RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6501
(174 letters)
>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding,
transcription; NMR {Trichoderma reesei}
Length = 107
Score = 89.6 bits (222), Expect = 5e-24
Identities = 31/92 (33%), Positives = 47/92 (51%), Gaps = 4/92 (4%)
Query: 2 AGTNKQPGTT--KNTAKLDRETEELKHEKVPLDLAKLLMQGRQA--KGWSQKDLATKINE 57
A + G T + K+DR + +K + V ++ K + QGRQ +Q +L +I E
Sbjct: 2 AMDPEFAGGTEGQRLTKVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGE 61
Query: 58 KPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
V YE G P+Q I+ KMER L ++LR
Sbjct: 62 TAATVASYERGTATPDQNILSKMERVLNVKLR 93
Score = 82.3 bits (203), Expect = 3e-21
Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 4/87 (4%)
Query: 92 AGTNKQPGTT--KNTAKLDRETEELKHEKVPLDLAKLLMQGRQA--KGWSQKDLATKINE 147
A + G T + K+DR + +K + V ++ K + QGRQ +Q +L +I E
Sbjct: 2 AMDPEFAGGTEGQRLTKVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGE 61
Query: 148 KPQIVNDYEGGRGIPNQAIIGKMERAL 174
V YE G P+Q I+ KMER L
Sbjct: 62 TAATVASYERGTATPDQNILSKMERVL 88
>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha,
helix-turn-helix, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: a.35.1.12
Length = 91
Score = 83.3 bits (206), Expect = 9e-22
Identities = 38/69 (55%), Positives = 55/69 (79%)
Query: 21 TEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 80
+ ++V L++ K++ QGRQ+KG +QKDLATKINEKPQ++ DYE GR IPN ++GK+
Sbjct: 2 SSGSSGDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKI 61
Query: 81 ERALGIRLR 89
ERA+G++LR
Sbjct: 62 ERAIGLKLR 70
Score = 76.3 bits (188), Expect = 4e-19
Identities = 35/64 (54%), Positives = 50/64 (78%)
Query: 111 TEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 170
+ ++V L++ K++ QGRQ+KG +QKDLATKINEKPQ++ DYE GR IPN ++GK+
Sbjct: 2 SSGSSGDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKI 61
Query: 171 ERAL 174
ERA+
Sbjct: 62 ERAI 65
>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria
phage P22} SCOP: a.35.1.2
Length = 76
Score = 43.0 bits (102), Expect = 1e-06
Identities = 8/55 (14%), Positives = 19/55 (34%)
Query: 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
+ + + R+ Q L + ++ +E PN + + +AL
Sbjct: 5 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQC 59
Score = 40.7 bits (96), Expect = 1e-05
Identities = 8/53 (15%), Positives = 19/53 (35%)
Query: 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
+ + + R+ Q L + ++ +E PN + + +AL
Sbjct: 5 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKAL 57
>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription
complex, serine kinase, DNA-bindin mercury derivative,
repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B*
3hzi_B*
Length = 88
Score = 43.3 bits (102), Expect = 2e-06
Identities = 19/72 (26%), Positives = 33/72 (45%)
Query: 30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
P LA + RQ GW+Q +LA KI K ++++E K+ ++L + +
Sbjct: 10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMT 69
Query: 90 VNAGTNKQPGTT 101
+ N P +T
Sbjct: 70 LCDAKNASPEST 81
Score = 38.3 bits (89), Expect = 1e-04
Identities = 16/55 (29%), Positives = 26/55 (47%)
Query: 120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
P LA + RQ GW+Q +LA KI K ++++E K+ ++L
Sbjct: 10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSL 64
>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix,
DNA-binding, transcription, transcription regulation;
1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB:
3jxb_C 3jxc_L 3jxd_L
Length = 68
Score = 41.8 bits (99), Expect = 4e-06
Identities = 8/55 (14%), Positives = 19/55 (34%)
Query: 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
+ + + R+ Q L + ++ +E PN + + +AL
Sbjct: 5 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQC 59
Score = 39.5 bits (93), Expect = 3e-05
Identities = 8/53 (15%), Positives = 19/53 (35%)
Query: 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
+ + + R+ Q L + ++ +E PN + + +AL
Sbjct: 5 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKAL 57
>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT,
structural genomics, PSI-2, protein structure
initiative; NMR {Eubacterium rectale atcc 33656}
Length = 94
Score = 42.0 bits (99), Expect = 5e-06
Identities = 11/54 (20%), Positives = 19/54 (35%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
++ L +Q ++A I PQ N + G IP + + I
Sbjct: 10 FSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNI 63
Score = 40.1 bits (94), Expect = 3e-05
Identities = 10/48 (20%), Positives = 18/48 (37%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 170
++ L +Q ++A I PQ N + G IP + +
Sbjct: 10 FSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQAL 57
>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein
structure initiative, MI center for structural
genomics, MCSG; 1.65A {Cytophaga hutchinsonii}
Length = 73
Score = 40.8 bits (96), Expect = 9e-06
Identities = 8/49 (16%), Positives = 19/49 (38%)
Query: 41 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
KG + L +++ V+ + P+ + + AL + +R
Sbjct: 17 LAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVR 65
Score = 38.1 bits (89), Expect = 9e-05
Identities = 7/44 (15%), Positives = 16/44 (36%)
Query: 131 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
KG + L +++ V+ + P+ + + AL
Sbjct: 17 LAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEAL 60
>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing
system, phosphoryltransferase, HEL helix motif,
transcription regulator; 3.20A {Streptococcus
pneumoniae}
Length = 158
Score = 41.1 bits (96), Expect = 4e-05
Identities = 19/127 (14%), Positives = 44/127 (34%), Gaps = 3/127 (2%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA 92
+ K + R+ +Q + A + ++ YE G + +I + + +
Sbjct: 2 IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYVDIV 61
Query: 93 GTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIV 152
G +K +L + E +K +L L + + ++G S D + +
Sbjct: 62 GEDKML-NPVEDYELTLKIEIVKERG--ANLLSRLYRYQDSQGISIDDESNPWILMSDDL 118
Query: 153 NDYEGGR 159
+D
Sbjct: 119 SDLIHTN 125
Score = 38.4 bits (89), Expect = 3e-04
Identities = 8/48 (16%), Positives = 19/48 (39%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 170
+ K + R+ +Q + A + ++ YE G + +I +
Sbjct: 2 IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDII 49
>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics,
PSI-2, protein structure initiative; HET: MSE; 1.65A
{Bacteroides fragilis}
Length = 76
Score = 39.2 bits (92), Expect = 4e-05
Identities = 7/49 (14%), Positives = 21/49 (42%)
Query: 41 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
K + + LA ++ + ++ + + P+ ++ K+ L + R
Sbjct: 19 LAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELLNVDPR 67
Score = 36.5 bits (85), Expect = 4e-04
Identities = 6/44 (13%), Positives = 19/44 (43%)
Query: 131 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
K + + LA ++ + ++ + + P+ ++ K+ L
Sbjct: 19 LAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELL 62
>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein,
xenobiotic response E family of transcriptional
regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae
PV}
Length = 83
Score = 39.3 bits (92), Expect = 5e-05
Identities = 14/56 (25%), Positives = 23/56 (41%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
L LL++ R A G +QK+LA ++ V+ E + R +G
Sbjct: 15 LLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDP 70
Score = 35.8 bits (83), Expect = 8e-04
Identities = 13/52 (25%), Positives = 22/52 (42%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
L LL++ R A G +QK+LA ++ V+ E + R +
Sbjct: 15 LLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGI 66
>3ivp_A Putative transposon-related DNA-binding protein; APC62618,
clostridium diffic structural genomics, PSI-2, protein
structure initiative; HET: PG4; 2.02A {Clostridium
difficile}
Length = 126
Score = 39.0 bits (91), Expect = 1e-04
Identities = 10/105 (9%), Positives = 40/105 (38%), Gaps = 2/105 (1%)
Query: 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN 91
L + + R+ +G +++ + I P+ + + E P+ ++ + L + +
Sbjct: 12 ALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSVDEF 71
Query: 92 AGTNKQPGTTKNTAKLDRETEELKHEKVPL--DLAKLLMQGRQAK 134
+ +L+ + + + + +A +++ ++
Sbjct: 72 FLPASSQVKSTKRRQLENKIDNFTDADLVIMESVADGIVKSKEVG 116
Score = 36.0 bits (83), Expect = 0.002
Identities = 8/53 (15%), Positives = 23/53 (43%)
Query: 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
L + + R+ +G +++ + I P+ + + E P+ ++ + L
Sbjct: 12 ALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLL 64
>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA
binding protein, transcription regulator; HET: CME;
1.95A {Enterobacteria phage P2}
Length = 84
Score = 38.2 bits (89), Expect = 1e-04
Identities = 11/58 (18%), Positives = 24/58 (41%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRV 90
L +LL + R+ SQ +LA + ++ E + + ++ + RL +
Sbjct: 11 LVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVVASRLGL 68
Score = 34.0 bits (78), Expect = 0.004
Identities = 9/52 (17%), Positives = 21/52 (40%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
L +LL + R+ SQ +LA + ++ E + + ++ +
Sbjct: 11 LVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVV 62
>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein
fold, OPPF, STRU genomics, oxford protein production
facility; 2.80A {Neisseria gonorrhoeae}
Length = 141
Score = 39.1 bits (91), Expect = 1e-04
Identities = 15/77 (19%), Positives = 30/77 (38%)
Query: 12 KNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI 71
+ A +DR + + + + R KG++Q +LAT ++ E +
Sbjct: 48 RRKAAMDRAAARIADKIALKAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQS 107
Query: 72 PNQAIIGKMERALGIRL 88
+ K+ ALG+
Sbjct: 108 LQDKTVQKLANALGVSP 124
Score = 35.6 bits (82), Expect = 0.002
Identities = 14/73 (19%), Positives = 28/73 (38%)
Query: 102 KNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI 161
+ A +DR + + + + R KG++Q +LAT ++ E +
Sbjct: 48 RRKAAMDRAAARIADKIALKAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQS 107
Query: 162 PNQAIIGKMERAL 174
+ K+ AL
Sbjct: 108 LQDKTVQKLANAL 120
>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure
initiative, MI center for structural genomics, MCSG,
transcription regulat; HET: MSE; 1.90A {Listeria
innocua}
Length = 114
Score = 38.6 bits (90), Expect = 2e-04
Identities = 9/54 (16%), Positives = 22/54 (40%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
A+ L + ++ G +A +N + + V Y G P+ + ++ +
Sbjct: 10 FAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHL 63
Score = 38.2 bits (89), Expect = 2e-04
Identities = 9/48 (18%), Positives = 21/48 (43%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 170
A+ L + ++ G +A +N + + V Y G P+ + ++
Sbjct: 10 FAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRL 57
>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434}
SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L*
1r63_A 2r63_A 1sq8_A
Length = 69
Score = 36.8 bits (86), Expect = 2e-04
Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
++ + R G +Q +LA K+ Q + E G+ + ++ ALG+
Sbjct: 2 ISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGK-TKRPRFLPELASALGV 54
Score = 34.9 bits (81), Expect = 0.001
Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
++ + R G +Q +LA K+ Q + E G+ + ++ AL
Sbjct: 2 ISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGK-TKRPRFLPELASAL 52
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A
{Enterobacteria phage lambda}
Length = 236
Score = 38.8 bits (90), Expect = 3e-04
Identities = 10/54 (18%), Positives = 19/54 (35%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
L + + + G SQ+ +A K+ V G N + + L +
Sbjct: 18 LKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKV 71
Score = 36.9 bits (85), Expect = 0.002
Identities = 10/52 (19%), Positives = 18/52 (34%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
L + + + G SQ+ +A K+ V G N + + L
Sbjct: 18 LKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKIL 69
>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding
protein, helix-turn-H restriction-modification,
transcription; 2.00A {Citrobacter SP} PDB: 3lis_A
Length = 98
Score = 37.2 bits (86), Expect = 4e-04
Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 4/60 (6%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQ----IVNDYEGGRGIPNQAIIGKMERALGIRL 88
L + L R G SQ+ L +N YE G+ P+ + ++ + L I +
Sbjct: 2 LIRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKIPV 61
Score = 35.2 bits (81), Expect = 0.002
Identities = 13/56 (23%), Positives = 22/56 (39%), Gaps = 4/56 (7%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQ----IVNDYEGGRGIPNQAIIGKMERAL 174
L + L R G SQ+ L +N YE G+ P+ + ++ + L
Sbjct: 2 LIRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVL 57
>1zug_A Phage 434 CRO protein; gene regulating protein, transcription
regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A
3cro_L*
Length = 71
Score = 36.1 bits (84), Expect = 4e-04
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
L++ L + R A +Q +LATK K Q + E G + + ++ AL
Sbjct: 4 LSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRFLF-EIAMALNC 56
Score = 34.2 bits (79), Expect = 0.002
Identities = 13/45 (28%), Positives = 21/45 (46%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII 167
L++ L + R A +Q +LATK K Q + E G + +
Sbjct: 4 LSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRFLF 48
>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional
regulator, transcription regulator; 1.69A {Aeromonas
hydrophila} SCOP: a.35.1.3
Length = 74
Score = 35.7 bits (83), Expect = 8e-04
Identities = 18/68 (26%), Positives = 25/68 (36%)
Query: 21 TEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 80
H + + L + R AKG SQ+ LA V E G+ + I K+
Sbjct: 2 QSHHDHYADLVKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKL 61
Query: 81 ERALGIRL 88
AL I
Sbjct: 62 ATALDIEP 69
Score = 31.9 bits (73), Expect = 0.018
Identities = 17/64 (26%), Positives = 24/64 (37%)
Query: 111 TEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 170
H + + L + R AKG SQ+ LA V E G+ + I K+
Sbjct: 2 QSHHDHYADLVKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKL 61
Query: 171 ERAL 174
AL
Sbjct: 62 ATAL 65
>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein
structure initiative, midwest center for structural
genomic binding; 1.80A {Silicibacter pomeroyi}
Length = 86
Score = 33.7 bits (77), Expect = 0.006
Identities = 13/53 (24%), Positives = 20/53 (37%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALG 85
L + L Q R G +Q DLA ++++ V E + K A
Sbjct: 15 LCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWMAACE 67
Score = 33.3 bits (76), Expect = 0.007
Identities = 11/37 (29%), Positives = 17/37 (45%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR 159
L + L Q R G +Q DLA ++++ V E
Sbjct: 15 LCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRE 51
>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription
factor, DNA binding protein; 1.88A {Neisseria
meningitidis}
Length = 114
Score = 34.0 bits (78), Expect = 0.006
Identities = 19/56 (33%), Positives = 26/56 (46%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
LA + R KGWSQ++LA + V+ E R + I KM ALG+
Sbjct: 22 LAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVERKRWNIALSNIEKMAAALGVAA 77
Score = 30.6 bits (69), Expect = 0.095
Identities = 18/52 (34%), Positives = 24/52 (46%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
LA + R KGWSQ++LA + V+ E R + I KM AL
Sbjct: 22 LAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVERKRWNIALSNIEKMAAAL 73
>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of
BLDD; 1.81A {Streptomyces coelicolor}
Length = 71
Score = 32.8 bits (75), Expect = 0.008
Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 2/52 (3%)
Query: 37 LMQGRQAKGWSQKDLATKINE--KPQIVNDYEGGRGIPNQAIIGKMERALGI 86
L R +G S + K K +V YE G + ++ G+
Sbjct: 13 LRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDRAVTVQRLAELADFYGV 64
Score = 30.1 bits (68), Expect = 0.065
Identities = 10/50 (20%), Positives = 16/50 (32%), Gaps = 2/50 (4%)
Query: 127 LMQGRQAKGWSQKDLATKINE--KPQIVNDYEGGRGIPNQAIIGKMERAL 174
L R +G S + K K +V YE G + ++
Sbjct: 13 LRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDRAVTVQRLAELADFY 62
>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA
binding motif, transcriptional regulator, bacter
antitoxin, Zn binding protein, transcription
regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB:
3gn5_A* 3gn5_B* 2kz8_A
Length = 133
Score = 33.6 bits (76), Expect = 0.010
Identities = 8/53 (15%), Positives = 19/53 (35%)
Query: 25 KHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII 77
+ +++ R+ +QK+ + + YE G P+ + I
Sbjct: 64 ASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTI 116
Score = 33.6 bits (76), Expect = 0.010
Identities = 8/53 (15%), Positives = 19/53 (35%)
Query: 115 KHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII 167
+ +++ R+ +QK+ + + YE G P+ + I
Sbjct: 64 ASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTI 116
>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif,
transcriptional ACTI human pathogen, transcription
activator; 1.75A {Corynebacterium glutamicum} PDB:
3f51_A
Length = 117
Score = 32.7 bits (74), Expect = 0.017
Identities = 12/48 (25%), Positives = 23/48 (47%)
Query: 41 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
R KG + ++LA P +++ E GR + ++ + ALG +
Sbjct: 37 RADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHALGASV 84
Score = 28.8 bits (64), Expect = 0.40
Identities = 11/44 (25%), Positives = 21/44 (47%)
Query: 131 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
R KG + ++LA P +++ E GR + ++ + AL
Sbjct: 37 RADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHAL 80
>4ghj_A Probable transcriptional regulator; structural genomics, niaid,
national institute of allergy AN infectious diseases;
HET: MSE; 1.75A {Vibrio vulnificus}
Length = 101
Score = 32.6 bits (74), Expect = 0.018
Identities = 13/76 (17%), Positives = 29/76 (38%), Gaps = 2/76 (2%)
Query: 11 TKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG 70
T+N + + + ++ L Q R + +Q ++A + V + E G+
Sbjct: 15 TENLYFQSNAMKHVTAAALAEEIGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAEKGKV 74
Query: 71 IPNQAIIGKMERALGI 86
I+ + AL +
Sbjct: 75 QL--DIMIAILMALDL 88
Score = 31.5 bits (71), Expect = 0.046
Identities = 10/62 (16%), Positives = 23/62 (37%)
Query: 101 TKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG 160
T+N + + + ++ L Q R + +Q ++A + V + E G+
Sbjct: 15 TENLYFQSNAMKHVTAAALAEEIGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAEKGKV 74
Query: 161 IP 162
Sbjct: 75 QL 76
>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix,
transcription/DNA complex; HET: DNA; 1.80A
{Enterobacteria phage lambda} SCOP: a.35.1.2 PDB:
1lrp_A 1rio_A 1lli_A*
Length = 92
Score = 32.3 bits (73), Expect = 0.021
Identities = 10/55 (18%), Positives = 19/55 (34%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR 87
L + + + G SQ+ +A K+ V G N + + L +
Sbjct: 18 LKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVS 72
>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding
protein, binding protein; NMR {Enterobacteria phage P2}
PDB: 2xcj_A
Length = 99
Score = 32.2 bits (73), Expect = 0.023
Identities = 9/56 (16%), Positives = 25/56 (44%)
Query: 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR 87
+++ ++ R+++ S++ LA ++ YE GR P ++ + +
Sbjct: 4 TISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQTPQFT 59
Score = 31.4 bits (71), Expect = 0.037
Identities = 9/49 (18%), Positives = 24/49 (48%)
Query: 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 170
+++ ++ R+++ S++ LA ++ YE GR P ++ +
Sbjct: 4 TISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNI 52
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 33.9 bits (77), Expect = 0.025
Identities = 21/123 (17%), Positives = 35/123 (28%), Gaps = 40/123 (32%)
Query: 39 QGRQAKG---------------WSQKDLATK----------INEKPQIVNDYEGGRGIPN 73
QG Q +G W++ D K + P + + GG
Sbjct: 1624 QGSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEK--- 1680
Query: 74 QAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEEL--KHEKVPLDL------AK 125
GK R + + + T K +++ + + EK L A
Sbjct: 1681 ----GKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPAL 1736
Query: 126 LLM 128
LM
Sbjct: 1737 TLM 1739
Score = 32.7 bits (74), Expect = 0.052
Identities = 16/95 (16%), Positives = 28/95 (29%), Gaps = 35/95 (36%)
Query: 40 GRQAKGWSQKDL-------ATKINEKPQIVND-YEGGRGIPNQAIIGKMERALGIRLRVN 91
GR A +SQ+ L + +IVN E Q +
Sbjct: 1815 GRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQ-----QYVAA------------- 1856
Query: 92 AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKL 126
G + + +K +K+ D+ +L
Sbjct: 1857 -------GDLRALDTVTNVLNFIKLQKI--DIIEL 1882
Score = 26.9 bits (59), Expect = 5.0
Identities = 12/61 (19%), Positives = 17/61 (27%), Gaps = 28/61 (45%)
Query: 129 QGRQAKG---------------WSQKDLATK----------INEKPQ---IVNDYEGGRG 160
QG Q +G W++ D K + P I E G+
Sbjct: 1624 QGSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKR 1683
Query: 161 I 161
I
Sbjct: 1684 I 1684
>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix
XRE-family like protei transcription regulator, PSI-2;
2.60A {Staphylococcus aureus subsp}
Length = 111
Score = 32.0 bits (72), Expect = 0.030
Identities = 8/46 (17%), Positives = 17/46 (36%)
Query: 41 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
R G +QK+L + + + E +++ K A +
Sbjct: 32 RTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAFNV 77
Score = 30.0 bits (67), Expect = 0.16
Identities = 8/44 (18%), Positives = 16/44 (36%)
Query: 131 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
R G +QK+L + + + E +++ K A
Sbjct: 32 RTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAF 75
>2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif,
XRE-family, structural genomics, PSI-2, protein
structure initiative; 2.00A {Agrobacterium tumefaciens
str} SCOP: a.35.1.3
Length = 99
Score = 31.9 bits (72), Expect = 0.031
Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 18 DRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQA 75
E+L + + R+A +Q++ + + + + D+E GR P+Q
Sbjct: 20 PLSAEQLASAPRMPRIKII----RRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQP 73
Score = 31.9 bits (72), Expect = 0.031
Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 108 DRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQA 165
E+L + + R+A +Q++ + + + + D+E GR P+Q
Sbjct: 20 PLSAEQLASAPRMPRIKII----RRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQP 73
>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix;
HET: DNA; 2.10A {Enterobacter SP} PDB: 3clc_A*
Length = 82
Score = 31.5 bits (72), Expect = 0.034
Identities = 11/56 (19%), Positives = 24/56 (42%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
++ ++ + R KG +Q+DLA K N ++ E + + + L +
Sbjct: 12 VSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSD 67
Score = 27.6 bits (62), Expect = 0.75
Identities = 11/52 (21%), Positives = 23/52 (44%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
++ ++ + R KG +Q+DLA K N ++ E + + + L
Sbjct: 12 VSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGL 63
>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus
caldolyticus} SCOP: a.35.1.3
Length = 77
Score = 30.7 bits (70), Expect = 0.054
Identities = 15/56 (26%), Positives = 24/56 (42%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
+ L + R KG SQ++LA +++ E G + I K+ AL I
Sbjct: 11 FGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPA 66
Score = 27.2 bits (61), Expect = 0.98
Identities = 14/52 (26%), Positives = 23/52 (44%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
+ L + R KG SQ++LA +++ E G + I K+ AL
Sbjct: 11 FGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAAL 62
>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix,
restriction- modification, transcription regulator;
2.80A {Enterobacter SP} PDB: 3fya_A
Length = 99
Score = 31.2 bits (71), Expect = 0.056
Identities = 11/56 (19%), Positives = 24/56 (42%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
++ ++ + R KG +Q+DLA K N ++ E + + + L +
Sbjct: 29 VSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSD 84
Score = 27.4 bits (61), Expect = 1.2
Identities = 11/52 (21%), Positives = 23/52 (44%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
++ ++ + R KG +Q+DLA K N ++ E + + + L
Sbjct: 29 VSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGL 80
>2bnm_A Epoxidase; oxidoreductase, cupin, HTH, cation-dependant, zinc,
fosfomycin; 1.7A {Streptomyces wedmorensis} SCOP:
a.35.1.3 b.82.1.10 PDB: 1zz7_A 1zz8_A 1zz9_A 1zzb_A
1zz6_A 1zzc_A 2bnn_A 2bno_A 3scf_A 3scg_A 3sch_A
Length = 198
Score = 31.4 bits (71), Expect = 0.091
Identities = 20/108 (18%), Positives = 38/108 (35%), Gaps = 3/108 (2%)
Query: 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIP-NQAIIGKMERALGIRLR- 89
A+LL R+ LA+ + E P+ V +E G G +G++ LG +
Sbjct: 10 GFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGA 69
Query: 90 -VNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGW 136
N +R + + V + L++ ++A
Sbjct: 70 LTPPAGNDLDDGVIIQMPDERPILKGVRDNVDYYVYNCLVRTKRAPSL 117
Score = 26.8 bits (59), Expect = 3.0
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIP-NQAIIGKMERAL 174
A+LL R+ LA+ + E P+ V +E G G +G++ L
Sbjct: 10 GFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVL 63
>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus
thuringiensis serovar ISRAELE35646}
Length = 293
Score = 31.3 bits (70), Expect = 0.12
Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
L + + R +G +QK L+ I + ++ E G P+ I+ + L I +
Sbjct: 4 EKLGSEIKKIRVLRGLTQKQLSENICHQSEVSR-IESGAVYPSMDILQGIAAKLQIPII 61
Score = 29.4 bits (65), Expect = 0.55
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
L + + R +G +QK L+ I + ++ E G P+ I+ + L
Sbjct: 4 EKLGSEIKKIRVLRGLTQKQLSENICHQSEVSR-IESGAVYPSMDILQGIAAKL 56
>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif,
biofilm, repressor, SINI; 1.90A {Bacillus subtilis}
Length = 78
Score = 29.6 bits (67), Expect = 0.15
Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 1/65 (1%)
Query: 25 KHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE-GGRGIPNQAIIGKMERA 83
H + + + Q R+ KG+S +LA K ++ E + P+ + K+
Sbjct: 3 SHHHHHHMIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAV 62
Query: 84 LGIRL 88
L + +
Sbjct: 63 LDVSV 67
Score = 26.1 bits (58), Expect = 2.2
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 1/61 (1%)
Query: 115 KHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE-GGRGIPNQAIIGKMERA 173
H + + + Q R+ KG+S +LA K ++ E + P+ + K+
Sbjct: 3 SHHHHHHMIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAV 62
Query: 174 L 174
L
Sbjct: 63 L 63
>3kz3_A Repressor protein CI; five helix bundle, DNA-binding,
transcription, transcription regulation; 1.64A
{Enterobacteria phage lambda}
Length = 80
Score = 28.8 bits (64), Expect = 0.27
Identities = 9/55 (16%), Positives = 18/55 (32%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR 87
L + + + G S + +A K+ V G N + + L +
Sbjct: 13 LKAIWEKKKNELGLSYESVADKMGMGQSAVAALFNGINALNAYNAALLAKILKVS 67
>1b0n_A Protein (SINR protein); transcription regulator, antagonist,
sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1
a.35.1.3 PDB: 2yal_A
Length = 111
Score = 29.4 bits (66), Expect = 0.29
Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE-GGRGIPNQAIIGKMERALGIRL 88
+ + + Q R+ KG+S +LA K ++ E + P+ + K+ L + +
Sbjct: 2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSV 58
Score = 26.3 bits (58), Expect = 3.1
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE-GGRGIPNQAIIGKMERAL 174
+ + + Q R+ KG+S +LA K ++ E + P+ + K+ L
Sbjct: 2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVL 54
>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding
protein; 1.00A {Staphylococcus aureus subsp}
Length = 130
Score = 29.0 bits (65), Expect = 0.38
Identities = 6/38 (15%), Positives = 15/38 (39%)
Query: 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR 69
+ + L R+ G + +L + K +++ E
Sbjct: 3 TVGEALKGRRERLGMTLTELEQRTGIKREMLVHIENNE 40
Score = 29.0 bits (65), Expect = 0.38
Identities = 6/38 (15%), Positives = 15/38 (39%)
Query: 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR 159
+ + L R+ G + +L + K +++ E
Sbjct: 3 TVGEALKGRRERLGMTLTELEQRTGIKREMLVHIENNE 40
>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET:
GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A*
2xj3_A 2xiu_A
Length = 66
Score = 27.9 bits (63), Expect = 0.43
Identities = 13/48 (27%), Positives = 21/48 (43%)
Query: 41 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
R+ K SQ +LA + Q +N E + P+ + K+ L L
Sbjct: 10 REKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPL 57
Score = 27.5 bits (62), Expect = 0.48
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 131 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIP 162
R+ K SQ +LA + Q +N E + P
Sbjct: 10 REKKKISQSELAALLEVSRQTINGIEKNKYNP 41
>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein
structure initiative, midwest center for structural
genomics; 2.00A {Lactobacillus plantarum WCFS1}
Length = 78
Score = 28.0 bits (63), Expect = 0.44
Identities = 12/49 (24%), Positives = 17/49 (34%), Gaps = 1/49 (2%)
Query: 41 RQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRL 88
+ + +AT VN GR P I K+ LGI +
Sbjct: 16 ITQQNLTINRVATLAGLNQSTVNAMFEGRSKRPTITTIRKVCGTLGISV 64
>2a6c_A Helix-turn-helix motif; putative transcriptional regulator,
structural genomics, JOI for structural genomics, JCSG;
HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13
Length = 83
Score = 28.2 bits (63), Expect = 0.48
Identities = 11/52 (21%), Positives = 20/52 (38%)
Query: 18 DRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR 69
D+ H K+ L +L + + G +Q A + V+D G+
Sbjct: 4 DKIHHHHHHMKMRSQLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGK 55
Score = 28.2 bits (63), Expect = 0.48
Identities = 11/52 (21%), Positives = 20/52 (38%)
Query: 108 DRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR 159
D+ H K+ L +L + + G +Q A + V+D G+
Sbjct: 4 DKIHHHHHHMKMRSQLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGK 55
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 28.5 bits (63), Expect = 0.85
Identities = 6/36 (16%), Positives = 11/36 (30%), Gaps = 6/36 (16%)
Query: 39 QGRQAKGWSQKDLATKI------NEKPQIVNDYEGG 68
+ G +L + P+IV + G
Sbjct: 6 SIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEG 41
Score = 28.5 bits (63), Expect = 0.85
Identities = 6/36 (16%), Positives = 11/36 (30%), Gaps = 6/36 (16%)
Query: 129 QGRQAKGWSQKDLATKI------NEKPQIVNDYEGG 158
+ G +L + P+IV + G
Sbjct: 6 SIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEG 41
>3h2y_A GTPase family protein; GTP-binding protein YQEH, possibly involved
in replication initiation, csgid, IDP90222; HET: DGI;
1.80A {Bacillus anthracis str}
Length = 368
Score = 28.4 bits (63), Expect = 1.3
Identities = 22/110 (20%), Positives = 34/110 (30%), Gaps = 10/110 (9%)
Query: 43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPN---QAIIGKMERALGIRLRVNAGTNKQPG 99
AKG +LA I + Y G N I +M + T+ PG
Sbjct: 142 AKGQGIAELADAIEYYRGGKDVY--VVGCTNVGKSTFINRMIKEFSDETENVITTSHFPG 199
Query: 100 TTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKP 149
TT + + L E D ++ + A ++ L K
Sbjct: 200 TTLDLIDIP-----LDEESSLYDTPGIINHHQMAHYVGKQSLKLITPTKE 244
>2wus_R RODZ, putative uncharacterized protein; structural protein, cell
WALL morphogenesis, bacterial cytos bacterial actin;
2.90A {Thermotoga maritima}
Length = 112
Score = 26.6 bits (59), Expect = 2.5
Identities = 7/38 (18%), Positives = 15/38 (39%)
Query: 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR 69
+L + + R+ + + D + N P + E G
Sbjct: 7 ELGETFRKKREERRITLLDASLFTNINPSKLKRIEEGD 44
Score = 26.6 bits (59), Expect = 2.5
Identities = 7/38 (18%), Positives = 15/38 (39%)
Query: 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR 159
+L + + R+ + + D + N P + E G
Sbjct: 7 ELGETFRKKREERRITLLDASLFTNINPSKLKRIEEGD 44
>1y9q_A Transcriptional regulator, HTH_3 family; transcriptional
regulaator, strucutral genomics, protein structure
initiative, PSI; 1.90A {Vibrio cholerae} SCOP: a.35.1.8
b.82.1.15
Length = 192
Score = 26.9 bits (60), Expect = 3.5
Identities = 13/52 (25%), Positives = 18/52 (34%), Gaps = 8/52 (15%)
Query: 41 RQAKGWSQKDLATKIN-EKP---QIVNDYEGGRGIPNQAIIGKMERALGIRL 88
R+++G S A K QI E G P A + K+ L
Sbjct: 20 RKSRGLSLDATAQLTGVSKAMLGQI----ERGESSPTIATLWKIASGLEASF 67
>1dw9_A Cyanate lyase; cyanate degradation, structural genomics, PSI,
protei structure initiative, midwest center for
structural genomic; HET: SO4; 1.65A {Escherichia coli}
SCOP: a.35.1.4 d.72.1.1 PDB: 1dwk_A* 2ivq_A 2ivb_A
2iu7_A 2iv1_A 2iuo_A 2ivg_A
Length = 156
Score = 26.1 bits (57), Expect = 4.5
Identities = 10/56 (17%), Positives = 18/56 (32%)
Query: 31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
LDLA ++ + K S ++A V G+ + L +
Sbjct: 12 LDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDL 67
Score = 25.3 bits (55), Expect = 8.3
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 121 LDLAKLLMQGRQAKGWSQKDLATKI 145
LDLA ++ + K S ++A
Sbjct: 12 LDLADAILLSKAKKDLSFAEIADGT 36
>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage,
structural evolution, transcription; 1.40A {Xylella
fastidiosa}
Length = 79
Score = 24.9 bits (54), Expect = 5.6
Identities = 7/39 (17%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 47 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALG 85
S LA + + ++++ +P + I +ER
Sbjct: 13 SVSALAASLGVRQSAISNWRARGRVPAERCI-DIERVTN 50
Score = 24.9 bits (54), Expect = 7.4
Identities = 4/26 (15%), Positives = 11/26 (42%)
Query: 137 SQKDLATKINEKPQIVNDYEGGRGIP 162
S LA + + ++++ +P
Sbjct: 13 SVSALAASLGVRQSAISNWRARGRVP 38
>2o38_A Hypothetical protein; alpha-beta, helix-turn-helix, structural
genomics, PSI-2, PR structure initiative; 1.83A
{Rhodopseudomonas palustris} SCOP: a.35.1.13
Length = 120
Score = 25.7 bits (56), Expect = 6.0
Identities = 7/38 (18%), Positives = 11/38 (28%)
Query: 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR 69
LA L SQ A ++ V+ +
Sbjct: 40 RLAYALNAVIDRARLSQAAAAARLGINQPKVSALRNYK 77
Score = 25.7 bits (56), Expect = 6.0
Identities = 7/38 (18%), Positives = 11/38 (28%)
Query: 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR 159
LA L SQ A ++ V+ +
Sbjct: 40 RLAYALNAVIDRARLSQAAAAARLGINQPKVSALRNYK 77
>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021);
helix-turn-helix, DNA-binding, transcription
regulation, DNA binding protein; HET: MEQ; 1.40A
{Escherichia coli k-12}
Length = 73
Score = 24.5 bits (53), Expect = 7.8
Identities = 8/37 (21%), Positives = 15/37 (40%)
Query: 41 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII 77
R+ +QK+ + + YE G P+ + I
Sbjct: 20 RKKLSLTQKEASEIFGGGVNAFSRYEKGNAXPHPSTI 56
Score = 24.5 bits (53), Expect = 7.8
Identities = 8/37 (21%), Positives = 15/37 (40%)
Query: 131 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII 167
R+ +QK+ + + YE G P+ + I
Sbjct: 20 RKKLSLTQKEASEIFGGGVNAFSRYEKGNAXPHPSTI 56
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.309 0.130 0.364
Gapped
Lambda K H
0.267 0.0581 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,512,182
Number of extensions: 139084
Number of successful extensions: 209
Number of sequences better than 10.0: 1
Number of HSP's gapped: 206
Number of HSP's successfully gapped: 108
Length of query: 174
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 87
Effective length of database: 4,272,666
Effective search space: 371721942
Effective search space used: 371721942
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (24.9 bits)