RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780282|ref|YP_003064695.1| putative transcription
regulator protein [Candidatus Liberibacter asiaticus str. psy62]
(299 letters)
>3mz1_A Putative transcriptional regulator; structural genomics, PSI-2,
protein structure initiative, MI center for STR uctural
genomics, MCSG; 1.88A {Sinorhizobium meliloti}
Length = 300
Score = 203 bits (516), Expect = 6e-53
Identities = 67/286 (23%), Positives = 126/286 (44%), Gaps = 4/286 (1%)
Query: 8 LRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLH 67
+R F V +G+FT A+ L++ +++++ I GLE + KL R R + +T G+ +
Sbjct: 3 MRAFLRVVETGNFTRASASLNMPKATVTNLIQGLEAHLRTKLLNRTTRRVLVTPDGALYY 62
Query: 68 RVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLI 127
+ + L+ L + P G+LR+ T ++ L EF YPDIQI L
Sbjct: 63 ERAARLLSDLDELDGSLSTAQSLPKGRLRVETASAFANLVIIPALPEFHKKYPDIQIDLG 122
Query: 128 LDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELD 187
+ ++ ID + DCAIR + SLI R++ + A A+ +L+ P +L+
Sbjct: 123 VSDRTIDYLAENVDCAIRAG-TLTDQSLIARRITEMKFVACASRDFLERHPVPQHPSDLE 181
Query: 188 KHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDY 247
K+ + L + + I + N + + G G+ P +
Sbjct: 182 KNCYVVGYFLPKTGQQMPFHFRRGNEEIEVSGRYTMAANESTTYLAAARAGLGVIQAPLF 241
Query: 248 IVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
+V++ N +V ++ D +Y YP + +L+ F +++
Sbjct: 242 MVREDLRNGTMVPVLPDWQVEPMPIYLVYPPNRHLSSRLRVFADWV 287
>3hhg_A Transcriptional regulator, LYSR family; transcription factor,
structural genomics, oxford protein production facility,
OPPF; 3.20A {Neisseria meningitidis serogroup B}
Length = 306
Score = 182 bits (462), Expect = 1e-46
Identities = 74/294 (25%), Positives = 130/294 (44%), Gaps = 9/294 (3%)
Query: 1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT 60
M + ++L VF V SGSF+ AAEQL ++ S++SR + LE ++G+ L R R L+LT
Sbjct: 1 MKTNSEELTVFVQVVESGSFSRAAEQLAMANSAVSRIVKRLEEKLGVNLLNRTTRQLSLT 60
Query: 61 EQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYP 120
E+G++ R + ++ + E+ P G L + + + + +LL +F YP
Sbjct: 61 EEGAQYFRRAQRILQEMAAAETEMLAVHEIPQGVLSVDSAMPMVLHLLAPLAAKFNERYP 120
Query: 121 DIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREP 180
I++ L+ I++ D A+R + S L R L A+P YL P
Sbjct: 121 HIRLSLVSSEGYINLIERKVDIALRAG-ELDDSGLRARHLFDSRFRVIASPEYLAKHGTP 179
Query: 181 LSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSG 240
S +EL H + F + P + + L P +S + C+ G G
Sbjct: 180 QSTEELAGHQCLGFTE--PGSLNTWAVLDAQGNPYKISPHFT--ASSGEILRSLCLSGCG 235
Query: 241 IALLPDYIVKD---NPNLVRIMEDVITP-SFTVYFCYPEALKNTGKLKAFRNFI 290
I L D++V + L+ ++ + + + Y +L+ F +F+
Sbjct: 236 IVCLSDFLVDNDIAEGKLIPLLAEQTSDKTHPFNAVYYSDKAVNLRLRVFLDFL 289
>1ixc_A CBNR, LYSR-type regulatory protein; long alpha helix connecting DNA
binding and regulatory domains, DNA binding protein;
2.20A {Cupriavidus necator} SCOP: a.4.5.37 c.94.1.1 PDB:
1iz1_A
Length = 294
Score = 148 bits (374), Expect = 1e-36
Identities = 50/296 (16%), Positives = 104/296 (35%), Gaps = 6/296 (2%)
Query: 4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
++ +L+ F VA +G+ AA++LH+SQ I+RQ+ LE ++G+ L R RG+ LT G
Sbjct: 2 EFRQLKYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERSHRGIELTAAG 61
Query: 64 SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123
+ + + ++ G+L +A L L+ FL P
Sbjct: 62 HAFLEDARRILELAGRSGDRSRAAARGDVGELSVAYFGTPIYRSLPLLLRAFLTSTPTAT 121
Query: 124 IQLILD--NKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPL 181
+ L ++ ++ + R + + + ++ +
Sbjct: 122 VSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIEIVNIAQEDLYLAVHRSQSGKFGKTC 181
Query: 182 SIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI 241
+ +L L F + + EPRI V + + + G+
Sbjct: 182 KLADLRAVELTLF-PRGGRPSFADEVIGLFKHAGIEPRI-ARVVEDATAALALTMAGAAS 239
Query: 242 ALLPDYIVK-DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296
+++P + P++ + + + K L F + A+D
Sbjct: 240 SIVPASVAAIRWPDIAFARIVGTRVKVPISCIFRKE-KQPPILARFVEHVRRSAKD 294
>3fxq_A LYSR type regulator of TSAMBCD; transcriptional regulator, LTTR,
TSAR, WHTH, DNA- binding, plasmid, transcription; 1.85A
{Comamonas testosteroni} PDB: 3fxr_A* 3fxu_A* 3fzj_A
Length = 305
Score = 147 bits (372), Expect = 2e-36
Identities = 53/294 (18%), Positives = 92/294 (31%), Gaps = 12/294 (4%)
Query: 4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
L+ + GS AA+ LHLSQ ++S I LE E+ L R RG++LT G
Sbjct: 3 KLQTLQALICIEEVGSLRAAAQLLHLSQPALSAAIQQLEDELKAPLLVRTKRGVSLTSFG 62
Query: 64 SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123
+ + + Q E+ + + G + A + + L L F +PD+
Sbjct: 63 QAFMKHARLIVTESRRAQEEIGQLRGRWEGHITFAASPAIALAALPLALASFAREFPDVT 122
Query: 124 IQLILDNKDI---DISMDYADCAI-RLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCRE 179
+ + + D A+ K + L + L + +
Sbjct: 123 VNVRDGMYPAVSPQLRDGTLDFALTAAHKHDIDTDLEAQPLYVSDVVIVGQRQHP--MAN 180
Query: 180 PLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239
+ EL + N A P L S+L++
Sbjct: 181 ATRLAELQECRWAFSSAPRGPGAIIRNAFARYGLP---EPKLGLVCESFLALPGVVAHSD 237
Query: 240 GIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
+ +P + + L I P+ T+Y L T +I
Sbjct: 238 LLTTMPRTLYERNAFKDQLCSIPLQDALPNPTIYVLRRHDLPVTPAAAGLIRWI 291
>3isp_A HTH-type transcriptional regulator RV1985C/MT2039; ROD shaped
structure, DNA binding domain, regulatory domain,
DNA-binding; 2.70A {Mycobacterium tuberculosis}
Length = 303
Score = 137 bits (346), Expect = 2e-33
Identities = 47/299 (15%), Positives = 99/299 (33%), Gaps = 16/299 (5%)
Query: 3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ 62
D +L V GSF AAE+LH++ S++S++I LE +VG L R + T
Sbjct: 6 LDGPQLAALAAVVELGSFDAAAERLHVTPSAVSQRIKSLEQQVGQVLVVRE-KPCRATTA 64
Query: 63 GSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDI 122
G L R+ ++ E+ ++ ++ IA D + D+
Sbjct: 65 GIPLLRLAAQTALLESEALAEMGGNASLKRTRITIAVNADSMATWFSAVFDGLGDVLLDV 124
Query: 123 QIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYL-KNCREPL 181
+I+ + + A A+ + L + A+ ++ ++ +
Sbjct: 125 RIEDQDHSARLLRE-GVAMGAVTTERN-PVPGCRVHPLGEMRYLPVASRPFVQRHLSDGF 182
Query: 182 SIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI 241
+ K + + ++D R I P V + G G
Sbjct: 183 TXXXXXKAPSLAWNR--DDGLQDMLVRKAFRRAITRPTH---FVPTTEGFTAAARAGLGW 237
Query: 242 ALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW 297
+ P+ + + + VR+ + V + ++ + + + A
Sbjct: 238 GMFPEKLAASPLADGSFVRVCD----IHLDVPLYWQCWKLDSPIIARITDTVRAAASGL 292
>3fzv_A Probable transcriptional regulator; LYSR, structural genomics,
PSI-2, protein structure initiative; 2.71A {Pseudomonas
aeruginosa PA01}
Length = 306
Score = 136 bits (343), Expect = 5e-33
Identities = 52/297 (17%), Positives = 111/297 (37%), Gaps = 13/297 (4%)
Query: 2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYR-HARGLTLT 60
S+ +L+ F GS A+ +L+++Q SIS + GLE G++LF R HA+G++LT
Sbjct: 3 SYTLRQLKYFVTTVECGSVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRHHAQGVSLT 62
Query: 61 EQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYP 120
G++ +R E+ + + +G++ I + L G + F YP
Sbjct: 63 PAGARFYRKAQELLRMAHEFEQNALADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYP 122
Query: 121 DIQIQLILDNKDI---DISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNC 177
++I++ + ++ D A + S+ + + HA +
Sbjct: 123 GVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDSTIETEPLMPPQRPHALLPEGHRFAG 182
Query: 178 REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237
+ +S+++L +I + ++ +G S +
Sbjct: 183 QAQVSLRDLCLEPMILL-----DVQPSRTYFVSLFEELGLTPNIAFSSPSIEMVRGMVGQ 237
Query: 238 GSGIALLPDYIV----KDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
G G +LL D +V + + + + + + T + F ++
Sbjct: 238 GFGFSLLVTRPHSECTYDGKKVVMVDLAEPVSTSGLAAAWLKRAQLTKPARLFVDYC 294
>1uth_A LYSR-type regulatory protein; transcription regulation,
transcriptional regulator; 2.2A {Burkholderia SP} SCOP:
c.94.1.1 PDB: 1utb_A 1utb_B 1uth_B 2uyf_A 2uye_A
Length = 315
Score = 130 bits (328), Expect = 3e-31
Identities = 49/296 (16%), Positives = 83/296 (28%), Gaps = 13/296 (4%)
Query: 2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61
D + L VF + S + A E+L L+Q ++S + L T + LF R ++G+ T
Sbjct: 13 DIDLNLLVVFNQLLLDRSVSTAGEKLGLTQPAVSNSLKRLRTALNDDLFLRTSKGMEPTP 72
Query: 62 QGSKLHRVTSEVYHKLETTQIELQ-ESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYP 120
L + L+T + +A T + ++ P
Sbjct: 73 YALHLAEPVIYALNTLQTALTTRNSFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAP 132
Query: 121 DIQIQLILDNKD---IDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNC 177
IQI + N D+ D A+ L P + QR+L +
Sbjct: 133 HIQISTLRPNAGNLKEDMESGAVDLALGLL-PELQTGFFQRRLFRHRYVCMFRKDHPSAK 191
Query: 178 REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL 237
Q + ++ D G R L V +++I
Sbjct: 192 SPMSLKQFSELEHVGVVALNTGHGEVDGLL-----ERAGIKRRMRLVVPHFIAIGPILHS 246
Query: 238 GSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
IA +P L P + + R
Sbjct: 247 TDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLF 302
>1al3_A Cys regulon transcriptional activator CYSB; LYSR family, cysteine
biosynthesis, transcription regulation; 1.80A
{Klebsiella aerogenes} SCOP: c.94.1.1
Length = 324
Score = 130 bits (326), Expect = 5e-31
Identities = 65/294 (22%), Positives = 113/294 (38%), Gaps = 11/294 (3%)
Query: 4 DWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-LTE 61
+LR V + + AE L+ SQ IS+Q+ LE E+GI++F R + LT +T
Sbjct: 2 KLQQLRYIVEVVNHNLNVSSTAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTP 61
Query: 62 QGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPD 121
G ++ R+ EV K++ + E + G L +ATT + L G +K F+ YP
Sbjct: 62 AGQEIIRIAREVLSKVDAIKSVAGEHTWPDKGSLYVATTHTQARYALPGVIKGFIERYPR 121
Query: 122 IQIQLILDNKDIDISM---DYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCR 178
+ + + + AD AI L+ + P + +
Sbjct: 122 VSLHMHQGSPTQIAEAVSKGNADFAIATEALHLYDDLVMLPCYHWNRSIVVTPEHPLATK 181
Query: 179 EPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG 238
+SI+EL ++ L+T+ + L T G I Y LG
Sbjct: 182 GSVSIEELAQYPLVTY----TFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVRLG 237
Query: 239 SGIALLPDYIVK--DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
G+ ++ V +P+LV++ + I T + + + F
Sbjct: 238 LGVGVIASMAVDPVSDPDLVKLDANGIFSHSTTKIGFRRSTFLRSYMYDFIQRF 291
>2h9b_A HTH-type transcriptional regulator BENM; LTTR, transcriptional
activator, LYSR-type transcriptional regulator; 1.80A
{Acinetobacter SP} PDB: 2h99_A 2f7a_A* 2f6p_A 2f78_A
2f6g_A* 2f8d_A 2f97_A*
Length = 312
Score = 126 bits (317), Expect = 5e-30
Identities = 48/294 (16%), Positives = 103/294 (35%), Gaps = 13/294 (4%)
Query: 4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
+ LR F V SFT AA++L ++Q +SRQI LE E+GI+L R +R + T +G
Sbjct: 2 ELRHLRYFVAVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVKTTPEG 61
Query: 64 SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123
++ ++ ++ + +RI L LL + + +P+++
Sbjct: 62 HFFYQYAIKLLSNVDQMVSMTKR-IASVEKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLR 120
Query: 124 IQLILDNKDIDISM----DYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCRE 179
I+L RL+ + + + + +A+ + +
Sbjct: 121 IELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKHSLLRNERLMVAVHASHPLNQMKDK 180
Query: 180 PLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239
+ + +L ++ + D + + +V + G
Sbjct: 181 GVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTK--INEVREVQLALGLVAAGE 238
Query: 240 GIALLPDYIVKDNPN---LVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
GI+L+P V +++ +Y ++T + + I
Sbjct: 239 GISLVPASTQSIQLFNLSYVPLLDPD--AITPIYIAVRNMEEST-YIYSLYETI 289
>2h98_A HTH-type transcriptional regulator CATM; BENM, LTTR; 1.80A
{Acinetobacter SP} PDB: 2h9q_A* 2f7b_A 2f7c_A* 3glb_A*
Length = 313
Score = 120 bits (302), Expect = 3e-28
Identities = 51/292 (17%), Positives = 93/292 (31%), Gaps = 9/292 (3%)
Query: 4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG 63
+ LR F V S + AAE+L ++Q +SRQI LE E+GI+LF R R +TE G
Sbjct: 2 ELRHLRYFVTVVEEQSISKAAEKLCIAQPPLSRQIQKLEEELGIQLFERGFRPAKVTEAG 61
Query: 64 SKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQ 123
++ ++ + + LRI L LL + F P+I
Sbjct: 62 MFFYQHAVQILTHTAQASSMAKRIATVSQ-TLRIGYVSSLLYGLLPEIIYLFRQQNPEIH 120
Query: 124 IQLILDNKD---IDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLK-NCRE 179
I+LI + D K + A H+L
Sbjct: 121 IELIECGTKDQINALKQGKIDLGFGRLKITDPAIRRIMLHKEQLKLAIHKHHHLNQFAAT 180
Query: 180 PLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS 239
+ + ++ ++ + F +G ++ + G
Sbjct: 181 GVHLSQIIDEPMLLYPVSQKPNFATFIQSL--FTELGLVPSKLTEIREIQLALGLVAAGE 238
Query: 240 GIALLPDYIVKDN-PNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
G+ ++P + NL+ I + ++ + +
Sbjct: 239 GVCIVPASAMDIGVKNLLYIPILDDDAYSPISLAVRNM-DHSNYIPKILACV 289
>2esn_A Probable transcriptional regulator; PA0477, APC5828,transcription,
PSI, protein structure initiative, MCSG; 2.10A
{Pseudomonas aeruginosa} SCOP: a.4.5.37 c.94.1.1
Length = 310
Score = 115 bits (288), Expect = 1e-26
Identities = 37/298 (12%), Positives = 76/298 (25%), Gaps = 14/298 (4%)
Query: 2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE 61
D + L VF + R + AA +L +S S+ S + L + +LF R + T+
Sbjct: 9 RLDLNLLLVFDALYRHRNVGTAASELAISASAFSHALGRLRQGLDDELFLRQGNRMQPTQ 68
Query: 62 QGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPD 121
+ L + L E + S + + D L L L
Sbjct: 69 RAEHLAAAVAAALRALGEGLEEWRPFVPGQSQRTFVFAATDYTAFALLPPLMNRLQHSAP 128
Query: 122 IQIQLILDNKDIDISMDYADCAIRL------RKPIQSSSLIQRKLVTIHMHAYAAPHYLK 175
+++ + A I + A + +
Sbjct: 129 GVRLRLVNAERKLSVEALASGRIDFALGYDEEHERLPEGIQAHDWFADRYVVVARRDHPR 188
Query: 176 NCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYC 235
P L + + + + D G R +Q+ + L+ +
Sbjct: 189 LAGAPTLEGYLAERHAVVTPWNEDSGVIDRLL-----ARSGLRREVAVQLPTVLAALFLA 243
Query: 236 VLGSGIALLPDYIVK---DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
+ P + + + L P + + +
Sbjct: 244 GSTDFLLTAPRHAARALAEAAGLALYPAPFDIPPYVLRLYSHVQHVGRDAHAWMIGQL 301
>3hhf_B Transcriptional regulator, LYSR family; transcription factor,
structural genomics, oxford protein production facility,
OPPF; 2.30A {Neisseria meningitidis serogroup B}
Length = 213
Score = 107 bits (267), Expect = 4e-24
Identities = 42/205 (20%), Positives = 75/205 (36%), Gaps = 9/205 (4%)
Query: 90 KPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKP 149
P G L + + + + +LL +F YP I++ L+ I++ D A+R +
Sbjct: 4 IPQGVLSVDSAMPMVLHLLAPLAAKFNERYPHIRLSLVSSEGYINLIERKVDIALRAGEL 63
Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209
S L R L A+P YL P S +EL H + F + W
Sbjct: 64 DD-SGLRARHLFDSRFRVIASPEYLAKHGTPQSTEELAGHQCLGFTE----PGSLNTWAV 118
Query: 210 TVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMED-VITP 265
+ +S + C+ G GI L D++V + L+ ++ +
Sbjct: 119 LDAQGNPYKISPHFTASSGEILRSLCLSGCGIVCLSDFLVDNDIAEGKLIPLLAEQTSDK 178
Query: 266 SFTVYFCYPEALKNTGKLKAFRNFI 290
+ Y +L+ F +F+
Sbjct: 179 THPFNAVYYSDKAVNLRLRVFLDFL 203
>3kos_A HTH-type transcriptional activator AMPR; alpha-beta sandwich,
DNA-binding, transcription regulation; HET: MES; 1.83A
{Citrobacter freundii} PDB: 3kot_A
Length = 219
Score = 99.0 bits (246), Expect = 1e-21
Identities = 34/207 (16%), Positives = 74/207 (35%), Gaps = 12/207 (5%)
Query: 87 SSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRL 146
++ + KL+I L L +F YP I + + N +D + + D IR
Sbjct: 6 ATKQTQEKLKIGVVGTFAIGCLFPLLSDFKRSYPHIDLHISTHNNRVDPAAEGLDYTIRY 65
Query: 147 RKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFN 206
+ L + M +P + P ++ K L+ E
Sbjct: 66 G-GGAWHDTDAQYLCSALMSPLCSPTLASQIQTP---ADILKFPLLRSYR----RDEWAL 117
Query: 207 WLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVI 263
W+ TV P + + +S +++++ G G+A+ P + + +V+ I
Sbjct: 118 WMQTVGEAPPSPTHNVMVFDSSVTMLEAAQAGMGVAIAPVRMFTHLLSSERIVQPFLTQI 177
Query: 264 TPSFTVYFCYPEALKNTGKLKAFRNFI 290
+ + ++ T ++ F ++
Sbjct: 178 -DLGSYWITRLQSRPETPAMREFSRWL 203
>3fd3_A Chromosome replication initiation inhibitor protein; structural
genomics, LYSR, PSI-2, protein structure initiative;
HET: MSE P33 PG4; 1.70A {Agrobacterium tumefaciens str}
Length = 208
Score = 89.4 bits (221), Expect = 1e-18
Identities = 29/212 (13%), Positives = 62/212 (29%), Gaps = 17/212 (8%)
Query: 93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISM---DYADCAIRLRKP 149
L IAT D + +F + + +D++D + A+
Sbjct: 2 VTLNIATNADSLGTWFLDAVSKFTGGSD-YLVNIAVDDQDHTVEWLRGGRVLAAVTAH-D 59
Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYL-KNCREPLSIQELDKHNLITFGDLIPKCMEDFNWL 208
L + HA A+P ++ ++ + ++ L + +TF +
Sbjct: 60 KPVQGCRVTPLGVLRYHATASPDFMARHFADGVTPAALARAPGLTFNQ-----KDRLQAS 114
Query: 209 ATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVITP 265
+ + S ++ + G G L P +V + LV +M
Sbjct: 115 WIRTALGEDVSYPTHWLPSTDGFVKASLAGMGWGLNPVQLVAEHLAAGRLVELMPG---T 171
Query: 266 SFTVYFCYPEALKNTGKLKAFRNFIFLKARDW 297
+ + +L + AR
Sbjct: 172 PLDIPLYWQVNRLAAERLAGLTANMVGTARVV 203
>1b9m_A Protein (mode); DNA-binding, gene regulation, winged helix turn
helix, molybdate, OB fold; 1.75A {Escherichia coli}
SCOP: a.4.5.8 b.40.6.2 b.40.6.2 PDB: 1b9n_A 1o7l_A
1h9s_A 1h9r_A 1h9s_B
Length = 265
Score = 81.1 bits (199), Expect = 3e-16
Identities = 32/198 (16%), Positives = 63/198 (31%), Gaps = 10/198 (5%)
Query: 1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-- 58
+ D ++ + +A SGS + A+ +S S I+ + L R G
Sbjct: 18 LFADPRRISLLKHIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGG 77
Query: 59 ---LTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQ----NLLQGN 111
LT G +L ++ + + L + P L A + Q N G
Sbjct: 78 GAVLTRYGQRLIQLYDLLAQIQQKAFDVLSDDDALPLNSLLAAISRFSLQTSARNQWFGT 137
Query: 112 LKEFLLLYPDIQIQLILDNKDIDISMDYA-DCAIRLRKPIQSSSLIQRKLVTIHMHAYAA 170
+ + ++L + + + RL LI K + + A
Sbjct: 138 ITARDHDDVQQHVDVLLADGKTRLKVAITAQSGARLGLDEGKEVLILLKAPWVGITQDEA 197
Query: 171 PHYLKNCREPLSIQELDK 188
+ + P I +++
Sbjct: 198 VAQNADNQLPGIISHIER 215
>3jv9_A OXYR, transcriptional regulator, LYSR family; LYSR-type
transcriptional regulator, LTTR, redox, structural
genomics, OPPF; 2.39A {Neisseria meningitidis}
Length = 219
Score = 77.8 bits (191), Expect = 3e-15
Identities = 29/204 (14%), Positives = 64/204 (31%), Gaps = 5/204 (2%)
Query: 92 SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--IDISMDYADCAIRLRKP 149
G ++ + LL + P + + L + + AI + +P
Sbjct: 3 EGAFKLGLIFTVAPYLLPKLIVSLRRTAPKMPLMLEENYTHTLTESLKRGDVDAIIVAEP 62
Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209
Q ++ L + + +S + L + ++ + + + +
Sbjct: 63 FQEPGIVTEPLYDEPFFVIVPKGHSFEELDAVSPRMLGEEQVLLLTEGNCMRDQVLSSCS 122
Query: 210 TVD-RPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVK--DNPNLVRIMEDVITPS 266
+ + + + LQ +S +I G I++LP + D+ I + PS
Sbjct: 123 ELAAKQRIQGLTNTLQGSSINTIRHMVASGLAISVLPATALTENDHMLFSIIPFEGTPPS 182
Query: 267 FTVYFCYPEALKNTGKLKAFRNFI 290
V Y L A + I
Sbjct: 183 RRVVLAYRRNFVRPKALSAMKAAI 206
>1i6a_A OXYR, hydrogen peroxide-inducible genes activator; OXYR regulatory
domain, oxidized form, transcription; 2.30A {Escherichia
coli} SCOP: c.94.1.1 PDB: 1i69_A
Length = 219
Score = 73.5 bits (179), Expect = 5e-14
Identities = 35/204 (17%), Positives = 62/204 (30%), Gaps = 9/204 (4%)
Query: 92 SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--IDISMDYADCAIRLRKP 149
SG L I +G LL + +P +++ L + A+ L
Sbjct: 4 SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALV 63
Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209
+S + I+ L M + RE + + +L L+ D + +
Sbjct: 64 KESEAFIEVPLFDEPMLLAIYEDHPWANREAVPMADLAGEKLLMLEDGHCLRDQAMGFC- 122
Query: 210 TVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMEDVITPS 266
G + + S ++ GSGI LLP V +V + P
Sbjct: 123 ---FEAGADEDTHFRATSLETLRNMVAAGSGITLLPALAVPPERKRDGVVYLPAIKPEPR 179
Query: 267 FTVYFCYPEALKNTGKLKAFRNFI 290
T+ Y + + I
Sbjct: 180 RTIGLVYRPGSPLRSRYEQLAEAI 203
>2qsx_A Putative transcriptional regulator, LYSR family; the putative
transcriptional regulator, PSI-2; 1.64A {Vibrio
parahaemolyticus rimd 2210633}
Length = 218
Score = 73.2 bits (178), Expect = 6e-14
Identities = 27/223 (12%), Positives = 73/223 (32%), Gaps = 13/223 (5%)
Query: 77 LETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDIS 136
++ L +++ L + T L N+ +F +P+I+++++ + +
Sbjct: 4 IQHATASLIQTN-TDQELLVVDVTPSFASLWLVPNINDFHQRHPNIRVKILTGDGAVKNI 62
Query: 137 MDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGD 196
+D +R P+ + + L + + K Q + + I
Sbjct: 63 HGESDLHVRCL-PLSTHYEYSQLLCEETLLLIGNTNLPKLSD----NQAISHYPFIPQTT 117
Query: 197 LIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NP 253
+ + + + + + + G+ALLPD++ +
Sbjct: 118 ----RPQLWEQFKQENDLECPITYHSVGFEHFYLACEAVRMEKGLALLPDFMAQFSILRG 173
Query: 254 NLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD 296
++ I + + Y P + K+ F +++ K
Sbjct: 174 DIQHIGNLKLHSGYGYYVVIPNFRLTSRKVALFHDWLKDKLTH 216
>3ho7_A OXYR; beta-alpha-barrels, DNA-binding, transcription, transcriptio
regulation; 1.58A {Porphyromonas gingivalis}
Length = 232
Score = 70.5 bits (172), Expect = 5e-13
Identities = 26/213 (12%), Positives = 59/213 (27%), Gaps = 11/213 (5%)
Query: 83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--IDISMDYA 140
E Q+S +G+L IA + LL + ++I + + +
Sbjct: 4 EEQQS---LTGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGE 60
Query: 141 DCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPK 200
+ ++ L L Y + ++ + E++ H L +
Sbjct: 61 IDMAIIASKAETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWLLDEGHCF 120
Query: 201 CMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVK---DNPNLVR 257
+ + R + S + M+ G GI +P V+ + +
Sbjct: 121 RDQLVRFCQMKGL---HERQTAYSGGSMEAFMRLVESGQGITFIPQLTVEQLSPSQKELV 177
Query: 258 IMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI 290
+ P V + + +
Sbjct: 178 RPFGMPRPVREVRLAVRQDYSRRKLREQLIGLL 210
>2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor;
structural genomics, DNA-binding protein, PSI-2; 2.30A
{Agrobacterium tumefaciens str}
Length = 135
Score = 70.5 bits (172), Expect = 5e-13
Identities = 16/107 (14%), Positives = 34/107 (31%), Gaps = 8/107 (7%)
Query: 1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRH-----AR 55
K+ + ++A +GS + A + +S + L +
Sbjct: 22 ERLGHGKVELMQLIAETGSISAAGRAMDMSYRRAWLLVDALNHMFRQPVICSQRGGKQGG 81
Query: 56 GLTLTEQGSKLHRVTSEVYHKLETT---QIELQESSVKPSGKLRIAT 99
G LT G++L + ++ I+ E++ P L
Sbjct: 82 GAALTVFGAELLERYRGMEERMNEALREDIDWLEANRNPQDALNRDR 128
>2ql3_A Probable transcriptional regulator, LYSR family protein; APC7314,
rhodococcus SP. RHA1, structural genomics, PSI-2,
protein structure initiative; HET: MSE; 2.05A
{Rhodococcus SP}
Length = 209
Score = 68.2 bits (165), Expect = 2e-12
Identities = 34/207 (16%), Positives = 65/207 (31%), Gaps = 13/207 (6%)
Query: 92 SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD---IDISMDYADCAIRLRK 148
+G + + LG +L L F YP ++ D ++ + D AI
Sbjct: 4 AGPIAVGCYPALGPTILPSMLYAFTAEYPRASVEFREDTQNRLRTQLEGGELDVAIVYDL 63
Query: 149 PIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWL 208
+ + M A H L P+ + +L +H ++ N
Sbjct: 64 DLSPEWQTVPLMTREPMVVLGAEHPLAGVDGPVRLADLAEHPMVLL-----DAPPSTNHA 118
Query: 209 ATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKDNPN-----LVRIMEDVI 263
V R G + ++ + + G G LL D +V+ + +
Sbjct: 119 MDVCREAGFAPRVAYRTANFETARAFVGRGLGWTLLLQRPRVDVTYEGLPVVVKPIAEPK 178
Query: 264 TPSFTVYFCYPEALKNTGKLKAFRNFI 290
S V + + + +AF F+
Sbjct: 179 PASVAVVVAWHQEATLSRVARAFIRFV 205
>2hxr_A HTH-type transcriptional regulator CYNR; CYNR transcriptional
regulator LYSR structural genomics, PSI-2, protein
structure initiative; 2.05A {Escherichia coli K12} PDB:
3hfu_A
Length = 238
Score = 57.1 bits (136), Expect = 4e-09
Identities = 39/244 (15%), Positives = 73/244 (29%), Gaps = 22/244 (9%)
Query: 49 LFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLL 108
++ ++A +L + + + + G LRIA T +
Sbjct: 2 VWRQYAS----------------RALQELGAGKRAIHDVADLTRGSLRIAVTPTFTSYFI 45
Query: 109 QGNLKEFLLLY--PDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMH 166
+ +F Y +Q+Q + K D+ P+ S L L+T +
Sbjct: 46 GPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLA 105
Query: 167 AYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVN 226
A H+ E +++ L L+ + G ++ N
Sbjct: 106 LVVAQHHPLAVHEQVALSRLHDEKLVLL----SAEFATREQIDHYCEKAGLHPQVVIEAN 161
Query: 227 SYLSIMQYCVLGSGIALLPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAF 286
S ++++ S LLP I + L I T + T KAF
Sbjct: 162 SISAVLELIRRTSLSTLLPAAIATQHDGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAF 221
Query: 287 RNFI 290
+
Sbjct: 222 LHMA 225
>2fyi_A HTH-type transcriptional regulator CBL; Lys-R family,
cofactor-binding domain, cysteine biosynthesis; 2.80A
{Escherichia coli K12} SCOP: c.94.1.1
Length = 228
Score = 55.6 bits (132), Expect = 1e-08
Identities = 34/202 (16%), Positives = 62/202 (30%), Gaps = 3/202 (1%)
Query: 91 PSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPI 150
SG L IATT + L +K F L+P+++++LI ++ A
Sbjct: 12 TSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASE 71
Query: 151 QSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLAT 210
+ S+ Q ++ + +S L+
Sbjct: 72 RLSNDPQLVAFPWFRWHHSLLVPHDHPLTQISPLTLESIAKWPLITYRQGITGRSRIDDA 131
Query: 211 VDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD--NPNLVRIMEDVITPSFT 268
R I +S + Y LG GI L+ + + NL+R+ + + T
Sbjct: 132 FARKGLLADIVLSAQDSDVIKT-YVALGLGIGLVAEQSSGEQEEENLIRLDTRHLFDANT 190
Query: 269 VYFCYPEALKNTGKLKAFRNFI 290
V+ + F
Sbjct: 191 VWLGLKRGQLQRNYVWRFLELC 212
>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein
structure initiative; 2.20A {Thermoplasma acidophilum
dsm 1728} SCOP: a.4.5.28 b.43.5.2
Length = 230
Score = 46.1 bits (109), Expect = 9e-06
Identities = 31/201 (15%), Positives = 69/201 (34%), Gaps = 21/201 (10%)
Query: 1 MSFD-----WDKLRVFYVVARSG-----SFTHAAEQLHLSQSSISRQISGLETEVGI-KL 49
MS + + ++ A + + + A+ L +SQ S SR I LE I +
Sbjct: 1 MSLETDDQYYRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRT 60
Query: 50 FYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQ 109
+ + L +TE+G + ++ + + + SG + Q ++Q
Sbjct: 61 VTKRGQILNITEKGLDVLYTEFADLSRILAIKNNVVITGTVTSGMGEGRYYVARKQYIIQ 120
Query: 110 GNLKEFLLLYP-DIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAY 168
K ++ Y + I++ + + I + R ++
Sbjct: 121 FQEKLGIIPYLGTLNIKVDQASLPELRKIRGFR-GIHIEGFKTED----RTFGSVK---- 171
Query: 169 AAPHYLKNCREPLSIQELDKH 189
A P ++N + + E +
Sbjct: 172 AFPAKIQNIPCFVIMPERTVY 192
>3oxn_A Putative transcriptional regulator, LYSR family; structural
genomics, PSI-2, protein structure initiative; 2.70A
{Vibrio parahaemolyticus}
Length = 241
Score = 45.0 bits (106), Expect = 2e-05
Identities = 25/205 (12%), Positives = 50/205 (24%), Gaps = 11/205 (5%)
Query: 92 SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--IDISMDYADCAIRLRKP 149
IATT Q +L L P++ + D D R
Sbjct: 18 DQTFTIATTDYAMQTILPFALPRIYQEAPNVSFNFLPLQHDRLSDQLTYEGADLAICRPT 77
Query: 150 IQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLA 209
L L + + + + +E S+ + H L
Sbjct: 78 GPVEPLRSEILGRVGVLCLLSKQHPLANQEM-SLDDYLSHPHAMIAISDGVKALIEQALI 136
Query: 210 TVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVK---DNPNLVRIMEDVITPS 266
R L+ + + I +P + + +LV
Sbjct: 137 D-----KPQRKMVLRAYHLEAALAIVDTLPIIITVPADLAYLVAERYDLVVKPLPFQFTP 191
Query: 267 FTVYFCYPEALKNTGKLKAFRNFIF 291
F + +++ + R+ +
Sbjct: 192 FDYSMIWHARCEHSPAQEWLRSVVR 216
>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix
prnai nucleotide-binding domain; HET: MSE; 1.80A
{Sulfolobus solfataricus}
Length = 244
Score = 39.7 bits (92), Expect = 8e-04
Identities = 15/85 (17%), Positives = 38/85 (44%), Gaps = 3/85 (3%)
Query: 8 LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSK 65
+++ V+ + A+ L S+ ++ +I+ L+ GI R + L E G
Sbjct: 155 MKLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKF-GILTQKGKDRKVELNELGLN 213
Query: 66 LHRVTSEVYHKLETTQIELQESSVK 90
+ ++ V ++++ ++E+ K
Sbjct: 214 VIKLNKSVIESSKSSEELVKENKGK 238
>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription
regulator, activator, DNA-binding, repressor; HET: SAL;
2.30A {Salmonella typhimurium} SCOP: a.4.5.28
Length = 166
Score = 36.0 bits (83), Expect = 0.011
Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 7/78 (8%)
Query: 8 LRVFYVVARSG---SFTHAAEQLHLSQSSISRQISGLE----TEVGIKLFYRHARGLTLT 60
+ + + S A+ + + Q S+ R + LE R A+ + LT
Sbjct: 56 WVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLT 115
Query: 61 EQGSKLHRVTSEVYHKLE 78
E+ L EV HK
Sbjct: 116 EKAEPLIAEMEEVIHKTR 133
>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor,
winged helix motif, DNA-binding; 1.40A {Methanobacterium
thermoautotrophicum} PDB: 3bpx_A*
Length = 138
Score = 35.7 bits (82), Expect = 0.012
Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 6/77 (7%)
Query: 8 LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFY----RHARGLTLTE 61
+ + R A H+ + +I+R + LE I+ R L +T
Sbjct: 32 VACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDPENRRRYILEVTR 91
Query: 62 QGSKLHRVTSEVYHKLE 78
+G ++ + +V + E
Sbjct: 92 RGEEIIPLILKVEERWE 108
>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural
genomics, MI center for structural genomics, MCSG,
unknown function; 1.78A {Listeria innocua}
Length = 143
Score = 35.4 bits (82), Expect = 0.016
Identities = 11/76 (14%), Positives = 24/76 (31%), Gaps = 6/76 (7%)
Query: 9 RVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFY----RHARGLTLTEQ 62
V + + + A +++R + L + I R L+LT++
Sbjct: 41 SVLEGIEANEPISQKEIALWTKKDTPTVNRIVDVLLRKELIVREISTEDRRISLLSLTDK 100
Query: 63 GSKLHRVTSEVYHKLE 78
G K ++
Sbjct: 101 GRKETTELRDIVEASC 116
>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine
disulfide, MARR-family transcriptional regulator,
DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB:
3hse_A 3hrm_A
Length = 140
Score = 34.5 bits (79), Expect = 0.030
Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 6/77 (7%)
Query: 8 LRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGI----KLFYRHARGLTLTE 61
V + + E++ L +++ + LE + + + ++LTE
Sbjct: 39 YIVLMAIENDEKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRTREEKDERNLQISLTE 98
Query: 62 QGSKLHRVTSEVYHKLE 78
QG + +E+ K+
Sbjct: 99 QGKAIKSPLAEISVKVF 115
>1jgs_A Multiple antibiotic resistance protein MARR; transcription
regulation, DNA-binding, repressor; HET: SAL; 2.30A
{Escherichia coli} SCOP: a.4.5.28
Length = 138
Score = 32.9 bits (75), Expect = 0.083
Identities = 8/75 (10%), Positives = 27/75 (36%), Gaps = 6/75 (8%)
Query: 8 LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKL----FYRHARGLTLTE 61
+V + + T + L + +++R + L + ++ + + LT
Sbjct: 37 FKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTT 96
Query: 62 QGSKLHRVTSEVYHK 76
G+ + ++ +
Sbjct: 97 GGAAICEQCHQLVGQ 111
>2vh1_A FTSQ, cell division protein FTSQ; potra, membrane, septation, cell
cycle, transmembrane, inner membrane; 2.7A {Escherichia
coli}
Length = 220
Score = 32.8 bits (74), Expect = 0.094
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 3/63 (4%)
Query: 99 TTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDID-ISMDYAD-CAIRLRKPIQSSSLI 156
++LG+ L F+ LYP +Q Q D K I + + Y A+ P+
Sbjct: 151 IKLNLGRGDTMKRLARFVELYPVLQQQAQTDGKRISYVDLRYDSGAAVGW-APLPPEEST 209
Query: 157 QRK 159
Q++
Sbjct: 210 QQQ 212
>2fxa_A Protease production regulatory protein HPR; protease porduction,
regulation, structural genomics, PSI, protein structure
initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis}
SCOP: a.4.5.28
Length = 207
Score = 32.7 bits (74), Expect = 0.11
Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 6/76 (7%)
Query: 9 RVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLE----TEVGIKLFYRHARGLTLTEQ 62
+ ++ + S + A+ + S+ LE +L + + LTE+
Sbjct: 52 HILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEE 111
Query: 63 GSKLHRVTSEVYHKLE 78
G+++ E +
Sbjct: 112 GTEVFWSLLEEFDPTR 127
>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for
structural genomics, PSI, protein structure initiative,
MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28
Length = 145
Score = 32.3 bits (73), Expect = 0.14
Identities = 11/77 (14%), Positives = 27/77 (35%), Gaps = 6/77 (7%)
Query: 8 LRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFY----RHARGLTLTE 61
+ + G + L +++S+++ + LE + + R A L +T
Sbjct: 36 FDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITR 95
Query: 62 QGSKLHRVTSEVYHKLE 78
+G ++ E
Sbjct: 96 KGEEVIEKVIERRENFI 112
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.9 bits (71), Expect = 0.17
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 11/32 (34%)
Query: 105 QNL--LQGNLKEFLLLY-----PDIQIQLILD 129
Q L LQ +LK LY P + I+ ++
Sbjct: 20 QALKKLQASLK----LYADDSAPALAIKATME 47
>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance
regulator, virulence determinant, transcriptional
factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28
Length = 142
Score = 31.8 bits (72), Expect = 0.18
Identities = 11/77 (14%), Positives = 24/77 (31%), Gaps = 6/77 (7%)
Query: 8 LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLF----YRHARGLTLTE 61
V ++ +L L ++S + +E IK + + LT+
Sbjct: 40 FLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTD 99
Query: 62 QGSKLHRVTSEVYHKLE 78
+ + S K+
Sbjct: 100 KSETIRPELSNASDKVA 116
>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1,
putative MARR-like transcription regulator, structural
genomics; 2.38A {Bacillus cereus atcc 10987}
Length = 139
Score = 31.1 bits (70), Expect = 0.33
Identities = 12/77 (15%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 8 LRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLF----YRHARGLTLTE 61
V V+A+SG + + E + S+++ I ++ + + + + LT+
Sbjct: 36 FGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTEKNPNDQRETLVYLTK 95
Query: 62 QGSKLHRVTSEVYHKLE 78
+G + + Y
Sbjct: 96 KGEETKKQVDVQYSDFL 112
>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator,
APC5857, structural genomics, PSI, protein structure
initiative; 1.80A {Pseudomonas aeruginosa} SCOP:
a.4.5.28
Length = 146
Score = 30.4 bits (68), Expect = 0.45
Identities = 10/59 (16%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 24 AEQLHLSQSSISRQISGLETEVGIKLFY----RHARGLTLTEQGSKLHRVTSEVYHKLE 78
A+ + + +++R + GLE++ ++ R A+ + LT + L + +
Sbjct: 59 AQSVGVEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIADIEAIAASVR 117
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 29.5 bits (66), Expect = 0.85
Identities = 22/187 (11%), Positives = 46/187 (24%), Gaps = 81/187 (43%)
Query: 166 HAYAAPHYLKNCREPLSIQELDKH-----------------------NLITFGDLIPKCM 202
+ P + + L+ +++ + NL+ G P+ +
Sbjct: 330 NNEGVPSPMLSISN-LTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGP--PQSL 386
Query: 203 EDFN-WLATVDRPIGE-----------PRISCLQVNSYLSIMQYCVLGSGIALLP---DY 247
N L P G + S N +L + P
Sbjct: 387 YGLNLTLRKAKAPSGLDQSRIPFSERKLKFS----NRFLPVA-----------SPFHSHL 431
Query: 248 IVKDNPNLVRIMEDVITPSFTVYFCYPEALK------NTGKLKAFRNF-----------I 290
+V + I +D++ + + F + ++ G R I
Sbjct: 432 LVPASD---LINKDLVKNNVS--FN-AKDIQIPVYDTFDG--SDLRVLSGSISERIVDCI 483
Query: 291 FLKARDW 297
W
Sbjct: 484 IRLPVKW 490
>2vh2_A FTSQ, cell division protein FTSQ; potra, cell cycle; 3.4A {Yersinia
enterocolitica}
Length = 255
Score = 29.4 bits (65), Expect = 1.00
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 99 TTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYAD-CAIRLR 147
++LG++ G L+ F+ LYP +Q Q +D + Y AI
Sbjct: 177 VRLELGRDDRMGRLQRFIELYPMLQQQPDKRVSYVD--LRYETGAAIGWA 224
>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structural
genomics, protein structure initiative; HET: GOL; 2.00A
{Rhodococcus jostii RHA1}
Length = 150
Score = 28.4 bits (63), Expect = 2.0
Identities = 12/77 (15%), Positives = 21/77 (27%), Gaps = 7/77 (9%)
Query: 9 RVFYVVARSG---SFTHAAEQLHLSQSSISRQISGLETEVGIKL----FYRHARGLTLTE 61
V + + A + L S I + LE + R + + TE
Sbjct: 43 SVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATE 102
Query: 62 QGSKLHRVTSEVYHKLE 78
+G +L
Sbjct: 103 EGRRLRDDAKARVDAAH 119
>1fjm_A Protein serine/threonine phosphatase-1 (alpha isoform, type 1);
hydrolase, complex (hydrolase/toxin) complex; HET: ADD;
2.10A {Oryctolagus cuniculus} SCOP: d.159.1.3
Length = 330
Score = 28.1 bits (62), Expect = 2.2
Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 9/67 (13%)
Query: 158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFG--DLIPKCMEDFNWLATVD--- 212
R+LVT+ ++AP+Y ++ +D+ + +F K + + ++
Sbjct: 261 RQLVTL----FSAPNYCGEFDNAGAMMSVDETLMCSFQILKPADKNKGKYGQFSGLNPGG 316
Query: 213 RPIGEPR 219
RPI PR
Sbjct: 317 RPITPPR 323
>1z91_A Organic hydroperoxide resistance transcriptional regulator; OHRR,
MARR family, bacterial transcription factor, DNA binding
protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB:
1z9c_A*
Length = 147
Score = 27.3 bits (60), Expect = 4.0
Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 24 AEQLHLSQSSISRQISGLETEVGIKLF----YRHARGLTLTEQGSKLHRVTSEVYHKLE 78
EQL+L +++ + +E + I + ++LTE G+ L ++ +
Sbjct: 61 GEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTIL 119
>2wus_R RODZ, putative uncharacterized protein; structural protein, cell
WALL morphogenesis, bacterial cytos bacterial actin;
2.90A {Thermotoga maritima}
Length = 112
Score = 27.3 bits (60), Expect = 4.8
Identities = 10/73 (13%), Positives = 29/73 (39%), Gaps = 3/73 (4%)
Query: 44 EVGIKL-FYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLR-IATTI 101
E+G R R +TL + + + ++E ++ ++ V ++ + +
Sbjct: 7 ELGETFRKKREERRITLLDASLFTN-INPSKLKRIEEGDLKGLDAEVYIKSYIKRYSEFL 65
Query: 102 DLGQNLLQGNLKE 114
+L + + +E
Sbjct: 66 ELSPDEMLKLYEE 78
>3pfd_A Acyl-COA dehydrogenase; structural genomics, seattle structural
genomics center for infectious disease, ssgcid; HET:
FDA; 2.10A {Mycobacterium thermoresistibile}
Length = 393
Score = 27.1 bits (60), Expect = 4.9
Identities = 8/41 (19%), Positives = 17/41 (41%)
Query: 133 IDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHY 173
+D ++ Y + +P+ + +Q L + M AA
Sbjct: 271 LDAAIAYTKERKQFGRPVSDNQGVQFMLADMAMKIEAARLM 311
>1z05_A Transcriptional regulator, ROK family; structural genomics, PSI,
protein structure initiative; 2.00A {Vibrio cholerae o1
biovar eltor str} SCOP: a.4.5.63 c.55.1.10 c.55.1.10
Length = 429
Score = 27.2 bits (59), Expect = 5.4
Identities = 7/38 (18%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 9 RVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETE 44
RV+ ++ + G + +++ L+ +SI++ L
Sbjct: 43 RVYKLIDQKGPISRIDLSKESELAPASITKITRELIDA 80
>1qgc_4 Protein (inmunoglobuline); virus-antibody complex, icosahedral
virus, virus/immune system complex; 30.00A {Mus
musculus} SCOP: i.6.1.1
Length = 438
Score = 26.9 bits (59), Expect = 6.3
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 15/56 (26%)
Query: 57 LTLT-EQGSKLHRVTSEVYHKLETT-----------QIELQES---SVKPSGKLRI 97
LTLT ++ + + T E HK T+ ++ L ES VKP G L++
Sbjct: 183 LTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNECEVMLVESGGGLVKPGGSLKL 238
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.323 0.138 0.410
Gapped
Lambda K H
0.267 0.0642 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,556,784
Number of extensions: 114819
Number of successful extensions: 354
Number of sequences better than 10.0: 1
Number of HSP's gapped: 322
Number of HSP's successfully gapped: 54
Length of query: 299
Length of database: 5,693,230
Length adjustment: 92
Effective length of query: 207
Effective length of database: 3,462,782
Effective search space: 716795874
Effective search space used: 716795874
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: 56 (25.5 bits)