SQ ++SR+++  E  +G+KLF R  RG L  
Sbjct: 2   AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFER-VRGRLHP 60

Query: 60  TEQGSKLHRVTSEVYHKLETTQIELQESSVKP--SGKLRIATTIDLGQNLLQGNLKEFLL 117
           T QG +L       Y+ L+  +I     S++    G+L IA      Q+LL G  + FL 
Sbjct: 61  TVQGLRLFEEVQRSYYGLD--RIVSAAESLREFRQGQLSIACLPVFSQSLLPGLCQPFLA 118

Query: 118 LYPDIQIQLI 127
            YPD+ + ++
Sbjct: 119 RYPDVSLNIV 128


>gnl|CDD|183989 PRK13348, PRK13348, chromosome replication initiation inhibitor
          protein; Provisional.
          Length = 294

 Score = 53.8 bits (130), Expect = 5e-08
 Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 10/85 (11%)

Query: 3  FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62
           D+ +L     V  +GSF  AA +LH++ S++S++I  LE  +G  L  R  R    T  
Sbjct: 2  LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPA 60

Query: 63 GSKLHRVTSEVYHKLETTQIELQES 87
          G +L R      H     Q+ L E+
Sbjct: 61 GQRLLR------H---LRQVALLEA 76


>gnl|CDD|185319 PRK15421, PRK15421, DNA-binding transcriptional regulator MetR;
           Provisional.
          Length = 317

 Score = 53.9 bits (129), Expect = 6e-08
 Identities = 34/117 (29%), Positives = 56/117 (47%), Gaps = 3/117 (2%)

Query: 8   LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLH 67
           L+    +   GS   AA  LH +QS++S Q S LE  +G +LF R ++ L  T QG  L 
Sbjct: 7   LKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILL 66

Query: 68  RVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQI 124
           ++ ++V  ++      LQ  +     +LRIA         L   L+ F   +P +++
Sbjct: 67  QLANQVLPQISQA---LQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEM 120


>gnl|CDD|179604 PRK03601, PRK03601, transcriptional regulator HdfR; Provisional.
          Length = 275

 Score = 53.9 bits (130), Expect = 6e-08
 Identities = 26/63 (41%), Positives = 40/63 (63%)

Query: 4  DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
          D + L+ F  V+R+  F  AAE L+L+QS++S +I  LE ++G+ LF RH   + LT  G
Sbjct: 2  DTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG 61

Query: 64 SKL 66
           +L
Sbjct: 62 ERL 64


>gnl|CDD|183045 PRK11233, PRK11233, nitrogen assimilation transcriptional
          regulator; Provisional.
          Length = 305

 Score = 52.4 bits (126), Expect = 1e-07
 Identities = 25/62 (40%), Positives = 39/62 (62%)

Query: 7  KLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL 66
          +L+ F  +   GS T AAE LH++Q ++S+Q++ LE E+  +L  R  RG+T TE G  L
Sbjct: 5  RLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKIL 64

Query: 67 HR 68
          + 
Sbjct: 65 YT 66


>gnl|CDD|179616 PRK03635, PRK03635, chromosome replication initiation inhibitor
           protein; Validated.
          Length = 294

 Score = 51.7 bits (125), Expect = 2e-07
 Identities = 36/101 (35%), Positives = 49/101 (48%), Gaps = 4/101 (3%)

Query: 3   FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62
            D+ +L     V R GSF  AA++LH++QS++S++I  LE  VG  L  R  +    TE 
Sbjct: 2   LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEA 60

Query: 63  GSKLHRVTSEVYHKLET-TQIELQESSVKPSGKLRIATTID 102
           G +L R   +V   LE     EL      P   L IA   D
Sbjct: 61  GQRLLRHARQVRL-LEAELLGELPALDGTPL-TLSIAVNAD 99


>gnl|CDD|182938 PRK11062, nhaR, transcriptional activator NhaR; Provisional.
          Length = 296

 Score = 47.7 bits (114), Expect = 4e-06
 Identities = 25/56 (44%), Positives = 32/56 (57%)

Query: 8  LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
          L  F++V + GS   AAE L L+  +I+ QI  LE  +  KLF R  RGL  TE G
Sbjct: 9  LYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG 64


>gnl|CDD|185155 PRK15243, PRK15243, transcriptional regulator SpvR; Provisional.
          Length = 297

 Score = 45.0 bits (106), Expect = 2e-05
 Identities = 29/92 (31%), Positives = 49/92 (53%), Gaps = 9/92 (9%)

Query: 7  KLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL 66
          KL++F  +  +GSF+ A   L+++++ +SR IS LE E+  +LF R    L  TE     
Sbjct: 8  KLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTE----- 62

Query: 67 HRVTSEVYHKLETTQIELQ--ESSVKPSGKLR 96
                +Y K+++  I L   E  + P+GK +
Sbjct: 63 --FAQTIYRKVKSHYIFLHALEQEIGPTGKTK 92


>gnl|CDD|182999 PRK11151, PRK11151, DNA-binding transcriptional regulator OxyR;
          Provisional.
          Length = 305

 Score = 44.3 bits (105), Expect = 4e-05
 Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 10/61 (16%)

Query: 20 FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHAR-------GLTLTEQGSKLHRVTSE 72
          F  AA+  H+SQ ++S QI  LE E+G+ L  R +R       GL L +Q      V  E
Sbjct: 18 FRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQAR---TVLRE 74

Query: 73 V 73
          V
Sbjct: 75 V 75


>gnl|CDD|183677 PRK12680, PRK12680, transcriptional regulator CysB-like protein;
           Reviewed.
          Length = 327

 Score = 37.3 bits (86), Expect = 0.004
 Identities = 34/143 (23%), Positives = 63/143 (44%), Gaps = 12/143 (8%)

Query: 7   KLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL-TLTEQGS 64
           +LR    +A +  + T AA ++H +Q  +S+Q+  LE E+G  LF R  R L ++T  G 
Sbjct: 5   QLRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESVTPAGV 64

Query: 65  KLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQI 124
           ++      V  +    +        +  G+L + TT    + +L   + +    YP + +
Sbjct: 65  EVIERARAVLSEANNIRTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSV 124

Query: 125 QL----------ILDNKDIDISM 137
            L          +L   D DI++
Sbjct: 125 HLQQAAESAALDLLGQGDADIAI 147


>gnl|CDD|181918 PRK09508, leuO, leucine transcriptional activator; Reviewed.
          Length = 314

 Score = 32.3 bits (74), Expect = 0.17
 Identities = 20/65 (30%), Positives = 34/65 (52%)

Query: 2  SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61
            D + L VF  V +  + T AA  L +SQ ++S  ++ L+     +LF R+ RG+  T 
Sbjct: 21 MVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTA 80

Query: 62 QGSKL 66
          +  +L
Sbjct: 81 RARQL 85


>gnl|CDD|183359 PRK11886, PRK11886, bifunctional biotin--[acetyl-CoA-carboxylase]
          synthetase/biotin operon repressor; Provisional.
          Length = 319

 Score = 31.7 bits (73), Expect = 0.26
 Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 14/72 (19%)

Query: 24 AEQLHLSQSSISRQISGLETEVGIKLF------YRHARGLTL-----TEQGSKLHRVTSE 72
           E+L +S+++I + I  LE E G+ +F      YR A  L L             RV   
Sbjct: 25 GEELGISRAAIWKHIQTLE-EWGLDIFSVKGKGYRLAEPLDLLDPERISSQLPPGRV--T 81

Query: 73 VYHKLETTQIEL 84
          V   +++T   L
Sbjct: 82 VLPVIDSTNQYL 93


>gnl|CDD|183159 PRK11482, PRK11482, putative DNA-binding transcriptional
          regulator; Provisional.
          Length = 317

 Score = 30.5 bits (69), Expect = 0.60
 Identities = 22/69 (31%), Positives = 34/69 (49%)

Query: 4  DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
          D + L +F  V       +AA+ L+L+ S+IS+ I  L       LF R  +G+T T   
Sbjct: 30 DLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYA 89

Query: 64 SKLHRVTSE 72
          + LH   S+
Sbjct: 90 THLHEYISQ 98


>gnl|CDD|163099 TIGR03007, pepcterm_ChnLen, polysaccharide chain length determinant
           protein, PEP-CTERM locus subfamily.  Members of this
           protein family belong to the family of polysaccharide
           chain length determinant proteins (pfam02706). All are
           found in species that encode the PEP-CTERM/exosortase
           system predicted to act in protein sorting in a number
           of Gram-negative bacteria, and are found near the epsH
           homolog that is the putative exosortase gene.
          Length = 498

 Score = 30.0 bits (68), Expect = 0.74
 Identities = 24/114 (21%), Positives = 39/114 (34%), Gaps = 25/114 (21%)

Query: 34  ISRQISGLETEVG-----IKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQE-- 86
           I  QI   E ++      +K F +   G  L +Q    +   SE   +LE  ++EL E  
Sbjct: 166 IDEQIKTYEKKLEAAENRLKAF-KQENGGILPDQEGDYYSEISEAQEELEAARLELNEAI 224

Query: 87  -------------SSVKPSGKLRIATTIDLGQNLLQGNLKEFLL----LYPDIQ 123
                          V  +G     + +D     L+  L    L     +PD+ 
Sbjct: 225 AQRDALKRQLGGEEPVLLAGSSVANSELDGRIEALEKQLDALRLRYTDKHPDVI 278


>gnl|CDD|180478 PRK06224, PRK06224, citrate synthase; Provisional.
          Length = 263

 Score = 28.3 bits (64), Expect = 2.6
 Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 1/28 (3%)

Query: 1   MSFDWDKLRVFYVVARS-GSFTHAAEQL 27
           + F     R  +V++R+ G   H  E+L
Sbjct: 209 LGFPPALARGLFVISRAAGLVAHVWEEL 236


>gnl|CDD|162837 TIGR02395, rpoN_sigma, RNA polymerase sigma-54 factor.  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 sigma-54, or RpoN (unrelated to
           sigma 70-type factors such as RpoD/SigA). RpoN is
           responsible for enhancer-dependent transcription, and
           its presence characteristically is associated with
           varied panels of activators, most of which are
           enhancer-binding proteins (but see Brahmachary, et al.,
           PubMed:15231786). RpoN may be responsible for
           transcription of nitrogen fixation genes, flagellins,
           pilins, etc., and synonyms for the gene symbol rpoN,
           such as ntrA, reflect these observations.
          Length = 429

 Score = 28.0 bits (63), Expect = 3.1
 Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 21  THAAEQLHLSQSSISRQISG--LETEVGI 47
              AE+L L +S+ISR I+   L+T  G+
Sbjct: 322 REVAEELGLHESTISRAINNKYLQTPRGV 350


>gnl|CDD|152978 pfam12544, LAM_C, Lysine-2,3-aminomutase.  This domain family is
           found in bacteria, archaea and eukaryotes, and is
           typically between 111 and 127 amino acids in length. The
           family is found in association with pfam04055. LAM
           catalyses the interconversion of L-alpha-lysine and
           L-beta-lysine, which proceeds by migration of the amino
           group from C2 to C3 concomitant with cross-migration of
           the 3-pro-R hydrogen of L-alpha-lysine to the 2-pro-R
           position of L-beta-lysine.
          Length = 127

 Score = 27.7 bits (62), Expect = 3.7
 Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 9/40 (22%)

Query: 238 GSGIALLPDYIVKDNPNLV--RIMEDVITPSFTVYFCYPE 275
           G  IAL P+Y++  +P+ V  R  E VIT        YPE
Sbjct: 24  GGKIALQPNYLISQSPDKVVLRNFEGVIT-------TYPE 56


>gnl|CDD|128802 smart00529, HTH_DTXR, Helix-turn-helix diphteria tox regulatory
          element.  iron dependent repressor.
          Length = 96

 Score = 27.2 bits (61), Expect = 5.6
 Identities = 15/43 (34%), Positives = 29/43 (67%), Gaps = 2/43 (4%)

Query: 24 AEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL 66
          AE+L++S  ++++ +  LE +  ++  Y   RG+TLTE+G +L
Sbjct: 6  AERLNVSPPTVTQMLKKLEKDGLVE--YEPYRGITLTEKGRRL 46


>gnl|CDD|162596 TIGR01910, DapE-ArgE, acetylornithine deacetylase or
           succinyl-diaminopimelate desuccinylase.  This group of
           sequences contains annotations for both acetylornithine
           deacetylase and succinyl-diaminopimelate desuccinylase,
           but does not contain any members with experimental
           characterization. Bacillus, Staphylococcus and
           Sulfolobus species contain multiple hits to this
           subfamily and each may have a separate activity.
           Determining which is which must await further laboratory
           research.
          Length = 375

 Score = 27.0 bits (60), Expect = 5.9
 Identities = 5/21 (23%), Positives = 14/21 (66%)

Query: 82  IELQESSVKPSGKLRIATTID 102
             ++E+ +KP+G + + + +D
Sbjct: 118 KAIREAGIKPNGNIILQSVVD 138


>gnl|CDD|115045 pfam06363, Picorna_P3A, Picornaviridae P3A protein.  This family
           consists of the P3A protein of picornaviridae. P3A has
           been identified as a genome-linked protein (VPg) and is
           involved in replication.
          Length = 100

 Score = 26.8 bits (59), Expect = 6.4
 Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 13/60 (21%)

Query: 244 LPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNT-------------GKLKAFRNFI 290
           + +Y+  +   L+  ME  I P  +V+ C+   L +              GK+K+  NF+
Sbjct: 6   IDEYLNIEMSTLIEQMEAFIEPRPSVFKCFASKLPHKPKTASRKVKAWVKGKMKSMLNFV 65


>gnl|CDD|182720 PRK10775, PRK10775, cell division protein FtsQ; Provisional.
          Length = 276

 Score = 27.0 bits (60), Expect = 6.8
 Identities = 12/36 (33%), Positives = 17/36 (47%)

Query: 99  TTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDID 134
             ++LG+      L  F+ LYP +Q Q   D K I 
Sbjct: 207 IRLELGRGDTMKRLARFIELYPVLQQQAQTDGKRIS 242


>gnl|CDD|162841 TIGR02401, trehalose_TreY, malto-oligosyltrehalose synthase.  This
           enzyme, formally named (1->4)-alpha-D-glucan
           1-alpha-D-glucosylmutase, is the TreY enzyme of the
           TreYZ pathway of trehalose biosynthesis, an alternative
           to the OtsAB pathway. Trehalose may be incorporated into
           more complex compounds but is best known as compatible
           solute. It is one of the most effective osmoprotectants,
           and unlike the various betaines does not require
           nitrogen for its synthesis.
          Length = 825

 Score = 26.6 bits (59), Expect = 7.9
 Identities = 9/19 (47%), Positives = 11/19 (57%)

Query: 50  FYRHARGLTLTEQGSKLHR 68
           FYR+ R L+L E G    R
Sbjct: 470 FYRYNRLLSLNEVGGDPGR 488


  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    0.138    0.410 

Gapped
Lambda     K      H
   0.267   0.0662    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,775,577
Number of extensions: 295028
Number of successful extensions: 548
Number of sequences better than 10.0: 1
Number of HSP's gapped: 531
Number of HSP's successfully gapped: 55
Length of query: 299
Length of database: 5,994,473
Length adjustment: 93
Effective length of query: 206
Effective length of database: 3,984,929
Effective search space: 820895374
Effective search space used: 820895374
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: 57 (25.9 bits)