RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254781218|ref|YP_003065631.1| hypothetical protein
CLIBASIA_05625 [Candidatus Liberibacter asiaticus str. psy62]
(205 letters)
>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 = 64.6 bits (157), Expect = 1e-11
Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 7/92 (7%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTK--KHLDW 171
I ++ +RK + +S+ + L G+P TLS YE GR+ P I Q + K+ W
Sbjct: 5 ISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQTPQFTKYTLW 64
Query: 172 IYFGDEV-----IVPKSIKRAKGNQSSKKSKK 198
I P + +S S +
Sbjct: 65 FMTNQIAPESGQIAPALAHFGQNETTSPHSGQ 96
Score = 39.1 bits (91), Expect = 7e-04
Identities = 8/68 (11%), Positives = 27/68 (39%), Gaps = 2/68 (2%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENG--MCSTSIRYALYLRNEYEISF 87
+ +I +RK+ +++++A ++ +E+G T + + ++
Sbjct: 3 NTISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQTPQFTKYT 62
Query: 88 DWIYDGEV 95
W ++
Sbjct: 63 LWFMTNQI 70
>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 = 59.5 bits (144), Expect = 6e-10
Identities = 16/63 (25%), Positives = 33/63 (52%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
+G R+++ RK + Q GK++G+ N +S +E+ T P + + + + D++
Sbjct: 6 MGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLL 65
Query: 174 FGD 176
GD
Sbjct: 66 KGD 68
Score = 46.0 bits (109), Expect = 6e-06
Identities = 13/65 (20%), Positives = 25/65 (38%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+ +G RI+ RK Q + A++ +E + L L + S D+
Sbjct: 4 QLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDY 63
Query: 90 IYDGE 94
+ G+
Sbjct: 64 LLKGD 68
>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 = 58.3 bits (141), Expect = 1e-09
Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 2/90 (2%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
LK +R D G++Q E G L + + T+ N E+ T + K D I+
Sbjct: 24 AMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAFNVKYDDIF 83
Query: 174 FGDEVIVPKSIKRAKGNQSSKKSKKDKKSS 203
G+E K +S + K+K++S
Sbjct: 84 LGNEYENFVFTNDKK--KSIILAFKEKQTS 111
Score = 46.4 bits (110), Expect = 4e-06
Identities = 12/80 (15%), Positives = 26/80 (32%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+ +K++R TQKE+ + E + + + + +D
Sbjct: 22 SNAMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAFNVKYDD 81
Query: 90 IYDGEVIDRRYEDVTNKKRL 109
I+ G + KK +
Sbjct: 82 IFLGNEYENFVFTNDKKKSI 101
>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein
fold, OPPF, structural genomics, oxford protein
production facility; 2.80A {Neisseria gonorrhoeae}
Length = 141
Score = 58.4 bits (141), Expect = 1e-09
Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 2/82 (2%)
Query: 96 IDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEI 155
+DR + +K + A G S+R KG +Q E G+P LS E + +
Sbjct: 53 MDRAAARIADK--IALKAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQD 110
Query: 156 KPARKIKQVTKKHLDWIYFGDE 177
K +K+ + E
Sbjct: 111 KTVQKLANALGVSPLEVRAAFE 132
Score = 44.2 bits (104), Expect = 2e-05
Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 2/74 (2%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
K G +R TQ E+A A + ++ EN S + L N +S
Sbjct: 67 KAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLE 126
Query: 90 IYDGEVIDRRYEDV 103
+ +RRYE +
Sbjct: 127 VRAA--FERRYEYM 138
>1adr_A P22 C2 repressor; transcription regulation; NMR {Bacteriophage P22}
SCOP: a.35.1.2
Length = 76
Score = 57.2 bits (138), Expect = 3e-09
Identities = 16/64 (25%), Positives = 33/64 (51%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
+G R+++ RK + Q GK++G+ N +S +E+ T P + + + + D++
Sbjct: 6 MGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLL 65
Query: 174 FGDE 177
GD
Sbjct: 66 KGDL 69
Score = 44.5 bits (105), Expect = 2e-05
Identities = 13/66 (19%), Positives = 26/66 (39%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+ +G RI+ RK Q + A++ +E + L L + S D+
Sbjct: 4 QLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDY 63
Query: 90 IYDGEV 95
+ G++
Sbjct: 64 LLKGDL 69
>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 = 56.0 bits (135), Expect = 6e-09
Identities = 15/69 (21%), Positives = 27/69 (39%)
Query: 105 NKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQV 164
+ D G RL+ +R KG+SQ L G+ S + E+G+ + K+
Sbjct: 5 HDHYADLVKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATA 64
Query: 165 TKKHLDWIY 173
++
Sbjct: 65 LDIEPRELF 73
Score = 39.8 bits (93), Expect = 4e-04
Identities = 14/60 (23%), Positives = 27/60 (45%)
Query: 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIY 91
G R++++R A +Q+ +A + S V E G + S+ L L +I ++
Sbjct: 14 FGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPRELF 73
>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 = 56.1 bits (135), Expect = 6e-09
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 106 KKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT 165
++L R+K IR+ ++Q EF +P TL ++EQGR+ P+ PAR ++
Sbjct: 23 AEQLASAPRMPRIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQ-PARAYLKII 81
Query: 166 KKHLDWI 172
+
Sbjct: 82 AVDPEGT 88
Score = 30.7 bits (69), Expect = 0.22
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENG 67
RIK IR+A TQ+E + + + +E G
Sbjct: 32 MPRIKIIRRALKLTQEEFSARYHIPLGTLRDWEQG 66
>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 = 55.9 bits (135), Expect = 7e-09
Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172
+I +R+KS R G++Q E + +G ++ E G+T + ++ +DW+
Sbjct: 1 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKT-KRPRFLPELASALGVSVDWL 59
Query: 173 YFGDE 177
G
Sbjct: 60 LNGTS 64
Score = 39.3 bits (92), Expect = 6e-04
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 1/63 (1%)
Query: 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIY 91
+ +R+K R Q E+A + ++ ENG + R+ L + +S DW+
Sbjct: 2 ISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGK-TKRPRFLPELASALGVSVDWLL 60
Query: 92 DGE 94
+G
Sbjct: 61 NGT 63
>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing
system, phosphoryltransferase, helix-turn-helix motif,
transcription regulator; 3.20A {Streptococcus pneumoniae
TIGR4}
Length = 158
Score = 55.5 bits (133), Expect = 8e-09
Identities = 20/75 (26%), Positives = 36/75 (48%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
IG +KS+RK ++Q+EF +++G+ ++LS YE G + + I Q I
Sbjct: 2 IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYVDIV 61
Query: 174 FGDEVIVPKSIKRAK 188
D+++ P
Sbjct: 62 GEDKMLNPVEDYELT 76
Score = 44.0 bits (103), Expect = 2e-05
Identities = 29/146 (19%), Positives = 63/146 (43%), Gaps = 7/146 (4%)
Query: 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIY 91
+G IK +RK ++ TQ E A ++++ +ENG S S + ++ +S+ I
Sbjct: 2 IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYVDIV 61
Query: 92 DGEVIDRRYEDVTNKKRLD-----PYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNY 146
+ + ED +++ + +RL + +G+S + + + LS+
Sbjct: 62 GEDKMLNPVEDYELTLKIEIVKERGANLLSRLYRYQDSQGISIDDESNPWILMSDDLSDL 121
Query: 147 EQGRTIPEIKPARKIKQVTKKHLDWI 172
I ++ +I++ +LD I
Sbjct: 122 IHTN-IYLVETFDEIERY-SGYLDGI 145
>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 = 55.3 bits (132), Expect = 9e-09
Identities = 17/68 (25%), Positives = 31/68 (45%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
I +LK++RK +G+S +L G+ + L E+G + P I KI + +
Sbjct: 12 IANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASFSAFF 71
Query: 174 FGDEVIVP 181
D ++
Sbjct: 72 ANDPQLLS 79
Score = 44.1 bits (103), Expect = 2e-05
Identities = 12/72 (16%), Positives = 27/72 (37%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+ ++K++RK+ + A ++ + E G S +I + + E SF
Sbjct: 10 SQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASFSA 69
Query: 90 IYDGEVIDRRYE 101
+ + E
Sbjct: 70 FFANDPQLLSSE 81
>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 = 55.1 bits (132), Expect = 1e-08
Identities = 17/97 (17%), Positives = 40/97 (41%)
Query: 105 NKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQV 164
+ + D A+G +K RK +G+++ + G ++ + L+N E P ++ + +
Sbjct: 4 KEDKYDFRALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSL 63
Query: 165 TKKHLDWIYFGDEVIVPKSIKRAKGNQSSKKSKKDKK 201
+D + V + +R N+ + D
Sbjct: 64 LNVSVDEFFLPASSQVKSTKRRQLENKIDNFTDADLV 100
Score = 39.7 bits (92), Expect = 5e-04
Identities = 13/71 (18%), Positives = 28/71 (39%)
Query: 24 EIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEY 83
E + ++ +G IK+ RK T++++ + EN S++ L +
Sbjct: 5 EDKYDFRALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLL 64
Query: 84 EISFDWIYDGE 94
+S D +
Sbjct: 65 NVSVDEFFLPA 75
>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus
caldolyticus} SCOP: a.35.1.3
Length = 77
Score = 54.4 bits (131), Expect = 2e-08
Identities = 18/65 (27%), Positives = 25/65 (38%)
Query: 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172
G LK IR KG+SQ E L G+ + +S E+G + KI
Sbjct: 10 KFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPASTF 69
Query: 173 YFGDE 177
+ E
Sbjct: 70 FRKME 74
Score = 40.5 bits (95), Expect = 3e-04
Identities = 12/65 (18%), Positives = 25/65 (38%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+ G +K IR +Q+E+A A + ++ E G + S+ + +I
Sbjct: 9 RKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPAST 68
Query: 90 IYDGE 94
+
Sbjct: 69 FFRKM 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 = 52.7 bits (126), Expect = 5e-08
Identities = 16/72 (22%), Positives = 31/72 (43%)
Query: 106 KKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVT 165
+K P + +K +R+ G +Q E K +G+ +T+SN+E + KI Q
Sbjct: 5 QKIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSL 64
Query: 166 KKHLDWIYFGDE 177
+ + +
Sbjct: 65 ELSMTLCDAKNA 76
Score = 39.2 bits (91), Expect = 7e-04
Identities = 13/65 (20%), Positives = 27/65 (41%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+ +K +R+ N TQ E+A ++ ++ FEN +T++ + E+S
Sbjct: 11 TQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTL 70
Query: 90 IYDGE 94
Sbjct: 71 CDAKN 75
>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein
structure initiative, midwest center for structural
genomics; 1.80A {Silicibacter pomeroyi}
Length = 86
Score = 51.4 bits (123), Expect = 2e-07
Identities = 11/49 (22%), Positives = 21/49 (42%)
Query: 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKI 161
+ RL+ R D G++Q + + L P S ++ E ++ K
Sbjct: 14 YLCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKW 62
Score = 31.7 bits (72), Expect = 0.13
Identities = 8/42 (19%), Positives = 17/42 (40%)
Query: 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSI 73
+ R++ R TQ ++A ++ +S V E +
Sbjct: 15 LCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDV 56
>2jvl_A TRMBF1; coactivator, helix-turn-helix, protein binding,
transcription; NMR {Trichoderma reesei}
Length = 107
Score = 51.1 bits (122), Expect = 2e-07
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 3/86 (3%)
Query: 99 RYEDVTNKKRLDPYAIGARLKSIRK--DKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIK 156
R +D+ K + +G ++ R+ + M+Q E GK +G +T+++YE+G P+
Sbjct: 21 RSDDIIKPKTVGK-EVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYERGTATPDQN 79
Query: 157 PARKIKQVTKKHLDWIYFGDEVIVPK 182
K+++V L G + PK
Sbjct: 80 ILSKMERVLNVKLRGANIGAPRLGPK 105
Score = 33.0 bits (75), Expect = 0.052
Identities = 12/67 (17%), Positives = 22/67 (32%), Gaps = 2/67 (2%)
Query: 30 KDVGTRIKDIRKANNK--TQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISF 87
K+VG I+ R+ TQ E+ + + V +E G + + +
Sbjct: 33 KEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYERGTATPDQNILSKMERVLNVKL 92
Query: 88 DWIYDGE 94
G
Sbjct: 93 RGANIGA 99
>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 = 51.0 bits (122), Expect = 2e-07
Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 1/64 (1%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
+ RLK R M+Q E G+ ++ E G T +I W+
Sbjct: 4 LSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRF-LFEIAMALNCDPVWLQ 62
Query: 174 FGDE 177
+G +
Sbjct: 63 YGTK 66
Score = 37.1 bits (86), Expect = 0.003
Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 1/65 (1%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+ + R+K R A TQ E+A A + ++ L E G+ + R+ + W
Sbjct: 2 QTLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGV-TKRPRFLFEIAMALNCDPVW 60
Query: 90 IYDGE 94
+ G
Sbjct: 61 LQYGT 65
>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 = 50.8 bits (121), Expect = 2e-07
Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 1/90 (1%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG-RTIPEIKPARKIKQVTKKHLDWI 172
IG R+K RK+KG S E + G+ S LS+ E+ +T P I+ K+ V + +
Sbjct: 2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTL 61
Query: 173 YFGDEVIVPKSIKRAKGNQSSKKSKKDKKS 202
++ + + + S
Sbjct: 62 LDEKHETEYDGQLDSEWEKLVRDAMTSGVS 91
Score = 38.9 bits (90), Expect = 9e-04
Identities = 19/105 (18%), Positives = 40/105 (38%), Gaps = 3/105 (2%)
Query: 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCST-SIRYALYLRNEYEISFDWI 90
+G RIK RK + E+A A +S ++ E + + SI++ + ++S +
Sbjct: 2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTL 61
Query: 91 YDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKL 135
D + D + A + K + +++ K
Sbjct: 62 LDEK--HETEYDGQLDSEWEKLVRDAMTSGVSKKQFREFLDYQKW 104
>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 = 50.6 bits (121), Expect = 3e-07
Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 1/59 (1%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172
+ +RK ++Q E ++ G + S YE+G P K+ +V KH + +
Sbjct: 12 APEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAXPH-PSTIKLLRVLDKHPELL 69
Score = 28.7 bits (64), Expect = 0.98
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENG 67
I +RK + TQKE + +A + +E G
Sbjct: 12 APEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKG 47
>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 = 50.5 bits (120), Expect = 3e-07
Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 2/75 (2%)
Query: 90 IYDGEVIDRRYEDVTNKKRLDPYAI--GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147
I + E D V + + +RK ++Q E ++ G + S YE
Sbjct: 46 IMNKEESDAFMAQVKAFRASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYE 105
Query: 148 QGRTIPEIKPARKIK 162
+G P + ++
Sbjct: 106 KGNAQPHPSTIKLLR 120
Score = 31.6 bits (71), Expect = 0.12
Identities = 14/61 (22%), Positives = 21/61 (34%), Gaps = 10/61 (16%)
Query: 20 IITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYL 79
+ PE I +RK + TQKE + +A + +E G L
Sbjct: 70 TVAPE----------FIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLL 119
Query: 80 R 80
R
Sbjct: 120 R 120
>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 = 50.6 bits (120), Expect = 3e-07
Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 2/75 (2%)
Query: 90 IYDGEVIDRRYEDVTNKKRLDPYAI--GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYE 147
I + E D V + + +RK ++Q E ++ G + S YE
Sbjct: 46 IMNKEESDAFMAQVKAFRASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYE 105
Query: 148 QGRTIPEIKPARKIK 162
+G P + ++
Sbjct: 106 KGNAQPHPSTIKLLR 120
Score = 31.7 bits (71), Expect = 0.13
Identities = 14/71 (19%), Positives = 25/71 (35%), Gaps = 12/71 (16%)
Query: 20 IITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYL 79
+ PE I +RK + TQKE + +A + +E G L
Sbjct: 70 TVAPE----------FIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLL 119
Query: 80 R--NEYEISFD 88
R +++ +
Sbjct: 120 RVLDKHPELLN 130
>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 = 49.1 bits (117), Expect = 6e-07
Identities = 13/74 (17%), Positives = 21/74 (28%), Gaps = 4/74 (5%)
Query: 81 NEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPN 140
E+E S +W D Y + +S + LG+
Sbjct: 61 AEWEGSVEWFDTEFGRDNVYAWAKEQAGEVS---HEMFGDWMHRNNLSLTTAAEALGISR 117
Query: 141 STLSNYEQG-RTIP 153
+S Y + IP
Sbjct: 118 RMVSYYRTAHKIIP 131
Score = 31.4 bits (71), Expect = 0.14
Identities = 6/48 (12%), Positives = 9/48 (18%)
Query: 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLR 80
D NN + A V+ + L
Sbjct: 92 HEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIWLACL 139
>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 = 49.2 bits (117), Expect = 7e-07
Identities = 15/68 (22%), Positives = 30/68 (44%)
Query: 111 PYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLD 170
+G ++ R+ KG++Q + + +++YE GR IP + KI++ L
Sbjct: 11 TLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLR 70
Query: 171 WIYFGDEV 178
G +
Sbjct: 71 GKDIGKPI 78
Score = 34.2 bits (78), Expect = 0.020
Identities = 13/68 (19%), Positives = 30/68 (44%)
Query: 31 DVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWI 90
+VG I+ R++ TQK++A N+ + +E+G + + + +
Sbjct: 13 EVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRGK 72
Query: 91 YDGEVIDR 98
G+ I++
Sbjct: 73 DIGKPIEK 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
Length = 198
Score = 48.3 bits (114), Expect = 1e-06
Identities = 14/89 (15%), Positives = 27/89 (30%), Gaps = 2/89 (2%)
Query: 104 TNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRT-IPEIKPARKIK 162
+N K LK R+ M LLG T++ +E G + +I
Sbjct: 2 SNTKTAS-TGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIA 60
Query: 163 QVTKKHLDWIYFGDEVIVPKSIKRAKGNQ 191
V + + + + ++
Sbjct: 61 HVLGTSIGALTPPAGNDLDDGVIIQMPDE 89
Score = 34.5 bits (78), Expect = 0.017
Identities = 13/89 (14%), Positives = 24/89 (26%), Gaps = 1/89 (1%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENG-MCSTSIRYALYLRNEYEISFD 88
+KD R+ +A + V +ENG ++ + + S
Sbjct: 9 TGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIG 68
Query: 89 WIYDGEVIDRRYEDVTNKKRLDPYAIGAR 117
+ D + P G R
Sbjct: 69 ALTPPAGNDLDDGVIIQMPDERPILKGVR 97
>3kz3_A Repressor protein CI; five helix bundle, DNA-binding,
transcription, transcription regulation; 1.64A
{Enterobacteria phage lambda}
Length = 80
Score = 48.0 bits (114), Expect = 2e-06
Identities = 12/72 (16%), Positives = 27/72 (37%), Gaps = 5/72 (6%)
Query: 101 EDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARK 160
E + + +RL A + + + G+S +GM S ++ G A
Sbjct: 5 EQLEDARRL-----KAIWEKKKNELGLSYESVADKMGMGQSAVAALFNGINALNAYNAAL 59
Query: 161 IKQVTKKHLDWI 172
+ ++ K ++
Sbjct: 60 LAKILKVSVEEF 71
Score = 39.1 bits (91), Expect = 7e-04
Identities = 11/70 (15%), Positives = 27/70 (38%)
Query: 21 ITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLR 80
+T E + + + + + + + +A +SAV NG+ + + A L
Sbjct: 2 LTQEQLEDARRLKAIWEKKKNELGLSYESVADKMGMGQSAVAALFNGINALNAYNAALLA 61
Query: 81 NEYEISFDWI 90
++S +
Sbjct: 62 KILKVSVEEF 71
>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein
structure initiative, MI center for structural genomics,
MCSG; 1.65A {Cytophaga hutchinsonii}
Length = 73
Score = 46.3 bits (110), Expect = 4e-06
Identities = 12/64 (18%), Positives = 26/64 (40%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
I RLKS+ +KG + + + L +T+S + P ++ I + + +
Sbjct: 9 IFNRLKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVRELI 68
Query: 174 FGDE 177
+
Sbjct: 69 VSTK 72
Score = 38.2 bits (89), Expect = 0.001
Identities = 6/61 (9%), Positives = 21/61 (34%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+ + R+K + KT + ++ ++ V+ + S+ + +
Sbjct: 7 RKIFNRLKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVRE 66
Query: 90 I 90
+
Sbjct: 67 L 67
>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 = 46.1 bits (109), Expect = 5e-06
Identities = 19/64 (29%), Positives = 30/64 (46%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
I LK IR+ K +SQ E LL + T++ E+ + P ++ A KI L+ I+
Sbjct: 2 IINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIF 61
Query: 174 FGDE 177
Sbjct: 62 QWQP 65
Score = 35.7 bits (82), Expect = 0.008
Identities = 12/63 (19%), Positives = 25/63 (39%)
Query: 32 VGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIY 91
+ +K IR+ +Q E+A +N E + S++ AL + + I+
Sbjct: 2 IINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIF 61
Query: 92 DGE 94
+
Sbjct: 62 QWQ 64
>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 = 46.1 bits (109), Expect = 5e-06
Identities = 13/65 (20%), Positives = 31/65 (47%)
Query: 100 YEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPAR 159
++D+T+ + + P G + I D ++ F ++LG+ N T+ G+ + A
Sbjct: 5 WQDITDDRLVRPIHPGEVIADILDDLDINTANFAEILGVSNQTIQEVINGQRSITVDIAI 64
Query: 160 KIKQV 164
++ +
Sbjct: 65 RLGKA 69
Score = 28.4 bits (63), Expect = 1.1
Identities = 9/45 (20%), Positives = 14/45 (31%)
Query: 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYAL 77
G I DI + A + NG S ++ A+
Sbjct: 20 GEVIADILDDLDINTANFAEILGVSNQTIQEVINGQRSITVDIAI 64
>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 = 46.1 bits (109), Expect = 6e-06
Identities = 14/69 (20%), Positives = 23/69 (33%)
Query: 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172
A+ L R G++Q E LG P S +S E ++ + +
Sbjct: 14 ALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPYAL 73
Query: 173 YFGDEVIVP 181
E + P
Sbjct: 74 LSKLEAMTP 82
Score = 34.2 bits (78), Expect = 0.020
Identities = 11/64 (17%), Positives = 22/64 (34%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+ + + + R A TQKE+A + +S V+ EN + +
Sbjct: 13 QALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPYA 72
Query: 90 IYDG 93
+
Sbjct: 73 LLSK 76
>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 = 45.6 bits (108), Expect = 8e-06
Identities = 12/64 (18%), Positives = 28/64 (43%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
L ++K+ G+ + +LL + T++ Y G T P+I+ ++ +D +
Sbjct: 10 FAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHLSIDELV 69
Query: 174 FGDE 177
+
Sbjct: 70 GYVQ 73
Score = 44.8 bits (106), Expect = 1e-05
Identities = 13/81 (16%), Positives = 30/81 (37%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+ ++K + ++A N V + +G I + L + +S D
Sbjct: 8 HQFAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHLSIDE 67
Query: 90 IYDGEVIDRRYEDVTNKKRLD 110
+ D+ + D++ K+ L
Sbjct: 68 LVGYVQEDKVWNDLSLKQWLL 88
>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 = 44.6 bits (105), Expect = 2e-05
Identities = 14/75 (18%), Positives = 26/75 (34%), Gaps = 6/75 (8%)
Query: 104 TNKKRLDPY------AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKP 157
T KK L + A + + + G+SQ +GM S + G
Sbjct: 2 TKKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYN 61
Query: 158 ARKIKQVTKKHLDWI 172
A + ++ K ++
Sbjct: 62 AALLAKILKVSVEEF 76
Score = 39.2 bits (91), Expect = 7e-04
Identities = 15/86 (17%), Positives = 32/86 (37%), Gaps = 2/86 (2%)
Query: 21 ITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLR 80
+T E + + + + + +Q+ +A +S V NG+ + + A L
Sbjct: 7 LTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLA 66
Query: 81 NEYEISFDWIYDG--EVIDRRYEDVT 104
++S + I YE V+
Sbjct: 67 KILKVSVEEFSPSIAREIYEMYEAVS 92
>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 = 43.0 bits (101), Expect = 5e-05
Identities = 12/52 (23%), Positives = 22/52 (42%)
Query: 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQV 164
+ L +RK+ +SQ E LG+ S +S E + ++ +V
Sbjct: 10 CLVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEV 61
Score = 32.2 bits (73), Expect = 0.084
Identities = 10/64 (15%), Positives = 22/64 (34%)
Query: 29 WKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFD 88
++ + + +RK + +Q E+AI +S ++ E+ L
Sbjct: 8 YRCLVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVVASRLG 67
Query: 89 WIYD 92
D
Sbjct: 68 LPMD 71
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A
{Enterobacteria phage lambda}
Length = 236
Score = 42.3 bits (98), Expect = 8e-05
Identities = 12/72 (16%), Positives = 27/72 (37%)
Query: 103 VTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIK 162
+T ++ D + A + + + G+SQ +GM S + G A +
Sbjct: 7 LTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLA 66
Query: 163 QVTKKHLDWIYF 174
++ K ++
Sbjct: 67 KILKVSVEEFSP 78
Score = 33.1 bits (74), Expect = 0.045
Identities = 11/71 (15%), Positives = 27/71 (38%)
Query: 21 ITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLR 80
+T E + + + + + +Q+ +A +S V NG+ + + A L
Sbjct: 7 LTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLA 66
Query: 81 NEYEISFDWIY 91
++S +
Sbjct: 67 KILKVSVEEFS 77
>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 = 41.5 bits (97), Expect = 1e-04
Identities = 12/60 (20%), Positives = 24/60 (40%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
+ +K IR +KGM+Q + + + +S E+ IK I + + +
Sbjct: 12 VSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFF 71
Score = 36.9 bits (85), Expect = 0.003
Identities = 14/73 (19%), Positives = 30/73 (41%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
V IK IR TQ+++A +N + ++ E + +I+ + E+S
Sbjct: 10 SKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVV 69
Query: 90 IYDGEVIDRRYED 102
++ + + D
Sbjct: 70 FFEMLIKEILKHD 82
>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus
thuringiensis serovarisraelensis atcc 35646}
Length = 293
Score = 41.3 bits (95), Expect = 2e-04
Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 1/78 (1%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
+G+ +K IR +G++Q + + + S +S E G P + + I + + Y
Sbjct: 6 LGSEIKKIRVLRGLTQKQLSENI-CHQSEVSRIESGAVYPSMDILQGIAAKLQIPIIHFY 64
Query: 174 FGDEVIVPKSIKRAKGNQ 191
+ K+ K
Sbjct: 65 EVLIYSDIERKKQFKDQV 82
Score = 35.9 bits (81), Expect = 0.006
Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+ +G+ IK IR TQK+++ +S V+ E+G S+ + + +I
Sbjct: 4 EKLGSEIKKIRVLRGLTQKQLSENICH-QSEVSRIESGAVYPSMDILQGIAAKLQIPIIH 62
Query: 90 IYDGE 94
Y+
Sbjct: 63 FYEVL 67
>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 = 39.9 bits (93), Expect = 4e-04
Identities = 39/241 (16%), Positives = 68/241 (28%), Gaps = 98/241 (40%)
Query: 6 FLETSLK-----------SLQEY-TLIITPEIRQYWKDV-----GT-----RIKDIRKAN 43
F + K + Y + P I + D G I ++ +
Sbjct: 292 FFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILE---DSLENNEGVPSPMLSISNLTQ-- 346
Query: 44 NKTQKEMAIGA-NQ-L-ES---AVNLFENG----MCS---TSIRYAL--YLR-------- 80
Q + + N L ++L NG + S S+ Y L LR
Sbjct: 347 --EQVQDYVNKTNSHLPAGKQVEISLV-NGAKNLVVSGPPQSL-YGLNLTLRKAKAPSGL 402
Query: 81 NEYEISFDWIYDGEVIDRRYEDVTNKKRLDP--------YAIGARLKSIRKDKGMSQIEF 132
++ I F +R+ + +N R P + A I KD + + F
Sbjct: 403 DQSRIPFS--------ERKLK-FSN--RFLPVASPFHSHLLVPAS-DLINKDLVKNNVSF 450
Query: 133 -GKLLGMP---NST---LSNYEQGRTIPEIKPARKIKQVTKKHLDW-----------IYF 174
K + +P L G I + + + + W + F
Sbjct: 451 NAKDIQIPVYDTFDGSDLRVL-SGSISERI-----VDCIIRLPVKWETTTQFKATHILDF 504
Query: 175 G 175
G
Sbjct: 505 G 505
>2wus_R RODZ, putative uncharacterized protein; structural protein, cell
WALL morphogenesis, bacterial cytos bacterial actin;
2.90A {Thermotoga maritima}
Length = 112
Score = 39.3 bits (91), Expect = 6e-04
Identities = 12/94 (12%), Positives = 34/94 (36%), Gaps = 6/94 (6%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPA------RKIKQVTKK 167
+G + R+++ ++ ++ + S L E+G ++ + +
Sbjct: 8 LGETFRKKREERRITLLDASLFTNINPSKLKRIEEGDLKGLDAEVYIKSYIKRYSEFLEL 67
Query: 168 HLDWIYFGDEVIVPKSIKRAKGNQSSKKSKKDKK 201
D + E + + + + KK +K+K
Sbjct: 68 SPDEMLKLYEEGKEEVAEEVEEKKPRKKKEKEKT 101
Score = 29.3 bits (65), Expect = 0.63
Identities = 9/41 (21%), Positives = 18/41 (43%)
Query: 27 QYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENG 67
+ WK++G + R+ T + ++ N S + E G
Sbjct: 3 EKWKELGETFRKKREERRITLLDASLFTNINPSKLKRIEEG 43
>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 = 39.2 bits (91), Expect = 7e-04
Identities = 15/91 (16%), Positives = 27/91 (29%), Gaps = 1/91 (1%)
Query: 112 YAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDW 171
+ IG+ LK IR++ QI+ M S E ++ K + +
Sbjct: 2 FKIGSVLKQIRQELNYHQIDLYS-GIMSKSVYIKVEADSRPISVEELSKFSERLGVNFFE 60
Query: 172 IYFGDEVIVPKSIKRAKGNQSSKKSKKDKKS 202
I + + K K +
Sbjct: 61 ILNRAGMNTKSVNETGKEKLLISKIFTNPDL 91
Score = 32.3 bits (73), Expect = 0.084
Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 1/63 (1%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+G+ +K IR+ N Q ++ +S E S+ ++F
Sbjct: 2 FKIGSVLKQIRQELNYHQIDLY-SGIMSKSVYIKVEADSRPISVEELSKFSERLGVNFFE 60
Query: 90 IYD 92
I +
Sbjct: 61 ILN 63
>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 = 38.1 bits (88), Expect = 0.001
Identities = 5/36 (13%), Positives = 14/36 (38%)
Query: 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148
+ L + + ++ L G+ ST++ +
Sbjct: 7 FVSEHLMELITQQNLTINRVATLAGLNQSTVNAMFE 42
Score = 29.6 bits (66), Expect = 0.57
Identities = 12/69 (17%), Positives = 22/69 (31%), Gaps = 1/69 (1%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALY-LRNEYEISFD 88
+ V + ++ N T +A A +S VN G + + IS
Sbjct: 6 EFVSEHLMELITQQNLTINRVATLAGLNQSTVNAMFEGRSKRPTITTIRKVCGTLGISVH 65
Query: 89 WIYDGEVID 97
+D +
Sbjct: 66 DFFDFPPYN 74
>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix,
restriction- modification, transcription regulator;
2.80A {Enterobacter SP} PDB: 3fya_A
Length = 99
Score = 38.2 bits (88), Expect = 0.001
Identities = 12/60 (20%), Positives = 24/60 (40%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
+ +K IR +KGM+Q + + + +S E+ IK I + + +
Sbjct: 29 VSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFF 88
Score = 36.2 bits (83), Expect = 0.005
Identities = 14/73 (19%), Positives = 30/73 (41%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
V IK IR TQ+++A +N + ++ E + +I+ + E+S
Sbjct: 27 SKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVV 86
Query: 90 IYDGEVIDRRYED 102
++ + + D
Sbjct: 87 FFEMLIKEILKHD 99
>3g7d_A PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic protein;
1.80A {Streptomyces viridochromogenes} PDB: 3gbf_A
Length = 443
Score = 37.2 bits (86), Expect = 0.003
Identities = 9/89 (10%), Positives = 28/89 (31%), Gaps = 2/89 (2%)
Query: 115 GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ-GRTIPEIKPARKIKQVTKKHLDWIY 173
G+ L + ++ + G+P + L + + + R + +
Sbjct: 232 GSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSPASETGLTVLRTLGRALGFDYRV-L 290
Query: 174 FGDEVIVPKSIKRAKGNQSSKKSKKDKKS 202
+ K + S++S++ +
Sbjct: 291 LPADDQHDGVGKTWTTIEDSRRSRRTFGT 319
>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding
protein; 1.00A {Staphylococcus aureus subsp}
Length = 130
Score = 37.0 bits (85), Expect = 0.003
Identities = 10/45 (22%), Positives = 16/45 (35%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPA 158
+G LK R+ GM+ E + G+ L + E
Sbjct: 4 VGEALKGRRERLGMTLTELEQRTGIKREMLVHIENNEFDQLPNKN 48
>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 = 36.5 bits (84), Expect = 0.005
Identities = 12/58 (20%), Positives = 23/58 (39%)
Query: 107 KRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQV 164
K + G ++ + +S EF + + + ST S G+ + A K+ V
Sbjct: 2 KMANHPRPGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVV 59
Score = 33.0 bits (75), Expect = 0.052
Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 7/83 (8%)
Query: 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFD-WI- 90
G I++ N + +E A S + G + + A+ L S W+
Sbjct: 10 GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLN 69
Query: 91 ----YDGEVIDRRYEDVTNKKRL 109
+ ++ DV+ +RL
Sbjct: 70 LQNAWSLAEAEKT-VDVSRLRRL 91
>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity,
transcription regulator; 1.95A {Enterobacteria phage
186} PDB: 2fkd_A
Length = 189
Score = 36.2 bits (83), Expect = 0.006
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 2/68 (2%)
Query: 117 RLKSIRKDKGM-SQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYFG 175
L I + G +I+ + +S+LSN I A T +L W+ G
Sbjct: 10 VLDRICEAYGFSQKIQLANHFDIASSSLSNRYTRGAISYDF-AAHCALETGANLQWLLTG 68
Query: 176 DEVIVPKS 183
+ +
Sbjct: 69 EGEAFVNN 76
>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 = 34.1 bits (77), Expect = 0.022
Identities = 15/65 (23%), Positives = 26/65 (40%)
Query: 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWI 172
A+GA L+S R DKG++ E + + LS E+GR + + + +
Sbjct: 28 ALGAALRSFRADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHALGASVADV 87
Query: 173 YFGDE 177
Sbjct: 88 LIEAA 92
Score = 31.8 bits (71), Expect = 0.12
Identities = 11/72 (15%), Positives = 24/72 (33%), Gaps = 3/72 (4%)
Query: 23 PEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNE 82
P +R+ +G ++ R T +E+A + ++ E G S + +
Sbjct: 23 PLLRE---ALGAALRSFRADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHA 79
Query: 83 YEISFDWIYDGE 94
S +
Sbjct: 80 LGASVADVLIEA 91
>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 = 0.029
Identities = 10/71 (14%), Positives = 26/71 (36%), Gaps = 3/71 (4%)
Query: 21 ITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGM-CSTSIRYALYL 79
+T E + + +G ++ R + + +A A + E G + + +
Sbjct: 6 LTAEELERGQRLGELLRSARG--DMSMVTVAFDAGISVETLRKIETGRIATPAFFTIAAV 63
Query: 80 RNEYEISFDWI 90
++S D +
Sbjct: 64 ARVLDLSLDDV 74
Score = 28.6 bits (63), Expect = 1.1
Identities = 15/60 (25%), Positives = 22/60 (36%), Gaps = 3/60 (5%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPE-IKPARKIKQVTKKHLDWI 172
+G L+S R MS + G+ TL E GR + +V LD +
Sbjct: 17 LGELLRSAR--GDMSMVTVAFDAGISVETLRKIETGRIATPAFFTIAAVARVLDLSLDDV 74
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 33.2 bits (75), Expect = 0.036
Identities = 35/148 (23%), Positives = 55/148 (37%), Gaps = 49/148 (33%)
Query: 25 IRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLF----------ENGMCSTSIR 74
+R +KD R KD N+ Q+ N + + VN+ G C+TS+
Sbjct: 1058 LRGMFKD---RFKDEPVQNDILQESFI---NTMSAWVNMLLISSSGPIKTPVGACATSVE 1111
Query: 75 YALYLRNEYEISFDWIYDGEV---IDRRYEDVTNKKRLDPYAIGARLKSIRKDKGMSQIE 131
+I + I G+ I Y+D +++G E
Sbjct: 1112 -------SVDIGVETILSGKARICIVGGYDDF-------------------QEEG--SFE 1143
Query: 132 FGKLLGMPNSTLSNYEQGRTIPEI-KPA 158
FG + N TL +E GRT E+ +PA
Sbjct: 1144 FGNMKATSN-TLEEFEHGRTPAEMSRPA 1170
Score = 30.2 bits (67), Expect = 0.39
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 153 PEIKPARKIKQVTKKHLDWIYFGDEVIV 180
PE+KP +++KQ+ L+ + + VIV
Sbjct: 794 PELKPYKQVKQIAPAELEGLLDLERVIV 821
>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 = 33.3 bits (75), Expect = 0.039
Identities = 8/66 (12%), Positives = 28/66 (42%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDW 89
+ + RIK + +T + +A + E+ ++ + + S+ + + +
Sbjct: 9 QMMLNRIKVVLAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELLNVDPRQ 68
Query: 90 IYDGEV 95
+ +G++
Sbjct: 69 LINGKI 74
Score = 29.1 bits (64), Expect = 0.79
Identities = 9/64 (14%), Positives = 26/64 (40%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
+ R+K + +K + + +G +T+S + ++ P + K+ ++ +
Sbjct: 11 MLNRIKVVLAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELLNVDPRQLI 70
Query: 174 FGDE 177
G
Sbjct: 71 NGKI 74
>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT,
structural genomics, PSI-2, protein structure
initiative; NMR {Eubacterium rectale atcc 33656}
Length = 94
Score = 31.7 bits (71), Expect = 0.11
Identities = 9/65 (13%), Positives = 23/65 (35%)
Query: 33 GTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYD 92
+ + KTQ E+A N + G+ + L + + I+ + +
Sbjct: 11 SENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNINKSDLIE 70
Query: 93 GEVID 97
+ ++
Sbjct: 71 DKKLN 75
Score = 30.9 bits (69), Expect = 0.19
Identities = 10/65 (15%), Positives = 24/65 (36%)
Query: 114 IGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173
L S +Q+E K +G+ T + + +G IP + + + + +
Sbjct: 10 FSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNINKSDLI 69
Query: 174 FGDEV 178
++
Sbjct: 70 EDKKL 74
>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress,
MERR family, 2Fe-2S; HET: DNA; 2.80A {Escherichia coli
K12} PDB: 2zhh_A
Length = 154
Score = 31.6 bits (71), Expect = 0.12
Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 119 KSIRKDKGMSQI-EFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIYF 174
K + + K + E K G+ S L YE I I+ + ++ + L ++
Sbjct: 3 KKLPRIKALLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAI 59
>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD;
1.81A {Streptomyces coelicolor A3}
Length = 71
Score = 29.8 bits (66), Expect = 0.42
Identities = 10/62 (16%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 113 AIGARLKSIRKDKGMSQIEFGKLLGMP--NSTLSNYEQGRTIPEIKPARKIKQVTKKHLD 170
+GA+L++IR +G+S + + +YE+G ++ ++ +
Sbjct: 8 QLGAKLRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDRAVTVQRLAELADFYGVPVQ 67
Query: 171 WI 172
+
Sbjct: 68 EL 69
Score = 28.7 bits (63), Expect = 0.91
Identities = 10/66 (15%), Positives = 25/66 (37%), Gaps = 2/66 (3%)
Query: 27 QYWKDVGTRIKDIRKANNKTQKEMA--IGANQLESAVNLFENGMCSTSIRYALYLRNEYE 84
+Y K +G +++ IR + + V +E G + +++ L + Y
Sbjct: 4 EYAKQLGAKLRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDRAVTVQRLAELADFYG 63
Query: 85 ISFDWI 90
+ +
Sbjct: 64 VPVQEL 69
>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 = 29.1 bits (64), Expect = 0.71
Identities = 7/36 (19%), Positives = 19/36 (52%)
Query: 113 AIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQ 148
+ L+ ++ G++Q + +LLG+ +S+ +
Sbjct: 18 QLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMR 53
Score = 25.6 bits (55), Expect = 9.1
Identities = 5/42 (11%), Positives = 14/42 (33%)
Query: 30 KDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCST 71
+ +++ + + TQ + A + V+ G
Sbjct: 17 SQLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKIDL 58
>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical
protein, JW0472, structural genomics, NPPSFA; 2.25A
{Escherichia coli}
Length = 113
Score = 28.0 bits (62), Expect = 1.4
Identities = 11/83 (13%), Positives = 28/83 (33%), Gaps = 6/83 (7%)
Query: 37 KDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFD-WI----- 90
+ + + E+A + ++V+ N + A L ++ + D W+
Sbjct: 17 YEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFWLNLQAA 76
Query: 91 YDGEVIDRRYEDVTNKKRLDPYA 113
D ++ R++ A
Sbjct: 77 VDLWEVENNMRTQEELGRIETVA 99
>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA
binding protein, helix-turn-helix, phosphotransferase
system, metalloprotein; 2.70A {Escherichia coli} SCOP:
a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A
Length = 406
Score = 28.0 bits (61), Expect = 1.6
Identities = 4/28 (14%), Positives = 15/28 (53%)
Query: 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSN 145
+ I + +S+I+ +L + ++++
Sbjct: 22 YRLIDQLGPVSRIDLSRLAQLAPASITK 49
>3bvx_A Alpha-mannosidase 2; family 38 glycoysl hydrolase, glycosidase,
golgi apparatus, membrane, signal-anchor, transmembrane;
HET: WZ5; 1.10A {Drosophila melanogaster} SCOP: a.8.3.1
b.30.5.6 c.6.2.1 PDB: 3bud_A 3buq_A* 3bvt_A* 3bui_A*
3bvv_A* 3bvw_A* 3bvu_A* 3cv5_A* 3czn_A* 3czs_A* 2ow6_A*
1r33_A* 1r34_A* 1tqs_A* 1tqt_A* 1tqu_A* 1tqv_A* 1tqw_A*
2alw_A* 2f18_A* ...
Length = 1045
Score = 27.8 bits (61), Expect = 1.9
Identities = 9/105 (8%), Positives = 27/105 (25%), Gaps = 2/105 (1%)
Query: 15 QEYTLIITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVNLFENGMCSTSIR 74
++ Q + + +LES+V++ + +I
Sbjct: 710 FKFLKYGVRSHGDRSGAYLFLPNGPASPVELGQPVVLVTKGKLESSVSVGLPSVVHQTIM 769
Query: 75 YALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRL--DPYAIGAR 117
+ + + E++ R + + D +
Sbjct: 770 RGGAPEIRNLVDIGSLDNTEIVMRLETHIDSGDIFYTDLNGLQFI 814
>2dg6_A Putative transcriptional regulator; winged-helix motif, MERR
family, gene regulation; 2.20A {Streptomyces coelicolor
A3}
Length = 222
Score = 27.4 bits (60), Expect = 2.2
Identities = 8/59 (13%), Positives = 19/59 (32%), Gaps = 10/59 (16%)
Query: 131 EFGKLLGMPNSTLSNYEQ-GRTIPEIKPARKIKQVTKKHLDWIYFGDEVIVPKSIKRAK 188
+ K G+ +T+ Y + G P + + + HL + ++
Sbjct: 5 DLSKRSGVSTATIKYYLREGLLPPGRQVNATTAEYDEDHLRRLRL---------VRALI 54
>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 = 2.9
Identities = 5/28 (17%), Positives = 14/28 (50%)
Query: 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSN 145
K I + +S+I+ K + ++++
Sbjct: 45 YKLIDQKGPISRIDLSKESELAPASITK 72
>2zru_A Isopentenyl-diphosphate delta-isomerase; type 2, IDI, FMN,
isopentenyl diphosphate isomerase, cytoplasm,
flavoprotein, isoprene biosynthesis; HET: FMN; 2.00A
{Sulfolobus shibatae} PDB: 2zrv_A* 2zrw_A* 2zrx_A*
2zry_A* 2zrz_A*
Length = 368
Score = 26.7 bits (58), Expect = 4.3
Identities = 4/41 (9%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 9 TSLKSLQEYTLIITPEIRQYWKDVGTRIKDIRKANNKTQKE 49
+ +L++ +++I +++++ + G ++ ++E
Sbjct: 331 KDVDALKKTSIVILGKLKEWAEYRGI---NLSIYEKVRKRE 368
>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ ATPase, DNA polymerase; HET: ATG
ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1
c.37.1.20
Length = 516
Score = 26.4 bits (57), Expect = 4.8
Identities = 23/162 (14%), Positives = 53/162 (32%), Gaps = 19/162 (11%)
Query: 8 ETSLKSLQEYTLIITPEIRQYWKDVGTRIKDIRKANNKTQKEMAIGANQLESAVN----- 62
+ +++ E + I D+ ++ D + ++ + + +
Sbjct: 261 TINHENINEISKAWEKNIALKPFDIAHKMLDGQIYSDIGSRNFTLNDKIALYFDDFDFTP 320
Query: 63 --LFEN--GMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARL 118
+ EN + ++ + + I G++++++ L P A L
Sbjct: 321 LMIQENYLSTRPSVLKPGQSHLEAVAEAANCISLGDIVEKKIRSSEQLWSLLPLH--AVL 378
Query: 119 KSIR-----KDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEI 155
S+ +I F LG NS + Y R + EI
Sbjct: 379 SSVYPASKVAGHMAGRINFTAWLGQ-NSKSAKYY--RLLQEI 417
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 26.2 bits (57), Expect = 5.0
Identities = 10/45 (22%), Positives = 17/45 (37%)
Query: 107 KRLDPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRT 151
DP+ +K + + Q E + G+ S LS + T
Sbjct: 25 LSEDPWRAAKMIKGYMQQHNIPQREVVDVTGLNQSHLSQHLNKGT 69
>3juk_A UDP-glucose pyrophosphorylase (GALU); transfer; HET: UPG; 2.30A
{Helicobacter pylori} PDB: 3juj_A*
Length = 281
Score = 26.2 bits (57), Expect = 5.5
Identities = 4/21 (19%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 24 EIRQYWKDVGTRIKDIRKANN 44
+ + D G+ ++ +A+N
Sbjct: 247 QFKGKRYDCGS-VEGYIEASN 266
>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-
binding, transcription regulator, PSI-2; 1.85A {Listeria
monocytogenes str}
Length = 142
Score = 25.8 bits (56), Expect = 7.8
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 127 MSQIEFGKLLGMPNSTLSNYEQ-GRTIPEIKPARKIKQVTKKHLDWIYFG 175
++ E + G+ T+ YE+ G P + +++ + L WI F
Sbjct: 3 LNIKEASEKSGVSADTIRYYERIGLIPPIHRNESGVRKFGAEDLRWILFT 52
>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 = 25.6 bits (56), Expect = 8.7
Identities = 10/55 (18%), Positives = 23/55 (41%), Gaps = 9/55 (16%)
Query: 96 IDRRYEDVTNKKRLDPYAIGAR----LKSIRKDKGMSQIEFGKLLGMPNSTLSNY 146
I ++Y L Y + L +I D+ ++ + G+ + + + TL+
Sbjct: 21 IIKKY-----TNYLKEYDLTYTGYIVLMAIENDEKLNIKKLGERVFLDSGTLTPL 70
>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor,
winged helix motif, DNA-binding; 1.40A {Methanobacterium
thermoautotrophicum} PDB: 3bpx_A*
Length = 138
Score = 25.6 bits (56), Expect = 9.0
Identities = 9/55 (16%), Positives = 19/55 (34%), Gaps = 5/55 (9%)
Query: 95 VIDRRYEDVTNKKRLDPYAIGAR----LKSIRKDKGMSQIEFGKLLGMPNSTLSN 145
+I R + + L + L I ++ G+ Q E + T++
Sbjct: 9 IILRSHRVFIGR-ELGHLNLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIAR 62
>1nh1_A Avirulence B protein; helix bundle, avirulence protein; 2.20A
{Pseudomonas syringae} SCOP: e.45.1.1 PDB: 2nud_A
2nun_A*
Length = 330
Score = 25.3 bits (55), Expect = 9.3
Identities = 8/47 (17%), Positives = 18/47 (38%), Gaps = 2/47 (4%)
Query: 110 DPYAIGARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIK 156
D + R+ +R + G ++ P+ ++ +P IK
Sbjct: 183 DTEYLRDRVAHLRTELGAKALKQHLQRYNPD--RIDHTNASYLPIIK 227
>1wh8_A CUT-like 2, homeobox protein CUX-2; CUT domain, structural
genomics, riken structural genomics/proteomics
initiative, RSGI, transcription; NMR {Homo sapiens}
SCOP: a.35.1.7
Length = 111
Score = 25.6 bits (56), Expect = 9.4
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 100 YEDVTNKKRLDPYAIGARLKSIRKDKGMSQIEFGKL-LGMPNSTLS 144
E V LD Y+I R+K + D + Q FG+ LG+ ++S
Sbjct: 18 QEIVAMSPELDTYSITKRVKEVLTDNNLGQRLFGESILGLTQGSVS 63
>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix
prnai nucleotide-binding domain; HET: MSE; 1.80A
{Sulfolobus solfataricus}
Length = 244
Score = 25.4 bits (55), Expect = 9.4
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 118 LKSIRKDKGMSQIEFGKLLGMPNSTLSN 145
L + + KG E K+L TL N
Sbjct: 158 LNVLYETKGTGITELAKMLDKSEKTLIN 185
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
0.315 0.133 0.379
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: 1,768,568
Number of extensions: 82040
Number of successful extensions: 318
Number of sequences better than 10.0: 1
Number of HSP's gapped: 315
Number of HSP's successfully gapped: 135
Length of query: 205
Length of database: 5,693,230
Length adjustment: 88
Effective length of query: 117
Effective length of database: 3,559,758
Effective search space: 416491686
Effective search space used: 416491686
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (24.8 bits)