RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780424|ref|YP_003064837.1| transcriptional regulator
protein [Candidatus Liberibacter asiaticus str. psy62]
(144 letters)
>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein
structure initiative, midwest center for structural
genomics; 1.80A {Silicibacter pomeroyi}
Length = 86
Score = 61.0 bits (148), Expect = 1e-10
Identities = 15/65 (23%), Positives = 24/65 (36%)
Query: 4 NKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHIS 63
K + P + + +R+R R+ G++Q L E L V K E R+
Sbjct: 4 TKTLRTPEHVYLCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWM 63
Query: 64 EVLES 68
E
Sbjct: 64 AACEG 68
>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 = 59.0 bits (143), Expect = 3e-10
Identities = 16/62 (25%), Positives = 26/62 (41%)
Query: 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISF 72
+ G+R+R R G+SQE L G+ V E+G V + ++ L+
Sbjct: 12 VKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPRE 71
Query: 73 FF 74
F
Sbjct: 72 LF 73
>2wiu_B HTH-type transcriptional regulator HIPB; transferase
transcription complex, bacterial persistence, serine
kinase, mercury derivative, SAD; 2.35A {Escherichia
coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B*
Length = 88
Score = 59.2 bits (143), Expect = 4e-10
Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 2/79 (2%)
Query: 1 MVGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQ 60
M+ +KI +P + ++L R G +Q +L + +GI + +E + +
Sbjct: 1 MMSFQKIYSPTQL--ANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFF 58
Query: 61 HISEVLESPISFFFDVSPT 79
I + LE ++ + +
Sbjct: 59 KILQSLELSMTLCDAKNAS 77
>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 = 57.2 bits (138), Expect = 2e-09
Identities = 13/61 (21%), Positives = 25/61 (40%)
Query: 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73
N K ++ R G++Q++LG+ ++ + +Q EK + S L
Sbjct: 23 NAMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAFNVKYDDI 82
Query: 74 F 74
F
Sbjct: 83 F 83
>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
Length = 68
Score = 56.8 bits (137), Expect = 2e-09
Identities = 15/60 (25%), Positives = 30/60 (50%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74
+G+RIR RR L + Q LG+ +G++ + ++E+ L +S+ L+ +
Sbjct: 6 MGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLL 65
>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus
caldolyticus} SCOP: a.35.1.3
Length = 77
Score = 56.3 bits (136), Expect = 2e-09
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 9 NPVDIN--VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVL 66
N ++I G+ ++ R G+SQE+L + G+ + + E+G + + I L
Sbjct: 3 NEIEIKRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAAL 62
Query: 67 ESPISFFFD 75
+ P S FF
Sbjct: 63 DIPASTFFR 71
>1adr_A P22 C2 repressor; transcription regulation; NMR {Bacteriophage
P22} SCOP: a.35.1.2
Length = 76
Score = 56.0 bits (135), Expect = 3e-09
Identities = 15/61 (24%), Positives = 30/61 (49%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74
+G+RIR RR L + Q LG+ +G++ + ++E+ L +S+ L+ +
Sbjct: 6 MGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLL 65
Query: 75 D 75
Sbjct: 66 K 66
>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 = 55.6 bits (134), Expect = 4e-09
Identities = 11/101 (10%), Positives = 31/101 (30%)
Query: 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73
+ + + G+ ++ E L + + V Y G + +L ++ I
Sbjct: 9 QFAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHLSIDEL 68
Query: 74 FDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVK 114
+ ++ ++ + I +D V+
Sbjct: 69 VGYVQEDKVWNDLSLKQWLLSLNLRSEEEIAKIKILVDTVE 109
>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 = 55.1 bits (133), Expect = 6e-09
Identities = 13/62 (20%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73
++ R++ +R+ LG++Q +L + +G T Q +++ E G + L ++ L + +
Sbjct: 1 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTK-RPRFLPELASALGVSVDWL 59
Query: 74 FD 75
+
Sbjct: 60 LN 61
>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus
thuringiensis serovarisraelensis atcc 35646}
Length = 293
Score = 55.2 bits (131), Expect = 6e-09
Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73
+G I+ R++ G++Q++L E +V + E G LQ I+ L+ PI F
Sbjct: 5 KLGSEIKKIRVLRGLTQKQLSE-NICHQSEVSRIESGAVYPSMDILQGIAAKLQIPIIHF 63
Query: 74 FDVSPTVCSDISSEENNVM 92
++V + + + +
Sbjct: 64 YEVLIYSDIERKKQFKDQV 82
>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing
system, phosphoryltransferase, helix-turn-helix motif,
transcription regulator; 3.20A {Streptococcus pneumoniae
TIGR4}
Length = 158
Score = 55.1 bits (132), Expect = 6e-09
Identities = 17/116 (14%), Positives = 39/116 (33%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74
+GK I+ R ++Q + +GI+ + +YE G + V + I +
Sbjct: 2 IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYVDIV 61
Query: 75 DVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIELVRSIVSSE 130
+ E ++ + L+R + D + ++S +
Sbjct: 62 GEDKMLNPVEDYELTLKIEIVKERGANLLSRLYRYQDSQGISIDDESNPWILMSDD 117
>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein
fold, OPPF, structural genomics, oxford protein
production facility; 2.80A {Neisseria gonorrhoeae}
Length = 141
Score = 54.2 bits (130), Expect = 1e-08
Identities = 10/60 (16%), Positives = 20/60 (33%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74
G+ RM G +Q +L G+ + + E + +Q ++ L
Sbjct: 69 GGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLEVR 128
>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 = 53.4 bits (128), Expect = 2e-08
Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 4/76 (5%)
Query: 4 NKKIPNPVDINVGKR----IRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRL 59
KK + +R ++ LG+SQE + + +G+ V G+N + A
Sbjct: 3 KKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNA 62
Query: 60 QHISEVLESPISFFFD 75
++++L+ + F
Sbjct: 63 ALLAKILKVSVEEFSP 78
>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 = 52.7 bits (126), Expect = 3e-08
Identities = 15/64 (23%), Positives = 25/64 (39%)
Query: 8 PNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLE 67
+ V + VGK I+ R G++Q+ L + Q + YE G L I +
Sbjct: 7 GDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIG 66
Query: 68 SPIS 71
+
Sbjct: 67 LKLR 70
>2jvl_A TRMBF1; coactivator, helix-turn-helix, protein binding,
transcription; NMR {Trichoderma reesei}
Length = 107
Score = 52.2 bits (125), Expect = 4e-08
Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 2/73 (2%)
Query: 8 PNPVDINVGKRIRLRRMIL--GMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEV 65
P V VGK I R M+Q +LG+ +G T V YE+G + L + V
Sbjct: 28 PKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYERGTATPDQNILSKMERV 87
Query: 66 LESPISFFFDVSP 78
L + +P
Sbjct: 88 LNVKLRGANIGAP 100
>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein,
xenobiotic response element family of transcriptional
regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae
PV}
Length = 83
Score = 52.3 bits (125), Expect = 4e-08
Identities = 13/71 (18%), Positives = 22/71 (30%)
Query: 5 KKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISE 64
K I N + + R G++Q++L LG V K E R+
Sbjct: 5 KTIHNARYQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCR 64
Query: 65 VLESPISFFFD 75
+ +
Sbjct: 65 GIGTDPYALLS 75
>3clc_A Regulatory protein; protein-DNA complex, transcriptional
regulator, helix-turn- helix, DNA-bending, plasmid,
transcription regulator/DNA complex; 2.80A
{Enterobacter SP}
Length = 82
Score = 52.3 bits (125), Expect = 5e-08
Identities = 15/62 (24%), Positives = 25/62 (40%)
Query: 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73
V I+ R+ GM+QE L + + E+ + L+ I + LE F
Sbjct: 11 KVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVF 70
Query: 74 FD 75
F+
Sbjct: 71 FE 72
>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 = 51.8 bits (123), Expect = 6e-08
Identities = 13/61 (21%), Positives = 29/61 (47%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74
+ +++ R G+S + + G++ + + E+G + + L I+ LE+ S FF
Sbjct: 12 IANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASFSAFF 71
Query: 75 D 75
Sbjct: 72 A 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 = 51.8 bits (124), Expect = 6e-08
Identities = 10/58 (17%), Positives = 26/58 (44%)
Query: 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPIS 71
+ ++I L R +S+++L + G+ + + YE G + + +I + +
Sbjct: 4 TISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQTPQFTKY 61
>3kz3_A Repressor protein CI; five helix bundle, DNA-binding,
transcription, transcription regulation; 1.64A
{Enterobacteria phage lambda}
Length = 80
Score = 51.5 bits (123), Expect = 7e-08
Identities = 11/59 (18%), Positives = 26/59 (44%)
Query: 16 GKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74
++ LG+S E + + +G+ V G+N + A ++++L+ + F
Sbjct: 14 KAIWEKKKNELGLSYESVADKMGMGQSAVAALFNGINALNAYNAALLAKILKVSVEEFS 72
>3ivp_A Putative transposon-related DNA-binding protein; APC62618,
structural genomics, PSI-2, protein structure
initiative; HET: PG4; 2.02A {Clostridium difficile 630}
Length = 126
Score = 51.2 bits (122), Expect = 8e-08
Identities = 17/107 (15%), Positives = 40/107 (37%), Gaps = 2/107 (1%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74
+G I+ R G+++E++G + I + + E L + +L + FF
Sbjct: 13 LGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSVDEFF 72
Query: 75 DVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIE 121
+ + S++ + + I L D + +++ E
Sbjct: 73 LPASS--QVKSTKRRQLENKIDNFTDADLVIMESVADGIVKSKEVGE 117
>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 = 50.4 bits (120), Expect = 2e-07
Identities = 16/70 (22%), Positives = 30/70 (42%)
Query: 7 IPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVL 66
I + + + + R +SQ +L LG++ + K E R+ A L + EV+
Sbjct: 3 IHDHRYRCLVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVV 62
Query: 67 ESPISFFFDV 76
S + D+
Sbjct: 63 ASRLGLPMDI 72
>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
Length = 198
Score = 49.5 bits (117), Expect = 3e-07
Identities = 15/66 (22%), Positives = 26/66 (39%), Gaps = 1/66 (1%)
Query: 11 VDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVN-RVGASRLQHISEVLESP 69
+ ++ RR + M L LG T + V +E G + ++L I+ VL +
Sbjct: 7 ASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTS 66
Query: 70 ISFFFD 75
I
Sbjct: 67 IGALTP 72
>1b0n_A Protein (SINR protein); transcription regulator, antagonist,
sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1
a.35.1.3
Length = 111
Score = 49.7 bits (118), Expect = 3e-07
Identities = 24/108 (22%), Positives = 42/108 (38%), Gaps = 4/108 (3%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNR-VGASRLQHISEVLESPISFF 73
+G+RI+ R G S +L E G+ + E+ + L+ +S VL+ +
Sbjct: 2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTL 61
Query: 74 FDVSPTVCSD---ISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQK 118
D D S E V D +++ + R F+ + QK
Sbjct: 62 LDEKHETEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQK 109
>1utx_A CYLR2; DNA-binding protein, transcriptional repressor, regulation
of cytolysin operon, helix-turn-helix; 1.90A
{Enterococcus faecalis} SCOP: a.35.1.3 PDB: 2gzu_A
Length = 66
Score = 49.2 bits (117), Expect = 3e-07
Identities = 14/64 (21%), Positives = 25/64 (39%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74
+ ++L R +SQ +L L ++ Q + EK I+ L +P+ F
Sbjct: 2 IINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIF 61
Query: 75 DVSP 78
P
Sbjct: 62 QWQP 65
>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein
structure initiative, MI center for structural
genomics, MCSG; 1.65A {Cytophaga hutchinsonii}
Length = 73
Score = 49.0 bits (117), Expect = 4e-07
Identities = 11/61 (18%), Positives = 19/61 (31%)
Query: 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73
+ R++ G + L E L V K+ + L I+E L +
Sbjct: 8 KIFNRLKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVREL 67
Query: 74 F 74
Sbjct: 68 I 68
>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix,
restriction- modification, transcription regulator;
2.80A {Enterobacter SP} PDB: 3fya_A
Length = 99
Score = 47.8 bits (113), Expect = 1e-06
Identities = 15/62 (24%), Positives = 25/62 (40%)
Query: 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73
V I+ R+ GM+QE L + + E+ + L+ I + LE F
Sbjct: 28 KVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVF 87
Query: 74 FD 75
F+
Sbjct: 88 FE 89
>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 = 47.5 bits (113), Expect = 1e-06
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73
+ +R++ RR+ L M+Q +L G+ Q +Q E G L I+ L +
Sbjct: 3 TLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAG-VTKRPRFLFEIAMALNCDPVWL 61
Query: 74 F 74
Sbjct: 62 Q 62
>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural
genomics, PSI, protein structure initiative; 1.85A
{Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1
Length = 170
Score = 46.0 bits (109), Expect = 4e-06
Identities = 7/39 (17%), Positives = 12/39 (30%)
Query: 16 GKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRV 54
+ +S E LGI+ + V Y +
Sbjct: 92 HEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKII 130
>2awi_A PRGX; repressor, pheromone, DNA binding, regulatory domain,
transcription; 2.25A {Enterococcus faecalis} SCOP:
a.35.1.11 a.118.8.4 PDB: 2axv_A 2axu_A 2aw6_A 2axz_A
2grl_A 2grm_A
Length = 317
Score = 45.4 bits (107), Expect = 5e-06
Identities = 17/133 (12%), Positives = 38/133 (28%), Gaps = 2/133 (1%)
Query: 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLE-SPIS 71
+G ++ R L Q L ++ K E + L SE L +
Sbjct: 2 FKIGSVLKQIRQELNYHQIDLYS-GIMSKSVYIKVEADSRPISVEELSKFSERLGVNFFE 60
Query: 72 FFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIELVRSIVSSEK 131
S + + ++ + ++ F +I+ ++ + S
Sbjct: 61 ILNRAGMNTKSVNETGKEKLLISKIFTNPDLFDKNFQRIEPKRLTSLQYFSIYLGYISIA 120
Query: 132 KYRTIEEECMVEQ 144
+ IE +
Sbjct: 121 HHYNIEVPTFNKT 133
>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 = 43.8 bits (103), Expect = 1e-05
Identities = 10/54 (18%), Positives = 23/54 (42%)
Query: 16 GKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESP 69
RI++ R L ++QE+ I ++ +E+G + ++ + P
Sbjct: 32 MPRIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPARAYLKIIAVDP 85
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A
{Enterobacteria phage lambda}
Length = 236
Score = 43.1 bits (100), Expect = 2e-05
Identities = 12/67 (17%), Positives = 28/67 (41%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74
+ ++ LG+SQE + + +G+ V G+N + A ++++L+ + F
Sbjct: 18 LKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEFS 77
Query: 75 DVSPTVC 81
Sbjct: 78 PSIAREI 84
>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 = 40.7 bits (95), Expect = 1e-04
Identities = 9/65 (13%), Positives = 21/65 (32%), Gaps = 1/65 (1%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQH-ISEVLESPISFF 73
V + + ++ ++ G+ V +G ++ + L + F
Sbjct: 8 VSEHLMELITQQNLTINRVATLAGLNQSTVNAMFEGRSKRPTITTIRKVCGTLGISVHDF 67
Query: 74 FDVSP 78
FD P
Sbjct: 68 FDFPP 72
>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 = 39.1 bits (91), Expect = 4e-04
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50
+ I R L ++Q++ E G +YEKG
Sbjct: 12 APEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKG 47
>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif,
transcriptional activator, human pathogen,
transcription activator; 1.75A {Corynebacterium
glutamicum} PDB: 3f51_A
Length = 117
Score = 39.1 bits (90), Expect = 4e-04
Identities = 11/61 (18%), Positives = 26/61 (42%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74
+G +R R G++ +L E ++ + + E+G V + L + L + ++
Sbjct: 29 LGAALRSFRADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHALGASVADVL 88
Query: 75 D 75
Sbjct: 89 I 89
>3gn5_A HTH-type transcriptional regulator MQSA (YGIT/B3021); Zn-binding
protein, HTH-XRE DNA binding motif, DNA-binding,
transcription regulation; HET: MEQ; 2.15A {Escherichia
coli k-12} PDB: 3gn5_B*
Length = 133
Score = 38.2 bits (88), Expect = 7e-04
Identities = 12/61 (19%), Positives = 25/61 (40%)
Query: 12 DINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPIS 71
+ + I R L ++Q++ E G +YEKG + S ++ + + + P
Sbjct: 69 ETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLLRVLDKHPEL 128
Query: 72 F 72
Sbjct: 129 L 129
>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium; 1.63A {Escherichia coli CFT073}
SCOP: a.35.1.3 PDB: 2icp_A
Length = 94
Score = 37.3 bits (86), Expect = 0.001
Identities = 11/68 (16%), Positives = 21/68 (30%), Gaps = 2/68 (2%)
Query: 6 KIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEV 65
K+ N G I+ L +S + + I + G + +S V
Sbjct: 2 KMANH--PRPGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVV 59
Query: 66 LESPISFF 73
+ S +
Sbjct: 60 IGSSPQMW 67
>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*
Length = 133
Score = 37.1 bits (85), Expect = 0.002
Identities = 12/57 (21%), Positives = 24/57 (42%)
Query: 16 GKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISF 72
+ I R L ++Q++ E G +YEKG + S ++ + + + P
Sbjct: 73 PEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLLRVLDKHPELL 129
>3cec_A Putative antidote protein of plasmid maintenance system;
ZP_00107635.1, structural genomics, joint center for
structural genomics; HET: MSE; 1.60A {Nostoc
punctiforme pcc 73102}
Length = 104
Score = 36.1 bits (83), Expect = 0.003
Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 2/72 (2%)
Query: 2 VGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQH 61
+ + ++ P I+ G+ I L ++ E LG++ Q +Q+ G +
Sbjct: 8 ITDDRLVRP--IHPGEVIADILDDLDINTANFAEILGVSNQTIQEVINGQRSITVDIAIR 65
Query: 62 ISEVLESPISFF 73
+ + L + +
Sbjct: 66 LGKALGNGPRLW 77
>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of
BLDD; 1.81A {Streptomyces coelicolor A3}
Length = 71
Score = 34.1 bits (77), Expect = 0.012
Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 2/69 (2%)
Query: 8 PNPVDINVGKRIRLRRMILGMSQEKLGECLG--ITFQQVQKYEKGVNRVGASRLQHISEV 65
+ +G ++R R G+S + E V YE+G V RL +++
Sbjct: 2 SSEYAKQLGAKLRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDRAVTVQRLAELADF 61
Query: 66 LESPISFFF 74
P+
Sbjct: 62 YGVPVQELL 70
>2ofy_A Putative XRE-family transcriptional regulator; transcription
regulator, structural genomics, PSI, protein structure
initiative; 1.70A {Rhodococcus SP} SCOP: a.35.1.3
Length = 86
Score = 33.9 bits (77), Expect = 0.015
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 3/75 (4%)
Query: 9 NPVDINVGKRI--RLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGA-SRLQHISEV 65
++ G+R+ LR MS + GI+ + ++K E G A + ++ V
Sbjct: 7 TAEELERGQRLGELLRSARGDMSMVTVAFDAGISVETLRKIETGRIATPAFFTIAAVARV 66
Query: 66 LESPISFFFDVSPTV 80
L+ + V
Sbjct: 67 LDLSLDDVAAVVTFG 81
>2wus_R RODZ, putative uncharacterized protein; structural protein, cell
WALL morphogenesis, bacterial cytos bacterial actin;
2.90A {Thermotoga maritima}
Length = 112
Score = 32.0 bits (72), Expect = 0.050
Identities = 6/37 (16%), Positives = 16/37 (43%)
Query: 14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50
+G+ R +R ++ I ++++ E+G
Sbjct: 7 ELGETFRKKREERRITLLDASLFTNINPSKLKRIEEG 43
>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical
protein, JW0472, structural genomics, NPPSFA; 2.25A
{Escherichia coli}
Length = 113
Score = 31.1 bits (70), Expect = 0.088
Identities = 7/50 (14%), Positives = 20/50 (40%)
Query: 26 LGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFD 75
L + +L E L + V ++ +++V ++ + F+ +
Sbjct: 23 LDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFWLN 72
>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding
protein; 1.00A {Staphylococcus aureus subsp}
Length = 130
Score = 30.8 bits (69), Expect = 0.11
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50
VG+ ++ RR LGM+ +L + GI + + E
Sbjct: 4 VGEALKGRRERLGMTLTELEQRTGIKREMLVHIENN 39
>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 = 0.27
Identities = 20/101 (19%), Positives = 33/101 (32%), Gaps = 36/101 (35%)
Query: 38 GITFQQVQKYEKGVNRVGASRL---QHISEVLESPISFFFDVSPTVCSDISSEENNVMDF 94
+T +QVQ Y N L + + IS ++ +N
Sbjct: 343 NLTQEQVQDYVNKTNS----HLPAGKQVE------ISL-----------VNGAKN----L 377
Query: 95 IST--PDGLQ-LNRYFIQIDDVKVRQKIIELVRSIVSSEKK 132
+ + P L LN + K ++ R I SE+K
Sbjct: 378 VVSGPPQSLYGLNLT---LRKAKAPSG-LDQSR-IPFSERK 413
>2nw5_A Methionine aminopeptidase 2; metap2, structural genomics, PSI-2,
protein structure initiative; 2.18A {Encephalitozoon
cuniculi} PDB: 3cmk_A* 3d0d_A* 3fm3_A 3fmq_A* 3fmr_A*
Length = 360
Score = 29.0 bits (64), Expect = 0.42
Identities = 12/63 (19%), Positives = 24/63 (38%), Gaps = 1/63 (1%)
Query: 62 ISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIE 121
+++ E PI F + N ++ + D LQ R + + R ++
Sbjct: 8 LNQAEELPIEFLPKDGVYGKGKLFDSRNMEIENFTESDILQDARRAAEAHR-RARYRVQS 66
Query: 122 LVR 124
+VR
Sbjct: 67 IVR 69
>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics,
PSI-2, protein structure initiative; HET: MSE; 1.65A
{Bacteroides fragilis nctc 9343}
Length = 76
Score = 28.7 bits (63), Expect = 0.52
Identities = 8/61 (13%), Positives = 23/61 (37%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFF 74
+ RI++ + L E +G + + ++ ++ L ++E+L
Sbjct: 11 MLNRIKVVLAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELLNVDPRQLI 70
Query: 75 D 75
+
Sbjct: 71 N 71
>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT,
structural genomics, PSI-2, protein structure
initiative; NMR {Eubacterium rectale atcc 33656}
Length = 94
Score = 27.9 bits (61), Expect = 0.83
Identities = 7/60 (11%), Positives = 24/60 (40%)
Query: 16 GKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFD 75
+ + +Q ++ + +G++ Q + KG+ ++Q +++ S +
Sbjct: 11 SENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNINKSDLIE 70
>2a6c_A Helix-turn-helix motif; NP_841403.1, , structural genomics, joint
center for structural genomics, JCSG, protein structure
initiative, PSI; HET: CIT; 1.90A {Nitrosomonas
europaea} SCOP: a.35.1.13
Length = 83
Score = 27.2 bits (59), Expect = 1.4
Identities = 10/61 (16%), Positives = 21/61 (34%), Gaps = 1/61 (1%)
Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNR-VGASRLQHISEVLESPISFF 73
+ ++ G++Q K E LG+T +V +G L + + +
Sbjct: 19 LLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKIDLFSLESLIDMITSIGLKVEIN 78
Query: 74 F 74
Sbjct: 79 I 79
>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity,
transcription regulator; 1.95A {Enterobacteria phage
186} PDB: 2fkd_A
Length = 189
Score = 26.6 bits (58), Expect = 2.0
Identities = 4/72 (5%), Positives = 15/72 (20%), Gaps = 1/72 (1%)
Query: 20 RLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPT 79
R+ + +L I + + H + + + +
Sbjct: 13 RICEAYGFSQKIQLANHFDIASSSLSNRYTR-GAISYDFAAHCALETGANLQWLLTGEGE 71
Query: 80 VCSDISSEENNV 91
+ +
Sbjct: 72 AFVNNRESSDAK 83
>3ngj_A Deoxyribose-phosphate aldolase; lyase, structural genomics,
structural genomics center for infectious disease,
ssgcid; 1.70A {Entamoeba histolytica}
Length = 239
Score = 25.7 bits (56), Expect = 4.0
Identities = 11/27 (40%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 38 GI-TFQQVQKY-EKGVNRVGASRLQHI 62
GI TF K G +R+GAS I
Sbjct: 208 GIRTFDDAMKMINNGASRIGASAGIAI 234
>3glc_A Aldolase LSRF; TIM barrel, cytoplasm, lyase, schiff base; HET:
R5P; 2.50A {Escherichia coli k-12} PDB: 3gnd_A* 3gkf_O
Length = 295
Score = 24.5 bits (53), Expect = 8.7
Identities = 4/19 (21%), Positives = 9/19 (47%)
Query: 7 IPNPVDINVGKRIRLRRMI 25
+ ++ G + RL R+
Sbjct: 30 LKGCGALDWGMQSRLSRIF 48
>2ozu_A Histone acetyltransferase MYST3; structural genomics, structural
genomics consortium, SGC; HET: ALY ACO; 2.30A {Homo
sapiens} SCOP: d.108.1.1 PDB: 2rc4_A* 1m36_A
Length = 284
Score = 24.8 bits (54), Expect = 8.9
Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 1/61 (1%)
Query: 83 DISSEEN-NVMDFISTPDGLQLNRYFIQIDDVKVRQKIIELVRSIVSSEKKYRTIEEECM 141
+S D ST L++ + + R+K+I+ + + + ++ EC+
Sbjct: 219 KLSKLTGICPQDITSTLHHLRMLDFRSDQFVIIRREKLIQDHMAKLQLNLRPVDVDPECL 278
Query: 142 V 142
Sbjct: 279 R 279
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
0.319 0.137 0.378
Gapped
Lambda K H
0.267 0.0632 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,229,074
Number of extensions: 51958
Number of successful extensions: 208
Number of sequences better than 10.0: 1
Number of HSP's gapped: 206
Number of HSP's successfully gapped: 61
Length of query: 144
Length of database: 5,693,230
Length adjustment: 83
Effective length of query: 61
Effective length of database: 3,680,978
Effective search space: 224539658
Effective search space used: 224539658
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.0 bits)